Issue 5933: Type association between BioSample and OntologyEntry (gene-expression-ftf) Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody) Nature: Uncategorized Issue Severity: Summary: The Type association between BioSample and OntologyEntry needs to be optional. The cardinality of the OntologyEntry end will change from 1..1 to 0..1. Resolution: see below Revised Text: Changes to the Specification: Section 2.1.10, BioMaterial Modify the BioSample documentation: Currently: " \btype\b : OntologyEntry (1..1) " Becomes: " \btype\b : OntologyEntry (0..1) " Replace Figure 2-11 MAGE-OM and the generated MAGE.xmi are updated, adding the association from OntologyEntry to itself. MAGE-ML.dtd Modify Element declaration for BioSample Currently: " <!ELEMENT BioSample ((%BioMaterial_content;), Type_assn) > " Becomes: " <!ELEMENT BioSample ((%BioMaterial_content;), Type_assn?) > " Actions taken: May 2, 2003: received issue November 6, 2003: closed issue Discussion: Requested by the Ontology group 1/15/03: The Type association between BioSample and OntologyEntry needs to be optional. The cardinality of the OntologyEntry end will change from 1..1 to 0..1. 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 7: The Type association between BioSample and OntologyEntry needs to be optional. The cardinality of the OntologyEntry end will change from 1..1 to 0..1. Discussion: Requested by the Ontology group 1/15/03