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search_index.json
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project hosts the PSICQUIC Reference Implementation, an implementation of the PSICQUIC Specification. A publication about PSICQUIC can be found in Nature Methods.\nYou can see PSICQUIC in action with the PSICQUIC View.\nWhat is PSICQUIC?\nPSICQUIC is an effort from the HUPO Proteomics Standard Initiative (HUPO-PSI) to standardise the access to molecular interaction databases programmatically.\n\nBasically, PSICQUIC specifies:\n\nA standard web service with a well-defined list of methods, accessible using SOAP or REST.\nA common query language (MIQL) \n\nMany interaction databases are already implementing PSICQUIC. You can check the Registry to see the most up to date list of providers and their status.\nIf you are a user in need of a convenient and standard way to fetch molecular interaction data from different sources, check the following section Information for Users. If you are a service provider willing to facilitate your data so it can reach more users with very little effort, check the section Information for Molecular Interaction providers below.\nInformation for Users\nPSICQUIC is a web service so it is meant to be use in machine-to-machine communications. However, you can get PSI-MITAB data directly in your browser by using the REST access, like in this example.\n\nHow to retrieve molecular interactions: using SOAP or REST\nList of PSICQUIC Service Providers.\nThere are two available JAVA clients for PSICQUIC. If you are a JAVA programmer start using PSICQUIC right away, find the documentations about the clients here.\nA Bioconductor package has also been developed for PSICQUIC. You can find more documentation here.\nYou can find more examples, including examples in Perl or Python.\nThe MIQL (Molecular Interaction Query Language) reference that can be used to perform more complex queries. \nIf you want to see a real use case of PSICQUIC, check the PSICQUIC View application (then just click on Search). It uses PSICQUIC behind the scenes.\nYou can also find the different PSICQUIC services in BioCatalogue.\nYou can use PSICQUIC directly from the latest Cytoscape version. Check this page if you want to know how.\nOther projects are using PSICQUIC too.\n\nInformation for Molecular Interaction providers\nImplementing PSICQUIC is relatively simple. If you can generate a PSI-MITAB file (versions 2.5, 2.6, 2.7 or 2.8), you can start using the Reference Implementation of PSICQUIC right away. For instructions, check these links:\n\nHow to install the PSICQUIC Reference Implementation: step by step guide for molecular interaction providers. \n\nCiting PSICQUIC\nTo cite PSICQUIC please use:\nAranda, B. et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Meth 8, 528-529 (2011).\ndoi:10.1038/nmeth.1637 http://www.nature.com/nmeth/journal/v8/n7/full/nmeth.1637.html\n"},"PsicquicSpecification.html":{"url":"PsicquicSpecification.html","title":"Specification","body":"Introduction\nPSICQUIC is an effort from the HUPO Proteomics Standard Initiative (HUPO-PSI) to standardise the access to molecular interaction databases programmatically.\n\nBasically, PSICQUIC specifies:\n\nA standard web service with a well-defined list of methods.\nA common query language (MIQL)\n\nThis page lists the main features of the different versions of the specification.\nVersion 1.0\nDetailed documents about the version 1.0 of the specification are available here for SOAP and here for REST.\nThis is the first version of the service and contains the following methods:\n\ngetByQuery\ngetByInteractor\ngetByInteractorList\ngetByInteraction\ngetByInteractionList\ngetByQuery\n\nAnd these metadata methods:\n\ngetSupportedReturnTypes\ngetSupportedDbAcs\ngetVersion\n\nVersion 1.1\nDetailed documents about the version 1.1 of the specification are available here for SOAP and here for REST.\nThe basic change since version 1.0 is the addition of two new metadata methods:\n\ngetProperty\ngetProperties\n\nVersion 1.2\nDetailed documents about the version 1.2 of the specification are available here for SOAP and here for REST.\nThe basic change since version 1.1 is the addition of two new metadata methods:\n\nData can be retrieved in a compressed form to save bandwidth.\nHTTP headers X-PSICQUIC-* are not part of the response.\nXGMML format available.\nRDF, Biopax formats available\n\nVersion 1.3\nDetailed documents about the version 1.3 of the specification are available here for SOAP and here for REST.\nThe most important changes since version 1.2 is the support of MITAB 2.6 and MITAB 2.7 formats. It is fully supporting all the fields of MIQL 2.7 and is based on a solr index.\n\nXGMML format available without any limitation in number of interactions to be exported\nBug fix when exporting data in RDF and biopax\nLimitation of 500 interactions when exporting in XML, Biopax and RDF. PSICQUIC returns a HTTP 400 error when trying to download more than 500 interactions at once in XML. Pagination is strongly recommended.\nBy default, negative interactions are excluded from the results returned by PSICQUIC. If a user wants to export both positive and negative interactions, he has to add a filter negative:(true OR false) to the query. Negative interactions cannot be exported with format tab25.\n\nVersion 1.4\nDetailed documents about the version 1.4 of the specification are available here for SOAP and here for REST.\nThe most important change since version 1.3 is the support of the MITAB 2.8 format for the REST service. It is supporting all the fields of MIQL 2.8 and is based on a solr index.\n"},"PsicquicSpec_1_4_Soap.html":{"url":"PsicquicSpec_1_4_Soap.html","title":"SOAP","body":"Version 1.4\nThe documentation in this page corresponds to the version 1.4 of the PSICQUIC specification.\nUsing SOAP is the traditional way to access a web service. The PSICQUIC specification defines a standard WSDL that all the implementations must comply with. This file contains the list of web service methods available for users.\nThe SOAP URL for the different interaction databases can be found in the Registry. To fetch the WSDL just append ?wsdl to the SOAP URL (example).\nImportant note: the maximum number of interactions in XML format that can be returned by a SOAP request is 500. If you want to retrieve more results, do an iteration of requests incrementing the firstResult parameter by 500 until you reach the total number of results.\nDifferences from previous versions\nFrom version 1.3\n\nThe WSDL file has not been updated so the SOAP methods are the same as for the 1.3, 1.2 and 1.1 versions.\npsi-mi/tab28 is now accepted. The ResultSet returned by the SOAP service will contain the MITAB (2.5, 2.6, 2.7 or 2.8) as a String (same as for the previous versions explaining why the WSDL file has not been updated since version 1.1)\n\nFrom version 1.2\n\nThe WSDL file has not been updated so the SOAP methods are the same as for 1.2 and 1.1.\npsi-mi/tab26 and psi-mi/tab27 are now accepted. The ResultSet returned by the SOAP service will contain the MITAB (2.5, 2.6 or 2.7) as a String (same as for the previous versions explaining why the WSDL file has not been updated since version 1.1)\nWhen returning MITAB (2.5, 2.6 or 2.7), there is no limit in the number of binary interactions returned by the SOAP service as it is doing some pagination internally. However, the maximum number of interaction to be returned in XML is 500. If the user ask for more than 500 results in XML, the SOAP service will return a 400 HTTP error code.\n\nFrom version 1.1\nNone. As the REST implementation has changed, we also updated the SOAP version. The WSDL file is the same as for version 1.1\nFrom version 1.0\nMethods to retrieve properties from the service have been added. These properties are used by the provider to define characteristics of the service.\nMethod Summary\n\n\n\nMethod Name\nDescription\n\n\n\n\ngetByQuery\nRetrieve data using a MIQL query\n\n\ngetByInteractor\nRetrieve data using a specific participant identifier\n\n\ngetByInteractorList\nRetrieve data using a list of participant identifiers. This method can be used to retrieve interactions where the two or more participants passed as arguments are found. To do so, set the operand to AND.\n\n\ngetByInteraction\nRetrieve a specific interaction using its identifier\n\n\ngetByInteractionList\nRetrieve a list of interactions, using the identifiers\n\n\n\nOther methods to retrieve information about the service itself (metadata) are also available:\n\n\n\nMethod Name\nDescription\n\n\n\n\ngetSupportedReturnTypes\nReturns the list of possible formats for the retrieved data\n\n\ngetSupportedDbAcs\nSupported database accessions\n\n\ngetVersion\nGets the version of the service\n\n\ngetProperties\nRetrieve a list of the property objects defined in a service by the provider. Each property object have a key and a value\n\n\ngetProperty\nRetrieve a property from the service\n\n\n\nMethods\nThis section explains the parameters that can be used in the above methods.\nMethod: getByQuery\nDescription: Retrieves data using a MIQL query. This is the more general method an can be used to perform the most flexible queries by using MIQL. The other methods of the web service are just convenience methods that just reduce the scope of the query, hence what the other methods do can be done through this one.\nInput parameters:\n\n\n\nName\nType\nRequired\nDescription\nExample(s)\n\n\n\n\nquery\nString\nYes\nThe MIQL query to use\n\n\n\ninfoRequest\ninfoRequest\nYes\nUsed to describe the format our to define the pagination\n\n\n\nOutput parameters:\n\n\n\nName\nType\nDescription\n\n\n\n\nqueryResponse\nqueryResponse\nComplex object containing the resulting data and some metadata about the results\n\n\n\nMethod: getByInteractor\nDescription: Retrieves data using a specific participant identifier.\nInput parameters:\n\n\n\nName\nType\nRequired\nDescription\nExample(s)\n\n\n\n\ndbRef\ndbRef\nYes\nThe identifier to search for\n\n\n\ninfoRequest\ninfoRequest\nYes\nUsed to describe the format our to define the pagination\n\n\n\nOutput parameters:\n\n\n\nName\nType\nDescription\n\n\n\n\nqueryResponse\nqueryResponse\nComplex object containing the resulting data and some metadata about the results\n\n\n\nMethod: getByInteractorList\nDescription: Retrieve data using a list of participant identifiers. This method can be used to retrieve interactions where the two or more participants passed as arguments are found. To do so, set the operand to AND.\nInput parameters:\n\n\n\nName\nType\nRequired\nDescription\nExample(s)\n\n\n\n\ndbRefs\nList of dbRef\nYes\nThe identifiers to search for\n\n\n\ninfoRequest\ninfoRequest\nYes\nUsed to describe the format our to define the pagination\n\n\n\nOperand\nString\nNo\nWhen multiple identifiers are provided two options are possible, dependening if we want to (a) find the interaction where ALL the provided identifiers are found or (b) just get a list of interactions where ANY of the identifiers is found. For (a) the value of operand is 'AND', whereas for (b) is 'OR' (default)\nAND, OR\n\n\n\nOutput parameters:\n\n\n\nName\nType\nDescription\n\n\n\n\nqueryResponse\nqueryResponse\nComplex object containing the resulting data and some metadata about the results\n\n\n\nMethod: getByInteraction\nDescription: Retrieves a specific interaction using its identifier. This method is identical to the getByInteractor, but requiring interaction accessions instead.\nInput parameters:\n\n\n\nName\nType\nRequired\nDescription\nExample(s)\n\n\n\n\ndbRef\ndbRef\nYes\nThe identifier to search for\n\n\n\ninfoRequest\ninfoRequest\nYes\nUsed to describe the format our to define the pagination\n\n\n\nOutput parameters:\n\n\n\nName\nType\nDescription\n\n\n\n\nqueryResponse\nqueryResponse\nComplex object containing the resulting data and some metadata about the results\n\n\n\nMethod: getByInteractionList\nDescription: Retrieves a list of interactions, using the identifiers.\nInput parameters:\n\n\n\nName\nType\nRequired\nDescription\nExample(s)\n\n\n\n\ndbRefs\nList of dbRef\nYes\nThe identifiers to search for\n\n\n\ninfoRequest\ninfoRequest\nYes\nUsed to describe the format our to define the pagination\n\n\n\nOutput parameters:\n\n\n\nName\nType\nDescription\n\n\n\n\nqueryResponse\nqueryResponse\nComplex object containing the resulting data and some metadata about the results\n\n\n\nComplex Objects\ndbRef\n\n\n\nName\nType\nRequired\nDescription\nExample(s)\n\n\n\n\nid\nString\nYes\nIdentifier to use\nbrca2P12345\n\n\ndbAc\nString\nNo\nAccession number of the database. Use it to avoid ambiguity if two databases contain the same parameter. Rarely used and not supported throughout\n\n\n\ninfoRequest\n\n\n\nName\nType\nRequired\nDescription\nDefault\n\n\n\n\nresultType\nString\nNo\nFormat of the returned results. Possible options are: 'psi-mi/tab25' (default): MITAB format. 'psi-mi/tab26': MITAB 26 format (not all services provide this format). 'psi-mi/tab27': MITAB 27 format (not all services provide this format). 'psi-mi/tab28': MITAB 28 format (not all services provide this format). 'psi-mi/xml25': PSI-MI XML 2.5.4 format.'count': just contains the result counts.\npsi-mi/tab25\n\n\nfirstResult\nInteger\nNo\nIndex for the first returned value (offset)\n0\n\n\nblockSize\nInteger\nNo\nNumber of results to be returned. Maximum is 200, so higher values will be ignored.\n0\n\n\n\nWhen doing queries, the results must be paginated to avoid memory problems. All methods accept the parameters firstResult and blockSize, which are used to define the starting interaction and the number of interactions to be retrieved. Use them to retrieve your data in batches.\nqueryResponse\n\n\n\nName\nType\nDescription\n\n\n\n\nresultSet\nresultSet\nContains the results of the query\n\n\nresultInfo\nresultInfo\nInformation about the query, such as the total number of results found\n\n\n\nresultSet\n\n\n\nName\nType\nDescription\n\n\n\n\nmitab\nString\nWhen the psi-mi/tab25, psi-mi/tab26, psi-mi/tab27 or psi-mi/tab28 format is used, this element contains the resulting data as a String in MITAB format. Lines are separated by a carriage return.\n\n\nentrySet\nPSI-MI XML 2.5\nWhen the psi-mi/xml25 format is used, the XML file with the results is embedded in the response\n\n\n\nresultInfo\n\n\n\nName\nType\nDescription\n\n\n\n\nfirstResult\nInteger\nThe offset used when querying the service\n\n\nblockSize\nInteger\nThe number of results returned. If the service returns a different number of results than those asked for (e.g. the number provided was higher than the server maximum), this value shows how much data was returned by the service\n\n\ntotalResults\nInteger\nThe total number of interaction evidences found, irrespectively of the firstResult and blockSize.\n\n\n\nQuerying the service\nTo query the SOAP service specific libraries may be needed by your programs. There is a JAVA client already implemented, but if you are not using JAVA you may need to create the service yourself (and if it is generic, contributing it to the project would be great!).\nWhen doing queries, the results in XML must be paginated to avoid memory problems. All methods accept the parameters firstResult and maxResults, which are used to define the starting interaction and the number of interactions to be retrieved. Use them to retrieve your data in batches.\nThe default return types are:\n\npsi-mi/tab25: returns PSI-MI TAB 2.5 format.\npsi-mi/tab26: returns PSI-MI TAB 2.6 format. (not all services provide this format)\npsi-mi/tab27: returns PSI-MI TAB 2.7 format. (not all services provide this format)\npsi-mi/tab28: returns PSI-MI TAB 2.8 format. (not all services provide this format)\npsi-mi/xml25: returns PSI-MI XML 2.5.4 format.\n\n"},"PsicquicSpec_1_4_Rest.html":{"url":"PsicquicSpec_1_4_Rest.html","title":"REST","body":"Version 1.4\nPSICQUIC is meant to be a RESTful service. Hence, it is possible to retrieve data using simple URLs through HTTP.\nSOAP can be too cumbersome for some users or developers as usually a client may be needed. With REST, none of this is necessary because it is possible to do a query through HTTP and get the data back. The simplest way to do it is to do queries using your browser, but REST is a convenient way to access the data for scripts.\nDifferent methods are available using REST. It is possible to fetch data by using:\n\nOne or many interactor/participant identifiers.\nOne or many interaction identifiers.\nA MIQL flexible query.\n\nThe first two methods are just a convenient modification of the third method. The only difference is that the appropriate MIQL field is automatically added for you behind the scenes.\nOther methods exist to get additional information about the service, such as specific properties or the version.\nDifferences from previous versions\nFrom version 1.3\n\nSupport all the fields of MIQL 2.8\nMITAB 2.8 is supported (combatibility with previous versions is maintained)\nRDF format support is no longer maintained\n\nFrom version 1.2\n\nSupport all the fields of MIQL 2.7\nXGMML format is available without any restrictions in number of interactions\nMITAB 2.6 and MITAB 2.7 are supported\nNow based on a SOLR index\nBug fixed when exporting in Biopax\nRDF format support is no longer maintained\nReturns HTTP 400 error if we try to download more than 500 interactions in XML or Biopax in one request.\n\nFrom version 1.1\n\nData can be retrieved in a compressed form to save bandwidth.\nHTTP headers X-PSICQUIC-* are not part of the response.\nXGMML format available.\nBiopax format available\nRDF format support is no longer maintained\n\nFrom version 1.0\n\nMethods have been added to retrieve properties about the service.\n\nURL syntax\nThe structure of the URL to fetch data from PSICQUIC is this one:\n\ne.g. http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/species:human?firstResult=0&maxResults=100\nThe URL contains different parts:\nPSICQUIC_URL\nThe first element of the URL is, of course, the location of the web service. Check the page for the providers for specific addresses.\nVERSION\nAt this moment there are 5 versions of PSICQUIC implemented. The possible values are:\n\n\n\nVersion\nDescription\n\n\n\n\nv1.0\nVersion 1.0 of the REST PSICQUIC specification\n\n\nv1.1\nVersion 1.1 of the REST PSICQUIC specification\n\n\nv1.2\nVersion 1.2 of the REST PSICQUIC specification\n\n\nv1.3\nVersion 1.3 of the REST PSICQUIC specification\n\n\nv1.4\nVersion 1.4 of the REST PSICQUIC specification\n\n\ncurrent\nWill map always to the most current version. It works as a symbolic link\n\n\n\nMETHODS TO RETRIEVE MOLECULAR INTERACTION DATA\nAs we said before, there are different methods available to retrieve data:\n\n\n\nMethod\nSince spec version\nDescription\n\n\n\n\ninteractor\nv1.0\nTo search using interactor identifiers or aliases\n\n\ninteraction\nv1.0\nTo search using interaction identifiers\n\n\nquery\nv1.0\nTo search using MIQL queries\n\n\n\nMETHODS WITH INFORMATION ABOUT THE SERVICE\nThese metadata methods return information about the service:\n\n\n\nMethod\nSince spec version\nDescription\n\n\n\n\nproperty\nv1.1\nTo get the value of a property\n\n\nproperties\nv1.1\nLists all the available properties\n\n\nformats\nv1.0\nLists the return formats supported by the service\n\n\nversion\nv1.0\nImplementation version\n\n\n\nQUERY\nThis is the place where we define the actual query. Depending on the method different queries may be used. When searching for interactors or interactions, the query must be one or many identifiers separater by the operands AND or OR (e.g. facd AND brca2).\nWhen using the query method, the query can be anything.\nFor users accessing RESTful PSICQUIC using scripts, the query must be properly encoded to avoid illegal URIs. For instance, all spaces in the query must be replaced by %20. Most programming languages contain already methods to do this. For clever web browsers, this is not necessary.\nPARAMETERS\nWhereas the rest of parts of the URL are mandatory, parameters are optional. We can use the parameters to choose the output format or to paginate the query. The parameters available in the reference implementation are the following:\n\n\n\nParameter Name\nPossible values\n\n\n\n\nformat\nFormat of the returned data. See the next section for the possible values\n\n\nfirstResult\nInteger value that defines the first element to be shown. If the whole result set contains 100 interactions and we use firstResult=40, the first row to be returned will be the 40\n\n\nmaxResults\nInteger value that defines the maximum number of interactions to be returned. For instance, a value of maxResults=20 will limit the results to 20 interactions.\n\n\n\nIt is possible to iterate through the results using "pages" by changing the value of firstResult while maintaining an immutable maxResults value. For example:\n ...?firstResult=0&maxResults=20\n ...?firstResult=20&maxResults=20\n ...?firstResult=40&maxResults=20\n etc\nIf you don't want to show the whole results at once, this "pagination" method is very effective memory and speedwise.