Gene Expression Avatar
  1. OMG Specification

Gene Expression — Closed Issues

  • Acronym: GENE
  • Issues Count: 26
  • Description: Issues resolved by a task force and approved by Board
Closed All
Issues resolved by a task force and approved by Board

Issues Summary

Key Issue Reported Fixed Disposition Status
GENE-26 group BioSequences that share the same type, PolymerType, and Species infor GENE 1.0b1 GENE 1.0 Resolved closed
GENE-25 For interoperability, need a rule for formatting numbers GENE 1.0b1 GENE 1.0 Resolved closed
GENE-24 Attribute to be added to describe its type GENE 1.0b1 GENE 1.0 Resolved closed
GENE-23 Database role to be associated with person/organization GENE 1.0b1 GENE 1.0 Resolved closed
GENE-22 Instances of OntologyEntries need a way to be further qualified GENE 1.0b1 GENE 1.0 Resolved closed
GENE-21 Specifying a FactorValue needs to be more flexible GENE 1.0b1 GENE 1.0 Resolved closed
GENE-20 ExperimentFactor needs an OntologyEntry association GENE 1.0b1 GENE 1.0 Resolved closed
GENE-19 Need a way to model features that are associated with a BioMaterial GENE 1.0b1 GENE 1.0 Resolved closed
GENE-18 It should be possible to assign default values to parameters GENE 1.0b1 GENE 1.0 Resolved closed
GENE-17 association from FeatureExtraction to QuantitationTypeMapping needed GENE 1.0b1 GENE 1.0 Resolved closed
GENE-16 QuantitationType issue GENE 1.0b1 GENE 1.0 Resolved closed
GENE-15 Allowing a person to belong to only one organization is too restrictive. GENE 1.0b1 GENE 1.0 Resolved closed
GENE-14 Make association from DerivedBioAssay to BioAssayMap navigable both ways GENE 1.0b1 GENE 1.0 Resolved closed
GENE-13 Recommend adding optional association from Compound to DatabaseEntry GENE 1.0b1 GENE 1.0 Resolved closed
GENE-12 Recommend changing cardinality of BioSource:sourceContacts GENE 1.0b1 GENE 1.0 Resolved closed
GENE-11 Recommend adding StandardQuantitationType, 'Failed' of type boolean GENE 1.0b1 GENE 1.0 Resolved closed
GENE-10 Attribute to be added to Description called URI of type string and optional GENE 1.0b1 GENE 1.0 Resolved closed
GENE-9 Recommend that FeatureLocation derive from Extendable GENE 1.0b1 GENE 1.0 Resolved closed
GENE-8 Change owner association from Security to Contact from 1..1 to 0..n GENE 1.0b1 GENE 1.0 Resolved closed
GENE-7 abstract base classes should be removed from ref entity declarations in DTD GENE 1.0b1 GENE 1.0 Resolved closed
GENE-6 Parent association from Organization to itself is marked GENE 1.0b1 GENE 1.0 Resolved closed
GENE-5 Change in the DesignElement package GENE 1.0b1 GENE 1.0 Resolved closed
GENE-4 Changing name of Association from "featureShape" to "FeatureShape" GENE 1.0b1 GENE 1.0 Resolved closed
GENE-3 dimension elements be transformed to be optional GENE 1.0b1 GENE 1.0 Resolved closed
GENE-2 order attribute be be added for BioDataCube in model (and, hence, the DTD) GENE 1.0b1 GENE 1.0 Resolved closed
GENE-1 transformed DTD should keep dimensions in content list of the BioAssayData GENE 1.0b1 GENE 1.0 Resolved closed

Issues Descriptions

group BioSequences that share the same type, PolymerType, and Species infor

  • Key: GENE-26
  • Legacy Issue Number: 5561
  • Status: closed  
  • Source: Affymetrix, Inc. ( Steve Chervitz)
  • Summary:

    It would be useful to have a way to group BioSequences that share the same
    Type, PolymerType, and Species information.

