Issue 5932: MerckIndex association between Compound and OntologyEntry (gene-expression-ftf) Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody) Nature: Uncategorized Issue Severity: Summary: The MerckIndex association between Compound and OntologyEntry is too specific. The association should become more general and allow more than one kind of Index. The name of the association and end role will change to 'CompoundIndices' and 'compoundIndices' and the OntologyEntry end will change its cardinality to 0..n Resolution: see below Revised Text: Changes to the Specification: Section 2.1.10, BioMaterial Change to the Compound Association documentation: Currently: " \bmerckIndex\b : OntologyEntry (0..1) The Merck Index of this Compound. " Becomes: " \bcompoundIndices\b : OntologyEntry (0..n) Indices into common Compound Indices, such as the Merck Index, for this Compound. " Replace Figure 2-11 MAGE-OM and the generated MAGE.xmi are updated, modifying the association to OntologyEntry from Compound. MAGE-ML.dtd Modify Element declarations for Compund Currently: " merckIndex: The Merck Index of this Compound. " Becomes: " compoundIndices: Indices into common Compound Indices, such as the Merck Index, for this Compound. " Currently: " <!ELEMENT Compound ((%Identifiable_content;), MerckIndex_assn?, ComponentCompounds_assnlist?, ExternalLIMS_assn?) > " Becomes: " <!ELEMENT Compound ((%Identifiable_content;), CompoundIndices_assnlist?, ComponentCompounds_assnlist?, ExternalLIMS_assn?) > " Currently for OntologyEntry declarations: " <!ELEMENT MerckIndex_assn (OntologyEntry) > " Becomes: " <!ELEMENT CompoundIndices_assnlist (OntologyEntry+) > " Actions taken: May 2, 2003: received issue November 6, 2003: closed issue Discussion: The MerckIndex association between Compound and OntologyEntry is too specific. The association should become more general and allow more than one kind of Index. The name of the association and end role will change to 'CompoundIndices' and 'compoundIndices' and the OntologyEntry end will change its cardinality to 0..n Issue was raised for the FTF on the mailing list but was overlooked. 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 6: The MerckIndex association between Compound and OntologyEntry is too specific. The association should become more general and allow more than one kind of Index. The name of the association and end role will change to 'CompoundIndices' and 'compoundIndices' and the OntologyEntry end will change its cardinality to 0..n Discussion: Issue was raised for the FTF on the mailing list but was overlooked.