Notes
user@computer:~$represents an example terminal prompt name. Actual command/argument input is after the$.- Replace
[email protected]with your email address.\followed by>on the next line represents continued terminal input. You will need to delete the>symbol in order to run the scripts as a copy/paste into terminal.- You should validate your own EDirect scripts and results as there may be unintentional mistakes in these recipes. A convenient method is to compare your EDirect results to the NCBI Web interface search results: https://www.ncbi.nlm.nih.gov/.
We can view available Entrez databases, data fields, and links (connected records) with the EDirect einfo function. To retrieve a list of all databases, use the -dbs argument:
user@computer:~$ einfo -email [email protected] -dbs
annotinfo
assembly
biocollections
bioproject
biosample
biosystems
blastdbinfo
books
cdd
clinvar
dbvar
gap
gapplus
gds
gene
genome
geoprofiles
grasp
gtr
homologene
ipg
medgen
mesh
ncbisearch
nlmcatalog
nuccore
nucleotide
omim
orgtrack
pcassay
pccompound
pcsubstance
pmc
popset
protein
proteinclusters
protfam
pubmed
seqannot
snp
sra
structure
taxonomy
This EDirectChemInfo repository focuses on searching the PubChem Compound, PubMed, and PubChem BioAssay databases. So let's take a closer look at these three databases, starting with the PubChem Compound (-db pccompound) database. The einfo arguments -fields and -links provide information about the available data fields and linked information, respectively:
user@computer:~$ einfo -email [email protected] -db pccompound -fields
AC ActiveAidCount
ACC AtomChiralCount
ACDC AtomChiralDefCount
ACUC AtomChiralUndefCount
ALL All Fields
BCC BondChiralCount
BCDC BondChiralDefCount
BCUC BondChiralUndefCount
CDAT CreateDate
CPLX Complexity
CSYN CompleteSynonym
CUC CovalentUnitCount
DCNT DepositorCount
DCSY DepositorCompleteSynonym
DSYN DepositorSynonym
ELMT Element
EMAS ExactMass
FILT Filter
HAC HeavyAtomCount
HBAC HydrogenBondAcceptorCount
HBDC HydrogenBondDonorCount
IAC IsotopeAtomCount
IKEY InChIKey
INCH InChI
MMAS MonoisotopicMass
MSHT MeSHTerm
MW MolecularWeight
PAID PharmActionID
PHMA PharmAction
RBC RotatableBondCount
SID SubstanceID
SRCC SourceCategory
SRC SourceName
STID StructureID
SYNO Synonym
TAC TotalAidCount
TFC TotalFormalCharge
TPSA TPSA
UID CompoundID
UPAC IUPACName
XLGP XLogP
user@computer:~$ einfo -email [email protected] -db pccompound -links
pccompound_biosystems BioSystems
pccompound_gene Gene
pccompound_mesh MeSH Keyword
pccompound_nuccore Nucleotide Sequences
pccompound_omim OMIM
pccompound_pcassay BioAssays
pccompound_pcassay_active BioAssays, Active
pccompound_pcassay_activityconcmicromolar BioAssays, activity concentration at/below 1 uM
pccompound_pcassay_activityconcnanomolar BioAssays, activity concentration at/below 1 nM
pccompound_pcassay_inactive BioAssays, Inactive
pccompound_pcassay_probe BioAssays, Probe
pccompound_pccompound Similar Compounds
pccompound_pccompound_3d Similar Conformers
pccompound_pccompound_mixture Mixture/Component Compounds
pccompound_pccompound_parent Parent Compound
pccompound_pccompound_parent_connectivity_pulldown Same Parent, Connectivity
pccompound_pccompound_parent_isotopes_pulldown Same Parent, Isotopes