    Request from Steve Chervitz, Affymetrix, that the model be modified in
    some way to make it possible to group together sequences that shared these
    common characteristics.

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    No Data Available

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

For interoperability, need a rule for formatting numbers

  • Key: GENE-25
  • Legacy Issue Number: 5560
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Request from Michael Miller, Rosetta Biosoftware, for clarification
    on how numbers should be formatted:

    • integer values are just digits
    • floating point numbers use a '.' (period), with an optional leading
      zero and an optional leading +/- sign:
    • -0.912
    • scientific notation: optional leading zero, optional leading +/-
      sign on the exponent and mantissa:
    • -2.34E-12
  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    reject the change but then see below

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

Attribute to be added to describe its type

  • Key: GENE-24
  • Legacy Issue Number: 5559
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Request from Hilmar Lapp, GNF, and Michael Miller, Rosetta Biosoftware,
    that an attribute be added to Parameter to describe its type:

    • name: type
    • required: true
    • enumeration: {IN, INOUT, OUT}
    • default: IN

    This would allow Protocol/ProtocolApplication to allow return values.

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    No Action Taken.

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

Database role to be associated with person/organization

  • Key: GENE-23
  • Legacy Issue Number: 5558
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Request from Catherine Ball, from Stanford University, that a database
    role be associated with person/organization. These roles will describe
    the types of privileges a person has with the data, not the type of
    occupation the person has. (see also MAGE ISSUE 103)

    (MAGE ISSUE 121)

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    reject the change

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

Instances of OntologyEntries need a way to be further qualified

  • Key: GENE-22
  • Legacy Issue Number: 5557
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Some ontologies, such as GeneOntology, don't have this concept but others,
    such as MGED's, do.

    Request from a number of sources to modify the model:

    • add a new class named "Slot" to the Description package with the
      following:
    • attribute: "name" of type String, required
    • parent base class: Extendable
    • association to Measurement named "Measurement"
      Slot end:
    • aggregates Measurement end
    • cardinality: 1..1
      Measurement End:
    • name: "measurement"
    • cardinality: 0..1
    • navigable
    • association to OntologyEntry named "SlotValue"
      Slot end:
    • aggregates OntologyEntry end
    • cardinality: 1..1
      OntologyEntry end:
    • name: slotValue
    • cardinality: 0..1
    • navigable
    • add rule that Slot has either measurement or ontologyEntry, exclusive
    • OntologyEntry has association to Slot named "Slots"
      OntologyEntry end:
    • aggregates Slot end
    • cardinality: 1..1
      Slot end:
    • name: slots
    • cardinality: 0..N
    • navigable

    An simpler alternative would be an association from OntologyEntry to
    itself named "Associations":
    1st OntologyEntry end:

    • aggregates 2nd OntologyEntry end
    • cardinality: 1..1
      2nd OntologyEntry end:
    • name: associations
    • cardinality: 0..N
    • navigable

    (MAGE ISSUE 7)

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Specifying a FactorValue needs to be more flexible

  • Key: GENE-21
  • Legacy Issue Number: 5556
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Request, made at MGED IV, to modify the model:

    • add association from FactorValue to OntologyEntry named "Value"
      FactorValue end:
    • aggregates OntologyEntry end
    • cardinality: 1..1
      OntologyEntry end:
    • name: value
    • cardinality: 0..1
    • navigable
    • make cardinality of association from FactorValue to Measurement
      become 0..1
    • add a rule that FactorValue has either a Measurement or a
      OntologyEntry
      (exclusive)
  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

ExperimentFactor needs an OntologyEntry association

  • Key: GENE-20
  • Legacy Issue Number: 5555
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    ExperimentFactor needs an OntologyEntry association for describing
    additional information.

    Request, made at MGED IV, that ExperimentFactor have an association
    to OntologyEntry to capture things like concentration of Tamoxafin
    with a CASRegistry #.

