Gene Expression Avatar
  1. OMG Specification

Gene Expression — Closed Issues

  • Acronym: GENE
  • Issues Count: 7
  • Description: Issues resolved by a task force and approved by Board
Closed All
Issues resolved by a task force and approved by Board

Issues Descriptions

BibliographicReference

  • Key: GENE11-5
  • Legacy Issue Number: 5931
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • 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

  • Reported: GENE 1.0 — Fri, 2 May 2003 04:00 GMT
  • Disposition: Resolved — GENE 1.1
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Type association between BioSample and OntologyEntry

  • Key: GENE11-7
  • Legacy Issue Number: 5933
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • 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.

  • Reported: GENE 1.0 — Fri, 2 May 2003 04:00 GMT
  • Disposition: Resolved — GENE 1.1
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

rule in the ExperimentDesign package

  • Key: GENE11-4
  • Legacy Issue Number: 5930
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    The rule in the ExperimentDesign package that only allows a single
    FactorValue per TopLevelBioAssay hinders proper description of
    multi-channel experiments and should be dropped

    Discussion:
    Raised by Angel Pizarro 3/4/03

    "During the MGED Ontology workshop, we came across a situation that does
    not allow you to describe certain ExperimentDesigns. For instance in a
    loop design, you compare conditions A,B,C as follows:
    A -> B
    B -> C

    If A,B & C represent different values of the same ExperimentalFactor, how
    do you encode that a single top-level BioAssay is A -> B? Remember that
    there is a Rule in the ExperimentDesign package that states that each
    TopLevelBioAssay can only have a single FactorValue per
    ExperimentalFactor."

  • Reported: GENE 1.0 — Fri, 2 May 2003 04:00 GMT
  • Disposition: Resolved — GENE 1.1
  • Disposition Summary:

    Reject the Change

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Clarify and expand the documentation for the MAGE-OM model

  • Key: GENE11-1
  • Legacy Issue Number: 5927
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Discussion:
    A draft was created by Cathy Ball and her group that is included
    as a separate document

    Issues:
    The changes were done on a previous version of the standard and
    need to be merged to the available standard

    The changes need to be backed merged into the UML model to keep
    the documentation in synch in the generated DTD and code.

  • Reported: GENE 1.0 — Fri, 2 May 2003 04:00 GMT
  • Disposition: Resolved — GENE 1.1
  • Disposition Summary:

    no action taken

  • Updated: Fri, 6 Mar 2015 20:58 GMT

Features should be able to know what their Reporter is

  • Key: GENE11-3
  • Legacy Issue Number: 5929
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • 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."

  • Reported: GENE 1.0 — Fri, 2 May 2003 04:00 GMT
  • Disposition: Resolved — GENE 1.1
  • Disposition Summary:

    Reject the change.

  • Updated: Fri, 6 Mar 2015 20:58 GMT

association ExperimentDesign

  • Key: GENE11-2
  • Legacy Issue Number: 5928
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    The association ExperimentDesign should be
    Experiment(1..1)-->ExperimentDesign(1..n)

    instead of

    Experiment(1..1)-->ExperimentDesign(1..1)

    and the association name and end role should become 'ExperimentDesigns'
    and 'experimentDesigns'

    Discussion:
    Raised by Angel Pizarro 9/9/02 and requested by the Ontology Group

  • Reported: GENE 1.0 — Fri, 2 May 2003 04:00 GMT
  • Disposition: Resolved — GENE 1.1
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT

MerckIndex association between Compound and OntologyEntry

  • Key: GENE11-6
  • Legacy Issue Number: 5932
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • 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

  • Reported: GENE 1.0 — Fri, 2 May 2003 04:00 GMT
  • Disposition: Resolved — GENE 1.1
  • Disposition Summary:

    see below

  • Updated: Fri, 6 Mar 2015 20:58 GMT