pccompound_pccompound_parent_pulldown Same Parent
pccompound_pccompound_parent_stereo_pulldown Same Parent, Stereochemistry
pccompound_pccompound_parent_tautomer_pulldown Same Parent, Any Tautomer
pccompound_pccompound_sameanytautomer_pulldown Same, Any Tautomer
pccompound_pccompound_sameconnectivity_pulldown Same, Connectivity
pccompound_pccompound_sameisotopic_pulldown Same, Isotopes
pccompound_pccompound_samestereochem_pulldown Same, Stereochemistry
pccompound_pcsubstance PubChem Mixture Substances
pccompound_pcsubstance_same PubChem Same Substances
pccompound_pmc PMC Articles
pccompound_protein Protein Sequences
pccompound_pubmed PubMed Citations
pccompound_pubmed_mesh PubMed (MeSH Keyword)
pccompound_pubmed_publisher PubMed (Publisher)
pccompound_structure Protein Structures
pccompound_taxonomy Taxonomy
Now that we have an understanding about what kind of data is available in the PubChem Compound database, let's take a look at a PubChem Compound record using the esearch and efetch functions:
user@computer:~$ esearch -email [email protected] -db pccompound -query 512323[UID]
<ENTREZ_DIRECT>
<Db>pccompound</Db>
<WebEnv>MCID...</WebEnv>
<QueryKey>1</QueryKey>
<Count>1</Count>
<Step>1</Step>
<Email>[email protected]</Email>
</ENTREZ_DIRECT>
We searched PubChem for the Compound Identifier 512323 using esearch, and the NCBI Entrez server returned a summary of the search results. The WebEnV and QueryKey specify the location of the search results on the NCBI server. In order to retrieve the data, we can pipe (|) the esearch results directly into the efetch function:
user@computer:~$ esearch -email [email protected] -db pccompound -query 512323[UID] | \
> efetch -format docsum
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE DocumentSummarySet PUBLIC "-//NLM//DTD esummary pccompound 20170720//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20170720/esummary_pccompound.dtd">
<DocumentSummarySet status="OK">
<DbBuild>Build210125-0720m.1</DbBuild>
<DocumentSummary>
<Id>512323</Id>
<CID>512323</CID>
<SourceCategoryList>
<string>Chemical Vendors</string>
<string>Governmental Organizations</string>
<string>Subscription Services</string>
<string>Curation Efforts</string>
<string>Journal Publishers</string>
<string>Research and Development</string>
<string>Legacy Depositors</string>
</SourceCategoryList>
<CreateDate>2005/08/01 00:00</CreateDate>
<SynonymList>
<string>CHEMBL1791149</string>
<string>89647-10-9</string>
<string>Uridine, 2'-deoxy-5-(2-thienyl)-</string>
<string>5-(2'-Thienyl)-2'-beta-deoxyuridine</string>
<string>SCHEMBL1635430</string>
<string>5-thien-2-yl-2'-deoxyuridine</string>
<string>CTK2J2646</string>
<string>5-(2-thienyl)-2'-deoxyuridine</string>
<string>5-(2'-Thienyl)-2'-deoxyuridine-</string>
<string>BDBM50407986</string>
<string>1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-thiophen-2-ylpyrimidine-2,4-dione</string>
<string>1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-(2-thienyl)pyrimidine-2,4-dione</string>
</SynonymList>
<IUPACName>1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-thiophen-2-ylpyrimidine-2,4-dione</IUPACName>
<CanonicalSmiles>C1C(C(OC1N2C=C(C(=O)NC2=O)C3=CC=CS3)CO)O</CanonicalSmiles>