    (MAGE ISSUE 116)

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Need a way to model features that are associated with a BioMaterial

  • Key: GENE-19
  • Legacy Issue Number: 5554
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Need a way to model features that are associated with a BioMaterial
    rather than a BioSequence

    Request from several sources that there be a way to specify that
    a Feature is associated with something other than Biosequences,
    such as solutions, Cy5, etc., when that decision is made at the
    ArrayDesign stage.

    (MAGE ISSUE 114)

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    no action taken

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

It should be possible to assign default values to parameters

  • Key: GENE-18
  • Legacy Issue Number: 5553
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    It should be possible to assign default values to parameters

    Request from Hilmar Lapp, GNF, that default values can be associated with
    a Parameterizable's Parameters. This could be done by replacing the
    current Unit association to an association called "DefaultValue" to
    Measurement. The Parameterizable end would aggregate the Measurement
    end and have a cardinality of 1. The Measurement end would have a
    cardinality of 0..1 and be named "defaultValue".

    (MAGE ISSUE 113)

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

association from FeatureExtraction to QuantitationTypeMapping needed

  • Key: GENE-17
  • Legacy Issue Number: 5552
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Currently, if software, for instance, calculates a Ratio
    from two channel images, there is no direct way to record how it was
    derived, other than burying it in the protocol.

    Request from Michael Miller, Rosetta Biosoftware, that there be an
    association from FeatureExtraction to QuantitationTypeMapping.
    The association would have the same names and characteristics as
    the Transformation to QuantitationTypeMapping Mapping association
    with a constraint of "rank: 3" on the QuantitationTypeMapping end.
    This association would allow a natural way to describe additional
    work of FeatureExtraction beyond reading the image.

    (MAGE ISSUE 109)

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    no action taken

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

QuantitationType issue

  • Key: GENE-16
  • Legacy Issue Number: 5551
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Allowing a QuantitationType to know how it was derived
    would make navigation easier.

    Request from Ugis Sarkans, EBI, that the Target association be
    navigable from QuantitationType to QuantitationTypeMap. The
    association end would be named quantitationTypeMaps.

    (MAGE ISSUE 108)

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Allowing a person to belong to only one organization is too restrictive.

  • Key: GENE-15
  • Legacy Issue Number: 5550
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Allowing a person to belong to only one organization is too restrictive.

    Request from John Yost, NCI, that the affiliation association between
    Person and Organization be changed so that the Organization end is
    changed from 0..1 to 0..n.

  • Reported: GENE 1.0b1 — Mon, 29 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    No action taken

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

Make association from DerivedBioAssay to BioAssayMap navigable both ways

  • Key: GENE-14
  • Legacy Issue Number: 5535
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend making association from DerivedBioAssay to BioAssayMap
    navigable both ways. It currently is only navigable from BioAssayMap
    to DerivedBioAssay. This will make it easier to find what BioAssays
    were used to producea BioAssay. The association end should be named
    derivedBioAssayMap

    Resolution of the issue would change:
    MAGE-OM and the generated MAGE.xmi
    MAGE-ML.dtd
    3.1.12, "BioAssayData" of the documentation

  • Reported: GENE 1.0b1 — Sat, 20 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Recommend adding optional association from Compound to DatabaseEntry

  • Key: GENE-13
  • Legacy Issue Number: 5534
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend adding optional association from Compound to DatabaseEntry
    called 'ExternalLIMS' to reference an external LIMS system entry.

    Resolution of the issue would change:
    MAGE-OM and the generated MAGE.xmi
    MAGE-ML.dtd
    3.1.10, "BioMaterial" of the documentation

  • Reported: GENE 1.0b1 — Sat, 20 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Recommend changing cardinality of BioSource:sourceContacts

  • Key: GENE-12
  • Legacy Issue Number: 5533
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend changing cardinality of BioSource:sourceContacts from
    0..1 to 0..N to allow multiple contacts for a BioSource.

