Issue 5931: BibliographicReference (gene-expression-ftf) Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody) Nature: Uncategorized Issue Severity: Summary: BibliographicReference needs to be able to point to multiple database entries. An association will be added between BibliographicReference and DatabaseEntry which will be named 'Accessions' with the end role name of 'accessions' on the DatabaseEntry end. It will be navigable from BibliographicReference to DatabaseEntry and its aggregation will be of type composite. The cardinality of the BibliographicReference end will be 1..1 and the cardinality of the DatabaseEntry end will be 0..n Resolution: see below Revised Text: Changes to the Specification: Section 2.1.4, BQS Add to the BibliographicReference Association documentation: "\baccessions\b : DatabaseEntry (0..n) References in publications, eg Medline and PubMed, for this BibliographicReference. " Replace Figure 2-4 MAGE-OM and the generated MAGE.xmi are updated, adding the association from BibliographicReference to OntologyEntry . MAGE-ML.dtd Modify Element declaration for BibliographicReference Add: "accessions: References in publications, eg Medline and PubMed, for this BibliographicReference. " Currently: " <!ELEMENT BibliographicReference ((%Describable_content;), Parameters_assnlist) > " Becomes: " <!ELEMENT BibliographicReference ((%Describable_content;), Parameters_assnlist, Accessions_assnlist?) > " Add to association declarations for OntologyEntry “ <!ELEMENT Accessions_assnlist (DatabaseEntry+) >” Actions taken: May 2, 2003: received issue November 6, 2003: closed issue Discussion: Raised by Helen Parkinson 3/18/03: BibliographicReference needs to be able to point to multiple database entries. We have come across a problem adding id's for papers to eg Medline and PubMed. Accession is not an attribute of Bibliographic reference and it's hard to explicitly link to an accession if the uri has already been used for the journal. Add an optional association from BibliographicReference to OntologyEntry. The association should be 0..n and named Accession. End of Annotations:===== X-Server-Uuid: F7D3E4A3-3C15-41D2-AC5D-A7D3F094E28F From: "Miller, Michael (Rosetta)" To: "'mged mage'" , "'gene-expression-ftf@omg.org'" Subject: RTF Issues Date: Thu, 1 May 2003 12:45:16 -0700 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 12AFA98819003-01-01 All, Finally getting this list of proposed changes out. Many thanks to Ugis for reminding me and helping to bring these out. We are under a bit of a tight deadline due to the lateness of my putting these together, the RTF report is due at the OMG on May 12th. It is exactly the same process as the FTF report was, so I would like to gather thoughts and additional discussions on these issues and any other that people think fall into the scope of MAGE v1.1. Remember, v2.0 is where the major changes will take place, these items are mainly changes to associations to make them more usable and the doc/specifications changes made at the Stanford Programming Jamboree. I will be then mailing out a vote to the OMG Gene Expression Revised Task Force whose members are: Steve Chervitz, Affymetrix; Charles Troup, Agilent Technologies; Ugis Sarkans, European Bioinformatics Institute; Michael Niemi, International Business Machines; Tony Parsons, Pfizer; Michael D Miller, Rosetta Biosoftware Business Unit Michael Michael Miller Senior Application Developer Rosetta Biosoftware michael_miller@rosettabio.com www.rosettabio.com These will change the DTD but looking at it from a developer point of view I don't anticipate much problem being able to cope with either v1.0 or 1.1. Currently I've specifying the doctype as: and will use for documents with the revised changes. I've also been successful at going to the OMG site go fetch the DTD at when receiving the SAX resolveEntity() callback (though it is always good to have a backup location): http://schema.omg.org/lsr/gene_expression/1.0/MAGE-ML.dtd If any changes are accepted, there will then be posted a http://schema.omg.org/lsr/gene_expression/1.1/MAGE-ML.dtd List of Issues for the Gene Expression Revision Task Force (MAGE v1.1) (The numbering is tentative, the OMG will assign their numbers when they are submitted) Michael Miller 05/01/2003 RTF ISSUE 5: BibliographicReference needs to be able to point to multiple database entries. An association will be added between BibliographicReference and DatabaseEntry which will be named 'Accessions' with the end role name of 'accessions' on the DatabaseEntry end. It will be navigable from BibliographicReference to DatabaseEntry and its aggregation will be of type composite. The cardinality of the BibliographicReference end will be 1..1 and the cardinality of the DatabaseEntry end will be 0..n Discussion: Raised by Helen Parkinson 3/18/03 "we have come across a problem adding id's for papers to eg Medline and PubMed. Accession is not an attribute of Bibliographic reference and it's hard to explicitly link to an accession if the uri has already been used for the journal. We have been providing medline and pubmed id's via the DatabaseEntry_assn to OntologyEntry, but this is actually a subversion of the intended use, as DatabaseEntry should refer to the Ontologyentry and not the accession of the BibliographicReference in an external DB (example below). Ugis and I discussed a few solutions: 1. add an attribute accession and database to Bibiliographic reference 2. Code two ontology entries for each BQS, one that is used correctly to specificy the type of BQS , and create a second, where the value is the id of the medline record and the DatabaseEntry is the same id of the medline record. 3. Create each 1 Description per BibliographicRef and use the DatabaseReferences_assn from Decription to DatabaseEntry to code the Medline information." Michael Miller replied 3/18/03: "That seems reasonable to me also to do 1) as an optional association. Basically it means that bibliographic references can be identified by more than one source. It seems the association should be 0..n and named Accession?"