<IsomericSmiles>C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C3=CC=CS3)CO)O</IsomericSmiles>
<RotatableBondCount>3</RotatableBondCount>
<MolecularFormula>C13H14N2O5S</MolecularFormula>
<MolecularWeight>310.330</MolecularWeight>
<MolecularWeightSort>310330</MolecularWeightSort>
<TotalFormalCharge>0</TotalFormalCharge>
<XLogP>-0.2</XLogP>
<HydrogenBondDonorCount>3</HydrogenBondDonorCount>
<HydrogenBondAcceptorCount>6</HydrogenBondAcceptorCount>
<Complexity>483.000</Complexity>
<ComplexitySort>483000</ComplexitySort>
<HeavyAtomCount>21</HeavyAtomCount>
<AtomChiralCount>3</AtomChiralCount>
<AtomChiralDefCount>3</AtomChiralDefCount>
<AtomChiralUndefCount>0</AtomChiralUndefCount>
<BondChiralCount>0</BondChiralCount>
<BondChiralDefCount>0</BondChiralDefCount>
<BondChiralUndefCount>0</BondChiralUndefCount>
<IsotopeAtomCount>0</IsotopeAtomCount>
<CovalentUnitCount>1</CovalentUnitCount>
<TPSA>127</TPSA>
<ActiveAidCount>1</ActiveAidCount>
<TotalAidCount>37</TotalAidCount>
<InChIKey>PCDQBRGMSMVLDZ-IQJOONFLSA-N</InChIKey>
<ProbeAidCount>0</ProbeAidCount>
<InChI>InChI=1S/C13H14N2O5S/c16-6-9-8(17)4-11(20-9)15-5-7(10-2-1-3-21-10)12(18)14-13(15)19/h1-3,5,8-9,11,16-17H,4,6H2,(H,14,18,19)/t8-,9+,11+/m0/s1</InChI>
</DocumentSummary>
</DocumentSummarySet>
efetch returned the CID record data as document summary XML format (for other formats see efetch -help). XML is useful, but we probably want to parse the data into a table for easier viewing and analysis. EDirect contains a function called xtract that can convert the Entrez XML data into tables. See xtract -help for more information. In brief, you will need to select a main XML heading tag to define the extract pattern and then specify the data you want to extract with the sub-heading tag names (elements). For example, in the above CID record data, we can set the pattern to DocumentSummary (the first main XML tag in this case), and then the elements to a few of the sub-heading tags we are interested such as IsomericSmiles, CID, InChIKey, MolecularFormula, and MolecularWeight:
user@computer:~$ esearch -email [email protected] -db pccompound -query 512323[UID] | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID InChIKey MolecularFormula MolecularWeight
C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C3=CC=CS3)CO)O 512323 PCDQBRGMSMVLDZ-IQJOONFLSA-N C13H14N2O5S 310.330
Similarly to PubChem Compound, let's preview the available PubMed database indexed fields, links, and data structure:
user@computer:~$ einfo -email [email protected] -db pubmed -fields
AFFL Affiliation
ALL All Fields
AUCL Author Cluster ID
AUID Author - Identifier
AUTH Author
BOOK Book
CDAT Date - Completion
CNTY Place of Publication
COIS Conflict of Interest Statements
COLN Author - Corporate
CRDT Date - Create
DSO DSO
ECNO EC/RN Number
EDAT Date - Entrez
ED Editor
EID Extended PMID
EPDT Electronic Publication Date
FAUT Author - First
FILT Filter
FINV Investigator - Full
FULL Author - Full
GRNT Grant Number
INVR Investigator
ISBN ISBN
ISS Issue
JOUR Journal
LANG Language
LAUT Author - Last
LID Location ID
MAJR MeSH Major Topic
MDAT Date - Modification
MESH MeSH Terms
MHDA Date - MeSH
OTRM Other Term
PAGE Pagination
PAPX Pharmacological Action