    Resolution of the issue would change:
    MAGE-OM and the generated MAGE.xmi
    MAGE-ML.dtd
    3.1.10, "BioMaterial" of the documentation

  • Reported: GENE 1.0b1 — Wed, 24 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Recommend adding StandardQuantitationType, 'Failed' of type boolean

  • Key: GENE-11
  • Legacy Issue Number: 5532
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend adding StandardQuantitationType, 'Failed' of type boolean,
    to represent overall failure

    Resolution of the issue would change:
    MAGE-OM and the generated MAGE.xmi
    MAGE-ML.dtd
    3.1.17, "QuantitationType" of the documentation

  • Reported: GENE 1.0b1 — Sat, 20 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Attribute to be added to Description called URI of type string and optional

  • Key: GENE-10
  • Legacy Issue Number: 5531
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend that an atribute be added to Description called URI of
    type string and optional. This will allow a description to reference
    an external MIME type

    Resolution of the issue would change:
    MAGE-OM and the generated MAGE.xmi
    MAGE-ML.dtd
    Section 3.1.3, "Description" of the documentation

  • Reported: GENE 1.0b1 — Sat, 20 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Recommend that FeatureLocation derive from Extendable

  • Key: GENE-9
  • Legacy Issue Number: 5530
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend that FeatureLocation derive from Extendable. It was an
    oversight that this was not done in the first palce

    Resolution of the issue would change:
    MAGE-OM and the generated MAGE.xmi
    MAGE-ML.dtd
    Section 3.1.7, "DesignElement" of the documentation

  • Reported: GENE 1.0b1 — Sat, 20 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Change owner association from Security to Contact from 1..1 to 0..n

  • Key: GENE-8
  • Legacy Issue Number: 5529
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend that the owner association from Security to Contact be
    changed from 1..1 to be 0..n. It was brought up that there may be many
    contacts with permission to change Security and, separately, that
    there may be no ownership concept.

    Resolution of the issue would change:
    MAGE-OM and the generated MAGE.xmi
    MAGE-ML.dtd
    Section 3.1.3, "Description" of the documentation

  • Reported: GENE 1.0b1 — Sat, 20 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

abstract base classes should be removed from ref entity declarations in DTD

  • Key: GENE-7
  • Legacy Issue Number: 5528
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    The DTD currently is generated with the rule that the *_ref entity
    includes abstract class refs. Since these can't be instantiated,
    implementations break when trying to figure out which class
    to map to. This is because the identifier concept allows using
    the identifier to be an alternative key in the case that the
    identifier isn't immediately resolvable. But without knowing the
    actually base class, this won't work. This is a particular
    problem for use in disconnected inhouse high through-put pipelines.

    Recommend that the abstract base classes be removed from the ref
    entity declarations in the DTD.

    Resolution of the issue would change:
    MAGE-ML.dtd
    (through a change to WriteDTDClassElement)
    Section 4.1.2, "Mapping from MAGE-OM to MAGE-ML"

  • Reported: GENE 1.0b1 — Sat, 20 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Parent association from Organization to itself is marked

  • Key: GENE-6
  • Legacy Issue Number: 5491
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    The Parent association from Organization to itself is wrongly marked as
    composite
    on the unnamed end. Recommend, in AuditAndSecurity Package, that the Parent
    Association be
    modified by changing the unnamed end (representing child organization) to be
    a non-composite
    aggregation and to change its cardinality from unknown to 0..n. Otherwise,
    because of the
    constraint in the dtd, the Parent is owned by the Child and can, wrongly,
    only belong to one
    Child.

