Phenotype and Genotype Object Model Avatar
  1. OMG Specification

Phenotype and Genotype Object Model — Closed Issues

  • Acronym: PAGE-OM
  • Issues Count: 35
  • 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
PAGEOM_-35 PAGE-OM package PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-34 "accompanied files", PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-32 There is no acronym table PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-30 The spec occasionally calls out "human genetics" but nowhere says that it limits itself to humans PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-33 References to other specs, OMG and external, are very weak and poorly stated PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-31 The modeling tool used (Sparx EA) is inadequately referenced in several places, PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-25 Figures are sometimes unexplained PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-28 Seven concepts PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-27 no statement that the spec was normative PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-29 Diagrams are confusing and hard to read PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-26 Associations in the model not really documented PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-24 textual descriptions of the model objects are nearly completely absent PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-23 PAGE-OM issue: errors in associations PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-22 PAGE-OM issue: most attributes should be optional PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-21 PAGE-OM issue: missing cardinalities PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-20 abstract Genotype_phenotype_correlation_experiment PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-18 Clarify conformance section PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-17 Figure 7.5: The description of the Identifiable is not fully correct PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-19 PAGE-OM: top level XML tag PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-16 Add a new inheritance relationship PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-15 several unsufficient cardinalities should be revised PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-13 Move association PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-12 Do not include the XSD stereotypes for the classes in the PIM. PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-14 Rename attribute 'sex' in snp2::Individual to 'gender'. PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-11 remove stereotypes PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-10 redundant association from Enum to Value. PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-7 Rename the association from Consensus_genomic_genotype to Latent_genotype PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-6 duplicated attributes and associations PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-9 Rename the association from Multi_variation_assay to Genomic_variation PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-8 Remove the inheritance from Identifiable in Set_of_haplotypes. PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-5 change name of some associations PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-4 remove duplicated attributes PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-2 The PSM namespaces should be rooted on the OMG spec directory URL PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-1 reference to an OMG rooted URL PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed
PAGEOM_-3 There are missing attributes 'schemaLocation' in the *.xsd files. PAGE-OM 1.0b2 PAGE-OM 1.0 Resolved closed

Issues Descriptions

PAGE-OM package

  • Key: PAGEOM_-35
  • Legacy Issue Number: 13817
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    I understand that the PAGE-OM package was added in response to Issue #13023. However, the role of the contained class "Page" (Section 7.1.1.1) is thoroughly unclear. Please document the purpose of the Page class and the reason that it contains 69 associations, apparently one to every other class in the model. If you can't clearly document the purpose of this class and its associations, you should remove it. Note also that the name of the class "Page" (Section 7.1.1.1) conflicts with the "PAGE" package (Section 7.1.2); this may not generate a syntax error in most tools, but it is certainly confusing for the human reader.

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    1) PAGE package gone (see the issue 13811). Its contents is
    incorporated into the main package PAGE-OM.

    2) Therefore, the class Page does not have anymore a confusing
    name. Also, its description was updated.

    Resolution:

    • The changes of package name for classes previously in the package PAGE are in the generated documentation (Chapter 7).
    • The PAGE class got a better description (again, it is generated directly from the model into Chapter 7): "This class does not contain any scientific meaning. Its mainpurpose is to be the root element for the situations where this specification is used for data exchange formats (e.g. xml-schema). Therefore, it has optional direct associations to all important classes so that implementations can exchange only relevant data."
  • Updated: Sat, 7 Mar 2015 03:28 GMT

"accompanied files",

  • Key: PAGEOM_-34
  • Legacy Issue Number: 13816
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    In a number of places the spec refers to "accompanied files", meaning the XML and XMI files that come with the specification. The correct phrase for such files should probably be "accompanying files".

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Replace all occurrences of "accompanied files" by text "accompanying files".

  • Updated: Sat, 7 Mar 2015 03:28 GMT

There is no acronym table

  • Key: PAGEOM_-32
  • Legacy Issue Number: 13814
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    There is no acronym table. For example, two major sections of the model are called "SNP" and "SNP2" but nowhere does the spec say that "SNP" means "Single Nucleotide Polymorphism". There are a number of other examples.

