Single Nucleotide Polymorphisms Avatar
  1. OMG Specification

Single Nucleotide Polymorphisms — All Issues

  • Acronym: SNP
  • Issues Count: 20
  • Description: All Issues
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All Issues

Issues Summary

Key Issue Reported Fixed Disposition Status
SNP-20 Added classes for describing bibliographic references SNP 1.0b1 SNP 1.0 Resolved closed
SNP-18 Removed unnecessary multiple inheritances SNP 1.0b1 SNP 1.0 Resolved closed
SNP-19 Added abstact class Population to have associations visible SNP 1.0b1 SNP 1.0 Resolved closed
SNP-17 Value of 'strand' attribute of Reference_genomic_location SNP 1.0b1 SNP 1.0 Resolved closed
SNP-15 Panel has new attribute 'type' SNP 1.0b1 SNP 1.0 Resolved closed
SNP-16 Abstact class Ordered_location has now attribute 'position:string SNP 1.0b1 SNP 1.0 Resolved closed
SNP-14 type of all attributes of Geographic_location SNP 1.0b1 SNP 1.0 Resolved closed
SNP-10 Section 2.1 SNP 1.0b1 SNP 1.0 Resolved closed
SNP-11 Added attribute 'url:string' into Db_xref. SNP 1.0b1 SNP 1.0 Resolved closed
SNP-13 Make it possible to Individual have more attributes SNP 1.0b1 SNP 1.0 Resolved closed
SNP-12 Added attribute 'version:string' into Db_xref SNP 1.0b1 SNP 1.0 Resolved closed
SNP-9 Some typos in section 4.1 and elsewhere SNP 1.0b1 SNP 1.0 Resolved closed
SNP-8 Various - some associations are 'derived' SNP 1.0b1 SNP 1.0 Resolved closed
SNP-7 Section 3.18 - Page 20 SNP 1.0b1 SNP 1.0 Resolved closed
SNP-6 Section 3.1.1 SNP 1.0b1 SNP 1.0 Resolved closed
SNP-4 Attributes in a subtype SNP 1.0b1 SNP 1.0 Resolved closed
SNP-5 Section 1.5 SNP 1.0b1 SNP 1.0 Resolved closed
SNP-3 Discrepancies in Glossary section SNP 1.0b1 SNP 1.0 Resolved closed
SNP-2 translation rules should be better documented SNP 1.0b1 SNP 1.0 Resolved closed
SNP-1 current XMI expressing the normative PIM is not too compatible SNP 1.0b1 SNP 1.0 Resolved closed

Issues Descriptions

Added classes for describing bibliographic references

  • Key: SNP-20
  • Legacy Issue Number: 8805
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The model follows closely the OMG Bibliographic Query Service data
    model. Only differences are the way bibref subject descriptors are
    handles (giving more flexibility to mix different vocabularies) and
    addition of boolean 'et_at' attribute to Person to indicate that the
    list of, for example, authors is not complete.

    • All the added classes except Bibref_subject and Bibref_description
      inherit from Identifiable and can have additional properties added to
      them using Annotation and Db_xref. These two classes are mere
      groupings of attributes to Bibliographic_reference and can not exist
      independently.
  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Removed unnecessary multiple inheritances

  • Key: SNP-18
  • Legacy Issue Number: 8803
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Removed unnecessary multiple inheritances

    • Individual and Sequence were inherited explicitly from Identifiable.
  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Added abstact class Population to have associations visible

  • Key: SNP-19
  • Legacy Issue Number: 8804
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Added abstact class Population to have associations visible

  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Value of 'strand' attribute of Reference_genomic_location

  • Key: SNP-17
  • Legacy Issue Number: 8802
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:
    • Value of 'strand' attribute of Reference_genomic_location is now
      expressed as a 'string' rather than an 'integer'. Valid values are
      'forward', 'reverse' and 'unknown'. 'unknown' is default.
  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Panel has new attribute 'type'

  • Key: SNP-15
  • Legacy Issue Number: 8800
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Panel has new attribute 'type' that allows us to annotate how Panel is
    used. Among the possible uses are: plate, population sample,
    family.

