diff --git a/psi-ms.obo b/psi-ms.obo index e65f134..33046b6 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: 4.1.92 +data-version: 4.1.93 date: 07:01:2022 11:44 saved-by: Joshua Klein auto-generated-by: OBO-Edit 2.3.1 @@ -195,14 +195,14 @@ id: MS:1000001 name: sample number def: "A reference number relevant to the sample under study." [PSI:MS] is_a: MS:1000548 ! sample attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000002 name: sample name def: "A reference string relevant to the sample under study." [PSI:MS] is_a: MS:1000548 ! sample attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000003 @@ -216,7 +216,7 @@ name: sample mass def: "Total mass of sample used." [PSI:MS] is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000021 ! gram -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000005 @@ -224,7 +224,7 @@ name: sample volume def: "Total volume of solution used." [PSI:MS] is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000098 ! milliliter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000006 @@ -232,7 +232,7 @@ name: sample concentration def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS] is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000175 ! gram per liter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000007 @@ -265,7 +265,7 @@ id: MS:1000011 name: mass resolution def: "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS] is_a: MS:1000503 ! scan attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000012 @@ -287,7 +287,7 @@ def: "Accuracy is the degree of conformity of a measured mass to its actual valu is_a: MS:1000480 ! mass analyzer attribute relationship: has_units MS:1000040 ! m/z relationship: has_units UO:0000169 ! parts per million -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000015 @@ -295,7 +295,7 @@ name: scan rate def: "Rate in Th/sec for scanning analyzers." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units MS:1000807 ! Th/s -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000016 @@ -305,7 +305,7 @@ is_a: MS:1000503 ! scan attribute is_a: MS:1002345 ! PSM-level attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000017 @@ -346,7 +346,7 @@ name: TOF Total Path Length def: "The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS] is_a: MS:1000480 ! mass analyzer attribute relationship: has_units UO:0000008 ! meter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000023 @@ -355,14 +355,14 @@ def: "OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate app comment: This former purgatory term was made obsolete. relationship: has_units MS:1000040 ! m/z is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000024 name: final MS exponent def: "Final MS level achieved when performing PFF with the ion trap (e.g. MS E10)." [PSI:MS] is_a: MS:1000480 ! mass analyzer attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000025 @@ -372,7 +372,7 @@ synonym: "B" EXACT [] synonym: "Magnetic Field" RELATED [] is_a: MS:1000480 ! mass analyzer attribute relationship: has_units UO:0000228 ! tesla -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000026 @@ -391,7 +391,7 @@ id: MS:1000028 name: detector resolution def: "The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height." [PSI:MS] is_a: MS:1000481 ! detector attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000029 @@ -400,7 +400,7 @@ def: "The rate of signal sampling (measurement) with respect to time." [PSI:MS] synonym: "ADC Sampling Frequency" NARROW [] is_a: MS:1000481 ! detector attribute relationship: has_units UO:0000106 ! hertz -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000030 @@ -420,7 +420,7 @@ id: MS:1000032 name: customization def: "Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS] is_a: MS:1000496 ! instrument attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000033 @@ -484,7 +484,7 @@ def: "Number of net charges, positive or negative, on an ion." [PSI:MS] synonym: "z" EXACT [] is_a: MS:1000455 ! ion selection attribute is_a: MS:1000507 ! ion property -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000042 @@ -497,7 +497,7 @@ relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit relationship: part_of MS:1000231 ! peak -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000043 @@ -518,7 +518,7 @@ name: collision energy def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000046 @@ -569,7 +569,7 @@ id: MS:1000053 name: sample batch def: "Sample batch lot identifier." [PSI:MS] is_a: MS:1000548 ! sample attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000054 @@ -1090,7 +1090,7 @@ id: MS:1000132 name: percent of base peak def: "The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity." [PSI:MS] is_a: MS:1000043 ! intensity unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000133 @@ -1135,7 +1135,7 @@ name: normalized collision energy def: "Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions." [PSI:PI] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000139 @@ -1561,7 +1561,7 @@ def: "OBSOLETE An experimentally determined mass that is can be to determine a u comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000208 @@ -1570,7 +1570,7 @@ def: "OBSOLETE The mass of an ion or molecule calculated using the average mass comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000209 @@ -1580,7 +1580,7 @@ synonym: "AE" EXACT [] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000266 ! electronvolt is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000210 @@ -1594,7 +1594,7 @@ id: MS:1000211 name: OBSOLETE charge number def: "OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state." [PSI:MS] is_obsolete: true -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000212 @@ -1610,7 +1610,7 @@ def: "OBSOLETE The electron affinity of M is the minimum energy required for the comment: This child of the former purgatory term ion attribute was made obsolete. synonym: "EA" EXACT [] is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000214 @@ -1626,7 +1626,7 @@ def: "OBSOLETE The calculated mass of an ion or molecule containing a single iso comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000216 @@ -1648,7 +1648,7 @@ name: ionization efficiency def: "OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] comment: This term was made obsolete because it was replaced by ionization efficiency (MS:1000392). is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000219 @@ -1658,7 +1658,7 @@ synonym: "IE" EXACT [] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000266 ! electronvolt is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000220 @@ -1681,7 +1681,7 @@ def: "OBSOLETE The difference between the monoisotopic and nominal mass of a mol comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000223 @@ -1689,7 +1689,7 @@ name: mass number def: "OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. is_obsolete: true -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000224 @@ -1697,7 +1697,7 @@ name: molecular mass def: "Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass] is_a: MS:1000861 ! molecular entity property relationship: has_units UO:0000002 ! mass unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000225 @@ -1706,7 +1706,7 @@ def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the m comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000226 @@ -1737,7 +1737,7 @@ def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the m comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000230 @@ -1766,7 +1766,7 @@ def: "OBSOLETE The proton affinity of a species M is defined as the negative of synonym: "PA" EXACT [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000234 @@ -1774,7 +1774,7 @@ name: mass resolving power def: "OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported." [PSI:MS] comment: This term was made obsolete because it was replaced by mass resolving power (MS:1000800). is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000235 @@ -1788,7 +1788,7 @@ id: MS:1000236 name: transmission def: "The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS] is_a: MS:1000496 ! instrument attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000237 @@ -2154,7 +2154,7 @@ name: total ion current def: "The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum." [PSI:MS] synonym: "TIC" EXACT [] is_a: MS:1003058 ! spectrum property -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000286 @@ -2287,7 +2287,7 @@ name: accelerating voltage def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] is_a: MS:1000487 ! ion optics attribute relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000305 @@ -2315,7 +2315,7 @@ name: electric field strength def: "The magnitude of the force per unit charge at a given point in space." [PSI:MS] is_a: MS:1000487 ! ion optics attribute relationship: has_units UO:0000268 ! volt per meter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000309 @@ -2507,7 +2507,7 @@ id: MS:1000336 name: neutral loss def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS] is_a: MS:1001055 ! modification parameters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000337 @@ -2885,7 +2885,7 @@ id: MS:1000392 name: ionization efficiency def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] is_a: MS:1000482 ! source attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000393 @@ -3005,7 +3005,7 @@ id: MS:1000412 name: buffer gas def: "An inert gas used for collisional deactivation of internally excited ions." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000413 @@ -3054,7 +3054,7 @@ id: MS:1000419 name: collision gas def: "An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000420 @@ -3499,7 +3499,7 @@ name: source potential def: "Potential difference at the MS source in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000487 @@ -3590,7 +3590,7 @@ def: "The lower m/z bound of a mass spectrometer scan window." [PSI:MS] synonym: "mzRangeStop" RELATED [] is_a: MS:1000549 ! selection window attribute relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000501 @@ -3599,7 +3599,7 @@ def: "The upper m/z bound of a mass spectrometer scan window." [PSI:MS] synonym: "mzRangeStart" RELATED [] is_a: MS:1000549 ! selection window attribute relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000502 @@ -3609,7 +3609,7 @@ synonym: "Scan Duration" RELATED [] is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000503 @@ -3624,7 +3624,7 @@ name: base peak m/z def: "M/z value of the signal of highest intensity in the mass spectrum." [PSI:MS] is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000505 @@ -3636,7 +3636,7 @@ relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000506 @@ -3664,7 +3664,7 @@ name: activation energy def: "Activation Energy." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000510 @@ -3677,14 +3677,14 @@ id: MS:1000511 name: ms level def: "Stage number achieved in a multi stage mass spectrometry acquisition." [PSI:MS] is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000512 name: filter string def: "A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS] is_a: MS:1000503 ! scan attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000513 @@ -3793,7 +3793,7 @@ def: "Highest m/z value observed in the m/z array." [PSI:MS] is_a: MS:1000808 ! chromatogram attribute is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000528 @@ -3802,14 +3802,14 @@ def: "Lowest m/z value observed in the m/z array." [PSI:MS] is_a: MS:1000808 ! chromatogram attribute is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000529 name: instrument serial number def: "Serial Number of the instrument." [PSI:MS] is_a: MS:1000496 ! instrument attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000530 @@ -4073,14 +4073,14 @@ id: MS:1000568 name: MD5 def: "MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS] is_a: MS:1000561 ! data file checksum type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000569 name: SHA-1 def: "SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard." [PSI:MS] is_a: MS:1000561 ! data file checksum type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000570 @@ -4200,35 +4200,35 @@ id: MS:1000586 name: contact name def: "Name of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000587 name: contact address def: "Postal address of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000588 name: contact URL def: "Uniform Resource Locator related to the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000589 name: contact email def: "Email address of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000590 name: contact affiliation def: "Home institution of the contact person." [PSI:MS] is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000591 @@ -4397,7 +4397,7 @@ id: MS:1000616 name: preset scan configuration def: "A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo \"scan event\", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time." [PSI:MS] is_a: MS:1000503 ! scan attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000617 @@ -4415,7 +4415,7 @@ def: "Highest wavelength observed in an EMR spectrum." [PSI:MS] is_a: MS:1003058 ! spectrum property is_a: MS:1000808 ! chromatogram attribute relationship: has_units UO:0000018 ! nanometer -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000619 @@ -4424,7 +4424,7 @@ def: "Lowest wavelength observed in an EMR spectrum." [PSI:MS] is_a: MS:1003058 ! spectrum property is_a: MS:1000808 ! chromatogram attribute relationship: has_units UO:0000018 ! nanometer -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000620 @@ -4496,7 +4496,7 @@ relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000630 @@ -4514,7 +4514,7 @@ relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000632 @@ -4527,7 +4527,7 @@ id: MS:1000633 name: possible charge state def: "A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty." [PSI:MS] is_a: MS:1000455 ! ion selection attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000634 @@ -5274,7 +5274,7 @@ name: selected ion m/z def: "Mass-to-charge ratio of an selected ion." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000745 @@ -5293,7 +5293,7 @@ id: MS:1000747 name: completion time def: "The time that a data processing action was finished." [PSI:MS] is_a: MS:1000630 ! data processing parameter -relationship: has_value_type xsd\:dateTime ! The allowed value-type for this CV term +relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term [Term] id: MS:1000748 @@ -5553,7 +5553,7 @@ xref: binary-data-type:MS\:1000522 "64-bit integer" xref: binary-data-type:MS\:1000523 "64-bit float" xref: binary-data-type:MS\:1001479 "null-terminated ASCII string" is_a: MS:1000513 ! binary data array -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000787 @@ -5565,7 +5565,7 @@ relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000788 @@ -5577,7 +5577,7 @@ relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000789 @@ -5613,7 +5613,7 @@ comment: This term was obsoleted in favour of using a target, lower, upper offse is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000794 @@ -5623,7 +5623,7 @@ comment: This term was obsoleted in favour of using a target, lower, upper offse is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000795 @@ -5638,7 +5638,7 @@ def: "Free-form text title describing a spectrum, usually a series of key value comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list. is_a: MS:1001405 ! spectrum identification result details is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000797 @@ -5647,7 +5647,7 @@ def: "A list of scan numbers and or scan ranges associated with a peak list. If comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list. is_a: MS:1001405 ! spectrum identification result details is_a: MS:1003058 ! spectrum property -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000798 @@ -5656,21 +5656,21 @@ def: "A list of raw scans and or scan ranges used to generate a peak list. If po comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list. is_a: MS:1001405 ! spectrum identification result details is_a: MS:1003058 ! spectrum property -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000799 name: custom unreleased software tool def: "A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added." [PSI:MS] is_a: MS:1000531 ! software -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000800 name: mass resolving power def: "The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported." [PSI:MS] is_a: MS:1000503 ! scan attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000801 @@ -5692,7 +5692,7 @@ name: analyzer scan offset def: "Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000804 @@ -5735,7 +5735,7 @@ name: chromatogram title def: "A free-form text title describing a chromatogram." [PSI:MS] comment: This is the preferred storage place for the spectrum title. is_a: MS:1000808 ! chromatogram attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000810 @@ -5854,7 +5854,7 @@ def: "The time of elution from all used chromatographic columns (one or more) in is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000827 @@ -5862,7 +5862,7 @@ name: isolation window target m/z def: "The primary or reference m/z about which the isolation window is defined." [PSI:MS] is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000828 @@ -5870,7 +5870,7 @@ name: isolation window lower offset def: "The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000829 @@ -5878,7 +5878,7 @@ name: isolation window upper offset def: "The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000831 @@ -5904,7 +5904,7 @@ id: MS:1000834 name: matrix solution def: "Describes the chemical solution used as matrix." [PSI:MS] is_a: MS:1000832 ! MALDI matrix application -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000835 @@ -5912,7 +5912,7 @@ name: matrix solution concentration def: "Concentration of the chemical solution used as matrix." [PSI:MS] is_a: MS:1000832 ! MALDI matrix application relationship: has_units UO:0000175 ! gram per liter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000836 @@ -5965,7 +5965,7 @@ comment: This term was made obsolete because it was redundant with the Pato Onto is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000018 ! nanometer is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000844 @@ -5973,7 +5973,7 @@ name: focus diameter x def: "Describes the diameter of the laser beam in x direction." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000017 ! micrometer -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000845 @@ -5981,7 +5981,7 @@ name: focus diameter y def: "Describes the diameter of the laser beam in y direction." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000017 ! micrometer -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000846 @@ -5989,7 +5989,7 @@ name: pulse energy def: "Describes output energy of the laser system. May be attenuated by filters or other means." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000112 ! joule -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000847 @@ -5997,7 +5997,7 @@ name: pulse duration def: "Describes how long the laser beam was emitted from the laser device." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000150 ! nanosecond -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000848 @@ -6005,7 +6005,7 @@ name: attenuation def: "Describes the reduction of the intensity of the laser beam energy." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000849 @@ -6013,7 +6013,7 @@ name: impact angle def: "Describes the angle between the laser beam and the sample target." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000185 ! degree -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000850 @@ -6068,7 +6068,7 @@ id: MS:1000858 name: fraction identifier def: "Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information." [PSI:MS] is_a: MS:1000857 ! run attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000859 @@ -6094,7 +6094,7 @@ name: isoelectric point def: "The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS] synonym: "pI" EXACT [] is_a: MS:1000861 ! molecular entity property -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000863 @@ -6102,7 +6102,7 @@ name: predicted isoelectric point def: "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm." [PSI:MS] synonym: "predicted pI" EXACT [] is_a: MS:1000862 ! isoelectric point -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000864 @@ -6115,28 +6115,28 @@ id: MS:1000865 name: empirical formula def: "A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS] is_a: MS:1000864 ! chemical formula -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000866 name: molecular formula def: "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS] is_a: MS:1000864 ! chemical formula -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000867 name: structural formula def: "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS] is_a: MS:1000864 ! chemical formula -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000868 name: SMILES formula def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301] is_a: MS:1000864 ! chemical formula -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000869 @@ -6144,7 +6144,7 @@ name: collision gas pressure def: "The gas pressure of the collision gas used for collisional excitation." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000110 ! pascal -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000870 @@ -6184,7 +6184,7 @@ name: declustering potential def: "Potential difference between the orifice and the skimmer in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000876 @@ -6192,7 +6192,7 @@ name: cone voltage def: "Potential difference between the sampling cone/orifice in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000877 @@ -6200,7 +6200,7 @@ name: tube lens voltage def: "Potential difference setting of the tube lens in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000878 @@ -6213,7 +6213,7 @@ id: MS:1000879 name: PubMed identifier def: "A unique identifier for a publication in the PubMed database (MIR:00000015)." [PSI:MS] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1000880 @@ -6221,7 +6221,7 @@ name: interchannel delay def: "The duration of intervals between scanning, during which the instrument configuration is switched." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000881 @@ -6240,7 +6240,7 @@ id: MS:1000883 name: protein short name def: "A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN)." [PSI:MS] is_a: MS:1000884 ! protein attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000884 @@ -6255,14 +6255,14 @@ name: protein accession def: "Identifier for a specific protein in a database." [PSI:MS] is_a: MS:1000884 ! protein attribute is_a: MS:1003046 ! peptide-to-protein mapping attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000886 name: protein name def: "A long name describing the function of the protein." [PSI:MS] is_a: MS:1000884 ! protein attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000887 @@ -6275,7 +6275,7 @@ id: MS:1000888 name: stripped peptide sequence def: "Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away." [PSI:MS] is_a: MS:1003050 ! peptidoform attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000889 @@ -6283,7 +6283,7 @@ name: peptidoform sequence def: "Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present." [PSI:MS] comment: Make it more general as there are actually many other ways to display a modified peptide sequence. is_a: MS:1003050 ! peptidoform attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000890 @@ -6309,7 +6309,7 @@ id: MS:1000893 name: peptidoform group label def: "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label." [PSI:MS] is_a: MS:1003050 ! peptidoform attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000894 @@ -6318,7 +6318,7 @@ def: "A time interval from the start of chromatography when an analyte exits a c is_a: MS:1003050 ! peptidoform attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000895 @@ -6327,7 +6327,7 @@ def: "A time interval from the start of chromatography when an analyte exits an is_a: MS:1000894 ! retention time relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000896 @@ -6336,7 +6336,7 @@ def: "A time interval from the start of chromatography when an analyte exits a s is_a: MS:1000894 ! retention time relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000897 @@ -6345,7 +6345,7 @@ def: "A time interval from the start of chromatography when an analyte exits a c is_a: MS:1000894 ! retention time relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000898 @@ -6382,7 +6382,7 @@ id: MS:1000903 name: product ion series ordinal def: "The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion)." [PSI:PI] is_a: MS:1001221 ! product ion attribute -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000904 @@ -6396,7 +6396,7 @@ id: MS:1000905 name: percent of base peak times 100 def: "The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries." [PSI:MS] is_a: MS:1000043 ! intensity unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000906 @@ -6404,7 +6404,7 @@ name: peak intensity rank def: "Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: part_of MS:1000231 ! peak -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000907 @@ -6412,7 +6412,7 @@ name: peak targeting suitability rank def: "Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: part_of MS:1000231 ! peak -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000908 @@ -6471,7 +6471,7 @@ def: "The extent of the retention time window in time units below the target ret is_a: MS:1000915 ! retention time window attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000917 @@ -6480,7 +6480,7 @@ def: "The extent of the retention time window in time units above the target ret is_a: MS:1000915 ! retention time window attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000918 @@ -6538,7 +6538,7 @@ id: MS:1000926 name: product interpretation rank def: "The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1." [PSI:MS] is_a: MS:1001221 ! product ion attribute -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000927 @@ -6546,7 +6546,7 @@ name: ion injection time def: "The length of time spent filling an ion trapping device." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000028 ! millisecond -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000928 @@ -6583,14 +6583,14 @@ id: MS:1000933 name: protein modifications def: "Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation." [PSI:MS] is_a: MS:1000884 ! protein attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000934 name: gene name def: "Name of the gene from which the protein is translated." [PSI:MS] is_a: MS:1000884 ! protein attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000935 @@ -6620,7 +6620,7 @@ relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrom id: MS:1001005 name: SEQUEST:CleavesAt is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001006 @@ -6633,14 +6633,14 @@ id: MS:1001007 name: SEQUEST:OutputLines def: "Number of peptide results to show." [PSI:MS] is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001009 name: SEQUEST:DescriptionLines def: "Number of full protein descriptions to show for top N peptides." [PSI:MS] is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001010 @@ -6659,7 +6659,7 @@ id: MS:1001012 name: database source def: "The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other)." [PSI:PI] is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001013 @@ -6679,14 +6679,14 @@ id: MS:1001015 name: database original uri def: "URI, from where the search database was originally downloaded." [PSI:PI] is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001016 name: database version def: "Version of the search database. In mzIdentML use the attribute instead." [PSI:PI] is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001017 @@ -6694,7 +6694,7 @@ name: release date def: "Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term." [PSI:PI] is_a: MS:1001011 ! search database details is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:dateTime +relationship: has_value_type xsd:dateTime relationship: has_structured_representation_in_format MS:1002073 ! mzIdentML format [Term] @@ -6744,13 +6744,13 @@ id: MS:1001025 name: translation table def: "The translation table used to translate the nucleotides to amino acids." [PSI:PI] is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001026 name: SEQUEST:NormalizeXCorrValues is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001027 @@ -6763,14 +6763,14 @@ id: MS:1001028 name: SEQUEST:SequenceHeaderFilter def: "String in the header of a sequence entry for that entry to be searched." [PSI:MS] is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001029 name: number of sequences searched def: "The number of sequences (proteins / nucleotides) from the database search after filtering." [PSI:PI] is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001030 @@ -6778,7 +6778,7 @@ name: number of peptide seqs compared to each spectrum def: "Number of peptide seqs compared to each spectrum." [PSI:PI] is_a: MS:1001011 ! search database details is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001031 @@ -6790,7 +6790,7 @@ is_a: MS:1001080 ! search type id: MS:1001032 name: SEQUEST:SequencePartialFilter is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001035 @@ -6804,21 +6804,21 @@ id: MS:1001036 name: search time taken def: "The time taken to complete the search in seconds." [PSI:PI] is_a: MS:1001184 ! search statistics -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001037 name: SEQUEST:ShowFragmentIons def: "Flag indicating that fragment ions should be shown." [PSI:MS] is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001038 name: SEQUEST:Consensus def: "Specify depth as value of the CVParam." [PSI:PI] is_a: MS:1001006 ! SEQUEST:ViewCV -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001040 @@ -6837,7 +6837,7 @@ id: MS:1001042 name: SEQUEST:LimitTo def: "Specify \"number of dtas shown\" as value of the CVParam." [PSI:PI] is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001044 @@ -6856,56 +6856,56 @@ id: MS:1001046 name: SEQUEST:sort by dCn def: "Sort order of SEQUEST search results by the delta of the normalized correlation score." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001047 name: SEQUEST:sort by dM def: "Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001048 name: SEQUEST:sort by Ions def: "Sort order of SEQUEST search results given by the ions." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001049 name: SEQUEST:sort by MH+ def: "Sort order of SEQUEST search results given by the mass of the protonated ion." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001050 name: SEQUEST:sort by P def: "Sort order of SEQUEST search results given by the probability." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001051 name: multiple enzyme combination rules def: "OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any." [PSI:PI] is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001052 name: SEQUEST:sort by PreviousAminoAcid def: "Sort order of SEQUEST search results given by the previous amino acid." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001053 name: SEQUEST:sort by Ref def: "Sort order of SEQUEST search results given by the reference." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001055 @@ -6937,7 +6937,7 @@ id: MS:1001059 name: SEQUEST:sort by RSp def: "Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide)." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001060 @@ -6979,35 +6979,35 @@ id: MS:1001068 name: SEQUEST:sort by Sp def: "Sort order of SEQUEST search results by the Sp score." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001069 name: SEQUEST:sort by TIC def: "Sort order of SEQUEST search results given by the total ion current." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001070 name: SEQUEST:sort by Scan def: "Sort order of SEQUEST search results given by the scan number." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001071 name: SEQUEST:sort by Sequence def: "Sort order of SEQUEST search results given by the sequence." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001072 name: SEQUEST:sort by Sf def: "Sort order of SEQUEST search results given by the SEQUEST result 'Sf'." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001073 @@ -7062,7 +7062,7 @@ id: MS:1001086 name: SEQUEST:sort by XCorr def: "Sort order of SEQUEST search results by the correlation score." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001087 @@ -7076,7 +7076,7 @@ name: protein description def: "The protein description line from the sequence entry in the source database FASTA file." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute is_a: MS:1001342 ! database sequence details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001089 @@ -7085,7 +7085,7 @@ def: "The taxonomy of the resultant molecule from the search." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute is_a: MS:1001342 ! database sequence details is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001090 @@ -7116,55 +7116,55 @@ id: MS:1001093 name: sequence coverage def: "The percent coverage for the protein based upon the matched peptide sequences (can be calculated)." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:decimal ! The allowed value-type for this CV term +relationship: has_value_type xsd:decimal ! The allowed value-type for this CV term [Term] id: MS:1001094 name: SEQUEST:sort by z def: "Sort order of SEQUEST search results given by the charge." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001095 name: SEQUEST:ProcessAll is_a: MS:1001087 ! SEQUEST:ProcessCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001096 name: SEQUEST:TopPercentMostIntense def: "Specify \"percentage\" as value of the CVParam." [PSI:PI] is_a: MS:1001087 ! SEQUEST:ProcessCV -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001097 name: distinct peptide sequences def: "This counts distinct sequences hitting the protein without regard to a minimal confidence threshold." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001098 name: confident distinct peptide sequences def: "This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001099 name: confident peptide qualification def: "The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001100 name: confident peptide sequence number def: "This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001101 @@ -7176,13 +7176,13 @@ is_a: MS:1001085 ! protein-level identification attribute id: MS:1001102 name: SEQUEST:Chromatogram is_a: MS:1001006 ! SEQUEST:ViewCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001103 name: SEQUEST:InfoAndLog is_a: MS:1001006 ! SEQUEST:ViewCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001104 @@ -7201,7 +7201,7 @@ id: MS:1001106 name: SEQUEST:TopNumber def: "Specify \"number\" as value of the CVParam." [PSI:PI] is_a: MS:1001087 ! SEQUEST:ProcessCV -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001107 @@ -7220,7 +7220,7 @@ id: MS:1001109 name: SEQUEST:CullTo def: "Specify cull string as value of the CVParam." [PSI:PI] is_a: MS:1001087 ! SEQUEST:ProcessCV -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001110 @@ -7232,7 +7232,7 @@ is_a: MS:1002096 ! SEQUEST input parameter id: MS:1001111 name: SEQUEST:Full is_a: MS:1001110 ! SEQUEST:modeCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001112 @@ -7240,7 +7240,7 @@ name: n-terminal flanking residue def: "Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001113 @@ -7248,7 +7248,7 @@ name: c-terminal flanking residue def: "Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001114 @@ -7259,7 +7259,7 @@ is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001115 @@ -7280,7 +7280,7 @@ name: theoretical mass def: "The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001118 @@ -7298,14 +7298,14 @@ is_a: MS:1002473 ! ion series considered in search id: MS:1001120 name: SEQUEST:FormatAndLinks is_a: MS:1001110 ! SEQUEST:modeCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001121 name: number of matched peaks def: "The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001122 @@ -7318,14 +7318,14 @@ id: MS:1001123 name: number of peaks used def: "The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001124 name: number of peaks submitted def: "The number of peaks from the original peaks listed that were submitted to the search engine." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001125 @@ -7333,13 +7333,13 @@ name: manual validation def: "Result of quality estimation: decision of a manual validation." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001126 name: SEQUEST:Fast is_a: MS:1001110 ! SEQUEST:modeCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001127 @@ -7366,42 +7366,42 @@ def: "OBSOLETE Peptide raw area." [PSI:PI] comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844). is_a: MS:1002737 ! peptide-level quantification datatype is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001131 name: error on peptide area def: "Error on peptide area." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001132 name: peptide ratio def: "Peptide ratio." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001133 name: error on peptide ratio def: "Error on peptide ratio." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001134 name: protein ratio def: "Protein ratio." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001135 name: error on protein ratio def: "Error on protein ratio." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001136 @@ -7410,21 +7410,21 @@ def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI] comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855). is_a: MS:1002738 ! protein-level quantification datatype is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001137 name: absolute quantity def: "Absolute quantity in terms of real concentration or molecule copy number in sample." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001138 name: error on absolute quantity def: "Error on absolute quantity." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001139 @@ -7446,7 +7446,7 @@ id: MS:1001141 name: intensity of precursor ion def: "The intensity of the precursor ion." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001142 @@ -7524,7 +7524,7 @@ id: MS:1001154 name: SEQUEST:probability def: "The SEQUEST result 'Probability'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001155 @@ -7532,62 +7532,62 @@ name: SEQUEST:xcorr def: "The SEQUEST result 'XCorr'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001156 name: SEQUEST:deltacn def: "The SEQUEST result 'DeltaCn'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001157 name: SEQUEST:sp def: "The SEQUEST result 'Sp' (protein)." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001158 name: SEQUEST:Uniq is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001159 name: SEQUEST:expectation value def: "The SEQUEST result 'Expectation value'." [PSI:PI] is_a: MS:1001153 ! search engine specific score -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001160 name: SEQUEST:sf def: "The SEQUEST result 'Sf'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001161 name: SEQUEST:matched ions def: "The SEQUEST result 'Matched Ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001162 name: SEQUEST:total ions def: "The SEQUEST result 'Total Ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001163 name: SEQUEST:consensus score def: "The SEQUEST result 'Consensus Score'." [PSI:PI] is_a: MS:1001153 ! search engine specific score -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001164 @@ -7595,7 +7595,7 @@ name: Paragon:unused protscore def: "The Paragon result 'Unused ProtScore'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001165 @@ -7603,70 +7603,70 @@ name: Paragon:total protscore def: "The Paragon result 'Total ProtScore'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001166 name: Paragon:score def: "The Paragon result 'Score'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001167 name: Paragon:confidence def: "The Paragon result 'Confidence'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001168 name: Paragon:expression error factor def: "The Paragon result 'Expression Error Factor'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001169 name: Paragon:expression change p-value def: "The Paragon result 'Expression change P-value'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001170 name: Paragon:contrib def: "The Paragon result 'Contrib'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001171 name: Mascot:score def: "The Mascot result 'Score'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001172 name: Mascot:expectation value def: "The Mascot result 'expectation value'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001173 name: Mascot:matched ions def: "The Mascot result 'Matched ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001174 name: Mascot:total ions def: "The Mascot result 'Total ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001175 @@ -7685,7 +7685,7 @@ id: MS:1001177 name: number of molecular hypothesis considered def: "Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search." [PSI:PI] is_a: MS:1001184 ! search statistics -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001178 @@ -7726,7 +7726,7 @@ comment: This term was made obsolete because now is split into peptide and prote is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001198 ! protein identification confidence metric is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001192 @@ -7734,7 +7734,7 @@ name: Expect value def: "Result of quality estimation: Expect value." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001193 @@ -7742,14 +7742,14 @@ name: confidence score def: "Result of quality estimation: confidence score." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001194 name: quality estimation with decoy database def: "Quality estimation by decoy database." [PSI:PI] is_a: MS:1001060 ! quality estimation method details -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001195 @@ -7794,7 +7794,7 @@ def: "Maximum value of molecular weight filter." [PSI:PI] is_a: MS:1001512 ! Sequence database filters relationship: has_units UO:0000221 ! dalton relationship: has_units UO:0000222 ! kilodalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001202 @@ -7803,21 +7803,21 @@ def: "Minimum value of molecular weight filter." [PSI:PI] is_a: MS:1001512 ! Sequence database filters relationship: has_units UO:0000221 ! dalton relationship: has_units UO:0000222 ! kilodalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001203 name: DB PI filter maximum def: "Maximum value of isoelectric point filter." [PSI:PI] is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001204 name: DB PI filter minimum def: "Minimum value of isoelectric point filter." [PSI:PI] is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001207 @@ -7868,35 +7868,35 @@ name: protein-level global FDR def: "Estimation of the global false discovery rate of proteins." [PSI:PI] is_a: MS:1002705 ! protein-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001215 name: SEQUEST:PeptideSp def: "The SEQUEST result 'Sp' in out file (peptide)." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001217 name: SEQUEST:PeptideRankSp def: "The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001218 name: SEQUEST:PeptideNumber def: "The SEQUEST result '#' in out file (peptide)." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001219 name: SEQUEST:PeptideIdnumber def: "The SEQUEST result 'Id#' in out file (peptide)." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001220 @@ -8081,7 +8081,7 @@ name: local FDR def: "Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001251 @@ -8179,21 +8179,21 @@ id: MS:1001268 name: programmer def: "Programmer role." [PSI:PI] is_a: MS:1001266 ! role type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001269 name: instrument vendor def: "Instrument vendor role." [PSI:PI] is_a: MS:1001266 ! role type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001270 name: lab personnel def: "Lab personnel role." [PSI:PI] is_a: MS:1001266 ! role type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001271 @@ -8236,7 +8236,7 @@ id: MS:1001283 name: decoy DB accession regexp def: "Specify the regular expression for decoy accession numbers." [PSI:PI] is_a: MS:1001450 ! decoy DB details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001284 @@ -8357,7 +8357,7 @@ id: MS:1001301 name: protein rank def: "The rank of the protein in a list sorted by the search engine." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001302 @@ -8464,70 +8464,70 @@ id: MS:1001316 name: Mascot:SigThreshold def: "Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05)." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001317 name: Mascot:MaxProteinHits def: "The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001318 name: Mascot:ProteinScoringMethod def: "Mascot protein scoring method; either 'Standard' or 'MudPIT'." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001319 name: Mascot:MinMSMSThreshold def: "Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001320 name: Mascot:ShowHomologousProteinsWithSamePeptides def: "If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001321 name: Mascot:ShowHomologousProteinsWithSubsetOfPeptides def: "If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001322 name: Mascot:RequireBoldRed def: "Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001323 name: Mascot:UseUnigeneClustering def: "If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001324 name: Mascot:IncludeErrorTolerantMatches def: "If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included." [http://www.matrixscience.com/help/error_tolerant_help.html] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001325 name: Mascot:ShowDecoyMatches def: "If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001326 @@ -8541,28 +8541,28 @@ id: MS:1001328 name: OMSSA:evalue def: "OMSSA E-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001329 name: OMSSA:pvalue def: "OMSSA p-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001330 name: X\!Tandem:expect def: "The X!Tandem expectation value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001331 name: X\!Tandem:hyperscore def: "The X!Tandem hyperscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001332 @@ -8725,7 +8725,7 @@ id: MS:1001358 name: msmsEval quality def: "This term reports the quality of the spectrum assigned by msmsEval." [PSI:PI] is_a: MS:1001357 ! spectrum quality descriptions -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001359 @@ -8738,7 +8738,7 @@ id: MS:1001360 name: alternate single letter codes def: "List of standard residue one letter codes which are used to replace a non-standard." [PSI:PI] is_a: MS:1001359 ! ambiguous residues -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001361 @@ -8746,14 +8746,14 @@ name: alternate mass def: "List of masses a non-standard letter code is replaced with." [PSI:PI] is_a: MS:1001359 ! ambiguous residues relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001362 name: number of unmatched peaks def: "The number of unmatched peaks." [PSI:PI] is_a: MS:1002345 ! PSM-level attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001363 @@ -8767,7 +8767,7 @@ name: peptide sequence-level global FDR def: "Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1002703 ! peptide sequence-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001365 @@ -8804,166 +8804,166 @@ id: MS:1001370 name: Mascot:homology threshold def: "The Mascot result 'homology threshold'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001371 name: Mascot:identity threshold def: "The Mascot result 'identity threshold'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001372 name: SEQUEST:Sequences is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001373 name: SEQUEST:TIC def: "SEQUEST total ion current." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001374 name: SEQUEST:Sum is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001375 name: Phenyx:Instrument Type def: "The instrument type parameter value in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001376 name: Phenyx:Scoring Model def: "The selected scoring model in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001377 name: Phenyx:Default Parent Charge def: "The default parent charge value in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001378 name: Phenyx:Trust Parent Charge def: "The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001379 name: Phenyx:Turbo def: "The turbo mode parameter in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001380 name: Phenyx:Turbo:ErrorTol def: "The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001381 name: Phenyx:Turbo:Coverage def: "The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001382 name: Phenyx:Turbo:Series def: "The list of ion series considered in the turbo mode of Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001383 name: Phenyx:MinPepLength def: "The minimal number of residues for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001384 name: Phenyx:MinPepzscore def: "The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001385 name: Phenyx:MaxPepPvalue def: "The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001386 name: Phenyx:AC Score def: "The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001387 name: Phenyx:Conflict Resolution def: "The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001388 name: Phenyx:AC def: "The primary sequence database identifier of a protein in Phenyx." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001389 name: Phenyx:ID def: "A secondary sequence database identifier of a protein in Phenyx." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001390 name: Phenyx:Score def: "The protein score of a protein match in Phenyx." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001391 name: Phenyx:Peptides1 def: "First number of phenyx result \"#Peptides\"." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001392 name: Phenyx:Peptides2 def: "Second number of phenyx result \"#Peptides\"." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001393 name: Phenyx:Auto def: "The value of the automatic peptide acceptance filter in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001394 @@ -8971,14 +8971,14 @@ name: Phenyx:User def: "The value of the user-defined peptide acceptance filter in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001395 name: Phenyx:Pepzscore def: "The z-score value of a peptide sequence match in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001396 @@ -8986,14 +8986,14 @@ name: Phenyx:PepPvalue def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001397 name: Phenyx:NumberOfMC def: "The number of missed cleavages of a peptide sequence in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001398 @@ -9001,7 +9001,7 @@ name: Phenyx:Modif def: "The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001399 @@ -9056,7 +9056,7 @@ id: MS:1001410 name: translation start codons def: "The translation start codons used to translate the nucleotides to amino acids." [PSI:PI] is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001411 @@ -9072,7 +9072,7 @@ relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001413 @@ -9082,7 +9082,7 @@ relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001414 @@ -9091,7 +9091,7 @@ def: "OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the is_a: MS:1001405 ! spectrum identification result details is_obsolete: true replaced_by: MS:1000797 -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001415 @@ -9100,7 +9100,7 @@ def: "OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold is_a: MS:1001405 ! spectrum identification result details is_obsolete: true replaced_by: MS:1000798 -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001416 @@ -9109,35 +9109,35 @@ def: "OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum titl is_a: MS:1001405 ! spectrum identification result details is_obsolete: true replaced_by: MS:1000796 -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001417 name: SpectraST:dot def: "SpectraST dot product of two spectra, measuring spectral similarity." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001418 name: SpectraST:dot_bias def: "SpectraST measure of how much of the dot product is dominated by a few peaks." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001419 name: SpectraST:discriminant score F def: "SpectraST spectrum score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001420 name: SpectraST:delta def: "SpectraST normalised difference between dot product of top hit and runner-up." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001421 @@ -9156,188 +9156,188 @@ id: MS:1001423 name: translation table description def: "A URL that describes the translation table used to translate the nucleotides to amino acids." [PSI:PI] is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001424 name: ProteinExtractor:Methodname def: "Name of the used method in the ProteinExtractor algorithm." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001425 name: ProteinExtractor:GenerateNonRedundant def: "Flag indicating if a non redundant scoring should be generated." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001426 name: ProteinExtractor:IncludeIdentified def: "Flag indicating if identified proteins should be included." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001427 name: ProteinExtractor:MaxNumberOfProteins def: "The maximum number of proteins to consider." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001428 name: ProteinExtractor:MaxProteinMass def: "The maximum considered mass for a protein." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001429 name: ProteinExtractor:MinNumberOfPeptides def: "The minimum number of proteins to consider." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001430 name: ProteinExtractor:UseMascot def: "Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001431 name: ProteinExtractor:MascotPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001432 name: ProteinExtractor:MascotUniqueScore def: "In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001433 name: ProteinExtractor:MascotUseIdentityScore is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001434 name: ProteinExtractor:MascotWeighting def: "Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001435 name: ProteinExtractor:UseSequest def: "Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001436 name: ProteinExtractor:SequestPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001437 name: ProteinExtractor:SequestUniqueScore def: "In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001438 name: ProteinExtractor:SequestWeighting def: "Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001439 name: ProteinExtractor:UseProteinSolver def: "Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001440 name: ProteinExtractor:ProteinSolverPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001441 name: ProteinExtractor:ProteinSolverUniqueScore def: "In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001442 name: ProteinExtractor:ProteinSolverWeighting def: "Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001443 name: ProteinExtractor:UsePhenyx def: "Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001444 name: ProteinExtractor:PhenyxPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001445 name: ProteinExtractor:PhenyxUniqueScore def: "In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001446 name: ProteinExtractor:PhenyxWeighting def: "Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001447 name: prot:FDR threshold def: "False-discovery rate threshold for proteins." [PSI:PI] is_a: MS:1002485 ! protein-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001448 name: pep:FDR threshold def: "False-discovery rate threshold for peptides." [PSI:PI] is_a: MS:1002484 ! peptide-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001449 name: OMSSA e-value threshold def: "Threshold for OMSSA e-value for quality estimation." [PSI:PI] is_a: MS:1002099 ! OMSSA input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001450 @@ -9350,7 +9350,7 @@ id: MS:1001451 name: decoy DB generation algorithm def: "Name of algorithm used for decoy generation." [PSI:PI] is_a: MS:1001450 ! decoy DB details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001452 @@ -9442,28 +9442,28 @@ id: MS:1001467 name: taxonomy: NCBI TaxID def: "This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens." [PSI:PI] is_a: MS:1001089 ! molecule taxonomy -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001468 name: taxonomy: common name def: "This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] is_a: MS:1001089 ! molecule taxonomy -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001469 name: taxonomy: scientific name def: "This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] is_a: MS:1001089 ! molecule taxonomy -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001470 name: taxonomy: Swiss-Prot ID def: "This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] is_a: MS:1001089 ! molecule taxonomy -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001471 @@ -9601,21 +9601,21 @@ id: MS:1001491 name: percolator:Q value def: "Percolator:Q value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001492 name: percolator:score def: "Percolator:score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001493 name: percolator:PEP def: "Posterior error probability." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001494 @@ -9628,91 +9628,91 @@ id: MS:1001495 name: ProteinScape:SearchResultId def: "The SearchResultId of this peptide as SearchResult in the ProteinScape database." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001496 name: ProteinScape:SearchEventId def: "The SearchEventId of the SearchEvent in the ProteinScape database." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001497 name: ProteinScape:ProfoundProbability def: "The Profound probability score stored by ProteinScape." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001498 name: Profound:z value def: "The Profound z value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001499 name: Profound:Cluster def: "The Profound cluster score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001500 name: Profound:ClusterRank def: "The Profound cluster rank." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001501 name: MSFit:Mowse score def: "The MSFit Mowse score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001502 name: Sonar:Score def: "The Sonar score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001503 name: ProteinScape:PFFSolverExp def: "The ProteinSolver exp value stored by ProteinScape." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001504 name: ProteinScape:PFFSolverScore def: "The ProteinSolver score stored by ProteinScape." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001505 name: ProteinScape:IntensityCoverage def: "The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001506 name: ProteinScape:SequestMetaScore def: "The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001507 name: ProteinExtractor:Score def: "The score calculated by ProteinExtractor." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001508 @@ -9749,14 +9749,14 @@ id: MS:1001513 name: DB sequence filter pattern def: "DB sequence filter pattern." [PSI:MS] is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001514 name: DB accession filter string def: "DB accession filter string." [PSI:MS] is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001515 @@ -9818,7 +9818,7 @@ name: fragment neutral loss def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001525 @@ -9826,7 +9826,7 @@ name: precursor neutral loss def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001526 @@ -10084,42 +10084,42 @@ id: MS:1001568 name: Scaffold:Peptide Probability def: "Scaffold peptide probability score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001569 name: IdentityE Score def: "Waters IdentityE peptide score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001570 name: ProteinLynx:Log Likelihood def: "ProteinLynx log likelihood score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001571 name: ProteinLynx:Ladder Score def: "Waters ProteinLynx Ladder score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001572 name: SpectrumMill:Score def: "Spectrum mill peptide score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001573 name: SpectrumMill:SPI def: "SpectrumMill SPI score (%)." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001574 @@ -10132,42 +10132,42 @@ id: MS:1001575 name: Scaffold: Minimum Peptide Count def: "Minimum number of peptides a protein must have to be accepted." [PSI:PI] is_a: MS:1002106 ! Scaffold input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001576 name: Scaffold: Minimum Protein Probability def: "Minimum protein probability a protein must have to be accepted." [PSI:PI] is_a: MS:1002106 ! Scaffold input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001577 name: Scaffold: Minimum Peptide Probability def: "Minimum probability a peptide must have to be accepted for protein scoring." [PSI:PI] is_a: MS:1002106 ! Scaffold input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001578 name: minimum number of enzymatic termini def: "Minimum number of enzymatic termini a peptide must have to be accepted." [PSI:PI] is_a: MS:1002094 ! common search engine input parameter -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001579 name: Scaffold:Protein Probability def: "Scaffold protein probability score." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001580 name: SpectrumMill:Discriminant Score def: "Discriminant score from Agilent SpectrumMill software." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001581 @@ -10176,7 +10176,7 @@ def: "The DC potential applied to the asymmetric waveform in FAIMS that compensa synonym: "FAIMS CV" EXACT [] is_a: MS:1002892 ! ion mobility attribute relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001582 @@ -10243,14 +10243,14 @@ id: MS:1001591 name: anchor protein def: "A representative protein selected from a set of sequence same-set or spectrum same-set proteins." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001592 name: family member protein def: "A protein with significant homology to another protein, but some distinguishing peptide matches." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001593 @@ -10263,49 +10263,49 @@ id: MS:1001594 name: sequence same-set protein def: "A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001595 name: spectrum same-set protein def: "A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001596 name: sequence sub-set protein def: "A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001597 name: spectrum sub-set protein def: "A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001598 name: sequence subsumable protein def: "A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001599 name: spectrum subsumable protein def: "A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001600 name: protein inference confidence category def: "Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable)." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001601 @@ -10314,7 +10314,7 @@ def: "OBSOLETE Name and location of the .raw file or files." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001602 @@ -10323,7 +10323,7 @@ def: "OBSOLETE Path and name of the .srf (SEQUEST Result Format) file." [PSI:MS] comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001603 @@ -10332,7 +10332,7 @@ def: "OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, comment: This term was made obsolete because it's recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001604 @@ -10341,14 +10341,14 @@ def: "OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any)." [ comment: This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001605 name: ProteomeDiscoverer:Spectrum Selector:Lower RT Limit def: "Lower retention-time limit." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001606 @@ -10357,28 +10357,28 @@ def: "OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, Se comment: This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001607 name: ProteomeDiscoverer:Max Precursor Mass def: "Maximum mass limit of a singly charged precursor ion." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001608 name: ProteomeDiscoverer:Min Precursor Mass def: "Minimum mass limit of a singly charged precursor ion." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001609 name: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count def: "Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001610 @@ -10387,7 +10387,7 @@ def: "OBSOLETE Level of the mass spectrum (MS2 ... MS10)." [PSI:MS] comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001611 @@ -10396,21 +10396,21 @@ def: "OBSOLETE Polarity mode (positive or negative)." [PSI:MS] comment: This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001612 name: ProteomeDiscoverer:Spectrum Selector:Precursor Selection def: "Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001613 name: ProteomeDiscoverer:SN Threshold def: "Signal-to-Noise ratio below which peaks are removed." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001614 @@ -10419,119 +10419,119 @@ def: "OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001615 name: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold def: "Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001616 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements def: "Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001617 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements def: "Specifies the charge state of the precursor ions, if it is not defined in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001618 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements def: "Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001619 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements def: "Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001620 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements def: "Specifies the polarity of the ions monitored if it is not included in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001621 name: ProteomeDiscoverer:Spectrum Selector:Upper RT Limit def: "Upper retention-time limit." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001622 name: ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset def: "Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001623 name: ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass def: "Maximum allowed mass of a neutral loss." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001624 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor def: "Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001625 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks def: "Determines whether neutral loss peaks are removed from ETD and ECD spectra." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001626 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses def: "Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001627 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones def: "Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001628 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak def: "Determines whether precursor artifact peaks from the MS2 input spectra are removed." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001629 name: ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch def: "Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001630 name: ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch def: "Determines whether spectra from different MS order scans can be grouped together." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001631 @@ -10540,21 +10540,21 @@ def: "OBSOLETE Chromatographic window where precursors to be grouped must reside comment: This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001632 name: ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion def: "Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001633 name: ProteomeDiscoverer:Xtract:Highest Charge def: "Highest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001634 @@ -10563,14 +10563,14 @@ def: "OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measu comment: This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001635 name: ProteomeDiscoverer:Xtract:Lowest Charge def: "Lowest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001636 @@ -10579,70 +10579,70 @@ def: "OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measur comment: This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001637 name: ProteomeDiscoverer:Xtract:Monoisotopic Mass Only def: "Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001638 name: ProteomeDiscoverer:Xtract:Overlapping Remainder def: "Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001639 name: ProteomeDiscoverer:Xtract:Required Fitting Accuracy def: "Accuracy required for a pattern fit to be considered valid." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001640 name: ProteomeDiscoverer:Xtract:Resolution At 400 def: "Resolution at mass 400." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001641 name: ProteomeDiscoverer:Lowest Charge State def: "Minimum charge state below which peptides are filtered out." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001642 name: ProteomeDiscoverer:Highest Charge State def: "Maximum charge above which peptides are filtered out." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001643 name: ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores def: "Determines whether spectra with scores above the threshold score are retained rather than filtered out." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001644 name: ProteomeDiscoverer:Dynamic Modification def: "Determine dynamic post-translational modifications (PTMs)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001645 name: ProteomeDiscoverer:Static Modification def: "Static Modification to all occurrences of a named amino acid." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001646 @@ -10651,42 +10651,42 @@ def: "OBSOLETE Determines whether the Proteome Discoverer application searches a comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001647 name: ProteomeDiscoverer:Mascot:Error tolerant Search def: "Determines whether to search error-tolerant." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001648 name: ProteomeDiscoverer:Mascot:Max MGF File Size def: "Maximum size of the .mgf (Mascot Generic Format) file in MByte." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001649 name: ProteomeDiscoverer:Mascot:Mascot Server URL def: "URL (Uniform resource Locator) of the Mascot server." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001650 name: ProteomeDiscoverer:Mascot:Number of attempts to submit the search def: "Number of attempts to submit the Mascot search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001651 name: ProteomeDiscoverer:Mascot:X Static Modification def: "Number of attempts to submit the Mascot search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001652 @@ -10695,14 +10695,14 @@ def: "OBSOLETE Name of the user submitting the Mascot search." [PSI:MS] comment: This term was made obsolete because it's recommended to use researcher (MS:1001271) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001653 name: ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search def: "Time interval between attempts to submit a search in seconds." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001654 @@ -10711,7 +10711,7 @@ def: "OBSOLETE Specifies the enzyme reagent used for protein digestion." [PSI:MS comment: This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001655 @@ -10720,28 +10720,28 @@ def: "OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu." [P comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001656 name: Mascot:Instrument def: "Type of instrument used to acquire the data in the raw file." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001657 name: ProteomeDiscoverer:Maximum Missed Cleavage Sites def: "Maximum number of missed cleavage sites to consider during the digest." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001658 name: ProteomeDiscoverer:Mascot:Peptide CutOff Score def: "Minimum score in the IonScore column that each peptide must exceed in order to be reported." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001659 @@ -10750,14 +10750,14 @@ def: "OBSOLETE Mass window for which precursor ions are considered to be the sam comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001660 name: ProteomeDiscoverer:Mascot:Protein CutOff Score def: "Minimum protein score in the IonScore column that each protein must exceed in order to be reported." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001661 @@ -10766,28 +10766,28 @@ def: "OBSOLETE Database to use in the search (configured on the Mascot server)." comment: This term was made obsolete because it's recommended to use database name (MS:1001013) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001662 name: ProteomeDiscoverer:Mascot:Protein Relevance Factor def: "Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001663 name: ProteomeDiscoverer:Target FDR Relaxed def: "Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001664 name: ProteomeDiscoverer:Target FDR Strict def: "Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001665 @@ -10796,7 +10796,7 @@ def: "OBSOLETE Limits searches to entries from a particular species or group of comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001666 @@ -10805,7 +10805,7 @@ def: "OBSOLETE Use average mass for the precursor." [PSI:MS] comment: This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001667 @@ -10814,105 +10814,105 @@ def: "OBSOLETE Determines whether to use MudPIT or normal scoring." [PSI:MS] comment: This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead. is_a: MS:1002095 ! Mascot input parameter is_obsolete: true -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001668 name: ProteomeDiscoverer:Absolute XCorr Threshold def: "Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001669 name: ProteomeDiscoverer:SEQUEST:Calculate Probability Score def: "Determines whether to calculate a probability score for every peptide match." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001670 name: ProteomeDiscoverer:SEQUEST:CTerminal Modification def: "Dynamic C-terminal modification that is used during the search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001671 name: ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage def: "Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001672 name: ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide def: "Maximum number of identical modifications that a single peptide can have." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001673 name: ProteomeDiscoverer:Max Modifications Per Peptide def: "Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001674 name: ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered def: "Maximum number of peptides that are searched and scored per spectrum." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001675 name: ProteomeDiscoverer:Maximum Peptides Output def: "Maximum number of peptide matches reported per spectrum." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001676 name: ProteomeDiscoverer:Maximum Protein References Per Peptide def: "Maximum number of proteins that a single identified peptide can be associated with during protein assembly." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001677 name: ProteomeDiscoverer:SEQUEST:NTerminal Modification def: "Dynamic N-terminal modification that is used during the search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001678 name: ProteomeDiscoverer:Peptide CTerminus def: "Static modification for the C terminal of the peptide used during the search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001679 name: ProteomeDiscoverer:Peptide NTerminus def: "Static modification for the N terminal of the peptide used during the search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001680 name: ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor def: "Specifies a factor to apply to the protein score." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001681 name: ProteomeDiscoverer:Protein Relevance Threshold def: "Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001682 @@ -10921,133 +10921,133 @@ def: "OBSOLETE Determines whether the Proteome Discoverer application searches a comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001683 name: ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses def: "Use average masses for the fragments." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001684 name: ProteomeDiscoverer:Use Neutral Loss a Ions def: "Determines whether a ions with neutral loss are used for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001685 name: ProteomeDiscoverer:Use Neutral Loss b Ions def: "Determines whether b ions with neutral loss are used for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001686 name: ProteomeDiscoverer:Use Neutral Loss y Ions def: "Determines whether y ions with neutral loss are used for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001687 name: ProteomeDiscoverer:Use Neutral Loss z Ions def: "Determines whether z ions with neutral loss are used for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001688 name: ProteomeDiscoverer:SEQUEST:Weight of a Ions def: "Uses a ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001689 name: ProteomeDiscoverer:SEQUEST:Weight of b Ions def: "Uses b ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001690 name: ProteomeDiscoverer:SEQUEST:Weight of c Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001691 name: ProteomeDiscoverer:SEQUEST:Weight of d Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001692 name: ProteomeDiscoverer:SEQUEST:Weight of v Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001693 name: ProteomeDiscoverer:SEQUEST:Weight of w Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001694 name: ProteomeDiscoverer:SEQUEST:Weight of x Ions def: "Uses x ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001695 name: ProteomeDiscoverer:SEQUEST:Weight of y Ions def: "Uses y ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001696 name: ProteomeDiscoverer:SEQUEST:Weight of z Ions def: "Uses z ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001697 name: ProteomeDiscoverer:ZCore:Protein Score Cutoff def: "Sets a minimum protein score that each protein must exceed in order to be reported." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001698 name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method def: "Specifies which peak to select if more than one peak is found inside the integration window." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001699 name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance def: "Specifies the mass-to-charge window that enables one to look for the reporter peaks." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001700 name: ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method def: "Quantitation method for isobarically labeled quantitation." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001701 @@ -11056,133 +11056,133 @@ def: "OBSOLETE Format of the exported spectra (dta, mgf or mzData)." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001702 name: ProteomeDiscoverer:Spectrum Exporter:File name def: "Name of the output file that contains the exported data." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001703 name: ProteomeDiscoverer:Search Modifications Only For Identified Proteins def: "Influences the modifications search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001704 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1 def: "Standard high confidence XCorr parameter for charge = 1." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001705 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2 def: "Standard high confidence XCorr parameter for charge = 2." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001706 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3 def: "Standard high confidence XCorr parameter for charge = 3." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001707 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4 def: "Standard high confidence XCorr parameter for charge >= 4." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001708 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1 def: "Standard medium confidence XCorr parameter for charge = 1." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001709 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2 def: "Standard medium confidence XCorr parameter for charge = 2." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001710 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3 def: "Standard medium confidence XCorr parameter for charge = 3." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001711 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4 def: "Standard medium confidence XCorr parameter for charge >= 4." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001712 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1 def: "FT high confidence XCorr parameter for charge = 1." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001713 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2 def: "FT high confidence XCorr parameter for charge = 2." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001714 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3 def: "FT high confidence XCorr parameter for charge = 3." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001715 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4 def: "FT high confidence XCorr parameter for charge >= 4." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001716 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1 def: "FT medium confidence XCorr parameter for charge = 1." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001717 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2 def: "FT medium confidence XCorr parameter for charge = 2." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001718 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3 def: "FT medium confidence XCorr parameter for charge = 3." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001719 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4 def: "FT medium confidence XCorr parameter for charge >= 4." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001720 @@ -11191,7 +11191,7 @@ def: "OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001721 @@ -11200,7 +11200,7 @@ def: "OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001722 @@ -11209,7 +11209,7 @@ def: "OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001723 @@ -11218,77 +11218,77 @@ def: "OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001724 name: ProteomeDiscoverer:Static Modification for X def: "Static Modification for X." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001725 name: ProteomeDiscoverer:Initial minimal peptide probability def: "Minimal initial peptide probability to contribute to analysis." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001726 name: ProteomeDiscoverer:Minimal peptide probability def: "Minimum adjusted peptide probability contributing to protein probability." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001727 name: ProteomeDiscoverer:Minimal peptide weight def: "Minimum peptide weight contributing to protein probability." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001728 name: ProteomeDiscoverer:Number of input1 spectra def: "Number of spectra from 1+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001729 name: ProteomeDiscoverer:Number of input2 spectra def: "Number of spectra from 2+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001730 name: ProteomeDiscoverer:Number of input3 spectra def: "Number of spectra from 3+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001731 name: ProteomeDiscoverer:Number of input4 spectra def: "Number of spectra from 4+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001732 name: ProteomeDiscoverer:Number of input5 spectra def: "Number of spectra from 5+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001733 name: ProteomeDiscoverer:Number of predicted correct proteins def: "Total number of predicted correct protein ids (sum of probabilities)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001734 @@ -11297,7 +11297,7 @@ def: "OBSOLETE Sample organism (used for annotation purposes)." [PSI:MS] comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001735 @@ -11306,14 +11306,14 @@ def: "OBSOLETE Full path database name." [PSI:MS] comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001736 name: ProteomeDiscoverer:Residue substitution list def: "Residues considered equivalent when comparing peptides." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001737 @@ -11322,7 +11322,7 @@ def: "OBSOLETE File type (if not pepXML)." [PSI:MS] comment: This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001738 @@ -11331,7 +11331,7 @@ def: "OBSOLETE Input pepXML files." [PSI:MS] comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001739 @@ -11340,21 +11340,21 @@ def: "OBSOLETE Input pepXML files (old)." [PSI:MS] comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001740 name: ProteomeDiscoverer:WinCyg reference database def: "Windows full path for database." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001741 name: ProteomeDiscoverer:WinCyg source files def: "Windows pepXML file names." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001742 @@ -11367,126 +11367,126 @@ id: MS:1001743 name: ProteomeDiscoverer:Mascot:Weight of A Ions def: "Determines if to use A ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001744 name: ProteomeDiscoverer:Mascot:Weight of B Ions def: "Determines if to use B ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001745 name: ProteomeDiscoverer:Mascot:Weight of C Ions def: "Determines if to use C ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001746 name: ProteomeDiscoverer:Mascot:Weight of D Ions def: "Determines if to use D ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001747 name: ProteomeDiscoverer:Mascot:Weight of V Ions def: "Determines if to use V ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001748 name: ProteomeDiscoverer:Mascot:Weight of W Ions def: "Determines if to use W ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001749 name: ProteomeDiscoverer:Mascot:Weight of X Ions def: "Determines if to use X ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001750 name: ProteomeDiscoverer:Mascot:Weight of Y Ions def: "Determines if to use Y ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001751 name: ProteomeDiscoverer:Mascot:Weight of Z Ions def: "Determines if to use z ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001752 name: ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation def: "Determines if to use precursor reevaluation." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001753 name: ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly def: "Signal-to-Noise ratio below which peaks are removed (in FT mode only)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001754 name: ProteomeDiscoverer:Mascot:Please Do not Touch this def: "Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001755 name: contact phone number def: "Phone number of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001756 name: contact fax number def: "Fax number for the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001757 name: contact toll-free phone number def: "Toll-free phone number of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001758 name: Mascot:SigThresholdType def: "Significance threshold type used in Mascot reporting (either 'identity' or 'homology')." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001759 name: Mascot:ProteinGrouping def: "Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering')." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001760 name: Percolator:features def: "List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'." [PSI:MS] is_a: MS:1002107 ! Percolator input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001761 @@ -11685,7 +11685,7 @@ id: MS:1001793 name: Mascot:PreferredTaxonomy def: "NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001795 @@ -11779,7 +11779,7 @@ id: MS:1001808 name: technical replicate def: "The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'." [PSI:MS] is_a: MS:1001807 ! study variable attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001809 @@ -11816,21 +11816,21 @@ id: MS:1001814 name: generic experimental condition def: "The experimental condition is given in the value of this term." [PSI:MS] is_a: MS:1001807 ! study variable attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001815 name: time series, time point X def: "The experimental design followed a time series design. The time point of this run is given in the value of this term." [PSI:MS] is_a: MS:1001807 ! study variable attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001816 name: dilution series, concentration X def: "The experimental design followed a dilution series design. The concentration of this run is given in the value of this term." [PSI:MS] is_a: MS:1001807 ! study variable attribute -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001817 @@ -11909,7 +11909,7 @@ id: MS:1001829 name: SRM transition ID def: "Identifier for an SRM transition in an external document describing additional information about the transition." [PSI:MS] is_a: MS:1001828 ! feature attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001830 @@ -11929,7 +11929,7 @@ id: MS:1001832 name: quantitation software comment or customizations def: "Quantitation software comment or any customizations to the default setup of the software." [PSI:PI] is_a: MS:1001129 ! quantification information -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001833 @@ -11978,35 +11978,35 @@ id: MS:1001840 name: LC-MS feature intensity def: "Maximum peak intensity of the LC-MS feature." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001841 name: LC-MS feature volume def: "Real (intensity times area) volume of the LC-MS feature." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001842 name: sequence-level spectral count def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001843 name: MS1 feature maximum intensity def: "Maximum intensity of MS1 feature." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001844 name: MS1 feature area def: "Area of MS1 feature." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001845 @@ -12015,21 +12015,21 @@ def: "OBSOLETE Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI] comment: This term was made obsolete because it was a duplication of MS:1001844. is_a: MS:1001805 ! quantification datatype is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001846 name: isotopic pattern area def: "Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N)." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001847 name: reporter ion intensity def: "Intensity of MS2 reporter ion (e.g. iTraq)." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001848 @@ -12044,84 +12044,84 @@ def: "OBSOLETE Peptide quantification value calculated as sum of MatchedFeature comment: This term was made obsolete because the concept MatchedFeature was dropped. is_a: MS:1002735 ! feature-level quantification datatype is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001850 name: normalized peptide value def: "Normalized peptide value." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001851 name: protein value: sum of peptide values def: "Protein quantification value calculated as sum of peptide values." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001852 name: normalized protein value def: "Normalized protein value." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001853 name: max fold change def: "Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis)." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001854 name: ANOVA p-value def: "Global datatype: p-value of ANOVA of group means (e.g. Progenesis)." [PSI:PI] is_a: MS:1002072 ! p-value -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001855 name: t-test p-value def: "P-value of t-Test of two groups." [PSI:PI] is_a: MS:1002072 ! p-value -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001856 name: reporter ion raw value def: "Intensity (or area) of MS2 reporter ion (e.g. iTraq)." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001857 name: reporter ion normalized value def: "Normalized value of MS2 reporter ion (e.g. iTraq)." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001858 name: XIC area def: "Area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001859 name: normalized XIC area def: "Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001860 name: protein value: mean of peptide ratios def: "Protein quantification value calculated as mean of peptide ratios." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001861 @@ -12171,7 +12171,7 @@ name: distinct peptide-level q-value def: "Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry)." [PSI:PI] is_a: MS:1002484 ! peptide-level statistical threshold relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001869 @@ -12179,7 +12179,7 @@ name: protein-level q-value def: "Estimation of the q-value for proteins." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001870 @@ -12187,7 +12187,7 @@ name: peptide sequence-level p-value def: "Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001871 @@ -12195,7 +12195,7 @@ name: protein-level p-value def: "Estimation of the p-value for proteins." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001872 @@ -12203,7 +12203,7 @@ name: peptide sequence-level e-value def: "Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001873 @@ -12211,7 +12211,7 @@ name: protein-level e-value def: "Estimation of the e-value for proteins." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001874 @@ -12221,14 +12221,14 @@ comment: This term was made obsolete because it was split into the more specific is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001875 name: modification motif def: "The regular expression describing the sequence motif for a modification." [PSI:PI] is_a: MS:1001056 ! modification specificity rule -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001876 @@ -12257,7 +12257,7 @@ name: offset voltage def: "The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001880 @@ -12282,14 +12282,14 @@ id: MS:1001883 name: coefficient of variation def: "Variation of a set of signal measurements calculated as the standard deviation relative to the mean." [PSI:MS] is_a: MS:1001882 ! transition validation attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001884 name: signal-to-noise ratio def: "Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal." [PSI:MS] is_a: MS:1001882 ! transition validation attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001885 @@ -12297,7 +12297,7 @@ name: command-line parameters def: "Parameters string passed to a command-line interface software application, omitting the executable name." [PSI:MS] is_a: MS:1000630 ! data processing parameter is_a: MS:1003201 ! library provenance attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001886 @@ -12329,119 +12329,119 @@ id: MS:1001890 name: Progenesis:protein normalised abundance def: "The data type normalised abundance for proteins produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001891 name: Progenesis:peptide normalised abundance def: "The data type normalised abundance for peptides produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001892 name: Progenesis:protein raw abundance def: "The data type raw abundance for proteins produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001893 name: Progenesis:peptide raw abundance def: "The data type raw abundance for peptide produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001894 name: Progenesis:confidence score def: "The data type confidence score produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001895 name: Progenesis:peptide count def: "The data type peptide count produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001896 name: Progenesis:feature intensity def: "The data type feature intensity produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001897 name: MaxQuant:peptide counts (unique) def: "The data type peptide counts (unique) produced by MaxQuant." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001898 name: MaxQuant:peptide counts (all) def: "The data type peptide counts (all) produced by MaxQuant." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001899 name: MaxQuant:peptide counts (razor+unique) def: "The data type peptide counts (razor+unique) produced by MaxQuant." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001900 name: MaxQuant:sequence length def: "The data type sequence length produced by MaxQuant." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001901 name: MaxQuant:PEP def: "The data type PEP (posterior error probability) produced by MaxQuant." [PSI:MS] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001902 name: MaxQuant:LFQ intensity def: "The data type LFQ intensity produced by MaxQuant." [PSI:MS] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001903 name: MaxQuant:feature intensity def: "The data type feature intensity produced by MaxQuant." [PSI:MS] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001904 name: MaxQuant:MS/MS count def: "The data type MS2 count produced by MaxQuant." [PSI:MS] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001905 name: emPAI value def: "The emPAI value of protein abundance, produced from the emPAI algorithm." [PSI:MS] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001906 name: APEX value def: "The APEX value of protein abundance, produced from the APEX software." [PSI:MS] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001907 @@ -12450,7 +12450,7 @@ def: "The full width of a retention time window for a chromatographic peak." [PS is_a: MS:1000915 ! retention time window attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001908 @@ -12490,7 +12490,7 @@ name: S-lens voltage def: "Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001914 @@ -12533,14 +12533,14 @@ id: MS:1001919 name: ProteomeXchange accession number def: "Main identifier of a ProteomeXchange dataset." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001921 name: ProteomeXchange accession number version number def: "Version number of a ProteomeXchange accession number." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001922 @@ -12549,63 +12549,63 @@ def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org] synonym: "doi" EXACT [] is_a: MS:1000878 ! external reference identifier relationship: has_regexp MS:1002480 ! (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+) -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001923 name: external reference keyword def: "Free text attribute that can enrich the information about an entity." [PSI:PI] is_a: MS:1002840 ! external reference data -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001924 name: journal article keyword def: "Keyword present in a scientific publication." [PSI:PI] is_a: MS:1001923 ! external reference keyword -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001925 name: submitter keyword def: "Keyword assigned by the data submitter." [PSI:PI] is_a: MS:1001923 ! external reference keyword -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001926 name: curator keyword def: "Keyword assigned by a data curator." [PSI:PI] is_a: MS:1001923 ! external reference keyword -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001927 name: Tranche file hash def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001928 name: Tranche project hash def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001929 name: PRIDE experiment URI def: "URI that allows the access to one experiment in the PRIDE database." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001930 name: PRIDE project URI def: "URI that allows the access to one project in the PRIDE database." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001931 @@ -12618,14 +12618,14 @@ id: MS:1001932 name: source interface model def: "The source interface model." [PSI:MS] relationship: part_of MS:1001931 ! source interface -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001933 name: source sprayer def: "The source sprayer." [PSI:MS] relationship: part_of MS:1000458 ! source -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001934 @@ -12638,14 +12638,14 @@ id: MS:1001935 name: source sprayer manufacturer def: "The source sprayer manufacturer." [PSI:MS] relationship: part_of MS:1001933 ! source sprayer -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001936 name: source sprayer model def: "The source sprayer model." [PSI:MS] relationship: part_of MS:1001933 ! source sprayer -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001937 @@ -12696,7 +12696,7 @@ def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument i is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000218 ! volt synonym: "CXP" EXACT [] -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001945 @@ -12739,35 +12739,35 @@ id: MS:1001950 name: PEAKS:peptideScore def: "The PEAKS peptide '-10lgP Score'." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001951 name: PEAKS:proteinScore def: "The PEAKS protein '-10lgP Score'." [PSI:MS] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001952 name: ZCore:probScore def: "The ZCore probability score." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001953 name: source interface manufacturer def: "The source interface manufacturer." [PSI:MS] relationship: part_of MS:1001931 ! source interface -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001954 name: acquisition parameter def: "Parameters used in the mass spectrometry acquisition." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001955 @@ -12810,35 +12810,35 @@ id: MS:1001961 name: peptide spectrum match scoring algorithm def: "Algorithm used to score the match between a spectrum and a peptide ion." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001962 name: Mascot:C13 counts def: "C13 peaks to use in peak detection." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001963 name: ProteinExtractor:Weighting def: "Weighting factor for protein list compilation by ProteinExtractor." [PSI:MS] is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001964 name: ProteinScape:second round Mascot def: "Flag indicating a second round search with Mascot." [PSI:MS] is_a: MS:1002100 ! ProteinScape input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001965 name: ProteinScape:second round Phenyx def: "Flag indicating a second round search with Phenyx." [PSI:MS] is_a: MS:1002100 ! ProteinScape input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001966 @@ -12854,7 +12854,7 @@ is_a: MS:1002222 ! SRM transition attribute relationship: has_units UO:0000028 ! millisecond comment: This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476). is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001968 @@ -12868,7 +12868,7 @@ name: phosphoRS score def: "phosphoRS score for PTM site location at the PSM-level." [DOI:10.1021/pr200611n, PMID:22073976] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001970 @@ -12876,7 +12876,7 @@ name: phosphoRS sequence probability def: "Probability that the respective isoform is correct." [DOI:10.1021/pr200611n, PMID:22073976] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001971 @@ -12884,14 +12884,14 @@ name: phosphoRS site probability def: "Estimate of the probability that the respective site is truly phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001972 name: PTM scoring algorithm version def: "Version of the post-translational modification scoring algorithm." [PSI:MS] is_a: MS:1001471 ! peptide modification details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001973 @@ -12906,7 +12906,7 @@ def: "Score specific to DeBunker." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001975 @@ -12917,7 +12917,7 @@ is_a: MS:1001405 ! spectrum identification result details relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001976 @@ -12928,7 +12928,7 @@ is_a: MS:1001405 ! spectrum identification result details relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001977 @@ -12942,7 +12942,7 @@ name: MSQuant:PTM-score def: "The PTM score from MSQuant software." [DOI:10.1021/pr900721e, PMID:19888749] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001979 @@ -12950,7 +12950,7 @@ name: MaxQuant:PTM Score def: "The PTM score from MaxQuant software." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001980 @@ -12958,14 +12958,14 @@ name: MaxQuant:Phospho (STY) Probabilities def: "The Phospho (STY) Probabilities from MaxQuant software." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001981 name: MaxQuant:Phospho (STY) Score Diffs def: "The Phospho (STY) Score Diffs from MaxQuant software." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001982 @@ -12973,7 +12973,7 @@ name: MaxQuant:P-site localization probability def: "The P-site localization probability value from MaxQuant software." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001983 @@ -12981,7 +12981,7 @@ name: MaxQuant:PTM Delta Score def: "The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest)." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001984 @@ -12995,7 +12995,7 @@ name: Ascore def: "A-score for PTM site location at the PSM-level." [DOI:10.1038/nbt1240, PMID:16964243] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001986 @@ -13003,7 +13003,7 @@ name: H-Score def: "H-Score for peptide phosphorylation site location." [DOI:10.1021/pr1006813, PMID:20836569] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001987 @@ -13095,28 +13095,28 @@ id: MS:1002001 name: MS1 label-based raw feature quantitation def: "MS1 label-based raw feature quantitation." [PSI:PI] is_a: MS:1002018 ! MS1 label-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002002 name: MS1 label-based peptide level quantitation def: "MS1 label-based peptide level quantitation." [PSI:PI] is_a: MS:1002018 ! MS1 label-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002003 name: MS1 label-based protein level quantitation def: "MS1 label-based protein level quantitation." [PSI:PI] is_a: MS:1002018 ! MS1 label-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002004 name: MS1 label-based proteingroup level quantitation def: "MS1 label-based proteingroup level quantitation." [PSI:PI] is_a: MS:1002018 ! MS1 label-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002005 @@ -13170,7 +13170,7 @@ name: Mascot:PTM site assignment confidence def: "Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score)." [http://www.matrixscience.com/help/pt_mods_help.html#SITE] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002013 @@ -13178,7 +13178,7 @@ name: collision energy ramp start def: "Collision energy at the start of the collision energy ramp." [PSI:PI] is_a: MS:1000045 ! collision energy relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002014 @@ -13186,28 +13186,28 @@ name: collision energy ramp end def: "Collision energy at the end of the collision energy ramp." [PSI:PI] is_a: MS:1000045 ! collision energy relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002015 name: spectral count peptide level quantitation def: "Spectral count peptide level quantitation." [PSI:PI] is_a: MS:1001836 ! spectral counting quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002016 name: spectral count protein level quantitation def: "Spectral count protein level quantitation." [PSI:PI] is_a: MS:1001836 ! spectral counting quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002017 name: spectral count proteingroup level quantitation def: "Spectral count proteingroup level quantitation." [PSI:PI] is_a: MS:1001836 ! spectral counting quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002018 @@ -13220,28 +13220,28 @@ id: MS:1002019 name: label-free raw feature quantitation def: "Label-free raw feature quantitation." [PSI:PI] is_a: MS:1001834 ! LC-MS label-free quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002020 name: label-free peptide level quantitation def: "Label-free peptide level quantitation." [PSI:PI] is_a: MS:1001834 ! LC-MS label-free quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002021 name: label-free protein level quantitation def: "Label-free protein level quantitation." [PSI:PI] is_a: MS:1001834 ! LC-MS label-free quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002022 name: label-free proteingroup level quantitation def: "Label-free proteingroup level quantitation." [PSI:PI] is_a: MS:1001834 ! LC-MS label-free quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002023 @@ -13254,63 +13254,63 @@ id: MS:1002024 name: MS2 tag-based feature level quantitation def: "MS2 tag-based feature level quantitation." [PSI:PI] is_a: MS:1002023 ! MS2 tag-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002025 name: MS2 tag-based peptide level quantitation def: "MS2 tag-based peptide level quantitation." [PSI:PI] is_a: MS:1002023 ! MS2 tag-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002026 name: MS2 tag-based protein level quantitation def: "MS2 tag-based protein level quantitation." [PSI:PI] is_a: MS:1002023 ! MS2 tag-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002027 name: MS2 tag-based proteingroup level quantitation def: "MS2 tag-based proteingroup level quantitation." [PSI:PI] is_a: MS:1002023 ! MS2 tag-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002028 name: nucleic acid base modification def: "Nucleic acid base modification (substitution, insertion or deletion)." [PSI:PI] is_a: MS:1001471 ! peptide modification details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002029 name: original nucleic acid sequence def: "Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence." [PSI:PI] is_a: MS:1001471 ! peptide modification details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002030 name: modified nucleic acid sequence def: "Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence." [PSI:PI] is_a: MS:1001471 ! peptide modification details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002031 name: PASSEL transition group browser URI def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002032 name: PeptideAtlas dataset URI def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002033 @@ -13364,7 +13364,7 @@ is_a: MS:1000482 ! source attribute is_a: MS:1002039 ! inlet attribute relationship: has_units UO:0000012 ! kelvin relationship: has_units UO:0000027 ! degree Celsius -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002041 @@ -13373,7 +13373,7 @@ def: "The temperature of the source of a mass spectrometer." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000012 ! kelvin relationship: has_units UO:0000027 ! degree Celsius -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002042 @@ -13382,7 +13382,7 @@ def: "The duration of a complete cycle of modulation in a comprehensive two-dime is_a: MS:1000857 ! run attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002043 @@ -13395,21 +13395,21 @@ id: MS:1002044 name: ProteinProspector:score def: "The ProteinProspector result 'Score'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002045 name: ProteinProspector:expectation value def: "The ProteinProspector result 'Expectation value'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002046 name: native source path def: "The original source path used for directory-based sources." [PSI:MS] is_a: MS:1001458 ! spectrum generation information -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002047 @@ -13429,21 +13429,21 @@ id: MS:1002049 name: MS-GF:RawScore def: "MS-GF raw score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002050 name: MS-GF:DeNovoScore def: "MS-GF de novo score." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002051 name: MS-GF:Energy def: "MS-GF energy score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1002052 @@ -13452,7 +13452,7 @@ def: "MS-GF spectral E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002053 @@ -13461,7 +13461,7 @@ def: "MS-GF E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002054 @@ -13469,21 +13469,21 @@ name: MS-GF:QValue def: "MS-GF Q-value." [PSI:PI] is_a: MS:1002354 ! PSM-level q-value is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002055 name: MS-GF:PepQValue def: "MS-GF peptide-level Q-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002056 name: MS-GF:PEP def: "MS-GF posterior error probability." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002057 @@ -13533,28 +13533,28 @@ id: MS:1002064 name: peptide consensus RT def: "Peptide consensus retention time." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002065 name: peptide consensus m/z def: "Peptide consensus mass/charge ratio." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002066 name: ratio calculation method def: "Method used to calculate the ratio." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002067 name: protein value: median of peptide ratios def: "Protein quantification value calculated as median of peptide ratios." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002068 @@ -13567,21 +13567,21 @@ id: MS:1002069 name: metabolic labelling purity def: "Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape." [PSI:PI] is_a: MS:1001055 ! modification parameters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002070 name: t-test def: "Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed." [PSI:PI] is_a: MS:1001861 ! quantification data processing -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002071 name: ANOVA-test def: "Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed." [PSI:PI] is_a: MS:1001861 ! quantification data processing -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002072 @@ -13589,7 +13589,7 @@ name: p-value def: "P-value as result of one of the processing steps described. Specify in the description, which processing step it was." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002073 @@ -13628,7 +13628,7 @@ def: "OBSOLETE ProteomeDiscoverer's 1st static post-translational modification ( comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002079 @@ -13637,7 +13637,7 @@ def: "OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification ( comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002080 @@ -13645,7 +13645,7 @@ name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before def: "Precursor clipping range before." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002081 @@ -13653,7 +13653,7 @@ name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After def: "Precursor clipping range after." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002082 @@ -13662,7 +13662,7 @@ def: "The time of elution from the first chromatographic column in the chromatog is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002083 @@ -13671,7 +13671,7 @@ def: "The time of elution from the second chromatographic column in the chromato is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002084 @@ -13708,28 +13708,28 @@ id: MS:1002089 name: ProteomeDiscoverer:Peptide Without Protein XCorr Threshold def: "XCorr threshold for storing peptides that do not belong to a protein." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002090 name: Calculate Probability Scores def: "Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated." [PSI:MS] is_a: MS:1002094 ! common search engine input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002091 name: ProteomeDiscoverer:Maximum Delta Cn def: "Delta Cn threshold for filtering out PSM's." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002092 name: Percolator:Validation based on def: "Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator." [PSI:MS] is_a: MS:1002107 ! Percolator input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002093 @@ -13925,7 +13925,7 @@ comment: This term was made obsolete because it was split into the more specific is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002126 @@ -14095,7 +14095,7 @@ id: MS:1002153 name: protein level PSM counts def: "The number of spectra identified for this protein in spectral counting." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002154 @@ -14457,35 +14457,35 @@ id: MS:1002213 name: PAnalyzer:conclusive protein def: "A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] is_a: MS:1001600 ! protein inference confidence category -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002214 name: PAnalyzer:indistinguishable protein def: "A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] is_a: MS:1001600 ! protein inference confidence category -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002215 name: PAnalyzer:non-conclusive protein def: "A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] is_a: MS:1001600 ! protein inference confidence category -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002216 name: PAnalyzer:ambiguous group member def: "A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] is_a: MS:1001600 ! protein inference confidence category -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002217 name: decoy peptide def: "A putative identified peptide issued from a decoy sequence database." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002218 @@ -14493,7 +14493,7 @@ name: percent collision energy ramp start def: "Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] is_a: MS:1000138 ! normalized collision energy relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002219 @@ -14501,7 +14501,7 @@ name: percent collision energy ramp end def: "Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] is_a: MS:1000138 ! normalized collision energy relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002220 @@ -14528,14 +14528,14 @@ id: MS:1002223 name: precursor ion detection probability def: "Probability of detecting precursor when parent protein is present." [PSI:PI] is_a: MS:1002222 ! SRM transition attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002224 name: product ion detection probability def: "Probability of detecting product ion when precursor ion is present." [PSI:PI] is_a: MS:1002222 ! SRM transition attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002225 @@ -14562,28 +14562,28 @@ id: MS:1002227 name: number of product ion observations def: "The number of times the specific product ion has been observed in a series of SRM experiments." [PSI:PI] is_a: MS:1002222 ! SRM transition attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002228 name: number of precursor ion observations def: "The number of times the specific precursor ion has been observed in a series of SRM experiments." [PSI:PI] is_a: MS:1002222 ! SRM transition attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002229 name: ProteomeDiscoverer:Mascot:Significance Middle def: "Calculated relaxed significance when performing a decoy search for high-confidence peptides." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002230 name: ProteomeDiscoverer:Mascot:Significance High def: "Calculated relaxed significance when performing a decoy search for medium-confidence peptides." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002231 @@ -14603,7 +14603,7 @@ id: MS:1002233 name: ProteomeDiscoverer:SEQUEST:Low resolution spectra contained def: "Flag indicating if low-resolution spectra are taken into consideration." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002234 @@ -14612,21 +14612,21 @@ def: "Mass-to-charge ratio of a precursor ion selected for fragmentation." [PSI: synonym: "selected ion m/z" RELATED [] is_a: MS:1000455 ! ion selection attribute relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002235 name: ProteoGrouper:PDH score def: "A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002236 name: ProteoGrouper:PAG score def: "A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002237 @@ -14699,21 +14699,21 @@ id: MS:1002248 name: SEQUEST:spscore def: "The SEQUEST result 'SpScore'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002249 name: SEQUEST:sprank def: "The SEQUEST result 'SpRank'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002250 name: SEQUEST:deltacnstar def: "The SEQUEST result 'DeltaCnStar'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002251 @@ -14727,63 +14727,63 @@ name: Comet:xcorr def: "The Comet result 'XCorr'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002253 name: Comet:deltacn def: "The Comet result 'DeltaCn'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002254 name: Comet:deltacnstar def: "The Comet result 'DeltaCnStar'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002255 name: Comet:spscore def: "The Comet result 'SpScore'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002256 name: Comet:sprank def: "The Comet result 'SpRank'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002257 name: Comet:expectation value def: "The Comet result 'Expectation value'." [PSI:PI] is_a: MS:1001153 ! search engine specific score -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002258 name: Comet:matched ions def: "The Comet result 'Matched Ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002259 name: Comet:total ions def: "The Comet result 'Total Ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002260 name: PSM:FDR threshold def: "False-discovery rate threshold for peptide-spectrum matches." [PSI:PI] is_a: MS:1002483 ! PSM-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002261 @@ -14797,7 +14797,7 @@ name: Byonic:Score def: "The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002263 @@ -14805,7 +14805,7 @@ name: Byonic:Delta Score def: "The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002264 @@ -14813,7 +14813,7 @@ name: Byonic:DeltaMod Score def: "The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002265 @@ -14821,7 +14821,7 @@ name: Byonic:PEP def: "Byonic posterior error probability." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002266 @@ -14829,7 +14829,7 @@ name: Byonic:Peptide LogProb def: "The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002267 @@ -14838,7 +14838,7 @@ def: "The log p-value of the protein." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002268 @@ -14847,7 +14847,7 @@ def: "Best (most negative) log p-value of an individual PSM." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002269 @@ -14855,7 +14855,7 @@ name: Byonic:Best Score def: "Best (largest) Byonic score of a PSM." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002270 @@ -14881,7 +14881,7 @@ name: detector potential def: "Detector potential difference in volts." [PSI:MS] is_a: MS:1000481 ! detector attribute relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002274 @@ -15065,7 +15065,7 @@ id: MS:1002303 name: Bruker Container nativeID format def: "Native identifier (UUID)." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002304 @@ -15103,7 +15103,7 @@ name: Byonic: Peptide AbsLogProb def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002310 @@ -15111,7 +15111,7 @@ name: Byonic: Protein AbsLogProb def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002311 @@ -15119,7 +15119,7 @@ name: Byonic: Peptide AbsLogProb2D def: "The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002312 @@ -15150,98 +15150,98 @@ id: MS:1002316 name: ProteomeDiscoverer:Amanda:high confidence threshold def: "Strict confidence probability score." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002317 name: ProteomeDiscoverer:Amanda:middle confidence threshold def: "Relaxed confidence probability score." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002318 name: ProteomeDiscoverer:automatic workload def: "Flag indicating automatic estimation of the workload level." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002319 name: Amanda:AmandaScore def: "The Amanda score of the scoring function for a PSM." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002320 name: ProteomeDiscoverer:max differential modifications def: "Maximum dynamic modifications per PSM." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002321 name: ProteomeDiscoverer:max equal modifications def: "Maximum equal modifications per PSM." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002322 name: ProteomeDiscoverer:min peptide length def: "Minimum peptide length." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002323 name: ProteomeDiscoverer:max peptide length def: "Maximum peptide length." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002324 name: ProteomeDiscoverer:max number neutral loss def: "Maximum number of same neutral losses." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002325 name: ProteomeDiscoverer:max number neutral loss modifications def: "Max number of same neutral losses of modifications." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002326 name: ProteomeDiscoverer:use flanking ions def: "Flag for usage of flanking ions." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002327 name: ProteomeDiscoverer:max number of same modifs def: "The maximum number of possible equal modifications per PSM." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002328 name: ProteomeDiscoverer:perform deisotoping def: "Defines whether a simple deisotoping shall be performed." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002329 name: ProteomeDiscoverer:ion settings def: "Specifies the fragment ions and neutral losses that are calculated." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002330 @@ -15250,7 +15250,7 @@ def: "OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification ( comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002331 @@ -15259,7 +15259,7 @@ def: "OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002332 @@ -15303,28 +15303,28 @@ name: Andromeda:score def: "The probability based score of the Andromeda search engine." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002339 name: site:global FDR def: "Estimation of global false discovery rate of peptides with a post-translational modification." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002340 name: ProteomeXchange project tag def: "Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002341 name: second-pass peptide identification def: "A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002342 @@ -15383,7 +15383,7 @@ name: PSM-level global FDR def: "Estimation of the global false discovery rate of peptide spectrum matches." [PSI:PI] is_a: MS:1002701 ! PSM-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002351 @@ -15391,7 +15391,7 @@ name: PSM-level local FDR def: "Estimation of the local false discovery rate of peptide spectrum matches." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002352 @@ -15399,7 +15399,7 @@ name: PSM-level p-value def: "Estimation of the p-value for peptide spectrum matches." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002353 @@ -15407,7 +15407,7 @@ name: PSM-level e-value def: "Estimation of the e-value for peptide spectrum matches." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002354 @@ -15415,7 +15415,7 @@ name: PSM-level q-value def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002355 @@ -15424,7 +15424,7 @@ def: "mzidLibrary FDRScore for peptide spectrum matches." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002356 @@ -15433,7 +15433,7 @@ def: "mzidLibrary Combined FDRScore for peptide spectrum matches specifically ob is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002357 @@ -15441,7 +15441,7 @@ name: PSM-level probability def: "Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002358 @@ -15455,7 +15455,7 @@ name: peptide sequence-level local FDR def: "Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002360 @@ -15464,7 +15464,7 @@ def: "MzidLibrary FDRScore for distinct peptides once redundant identifications is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002361 @@ -15473,7 +15473,7 @@ def: "Combined FDRScore for peptides once redundant identifications of the same is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002362 @@ -15481,7 +15481,7 @@ name: peptide sequence-level probability def: "Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002363 @@ -15494,7 +15494,7 @@ id: MS:1002364 name: protein-level local FDR def: "Estimation of the local false discovery rate of proteins." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002365 @@ -15502,7 +15502,7 @@ name: FDRScore for proteins def: "MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002366 @@ -15510,7 +15510,7 @@ name: combined FDRScore for proteins def: "MzidLibrary Combined FDRScore for proteins." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002367 @@ -15518,7 +15518,7 @@ name: probability for proteins def: "Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002368 @@ -15531,14 +15531,14 @@ id: MS:1002369 name: protein group-level global FDR def: "Estimation of the global false discovery rate of protein groups." [PSI:PI] is_a: MS:1002706 ! protein group-level result list statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002370 name: protein group-level local FDR def: "Estimation of the local false discovery rate of protein groups." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002371 @@ -15546,7 +15546,7 @@ name: protein group-level p-value def: "Estimation of the p-value for protein groups." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002372 @@ -15554,7 +15554,7 @@ name: protein group-level e-value def: "Estimation of the e-value for protein groups." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002373 @@ -15562,7 +15562,7 @@ name: protein group-level q-value def: "Estimation of the q-value for protein groups." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002374 @@ -15570,7 +15570,7 @@ name: protein group-level FDRScore def: "mzidLibrary FDRScore for protein groups." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002375 @@ -15578,7 +15578,7 @@ name: protein group-level combined FDRScore def: "mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002376 @@ -15586,35 +15586,35 @@ name: protein group-level probability def: "Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002377 name: ProteomeDiscoverer:Relaxed Score Threshold def: "Specifies the threshold value for relaxed scoring." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002378 name: ProteomeDiscoverer:Strict Score Threshold def: "Specifies the threshold value for strict scoring." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002379 name: ProteomeDiscoverer:Peptide Without Protein Cut Off Score def: "Cut off score for storing peptides that do not belong to a protein." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002380 name: false localization rate def: "Estimation of the false localization rate for modification site assignment." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002381 @@ -15682,28 +15682,28 @@ id: MS:1002390 name: PIA:FDRScore calculated def: "Indicates whether the FDR score was calculated for the input file." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002391 name: PIA:Combined FDRScore calculated def: "Indicates whether the combined FDR score was calculated for the PIA compilation." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002392 name: PIA:PSM sets created def: "Indicates whether PSM sets were created." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002393 name: PIA:used top identifications for FDR def: "The number of top identifications per spectrum used for the FDR calculation, 0 means all." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1002394 @@ -15711,49 +15711,49 @@ name: PIA:protein score def: "The score given to a protein by any protein inference." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002395 name: PIA:protein inference def: "The used algorithm for the protein inference using PIA." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002396 name: PIA:protein inference filter def: "A filter used by PIA for the protein inference." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002397 name: PIA:protein inference scoring def: "The used scoring method for the protein inference using PIA." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002398 name: PIA:protein inference used score def: "The used base score for the protein inference using PIA." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002399 name: PIA:protein inference used PSMs def: "The method to determine the PSMs used for scoring by the protein inference." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002400 name: PIA:filter def: "A filter used for the report generation." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002401 @@ -15778,7 +15778,7 @@ id: MS:1002404 name: count of identified proteins def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI] is_a: MS:1002704 ! protein-level result list attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002405 @@ -15791,21 +15791,21 @@ id: MS:1002406 name: count of identified clusters def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [DOI:10.1002/pmic.201400080, PMID:25092112] is_a: MS:1002405 ! protein group-level result list attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002407 name: cluster identifier def: "An identifier applied to protein groups to indicate that they are linked by shared peptides." [PSI:PI] is_a: MS:1002698 ! protein cluster identification attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002408 name: number of distinct protein sequences def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [PSI:PI] is_a: MS:1002405 ! protein group-level result list attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002409 @@ -15831,14 +15831,14 @@ id: MS:1002412 name: total XIC area def: "Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM)." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002413 name: product background def: "The background area for the quantified transition." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002414 @@ -15851,7 +15851,7 @@ id: MS:1002415 name: protein group passes threshold def: "A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file." [PSI:PI] is_a: MS:1002346 ! protein group-level identification attribute -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002416 @@ -15882,7 +15882,7 @@ id: MS:1002420 name: PASSEL experiment URI def: "URI that allows access to a PASSEL experiment." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002421 @@ -15895,70 +15895,70 @@ id: MS:1002422 name: Paragon: sample type def: "The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002423 name: Paragon: cysteine alkylation def: "The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002424 name: Paragon: instrument setting def: "The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002425 name: Paragon: search effort def: "The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002426 name: Paragon: ID focus def: "A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002427 name: Paragon: FDR analysis def: "The Paragon method setting that controls whether FDR analysis is conducted." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002428 name: Paragon: quantitation def: "The Paragon method setting that controls whether quantitation analysis is conducted." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002429 name: Paragon: background correction def: "The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002430 name: Paragon: bias correction def: "The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002431 name: Paragon: channel to use as denominator in ratios def: "The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002432 @@ -15971,35 +15971,35 @@ id: MS:1002433 name: Paragon: modified data dictionary or parameter translation def: "This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result." [PSI:PI] is_a: MS:1002432 ! search engine specific input metadata -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002434 name: number of spectra searched def: "Number of spectra in a search." [PSI:PI] is_a: MS:1001249 ! search input details -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002435 name: data processing start time def: "The time that a data processing action was started." [PSI:MS] is_a: MS:1000630 ! data processing parameter -relationship: has_value_type xsd\:dateTime ! The allowed value-type for this CV term +relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term [Term] id: MS:1002436 name: Paragon: digestion def: "The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done." [PSI:PI] is_a: MS:1001249 ! search input details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002437 name: number of decoy sequences def: "The number of decoy sequences, if the concatenated target-decoy approach is used." [PSI:PI] is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1002438 @@ -16060,21 +16060,21 @@ id: MS:1002447 name: Paragon:special factor def: "The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002448 name: PEAKS:inChorusPeptideScore def: "The PEAKS inChorus peptide score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002449 name: PEAKS:inChorusProteinScore def: "The PEAKS inChorus protein score." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002450 @@ -16191,7 +16191,7 @@ name: PeptideShaker PSM score def: "The probability based PeptideShaker PSM score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002467 @@ -16199,7 +16199,7 @@ name: PeptideShaker PSM confidence def: "The probability based PeptideShaker PSM confidence." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002468 @@ -16208,7 +16208,7 @@ def: "The probability based PeptideShaker peptide score." [PSI:PI] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002469 @@ -16216,7 +16216,7 @@ name: PeptideShaker peptide confidence def: "The probability based PeptideShaker peptide confidence." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002470 @@ -16225,7 +16225,7 @@ def: "The probability based PeptideShaker protein group score." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002471 @@ -16233,7 +16233,7 @@ name: PeptideShaker protein group confidence def: "The probability based PeptideShaker protein group confidence." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002472 @@ -16253,14 +16253,14 @@ name: ProteoAnnotator:non-canonical gene model score def: "The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002475 name: ProteoAnnotator:count alternative peptides def: "The count of the number of peptide sequences mapped to non-canonical gene models only within the group." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002476 @@ -16269,7 +16269,7 @@ def: "Drift time of an ion or spectrum of ions as measured in an ion mobility ma is_a: MS:1000455 ! ion selection attribute is_a: MS:1002892 ! ion mobility attribute relationship: has_units UO:0000028 ! millisecond -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002477 @@ -16278,7 +16278,7 @@ def: "Array of population mean ion mobility values from a drift time device, rep is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002478 @@ -16340,14 +16340,14 @@ id: MS:1002487 name: MassIVE dataset identifier def: "Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002488 name: MassIVE dataset URI def: "URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002489 @@ -16423,7 +16423,7 @@ id: MS:1002500 name: peptide passes threshold def: "A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002501 @@ -16448,7 +16448,7 @@ id: MS:1002504 name: modification index def: "The order of modifications to be referenced elsewhere in the document." [PSI:PI] is_a: MS:1001055 ! modification parameters -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002505 @@ -16468,7 +16468,7 @@ name: modification rescoring:false localization rate def: "Mod position score: false localization rate." [PSI:PI] is_a: MS:1002506 ! modification position score relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002508 @@ -16481,35 +16481,35 @@ id: MS:1002509 name: cross-link donor def: "The Cross-linking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] is_a: MS:1002508 ! cross-linking attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002510 name: cross-link acceptor def: "Cross-linking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] is_a: MS:1002508 ! cross-linking attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002511 name: cross-link spectrum identification item def: "Cross-linked spectrum identification item." [PSI:PI] is_a: MS:1002508 ! cross-linking attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002512 name: cross-linking score def: "Cross-linking scoring value." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002513 name: molecules per cell def: "The absolute abundance of protein in a cell." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002514 @@ -16522,42 +16522,42 @@ id: MS:1002515 name: internal peptide reference used def: "States whether an internal peptide reference is used or not in absolute quantitation analysis." [PSI:PI] is_a: MS:1001832 ! quantitation software comment or customizations -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002516 name: internal protein reference used def: "States whether an internal protein reference is used or not in absolute quantitation analysis." [PSI:PI] is_a: MS:1001832 ! quantitation software comment or customizations -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002517 name: internal reference abundance def: "The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis." [PSI:PI] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002518 name: Progenesis:protein group normalised abundance def: "The data type normalised abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] is_a: MS:1002739 ! protein group-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002519 name: Progenesis:protein group raw abundance def: "The data type raw abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] is_a: MS:1002739 ! protein group-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002520 name: peptide group ID def: "Peptide group identifier for peptide-level stats." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002521 @@ -16570,7 +16570,7 @@ id: MS:1002522 name: ProteomeDiscoverer:1. Static Terminal Modification def: "Determine 1st static terminal post-translational modifications (PTMs)." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002523 @@ -16649,14 +16649,14 @@ name: ProLuCID:xcorr def: "The ProLuCID result 'XCorr'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002535 name: ProLuCID:deltacn def: "The ProLuCID result 'DeltaCn'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002536 @@ -16664,7 +16664,7 @@ name: D-Score def: "D-Score for PTM site location at the PSM-level." [PMID:23307401] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002537 @@ -16672,42 +16672,42 @@ name: MD-Score def: "MD-Score for PTM site location at the PSM-level." [PMID:21057138] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002538 name: PTM localization confidence metric def: "Localization confidence metric for a post translational modification (PTM)." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002539 name: PeptideShaker PTM confidence type def: "PeptideShaker quality criteria for the confidence of PTM localizations." [PSI:PI] is_a: MS:1002538 ! PTM localization confidence metric -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002540 name: PeptideShaker PSM confidence type def: "PeptideShaker quality criteria for the confidence of PSM's." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002541 name: PeptideShaker peptide confidence type def: "PeptideShaker quality criteria for the confidence of peptide identifications." [PSI:PI] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002542 name: PeptideShaker protein confidence type def: "PeptideShaker quality criteria for the confidence of protein identifications." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002543 @@ -16727,7 +16727,7 @@ name: xi:score def: "The xi result 'Score'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002546 @@ -16760,7 +16760,7 @@ name: peptide:phosphoRS score def: "phosphoRS score for PTM site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002551 @@ -16768,7 +16768,7 @@ name: peptide:Ascore def: "A-score for PTM site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002552 @@ -16776,7 +16776,7 @@ name: peptide:H-Score def: "H-Score for peptide phosphorylation site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002553 @@ -16784,7 +16784,7 @@ name: peptide:D-Score def: "D-Score for PTM site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002554 @@ -16792,7 +16792,7 @@ name: peptide:MD-Score def: "MD-Score for PTM site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002555 @@ -16805,112 +16805,112 @@ id: MS:1002556 name: Ascore threshold def: "Threshold for Ascore PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002557 name: D-Score threshold def: "Threshold for D-score PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002558 name: MD-Score threshold def: "Threshold for MD-score PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002559 name: H-Score threshold def: "Threshold for H-score PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002560 name: DeBunker:score threshold def: "Threshold for DeBunker PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002561 name: Mascot:PTM site assignment confidence threshold def: "Threshold for Mascot PTM site assignment confidence." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002562 name: MSQuant:PTM-score threshold def: "Threshold for MSQuant:PTM-score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002563 name: MaxQuant:PTM Score threshold def: "Threshold for MaxQuant:PTM Score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002564 name: MaxQuant:P-site localization probability threshold def: "Threshold for MaxQuant:P-site localization probability." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002565 name: MaxQuant:PTM Delta Score threshold def: "Threshold for MaxQuant:PTM Delta Score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002566 name: MaxQuant:Phospho (STY) Probabilities threshold def: "Threshold for MaxQuant:Phospho (STY) Probabilities." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002567 name: phosphoRS score threshold def: "Threshold for phosphoRS score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002568 name: phosphoRS site probability threshold def: "Threshold for phosphoRS site probability." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002569 name: ProteomeDiscoverer:Number of Spectra Processed At Once def: "Number of spectra processed at once in a ProteomeDiscoverer search." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002570 name: sequence multiply subsumable protein def: "A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002571 name: spectrum multiply subsumable protein def: "A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002572 @@ -17079,7 +17079,7 @@ id: MS:1002599 name: splash key def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832] is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002600 @@ -17281,14 +17281,14 @@ id: MS:1002632 name: jPOST dataset identifier def: "Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002633 name: jPOST dataset URI def: "URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002634 @@ -17313,14 +17313,14 @@ id: MS:1002637 name: chromosome name def: "The name or number of the chromosome to which a given peptide has been mapped." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002638 name: chromosome strand def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002639 @@ -17329,42 +17329,42 @@ def: "OBSOLETE The overall start position on the chromosome to which a peptide h comment: This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome. is_a: MS:1002636 ! proteogenomics attribute is_obsolete: true -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002640 name: peptide end on chromosome def: "The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002641 name: peptide exon count def: "The number of exons to which the peptide has been mapped." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002642 name: peptide exon nucleotide sizes def: "A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002643 name: peptide start positions on chromosome def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002644 name: genome reference version def: "The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002645 @@ -17385,35 +17385,35 @@ id: MS:1002647 name: Thermo nativeID format, combined spectra def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002648 name: Waters nativeID format, combined spectra def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002649 name: WIFF nativeID format, combined spectra def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002650 name: Bruker/Agilent YEP nativeID format, combined spectra def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002651 name: Bruker BAF nativeID format, combined spectra def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002652 @@ -17421,7 +17421,7 @@ name: Bruker FID nativeID format, combined spectra def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: The nativeID must be the same as the source file ID. is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002653 @@ -17429,7 +17429,7 @@ name: multiple peak list nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002654 @@ -17437,7 +17437,7 @@ name: single peak list nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002655 @@ -17445,7 +17445,7 @@ name: scan number only nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002656 @@ -17453,7 +17453,7 @@ name: spectrum identifier nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: Used for conversion from mzData. The spectrum id attribute is referenced. is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002657 @@ -17461,7 +17461,7 @@ name: mzML unique identifier, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: A unique identifier of a spectrum stored in an mzML file. is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002658 @@ -17493,7 +17493,7 @@ name: Morpheus:Morpheus score def: "Morpheus score for PSMs." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002663 @@ -17501,7 +17501,7 @@ name: Morpheus:summed Morpheus score def: "Summed Morpheus score for protein groups." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002664 @@ -17509,7 +17509,7 @@ name: interaction score derived from cross-linking def: "Parent term for interaction scores derived from cross-linking." [PSI:PI] is_a: MS:1002675 ! cross-linking result details relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})) -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002665 @@ -17534,28 +17534,28 @@ id: MS:1002668 name: frag: iTRAQ 4plex reporter ion def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002669 name: frag: iTRAQ 8plex reporter ion def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002670 name: frag: TMT reporter ion def: "Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002671 name: frag: TMT ETD reporter ion def: "Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002672 @@ -17588,7 +17588,7 @@ def: "Estimation of the global false discovery rate of proteins-pairs in cross-l is_a: MS:1002664 ! interaction score derived from cross-linking relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})) -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002677 @@ -17597,7 +17597,7 @@ def: "Estimation of the global false discovery rate of residue-pairs in cross-li is_a: MS:1002664 ! interaction score derived from cross-linking relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})) -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002678 @@ -17617,7 +17617,7 @@ name: supplemental collision energy def: "Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002681 @@ -17626,7 +17626,7 @@ def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002682 @@ -17635,7 +17635,7 @@ def: "OpenXQuest's cross-correlation of cross-linked ions subscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002683 @@ -17644,7 +17644,7 @@ def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002684 @@ -17654,7 +17654,7 @@ is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002685 @@ -17664,7 +17664,7 @@ is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002686 @@ -17674,7 +17674,7 @@ is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002687 @@ -17820,21 +17820,21 @@ id: MS:1002711 name: list of strings def: "A list of xsd:string." [] is_a: MS:1002710 ! list of type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002712 name: list of integers def: "A list of xsd:integer." [] is_a: MS:1002710 ! list of type -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002713 name: list of floats def: "A list of xsd:float." [] is_a: MS:1002710 ! list of type -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002719 @@ -17855,7 +17855,7 @@ def: "MSPathFinder spectral E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002722 @@ -17864,7 +17864,7 @@ def: "MSPathFinder E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002723 @@ -17872,21 +17872,21 @@ name: MSPathFinder:QValue def: "MSPathFinder Q-value." [PSI:PI] is_a: MS:1002354 ! PSM-level q-value is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002724 name: MSPathFinder:PepQValue def: "MSPathFinder peptide-level Q-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002725 name: MSPathFinder:RawScore def: "MSPathFinder raw score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002726 @@ -17935,14 +17935,14 @@ id: MS:1002733 name: peptide-level spectral count def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002734 name: peptide ion-level spectral count def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002735 @@ -18043,7 +18043,7 @@ id: MS:1002749 name: Mascot:IntegratedSpectralLibrarySearch def: "Means that Mascot has integrated the search results of database and spectral library search into a single data set." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002750 @@ -18412,7 +18412,7 @@ id: MS:1002810 name: adduct ion X m/z def: "Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." [PSI:MS] is_a: MS:1003056 ! adduct ion property -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000040 ! m/z [Term] @@ -18420,7 +18420,7 @@ id: MS:1002811 name: adduct ion isotope def: "Isotope of the matrix molecule M of an adduct formation." [PSI:MS] is_a: MS:1003056 ! adduct ion property -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002812 @@ -18434,7 +18434,7 @@ name: adduct ion formula def: "Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression." [PSI:MS] is_a: MS:1002809 ! adduct ion attribute relationship: has_regexp MS:1002812 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]) -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002814 @@ -18450,7 +18450,7 @@ def: "Ion mobility measurement for an ion or spectrum of ions as measured in an is_a: MS:1000455 ! ion selection attribute is_a: MS:1002892 ! ion mobility attribute relationship: has_units MS:1002814 ! volt-second per square centimeter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002816 @@ -18459,7 +18459,7 @@ def: "Array of population mean ion mobility values (K or K0) based on ion separa is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002817 @@ -18478,7 +18478,7 @@ id: MS:1002819 name: Bruker TDF nativeID format, combined spectra def: "Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002820 @@ -18530,7 +18530,7 @@ name: MetaMorpheus:score def: "MetaMorpheus score for PSMs." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002828 @@ -18538,35 +18538,35 @@ name: MetaMorpheus:protein score def: "MetaMorpheus score for protein groups." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002829 name: XCMS:into def: "Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002830 name: XCMS:intf def: "Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002831 name: XCMS:maxo def: "Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002832 name: XCMS:area def: "Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002833 @@ -18579,7 +18579,7 @@ id: MS:1002834 name: ProteomeDiscoverer:Delta Score def: "The Delta Score reported by Proteome Discoverer version 2." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002835 @@ -18592,14 +18592,14 @@ id: MS:1002836 name: iProX dataset identifier def: "Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002837 name: iProX dataset URI def: "URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002838 @@ -18624,7 +18624,7 @@ id: MS:1002841 name: external HDF5 dataset def: "The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the section of the BinaryDataArray." [PSI:PI] is_a: MS:1002840 ! external reference data -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002842 @@ -18632,7 +18632,7 @@ name: external offset def: "The position in the external data where the array begins." [PSI:PI] relationship: has_units UO:0000189 ! Count is_a: MS:1002840 ! external reference data -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1002843 @@ -18640,7 +18640,7 @@ name: external array length def: "Describes how many fields an array contains." [PSI:PI] relationship: has_units UO:0000189 ! Count is_a: MS:1002840 ! external reference data -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1002844 @@ -18653,56 +18653,56 @@ id: MS:1002845 name: Associated file URI def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002846 name: Associated raw file URI def: "URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002847 name: ProteomeCentral dataset URI def: "URI associated to one PX submission in ProteomeCentral." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002848 name: Result file URI def: "URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002849 name: Search engine output file URI def: "URI of one search engine output file associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002850 name: Peak list file URI def: "URI of one of one search engine output file associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002851 name: Other type file URI def: "URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002852 name: Dataset FTP location def: "FTP location of one entire PX data set." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002853 @@ -18745,28 +18745,28 @@ id: MS:1002859 name: Additional associated raw file URI def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI] is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002860 name: Gel image file URI def: "URI of one gel image file associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002861 name: Reprocessed complete dataset def: "All the raw files included in the original dataset (or group of original datasets) have been reanalysed." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002862 name: Reprocessed subset dataset def: "A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002863 @@ -18791,7 +18791,7 @@ id: MS:1002866 name: Reference def: "Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002867 @@ -18831,14 +18831,14 @@ id: MS:1002872 name: Panorama Public dataset identifier def: "Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002873 name: Panorama Public dataset URI def: "URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002874 @@ -18923,7 +18923,7 @@ id: MS:1002887 name: Progenesis QI normalised abundance def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI] is_a: MS:1002886 ! small molecule quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002888 @@ -18936,21 +18936,21 @@ id: MS:1002889 name: Progenesis MetaScope score def: "The confidence score produced by Progenesis QI." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002890 name: fragmentation score def: "The fragmentation confidence score." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002891 name: isotopic fit score def: "The isotopic fit confidence score." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002892 @@ -18970,7 +18970,7 @@ id: MS:1002894 name: InChIKey def: "Unique chemical structure identifier for chemical compounds." [PMID:273343401] is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002895 @@ -18983,7 +18983,7 @@ id: MS:1002896 name: compound identification confidence level def: "Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'." [PMID:29748461] is_a: MS:1002895 ! small molecule identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002897 @@ -18992,7 +18992,7 @@ def: "OBSOLETE Identifies a peak when no de-isotoping has been performed. The va comment: This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. is_a: MS:1000231 ! peak is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002898 @@ -19054,7 +19054,7 @@ name: proteoform-level global FDR def: "Estimation of the global false discovery rate of proteoforms." [PSI:PI] is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002908 @@ -19062,7 +19062,7 @@ name: proteoform-level local FDR def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI] is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002909 @@ -19075,14 +19075,14 @@ id: MS:1002910 name: proteoform-level global FDR threshold def: "Threshold for the global false discovery rate of proteoforms." [PSI:PI] is_a: MS:1002909 ! proteoform-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002911 name: proteoform-level local FDR threshold def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI] is_a: MS:1002909 ! proteoform-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002912 @@ -19107,70 +19107,70 @@ id: MS:1002915 name: TopPIC:error tolerance def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002916 name: TopPIC:max shift def: "Maximum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002917 name: TopPIC:min shift def: "Minimum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002918 name: TopPIC:shift num def: "Maximum number of unexpected modifications in a proteoform spectrum match." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002919 name: TopPIC:spectral cutoff type def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002920 name: TopPIC:spectral cutoff value def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002921 name: TopPIC:proteoform-level cutoff type def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002922 name: TopPIC:proteoform-level cutoff value def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002923 name: TopPIC:generating function def: "P-value and E-value estimation using generating function." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002924 name: TopPIC:combined spectrum number def: "Number of combined spectra." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002925 @@ -19183,14 +19183,14 @@ id: MS:1002926 name: TopPIC:thread number def: "Number of threads used in TopPIC." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002927 name: TopPIC:use TopFD feature def: "Proteoform identification using TopFD feature file." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002928 @@ -19199,7 +19199,7 @@ def: "TopPIC spectrum-level E-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002353 ! PSM-level e-value relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002929 @@ -19207,7 +19207,7 @@ name: TopPIC:spectral FDR def: "TopPIC spectrum-level FDR." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002351 ! PSM-level local FDR -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002930 @@ -19215,7 +19215,7 @@ name: TopPIC:proteoform-level FDR def: "TopPIC proteoform-level FDR." [PSI:PI] is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002906 ! search engine specific score for proteoforms -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002931 @@ -19223,21 +19223,21 @@ name: TopPIC:spectral p-value def: "TopPIC spectrum-level p-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002352 ! PSM-level p-value -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002932 name: TopPIC:MIScore def: "Modification identification score." [PMID:27291504] is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002933 name: TopPIC:MIScore threshold def: "TopPIC:MIScore threshold." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002934 @@ -19262,42 +19262,42 @@ id: MS:1002937 name: TopMG:error tolerance def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002938 name: TopMG:max shift def: "Maximum value of the mass shift (in Dalton)." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002939 name: TopMG:spectral cutoff type def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002940 name: TopMG:spectral cutoff value def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002941 name: TopMG:proteoform-level cutoff type def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002942 name: TopMG:proteoform-level cutoff value def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002943 @@ -19310,42 +19310,42 @@ id: MS:1002944 name: TopMG:thread number def: "Number of threads used in TopMG." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002945 name: TopMG:use TopFD feature def: "Proteoform identification using TopFD feature file." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002946 name: TopMG:proteoform graph gap size def: "Gap size in constructing proteoform graph." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002947 name: TopMG:variable PTM number def: "Maximum number of variable PTMs." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002948 name: TopMG:variable PTM number in proteoform graph gap def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002949 name: TopMG:use ASF-DIAGONAL def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814] is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002950 @@ -19354,7 +19354,7 @@ def: "TopMG spectrum-level E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002951 @@ -19362,7 +19362,7 @@ name: TopMG:spectral FDR def: "TopMG spectrum-level FDR." [PSI:PI] is_a: MS:1002351 ! PSM-level local FDR is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002952 @@ -19370,7 +19370,7 @@ name: TopMG:proteoform-level FDR def: "TopMG proteoform-level FDR." [PSI:PI] is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002906 ! search engine specific score for proteoforms -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002953 @@ -19378,7 +19378,7 @@ name: TopMG:spectral p-value def: "TopMG spectrum-level p-value." [PSI:PI] is_a: MS:1002352 ! PSM-level p-value is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002954 @@ -19386,56 +19386,56 @@ name: collisional cross sectional area def: "Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI] is_a: MS:1000861 ! molecular entity property relationship: has_units UO:0000324 ! square angstrom -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002955 name: hr-ms compound identification confidence level def: "Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540] is_a: MS:1002895 ! small molecule identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002956 name: isotopic ion MS peak def: "A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI] is_a: MS:1000231 ! peak -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002957 name: isotopomer MS peak def: "The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI] is_a: MS:1002956 ! isotopic ion MS peak -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002958 name: isotopologue MS peak def: "The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI] is_a: MS:1002956 ! isotopic ion MS peak -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002959 name: isomer def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html] is_a: MS:1000859 ! molecule -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002960 name: isotopomer def: "An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html] is_a: MS:1002959 ! isomer -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002961 name: isotopologue def: "A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html] is_a: MS:1002959 ! isomer -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002962 @@ -19614,7 +19614,7 @@ name: IdentiPy:RHNS def: "The IdentiPy result 'RHNS'." [PSI:PI] is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002989 @@ -19622,7 +19622,7 @@ name: IdentiPy:hyperscore def: "The IdentiPy result 'hyperscore'." [PSI:PI] is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002990 @@ -19643,7 +19643,7 @@ def: "Posterior error probability of the best identified peptide of the Andromed is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002996 @@ -19656,7 +19656,7 @@ id: MS:1002997 name: ProteomeXchange dataset identifier reanalysis number def: "Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD)." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1002998 @@ -19712,7 +19712,7 @@ name: mean inverse reduced ion mobility array def: "Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units MS:1002814 ! volt-second per square centimeter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003007 @@ -19721,7 +19721,7 @@ def: "Array of raw ion mobility values (K or K0) based on ion separation in gase is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003008 @@ -19729,7 +19729,7 @@ name: raw inverse reduced ion mobility array def: "Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units MS:1002814 ! volt-second per square centimeter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003009 @@ -19783,7 +19783,7 @@ is_a: MS:1002490 ! peptide-level scoring is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003017 @@ -19793,7 +19793,7 @@ is_a: MS:1002490 ! peptide-level scoring is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003018 @@ -19840,7 +19840,7 @@ def: "The OpenPepXL score for a cross-link spectrum match." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003025 @@ -19877,21 +19877,21 @@ id: MS:1003030 name: Mascot:MinNumSigUniqueSeqs def: "Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1003031 name: CPTAC accession number def: "Main identifier of a CPTAC dataset." [PSI:PI] is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003032 name: compound identification confidence code in MS-DIAL def: "The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program." [PMID:25938372, http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL] is_a: MS:1002895 ! small molecule identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003033 @@ -19982,7 +19982,7 @@ id: MS:1003047 name: protein sequence offset def: "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003048 @@ -20022,14 +20022,14 @@ id: MS:1003053 name: theoretical monoisotopic m/z def: "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003054 name: theoretical average m/z def: "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003055 @@ -20060,21 +20060,21 @@ id: MS:1003059 name: number of peaks def: "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI] is_a: MS:1003058 ! spectrum property -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003060 name: number of data points def: "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI] is_a: MS:1003058 ! spectrum property -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003061 name: library spectrum name def: "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI] is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term synonym: "spectrum name" EXACT [] [Term] @@ -20082,14 +20082,14 @@ id: MS:1003062 name: library spectrum index def: "Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0." [PSI:PI] is_a: MS:1003234 ! library spectrum attribute -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003063 name: universal spectrum identifier def: "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI] is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term synonym: "USI" EXACT [] [Term] @@ -20127,14 +20127,14 @@ id: MS:1003069 name: number of replicate spectra available def: "Number of replicate spectra available for use during the aggregation process." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003070 name: number of replicate spectra used def: "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003071 @@ -20195,7 +20195,7 @@ id: MS:1003080 name: top 20 peak unassigned intensity fraction def: "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003081 @@ -20203,7 +20203,7 @@ name: unidentified modification monoisotopic mass delta def: "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the element in mzIdentML." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003082 @@ -20223,7 +20223,7 @@ id: MS:1003084 name: processed data file def: "File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument." [PSI:MS] is_a: MS:1000577 ! source data file -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003085 @@ -20231,7 +20231,7 @@ name: previous MSn-1 scan precursor intensity def: "Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes." [PSI:MS] is_a: MS:1001141 ! intensity of precursor ion is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003086 @@ -20239,7 +20239,7 @@ name: precursor apex intensity def: "Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope." [PSI:MS] is_a: MS:1001141 ! intensity of precursor ion is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003087 @@ -20277,7 +20277,7 @@ id: MS:1003092 name: number of mantissa bits truncated def: "Number of extraneous mantissa bits truncated to improve subsequent compression." [PSI:MS] is_a: MS:1003091 ! binary data compression parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1003093 @@ -20309,42 +20309,42 @@ id: MS:1003097 name: MaxQuant protein group-level score def: "The probability based MaxQuant protein group score." [PSI:MS] is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003098 name: Andromeda peptide PEP def: "Peptide probability from Andromeda." [PSI:MS] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003099 name: MaxQuant-DIA peptide PEP def: "Peptide probability from MaxQuant-DIA algorithm." [PSI:MS] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003100 name: MaxQuant-DIA score def: "PSM evidence score from MaxQuant-DIA algorithm." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003101 name: MaxQuant-DIA PEP def: "PSM evidence PEP probability from MaxQuant-DIA algorithm." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003102 name: NIST msp comment def: "Term for a comment field withing the NIST msp file format" [PSI:MS] is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003103 @@ -20395,7 +20395,7 @@ name: SIM-XL score def: "SIM-XL identification search engine score" [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003111 @@ -20414,35 +20414,35 @@ id: MS:1003113 name: OpenMS:ConsensusID PEP def: "The OpenMS ConsesusID tool posterior error probability" [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003114 name: OpenMS:Best PSM Score def: "The score of the best PSM selected by the underlying identification tool" [PSI:MS] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003115 name: OpenMS:Target-decoy PSM q-value def: "The OpenMS Target-decoy q-values at PSM level" [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003116 name: OpenMS:Target-decoy peptide q-value def: "The OpenMS Target-decoy q-values at peptide sequence level" [PSI:MS] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003117 name: OpenMS:Target-decoy protein q-value def: "The OpenMS Target-decoy q-values at protein level" [PSI:MS] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003118 @@ -20456,21 +20456,21 @@ id: MS:1003119 name: EPIFANY:Protein posterior probability def: "Protein Posterior probability calculated by EPIFANY protein inference algorithm" [PSI:MS] is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003120 name: OpenMS:LFQ intensity def: "The data type LFQ intensity produced by OpenMS." [PSI:MS] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003121 name: OpenMS:LFQ spectral count def: "The data type LFQ spectral count produced by OpenMS." [PSI:MS] is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003122 @@ -20497,7 +20497,7 @@ def: "ProSight spectrum-level Q-value." [PSI:MS] is_a: MS:1002354 ! PSM-level q-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003126 @@ -20505,7 +20505,7 @@ name: ProSight:spectral P-score def: "ProSight spectrum-level P-score." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003127 @@ -20514,7 +20514,7 @@ def: "ProSight spectrum-level E-value." [PSI:MS] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003128 @@ -20522,7 +20522,7 @@ name: ProSight:spectral C-score def: "ProSight spectrum-level C-score." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003129 @@ -20531,7 +20531,7 @@ def: "Estimation of the Q-value for proteoforms." [PSI:MS] is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003130 @@ -20539,7 +20539,7 @@ name: ProSight:proteoform Q-value def: "ProSight proteoform-level Q-value." [PSI:MS] is_a: MS:1003129 ! proteoform-level Q-value relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003131 @@ -20559,7 +20559,7 @@ name: isoform-level Q-value def: "Estimation of the Q-value for isoforms." [PSI:MS] is_a: MS:1003132 ! isoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003134 @@ -20567,7 +20567,7 @@ name: ProSight:isoform Q-value def: "ProSight isoform-level Q-value." [PSI:MS] is_a: MS:1003133 ! isoform-level Q-value relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003135 @@ -20575,7 +20575,7 @@ name: ProSight:protein Q-value def: "ProSight protein-level Q-value." [PSI:MS] is_a: MS:1001869 ! protein-level q-value relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003136 @@ -20595,7 +20595,7 @@ name: ProSight:Run delta m mode def: "If true, runs delta m mode in ProSight." [PSI:MS] is_a: MS:1003136 ! ProSight input parameter is_a: MS:1003137 ! TDPortal input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1003139 @@ -20603,7 +20603,7 @@ name: ProSight:Run Subsequence Search mode def: "If true, runs Subsequence Search mode in ProSight." [PSI:MS] is_a: MS:1003136 ! ProSight input parameter is_a: MS:1003137 ! TDPortal input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1003140 @@ -20611,7 +20611,7 @@ name: ProSight:Run Annotated Proteoform Search mode def: "If true, runs Annotated Proteoform Search mode in ProSight." [PSI:MS] is_a: MS:1003136 ! ProSight input parameter is_a: MS:1003137 ! TDPortal input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1003141 @@ -20685,7 +20685,7 @@ id: MS:1003151 name: SHA-256 def: "SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [PSI:MS] is_a: MS:1000561 ! data file checksum type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003152 @@ -20700,7 +20700,7 @@ def: "Array of raw ion mobility values from a drift time device, reported in sec is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003154 @@ -20709,7 +20709,7 @@ def: "Array of ion mobility values (K or K0) based on ion separation in gaseous is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003155 @@ -20717,7 +20717,7 @@ name: deconvoluted inverse reduced ion mobility array def: "Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units MS:1002814 ! volt-second per square centimeter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003156 @@ -20726,7 +20726,7 @@ def: "Array of mean ion mobility values from a drift time device, reported in se is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003157 @@ -20734,7 +20734,7 @@ name: scanning quadrupole position lower bound m/z array def: "Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] is_a: MS:1000513 ! binary data array relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003158 @@ -20742,7 +20742,7 @@ name: scanning quadrupole position upper bound m/z array def: "Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] is_a: MS:1000513 ! binary data array relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003159 @@ -20794,28 +20794,28 @@ id: MS:1003166 name: assigned intensity fraction def: "Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum" [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003167 name: MSn-1 isolation window precursor purity def: "The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte" [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003168 name: library spectrum comment def: "A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools." [PSI:PI] is_a: MS:1003234 ! library spectrum attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003169 name: proforma peptidoform sequence def: "Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation" [PSI:PI] is_a: MS:1000889 ! peptidoform sequence -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003170 @@ -20840,64 +20840,64 @@ id: MS:1003173 name: numeric attribute def: "An attribute that takes on a numeric value" [PSI:PI] is_a: MS:1000547 ! object attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003174 name: attribute maximum def: "The maximum value for this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003175 name: attribute minimum def: "The minimum value for this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003176 name: attribute mean def: "The arithmetic mean value for this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003177 name: attribute standard deviation def: "The standard deviation (exact value of population, or estimate from sample) of this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003178 name: attribute coefficient of variation def: "The coefficient of variation of this attribute, i.e. standard deviation divided by the mean" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003179 name: attribute summary value def: "The most appropriate summary value of the attribute, usually but not necessarily the mean" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003180 name: attribute median def: "The median of this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003181 @@ -20935,42 +20935,42 @@ id: MS:1003186 name: library format version def: "Version number of the [PSI] library format specification" [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003187 name: library identifier def: "Short identifier for the library for easy reference, preferably but not necessarily globally unique" [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003188 name: library name def: "A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library." [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003189 name: library description def: "Extended free-text description of the library" [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003190 name: library version def: "Version number of the library, usually refering to a certain release of a continually updated library " [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003191 name: library URI def: "URI or URL that uniquely identifies the library" [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003192 @@ -21007,28 +21007,28 @@ id: MS:1003197 name: license URI def: "URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/)" [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003198 name: copyright notice def: "Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work" [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003199 name: change log def: "Extended free-text description of the difference from the previous version" [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003200 name: software version def: "Version number of the software package used for library creation" [PSI:PI] is_a: MS:1003171 ! spectral library attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003201 @@ -21048,28 +21048,28 @@ id: MS:1003203 name: constituent spectrum file def: "Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible." [PSI:PI] is_a: MS:1003201 ! library provenance attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003204 name: constituent identification file def: "Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible" [PSI:PI] is_a: MS:1003201 ! library provenance attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003205 name: constituent library file def: "Source library URI which(at least) a subset of spectra were extracted from." [PSI:PI] is_a: MS:1003201 ! library provenance attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003206 name: library creation log def: "String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \n" [PSI:PI] is_a: MS:1003201 ! library provenance attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003207 @@ -21084,7 +21084,7 @@ name: experimental precursor monoisotopic m/z def: "The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003209 @@ -21093,7 +21093,7 @@ def: "The measured monoisotopic m/z (as reported by the mass spectrometer acquis is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_units MS:1000040 ! m/z relationship: has_units UO:0000169 ! parts per million -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003210 @@ -21102,7 +21102,7 @@ def: "The measured average m/z (as reported by the mass spectrometer acquisition is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_units MS:1000040 ! m/z relationship: has_units UO:0000169 ! parts per million -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003211 @@ -21117,7 +21117,7 @@ def: "A name to refer to a library attribute set" [PSI:PI] relationship: part_of MS:1003211 ! library spectrum attribute set relationship: part_of MS:1003238 ! library analyte attribute set relationship: part_of MS:1003239 ! library interpretation attribute set -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003213 @@ -21268,7 +21268,7 @@ id: MS:1003237 name: library spectrum key def: "An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library." [PSI:PI] is_a: MS:1003234 ! library spectrum attribute -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003238 @@ -21305,14 +21305,14 @@ id: MS:1003243 name: adduct ion mass def: "The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule’s mass plus the mass of a proton)" [PSI:PI] is_a: MS:1003056 ! adduct ion property -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003244 name: peptide accession number def: "Accession number (e.g. in PeptideAtlas) of the peptide sequence" [PSI:PI] is_a: MS:1003050 ! peptidoform attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003245 @@ -21353,14 +21353,14 @@ id: MS:1003250 name: count of identified peptidoforms def: "The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] is_a: MS:1002702 ! peptide sequence-level result list attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1003251 name: count of identified spectra def: "The number of spectra that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] is_a: MS:1002700 ! PSM-level result list attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1003252 @@ -21417,14 +21417,14 @@ id: MS:1003260 name: related spectrum USI def: "A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI] is_a: MS:1003258 ! related spectrum -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003261 name: related spectrum description def: "A free-text string describing the related spectrum and/or its relationship to this spectrum" [PSI:PI] relationship: part_of MS:1003258 ! related spectrum -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003262 @@ -21444,7 +21444,7 @@ id: MS:1003264 name: similar spectrum USI def: "A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI] is_a: MS:1003262 ! similar spectrum -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003265 @@ -21463,7 +21463,7 @@ id: MS:1003267 name: spectrum cluster key def: "An ordinal number uniquely identifying a spectrum cluster. It should start with 1." [PSI:PI] is_a: MS:1003266 ! spectrum cluster attribute -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003268 @@ -21477,7 +21477,7 @@ id: MS:1003269 name: spectrum cluster member USI def: "A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier " [PSI:PI] is_a: MS:1003266 ! spectrum cluster attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003270 @@ -21640,7 +21640,7 @@ synonym: "XIC-WideFrac" EXACT [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept UO:0000191 ! fraction [Term] @@ -21654,7 +21654,7 @@ is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000018 ! XIC metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept MS:1000086 ! full width at half-maximum relationship: has_value_concept STATO:0000291 ! quantile relationship: has_units UO:0000010 ! second @@ -21670,7 +21670,7 @@ is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000018 ! XIC metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept STATO:0000105 ! log signal intensity ratio relationship: has_value_concept UO:0000191 ! fraction @@ -21683,7 +21683,7 @@ is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C25330 ! Duration relationship: has_units UO:0000010 ! second @@ -21700,7 +21700,7 @@ relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_metric_category MS:4000017 ! chromatogram metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000191 ! fraction [Term] @@ -21716,7 +21716,7 @@ relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000191 ! fraction [Term] @@ -21732,7 +21732,7 @@ relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000191 ! fraction [Term] @@ -21747,7 +21747,7 @@ relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept STATO:0000105 ! log signal intensity ratio [Term] @@ -21762,7 +21762,7 @@ relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept STATO:0000105 ! log signal intensity ratio [Term] @@ -21774,7 +21774,7 @@ is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] @@ -21786,7 +21786,7 @@ is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] @@ -21800,7 +21800,7 @@ is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C45781 ! Density relationship: has_units UO:0000189 ! count unit @@ -21815,7 +21815,7 @@ is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C45781 ! Density relationship: has_units UO:0000189 ! count unit @@ -21865,7 +21865,7 @@ is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000106 ! hertz [Term] @@ -21878,7 +21878,7 @@ is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000106 ! hertz [Term] @@ -21889,7 +21889,7 @@ is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000019 ! MS metric -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C25330 ! Duration relationship: has_units UO:0000010 ! second @@ -21936,7 +21936,7 @@ is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000017 ! chromatogram metric -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] @@ -22056,28 +22056,28 @@ id: MS:4000086 name: mzQC input reference def: "Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels." [PSI:MS] is_a: MS:4000080 ! QC non-metric term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:4000087 name: mzQC plot label def: "Used to supply alternative labels for plotting figures." [PSI:MS] is_a: MS:4000080 ! QC non-metric term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:4000088 name: batch label def: "Used to supply batch label information with any string value." [PSI:MS] is_a: MS:4000080 ! QC non-metric term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:4000089 name: injection sequence label def: "Used to supply injection sequence information with consecutive whole numbers." [PSI:MS] is_a: MS:4000080 ! QC non-metric term -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:4000090 @@ -22186,42 +22186,42 @@ id: PEFF:0000008 name: DbName def: "PEFF keyword for the sequence database name." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000009 name: Prefix def: "PEFF keyword for the sequence database prefix." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000010 name: DbDescription def: "PEFF keyword for the sequence database short description." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000011 name: Decoy def: "PEFF keyword for the specifying whether the sequence database is a decoy database." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: PEFF:0000012 name: DbSource def: "PEFF keyword for the source of the database file." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000013 name: DbVersion def: "PEFF keyword for the database version (release date) according to database provider." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000014 @@ -22236,14 +22236,14 @@ id: PEFF:0000015 name: NumberOfEntries def: "PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: PEFF:0000016 name: Conversion def: "PEFF keyword for the description of the conversion from original format to this current one." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000017 @@ -22251,56 +22251,56 @@ name: SequenceType def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_regexp PEFF:1002002 ! regular expression for PEFF molecular sequence type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000018 name: SpecificKey def: "PEFF keyword for database specific keywords not included in the current controlled vocabulary." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000019 name: SpecificValue def: "PEFF keyword for the specific values for a custom key." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000020 name: DatabaseDescription def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000021 name: GeneralComment def: "PEFF keyword for a general comment." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000022 name: ProteoformDb def: "PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000023 name: OptionalTagDef def: "PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000024 name: HasAnnotationIdentifiers def: "PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001001 @@ -22309,63 +22309,63 @@ def: "OBSOLETE Sequence database unique identifier." [PSI:PEFF] comment: This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant. is_a: PEFF:0000003 ! PEFF file sequence entry term is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001002 name: PName def: "PEFF keyword for the protein full name." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001003 name: NcbiTaxId def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: PEFF:0001004 name: TaxName def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001005 name: GName def: "PEFF keyword for the gene name." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001006 name: Length def: "PEFF keyword for the sequence length." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: PEFF:0001007 name: SV def: "PEFF keyword for the sequence version." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001008 name: EV def: "PEFF keyword for the entry version." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001009 name: PE def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: PEFF:0001010 @@ -22373,7 +22373,7 @@ name: Processed def: "PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001011 @@ -22383,7 +22383,7 @@ comment: This term was made obsolete in favor of VariantSimple and VariantComple is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001012 @@ -22391,7 +22391,7 @@ name: ModResPsi def: "PEFF keyword for the modified residue with PSI-MOD identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001013 @@ -22399,14 +22399,14 @@ name: ModRes def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001014 name: AltAC def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001015 @@ -22414,35 +22414,35 @@ name: SeqStatus def: "PEFF keyword for the sequence status. Complete or Fragment." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002003 ! regular expression for PEFF sequence status -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001016 name: CC def: "PEFF keyword for the entry associated comment." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001017 name: KW def: "PEFF keyword for the entry associated keyword(s)." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001018 name: GO def: "PEFF keyword for the Gene Ontology code." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001019 name: XRef def: "PEFF keyword for the cross-reference to an external resource." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001020 @@ -22450,7 +22450,7 @@ name: mature protein def: "Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001021 @@ -22458,7 +22458,7 @@ name: signal peptide def: "Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001022 @@ -22466,7 +22466,7 @@ name: transit peptide def: "Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001023 @@ -22474,28 +22474,28 @@ name: Conflict def: "PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001024 name: Crc64 def: "PEFF keyword for the Sequence checksum in crc64." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001025 name: Domain def: "PEFF keyword for the sequence range of a domain." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001026 name: ID def: "PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001027 @@ -22503,7 +22503,7 @@ name: ModResUnimod def: "PEFF keyword for the modified residue with UniMod identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001028 @@ -22511,7 +22511,7 @@ name: VariantSimple def: "PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001029 @@ -22519,21 +22519,21 @@ name: VariantComplex def: "PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001030 name: Proteoform def: "PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001031 name: DisulfideBond def: "PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001032 @@ -22546,7 +22546,7 @@ id: PEFF:0001033 name: Comment def: "PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001034 @@ -22554,7 +22554,7 @@ name: propeptide def: "Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001035 @@ -22562,7 +22562,7 @@ name: initiator methionine def: "N-terminal methionine residue of a protein that can be co-translationally cleaved." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:1002001