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Resolution explanation:

    We do not see a need for a separate acronym table. Except the package
    names, such as SNP, the abbreviations are of general
    knowledge. However, the package names should be explained. And they
    are explained (now) better directly in the paragraphs introducing
    them. So we have better explanation of the important terms but not in
    a separate acronym table.

    Regarding the package name SNP2, it does not exist anymore. Its
    contents was incorporated directly in the main package PAGE-OM (see
    issue 13811).

    Resolution:

    • Into the generated documentation (Chapter 7), where the package SNP starts, add the following text describing the SNP abbreviation: "Module replicating part of OMG specification SNP (Single Nucleotide Polymorphism)."
  • Updated: Sat, 7 Mar 2015 03:28 GMT

The spec occasionally calls out "human genetics" but nowhere says that it limits itself to humans

  • Key: PAGEOM_-30
  • Legacy Issue Number: 13812
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    The spec occasionally calls out "human genetics" but nowhere says that it limits itself to humans. Seems to me it would work for any organism, so "human" references should be removed.

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:
    • Remove the word "human" from the glossary item "Association Study",
      and from the descriptions in the model (which will become a part of
      the generated documentation (chapter 7).

    Disposition: Resolved

  • Updated: Sat, 7 Mar 2015 03:28 GMT

References to other specs, OMG and external, are very weak and poorly stated

  • Key: PAGEOM_-33
  • Legacy Issue Number: 13815
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    References to other specs, OMG and external, are very weak and poorly stated. A table of referenced external documents would seem essential. There are (strong?) hints that some motel objects specialize objects from other specs but which ones and from where are thoroughly obscure. The spec seems to assume substantial knowledge of other LifeSciences TF specs; this is not necessarily bad, but it should say so explicity and identify the referenced specifications precisely.

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Resolution explanation:

    The original PAGE-OM specification had a list of related existing OMG
    specifications. It disappeared during the editing process - and today,
    we are not able to trace where and when it happened. Therefore, we
    suggest to copy back what was previously in the specification,
    assuming that it was not an OMG intention to remove it.

    Resolution:
    Add the following text at the end of the section Preface -> OMG Specification (or into any other place that would be suitable from the point of OMG formatting procedure):

    • Relationship to Existing Domain OMG Specifications
      • Single Nucleotide Polymorphism (SNP)
        The described specification extends the "Single Nucleotide
        Polymorphism" (formal/2005-11-01, formal/2005-12-01). Because
        it requires some changes in the SNP specification, the original
        SNP entities are also mentioned here, in this PAGE-OM
        specification.
    • Bibliographic Query Service (BQS)
      This specification uses classes and attributes defined in the
      BQS (formal/02-05-03). It does not directly include the
      original BQS entities because its model is expressed as a CORBA
      model. However, it uses all bibliographic entities, except the
      query part (the query is not in the scope of this
      specification). The above is also true for the SNP
      specification. Therefore, this specification uses BQS only
      indirectly, via SNP.
    • Life Sciences Identifiers (LSID)
      It is used in the Identifiable class (again, as with BQS, only
      indirectly, via SNP specification).
  • Updated: Sat, 7 Mar 2015 03:28 GMT

The modeling tool used (Sparx EA) is inadequately referenced in several places,

  • Key: PAGEOM_-31
  • Legacy Issue Number: 13813
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    The modeling tool used (Sparx EA) is inadequately referenced in several places, meaning that a causal reader would not necessarily be able to find the correct tool on the internet. At minimum, cite the Sparx URL.

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:
    • Add (on several places as indicated by the change-bar document) the following URL: http://www.sparxsystems.com/. For example, in the first paragraph of the Conformance chapter, the updated text will be: "...using program Enterprise Architect (http://www.sparxsystems.com/)..."
      Disposition: Resolved
  • Updated: Sat, 7 Mar 2015 03:28 GMT

Figures are sometimes unexplained

  • Key: PAGEOM_-25
  • Legacy Issue Number: 13807
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    Figures are sometimes unexplained and arrangement (ie, poor paging) of the figures and text that does exist lead to misunderstandings on first reading.

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Resolution explanation:

    The diagram legends and class descriptions were mixed in the generated
    documentation - making unclear which diagrams belong to which packages
    and classes. We generate them now separately.