  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Abstact class Ordered_location has now attribute 'position:string

  • Key: SNP-16
  • Legacy Issue Number: 8801
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Abstact class Ordered_location has now attribute 'position:string'
    that allows for giving a value to inheriting classes, e.g.
    Cytogenetic_location

  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

type of all attributes of Geographic_location

  • Key: SNP-14
  • Legacy Issue Number: 8799
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The type of all attributes of Geographic_location are now 'double' to
    allow fractional degrees

    Definition: Location of an individual or population in a geographic
    map. Locations are expressed in decimal degrees. Northern latitides
    and eastern longitudes have positive values by convention.

  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Section 2.1

  • Key: SNP-10
  • Legacy Issue Number: 8717
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    10. Section 2.1 - The UML diagram here and elsewhere should have a
    figure # for easier cross reference.

    Proposed solution:

    Add numbers to all figures, in order as they appear in the document.

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Added attribute 'url:string' into Db_xref.

  • Key: SNP-11
  • Legacy Issue Number: 8796
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Added attribute 'url:string' into Db_xref.
    Definition: Full URL to the cross-refenced entry

  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Make it possible to Individual have more attributes

  • Key: SNP-13
  • Legacy Issue Number: 8798
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:
    • moved attributes 'size' and 'count_unit' from Population to Panel
    • made Individual to inherit from Population
    • removed association from Individual to Geographic_location and
      Taxon as they are now inherited from Population
    • removed associations from Molecular_sample to Panel and
      Individual and replaced them with one association to Population
    • Modified the association from Individual to Panel to allow more
      than one Panel

    The net result is that Individual can have new attributes

    • race
    • ethnicity
    • primary_language
    • language_family
      and it can be associated to more than one Panel
  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Added attribute 'version:string' into Db_xref

  • Key: SNP-12
  • Legacy Issue Number: 8797
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Added attribute 'version:string' into Db_xref
    Definition: Version of the database

  • Reported: SNP 1.0b1 — Fri, 20 May 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Some typos in section 4.1 and elsewhere

  • Key: SNP-9
  • Legacy Issue Number: 8716
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:
    • Section 4.1 - XLM instead of XML,
    • Section 2.0 - 'researches' - should be 'researchers' .
    • Section 3.1.1 - XSD and model refer to Anatomic_location, the text
      referes to 'Anatomical_location.
    • Section 3.14 - twice "information" in the phrase "contain
      information information".

    Proposed solution:

    Change typos in sections 4.1, 2.0, 3.1.1 as reported.

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Various - some associations are 'derived'

  • Key: SNP-8
  • Legacy Issue Number: 8715
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    8. Various - some associations are 'derived' - is this just
    documentation only or is there some derivation algorithm?

    Proposed solution:

    Add a bullet to the beginning of Section 3 with the following text:

    "The words 'derived from' are used in the UML model as comments, they
    do not imply any specific derivation algorithm."

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Section 3.18 - Page 20

  • Key: SNP-7
  • Legacy Issue Number: 8714
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    7. Section 3.18 - Page 20 - there is disrepancy between the diagram
    and the XSD. The XSD has an attribute 'url' - this is not in the
    diagram. It is not in the model either for the DB-xref class (I
    checked the XMI file) - Is there some other mapping rule that creates
    this attribute?

    Discussion:

    To modify PIM to add an attribute URL to the DB-xref class. The rest
    will be solved by new conversion software tool.

    Proposed solution:

    not yet

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Section 3.1.1

  • Key: SNP-6
  • Legacy Issue Number: 8713
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    6. Section 3.1.1 - In looking at the model and the XML Schema, it is not
    clear how the model maps to the schema. For example in looking at
    Assayed_genomic_genotype, the association cardinalities
    (multiplicities if you will) map differently. for example the '* *'
    between Polymorphism_Assay and Molecular_Sample, maps to minoccurs =
    1, maxoccurs = 1, but between Polymorphism_Assay and
    Consensus_genomic_genotype maps to minoccurs =0, max occurs = 1. So
    it is not clear if the semantics in the diagram and the XSD are
    consistent.