\nFormats\nThis is the list of available formats:\n\n\n\nFormat parameter\nSince Spec\nDescription\n\n\n\n\ntab25\n1.0\nPSI-MITAB 2.5\n\n\ntab26\n1.3\nPSI-MITAB 2.6\n\n\ntab27\n1.3\nPSI-MITAB 2.7\n\n\ntab28\n1.4\nPSI-MITAB 2.8\n\n\nxml25\n1.0\nPSI-MIXML 2.5.4\n\n\ncount\n1.0\nJust the total count\n\n\nbiopax\n1.2\nBioPAX - append -L2 or -L3 to the parameter if a specific level is desired\n\n\nxgmml\n1.2\nXGMML format, used in Cytoscape)\n\n\n\nHTTP Headers\nSince the spec 1.2, in order to help understanding the content of a response with results, some HTTP headers are used:\n\n\n\nHeader name\nDescription\n\n\n\n\nX-PSICQUIC-Count\nTotal count of results\n\n\nX-PSICQUIC-Impl\nName of the implementation\n\n\nX-PSICQUIC-Spec-Version\nVersion for the REST Spec used\n\n\nX-PSICQUIC-Supports-Formats\nList of supported formats\n\n\n\nFor example:\ncurl -I "http://localhost:9090/psicquic/webservices/current/search/query/*?firstResult=0&maxResults=10"\n\nHTTP/1.1 200 OK\nContent-Length: 0\nContent-Type: text/plain\nDate: Wed, 18 Jul 2018 16:23:35 GMT\nX-PSICQUIC-Count: 2\nX-PSICQUIC-Impl: Reference Implementation\nX-PSICQUIC-Impl-Version: 1.3.15-SNAPSHOT\nX-PSICQUIC-Spec-Version: 1.4\nX-PSICQUIC-Supports-Formats: xml25, tab25, tab26, tab27, tab28, biopax, xgmml, count, biopax-L2, biopax-L3\nServer: Jetty(8.1.0.RC5)\nError status codes\nREST relies on direct HTTP communication. Errors are reported using HTTP status codes in the header of the request:\n\n\n\nStatus code\nDescription\n\n\n\n\n200\nNot an error. Request is OK\n\n\n406\nFormat not supported\n\n\n400\nToo many results for exporting in XML and Biopax\n\n\n500\nInternal server error\n\n\n\nSome Examples\nBy Interactor\n\nGetting the result for "brca2_human" in PSI-MITAB 2.7 format\n\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/interactor/brca2_human?format=tab27\n\n\nGetting the result for "brca2_human" using the Uniprot accession P51587 in PSI-MITAB 2.7 format\n\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/interactor/P51587?format=tab27\n\n\nThe number of results in both cases is the same:\n\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/interactor/brca2_human?format=count\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/interactor/P51587?format=count\n\n\n\nBy Interaction\n\nGetting the result for all the interactions which accession number contains "IM-16571-" in PSI-MITAB 2.7 format. These interactions are part of the publication with imex id IM-16571 (PubMed id "15710747")\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/interaction/IM-16519-*?format=tab27\n\n\n\nBy Query\n\nGetting the result for "brca2" in PSI-MITAB 2.7 format\n\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/brca2?format=tab27\n\n\nThe same, in PSI-MI XML 2.5.4 format\n\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/brca2?format=xml25\n\n\nIt supports paging. For instance, search for "species:human" and get only the first 100 results\n\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/species:human?firstResult=0&maxResults=100\n\n\nAll of matrixdb in PSI-MITAB format\n\nhttp://matrixdb.univ-lyon1.fr:8080/psicquic/webservices/current/search/query/*\n\n\n\n"},"Registry.html":{"url":"Registry.html","title":"Registry","body":"The Registry\nA registry exists that shows which PSICQUIC services exist and what is their current state. It can be found here: http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS.\nThe registry also shows the number of total binary interactions that each resource has made available through PSICQUIC.\nAccess\nThere are different ways to access the service, depending if you just want to have a quick look or have an application that want to check the services status programmatically. The URL to access the Registry is RESTful, and follows this syntax:\n\nExcept for the action parameter, the rest are optional. The following tables show what values are available for each parameter:\nThe following table summarises the different parameters that can be passed to the URL.\n\n\n\nParameter\nMandatory\nDefault\nDescription\n\n\n\n\naction\nYes\n\nThe action to be done\n\n\nformat\nNo\n\nThe format to use when viewing the registry\n\n\nname\nNo\n\nFilters the list by name\n\n\nprotocol\nNo\nsoap\nAllows to retrieve soap or rest urls from the services\n\n\nrestricted\nNo\ny\nAllows to filter the restricted services from the list\n\n\ntags\nNo\n\nAllows to filter by tag the services from the list\n\n\n\nParameters\nThe 'action' parameter\nThis parameter is mandatory.\n\n\n\nValue\nDescription\nExample\n\n\n\n\nSTATUS\nLists all the services\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS\n\n\nACTIVE\nOnly shows the active services\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE\n\n\nINACTIVE\nOnly shows the inactive services\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=INACTIVE\n\n\n\nThe 'format' parameter\nThis parameter is optional. The default behaviour is to show an web page with the services.\n\n\n\nValue\nDescription\nExample\n\n\n\n\nnone\nShows a web page\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS\n\n\nxml\nReturns an XML response with all the available information\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=xml\n\n\ntxt\nSimple text page that contains the name and SOAP URLs of the services (but can retrieve REST URLs when combine with protocol=rest) separated by an '=' character\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&format=txt\n\n\ncount\nReturns just the count of services\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=count\n\n\n\nThe 'name' parameter\nThe name is optional and can be used just to get the information for one specific service. Examples:\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&name=IntAct\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&name=MINT&format=xml\nThe 'protocol' parameter\nThe protocol parameter is optional. It can be used to retrieve SOAP or REST URLs from the list of services.\n\n\n\nValue\nDescription\nExample\n\n\n\n\nrest\nREST URLs\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&format=txt&protocol=rest\n\n\nsoap\nSOAP URLs\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&format=txt&protocol=soap\n\n\n\nThe 'restricted' parameter\nThe restricted parameter is optional. It can be used to hide from the list those services that are restricted, normally due to licensing issues.\n\n\n\nValue\nDescription\nExample\n\n\n\n\ny\nAll services including restricted services\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&restricted=y\n\n\nn\nAll services excluding restricted services\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&restricted=n\n\n\n\nThe 'tags' parameter\nThe tags parameter is optional. it can be used to select a specific list of PSICQUIC services based on the tagging of their data content. There are currently 5 data content main categories described on the PsicquicServiceTags page. You can describe a specific tag by either using its name or its MI ontology identifier (e.g. MI:0960 is equivalent to 'imex curation'). You can build a query using the boolean operators AND, OR and NOT.Here are a few sample queries:\n\n\n\nDescription\nQuery\nURL\n\n\n\n\nOnly IMEx data providers\nimex curation\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&tags=imex curation\n\n\nprotein protein interaction and internally-curated\nprotein-protein AND internally-curated\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&tags=protein-protein AND internally-curated\n\n\nprotein protein interaction AND neither text mining nor predicted\nprotein-protein AND NOT (text-mining OR predicted)\nhttp://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&tags=protein-protein AND NOT (text-mining OR predicted) \n\n\n\nPlease note that when encoding the query into a URL you will have to encode special characters following standard guidelines. For your convenience we have summarised the main ones you will need with tags here:\n\n\n\nCharacter\nEncoding\n\n\n\n\nSpace\n%20\n\n\n-\n%2D\n\n\n:\n%3A\n\n\n(\n%28\n\n\n)\n%29\n\n\n\n"},"PsicquicServiceTags.html":{"url":"PsicquicServiceTags.html","title":"Registry Service Tags","body":"Why Tags ?\nIn addition to having all PSICQUIC services available via the Registry, some user do need to apply filters on the requested services in order to retrieve specific type of molecular interaction. Here are just a few examples:\n\nOnly IMEx data providers\nOnly manually curated data\nOnly protein-protein interactions and not (text-mining or predicted)\nOnly causal molecular interactions\n\nCurrent tags\nWe have so far put together the 6 categories of tags described below:\nInteracting molecules (MI:1046)\n\nprotein-protein (MI:1047)\nsmallmolecule-protein (MI:1048)\nnucleicacid-protein (MI:1049)\n\nInteraction representation (MI:1050)\n\nevidence (MI:1051)\nclustered (MI:1052)\n\nCuration depth (MI:0955)\n\nimex curation (MI:0959)\nmimix curation (MI:0960)\nrapid curation (MI:0961)\n\nSource (MI:1053)\n\nexperimentally-observed (MI:1054)\ninternally-curated (MI:1055)\ntext-mining (MI:1056)\npredicted (MI:1057)\nimported (MI:1058)\n\nComplex expansion (MI:1059)\n\nspoke expansion (MI:1060)\nmatrix expansion (MI:1061)\nbipartite expansion (MI:1062)\n\nCausal interactions (MI:2233)\n\ncausal interaction (MI:2233)\n\nYou can refer to the Registry documentation to find out how to use the tags to query for specific lists of PSICQUIC services based on the tagging of their data content.\nCurrent limitations\nFor the time being the definition of tags is done as a manual curation effort by the maintainers of the PSICQUIC Registry with input from PSICQUIC service providers. The current strategy has been adopted because it could be put in place quickly but suffers from a number of limitations, namely:\n\ncurrently the tags are set to describe a PSICQUIC service as a whole\nthe current tagging strategy do not allow to isolate specific part of the dataset and that further development is already planned to enable that feature.\nthat multiple tags per category can be used to describe specific conditions, for instance, if a provider has included manually curated data of their own as well as imported data from a third party source, both the tags imported and internally-curated should be used. This will now allow users to discriminate the underlying interactions but it is still very informative.\n\n"},"RegistryJavaClient.html":{"url":"RegistryJavaClient.html","title":"Java client","body":"Introduction\nThis page explains how to access the Registry using the provided Java client. If you want to query a PSICQUIC service with Java, check this page instead.\nGetting the client\nYou can download the latest client release version here, or use this Maven dependency in your project:\n <dependency>\n <groupId>org.hupo.psi.mi.psicquic</groupId>\n <artifactId>psicquic-registry-client</artifactId>\n <version>1.4.0</version>\n </dependency>\nThis dependency is hosted at the European Bioinformatics Institute (EBI) repository. You can add this repository in your pom.xml file like this:\n <repositories>\n <repository>\n <id>nexus-ebi-release-repo</id>\n <url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>\n </repository>\n </repositories>\nUsage\nPsicquicRegistryClient registryClient = new DefaultPsicquicRegistryClient();\n\nList<ServiceType> services = registryClient.listServices();\n\nfor (ServiceType service : services) {\n System.out.println(service.getName());\n}\nExamples\nFor an implementation of the example above see here.\n"},"MiqlDefinition.html":{"url":"MiqlDefinition.html","title":"Usage MIQL","body":"Querying PSICQUIC\nThe Molecular Interactions Query Language (MIQL) defines a way to allow more powerful and flexible queries by using a specific syntax when doing searches. If we have a common way to access the data (PSICQUIC), we need a common way to write the search queries.\nIn most cases, searches are done for a specific identifier or group of identifiers. However, the service is not limited to these. For instance, there are ways to search for specific organisms, interaction detection methods or publication identifiers. The MIQL defines how these kind of queries can be done.\nMIQL is a consensus between the different databases, so you should be able to use the same query across different repositories. It is based on the PSIMITAB format and allows to search for data in specific columns, by using the fields explained in the next section.\nThe MIQL syntax is based on Lucene's syntax. A query is broken into terms and operators:\n\nTerms: single words or phrases (group of words surrounded by quotes). E.g. brca2 or "pull down"\nFields: used to search in a specific column. See the next section for the specific field names. E.g. species:human\nTerm modifiers: wildcard searches, fuzzy searches, proximity and range searches. E.g. brc*\nOperands: OR (or space), AND, NOT, +, -. E.g. brca2 AND rpa1 or brca2 NOT mouse or +brca2 –mouse –expansion:spoke\nGrouping and field grouping: brca2 AND ( mouse "in vitro" )\n\nIMPORTANT: When using parenthesis in your queries, please add a space after and opening parenthesis and before a closing one, since some PSICQUIC implementations need it for correct parenthesis recognition.\nExisting versions\nThere are three versions of MIQL language which have been implemented so far.\n\nMIQL 2.5 is based on the PSIMITAB 2.5 format\nMIQL 2.7 is an extension of MIQL 2.5 and is based on the PSIMITAB 2.7 format.\nMIQL 2.8 is an extension of MIQL 2.7 and is based on the PSIMITAB 2.8 format.\n\n"},"MiqlReference.html":{"url":"MiqlReference.html","title":"MIQL Reference 2.5","body":"MIQL 2.5\nThe Molecular Interactions Query Language (MIQL) defines a way to allow more powerful and flexible queries by using a specific syntax when doing searches. If we have a common way to access the data (PSICQUIC), we need a common way to write the search queries.\nIn most cases, searches are done for a specific identifier or group of identifiers. However, the service is not limited to these. For instance, there are ways to search for specific organisms, interaction detection methods or publication identifiers. The MIQL defines how these kind of queries can be done.\nMIQL is a consensus between the different databases, so you should be able to use the same query across different repositories. It is based on the PSIMITAB 2.5 format and allows to search for data in specific columns, by using the fields explained in the next section.\nThe MIQL syntax is based on Lucene's syntax. A query is broken into terms and operators:\n\nTerms: single words or phrases (group of words surrounded by quotes). E.g. brca2 or "pull down"\nFields: used to search in a specific column. See the next section for the specific field names. E.g. species:human\nTerm modifiers: wildcard searches, fuzzy searches, proximity and range searches. E.g. brc*\nOperands: OR (or space), AND, NOT, +, -. E.g. brca2 AND rpa1 or brca2 NOT mouse or +brca2 –mouse \nGrouping and field grouping: brca2 AND ( mouse "in vitro" )\n\nIMPORTANT: When using parenthesis in your queries, please add a space after and opening parenthesis and before a closing one, since some PSICQUIC implementations need it for correct parenthesis recognition.\nFields\nThe following table shows the available standard fields that can be used in PSICQUIC searches:\n\n\n\nField Name\nSearches on\nMITAB 2.5 Columns\nExample\n\n\n\n\nidA\nIdentifier A\n1\nidA:P74565\n\n\nidB\nIdentifier B\n2\nidB:P74565\n\n\nid\nIdentifiers (A or B)\n1..4\nid:P74565\n\n\nalias\nAliases (A or B)\n5, 6\nalias:( KHDRBS1 OR HCK )\n\n\nidentifier\nIdentifiers (A or B) or Aliases (A or B)\n1..6\nidentifier:P74565\n\n\npubauth\nPublication 1st author(s)\n8\npubauth:scott\n\n\npubid\nPublication Identifier(s)\n9\npubid:( 10837477 OR 12029088 )\n\n\ntaxidA\nTax ID interactor A: be it the tax ID or the species name\n10\ntaxidA:mouse\n\n\ntaxidB\nTax ID interactor B: be it the tax ID or species name\n11\ntaxidB:9606\n\n\nspecies\nSpecies. Tax ID A and Tax ID B\n10, 11\nspecies:human\n\n\ntype\nInteraction type(s)\n12\ntype:"physical association"\n\n\ndetmethod\nInteraction Detection method(s)\n7\ndetmethod:"two hybrid*"\n\n\nsource\nInteraction source(s)\n13\npsi-mi:"MI:0469"(intact)\n\n\ninteraction_id\nInteraction identifier(s)\n14\ninteraction_id:EBI-761050\n\n\n\n"},"MiqlReference27.html":{"url":"MiqlReference27.html","title":"MIQL Extension 2.7","body":"MIQL 2.7\nThe Molecular Interactions Query Language (MIQL) defines a way to allow more powerful and flexible queries by using a specific syntax when doing searches. If we have a common way to access the data (PSICQUIC), we need a common way to write the search queries.\nIn most cases, searches are done for a specific identifier or group of identifiers. However, the service is not limited to these. For instance, there are ways to search for specific organisms, interaction detection methods or publication identifiers. The MIQL defines how these kind of queries can be done.\nMIQL is a consensus between the different databases, so you should be able to use the same query across different repositories. It is based on the PSIMITAB 2.7 format and allows to search for data in specific columns, by using the fields explained in the next section.\nThe MIQL syntax is based on Lucene's syntax. A query is broken into terms and operators:\n\nTerms: single words or phrases (group of words surrounded by quotes). E.g. brca2 or "pull down"\nFields: used to search in a specific column. See the next section for the specific field names. E.g. species:human\nTerm modifiers: wildcard searches, fuzzy searches, proximity and range searches. E.g. brc*\nOperands: OR (or space), AND, NOT, +, -. E.g. brca2 AND rpa1 or brca2 NOT mouse or +brca2 –mouse –complex:spoke\nGrouping and field grouping: brca2 AND ( mouse "in vitro" )\n\nIMPORTANT: When using parenthesis in your queries, please add a space after and opening parenthesis and before a closing one, since some PSICQUIC implementations need it for correct parenthesis recognition.\nFields\nThe following table shows the available standard fields that can be used in PSICQUIC searches:\n\n\n\nField Name\nSearches on\nMITAB 2.7 Columns\nExample\n\n\n\n\nidA\nIdentifier A\n1\nidA:P74565\n\n\nidB\nIdentifier B\n2\nidB:P74565\n\n\nid\nIdentifiers (A or B)\n1..4\nid:P74565\n\n\nalias\nAliases (A or B)\n5, 6\nalias:( KHDRBS1 OR HCK )\n\n\nidentifier\nIdentifiers (A or B) or Alternatives (A or B) Aliases (A or B)\n1..6\nidentifier:P74565\n\n\npubauth\nPublication 1st author(s)\n8\npubauth:scott\n\n\npubid\nPublication Identifier(s)\n9\npubid:( 10837477 OR 12029088 )\n\n\ntaxidA\nTax ID interactor A: be it the tax ID or the species name\n10\ntaxidA:mouse\n\n\ntaxidB\nTax ID interactor B: be it the tax ID or species name\n11\ntaxidB:9606\n\n\nspecies\nSpecies. Tax ID A and Tax ID B\n10, 11\nspecies:human\n\n\ntype\nInteraction type(s)\n12\ntype:"physical association"\n\n\ndetmethod\nInteraction Detection method(s)\n7\ndetmethod:"two hybrid*"\n\n\ninteraction_id\nInteraction identifier(s)\n14\ninteraction_id:EBI-761050\n\n\npbioroleA\nBiological role A\n17\npbioroleA:ancillary\n\n\npbioroleB\nBiological role B\n18\npbioroleB:"MI:0684"\n\n\npbiorole\nBiological roles (A or B)\n17, 18\npbiorole:enzyme\n\n\nptypeA\nInteractor type A\n21\nptypeA:protein\n\n\nptypeB\nInteractor type B\n22\nptypeB:"gene"\n\n\nptype\nInteractor types (A or B)\n21, 22\npbiorole:"small molecule"\n\n\npxrefA\nInteractor xref A (or Identifier A)\n23, 1\npxrefA:"GO:0003824"\n\n\npxrefB\nInteractor xref B (or Identifier B)\n24, 2\npxrefB:"GO:0003824"\n\n\npxref\nInteractor xrefs (A or B or Identifier A or Identifier B)\n23, 24, 1, 2\npxref:"catalytic activity"\n\n\nxref\nInteraction xrefs (or Interaction identifiers)\n25, 14\nxref:nuclear pore\n\n\nannot\nInteraction annotations and tags\n28\nannot:"internally curated"\n\n\nudate\nUpdate date\n32\nudate:[20100101 TO 20120101]\n\n\nnegative\nNegative interaction boolean\n36\nnegative:true\n\n\ncomplex\nComplex expansion\n16\ncomplex:"spoke expanded" or complex:"MI:1060"\n\n\nftypeA\nFeature type of participant A\n37\nftypeA:"sufficient to bind"\n\n\nftypeB\nFeature type of participant B\n38\nftypeB:mutation\n\n\nftype\nFeature type of participant A or B\n37, 38\nftype:"binding site"\n\n\npmethodA\nParticipant identification method A\n41\npmethodA:"western blot"\n\n\npmethodB\nParticipant identification method B\n42\npmethodB:"sequence tag identification"\n\n\npmethod\nParticipant identification methods (A or B)\n41, 42\npmethod:immunostaining\n\n\nstc\nStoichiometry (A or B). Only true or false, just to be able to filter interaction having stoichiometry available\n39, 40\nstc:true\n\n\nparam\nInteraction parameters. Only true or false, just to be able to filter interaction having parameters available\n30\nparam:true\n\n\n\n"},"MiqlReference28.html":{"url":"MiqlReference28.html","title":"MIQL Extension 2.8","body":"MIQL 2.8\nThe Molecular Interactions Query Language (MIQL) defines a way to allow more powerful and flexible queries by using a specific syntax when doing searches. If we have a common way to access the data (PSICQUIC), we need a common way to write the search queries.