    Resolution:

    • Generated separately a chapter with diagrams and a chapter with
      their descriptions (legend). They will become chapter 7.1 and 7.2
      (or whatever numbering the formatting of the resulting document
      requires).
    • Change the order of the diagrams and rename them in order to reflect
      better the importance of their contents to the whole
      specification. The new order and diagram names are now:

    01 Association study
    02 Sample
    03 Genotype overview
    04 Phenotype overview
    05 Genotype in details
    06 Frequency
    07 Haplotype
    08 Sequence
    09 Map
    90 Identifiable
    91 Evidence and Value

  • Updated: Sat, 7 Mar 2015 03:28 GMT

Seven concepts

  • Key: PAGEOM_-28
  • Legacy Issue Number: 13810
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    The Introduction describes that the model is packaged into seven concepts that can be used independently. This is a cool idea. But the oganization of the rest of the spec does not support identification of those seven concepts or how they might be isolated so that can be used independently. Naming of the model subdivisions does not even match the stated concepts. Do these seven concepts raise any conformance issues?

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Resolution explanation:

    There is a misunderstanding of the wording here, especially what
    "standalone" means here. The idea, still valid, is that the PAGE-OM
    has several components that can be used independently, on the
    conceptual level, but not necessarily on the level when using a
    modelling tool.

    Resolution:

    • Change the text in the last but one paragraph of the Introduction to this:
      To enable PAGE-OM to achieve its goals, it is structured as several high level concepts that can be used independently on the conceptual level (but not necessarily when using a modeling tool). Examples of these concepts are: Marker, Assay, Sample, Genotype, Frequency, Phenotype, and Experiment. For example: A company providing DNA analysis kits might only need to use the Marker and Assay parts of this model.
  • Updated: Sat, 7 Mar 2015 03:28 GMT

no statement that the spec was normative

  • Key: PAGEOM_-27
  • Legacy Issue Number: 13809
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    I found no statement that the spec was normative. There's a discussion of conformance but it is quite inadequate and I'd bet it's missing some important points. There is discussion about the XML/XMI files being normative, but not the spec. Please review the Conformance section for completeness.

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Resolution:

    • add text "(Chapter 7)" for Platform independent model
    • add text "(Chapter 8)" for Platform specific model

    in the first sentences of the chapter 2 (Conformace). In the final
    document, the added text may contain different chapter numbers if the
    editing of the whole document changes the chapter numbering).

    Disposition: Resolved

  • Updated: Sat, 7 Mar 2015 03:28 GMT

Diagrams are confusing and hard to read

  • Key: PAGEOM_-29
  • Legacy Issue Number: 13811
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    Diagrams are confusing and hard to read – lines overlapping boxes, too many objects in figures, little or no explanations. Graphics conventions (such as box color shading) are not discussed but seem to be meaningful. Perhaps the figures can be broken up into smaller, target fragments that are specific to sets of related class and distributed to relevant locations in the spec?

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Resolution explanation:

    1) We removed SNP2 package, making all its contents a direct part of
    the PAGE-OM package. We also removed package PAGE, making all its
    contents a direct part of the PAGE-OM package. This simplifies the
    model without losing any relationships.

    2) The color conventions are now simple: old classes (SNP, BREF,
    BasicTypes) are gray, new classes are green.

    Resolution:

    • Move all classes from SNP2 package to PAGE-OM (the main)package. Package SNP2 will cease to exist.
    • Move all classes from PAGE package to PAGE-OM (the main)package). Package PAGE will cease to exist.
    • Then, re-generate the documentation (chapter 7).
    • Make appropriate text changes in the description of the Platform specific model, i.e. to remove file name snp2.xsd.
  • Updated: Sat, 7 Mar 2015 03:28 GMT

Associations in the model not really documented

  • Key: PAGEOM_-26
  • Legacy Issue Number: 13808
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    There are a lot of associations in the model but not one of them is documented in any fashion beyond listing names and the classes they connect. Cardinalities can be found in the diagrams but direct documentation of the associations and their use is necessary to convey the intent of the specification. Associations should be individually documented to the extent that a reader can determine the characteristics of each association, its name, and the names, multiplicity, and ocnstraints of its ends in a single place in the spec. The reader should not have to harvest association characteristics scattered around figures and text.

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Resolution explanation:

    1) Cardinalities will be generated into the generated documentation of
    the model.