PDAT Date - Publication
PID Publisher ID
PPDT Print Publication Date
PS Subject - Personal Name
PTYP Publication Type
PUBN Publisher
SI Secondary Source ID
SUBH MeSH Subheading
SUBS Supplementary Concept
TIAB Title/Abstract
TITL Title
TT Transliterated Title
UID UID
VOL Volume
WORD Text Word
user@computer:~$ einfo -email [email protected] -db pubmed -links
pubmed_assembly Assembly
pubmed_bioproject Project Links
pubmed_biosample BioSample Links
pubmed_biosystems BioSystem Links
pubmed_books_refs Cited in Books
pubmed_cdd Conserved Domain Links
pubmed_clinvar_calculated ClinVar (calculated)
pubmed_clinvar ClinVar
pubmed_dbvar dbVar
pubmed_gap dbGaP Links
pubmed_gds GEO DataSet Links
pubmed_gene_bookrecords Gene (from Bookshelf)
pubmed_gene_citedinomim Gene (OMIM) Links
pubmed_gene Gene Links
pubmed_gene_pmc_nucleotide Gene (nucleotide/PMC)
pubmed_gene_rif Gene (GeneRIF) Links
pubmed_genome Genome Links
pubmed_geoprofiles GEO Profile Links
pubmed_homologene HomoloGene Links
pubmed_medgen_bookshelf_cited MedGen (Bookshelf cited)
pubmed_medgen_genereviews MedGen (GeneReviews)
pubmed_medgen MedGen
pubmed_medgen_omim MedGen (OMIM)
pubmed_nuccore Nucleotide Links
pubmed_nuccore_refseq Nucleotide (RefSeq) Links
pubmed_nuccore_weighted Nucleotide (Weighted) Links
pubmed_omim_bookrecords OMIM (from Bookshelf)
pubmed_omim_calculated OMIM (calculated) Links
pubmed_omim_cited OMIM (cited) Links
pubmed_pcassay PubChem BioAssay
pubmed_pccompound_mesh PubChem Compound (MeSH Keyword)
pubmed_pccompound PubChem Compound
pubmed_pccompound_publisher PubChem Compound (Publisher)
pubmed_pcsubstance_bookrecords PubChem Substance (from Bookshelf)
pubmed_pcsubstance PubChem Substance Links
pubmed_pcsubstance_publisher PubChem Substance (Publisher)
pubmed_pmc_bookrecords References in PMC for this Bookshelf citation
pubmed_pmc_embargo
pubmed_pmc_local
pubmed_pmc PMC Links
pubmed_pmc_refs Cited in PMC
pubmed_popset PopSet Links
pubmed_probe Probe Links
pubmed_proteinclusters Protein Cluster Links
pubmed_protein Protein Links
pubmed_protein_refseq Protein (RefSeq) Links
pubmed_protein_weighted Protein (Weighted) Links
pubmed_protfam Protein Family Models
pubmed_pubmed_alsoviewed Articles frequently viewed together
pubmed_pubmed_bookrecords References for this Bookshelf citation
pubmed_pubmed_refs References for PMC Articles
pubmed_pubmed Similar articles
pubmed_snp_cited SNP (Cited)
pubmed_snp SNP Links
pubmed_sra SRA Links
pubmed_structure Structure Links
pubmed_taxonomy_entrez Taxonomy via GenBank
And here is an example PubMed article record in abstract form:
user@computer:~$ esearch -email [email protected] -db pubmed -query "17630804"[PMID] |\
> efetch -format abstract
1. J Org Chem. 2007 Aug 17;72(17):6621-3. Epub 2007 Jul 14.
Total synthesis and absolute configuration determination of (+)-bruguierol C.
Solorio DM(1), Jennings MP.
Author information:
(1)Department of Chemistry, 500 Campus Drive, The University of Alabama,
Tuscaloosa, Alabama 35487-0336, USA.
The first total synthesis and absolute configuration of bruguierol C are
reported. The key step involved the diastereoselective capture of an in situ
generated oxocarbenium ion via an intramolecular Friedel-Crafts alkylation.