\nIn most cases, searches are done for a specific identifier or group of identifiers. However, the service is not limited to these. For instance, there are ways to search for specific organisms, interaction detection methods or publication identifiers. The MIQL defines how these kind of queries can be done.\nMIQL is a consensus between the different databases, so you should be able to use the same query across different repositories. It is based on the PSIMITAB 2.8 format and allows to search for data in specific columns, by using the fields explained in the next section.\nThe MIQL syntax is based on Lucene's syntax. A query is broken into terms and operators:\n\nTerms: single words or phrases (group of words surrounded by quotes). E.g. brca2 or "pull down"\nFields: used to search in a specific column. See the next section for the specific field names. E.g. species:human\nTerm modifiers: wildcard searches, fuzzy searches, proximity and range searches. E.g. brc*\nOperands: OR (or space), AND, NOT, +, -. E.g. brca2 AND rpa1 or brca2 NOT mouse or +brca2 –mouse –complex:spoke\nGrouping and field grouping: brca2 AND ( mouse "in vitro" )\n\nIMPORTANT: When using parenthesis in your queries, please add a space after and opening parenthesis and before a closing one, since some PSICQUIC implementations need it for correct parenthesis recognition.\nFields\nThe following table shows the available standard fields that can be used in PSICQUIC searches:\n\n\n\nField Name\nSearches on\nMITAB 2.8 Columns\nExample\n\n\n\n\nidA\nIdentifier A\n1\nidA:P74565\n\n\nidB\nIdentifier B\n2\nidB:P74565\n\n\nid\nIdentifiers (A or B)\n1..4\nid:P74565\n\n\nalias\nAliases (A or B)\n5, 6\nalias:( KHDRBS1 OR HCK )\n\n\nidentifier\nIdentifiers (A or B) or Alternatives (A or B) Aliases (A or B)\n1..6\nidentifier:P74565\n\n\npubauth\nPublication 1st author(s)\n8\npubauth:scott\n\n\npubid\nPublication Identifier(s)\n9\npubid:( 10837477 OR 12029088 )\n\n\ntaxidA\nTax ID interactor A: be it the tax ID or the species name\n10\ntaxidA:mouse\n\n\ntaxidB\nTax ID interactor B: be it the tax ID or species name\n11\ntaxidB:9606\n\n\nspecies\nSpecies. Tax ID A and Tax ID B\n10, 11\nspecies:human\n\n\ntype\nInteraction type(s)\n12\ntype:"physical association"\n\n\ndetmethod\nInteraction Detection method(s)\n7\ndetmethod:"two hybrid*"\n\n\ninteraction_id\nInteraction identifier(s)\n14\ninteraction_id:EBI-761050\n\n\npbioroleA\nBiological role A\n17\npbioroleA:ancillary\n\n\npbioroleB\nBiological role B\n18\npbioroleB:"MI:0684"\n\n\npbiorole\nBiological roles (A or B)\n17, 18\npbiorole:enzyme\n\n\nptypeA\nInteractor type A\n21\nptypeA:protein\n\n\nptypeB\nInteractor type B\n22\nptypeB:"gene"\n\n\nptype\nInteractor types (A or B)\n21, 22\npbiorole:"small molecule"\n\n\npxrefA\nInteractor xref A (or Identifier A)\n23, 1\npxrefA:"GO:0003824"\n\n\npxrefB\nInteractor xref B (or Identifier B)\n24, 2\npxrefB:"GO:0003824"\n\n\npxref\nInteractor xrefs (A or B or Identifier A or Identifier B)\n23, 24, 1, 2\npxref:"catalytic activity"\n\n\nxref\nInteraction xrefs (or Interaction identifiers)\n25, 14\nxref:nuclear pore\n\n\nannot\nInteraction annotations and tags\n28\nannot:"internally curated"\n\n\nudate\nUpdate date\n32\nudate:[20100101 TO 20120101]\n\n\nnegative\nNegative interaction boolean\n36\nnegative:true\n\n\ncomplex\nComplex expansion\n16\ncomplex:"spoke expanded" or complex:"MI:1060"\n\n\nftypeA\nFeature type of participant A\n37\nftypeA:"sufficient to bind"\n\n\nftypeB\nFeature type of participant B\n38\nftypeB:mutation\n\n\nftype\nFeature type of participant A or B\n37, 38\nftype:"binding site"\n\n\npmethodA\nParticipant identification method A\n41\npmethodA:"western blot"\n\n\npmethodB\nParticipant identification method B\n42\npmethodB:"sequence tag identification"\n\n\npmethod\nParticipant identification methods (A or B)\n41, 42\npmethod:immunostaining\n\n\nstc\nStoichiometry (A or B). Only true or false, just to be able to filter interaction having stoichiometry available\n39, 40\nstc:true\n\n\nparam\nInteraction parameters. Only true or false, just to be able to filter interaction having parameters available\n30\nparam:true\n\n\nbioeffectA\nBiological effect of participant A\n43\nbioeffectA:"kinase activity"\n\n\nbioeffectB\nBiological effect of participant B\n44\nbioeffectB:"antioxidant activity"\n\n\nbioeffect\nBiological effect of participant A or B\n43, 44\nbioeffect:"molecular carrier activity"\n\n\ncausalmechanism\nThe indirect causal regulatory mechanism between participants A and B\n45\ncausalmechanism:"MI:2245"\n\n\ncausalstatement\nThe causal statement describing the effect of participant A on participant B\n46\ncausalstatement:"up regulates"\n\n\n\n"},"Clients.html":{"url":"Clients.html","title":"Clients","body":"Clients and software tools that can be used to query the PSICQUIC service.\n"},"JavaClient.html":{"url":"JavaClient.html","title":"Java","body":"Java clients\nThere are two JAVA clients provided by the project at the moment:\n\nPSICQUIC Simple Client: it does not have dependencies. Provides basic access to the services by retrieving the raw data. It does not parse the results. It is REST based.\nPSICQUIC Client: it has more dependencies, because it contains different models to manipulate the results in a Java object oriented way. At the moment it uses SOAP access, but this will be soon replaced to use the Simple Client behind the scenes soon.\n\nYou can download the clients here, or obtain them using Maven.\nThe following table summarises the differences between the two clients, described in more detail below:\n\n\n\nPSICQUIC Client\nSimple\nUniversal\n\n\n\n\nJava lib dependencies\nNone\nMany\n\n\nProtocol used\nREST\nSOAP\n\n\nStreaming\nYes\nNo\n\n\nPagination\nYes\nYes\n\n\nIntegration with model\nNone (but easily integrated)\nFull integration with XML and MITAB models\n\n\nSpeed\nFaster\nSlower (due to response generation)\n\n\nBandwidth\nSmaller\nLarger (SOAP evelope and response)\n\n\nCompression\nYes\nYes\n\n\nCompatibility\nPSICQUIC 1.1 or higher\nPSICQUIC 1.0 or higher\n\n\n\nPSICQUIC Simple Client\nThis client is the simplest way to access the services using Java. It provides no-frills access to the data, hence it is quicker than the other client. You need to parse the results yourself though.\nIf you are using Maven, include the following in your project:\n\nLatest release version:\n\n <dependency>\n <groupId>org.hupo.psi.mi.psicquic</groupId>\n <artifactId>psicquic-simple-client</artifactId>\n <version>1.4.0</version>\n </dependency>\nThis dependency is hosted at the European Bioinformatics Institute (EBI) repository. You can add this repository in your pom.xml file like this:\n <repositories>\n <repository>\n <id>nexus-ebi-release-repo</id>\n <url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>\n </repository>\n </repositories>\nExamples of Use\nYou can find different examples in this folder.\nPSICQUIC Client (Standard)\nA JAVA client is provided already by this project. If your project is using Maven, you can start using the client right away just by adding this dependencies to your project.\nInclude the following dependency in your project:\n\nLatest released version:\n\n <dependency>\n <groupId>org.hupo.psi.mi.psicquic</groupId>\n <artifactId>psicquic-client</artifactId>\n <version>1.6.0</version>\n </dependency>\nThis dependency is hosted at the European Bioinformatics Institute (EBI) repository. You can add this repository in your pom.xml file like this:\n <repositories>\n <repository>\n <id>nexus-ebi-release-repo</id>\n <url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>\n </repository>\n </repositories>\nExamples of Use\nYou can find different examples in this folder to start using the PSICQUIC service.\nBuilding the client from sources\nThe sources for this client can be found as part of the project source code.\nOnce you have the code and you want to build the project, execute the Maven command:\ncd psicquic-client\nmvn clean install\nUsing other programming languages\nIf you are not using JAVA, you can generate your client code using the WSDL file directly. The WSDL can be found at:\n\nversion 1.0 : \nhttps://github.com/PSICQUIC/psicquic-solr-ws/blob/master/src/main/wsdl/psicquic10.wsdl\nversion 1.1 (recommended) : https://github.com/PSICQUIC/psicquic-solr-ws/blob/master/src/main/wsdl/psicquic11.wsdl\n\n"},"PerlCodeSamples.html":{"url":"PerlCodeSamples.html","title":"Perl","body":"PERL examples\nAll the PERL examples in this page use the REST access as it is straight-forward to use for scripting languages.\nAccessing the registry\n\nList all the Services and its base URL.\n\nQuerying PSICQUIC services\nThe following examples can be used to access PSICQUIC services.\n\nQuery one service.\nQuery all the services: It queries the registry to get all the services and then executes a query for one of them.\n\n"},"PythonCodeSamples.html":{"url":"PythonCodeSamples.html","title":"Python","body":"Python examples\nAll the Python examples in this page use the REST access as it is straight-forward to use for scripting languages.\nAccessing the registry\nPython 2.7 examples\n\nList all the Services and its base URL.\nList all the Services showing more details about the service.\n\nPython 3 examples\n\nList all the Services and its base URL.\nList all the Services showing more details about the service.\n\nQuerying PSICQUIC services\nThe following examples can be used to access PSICQUIC services.\nPython 2.7 examples\n\nQuery one service.\nQuery all the services: It queries the registry to get all the services and then executes a query for each one of them.\n\nPython 3 examples\n\nQuery one service.\nQuery all the services: It queries the registry to get all the services and then executes a query for each one of them.\n\n"},"CytoscapeClient.html":{"url":"CytoscapeClient.html","title":"Cytoscape","body":"PSICQUIC Client Plugin for Cytoscape Quick Start\nNews\n\n3/13/2014: Now PSICQUIC Client is a built-in core feature in Cytoscape 3.1. You do not have to install plugins to use it.\n6/1/2012: New Cytoscape Plugin version 0.31 released. This update is recommended for all current users. Please use with latest version of Cytoscape (2.8.3).\nSmart Label - Plugin adds more human-readable gene names to the node\nColor coding based on species name\nBug fixes for edge score import function\n\n\n5/30/2012: Now PSICQUIC Client is part of Cytoscape 3 core!\n7/28/2010: version 0.25 released. This is compatible with Cytoscape 2.7.0 or later.\n\nIntroduction\nCytoscape is an open source platform for general network data integration, analysis, and visualization. It is widely used in systems biology community and is expandable by plugins. PSICQUIC Universal Client is a Cytoscape plugin for querying multiple PSICQUIC-compliant interaction data services from a simple user interface.\nThe advantage of using PSICQUIC services with Cytoscape client is you can save your work as a snapshot (session file) and also you can use its powerful visualization features. For more information about Cytoscape, please visit official web site.\nOverview of Client User Interface\nPSICQUIC Client for Cytoscape is a part of Cytoscape's web service client framework. You can access PSICQUIC databases just like the other clients. From a single window, you can send your query to all of registered PSICQUIC services at once.\nHow to Use PSICQUIC Client in Cytoscape 2\nInstall Plugin\nThe PSICQUIC Client Plugin is compatible with Cytoscape 2.7.0 or later. If you have older versions, please download the latest version. The Plugin is available from Cytoscape Plugin Manager. Select Plugin-->Manage Plugins and then you can find the plugin under Network and Attribute IO section --> PSICQUICUniversalClient\nStart Plugin\nTo start the plugin, select the client from File-->Import-->Network from web services.... If PSICQUIC client is properly installed, you can find it in Data Source combo box.\nQuery Services\nThere are two search modes in the client:\n\nSearch by Interactor ID\nSearch by Query (MIQL)\n\nYou can switch the mode from Search Property tab.\nSearch by Interactor ID(s)\nIn this mode, Cytoscape sends list of identifiers as query. You can simply copy and paste list of identifiers to the text box. After the search process, it pops up a window, where you can select which data sets you want to import. If the result is 0 or the service is inactive, it will be ignored. When the import process is finished, you also have the option to edit the network titles if you want. If you press the Merge button, the Advanced Network Marge plugin will be started and you can merge imported networks manually.\nSearch by MIQL\nThis mode supports MIQL syntax. You can simply type the query in the text field. For more information about MIQL, please read the reference page.\nPSICQUIC Client in Cytoscape 3\nCytoscape 3.1.0 has been released since 2014 and the PSICQUIC client feature is a built-in function from that version. To try the new version, please visit here.\nNeed Help?\nPlease join our user mailing list. All core developers of Cytoscape are available to answer your questions.\n"},"formats.html":{"url":"formats.html","title":"Formats","body":"Available Data exchange formats:\n\nPSI MITAB\nPSI-MI XML\n\n"},"PSIMITAB.html":{"url":"PSIMITAB.html","title":"PSI-MI TAB","body":"The PSI-MI TAB data interchange format is a common tab-delimited molecular interactions format.\nVersions\n\nMITAB 2.5\nMITAB 2.6\nMITAB 2.7\nMITAB 2.8\n\n"},"MITAB25Format.html":{"url":"MITAB25Format.html","title":"MITAB 2.5","body":"PSI-MI TAB 2.5 Format\nIntroduction\nThe MITAB25 format is part of the PSI-MI 2.5 standard (1). It has been derived from the tabular format provided by BioGrid. MITAB25 only describes binary interactions, one pair of interactors per row. Columns are separated by tabulations. Tools allowing to manipulate this data format are available (2).\n(1) http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17925023\n(2) http://www.psidev.info/groups/molecular-interactions (Tools section)\nColumn definitions\nThe column contents should be as follows:\n\nUnique identifier for interactor A, represented as databaseName:ac, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the unique primary identifier of the molecule in the database. Identifiers from multiple databases can be separated by "|". It is recommended that proteins be identified by stable identifiers such as their UniProtKB or RefSeq accession number.\nUnique identifier for interactor B.\nAlternative identifier for interactor A, for example the official gene symbol as defined by a recognised nomenclature committee. Representation as databaseName:identifier. Multiple identifiers separated by "|".\nAlternative identifier for interactor B.\nAliases for A, separated by "|". Representation as databaseName:identifier. Multiple identifiers separated by "|".\nAliases for B.\nInteraction detection methods, taken from the corresponding PSI-MI controlled Vocabulary, and represented as darabaseName:identifier(methodName), separated by "|".\nFirst author surname(s) of the publication(s) in which this interaction has been shown, optionally followed by additional indicators, e.g. "Doe-2005-a". Separated by "|".\nIdentifier of the publication in which this interaction has been shown. Database name taken from the PSI-MI controlled vocabulary, represented as databaseName:identifier. Multiple identifiers separated by "|".\nNCBI Taxonomy identifier for interactor A. Database name for NCBI taxid taken from the PSI-MI controlled vocabulary, represented as databaseName:identifier (typicaly databaseName is set to 'taxid'). Multiple identifiers separated by "|". Note: In this column, the databaseName:identifier(speciesName) notation is only there for consistency. Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -1 to indicate "in vitro", -2 to indicate "chemical synthesis", -3 indicates "unknown", -4 indicates "in vivo" and -5 indicates "in silico".\nNCBI Taxonomy identifier for interactor B.\nInteraction types, taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(interactionType), separated by "|".\nSource databases and identifiers, taken from the corresponding PSI-MI controlled vocabulary, and represented as databaseName:identifier(sourceName). Multiple source databases can be separated by "|".\nInteraction identifier(s) in the corresponding source database, represented by databaseName:identifier\nConfidence score. Denoted as scoreType:value. There are many different types of confidence score, but so far no controlled vocabulary. Thus the only current recommendation is to use score types consistently within one source. Multiple scores separated by "|".\n\nAll columns are mandatory.\nSyntax\nColumns are normally formed by fields delimited by "|", with a structure like this one:\n<XREF>:<VALUE>(<DESCRIPTION>)\nDue to the unsafe use of reserved characters in the values, we have recently added the possibility to surround <XREF>, <VALUE> or <DESCRIPTION> with quotes if they contain a special symbol.\nIn MI-TAB, the reserved characters are:\n|\n(\n)\n:\n\\t (tabulation)\nWhenever this happen in your data, surround the value with double quotes:\n"<XREF_WITH_RESERVED_CHARS>":"<VALUE_WITH_RESERVED_CHARS>"("<DESCRIPTION>")\nNote that the quotes are before and after each part. The escaped data should look like in the following examples:\npsi-mi:"MI:0000"(a cv term)\npsi-mi:"MI:0000"("I can now use braces ()()() or pipes ||| here and ::colons::")\nIf you want to use a quote within a quote, escape it:\nuniprotkb:P12345("a \\"nice\\" protein")\n"},"MITAB26Format.html":{"url":"MITAB26Format.html","title":"MITAB 2.6","body":"PSI-MI TAB 2.6 Format\nIntroduction\nThe MITAB26 format is part of the PSI-MI 2.5 standard (1). It has been derived from the tabular format provided by BioGrid. MITAB26 only describes binary interactions, one pair of interactors per row. Columns are separated by tabulations. Tools allowing to manipulate this data format are available (2).\n(1) http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17925023\n(2) http://www.psidev.info/groups/molecular-interactions (Tools section)\nColumn definitions\nThe column contents should be as follows:\n\nUnique identifier for interactor A, represented as databaseName:ac, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the unique primary identifier of the molecule in the database. Identifiers from multiple databases can be separated by "|". It is recommended that proteins be identified by stable identifiers such as their UniProtKB or RefSeq accession number.\nUnique identifier for interactor B.\nAlternative identifier for interactor A, for example the official gene symbol as defined by a recognised nomenclature committee. Representation as databaseName:identifier. Multiple identifiers separated by "|".\nAlternative identifier for interactor B.\nAliases for A, separated by "|". Representation as databaseName:identifier. Multiple identifiers separated by "|".\nAliases for B.\nInteraction detection methods, taken from the corresponding PSI-MI controlled Vocabulary, and represented as darabaseName:identifier(methodName), separated by "|".\nFirst author surname(s) of the publication(s) in which this interaction has been shown, optionally followed by additional indicators, e.g. "Doe-2005-a". Separated by "|".\nIdentifier of the publication in which this interaction has been shown. Database name taken from the PSI-MI controlled vocabulary, represented as databaseName:identifier. Multiple identifiers separated by "|".\nNCBI Taxonomy identifier for interactor A. Database name for NCBI taxid taken from the PSI-MI controlled vocabulary, represented as databaseName:identifier (typicaly databaseName is set to 'taxid'). Multiple identifiers separated by "|". Note: In this column, the databaseName:identifier(speciesName) notation is only there for consistency. Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -1 to indicate "in vitro", -2 to indicate "chemical synthesis", -3 indicates "unknown", -4 indicates "in vivo" and -5 indicates "in silico".\nNCBI Taxonomy identifier for interactor B.\nInteraction types, taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(interactionType), separated by "|".\nSource databases and identifiers, taken from the corresponding PSI-MI controlled vocabulary, and represented as databaseName:identifier(sourceName). Multiple source databases can be separated by "|".\nInteraction identifier(s) in the corresponding source database, represented by databaseName:identifier\nConfidence score. Denoted as scoreType:value. There are many different types of confidence score, but so far no controlled vocabulary. Thus the only current recommendation is to use score types consistently within one source. Multiple scores separated by "|".\nExpansion. Model used to convert n-ary interactions into binary interactions for purpose of export in MITAB file. The known expansions are none (if true binary interaction), spoke, matrix or bipartite.\nBiological role A , taken from the corresponding PSI-MI controlled Vocabulary, and represented as dataBaseName:identifier(biological role name), separated by "|".\nBiological role B , taken from the corresponding PSI-MI controlled Vocabulary, and represented as dataBaseName:identifier(biological role name), separated by "|".