    Plus: Explicit cardinality is one (whenever it is not mentioned in the
    generated document).

    See also issue 14018 dealing with missing cardinalities.

    2) The rules for associations are:

    a) Many associations are described enough by the class names they
    connect. We have not changed them; we do not see a need for better
    documentation for these associations.

    b) Some of the remaining associations have on one or on both sides
    roles. We believe that the roles describe the association
    sufficiently.

    c) Many of the remaining associations have names that are sufficent
    for describing the association role. We added, however, some names:

    • Panel has subpanels.
    • Genotype_phenotype_correlation_experiment associated with itself:
      meta-experiments has sub-experiments.

    d) For the rest we added better description.

    3) In the model, we do not define (expect) any constraints - so no
    documentation needed for them.

    Resolution:

    • Few new descriptions added to the associations. Done directly in the
      model. Regenerate the whole documentation (chapter 7).
    • Add to the generated documentation roles and cardinalities. [Now,
      each class has two new rows labelled "Card" and "Role name". Often,
      however, on places that we consider self-explanatory, they are
      empty.]
  • Updated: Sat, 7 Mar 2015 03:28 GMT

textual descriptions of the model objects are nearly completely absent

  • Key: PAGEOM_-24
  • Legacy Issue Number: 13806
  • Status: closed  
  • Source: Thematix Partners LLC ( Doug Tolbert)
  • Summary:

    All of the model objects seem to be listed, and there are some diagrams, but textual descriptions of the model objects are nearly completely absent. Those that exist are often (but not always) merely copied from the glossary. There is little (often no) semantic descriptions of model objects that would help the reader understand their intent. purpose, or best usage.

  • Reported: PAGE-OM 1.0b2 — Thu, 19 Mar 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Many classes got now better descriptions. But it is hard to list the
    changes here, in the resolution of the issue, because the changes were
    made by the UML tool and the documentation was re-generated. The FTF
    made the best effort to produce a change-bar document where all these
    changes will be visible.

    Regarding glossary, it is actually vice-versa: the glossary items were
    copied from the documentation of the model. Therefore, glossary is not
    (and never was) a normative part of the documentation. Its only reason
    is that it contains classes (and their synonyms) in alphabetic order,
    across all packages.

    Resolution:

    • The class descriptions in the model have been updated. Regenerate
      documentation (chapter 7).
    • Generate glossary from the XMI and then replace the exiting
      glossary in full.
    • Add the following reference to the Annex C (References) - as the
      first reference in the table:

    Brookes et. al., The Phenotype and Genotype Experiment Object Model
    (PaGE-OM): A robust data structure for information related to DNA
    variation, Human Mutation (2009), vol 30, p. 1-16

  • Updated: Sat, 7 Mar 2015 03:28 GMT

PAGE-OM issue: errors in associations

  • Key: PAGEOM_-23
  • Legacy Issue Number: 14036
  • Status: closed  
  • Source: University of Helsinki ( Juha Muilu)
  • Summary:

    Association from Frequency to Variation_assay should be many to 0..1
    Association from Frequency to Genomic_variation should be many to 0..1
    Association from Assayed_genomic_genotype to
    Abstract_observation_target should be many to 1

    Reference_genomic_location_in_assembly has redundant relationship to
    reference_genomic_assembly. Remove association

    Directionality is wrong between Haplotype_derivation_method and
    Genomic_haplotype.
    Reverse directionality

    Directionality is wrong between Haplotype_derivation_methods and
    Consesus_genomic_genotype.
    Reverse directionality

  • Reported: PAGE-OM 1.0b2 — Tue, 30 Jun 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    No Data Available

  • Updated: Fri, 6 Mar 2015 21:47 GMT

PAGE-OM issue: most attributes should be optional

  • Key: PAGEOM_-22
  • Legacy Issue Number: 14019
  • Status: closed  
  • Source: University of Helsinki ( Juha Muilu)
  • Summary:

    All attributes are now mandatory in the model, but most of them should
    be optional.
    For example creation_date in Identifiable.

