Issue 5929: Features should be able to know what their Reporter is (gene-expression-ftf) Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody) Nature: Uncategorized Issue Severity: Summary: Features should be able to know what their Reporter is. The model currently has no way to navigate from a Feature to its Reporter Discussion: Raise by Michael Dondrup 10/2/02 "Given a particular Feature (eg. by selecting a spot on a image of an array), try to retrieve data for the BioSequence via its Reporter. I would suggest a direct association from Feature to Reporter. Or is this only adding redundancy to the model?' Reply from Paul Spellman 10/4/02 "there is a very good reason for this association not to exist. Features are immutable and confined to a single array, Reporters are flexible and can be present on multiple arrays. Requiring Features to know which Reporters they are in could in some cases be a logistical nightmare. This is best solved using a database query rather than the model." Resolution: Reject the change. Revised Text: Actions taken: May 2, 2003: received issue November 6, 2003: closed issue Discussion: Raise by Michael Dondrup 10/2/02: Features should be able to know what their Reporter is. The model currently has no way to navigate from a Feature to its Reporter. Applications are free to add (or not) explicit relationships outside the model. The model, as is, provides sufficient support for queries between Features and Reporters 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 3: Features should be able to know what their Reporter is. The model currently has no way to navigate from a Feature to its Reporter Discussion: Raise by Michael Dondrup 10/2/02 "Given a particular Feature (eg. by selecting a spot on a image of an array), try to retrieve data for the BioSequence via its Reporter. I would suggest a direct association from Feature to Reporter. Or is this only adding redundancy to the model?' Reply from Paul Spellman 10/4/02 "there is a very good reason for this association not to exist. Features are immutable and confined to a single array, Reporters are flexible and can be present on multiple arrays. Requiring Features to know which Reporters they are in could in some cases be a logistical nightmare. This is best solved using a database query rather than the model."