\nExperimental role A , taken from the corresponding PSI-MI controlled Vocabulary, and represented as dataBaseName:identifier(experimental role name), separated by "|".\nExperimental role B , taken from the corresponding PSI-MI controlled Vocabulary, and represented as dataBaseName:identifier(experimental role name), separated by "|".\nInteractor type A , taken from the corresponding PSI-MI controlled Vocabulary, and represented as dataBaseName:identifier(interactor type name), separated by "|".\nInteractor type B , taken from the corresponding PSI-MI controlled Vocabulary, and represented as dataBaseName:identifier(interactor type name), separated by "|".\nXref for interactor A, for example the gene ontology cross references associated. Representation as databaseName:identifier(text). Multiple cross references separated by "|".\nXref for interactor B, for example the gene ontology cross references associated. Representation as databaseName:identifier(text). Multiple cross references separated by "|".\nXref for the interaction, for example the gene ontology cross references associated (components, etc.) or OMIM cross references. Representation as databaseName:identifier(text). Multiple cross references separated by "|".\nAnnotations for interactor A, for example comments about this interactor. Representation as topic:text. Multiple annotations separated by "|".\nAnnotations for Interactor B, for example comments about this interactor. Representation as databaseName:identifier(text). Multiple annotations separated by "|".\nAnnotations for the interaction, for example comments about this interaction. Representation as topic:text. Multiple annotations separated by "|".\nNCBI Taxonomy identifier for the host organism. Database name for NCBI taxid taken from the PSI-MI controlled vocabulary, represented as databaseName:identifier (typicaly databaseName is set to 'taxid'). Multiple identifiers separated by "|". Note: In this column, the databaseName:identifier(speciesName) notation is only there for consistency. Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -1 to indicate "in vitro", -2 to indicate "chemical synthesis", -3 indicates "unknown", -4 indicates "in vivo" and -5 indicates "in silico".\nParameters of the interaction, for example kinetics. Representation as type:value(text). The type can be taken from the corresponding PSI-MI controlled vocabulary. Multiple parameters separated by "|".\nCreation date Representation as yyyy/mm/dd.\nUpdate date Representation as yyyy/mm/dd.\nChecksum for interactor A, for instance the ROGID of the interactor. Representation as databaseName:checksum\nChecksum for interactor B, for instance the ROGID of the interactor. Representation as databaseName:checksum\nChecksum for interaction, for instance the RIGID of the interaction. Representation as databaseName:checksum\nnegative Boolean value to distinguish positive interactions (negative = false) from negative interactions (negative = true)\n\nAll the columns are mandatory.\nSyntax\nColumns are normally formed by fields delimited by "|", with a structure like this one:\n<XREF>:<VALUE>(<DESCRIPTION>)\nDue to the unsafe use of reserved characters in the values, we have recently added the possibility to surround <XREF>, <VALUE> or <DESCRIPTION> with quotes if they contain a special symbol.\nIn MI-TAB, the reserved characters are:\n|\n(\n)\n:\n\\t (tabulation)\nWhenever this happen in your data, surround the value with double quotes:\n"<XREF_WITH_RESERVED_CHARS>":"<VALUE_WITH_RESERVED_CHARS>"("<DESCRIPTION>")\nNote that the quotes are before and after each part. The escaped data should look like in the following examples:\npsi-mi:"MI:0000"(a cv term)\npsi-mi:"MI:0000"("I can now use braces ()()() or pipes ||| here and ::colons::")\nIf you want to use a quote within a quote, escape it:\nuniprotkb:P12345("a \\"nice\\" protein")\n"},"MITAB27Format.html":{"url":"MITAB27Format.html","title":"MITAB 2.7","body":"PSI-MI TAB 2.7 Format\nIntroduction\nThe MITAB27 format is an extention of the PSI-MI 2.5 (1) and 2.6 standard. It has been derived from the tabular format provided by BioGrid. MITAB27 only describes binary interactions, one pair of interactors per row. Columns are separated by tabulations. Tools allowing to manipulate this data format are available (2).\n(1) http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17925023\n(2) http://www.psidev.info/groups/molecular-interactions (Tools section)\nColumn definitions\nThe column contents should be as follows:\n\nUnique identifier for interactor A, represented as databaseName:identifier, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and identifier is the unique primary identifier of the molecule in the database. Even though identifiers from multiple databases can be separated by "|", it is recommended to give only one identifier in this column. It is recommended that proteins be identified by stable identifiers such as their UniProtKB or RefSeq accession number. Small molecules should have Chebi identifiers, nucleic acids should have embl/ddbj/genbank identifiers and gene should have entrez gene/locuslink, ensembl, or ensemblGenome identifiers. This column should never be empty ('-') except for describing intra-molecular interactions or auto-catalysis. Ex: uniprotkb:P12346\nUnique identifier for interactor B.\nAlternative identifier for interactor A, represented as databaseName:ac, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the primary identifier of the molecule in the database. Multiple identifiers separated by "|". It is recommended to only give database identifiers in this column. Other cross references for interactor A such as GO xrefs should be moved to the column 'Interactor xrefs A' and interactor names such as gene names should be moved to the column 'Alias A'. Ex: refseq:NP_001013128|ensembl:ENSRNOP00000012946\nAlternative identifier for interactor B.\nAliases for A, separated by "|". Representation as databaseName:name(alias type), where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, name is the alias name and alias type is the name of the corresponding alias type as defined in the PSI-MI controlled vocabulary. In the absence of databaseName, one can use unknown. Multiple names separated by "|". In parenthesis, 'display_short' and 'display_long' are used to describe what name can be used for network display. Ex: uniprotkb:Tf(gene name)|uniprotkb:Serotransferrin(recommended name)|uniprotkb:Tf(display_short)\nAliases for B.\nInteraction detection methods, taken from the corresponding PSI-MI controlled Vocabulary, and represented as databaseName:identifier(methodName), separated by "|". As the detection methods are taken from the PSI-MI ontology, the database name is 'psi-mi'. Interaction detection method is recommended by MIMIx and can be used for scoring interactions so it is recommended to always give this information. It is also recommended to give one interaction detection method per MITAB line (for clustering purposes). Ex: psi-mi:"MI:0006"(anti bait coimmunoprecipitation)\nFirst author surname(s) of the publication(s) followed by 'et al.' and the publication year in parenthesis, e.g. Ciferri et al.(2005). Separated by "|".\nIdentifier of the publication in which this interaction has been shown. Database name taken from the PSI-MI controlled vocabulary, represented as databaseName:identifier. Multiple identifiers separated by "|". The publication identifier is used for clustering interactions from different data providers in PSICQUIC and can be used for scoring interactions so it is recommended to always give this information. It is recommended to give one pubmed id per MITAB line and IMEx ids can be added. Ex: pubmed:16980971|imex:IM-1\nNCBI Taxonomy identifier for interactor A. represented as taxid:identifier(organism name) where the identifier is the taxon id of the organism and organism name can either be the common name or scientific name. Even though multiple identifiers can be separated by "|", it is recommended to have one organism per interactor per MITAB line. If both scientific name and common name are given, they should be represented with : taxid:id1(common name1)|taxid:id1(scientific name1). Note: Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -2 to indicate "chemical synthesis" and -3 indicates "unknown". It is recommended to always give this information for proteins and genes. For small molecules and nucleic acids, this information should be given when available but can be left empty ('-') if not relevant.\nNCBI Taxonomy identifier for interactor B.\nInteraction types, taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(interactionType), separated by "|". As the interaction types are taken from the PSI-MI ontology, the database name is 'psi-mi'. Interaction type can be used for scoring interactions so it is recommended to always give this information. It is also recommended to give one interaction type per MITAB line (for clustering purposes). Ex: psi-mi:"MI:0914"(association)\nSource databases and identifiers, taken from the corresponding PSI-MI controlled vocabulary, and represented as databaseName:identifier(sourceName). As the detection methods are taken from the PSI-MI ontology, the database name is 'psi-mi'. Multiple source databases can be separated by "|". When the interaction has been imported and reported by different sources, it is recommended to give the original source plus the source that currently reports the interaction. Ex: psi-mi:"MI:0469"(intact)|psi-mi:"MI:0923"(irefindex)\nInteraction identifier(s) in the corresponding source database, represented by databaseName:identifier. It is recommended to always give a unique identifier per interaction (binary and n-ary) so in case of complexes which have been expanded, it would be possible to retrieve and re-build the original complex based on the interaction identifier. IrefIndex IDs go into the interaction checksum field. Other interaction references such as GO references go into the interaction xref field. Ex: intact:EBI-1547321|imex:IM-11865-3\nConfidence score. Denoted as scoreType:value where scoreType is taken from the corresponding PSI-MI controlled vocabulary. Multiple scores separated by "|". Ex: author-score:0.60|author-score:high|intact-miscore:0.36784992\nComplex expansion. Model used to convert n-ary interactions into binary interactions for purpose of export in MITAB file. It should be represented as databaseName:identifier(expansion name) and taken from the corresponding PSI-MI controlled vocabulary. It is recommended to always give this information when n-ary interactions have been expanded. In case of true binary interactions, this column should be empty ('-'). Ex: psi-mi:"MI:1060"(spoke expansion)\nBiological role A , taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(biological role name), separated by "|". As the biological roles are taken from the PSI-MI ontology, the database name is 'psi-mi'. Biological roles are recommended by MIMIx so it is recommended to always give this information. When the participant A does not have any specific biological roles, the term 'unspecified role' (MI:0499) should be used. Ex: psi-mi:"MI:0684"(ancillary)\nBiological role B.\nExperimental role A , taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(experimental role name), separated by "|". As the experimental roles are taken from the PSI-MI ontology, the database name is 'psi-mi'. Experimental roles are recommended by MIMIx so it is recommended to always give this information. When the participant A does not have any specific experimental roles, the term 'unspecified role' (MI:0499) should be used. Ex:psi-mi:"MI:0496"(bait)\nExperimental role B .\nInteractor type A , taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(interactor type name), separated by "|". As the interactor types are taken from the PSI-MI ontology, the database name is 'psi-mi'. It is recommended to always give this information as it can be useful for recognizing protein-protein, small molecule-proteins, nucleic acids-proteins and gene-proteins interactions. Ex: psi-mi:"MI:0326"(protein)\nInteractor type B.\nXref for interactor A, represented as databaseName:ac(text), where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the primary accession of the molecule in the database. For example the gene ontology cross references associated. The text can be used to describe the qualifier type of the cross reference (see the corresponding PSI-MI controlled vocabulary) or could be used to give the name of the GO term in case of cross references to ontology databases. Multiple cross references separated by "|". This column aims at adding more information to describe the interactor A but cannot be used to identify the interactor A. If some sequence database accessions are ambiguous (Ex : uniprot secondary accessions that are shared between different uniprot entries and so cannot be used as identifiers of interactor A), it is possible to report them in this column. Ex: go:"GO:0003824"(catalytic activity)\nXref for interactor B.\nXref for the interaction, represented as databaseName:ac(text), where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the primary accession in the database. For example the gene ontology cross references associated (components, etc.) or OMIM cross references. Multiple cross references separated by "|". The text can be used to describe the qualifier type of the cross reference (see the corresponding PSI-MI controlled vocabulary) or could be used to give the name of the GO term in case of cross references to ontology databases. Note, that this field is not meant not store interaction accessions or interaction checksums in this field. Ex:go:"GO:0005643"(nuclear pore)\nAnnotations for interactor A, represented as topic:"text", where topic is the name of the topic as defined in the PSI-MI controlled vocabulary and text is free text associated with the topic (linebreak and other MITAB reserved characters should be properly escaped, replaced and/or removed). For example comments about this interactor : comment:"sequence not available in uniprotKb". The text is optional and only a topic could be given, e.g. anti-bacterial. Multiple annotations separated by "|".\nAnnotations for Interactor B.\nAnnotations for the interaction, represented as topic:"text", where topic is the name of the topic as defined in the PSI-MI controlled vocabulary and text is free text associated with the topic (linebreak and other MITAB reserved characters should be properly escaped, replaced and/or removed). For example figure legends : figure legend:"Supp Tables 1 and 2". The text is optional and only a topic could be given. This column would also be used for tagging interactions and in such a case, topics for tags are also defined in the PSI-MI controlled vocabulary except for the complex expansion tags that have their own column. Ex: internally-curated Multiple annotations separated by "|".\nNCBI Taxonomy identifier for the host organism. represented as taxid:identifier(organism name) where the identifier is the taxon id of the organism and organism name can either be the common name or scientific name. Multiple identifiers can be separated by "|". Cells and tissues cannot be described in this column. If both scientific name and common name are given, they should be represented with : taxid:id1(common name1)|taxid:id1(scientific name1). Note: Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -1 to indicate "in vitro", -2 to indicate "chemical synthesis", -3 indicates "unknown", -4 indicates "in vivo" and -5 indicates "in silico".\nParameters of the interaction, for example kinetics. Representation as type:value(text). The type can be taken from the corresponding PSI-MI controlled vocabulary. Multiple parameters separated by "|". Ex: kd:"4.0x2^5 ~0.3"\nCreation date when the curation of the publication started. Representation as yyyy/mm/dd. This field is equivalent to the release date in the PSI-XML schema. Ex:2010/10/17\nUpdate date when the interaction was updated for the last time. Ex:2011/12/13 Representation as yyyy/mm/dd. This field does not have any equivalence in PSI-XML (could be the release date as well) and helps to keep track of changes in curated data.\nChecksum for interactor A, for instance the ROGID of the interactor which takes into consideration both the sequence and the organism of the interactor. Representation as methodName:checksum where methodName is the name of the method used to create the checksum. It is recommended to give the ROGID and CROGID for proteins and the standard Inchi key for small molecules. Ex: rogid:UcdngwpTSS6hG/pvQGgpp40u67I9606|crogid:UcdngwpTSS6hG/pvQGgpp40u67I9606\nChecksum for interactor B.\nChecksum for interaction, for instance the RIGID of the interaction. Representation as methodName:checksum where methodName is the name of the method used to create the checksum. Ex: rigid:"+++94o2VtVJcuk6jD3H2JZXaVYc"\nnegative Boolean value to distinguish positive interactions (false) from negative interactions (true). By default, if the column is empty ('-'), the negative value is considered to be false (positive interaction). Ex: true\nFeature(s) for interactor A: describe features for participant A such as binding sites, PTMs, tags, etc. Represented as feature_type:range(text), where feature_type is the feature type as described in the PSI-MI controlled vocabulary. For the PTMs, the MI ontology terms are obsolete and the PSI-MOD ontology should be used instead. The text can be used for feature type names, feature names, interpro cross references, etc. For instance : sufficient to bind:27-195,201-133 (IPR000785). The use of the following characters is allowed to describe a range position : ‘?’ (undetermined position), ‘n’ (n terminal range), ‘c’ (c-terminal range), ‘>x’ (greater than x), ‘<’ (less than x), ‘x1..x1’ (fuzzy range position Ex : 5..5-9..10). The character '-' is used to separate start position(s) from end position(s). Multiple features separated by '|'. Multiple ranges per feature separated by ','. However, It is not possible to represent linked features/ranges. Ex: gst tag:n-n(n-terminal region)|sufficient to bind:23-45. or binding site:23..24-46,33-33\nFeature(s) for interactor B.\nStoichiometry for interactor A: A numerical value describing the count of instance of the molecule participating in the interaction. If no stoichiometry is available for interactor A, the column should be empty ('-'), otherwise a positive Integer value should be given. Several specific cases should be taken into consideration : in case of auto-catalysis, only one interactor is given and the stoichiometry should be 1. In case of homodimers, homotrimers, etc., the stoichiometry of one interactor should be 0 and the stoichiometry of the other should be a valid positive Integer. In case of homo-oligomer, the stoichiometry of both interactors should be 0. Example: for self interactors e.g. a kinase occluding its kinase domain by an internal phospho-tyrosine/SH2 domain interaction, only Interactor A column will show the molecule accession number with the stoichiometry 1. The columns for Interactor B will be empty. Ex: 4\nStoichiometry for interactor B.\nParticipant identification method for interactor A: taken from the corresponding PSI-MI controlled Vocabulary, and represented as databaseName:identifier(methodName), separated by "|". As the identification methods are taken from the PSI-MI ontology, the database name is 'psi-mi'. Participant detection method is recommended by MIMIx so it is recommended to always give this information. Ex: psi-mi:"MI:0102"(sequence tag identification)\nParticipant identification method for interactor B.\n\nEmpty columns should be represented with '-' to keep track of the columns.\nSyntax\nColumns are normally formed by fields delimited by "|", with a structure like this one:\n<XREF>:<VALUE>(<DESCRIPTION>)\nDue to the unsafe use of reserved characters in the values, we have recently added the possibility to surround <XREF>, <VALUE> or <DESCRIPTION> with quotes if they contain a special symbol.\nIn MI-TAB, the reserved characters are:\n|\n(\n)\n:\n\\t (tabulation)\nWhenever this happen in your data, surround the value with double quotes:\n"<XREF_WITH_RESERVED_CHARS>":"<VALUE_WITH_RESERVED_CHARS>"("<DESCRIPTION>")\nNote that the quotes are before and after each part. The escaped data should look like in the following examples:\npsi-mi:"MI:0000"(a cv term)\npsi-mi:"MI:0000"("I can now use braces ()()() or pipes ||| here and ::colons::")\nIf you want to use a quote within a quote, escape it:\nuniprotkb:P12345("a \\"nice\\" protein")\n"},"MITAB28Format.html":{"url":"MITAB28Format.html","title":"MITAB 2.8","body":"PSI-MI TAB 2.8 Format\nIntroduction\nThe MITAB28 format is an extention of the PSI-MI 2.5 (1), 2.6 and 2.7 standards (2) and is suited to capture causal interactions among biological entities. It was initially derived from the tabular format provided by BioGrid and the newest columns are derived from Signor's CausalTAB format (3). MITAB28 describes binary interactions, one pair of interactors per row. Columns are separated by tabulations. Tools allowing to manipulate this data format are available (4).