    Requires modification of the following files:
    MAGE-ML.dtd
    The Model and the generated MAGE.xmi file
    <Foundation.Core.AssociationEnd.aggregation xmi.value = "composite"/>
    to
    <Foundation.Core.AssociationEnd.aggregation xmi.value = "none"/>

  • Reported: GENE 1.0b1 — Sun, 14 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Change in the DesignElement package

  • Key: GENE-5
  • Legacy Issue Number: 5490
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend to change, in the DesignElement package, the cardinality of the
    Position end
    of the DistanceUnit association between Position and DistanceUnit from 0..n
    to 1..1 since
    0..n and COMPOSITE are inconsistent with each other for an end role.
    (that is, since the DistanceUnit is a composite aggregation it must belong
    to one and
    only one Position)

    Only effects the Model and the generated MAGE.xmi file:
    <Foundation.Data_Types.MultiplicityRange.lower>0</Foundation.Data_Types.Mult
    iplicityRange.lower>
    <Foundation.Data_Types.MultiplicityRange.upper>-1</Foundation.Data_Types.Mul
    tiplicityRange.upper>
    to
    <Foundation.Data_Types.MultiplicityRange.lower>1</Foundation.Data_Types.Mult
    iplicityRange.lower>
    <Foundation.Data_Types.MultiplicityRange.upper>1</Foundation.Data_Types.Mult
    iplicityRange.upper>

  • Reported: GENE 1.0b1 — Sun, 14 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

Changing name of Association from "featureShape" to "FeatureShape"

  • Key: GENE-4
  • Legacy Issue Number: 5489
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend changing name of Association from "featureShape" to "FeatureShape"
    to be consistent
    with naming convention of initial capitals for Association names.

    Only effects the Model and the generated MAGE.xmi file:
    MAGE-OM::ArrayDesign::featureShape

    {3B72C550029B} [Association]
    to
    MAGE-OM::ArrayDesign::FeatureShape{3B72C550029B}

    [Association]

  • Reported: GENE 1.0b1 — Sun, 14 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

dimension elements be transformed to be optional

  • Key: GENE-3
  • Legacy Issue Number: 5488
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend that, in additional to MAGE Issue 11, the dimension elements be
    transformed
    to be optional, since the transformation of BioDataTuples makes specifying
    the
    dimensions redundant.

    The following will be effected by this change:
    The DTD
    (by modifying the generating code:
    generate_dtd\TransformBioAssayData.java,
    generate_classes\CreateFile.java)
    Section 4.1.4, "Transforming BioDataValues" of the submission

  • Reported: GENE 1.0b1 — Tue, 23 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

order attribute be be added for BioDataCube in model (and, hence, the DTD)

  • Key: GENE-2
  • Legacy Issue Number: 5487
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend that, in additional to MAGE Issue 11, an order attribute be added
    for
    BioDataCube in the model (and, hence, the DTD). This will specify the order
    of
    the dimensions in the accompanying data specified by either the DataInternal
    or
    DataExternal element. In addition, the rule specifying "the first dimension
    matches
    order of BioAssayDimension, second, the DesignElementDimension and the
    third, the
    QuantitationDimension" can be removed.
    Attribute to add: BioDataCube.order
    type: enum

    {BDQ | BQD | DBQ | DQB | QBD | QDB}

    default: 'BDQ'

    The following will be effected by this change:
    The model and MAGE.xmi file.
    The DTD
    Section 3.1.12, "BioAssayData" of the submission

    (MAGE Issue 25)

  • Reported: GENE 1.0b1 — Sun, 14 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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

transformed DTD should keep dimensions in content list of the BioAssayData

  • Key: GENE-1
  • Legacy Issue Number: 5486
  • Status: closed  
  • Source: Rosetta Biosoftware Business Unit ( Michael Miller)
  • Summary:

    Recommend that the transformed DTD should keep dimensions in the content
    list of the
    BioAssayData element instead of moving them to the BioDataCube and
    BioDataTuples
    content lists. This simplifies considerable the difference between the PIM
    and XML-DTD PSM.

    Requires modification of the following files:
    MAGE-ML.dtd
    (by modifying the generating code:
    generate_dtd\TransformBioAssayData.java)
    Section 4.1.4, Transforming BioDataValues of the submission

  • Reported: GENE 1.0b1 — Sun, 14 Jul 2002 04:00 GMT
  • Disposition: Resolved — GENE 1.0
  • Disposition Summary:

    see below

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