DOI: 10.1021/jo071035l
PMID: 17630804 [Indexed for MEDLINE]
and the same record in XML format:
user@computer:~$ esearch -email [email protected] -db pubmed -query "17630804"[PMID] |\
> efetch -format xml
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2019//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd">
<PubmedArticleSet>
<PubmedArticle>
<MedlineCitation Status="MEDLINE" Owner="NLM">
<PMID Version="1">17630804</PMID>
<DateCompleted>
<Year>2007</Year>
<Month>10</Month>
<Day>25</Day>
</DateCompleted>
<DateRevised>
<Year>2007</Year>
<Month>08</Month>
<Day>10</Day>
</DateRevised>
<Article PubModel="Print-Electronic">
<Journal>
<ISSN IssnType="Print">0022-3263</ISSN>
<JournalIssue CitedMedium="Print">
<Volume>72</Volume>
<Issue>17</Issue>
<PubDate>
<Year>2007</Year>
<Month>Aug</Month>
<Day>17</Day>
</PubDate>
</JournalIssue>
<Title>The Journal of organic chemistry</Title>
<ISOAbbreviation>J Org Chem</ISOAbbreviation>
</Journal>
<ArticleTitle>Total synthesis and absolute configuration determination of (+)-bruguierol C.</ArticleTitle>
<Pagination>
<MedlinePgn>6621-3</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>The first total synthesis and absolute configuration of bruguierol C are reported. The key step involved the diastereoselective capture of an in situ generated oxocarbenium ion via an intramolecular Friedel-Crafts alkylation.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Solorio</LastName>
<ForeName>Dionicio Martinez</ForeName>
<Initials>DM</Initials>
<AffiliationInfo>
<Affiliation>Department of Chemistry, 500 Campus Drive, The University of Alabama, Tuscaloosa, Alabama 35487-0336, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Jennings</LastName>
<ForeName>Michael P</ForeName>
<Initials>MP</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2007</Year>
<Month>07</Month>
<Day>14</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>United States</Country>
<MedlineTA>J Org Chem</MedlineTA>
<NlmUniqueID>2985193R</NlmUniqueID>
<ISSNLinking>0022-3263</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D006575">Heterocyclic Compounds, 3-Ring</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="C523709">bruguierol C</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D006575" MajorTopicYN="N">Heterocyclic Compounds, 3-Ring</DescriptorName>
<QualifierName UI="Q000138" MajorTopicYN="N">chemical synthesis</QualifierName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D009682" MajorTopicYN="N">Magnetic Resonance Spectroscopy</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D015394" MajorTopicYN="Y">Molecular Structure</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D021241" MajorTopicYN="N">Spectrometry, Mass, Electrospray Ionization</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013055" MajorTopicYN="N">Spectrophotometry, Infrared</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013237" MajorTopicYN="N">Stereoisomerism</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="pubmed">
<Year>2007</Year>
<Month>7</Month>
<Day>17</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2007</Year>
<Month>10</Month>
<Day>27</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>2007</Year>
<Month>7</Month>
<Day>17</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">17630804</ArticleId>
<ArticleId IdType="doi">10.1021/jo071035l</ArticleId>
</ArticleIdList>
</PubmedData>
</PubmedArticle>
</PubmedArticleSet>
The above returned XML PubMed record is hard to understand as it has many fields. We can use the xtract -outline argument to present a structured view of only the XML data tags:
user@computer:~$ esearch -email [email protected] -db pubmed -query "17630804"[PMID] | \
> efetch -format xml | \
> xtract -outline
PubmedArticle
MedlineCitation
PMID
DateCompleted
Year
Month
Day
DateRevised
Year
Month
Day
Article
Journal
ISSN
JournalIssue
Volume
Issue
PubDate
Year
Month
Day
Title
ISOAbbreviation
ArticleTitle
Pagination
MedlinePgn
Abstract
AbstractText
AuthorList
Author
LastName
ForeName
Initials
AffiliationInfo
Affiliation
Author
LastName
ForeName
Initials
Language
PublicationTypeList
PublicationType
PublicationType
PublicationType
ArticleDate
Year
Month
Day
MedlineJournalInfo
Country
MedlineTA
NlmUniqueID
ISSNLinking
ChemicalList
Chemical
RegistryNumber
NameOfSubstance
Chemical
RegistryNumber
NameOfSubstance
CitationSubset
MeshHeadingList
MeshHeading
DescriptorName
QualifierName
QualifierName
MeshHeading
DescriptorName
MeshHeading
DescriptorName
MeshHeading
DescriptorName
MeshHeading
DescriptorName
MeshHeading
DescriptorName
PubmedData
History
PubMedPubDate
Year
Month
Day
Hour
Minute
PubMedPubDate
Year
Month
Day
Hour
Minute
PubMedPubDate
Year
Month
Day
Hour
Minute
PublicationStatus
ArticleIdList
ArticleId
ArticleId
The above structured output makes it easier to view the XML formatting and determine which data elements we are interested in extracting out with xtract, such as the PMID, Author/LastName, Author/Initials, ISOAbbreviation, ArticleTitle, PubDate, Volume, Issue, and MedlinePgn:
user@computer:~$ esearch -email [email protected] -db pubmed -query "17630804"[PMID] | \
> efetch -format xml | \
> xtract -pattern PubmedArticle -element MedlineCitation/PMID -first Author/LastName Author/Initials \
> ISOAbbreviation ArticleTitle PubDate/Year Volume Issue MedlinePgn
17630804 Solorio DM J. Org. Chem. Total synthesis and absolute configuration determination of (+)-bruguierol C. 2007 72 17 6621-3
Note that in the above xtract argument, the element selection is specified with -first, so that only the first occurrence is extracted (e.g., first Author).