\n(1) http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17925023\n(2) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977660\n(3) https://signor.uniroma2.it/scripts/causalTabInfo.php\n(4) http://www.psidev.info/groups/molecular-interactions (Tools section)\nColumn definitions\nThe column contents should be as follows:\n\nUnique identifier for interactor A, represented as databaseName:identifier, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and identifier is the unique primary identifier of the molecule in the database. Even though identifiers from multiple databases can be separated by "|", it is recommended to give only one identifier in this column. It is recommended that proteins be identified by stable identifiers such as their UniProtKB or RefSeq accession number. Small molecules should have Chebi identifiers, nucleic acids should have embl/ddbj/genbank identifiers and gene should have entrez gene/locuslink, ensembl, or ensemblGenome identifiers. This column should never be empty ('-') except for describing intra-molecular interactions or auto-catalysis. Ex: uniprotkb:P12346\nUnique identifier for interactor B.\nAlternative identifier for interactor A, represented as databaseName:ac, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the primary identifier of the molecule in the database. Multiple identifiers separated by "|". It is recommended to only give database identifiers in this column. Other cross references for interactor A such as GO xrefs should be moved to the column 'Interactor xrefs A' and interactor names such as gene names should be moved to the column 'Alias A'. Ex: refseq:NP_001013128|ensembl:ENSRNOP00000012946\nAlternative identifier for interactor B.\nAliases for A, separated by "|". Representation as databaseName:name(alias type), where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, name is the alias name and alias type is the name of the corresponding alias type as defined in the PSI-MI controlled vocabulary. In the absence of databaseName, one can use unknown. Multiple names separated by "|". In parenthesis, 'display_short' and 'display_long' are used to describe what name can be used for network display. Ex: uniprotkb:Tf(gene name)|uniprotkb:Serotransferrin(recommended name)|uniprotkb:Tf(display_short)\nAliases for B.\nInteraction detection methods, taken from the corresponding PSI-MI controlled Vocabulary, and represented as databaseName:identifier(methodName), separated by "|". As the detection methods are taken from the PSI-MI ontology, the database name is 'psi-mi'. Interaction detection method is recommended by MIMIx and can be used for scoring interactions so it is recommended to always give this information. It is also recommended to give one interaction detection method per MITAB line (for clustering purposes). Ex: psi-mi:"MI:0006"(anti bait coimmunoprecipitation)\nFirst author: surname(s) of the publication(s) followed by 'et al.' and the publication year in parenthesis, e.g. Ciferri et al.(2005). Separated by "|".\nIdentifier of the publication in which this interaction has been shown. Database name taken from the PSI-MI controlled vocabulary, represented as databaseName:identifier. Multiple identifiers separated by "|". The publication identifier is used for clustering interactions from different data providers in PSICQUIC and can be used for scoring interactions so it is recommended to always give this information. It is recommended to give one pubmed id per MITAB line and IMEx ids can be added. Ex: pubmed:16980971|imex:IM-1\nNCBI Taxonomy identifier for interactor A, represented as taxid:identifier(organism name) where the identifier is the taxon id of the organism and organism name can either be the common name or scientific name. Even though multiple identifiers can be separated by "|", it is recommended to have one organism per interactor per MITAB line. If both scientific name and common name are given, they should be represented with : taxid:id1(common name1)|taxid:id1(scientific name1). Note: Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -2 to indicate "chemical synthesis" and -3 indicates "unknown". It is recommended to always give this information for proteins and genes. For small molecules and nucleic acids, this information should be given when available but can be left empty ('-') if not relevant.\nNCBI Taxonomy identifier for interactor B.\nInteraction types, taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(interactionType), separated by "|". As the interaction types are taken from the PSI-MI ontology, the database name is 'psi-mi'. Interaction type can be used for scoring interactions so it is recommended to always give this information. It is also recommended to give one interaction type per MITAB line (for clustering purposes). Ex: psi-mi:"MI:0914"(association)\nSource databases and identifiers, taken from the corresponding PSI-MI controlled vocabulary, and represented as databaseName:identifier(sourceName). As the detection methods are taken from the PSI-MI ontology, the database name is 'psi-mi'. Multiple source databases can be separated by "|". When the interaction has been imported and reported by different sources, it is recommended to give the original source plus the source that currently reports the interaction. Ex: psi-mi:"MI:0469"(intact)|psi-mi:"MI:0923"(irefindex)\nInteraction identifier(s) in the corresponding source database, represented by databaseName:identifier. It is recommended to always give a unique identifier per interaction (binary and n-ary) so in case of complexes which have been expanded, it would be possible to retrieve and re-build the original complex based on the interaction identifier. IrefIndex IDs go into the interaction checksum field. Other interaction references such as GO references go into the interaction xref field. Ex: intact:EBI-1547321|imex:IM-11865-3\nConfidence score: Denoted as scoreType:value where scoreType is taken from the corresponding PSI-MI controlled vocabulary. Multiple scores separated by "|". Ex: author-score:0.60|author-score:high|intact-miscore:0.36784992\nComplex expansion: Model used to convert n-ary interactions into binary interactions for purpose of export in MITAB file. It should be represented as databaseName:identifier(expansion name) and taken from the corresponding PSI-MI controlled vocabulary. It is recommended to always give this information when n-ary interactions have been expanded. In case of true binary interactions, this column should be empty ('-'). Ex: psi-mi:"MI:1060"(spoke expansion)\nBiological role A, taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(biological role name), separated by "|". As the biological roles are taken from the PSI-MI ontology, the database name is 'psi-mi'. Biological roles are recommended by MIMIx so it is recommended to always give this information. When the participant A does not have any specific biological roles, the term 'unspecified role' (MI:0499) should be used. Ex: psi-mi:"MI:0684"(ancillary)\nBiological role B.\nExperimental role A, taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(experimental role name), separated by "|". As the experimental roles are taken from the PSI-MI ontology, the database name is 'psi-mi'. Experimental roles are recommended by MIMIx so it is recommended to always give this information. When the participant A does not have any specific experimental roles, the term 'unspecified role' (MI:0499) should be used. Ex:psi-mi:"MI:0496"(bait)\nExperimental role B .\nInteractor type A, taken from the corresponding PSI-MI controlled vocabulary, and represented as dataBaseName:identifier(interactor type name), separated by "|". As the interactor types are taken from the PSI-MI ontology, the database name is 'psi-mi'. It is recommended to always give this information as it can be useful for recognizing protein-protein, small molecule-proteins, nucleic acids-proteins and gene-proteins interactions. Ex: psi-mi:"MI:0326"(protein)\nInteractor type B.\nXref for interactor A, represented as databaseName:ac(text), where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the primary accession of the molecule in the database. For example the gene ontology cross references associated. The text can be used to describe the qualifier type of the cross reference (see the corresponding PSI-MI controlled vocabulary) or could be used to give the name of the GO term in case of cross references to ontology databases. Multiple cross references separated by "|". This column aims at adding more information to describe the interactor A but cannot be used to identify the interactor A. If some sequence database accessions are ambiguous (Ex : uniprot secondary accessions that are shared between different uniprot entries and so cannot be used as identifiers of interactor A), it is possible to report them in this column. Ex: go:"GO:0003824"(catalytic activity)\nXref for interactor B.\nXref for the interaction, represented as databaseName:ac(text), where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the primary accession in the database. For example the gene ontology cross references associated (components, etc.) or OMIM cross references. Multiple cross references separated by "|". The text can be used to describe the qualifier type of the cross reference (see the corresponding PSI-MI controlled vocabulary) or could be used to give the name of the GO term in case of cross references to ontology databases. Note, that this field is not meant not store interaction accessions or interaction checksums in this field. Ex: go:"GO:0005643"(nuclear pore)\nAnnotations for interactor A, represented as topic:"text", where topic is the name of the topic as defined in the PSI-MI controlled vocabulary and text is free text associated with the topic (linebreak and other MITAB reserved characters should be properly escaped, replaced and/or removed). For example comments about this interactor : comment:"sequence not available in uniprotKb". The text is optional and only a topic could be given, e.g. anti-bacterial. Multiple annotations separated by "|".\nAnnotations for Interactor B.\nAnnotations for the interaction, represented as topic:"text", where topic is the name of the topic as defined in the PSI-MI controlled vocabulary and text is free text associated with the topic (linebreak and other MITAB reserved characters should be properly escaped, replaced and/or removed). For example figure legends : figure legend:"Supp Tables 1 and 2". The text is optional and only a topic could be given. This column would also be used for tagging interactions and in such a case, topics for tags are also defined in the PSI-MI controlled vocabulary except for the complex expansion tags that have their own column. Ex: internally-curated Multiple annotations separated by "|".\nNCBI Taxonomy identifier for the host organism, represented as taxid:identifier(organism name) where the identifier is the taxon id of the organism and organism name can either be the common name or scientific name. Multiple identifiers can be separated by "|". Cells and tissues cannot be described in this column. If both scientific name and common name are given, they should be represented with : taxid:id1(common name1)|taxid:id1(scientific name1). Note: Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -1 to indicate "in vitro", -2 to indicate "chemical synthesis", -3 indicates "unknown", -4 indicates "in vivo" and -5 indicates "in silico".\nParameters of the interaction, for example kinetics. Representation as type:value(text). The type can be taken from the corresponding PSI-MI controlled vocabulary. The value syntax format is factor x base ^ exponent ~uncertainty. Multiple parameters separated by "|". Ex: kd:"4.0x2^5 ~0.3"|kd:2.0\nCreation date: when the curation of the publication started. Representation as yyyy/mm/dd. This field is equivalent to the release date in the PSI-XML schema. Ex:2010/10/17\nUpdate date: when the interaction was updated for the last time. Ex:2011/12/13 Representation as yyyy/mm/dd. This field does not have any equivalence in PSI-XML (could be the release date as well) and helps to keep track of changes in curated data.\nChecksum for interactor A, for instance the ROGID of the interactor which takes into consideration both the sequence and the organism of the interactor. Representation as methodName:checksum where methodName is the name of the method used to create the checksum. It is recommended to give the ROGID and CROGID for proteins and the standard Inchi key for small molecules. Ex: rogid:UcdngwpTSS6hG/pvQGgpp40u67I9606|crogid:UcdngwpTSS6hG/pvQGgpp40u67I9606\nChecksum for interactor B.\nChecksum for interaction, for instance the RIGID of the interaction. Representation as methodName:checksum where methodName is the name of the method used to create the checksum. Ex: rigid:"+++94o2VtVJcuk6jD3H2JZXaVYc"\nnegative: Boolean value to distinguish positive interactions (false) from negative interactions (true). A molecular interaction between A and B entities is considered as negative (true) when an isoform of A interacts/binds to B and not A itself. For that particular isoform of A that interacts with entity B, in the corresponding binary interaction row, the negative value should be set to false. By default, if the column is empty ('-'), the negative value is considered to be false (positive interaction). Ex: true\nFeature(s) for interactor A: describe features for participant A such as binding sites, PTMs, tags, etc. Represented as feature_type:range(text), where feature_type is the feature type as described in the PSI-MI controlled vocabulary. For the PTMs, the MI ontology terms are obsolete and the PSI-MOD ontology should be used instead. The text can be used for feature type names, feature names, interpro cross references, etc. For instance : sufficient to bind:27-195,201-133 (IPR000785). The use of the following characters is allowed to describe a range position : ‘?’ (undetermined position), ‘n’ (n terminal range), ‘c’ (c-terminal range), ‘>x’ (greater than x), ‘<’ (less than x), ‘x1..x1’ (fuzzy range position Ex : 5..5-9..10). The character '-' is used to separate start position(s) from end position(s). Multiple features separated by '|'. Multiple ranges per feature separated by ','. However, It is not possible to represent linked features/ranges. Ex: gst tag:n-n(n-terminal region)|sufficient to bind:23-45. or binding site:23..24-46,33-33\nFeature(s) for interactor B.\nStoichiometry for interactor A: A numerical value describing the count of instance of the molecule participating in the interaction. If no stoichiometry is available for interactor A, the column should be empty ('-'), otherwise a positive Integer value should be given. Several specific cases should be taken into consideration : in case of auto-catalysis, only one interactor is given and the stoichiometry should be 1. In case of homodimers, homotrimers, etc., the stoichiometry of one interactor should be 0 and the stoichiometry of the other should be a valid positive Integer. In case of homo-oligomer, the stoichiometry of both interactors should be 0. Example: for self interactors e.g. a kinase occluding its kinase domain by an internal phospho-tyrosine/SH2 domain interaction, only Interactor A column will show the molecule accession number with the stoichiometry 1. The columns for Interactor B will be empty. Ex: 4\nStoichiometry for interactor B.\nParticipant identification method for interactor A: taken from the corresponding PSI-MI controlled Vocabulary, and represented as databaseName:identifier(methodName), separated by "|". As the identification methods are taken from the PSI-MI ontology, the database name is 'psi-mi'. Participant detection method is recommended by MIMIx so it is recommended to always give this information. Ex: psi-mi:"MI:0102"(sequence tag identification)\nParticipant identification method for interactor B.\nBiological effect of interactor A: The GO term associated with the molecular function of interactor A that is responsible for its regulatory activity. Represented as dataBaseName:identifier(biological effect name), separated by "|". As the biological effect is taken from the GO ontology, the database name should be 'go'. Also, it is recommended that at most one GO xref is given as a biological effect. Ex: go:"GO:0016301"(kinase activity)\nBiological effect of interactor B.\nCausal regulatory mechanism: This column describes the regulatory mechanism of indirect causal interactions, where the entity A is not immediately upstream of the entity B. It is taken from the corresponding PSI-MI controlled vocabulary and represented as dataBaseName:identifier(regulatoryMechanism), separated by "|". As the causal regulatory mechanism is taken from the PSI-MI ontology, the database name is 'psi-mi'. When the ‘Interaction Types’ column is equal to the psi-mi term: psi-mi:"MI:2286"(functional association), then the causal regulatory mechanism must be absolutely filled - otherwise it can be empty. Ex: psi-mi:"MI:2247"(transcriptional regulation)\nCausal statement: This column describes the effect of modulator entity A on a modulated entity B. It is taken from the corresponding PSI-MI controlled vocabulary and represented as dataBaseName:identifier(causalStatement), separated by "|". As the causal statement is taken from the PSI-MI ontology, the database name is 'psi-mi'. Ex: psi-mi:"MI:2240"(down regulates)\n\nEmpty columns should be represented with '-' to keep track of the columns.\nSyntax\nColumns are normally formed by fields delimited by "|", with a structure like this one:\n<XREF>:<VALUE>(<DESCRIPTION>)\nDue to the unsafe use of reserved characters in the values, we have recently added the possibility to surround <XREF>, <VALUE> or <DESCRIPTION> with quotes if they contain a special symbol.\nIn MI-TAB, the reserved characters are:\n|\n(\n)\n:\n\\t (tabulation)\nWhenever this happen in your data, surround the value with double quotes:\n"<XREF_WITH_RESERVED_CHARS>":"<VALUE_WITH_RESERVED_CHARS>"("<DESCRIPTION>")\nNote that the quotes are before and after each part. The escaped data should look like in the following examples:\npsi-mi:"MI:0000"(a cv term)\npsi-mi:"MI:0000"("I can now use braces ()()() or pipes ||| here and ::colons::")\nIf you want to use a quote within a quote, escape it:\nuniprotkb:P12345("a \\"nice\\" protein")\n"},"PSIMIXML.html":{"url":"PSIMIXML.html","title":"PSI-MI XML","body":"The PSI-MI XML (miXML) data interchange format is an XML-based molecular interactions format. The version currently used by PSICQUIC when returning results in XML is the PSI-MI XML 2.5 version.\nVersions\n\nPSI-MI XML 2.5\nPSI-MI XML 3.0\n\n"},"MIXML25Format.html":{"url":"MIXML25Format.html","title":"PSI-MI XML 2.5","body":"\nPSI-MI XML 2.5 Specifications and Guidelines\nPSI-MI XML 2.5.4 Schema documentation\nXSD Schema 2.5.4\n\n"},"MIXML30Format.html":{"url":"MIXML30Format.html","title":"PSI-MI XML 3.0","body":"\nPSI-MI XML 3.0.0 Schema documentation\nXSD Schema 3.0.0\n\n"},"PsicquicServiceProviders.html":{"url":"PsicquicServiceProviders.html","title":"Service providers","body":"PSICQUIC Providers\nThere are more than 30 PSICQUIC providers. As more molecular interaction databases implement PSICQUIC, this list of providers will grow.\nIt is possible to check dynamically on the status of each of this services by using the Registry.\nNotes:\n\nOnly those with version 1.0 or more support REST access.\nOnly those with version 1.2 or more support XGMML and RDF format.\nOnly those with version 1.3 or more support MITAB 2.7 and MITAB 2.6 format.\nOnly those with version 1.4 or more support the MITAB 2.8 format.\nThe webservices having a version inferior to 1.3 are based on LUCENE reference implementation and the webservices having a version superior or equal to 1.3 are based on SOLR reference implementation. The index is different but the data is the same.\n\n"},"HowToInstallPsicquicSolr.html":{"url":"HowToInstallPsicquicSolr.html","title":"How to install PSICQUIC Solr (recommened)","body":"PSICQUIC reference implementation based on SOLR (recommended)\nThe new PSICQUIC Reference Implementation is now based on SOLR which is an indexing software based on LUCENE. It can index MITAB 2.5, 2.6, 2.7 and 2.8 files.\nYou have two ways for building your psicquic webservice :\n\nHow to install PSICQUIC using a single jetty server\nIf you need to test quickly your webservice\nIf you want to start both the solr server and the PSICQUIC webservice using one single command line. However Both applications will be running on the same jetty server, which may not be what you want if you re-use your SOLR index/server for other applications -- eg -- when updating the solr server, it is better to leave the psiquic webservice running, this setup requires both to shut down at the same time.