    Discussion: will be solved by new conversion software tool

    Proposed solution:

    not yet

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Attributes in a subtype

  • Key: SNP-4
  • Legacy Issue Number: 8711
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    As I was reading the spec, I found out that attributes in a subtype
    are bold and the inherited ones are not. Would be nice if these
    conventions are spelled out somewhere in a 'how to read the spec
    section'.

    Discussion:

    It will probably be also solved by writing the new software conversion
    tool, and by re-generating the PSM part of the specification. But I
    would not rely on fonts indicating some meaning - they may be
    unintentionally changed by formatting the document. The inheritance
    is, however, already indicated by text like "defined at ..." that
    accompanies every attribute.

    Proposed solution:

    Reject the issue

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Section 1.5

  • Key: SNP-5
  • Legacy Issue Number: 8712
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Section 1.5 - Please refer to exact document numbers of related
    specs this proposal is based on (Example : Whether the LSID used in
    final adopted spec, available spec etc.). Add these references to the
    'references' section.

    Proposed solution:

    Add the following to Section 1.5

    • at the end of BQS section:
      "The relevant specification is available as OMG documents
      formal/02-05-03, formal/02-05-04 and dtc/02-02-01."
    • at the end of LSID section:
      "The relevant specification is available as OMG documents
      formal/2004-12-01 and dtc/04-08-03."

    Add the following to the Section 6 (References):

    [9] Bibliographic Query Service, an OMG specification,
    http://www.omg.org/technology/documents/formal/bibliographic_query.htm

    [10] Life Sciences Identifier, an OMG specification,
    http://www.omg.org/technology/documents/formal/life_sciences.htm

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

Discrepancies in Glossary section

  • Key: SNP-3
  • Legacy Issue Number: 8710
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    3. I like the way the Glossary is usually consistent with the model
    and the XSD. There are some discrepancies though.

    Discussion:

    The definitions of terms are already in section 3.2. Therefore there
    is no need to repeat them again in a separate section called
    "Glossary". Having them in one place will guarantee consistency.

    Proposed solution:

    Replace the complete chapter "Glossary" by text: "The used terms are
    defined in section "Model classes, attributes and associations
    (details)".

    Remove the third paragraph ("Conveniently, most of the used
    domain-specific terms are also collected in the Glossary section of
    this document.") from the beginning of the Section 3.

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

translation rules should be better documented

  • Key: SNP-2
  • Legacy Issue Number: 8709
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The use of UML to describe the conceptual model in UML (i.e PIM)
    and the data interchange model in XML Schema (i.e PSM) is good. It
    would be better if the translation rules are better documented (some
    of this is listed, but others are hidden in the tool implementation
    that is used to produce the schema).

    Discussion:

    At the monent we see two alternatives. Both of them, however, need
    first to solve the issue with UML tools interoperability (see above,
    number 1). They are:

    a) Keep the current way of transformation from the XMI to the XML
    Schema but:
    i) Better document the rules used in the manual translation from
    the XMI to the Excel spreadsheet, and
    ii) Make available the software tool used to transform the Excel
    spreadsheet to the final XML Schema.

    b) Write (and make available, including reasonable documentation) a
    new tool that would transform directly from the XMI to XML Schema.

    Actually, there is also the third way. We will use it if the resulting
    XMI (coming from the new version of Umbrello 1.4) is too different
    from the current XMI. In that case, we remove from the specification
    the description how to get from the XMI to XML Schema completely, and
    we will only keep there a statemant that that both XMI and XML Schema
    are normative.

    Proposed solution:

    none yet

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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

current XMI expressing the normative PIM is not too compatible

  • Key: SNP-1
  • Legacy Issue Number: 8708
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The current XMI expressing the normative PIM is not too
    compatible. It is possible to read it by the same UML tool that
    created it (Umbrello 1.2) but hardly by any other tool.

    Discussion:

    Because we are aware that there is a general problem with almost all
    UML tools regarding their interoperability, we will try to use the
    latest version of Umbrello (our UML tool of choice). That's all we can
    do/guarantee.

    Proposed solution:

    Replace file omgsnp-xmi12.xml in the accompanied document with its new
    version.

  • Reported: SNP 1.0b1 — Tue, 26 Apr 2005 04:00 GMT
  • Disposition: Resolved — SNP 1.0
  • Disposition Summary:

    No Data Available

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