Lastly, let's take a look at the PubChem BioAssay database indexed fields, links, and data structure:
user@computer:~$ einfo -email [email protected] -db pcassay -fields
AC Active Sid Count
ACMD Activity Outcome Method
ACMT Assay Comment
ADES Assay Description
ALL All Fields
ANAM Assay Name
APRJ Assay Project
APRL Assay Protocol
ASRD Assay Source ID
BSID BioSystems ID
CCMT Categorized Comment
CCT Categorized Comment Title
CELL Cell Line
CSNM Current Source Name
DDAT Deposit Date
DTMD Detection Method
FILT Filter
GBAC GenBank Accession
GRN Grant Number
GSYM Gene Symbol
HDAT Hold Until Date
JNAM Journal Name
MDAT Modify Date
NARD Nucleic Acid Reagent ID
NSAM Number of Sids With Activity Concentration micromolar
NSAN Number of Sids With Activity Concentration nanomolar
ORGN Organism
PCC Probe Cid Count
PIGI Pig GI
PSC Probe Sid Count
PTGI Protein Target GI
PTN Protein Target Name
RTGI RNA Target GI
SNME Source Name
SRCC Source Category
SYNT Synonym Tested
TCNT Target Count
TSC Total Sid Count
TXNM Taxonomy Name
UID Assay ID
UPAC UniProt Accession
user@computer:~$ einfo -email [email protected] -db pcassay -links
pcassay_books_probe MLP Chemical Probe Report
pcassay_cdd_protein_target Conserved Domains (Full) via Protein Target
pcassay_gene_rnai RNAi Target, Tested
pcassay_gene_rnai_active RNAi Target, Active
pcassay_gene_target Gene Target
pcassay_nuccore Nucleotide
pcassay_nuccore_rna_target Nucleotide RNA Target
pcassay_omim OMIM
pcassay_pcassay_activityneighbor_list Related BioAssays, by Activity Overlap (List)
pcassay_pcassay_assay_project Related Assay Projects
pcassay_pcassay_common_gene_list Related BioAssays, by Common Active Gene (List)
pcassay_pcassay_gene_interaction_list Related BioAssays, by Gene Interaction (List)
pcassay_pcassay_neighbor_list Related BioAssays, by Depositor (List)
pcassay_pcassay_same_assay_project_list Related BioAssays, by Same Project (List)
pcassay_pcassay_same_publication_list Related BioAssays, by Same Publication (List)
pcassay_pcassay_similar_publication_list Related BioAssays, by Similar Publication (List)
pcassay_pcassay_targetneighbor_list Related BioAssays, by Target Similarity (List)
pcassay_pccompound Compounds
pcassay_pccompound_active Compounds, Active
pcassay_pccompound_activityconcmicromolar Compounds, activity concentration at/below 1 uM
pcassay_pccompound_activityconcnanomolar Compounds, activity concentration at/below 1 nM
pcassay_pccompound_inactive Compounds, Inactive
pcassay_pccompound_probe Compounds, Probe
pcassay_pcsubstance Substances
pcassay_pcsubstance_active Substances, Active
pcassay_pcsubstance_activityconcmicromolar Substances, activity concentration at/below 1 uM
pcassay_pcsubstance_activityconcnanomolar Substances, activity concentration at/below 1 nM
pcassay_pcsubstance_inactive Substances, Inactive
pcassay_pcsubstance_probe Substances, Probe
pcassay_pmc PMC Articles
pcassay_probe Nucleic acid reagent
pcassay_protein_target Protein Target
pcassay_protein_target_pig Protein Target, Identical Sequence
pcassay_pubmed PubMed Citations
pcassay_sparcle_target Target Functional Class
pcassay_structure Protein Structures