\n\n\nHow to install PSICQUIC using a solr server independent from the PSICQUIC server\nIf you don't want to use jetty for running your PSICQUIC webservice\nIf you want to start the solr server in another server so you can reuse it in other applications independent from your PSICQUIC service\nIf you already have a solr server independent from the PSICQUIC server\n\n\n\n"},"HowToInstallPsicquicAndSolrJetty.html":{"url":"HowToInstallPsicquicAndSolrJetty.html","title":"Single jetty server","body":"Installation\nThis instructions are aimed to those who want to have its local instance of the PSICQUIC web service based on SOLR.\nRequirements\n\nJAVA (JDK 6)\nMaven 2 or 3 (3 is recommended)\n\nObtaining the Reference Implementation source code\nThere are two ways to obtain the source code:\n\nDownload the psicquic-solr-ws-1.4.0.zip\n\nUsing a git client, clone the code\ngit clone https://github.com/PSICQUIC/psicquic-solr-ws.git\n\n\nCreating a solr working directory\nThis solr working directory will contain solr-home, the MITAB index and solr war file. The content of solr working directory does not need to be there, it will be created automatically by the indexing script. If a solr-home, MITAB index or solr.war file already exists in the working directory, only the MITAB index will be overwritten by the MITAB indexing script.\nBuilding the index\nThe Reference Implementation uses SOLR (based on LUCENE) to index the data. This index can be generated in many ways but for your convenience, a class to create it from a PSIMITAB file (versions 2.5, 2.6, 2.7 and 2.8 are supported) is included as part of the web service. The PSIMITAB formats are described in MITAB25Format, MITAB26Format, MITAB27Format, MITAB28Format and we recommend data providers to read the Data Distribution Best Practices as well as the PSICQUIC FAQ before starting to generate a PSIMITAB dataset.\nCreating an index\nWhen the indexing job starts, it creates a file target/mitabIndexJob_currentTimeMillis which contains the job ID of the indexing process. This job ID will be necessary if you want to restart the indexing process from where it failed in case of a badly formatted MITAB line for instance.\n\nYou can run this bash script :\ncd psicquic-solr-ws\nbash indexMitab.sh /path/to/mitab-file /path/to/solr-workingdir\nwhere\n\n/path/to/mitab-file is the path to the MITAB file to index. This argument is mandatory.\n/path/to/solr-workingdir is the path to the solr working directory. If this argument is not provided, the script will consider the current working directory as the solr working directory.\n\n\n\n\nThe indexing can be executed using the Maven command (used by the bash script) :\ncd psicquic-solr-ws\nmvn clean install -PcreateIndex -DmitabFile=/path/to/mitab-file -Dsolr.workdir=/path/to/solr-workingdir -Dmaven.test.skip\nwhere\n\n/path/to/solr-workingdir is the path to the solr working directory. If this argument is not provided, the script will consider the current working directory as the solr working directory.\n/path/to/mitab-file is the path to the MITAB file to index. This argument is mandatory.\n\n\n\nRestarting the indexing process where it failed (in case it failed)\nIt can happen that the indexing process fails (bad formatted MITAB line for instance, solr server down, etc.). In this case you may want to restart the indexing process from where it failed (after fixing the badly formatted line for instance). Look at the job ID in the file target/mitabIndexJob_currentTimeMillis and then you have two ways of restarting the indexing:\n\nYou can run this bash script :\ncd psicquic-solr-ws\nbash restartIndexMitab.sh /path/to/mitab-file job-ID /path/to/solr-workingdir\nwhere\n\n/path/to/mitab-file is the path to the MITAB file to index. This argument is mandatory.\njob-ID is the job ID in the file target/mitabIndexJob_currentTimeMillis generated by the indexing script that failed. This argument is mandatory\n/path/to/solr-workingdir is the path to the solr working directory. If this argument is not provided, the script will consider the current working directory as the solr working directory.\n\n\n\n\nThe script can be executed using the Maven command (used by the bash script) :\ncd psicquic-solr-ws\nmvn install -PrestartIndex -DmitabFile=/path/to/mitab-file -Dsolr.workdir=/path/to/solr-workingdir -Dindexing.id=job-ID -Dmaven.test.skip\nwhere\n\n/path/to/mitab-file is the path to the MITAB file to index. This argument is mandatory.\njob-ID is the job ID in the file target/mitabIndexJob_currentTimeMillis generated by the indexing script that failed. This argument is mandatory\n/path/to/solr-workingdir is the path to the solr working directory. If this argument is not provided, the script will consider the current working directory as the solr working directory.\n\n\n\nStarting solr and the PSICQUIC service locally, using Jetty\nThe solr server will start with the PSICQUIC service using the same jetty server.\n\nYou can run this bash script :\ncd psicquic-solr-ws\nbash startPsicquicServerAndSolr.sh /path/to/solr-workingdir\nwhere\n\n/path/to/solr-workingdir is the path to the solr working directory (same as for indexing MITAB). If this argument is not provided, the script will consider the current working directory as the solr working directory.\n\n\n\n\nThe PSICQUIC service and solr can be started using the Maven command (used by the bash script):\ncd psicquic-solr-ws\nmvn clean install -Pstart-jetty-solr jetty:run -Dmaven.test.skip -Dsolr.workdir=/path/to/solr-workingdir\nwhere\n\n/path/to/solr-workingdir is the path to the solr working directory. If this argument is not provided, the script will consider the current working directory as the solr working directory.\n\n\n\nFrom PSICQUIC Spec 1.1 it is possible to define and expose properties about the service. You can set which properties your service is going to show by passing the psicquic.properties variable. Properties are defined using key=value pairs, comma-separated and all the expression is quoted.\nmvn clean install -Pstart-jetty-solr -Dmaven.test.skip -D psicquic.properties="owner=John Smith, contactinfo=My Address"\nIf you decide to use maven command, other parameters can be configured :\n\n-Djetty.port=9090\n-Dsolr.host=127.0.0.1 to set up the virtual host for the solr admin interface (by default private only)\n-Dpsicquic.properties=properties-file-name\n-Dpsicquic.filter=filter-query (define some filters for your service)\n-Dservice.name=name (the name of the service such as intact, mint, ... which will be used to create the war file). If no service name is provided, the default name is 'default'\n-Dlog.file.name=filename (define a log file where you want to log all the queries that have been sent to your service)\n\nHere is a sample query listing a limited number of available interactions in your local service:\nhttp://localhost:9090/psicquic/webservices/current/search/query/*?firstResult=0&maxResults=10\n"},"HowToInstallPsicquicSolrDifferentServers.html":{"url":"HowToInstallPsicquicSolrDifferentServers.html","title":"Using a solr server independent from the PSICQUIC server","body":"Installation\nThis instructions are aimed to those who want to have its local instance of the PSICQUIC web service based on SOLR.\nRequirements\n\nJAVA (JDK 6)\nMaven 2 or 3 (3 is recommended)\nSOLR 3.6.2\n\nInstalling solr and solr-home\nObtaining the solr schema used in the reference implementation\n\nClone the code :\n git clone https://github.com/PSICQUIC/psicquic-solr.git\n\nCopy solr-home directory (psicquic-solr/src/main/resources/solr-home/) in your solr working directory:\n cp -r psicquic-solr/src/main/resources/solr-home/ path/to/your/solr-workingdir\n\n\nStarting solr server\nThe solr.war file is available in psicquic-solr/src/main/resources/solr.war or you can download the solr 3.6.2 package from apache website http://archive.apache.org/dist/lucene/solr/3.6.2/\nIn the environment of your solr server, it is important to set the variable solr.solr.home which will point to the solr-home folder that you copied in your system. More information about how to install solr is available here http://wiki.apache.org/solr/SolrInstall\nObtaining the Reference Implementation source code\nThere are two ways to obtain the source code:\n\nDownload the psicquic-solr-ws-1.4.0.zip\n\nUsing a git client, clone the code\ngit clone https://github.com/PSICQUIC/psicquic-solr-ws.git\n\n\nBuilding the index\nThe Reference Implementation uses SOLR (based on LUCENE) to index the data. This index can be generated in many ways but for your convenience, a class to create it from a PSIMITAB files (versions 2.5, 2.6, 2.7 and 2.8 are supported) is included as part of the web service. The PSIMITAB formats are described in MITAB25Format, MITAB26Format, MITAB27Format, MITAB28Format and we recommend data providers to read the Data Distribution Best Practices as well as the PSICQUIC FAQ before starting to generate a PSIMITAB dataset.\nCreating an index\nWhen the indexing job starts, it creates a file target/mitabIndexJob_currentTimeMillis which contains the job ID of the indexing process. This job ID will be necessary if you want to restart the indexing process from where it failed in case of a badly formatted MITAB line for instance.\n\nYou can run this bash script:\ncd psicquic-solr-ws\nbash indexMitabWithSolrUrl.sh /path/to/mitab-file solr-server-url\nwhere\n\n/path/to/mitab-file is the path to the MITAB file to index. This argument is mandatory.\nsolr-server-url is the URL of your solr server. By default if not provided, it is http://localhost:9090/solr/. \n\n\n\n\nThe indexing can be executed using the Maven command (used by the bash script):\ncd psicquic-solr-ws\nmvn clean install -PcreateIndexWithSolrRunning -DmitabFile=/path/to/mitab-file -DsolrUrl=solr-server-url -Dmaven.test.skip\nwhere\n\n/path/to/mitab-file is the path to the MITAB file to index. This argument is mandatory.\nsolr-server-url is the URL of your solr server. By default if not provided, it is http://localhost:9090/solr/.\n\n\n\nRestarting the indexing process where it failed (in case it failed)\nIt can happen that the indexing process fails (bad formatted MITAB line for instance, solr server down, etc.). In this case you may want to restart the indexing process from where it failed (after fixing the badly formatted line for instance). Look at the job ID in the file target/mitabIndexJob_currentTimeMillis and then you have two ways of restarting the indexing:\n\nYou can run this bash script :\ncd psicquic-solr-ws\nbash restartIndexMitabWithSolrUrl.sh /path/to/mitab-file job-ID solr-server-url\nwhere\n\n/path/to/mitab-file is the path to the MITAB file to index. This argument is mandatory.\njob-ID is the job ID in the file target/mitabIndexJob_currentTimeMillis generated by the indexing script that failed. This argument is mandatory.\nsolr-server-url is the URL of your solr server. By default if not provided, it is http://localhost:9090/solr/.\n\n\n\n\nThe script can be executed using the Maven command (used by the bash script) :\ncd psicquic-solr-ws\nmvn install -PrestartIndexWithSolrRunning -Dmitab.file=/path/to/mitab-file -DsolrUrl=solr-server-url -Dindexing.id=job-ID -Dmaven.test.skip\nwhere\n\n/path/to/mitab-file is the path to the MITAB file to index. This argument is mandatory.\njob-ID is the job ID in the file target/mitabIndexJob_currentTimeMillis generated by the indexing script that failed. This argument is mandatory.\nsolr-server-url is the URL of your solr server. By default if not provided, it is http://localhost:9090/solr/.\n\n\n\nStarting the PSICQUIC service locally\nStarting with jetty\nYou can use jetty to start the psicquic service (good for testing but can be used in production as well)\n\nYou can run this bash script :\ncd psicquic-solr-ws\nbash startPsicquicServerOnly.sh solr-server-url\nwhere\n\nsolr-server-url is the URL of your solr server. By default if not provided, it is http://localhost:9090/solr/.\n\n\n\n\nThe PSICQUIC service and solr can be started using the Maven command (used by the bash script) :\ncd psicquic-solr-ws\nmvn clean jetty:run -Dmaven.test.skip -DsolrUrl=solr-server-url\nwhere\n\nsolr-server-url is the URL of your solr server. By default if not provided, it is http://localhost:9090/solr/.\n\n\n\nNote that if you get an error like Address already in use, then you have to setup the solr server on a different port than 9090 (which is used by default by the psicquic service).\nFrom PSICQUIC Spec 1.1 it is possible to define and expose properties about the service. You can set which properties your service is going to show by passing the psicquic.properties variable. Properties are defined using key=value pairs, comma-separated and all the expression is quoted.\nmvn clean jetty:run -Dmaven.test.skip -DsolrUrl=solr-server-url -D psicquic.properties="owner=John Smith, contactinfo=My Address"\nIf you decide to use maven command, other parameters can be configured :\n\n-Djetty.port=9090\n-Dsolr.host=127.0.0.1 to set up the virtual host for solr admin interface. By default is private only\n-Dpsicquic.properties=properties-file-name\n-Dpsicquic.filter=filter-query (define some filters for your service)\n-Dservice.name=name (the name of the service such as intact, mint, ... which will be used to create the war file). If no service name is provided, the default name is 'default'\n-Dlog.file.name=filename (define a log file where you want to log all the queries that have been sent to your service)\n\nUsing tomcat, or any other server\nIf the jetty hot launch does not work for you, you can package the application in a war file and deploy it in your favourite web server (e.g. Tomcat).\nTo create the war file with maven, use the following command:\nmvn clean package -DsolrUrl=solr-server-url\nwhere\n\nsolr-server-url is the URL of your solr server. By default if not provided, it is http://localhost:9090/solr/.\n\nHere is a sample query listing a limited number of available interactions in your local service:\nhttp://localhost:9090/psicquic/webservices/current/search/query/*?firstResult=0&maxResults=10\n"},"HowToInstallPsicquicLucene.html":{"url":"HowToInstallPsicquicLucene.html","title":"How to install PSICQUIC using LUCENE","body":"PSICQUIC reference implementation based on LUCENE\nThis is the original psicquic reference implementation which is able to index a MITAB 2.5 file and which is based on LUCENE. This implementation will not be further developed and the PSICQUIC reference implementation based on SOLR should be used instead. You can find more information about how to install PSICQUIC using LUCENE here.\n"},"HowToInstall.html":{"url":"HowToInstall.html","title":"Using LUCENE","body":"Installation\nThis instructions are aimed to those who want to have its local instance of the PSICQUIC web service.\nRequirements\n\nJAVA (JDK 6)\nMaven 2\n\nObtaining the Reference Implementation source code\nThere are two ways to obtain the source code:\n\nFrom the download section, downloading psicquic-ws-1.2.9 (.zip/.tar.gz) containing the sources\nUsing a git client, clone the code\ngit clone https://github.com/PSICQUIC/psicquic-webservice.git\n\n\nCreating an index\nThe Reference Implementation uses a Lucene index to store the data. This index can be generated in many ways but for your convenience, a class to create it from a PSIMITAB file is included as part of the web service. The PSIMITAB format is described here and we recommend data providers to read the Data Distribution Best Practices as well as the PSICQUIC FAQ before starting to generate a PSIMITAB dataset.\nThis class can be executed using Maven:\ncd psicquic-webservice\nmvn clean compile -P createIndex -D psicquic.index=/path/to/new.index -D mitabFile=/path/to/mitab.txt -D hasHeader=true\nReplace the psicquic.index (where the index will be created), mitabFile (mitab file to index) and hasHeader (whether the file has a header) values accordingly.\nIf for whatever reason this is not working to you, you can execute directly the class uk.ac.ebi.intact.psicquic.ws.utils.MitabIndexer that can be found in the psicquic-webservice project.\nRunning the service\nYou have two choices here:\nStarting the service locally, using Jetty\nThe web service project can be started with jetty directly. This is extremely useful when testing but can be used as well for production instances.\nmvn clean jetty:run -D psicquic.index=/path/to/new.index\nUse the psicquic.index created in the previous step.\nFrom PSICQUIC Spec 1.1 it is possible to define and expose properties about the service. You can set which properties your service is going to show by passing the psicquic.properties variable. Properties are defined using key=value pairs, comma-separated and all the expression is quoted.\nmvn clean jetty:run -D psicquic.index=/path/to/new.index -D psicquic.properties="owner=John Smith, contactinfo=My Address"\nHere is a sample query listing a limited number of available interactions in your local service:\nhttp://localhost:9090/psicquic/webservices/current/search/query/*?firstResult=0&maxResults=10\nUsing tomcat, or any other server\nIf the jetty hot launch does not work for you, you can package the application in a war file and deploy it in your favourite web server (e.g. Tomcat).\nTo create the war file with maven, use the following command:\nmvn clean package -D psicquic.index=/path/to/new.index\nUse the psicquic.index created in the index creation step. Make sure that you are using the full path to the index as othwerwise the web server would not find it. Once the command is run, you can find the war file in the target folder. Grab it and deploy it in any web server.\nYou can define properties as explained in the previous section:\nmvn clean package -D psicquic.index=/path/to/new.index -D psicquic.properties="owner=John Smith, contactinfo=My Address"\n"},"DataDistributionBestPractices.html":{"url":"DataDistributionBestPractices.html","title":"Data Distribution Best Practices","body":"Purpose\nThis document focuses on several aspects of the MITAB27 data representation in the context of data distribution via PSICQUIC services. As MITAB 2.7 is backward compatible with MITAB 2.5 and MITAB 2.6, the best practices also apply to these formats except for the new columns. The implementation of these best practices in the data served by a PSICQUIC services should improve users searches, data consistency and visualization as well as clustering of this data with other PSICQUIC services.\nBest Practices\nA. Describing an Interacting Molecule\nTypically, an interacting molecule is described using up to 12 columns of the MITAB format:\n\n\n\nColumn name\nColumns for Interactor A\nColumns for Interactor B\nDefinition\n\n\n\n\nUnique identifier\n1\n2\nrepresented as databaseName:ac, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the unique primary identifier of the molecule in the database. Even though the MITAB format can accept several identifiers from multiple databases (separated by "|") in the 'unique identifier' columns, it is recommended to give only one identifier. It is also recommended that proteins are identified by stable identifiers such as their UniProtKB, RefSeq, Ensembl, ddbj/genbank/embl or Chebi accession number.\n\n\nAlternative Identifier\n3\n4\nrepresented as databaseName:ac, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the primary identifier of the molecule in the database. Multiple identifiers separated by "|". It is recommended that only database identifiers for the interactors are given in these columns. Other cross references for these interactors such as GO xrefs should be moved to columns 23 and 24 and interactor names such as gene names should be moved to columns 5 and 6.\n\n\nAliases\n5\n6\nrepresented as databaseName:name, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and name is the name of the molecule in the database (Ex gene names, protein recommended name, ORF, locus name, drug name, Chebi recommended name, etc.). Multiple names separated by "|".\n\n\nXrefs\n23\n24\nrepresented as databaseName:ac, where databaseName is the name of the corresponding database as defined in the PSI-MI controlled vocabulary, and ac is the primary accession in the database. Multiple accessions separated by "|". This columns can contain for instance GO xrefs.\n\n\nNCBI Taxonomy identifier\n10\n11\nDatabase name for NCBI taxid taken from the PSI-MI controlled vocabulary, represented as taxid:identifier(organism common name). Even though the MITAB format can accept several taxon ids per column (Multiple identifiers separated by "|"), it is strongly recommended to have only one organism per protein per MITAB line. Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -2 to indicate "chemical synthesis" and -3 indicates "unknown".\n\n\nchecksum\n33\n34\nrepresented as methodName:value, where methodName is the name of the corresponding checksum method, and value is the checksum for this interactor. Multiple checksums separated by "|". This columns can contain for instance rogid, or standard inchi key\n\n\n\n\nIt is recommended that the unique identifier and alternative identifier column should be used as follow:\n\nunique identifier column: Ideally indicate a single reference to a chosen primary sequence database (e.g. one of UniProt or RefSeq). The unique identifier should not be ambiguous. If the interactor can match several RefSeq identifiers are used but only one master UniProt ac, it is recommended to give the master UniProt ac as 'unique identifier' and the RefSeq identifiers as 'alternative identifiers'.