pcassay_taxonomy TaxonomyAnd here is an example PubChem BioAssay record in docsum XML:
user@computer:~$ esearch -email [email protected] -db pcassay -query "1236573"[UID] | \
> efetch -format docsum
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE DocumentSummarySet PUBLIC "-//NLM//DTD esummary pcassay 20161116//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20161116/esummary_pcassay.dtd">
<DocumentSummarySet status="OK">
<DbBuild>Build200617-0952.1</DbBuild>
<DocumentSummary><Id>1236573</Id>
<AssayName>Cytotoxicity against human NCI/ADR cells</AssayName>
<CellLine></CellLine>
<AssayDescription>Title: Progress Toward the Development of Noscapine and Derivatives as Anticancer Agents. Abstract: Many nitrogen-moiety containing alkaloids derived from plant origins are bioactive and play a significant role in human health and emerging medicine. Noscapine, a phthalideisoquinoline alkaloid derived from Papaver somniferum, has been used as a cough suppressant since the mid 1950s, illustrating a good safety profile. Noscapine has since been discovered to arrest cells at mitosis, albeit with moderately weak activity. Immunofluorescence staining of microtubules after 24 h of noscapine exposure at 20 inverted question markM elucidated chromosomal abnormalities and the inability of chromosomes to complete congression to the equatorial plane for proper mitotic separation ( Proc. Natl. Acad. Sci. U. S. A. 1998 , 95 , 1601 - 1606 ). A number of noscapine analogues possessing various modifications have been described within the literature and have shown significantly improved antiprolific profiles for a large variety of cancer cell lines. Several semisynthetic antimitotic alkaloids are emerging as possible candidates as novel anticancer therapies. This perspective discusses the advancing understanding of noscapine and related analogues in the fight against malignant disease. </AssayDescription>
<AssaySourceID>1506980</AssaySourceID>
<SourceNameList>
<string>ChEMBL</string>
</SourceNameList>
<CurrentSourceName>ChEMBL</CurrentSourceName>
<DetectionMethod></DetectionMethod>
<ActiveSidCount>1</ActiveSidCount>
<ActivityOutcomeMethod>Confirmatory</ActivityOutcomeMethod>
<TotalSidCount>1</TotalSidCount>
<OnHold>No</OnHold>
<ModifyDate>2018/10/08 00:00</ModifyDate>
<DepositDate>2016/12/22 00:00</DepositDate>
<HoldUntilDate>1/01/01 00:00</HoldUntilDate>
<AID>1236573</AID>
<ProbeSidCount>0</ProbeSidCount>
<TargetCount>0</TargetCount>
<NumberofSidsWithActivityConcmicromolar>1</NumberofSidsWithActivityConcmicromolar>
<NumberofSidsWithActivityConcnanomolar>1</NumberofSidsWithActivityConcnanomolar>
<ProteinTargetList>
</ProteinTargetList>
</DocumentSummary>
</DocumentSummarySet>Similarly to the PubChem Compound and PubMed data, we can extract out specific data using the xtract function such as the AID, CurrentSourceName, AssayName, ActiveSidCount, and TargetCount:
user@computer:~$ esearch -email [email protected] -db pcassay -query "1236573"[UID] | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element AID CurrentSourceName AssayName ActiveSidCount TargetCount
1236573 ChEMBL Cytotoxicity against human NCI/ADR cells 1 0