\nalternative identifier column: any other database identifier referring to your interacting molecule. Here are two examples:\nif you are UniProt centric, you could add mapping to RefSeq,\nif you are a gene centric, you could add mapping to UniProt and/or RefSeq.\n\n\n\nThe first two columns 'unique identifier' should never be both empty columns. If a unique identifier to a sequence database cannot be found, it is important to give at least one identifier from the interaction database that created the interactor entry (Ex : IntAct accession, MINT accessions, etc.). One empty column is allowed in case of intra-molecular interactions (a single molecule interacts with itself). If one 'unique identifier' column is empty, it is expected to have empty columns for the matching 'alternative identifier', 'alias', 'taxid', 'interactor xref', 'checksum', 'biological role', 'experimental role', 'interactor type', 'feature', 'participant identification method'.\nIt is recommended to give gene names, ORF, locus names, gene synonyms, Chebi recommended name, drug name and/or protein recommended names in the alias columns.\nOther cross references which can describe the interactors but ARE NOT identifiers such as GO xrefs could be added in columns 23 and 24.\nIn a single MITAB line, the interactors should only be associated with a single taxon id.\nWhen it is available, a checksum of the interactor can be used in column 33 and 34 such as rogid, crogid and standard inchi key. These checksums could then be used for clustering interactors and taking into account their sequence.\nHere is a recommendation for various molecule types:\n1. Complexes\nIn case of complexes (several protein chains for instance), no reference database can be recommended. The UniprotKB database does not generate unique identifiers for complexes. For now, only identifiers generated by the interaction databases can be used. For clustering purposes, if one interaction database such as IntAct did create an entry for describing a specific complex, the accession of the interaction generated by the database (IntAct) could be used across several different interaction databases to point to the same complex.\n2. Proteins\n\n\n\nColumn\nData required\nExample(s)\n\n\n\n\nUnique identifier\nUse preferentially a single cross references to uniprotkb or RefSeq\nuniprotkb:P51587 uniprotkb:P51123-3 refseq:NP_000059\n\n\nAlternative identifier\nUse secondary cross references in primary database, Use model organism databases.\nuniprotkb:O00183\n\n\nInteractor Xrefs\nUse cross references to databases that can give more information about the protein but cannot be used as identifier. This columns can also contain secondary identifiers that are ambiguous (can be shared by two different proteins for instance, uniprot demerge) and that cannot be used to identify a single protein.\ngo:"GO:0003824"\n\n\nAlias\nuse the gene name found in your reference database. 'orf name', 'gene name synonym', 'locus names' and 'protein recommended name' can also be added\nuniprotkb:BRCA2(gene name) uniprotkb:FACD(gene name synonym)\n\n\nNCBI Taxonomy identifier\nThe taxid of the molecule (e.g. taxid:9606) should always be provided. In parenthesis, it is recommended to add the common name/scientific name of the organism.\ntaxid:9606 taxid:9606(human) taxid:9606(Homo sapiens)\n\n\nInteractor checksums (columns 33 and 34)\nUse rogid and crogid\nrogid:UcdngwpTSS6hG/pvQGgpp40u67I9606 crogid:UcdngwpTSS6hG/pvQGgpp40u67I9606\n\n\n\nWhat is a ROGID ?\nROGID (Redundant Object Group Identifier) is a SHA-1 digest of the protein interactor's primary amino acid sequence concatenated with the NCBI taxonomy identifier. The first 27 character of a ROGID is always the hash value (SEGUID) to which is appended the taxid. Please refer to the iRefIndex paper for more details.\nWhat is a CROGID ?\nThis is similar to ROGID but allows the description of Canonical Redundant Object Group. See below how a canonical sequence should be chosen.\n3. Small Molecules\n\n\n\nColumn\nData required\nExample(s)\n\n\n\n\nUnique identifier\nuse the standard inchi key if not ambiguous, otherwise use a non ambiguous identifier (Chebi recommended). As the standard inchi key is not a database identifier but more a checksum, a unique Chebi identifier would be recommended. The standard inchi key should only be used as identifier for enrichment purposes and it may be moved to the checksum columns after data enrichment. If the standard inchi key is used as an identifier, the database is unknown and we should write standard inchi key in parenthesis\nunknown:"KTUFNOKKBVMGRW-UHFFFAOYSA-N"(standard inchi key)\n\n\nAlternative identifier\nuse cross references to chebi or other small molecule database that can identify without ambiguity the small molecule.\nchebi:"CHEBI:45783"\n\n\nInteractor Xrefs\nUse cross references to databases that can give more information about the small molecule but cannot be used as identifier. This columns can also contain secondary identifiers that are ambiguous (can be shared by two different small molecules for instance) and that cannot be used to identify a single molecule.\npubchem:26697112\n\n\nAlias\nadd a standard inchi, smile, Chebi name, drug name\nunknown:"1S/C29H31N7O/c1-21-5-10-25(18-27(21)34-29-31-13-11-26(33-29)24-4-3-12-30-19-24)32-28(37)23-8-6-22(7-9-23)20-36-16-14-35(2)15-17-36/h3-13,18-19H,14-17,20H2,1-2H3,(H,32,37)(H,31,33,34)"(standard inchi)chebi:imatinib(chebi name)\n\n\nNCBI Taxonomy identifier\nit should be '-' if undefined, taxid:-3(unknown), taxid:-2(chemical synthesis) or a specific taxid if known\n\n\n\nInteractor checksums (columns 33 and 34)\nUse standard inchi key\nstandard inchi key:"KTUFNOKKBVMGRW-UHFFFAOYSA-N"\n\n\n\nShould the Standard InCHI Key not describe unambiguously a molecule, the data provider should use an other cross reference and keep the Standard InCHI Key as a checksum only.\nWhat is a Standard InChI ?\nIUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03.\nWhat is a Standard InChI Key ?\nThe standard InChI Key is a condensed, 27 character identifier that is a hashed version of the full standard InChI (using the SHA-256 algorithm), designed to allow for easy web searches of chemical compounds.\nThe InChI Trust has more information and software support for InChI related matters.\n4. Nucleic Acids\n\n\n\nColumn\nData required\nExample(s)\n\n\n\n\nUnique identifier\nuse a single cross references to embl/genebank/ddbj\nddbj/embl/genbank:U41813\n\n\nAlternative identifier\nuse other cross references to other nucleotide sequence databases such as Refseq nucleotides\n\n\n\nNCBI Taxonomy identifier\nThe taxid of the molecule (e.g. taxid:9606) should be provided when available. In parenthesis, it is recommended to add the common name/scientific name of the organism. It should be '-' if undefined, taxid:-3(unknown) or taxid:-2(chemical synthesis) otherwise.\n.\n\n\n\n5. Gene\nThis case is differentiated from 'Nucleic Acid' as not all nucleic acid sequence result in genes. Furthermore genes can be references to with set of public databases that differs from other Nucleic Acid based molecules.\n\n\n\nColumn\nData required\nExample(s)\n\n\n\n\nUnique identifier\nuse a unique cross references to entrez gene/locuslink, ensembl, or ensemblGenome\nentrez gene/locuslink:84665ensembl:X63509ensemblgenomes:AT1G66140\n\n\nAlternative identifier\nuse cross references to entrez gene/locuslink, ensembl and ensemblGenome that could not be used in 'unique identifier' columns.\n\n\n\nInteractor Xrefs\nuse other cross references to other databases that can add more information about the gene but cannot be used as identifier\n\n\n\nAlias\nuse gene names, ORF, locus names and/or gene synonyms\n\n\n\nNCBI Taxonomy identifier\nThe taxid of the molecule (e.g. taxid:9606) should always be provided. In parenthesis, the common name and/or scientific name should be given\ntaxid:9606(Homo sapiens)taxid:9606(human)\n\n\n\nB. Describing the publication\nCurrently, the publication can be described using up to 2 columns in MITAB. The publication information should be provided because can be used for PSICQUIC queries, clustering, scoring and linking to the original publication.\n\n\n\nColumn\nData required\nExample(s)\n\n\n\n\nidentifier of the publication (col 8)\nuse a unique cross references to pubmed or doi. If an IMEx id has been assigned to the publication, it should be added as well. If no pubmed id or DOI number can be used, another publication identifier could be used\npubmed:10655498pubmed:16980971imex:IM-1\n\n\nFirst Author\nuse the first author surname in the publication and the publication date in parenthesis\nCiferri et al.(2005)\n\n\n\nC. Describing the organism\nIn MITAB 2.7, three columns can describe organisms.\n\n\n\nColumn\nData required\nExample(s)\n\n\n\n\nNCBI Taxonomy identifier for interactor A (col 10 and 11)\nuse a unique taxId and in parenthesis gives the common name and/or scientific name. This information should always be provided for genes and proteins. For nucleic acids and small molecules, the column can be empty if the information is not relevant, -2 to indicate "chemical synthesis" and -3 to indicate "unknown"\ntaxid:9606(human)taxid:9606(human)taxid:9606(Homo sapiens)\n\n\nNCBI Taxonomy identifier for the host organism\nuse the taxId of the host organism only. -3 for unknown, -2 for chemical synthesis, -4 for in vivo and -5 for in sillico are allowed. In parenthesis, give the common name and/or scientific name of the organism. Cell types and tissues cannot be represented in this column. This information is recommended for MIMIx\ntaxid:9606(human)taxid:9606(human)taxid:9606(Homo sapiens)\n\n\n\nD. Describing controlled vocabularies\nIn MITAB 2.7, 12 columns are controlled vocabulary columns :\n\nMIMIx : interaction detection method (col 7), biological roles (col 17 and 18), experimental roles (col 19 and 20) and participant identification methods (col 41 and 42).\nComplex expansion should always be provided in column 16 when the binary interaction has been expanded and was originally part of a n-ary interaction\nIMEx : interaction type which can be used for scoring (col 12), interactor types which can be used to filter interactions (col 21 and 22)\nsource databases should always be provided in column 13\n\n\n\n\nColumn\nData format\nExample(s)\n\n\n\n\ncolumns 7, 12, 16, 17, 18, 19, 20, 21, 22, 41 and 42,\nuse a unique cross references to the PSI-MI ontology. In parenthesis, it should be the name of the MI term in the ontology\npsi-mi:"MI:0914"(association)\n\n\ncolumn 13\nuse one to several cross references to the PSI-MI ontology depending on the interaction which can be imported from other databases.\npsi-mi:"MI:0469"(intact)psi-mi:"MI:0923"(irefindex)\n\n\n\nE. Describing interaction and complex expansion\nIn MITAB 2.6 and MITAB 2.7, it is possible to tag n-ary interactions which have been expanded. When a binary intercation is expanded, the method to expand the complex should always be provided in column 16 for filtering and clustering purposes.\nHowever, this information is not enough to be able to re-build a complex from MITAB. The interaction AC column could be used to retrieve all the binary pairs composing the complex if the interaction AC is unique per interaction (true binary and n-ary interactions). If possible, the column 14 (Interaction identifiers) should always give an identifier for this purpose (could be the database accession of the interaction or an automatically generated identifier). This only concerns data providers which expand n-ary interactions. In case of true binary interactions, the column 14 is only used for linking to the proper database entry.\nEx :\npsi-mi:"MI:1060"(spoke expansion)\npsi-mi:"MI:1061"(matrix expansion)\npsi-mi:"MI:1062"(bipartite expansion)\nNegative interactions can be represented in MITAB 2.6 and MITAB 2.6 but the negative column (column 36) should always be 'true'. The column can be left empty for positive interactions or should be 'false'.\nSupplementary information could be given in column 25 (Interaction xrefs) such as GO xrefs.\nF. Describing annotations\nIn MITAB 2.6 and 2.7, it is possible to give annotations for interactors (col 26 and 27) and interaction which can be used for tagging (col 28). The topic of the interaction should always be provided (could be any participant attribute name in PSI-MI ontology for columns 26 and 27 and any interaction attribute name or curation content/curation quality tags in the PSI-MI ontology for column 28). The text is optional and if provided must be properly escaped (breakline, tabs, MITAB reserved characters).\nThe section K gives more information about how to tag interactions.\nG. Describing interaction parameters\n\n\n\nColumn\nData format\nExample(s)\n\n\n\n\nParamaters of the interaction (col 30)\nrepresented as type:value(text) where type is a parameter type name from the PSI-MI ontology. Multiple values can be separated by "|". Special characters should not be allowed in MITAB so to represent exponents, fractions or the real values could be used.\nkd:"4.0x2^5 ~0.3"\n\n\n\nH. Describing stoichiometry and self interactions\nIn MITAB 2.7, 2 columns can be used to specify the stoichiometry of the participants (columns 39 and 40). If no stoichiometry information are available, these columns should stay empty (-).\n\nThree different cases need to be specified :\n\nintra-molecular/auto-catalysis : only one interactor is given and the columns for the second interactor should all be empty (with a '-'). The stoichiometry of the interactor should be 1.\nhomodimers, trimers, etc. : two interactors are given (identifiers of interactor A are the same as identifiers for Interactor B). One of the stoichiometry column should be 0 and the other stoichiometry column should be a positive numeric value. Ex: for homodimers, stoichiometry is 2\nhomo oligomers : two interactors are given (identifiers of interactor A are the same as identifiers for Interactor B). Both stoichiometry columns should be 0.\n\nI. Describing features\nFeatures of participant A and B can be added in columns 37 and 39 of MITAB 2.7.\n\n\n\nColumn\nData format\nExample(s)\n\n\n\n\nFeatures for interactor A and B\ndescribe features or participant A such as binding sites, PTMs, tags, etc. Represented as feature_type:range(text), where feature_type is the feature type as described in the PSI-MI controlled vocabulary. For the PTMs, the MI ontology terms are obsolete and the PSI-MOD ontology should be used instead. The text can be used for feature type names, feature names, interpro cross references, etc. The use of the following characters is allowed to describe a range position : ‘?’ (undetermined position), ‘n’ (n terminal range), ‘c’ (c-terminal range), ‘>x’ (greater than x), ‘<’ (less than x), ‘x1..x1’ (fuzzy range position Ex : 5..5-9..10). The character '-' is used to separate start position(s) from end position(s). Multiple features separated by "|". Multiple ranges per feature separated by ','. However, It is not possible to represent linked features/ranges\nsufficient to bind:27-195,201-133 (IPR000785) gst tag:n-n(n-terminal region)sufficient to bind:23-45 binding site:23..24-46,33-33\n\n\n\nJ. Interaction confidence nomenclature\nA scoring nomenclature has been discussed during the PSI meeting 2012 and no final decision has been reached yet.\nThe current proposal is :\n\n{service}-{score method}-{profile}\n\nservice = Service or database which performed the score\nscore method = Name of the score method use to score interactions (CV term)\nprofile = Name used to define a specific way to calculate the score. This could include specific parameters or configuration for a scoring method.\n"service", "score method" and "profile" would be optional, but at least one of them should be present.\n\ne.g.intact-miscore-default:0.36 {service}-{score method}-{profile}\nmiscore-default:0.36 {score method}-{profile}\nmiscore-imex:0.20 {score method}-{profile}\nmiscore-psicquic:0.60 {score method}-{profile}\nThis level of detail is important as the score will differ not only with method, but also with the dataset over which the score is run and the parameters set.\nK. Interaction Evidence Clustering\nWhat is clustering ?\nStoring in a single MITAB line the content of multiple interaction evidence. The format is (to an extent) capable of representing this data by concatenating information in the respective columns. Interaction clustering is an commonly requested operation on molecular interactions query results. This allows for instance to identify a non redundant set of interacting molecule pairs.\nShould You Be Serving Clustered Data ?\nClustering can be performed by a data provider and the clustered data be served by PSICQUIC. However, this practice is not optimal as far as user queries are concerned. For instance, if a service is serving a clustered interaction that aggregates evidences detected by 'yeast two hybrid' and 'pull down' and the user searches for NOT "yeast two hybrid", the clustered line containing pull down would not be returned. The same problem can be reported for a service that is clustering two interactors from two different organisms but with the same sequence in the same column.\nClustering Algorithms\nTypically, clustering is performed by matching interacting molecule pairs using a predefined set of database cross references and aliases. For instance it could be performed by matching molecules based on UniProtKB, RefSeq, rogid, chebi, standard inchi key. Hence, if the recommendation on how to describe an interacting molecule was followed, interaction evidence clustering should work efficiently.\nHow To Present Clustered Data in MITAB\nClustering is currently only run over the single line representation of data in the MITAB format, where multiples pieces of information are separated by ‘|’. As these pieces of information often do not have a 1:1 relationship, for example one interaction method may be related to multiple interaction types, relationships between information will inevitably be lost. There was some discussion and to whether it was worth retaining these relationships by duplicating information but it was generally agreed that the records would then be less human-readable (which is the main reason for producing MITAB in the first place), and that MITAB should only contain the summary of the cluster and in a long term solution, XML could be used for keeping the relationships.\nL. Interaction Evidence Tagging\nCurrently, PSICQUIC tagging is done by the PSICQUIC Registry. Tagging the PSICQUIC service in the registry is important because it gives information about the content of each PSICQUIC registry and can help to focus queries on specific services depending on what the user is looking for (mainly for optimisation). However, this tagging approach presents the obvious limitation that a service, which provides mixed datasets matching different tags, can only be in or out, as opposed to filtering the data it hosts. We will describe in this section some recommendation to implement tagging at the interaction evidence level.\nWhat tags are currently available ?\nThe tags are fully integrated in the PSI-MI Ontology and they can be found here.\nTags useful at the interaction level\n\n\nmimix curation or rapid curation are useful. It is easy to detect interactions having imex-curation because they have an IMEx identifier in the interaction Acs column.\ncomplex expansion tags will be used in a specific 'Complex expansion' column in MITAB 2.7\nsome data source tags are useful at the level of interaction such as 'imported', 'internally curated'. The tags 'predicted', 'experimentally-observed' and 'text-mining' could be deduced from the interaction detection method so can already been filtered without tagging. Depending on the data provider, it is not necessary to tag at the level of the interaction for the data-source because only contain one specific data source.\nthe interacting molecule tags such as protein-protein, nucleicacid-protein or smallmolecule-protein are not really necessary in MITAB 2.7 and MITAB 2.6 because of the Interactor type(s) columns. As an interactor type can be any children of protein. nucleic acid and small molecule, being able to tag the interaction could avoid going back to the ontology to recognize proteins from nucleic acids and small molecules. However, with the interactor type information, we could have more filtering options (peptide-protein, gene-gene, etc.) without the need of new controlled vocabulary terms.\nthe interaction representation tags (clustered or evidence) are not really important at the interaction level because all the data providers are now providing evidence based interactions and not clustered interactions.\nthe curation coverage (full-curation or partial-curation) are tags that are interesting to add at the interaction level.\n\nHow to encode Tags ?\nIn MITAB2.7 onward it will be stored in column 28 (Interaction Annotation). The syntax for annotation columns in MITAB 2.7 is topic:text where topic is the annotation topic and text is free text. In the case of tags, only the topic will be given as described in the corresponding PSI-MI Ontology, example: evidence for the term 'evidence' (MI:1051).\nIn the PSI-MI XML 2.5 format, these tags will be stored under the interaction's attribute, example: <attribute name="evidence" nameAc="MI:1051" />\n\nM. Molecule Naming for Network Visualisation\nIn the context of network visualisation, where molecules are typically nodes and interaction edges. Nodes are usually labelled with the name of the molecule is represents. It would be helpful if data providers could indicate a chosen name for their interacting molecule. This could be enabled easily by simply adding an additional alias formatted as follow: psi-mi:label(display_short), where label is the chosen name for the molecule.\nThis topic has been discussed at the PSI-MI Spring meeting 2011 (Heidelberg) and 2012 (San Diego) and here is the consensus we have reached.\nThe group felt there was a need for two display names to be defined in order to reflect a overview (TODO: add MI CV for display short) and detailed (TODO: add MI CV for dislay long) naming of molecules. Examples of use will be given for specific molecule types below.\nThis information should be added by PSICQUIC data providers (and more generally MITAB producers) and stored under the respective aliases columns of molecule A and B (respectively 5 & 6). If not present, the Data Enricher could add this information. It has been agreed that it should be encoded as a psi-mi reference as this is the group that rubber stamped this specification.\n\nExamples:\n* `psi-mi:LSM7(display_short)`\n* `psi-mi:P12345-1_HUMAN(display_long)`\n\nThe recommendation is molecule type centric, the order column indicates the picking order depending on availability.\nProteins\n\n\n\nOrder\nValue\nLevel\nExample(s)\n\n\n\n\n1\nGene Symbol (gene name or gene synonym)\nOverview\npsi-mi:LSM7(display_short)\n\n\n2\nFirst sequence database identifier/accession\nDetailed & Overview\npsi-mi:P53905(display_long)\n\n\n3\nFirst available identifier\nDetailed & Overview\npsi-mi:EBI-1234(display_long)\n\n\n\nSmall Molecules\n\n\n\nOrder\nValue\nLevel\nExample(s)\n\n\n\n\n1\nChEBI recommended name or drug name\nOverview\npsi-mi:imatinib(display_short)\n\n\n3\nFirst available identifier\nDetailed & Overview\npsi-mi:CHEMBL340969(display_long)\n\n\n\nNucleic Acids\n\n\n\nOrder\nValue\nLevel\nExample(s)\n\n\n\n\n1\nFirst available identifier\nOverview and/or Detailed\npsi-mi:AF026397(display_long)\n\n\n\nGenes\n\n\n\nOrder\nValue\nLevel\nExample(s)\n\n\n\n\n1\nGene symbol( gene name or synonyms ) ending with 'gene'\nOverview and/or Detailed\npsi-mi:LSM7_gene(display_short)\n\n\n2\nFirst identifier\nOverview and/or Detailed\n.\n\n\n\nIt was agreed that in order to differentiate proteins (primarily described by gene symbol) from genes in a network display, we will append to the gene symbol the molecule type.\n"},"DataEnricher.html":{"url":"DataEnricher.html","title":"Data Enricher","body":"Purpose\nOne of the aim of this guideline is to provide the community with a tool that could help adding useful information to an existing MITAB 2.7 dataset (but because MITAB 2.7 is backward compatible with MITAB 2.5 and 2.6, the enricher can be used in MITAB 2.5 and 2.6 but will add less information than in MITAB 2.7). A tool, (referred later on as “Enricher”) could consume MITAB data, add extra information about molecules, controlled vocabularies, publication and return enriched MITAB content which follows the Data best practices. Below are a few data items that could be enriched automatically:\n\nmolecule identifiers, aliases, xrefs and checksum\nControlled vocabulary terms could have their names added provided an ontology identifier is present, eg:\ninteraction detection method (column #7),\ninteraction type (column #12),\nsource database (column #13);\ncomplex expansion (column #16);\nbiological roles (columns #17 and #18),\nexperimental roles (columns #19 and #20),\ninteractor types (columns #21 and #22),\nparticipant identification methods (columns #41 and #42)\n\n\npublication information such as author name (column #8) could be added provided there is a publication identifier (i.e. PMID);\norganism name (columns #10 & 11) could be added if a taxid is provided.\n\nData Enricher\nThe Enricher could use the following resources to retrieve data:\n\nOntology Lookup Service (aka. OLS) to access the psi-mi ontology;\nCiteExplore to access publication details;\nUniProtKB to access protein information, the sequence information could then be used to compute ROGID and CROGID;\nUniProt Taxonomy to access species information;\nPICR to perform computational mapping of protein identifier;\nChEBI to access small molecule information,\n\nMolecule enrichment\nThe Data enricher would use the identifiers in columns 1 and 2 (unique identifier) to collect information in PICR, UniProtKB and ChEBI. Here is a recommendation for various molecule types:\n1. Proteins\nFor higher organisms, the curator may have several isoforms of a protein to select from. In most cases, the experimental evidence will not be sufficient to make an unambiguous mapping. In such a case, most protein interaction databases will make a mapping to the canonical UniProtKB sequence e.g. P51123 to indicate that the interaction could be with some or all of the potential isoforms. Where a mapping to a specific isoform e.g. P51123-3 can be made, it will be. Gene-centric databases will map to the gene identifier in all cases. Whenever the curator has chosen a specific splice variant, its identifier should appear under the unique identifier column. Some examples of annotated proteins:\n\n\n\n\n\n\n\n\n\nensembl:ENSG00000136869\ninnatedb:IDBG-82738\n\n\nuniprotkb:O00206\nuniprotkb:TLR4_HUMAN\n\n\nrefseq:NM_138554\nrefseq:NP_612564\n\n\nrefseq:NR_024169\nrefseq:NR_024168\n\n\n\nHow to pick the canonical sequence for a given protein ?\nThe sequence defined at the top level of a UniProtKB entry is considered a canonical sequence i.e. P51123. All isoforms linked to this entries (having their own potential sequence variation) would link to this top level sequence which is the canonical sequence for the entry (note, it will be an exact match to one of the isoforms). For example: should your molecule be P51123-3, the canonical sequence would be P51123.\nShould the protein be described using a gene identifier (as seen in a minority of PSICQUIC services), it is recommended to map this identifier to the corresponding UniProt/Swiss-Prot canonical sequence, given a specific species, there should be only one corresponding UniProt/Swiss-Prot entry. If the entry is only in UniProtKB/TrEMBL, selecting the longest ORF for that gene is the conventional method for performing a 1:1 mapping.\nHow to map UniProtKB proteins to RefSeq ?\nSome proteins may have related isoforms resulting from different splice isoforms of the mRNA or from alternative promoter usage. UniProtKB does give different identifiers to these entities and it is possible to map them to RefSeq by using the PICR Identifier mapping service. In case of isoforms, PICR would be able to map it to the corresponding RefSeq identifier.\nHow would it work in practice ?\nFor proteins, the Data Enricher can:\n\nremap identifiers from any databases listed in PICR to a single UniProtKB identifier when possible. For that, it is important to give unambiguous identifiers in columns 1 and 2 and to give the organism of the protein in columns 10 and 11. The organism is very important to be able to remap to a single uniprot accession. The Data Enricher will always remap to the master uniprot entry (canonical sequence) even if an identifier can match a single uniprot splice variant identifier. When the remapping is successful, the Enricher will not delete the original identifier but just move it to 'alternative identifiers' in columns 3 and 4 and add the remapped uniprot accession in columns 1 and 2 for 'unique identifier'. In several cases, the remapping is too ambiguous and the enricher would not enrich the line but just log a warning:\nSeveral Swissprot entries can match\nSeveral Trembl entries can match and have the same sequence length (but different sequences)\nIdentifier cannot be remapped to a UniProtKb accession\n\n\nadd Refseq identifiers using PICR. The Data Enricher will add all the possible Refseq identifiers in the columns 3 and 4 'Alternatice identifiers'.\nenrich several columns :\nIn columns 5 and 6 for aliases, it will add gene name, gene synonym, protein recommended name, ORF and locus name. It will follow the Data best practices and add display_short and display_long aliases.\nIn columns 3 and 4 for alternative identifiers, it will add uniprotKb secondary accession when not ambiguous\nIn columns 23 and 24 for Interactor xrefs, it could add GO and interpro xrefs...\nIn columns 33 and 34 for Interactor checksums, it would add rogid and crogid\n\n\n\n\n\n\nProtein accession\nROGID\nCROGID\nRefSeq\n\n\n\n\nP51123\nrogid:DxUDrj8iljY131pQOBswejQxoxI7227\nrogid:DxUDrj8iljY131pQOBswejQxoxI7227\nNP_996160\n\n\nP51123-2\nrogid:nqWqHc3mUUZtYVGzCr3UZq60DRU7227\nrogid:DxUDrj8iljY131pQOBswejQxoxI7227\nNP_476956\n\n\n\n\n\n\n\nWhat information\nTarget Column\nData source\n\n\n\n\ngene name, gene name synonym, orf, locus name, recommended name, display_short and display_long\n5 & 6\nUniProtKB\n\n\nAdditional database cross references (e.g. primary database identifier such as RefSeq or UniProt), uniprot secondary AC\n3 & 4\nUniProtKB, PICR\n\n\nOrganism name (only if no conflicts with uniprot entry)\n10 & 11\nUniProt Taxonomy\n\n\nModel organism database (Flybase, TAIR, SGD...), GO, interpro,...\n23 & 24\nUniProtKB\n\n\nROGID, CROGID\n33 & 34\nUniProtKB\n\n\n\n2. Small Molecules\nShould the Standard InCHI Key not describe unambiguously a molecule, the data provider should use an other cross reference and keep the Standard InCHI Key as an alternative identifier.\nEnrichment Process\nFor small molecules, the Data Enricher can :\n\nremap identifiers from any databases cross referenced by ChEBI (some Drugbank identifiers, Pubchem, etc.) to a single ChEBI identifier when possible. For that, it is important to give unambiguous identifiers or standard Inchi keys in columns 1 and 2 and to give the organism of the small molecule in columns 10 and 11 when relevant. The organism could help to remap to a single ChEBI identifier. When giving the standard inchi key in column 1 and 2 or 3 and 4, it should be represented as 'unknown:xxxxx(standard inchi key)'. The Data Enricher will remap to manually curated compounds when it is possible. When the remapping is successful, the Enricher will not delete the original identifier but just move it to 'alternative identifiers' in columns 3 and 4 and add the remapped ChEBI accession in columns 1 and 2 for 'unique identifier'. If the original identifier is a standard inchi key, it will move it to the checksum columns 33 and 34. In several cases, the remapping is too ambiguous and the enricher would not enrich the line but just log a warning:\nSeveral compounds can match\nIdentifier cannot be found in ChEBI\n\n\nenrich several columns :\nIn columns 5 and 6 for aliases, it will add ChEBI name, standard inchi. It will follow the Data best practices and add display_short and display_long aliases.\nIn columns 3 and 4 for alternative identifiers, it will add ChEBI secondary accessions when not ambiguous\nIn columns 23 and 24 for Interactor xrefs, it could add PubChem or other xrefs (To be defined)...\nIn columns 33 and 34 for Interactor checksums, it would add standard inchi key and maybe smiles as well.\nThe enrichment process here would rely on the existence of a !ChEBI identifier in the unique identifier column. If the given identifier is unambiguously identifying a single small molecule and the taxids match, the enrichment below can take place.\n\n\n\n\n\n\nWhat information\nTarget Column\nData source\n\n\n\n\nstandard inchi, ChEBI name, display_sort and display_long\n5 & 6\nChEBI\n\n\nChEBI secondary acs and Standard InChI\n3 & 4\nChEBI\n\n\nOrganism name (only if no conflicts with ChEBI entry)\n10 & 11\nChEBI and uniprot taxonomy\n\n\nother xrefs which could be useful (to be defined)\n23 & 24\nChEBI\n\n\nstandard inchi key, smile\n33 & 34\nChEBI\n\n\n\n3. Nucleic Acids and genes\nIt was agreed during the PSI meeting 2012 that the Data Enricher will not enrich genes and nucleic acids. It will be up to the data provider to follow the data best practices and provide:\n\nunique embl/ddbj/genbank identifier for small nucleic acids in columns 1 and 2. It is recommended to move the other identifiers to alternative identifiers and Interactor xrefs.\nunique ensembl genome, ensembl or gene id/locus link identifier for genes in columns 1 and 2. It is recommended to move the other identifiers to alternative identifiers and Interactor xrefs.\ngene names should be provided for genes in aliases columns as well as display_short and display_long.\norganisms will be enriched using uniprot taxonomy but it will not check if there is a conflict with the identifiers\n\nOrganism enrichment\nTo be able to enrich the organism, it is important to give the taxid of the organism represented as 'taxid:taxon(text)'.\nIn case of proteins and small molecules, the organism enrichment will depend on the consistency between organism and the molecule identifiers.\nEnrichment Process\nFor organisms (interactor organisms in columns 10 and 11 and host organism in column 29), the Data Enricher can:\n\nadd the missing organism for proteins and small molecules (and genes as well?) when possible (columns 10 and 11 only)\nadd the common name and scientific name as defined in the data best practices (columns 10, 11 and 29)\n\nPublication enrichment\nTo be able to enrich the publication, a pubmed id (or IMEx id) is necessary in column 9 (identifier of the publication).\nEnrichment Process\nFor publications, the Data Enricher can:\n\nFor each pubmed id, it will add the first author name and publication date as defined in the data best practices\n\nControlled vocabulary enrichment\nThe Data Enricher will only enrich psi-mi ontology terms in columns 7, 13, 12, 16, 17, 18, 19, 20, 21, 22, 41 and 42 (cross references to psi-mi terms should be represented with 'psi-mi:"MI:xxxx"(term name)').\nThe Enricher will only add the term name in parenthesis if it is missing or not exact.\nFor other ontology terms such as GO that could be present in columns 23,24 and 25 (interactor and interaction xrefs), the enricher could also add the name in parenthesis.\n"},"Faq.html":{"url":"Faq.html","title":"FAQ","body":"\nAre there guidelines on how to create valid PSIMITAB ?\nThe original format (version 2.5) itself was first described in Kerrien et al. (2007) but you can also find it as part of the PSI-MI and PSICQUIC documentation. These documents only describe the various columns of the PSIMITAB format (2.5, 2.6, 2.7 and 2.8) and the syntax of the data that can be stored. In addition to the format, the PSI-MI workgroup has defined a guideline referred to as Data Distribution Best Practices that aims at standardising the use of the format to maximize its effectiveness. It is strongly recommended to read these documents before attempting to build a dataset using the PSIMITAB 2.5, PSIMITAB 2.6, PSIMITAB 2.7 or PSIMITAB 2.8 format.\n\nWhat identifier should I use to describe my Interacting Proteins ?\nMost PSICQUIC providers are using UniProtKB ACs to describe their proteins, and this allows these services to be easily combined together. For more information, look at the Data Distribution Best Practices.\n\nHow can I map my identifiers to UniProtKB AC ?\nIf you happen to be using another identifier space to describe your proteins, there are several tools you could be using to map to UniProtKB:\n\nPICR\nUniProt Mapping\n\n\nWhy are my ChEBI identifiers not linked properly in PSICQUIC View\nIf you are using ChEBI, or any database identifier using reserved character such as column (':') you will have to escape them as follow: CHEBI:"CHEBI:114264".\nHow can I easily browse the various ontology types of PSI-MI ?\nWe recommend you use the Ontology Lookup Service (OLS). You can browse the PSI-MI ontology as a simple tree structure here or perform the following searches from the OLS home page:\nsearch by term name (with auto-completion),\nsearch by term id.\n\nCan I cluster multiple interaction evidences into a single MITAB line ?\nYes you can, but we do not recommend you doing it if you are intending to distribute the data using PSICQUIC. While PSICQUIC isn’t affected by clustered data, it doesn’t allow users to effectively query the service.\nLet’s describe the issue using an example, say you have 2 MITAB lines:\n P12345 Q98765 - - - - two hybrid …\n P12345 Q98765 - - - - coip …\nNow let’s consider the clustered equivalent of these 2 lines:\n P12345 Q98765 - - - - two hybrid|coip …\nSo now if a user queries the non-clustered service with the following MIQL:\nNOT detmethod:coip\nthe response contains a single line (i.e. the two hybrid evidence).\nWhen the user runs the same query on the clustered service, the response shows no data because the whole line has been removed as it contains a coip evidence, leading the user to miss potentially critical information.\n\nHow do I define confidence values ?\nColumn 15 of MITAB was designed to accommodate this type of data. There are numerous methods in used and in most cases, data providers tend to design their own. For this reason, we have defined a set of controlled vocabulary terms to help categorising broad classes of scoring methods. You can view the current list on the Ontology Lookup Service.\n\nHow much additional information (i.e. alternative identifiers, aliases) should I add about my interacting molecules ?\nWhile providing a UniProtKB AC is a great start to providing a broadly accepted referencing system for your proteins, many users are searching PSICQUIC services using gene names. For this reason, columns 5 and 6 will allow the storage of aliases for, respectively, molecule A and B. It is strongly encouraged to stored in these columns information such as:\n\ngene name (e.g. uniprotkb:BRCA2(gene name))\norf name (e.g.uniprotkb:F14J9.23(orf name))\nlocus name (e.g. uniprotkb:At1g09570(locus name))\ngene name synonym (e.g. uniprotkb:Protein ELONGATED HYPOCOTYL 8(gene name synonym))\nThe data type that can be used are defined in this branch of the PSI-MI ontology.\n\n\nHow should I use the Unique Identifier/Alternative Identifier columns ?\nThese columns have different purposes, all of which are geared toward identifying the interacting molecule unambiguously. While the unique identifier is meant as a single cross reference to a public database, the alternative identifier column should be used to maintain a collection of alternative identifiers potentially encompassing secondary identifiers (e.g. UniProtKB), model organism databases (SGD, FlyBase...), translation to other biological concept (e.g. the molecule descibed is a protein but I could store an ensembl or entrez geneid). The Data Distribution Best Practices does give some additional information with respect to which specific cross reference to use.\n"},"WhoUsesPsicquic.html":{"url":"WhoUsesPsicquic.html","title":"Who uses PSICQUIC?","body":"Who uses PSICQUIC?\nThis is the list of some of the projects that use PSICQUIC to query molecular interaction data. There are more, but these are the ones known to us as of July 2011. If you are using PSICQUIC, please let us know and we will add you to this list.\n\nBio::Homology::InterologWalk: a Perl module to build putative protein-protein interaction networks through interolog mapping. [Publication]\n\nCytoscape: can create interation networks using a PSICQUIC plugin.\n\nEnVision 2: a visualization application for the Enfin project.\n\nIMEx Consortium: the data search in the consortium page is based on PSICQUIC to query all the IMEx members on-the-fly. [Link] [Publication]\n\nIntAct: the user is presented with counts and links to other PSICQUIC services when executing a query. [Link] [Publication]\n\nReactome: it exploits the PSICQUIC web services to overlay molecular interaction data in the Pathway Browser [Link] [Publication]\n\nTaverna: PSICQUIC workflows in Taverna. [Link]\n\n\n"},"PreparingARelease.html":{"url":"PreparingARelease.html","title":"How to release the project","body":"Introduction\nThe PSICQUIC Reference Implementation will be released from time to time. This page contains the instructions to do it.\nReleasing the Reference Implementation\nWhen everyone is happy about releasing a new version of the Reference Implementation, this must be done:\n\nChange the version in the POM file and commit the change.\nTag the project, running this command in the psicquic-solr-ws folder.\n\nmvn scm:tag -Dtag=psicquic-solr-ws-1.3.15\n\nCreate an assembly with the sources and upload the tar.gz bundle to the project, so it will be available as a download.\n\nmvn clean assembly:assembly -DdescriptorId=src\n\nUpdate the version of the project to the next SNAPSHOT version and commit.\n\n"}}}