  • Reported: PAGE-OM 1.0b2 — Mon, 22 Jun 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:
    • Change the model in order to define the following attributes either optionally or mandatory. Then generate new documentation (chapter 7).
      The following attributes have been kept mandatory (they are listed here for information; there is no change here):
      Boolean.value
      Db_xref.uid
      Evidence_code.code
      Float_value.value
      Identifiable.lsid
      Integer_value.value
      Location_on_plate.x
      Location_on_plate.y
      Ontology_term.term
      Reference_genomic_location.start
      String_value.value
      Time_accuracy.code
      Unit.type
      Value_range.max
      Value_range.min

    The following attributes have been changed to optional:

    Abstract_population.ethnicity
    Abstract_population.language_family
    Abstract_population.primary_language
    Abstract_population.race
    Algorithm.description
    Annotation.name
    Annotation.value
    Article.first_page
    Article.last_page
    Assayed_genomic_genotype.assay_failure
    Assayed_genomic_genotype.quality_score
    Bibliographic_reference.date
    Bibliographic_reference.format
    Bibliographic_reference.language
    Bibliographic_reference.rights
    Bibliographic_reference.title
    Bibliographic_reference.type
    Bibref_description.abstract_type
    Bibref_description.language
    Bibref_description.table_of_contents
    Bibref_description.the_abstract
    Bibref_description.toc_type
    Bibref_scope.spatial_location
    Bibref_scope.temporal_period
    Book.edition
    Book.isbn
    Book.series
    Book.volume
    Conclusion.p_value
    Constraint.description
    Contributor.date
    Db_xref.db
    Db_xref.db_version
    Db_xref.field
    Db_xref.url
    Defining_feature.type
    Entry_status.last_modified_date
    Entry_status.subset
    Frequency.count
    Frequency.value
    Gene_product_change.label
    Genomic_allele.bin
    Genomic_allele.repeat_count
    Genomic_allele.repeat_is_exact
    Genomic_gene_structure.gene_symbol
    Genomic_variation.flank_down
    Genomic_variation.flank_up
    Genomic_variation.is_mutation
    Genomic_variation.repeat_unit
    Genomic_variation.type
    Genomic_variation.validation_status
    Genotype_phenotype_correlation_experiment.objective
    Genotype_phenotype_correlation_experiment.outcome
    Genotype_phenotype_correlation_experiment.study_id
    Genotype_phenotype_correlation_experiment.type
    Geographic_location.max_latitude
    Geographic_location.max_longitude
    Geographic_location.min_latitude
    Geographic_location.min_longitude
    Hypothesis.description
    Identifiable.creation_date
    Identifiable.delete_date
    Identifiable.modify_date
    Identifiable.name
    Individual.birth_date
    Individual.death_date
    Individual.father_id
    Individual.gender
    Individual.mother_id
    Journal.abbreviation
    Journal.issn
    Journal_article.issue
    Journal_article.issue_supplement
    Journal_article.volume
    Molecular_sample.molecule
    Observed_value.time
    Ontology_source.ontology_URI
    Ordered_location.position
    Panel.count_unit
    Panel.pooled
    Panel.size
    Panel.type
    Patent.doc_number
    Patent.doc_office
    Patent.doc_type
    Person.affiliation
    Person.email
    Person.et_al
    Person.first_name
    Person.mid_initials
    Person.postal_address
    Person.surname
    Reference_genomic_location.end
    Reference_genomic_location.strand
    Reference_genomic_location_in_assembly.chromosome_name
    Residue_change.changed_residue
    Residue_change.original_residue
    Run.instrument
    Run.run_date
    Sequence.molecule
    Sequence.sequence
    Source.address
    Source.email
    Source.fax
    Source.institution
    Source.name
    Source.tel
    Study.abstract
    Study.acknowledgements
    Study.background
    Study.conclusions
    Study.key_results
    Study.limitations
    Study.objectives
    Study.source_of_bias
    Study.study_design
    Study.study_power
    Study.study_size_reason
    Study.submission_date
    Study.title
    Study.update_date
    Subject_descriptor.term
    Subject_descriptor.vocabulary_name
    Taxon.rank
    Taxon.scientific_name
    Transcription_change.changed_codon
    Transcription_change.codon_position
    Transcription_change.original_codon
    Variation_assay.description
    Web_resource.cost
    Web_resource.estimated_size
    Web_resource.url

  • Updated: Fri, 6 Mar 2015 21:47 GMT

PAGE-OM issue: missing cardinalities

  • Key: PAGEOM_-21
  • Legacy Issue Number: 14018
  • Status: closed  
  • Source: University of Helsinki ( Juha Muilu)
  • Summary:

    In page-om model there are some missing cardinalities, which means
    that default cardinality (one-to-one) is used, which is wrong.
    For example association between Assayed_genomic_genotype and
    Observation_target

  • Reported: PAGE-OM 1.0b2 — Mon, 22 Jun 2009 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:
    • Add the following text to the beginning of the Chapter 7.1 (Detailed Model Documentation) - just before the generated text:
    • Notes
      Those cardinalities that are not explicitly given in PIM should be interpreted as "0..1".
    • Change the following cardinalities in the model, then generate new documentation (chapter 7):
      Abstract_population-Geographic_location / Changed from: [0..*]>[undef..undef] to: [0..*]>[0..1]
      Abstract_value-Assayed_genomic_genotype / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Abstract_value-Band_size / Changed from: [1..1]<[undef..undef] to: [1..1]<[0..1]
      Abstract_value-Defining_feature / Changed from: [1..1]<[undef..undef] to: [1..1]<[0..1]
      Abstract_value-Melting_temperature / Changed from: [1..1]<[undef..undef] to: [1..1]<[0..1]
      Algorithm-Experiment_result / Changed from: [undef..undef]<[undef..undef] to: [0..1]<[0..1]
      Algorithm-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Anatomic_location-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Annotation-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Assayed_genomic_genotype-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Association_study-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Band_size-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Bibliographic_reference-Bibref_description / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Bibliographic_reference-Bibref_scope / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Bibliographic_reference-Bibref_subject / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Bibliographic_reference-Db_xref / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Bibliographic_reference-Entry_status / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Bibliographic_reference-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Bibliographic_reference-Provider / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Bibliographic_reference-Provider (2) / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Bibliographic_reference-Provider (3) / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Bibliographic_reference-Provider (4) / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Bibref_description-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Bibref_subject-Subject_descriptor / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Bibref_subject-Subject_descriptor (2) / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Bibref_subject-Subject_descriptor (3) / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Book-Book_article / Changed from: [1..1]<[undef..undef] to: [1..1]<[0..1]
      Book-Person / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      CDS-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Conclusion-Genotype_phenotype_correlation_experiment / Changed from: [undef..undef]<[undef..undef] to: [0..1]<[0..1]
      Conclusion-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Consensus_genomic_genotype-Haplotype_derivation_methods / Changed from: [undef..undef]>[0..*] to: [0..1]<[0..*]
      Constraint-Value / Changed from: [0..*]>[undef..undef] to: [0..*]>[0..1]
      Contributor-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Cytogenetic_location-Cytogenetic_map / Changed from: [0..*]>[undef..undef] to: [0..*]>[0..1]
      Cytogenetic_location-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Cytogenetic_map-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Db_xref-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Defining_feature-Latent_genotype_specification / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Enum-Value / Changed from: [undef..undef]<[0..*] to: [0..1]<[0..*]
      Environment_feature-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Error-Numeric_value / Changed from: [0..1]<[undef..undef] to: [0..1]<[0..1]
      Evidence-Identifiable [supporting_source] / Changed from: [undef..undef]<[0..*] to: [0..1]<[0..*]
      Evidence-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Evidence-Person / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Evidence-Value / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Evidence_code-Value [supporting_evidence] / Changed from: [0..*]>[undef..undef] to: [0..*]>[0..1]
      Exon-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Experiment_result-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Frequency-Frequency_set / Changed from: [1..*]>[undef..undef] to: [1..*]>[0..1]
      Frequency-Genomic_variation / Changed from: [0..*]>[undef..undef] to: [0..*]>[0..1]
      Frequency_set-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Functional_change-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Gene_based_haplotype-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genetic_location-Genetic_map / Changed from: [0..*]>[undef..undef] to: [0..*]>[0..1]
      Genetic_location-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genetic_map-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genic_variation-Genomic_gene_structure / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Genic_variation-Genomic_gene_structure (2) / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genic_variation-Genomic_variation / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Genic_variation-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genomic_allele-Genomic_reference_allele / Changed from: [undef..undef]<[undef..undef] to: [0..1]<[0..1]
      Genomic_allele-Genomic_variation / Changed from: [0..*]>[undef..undef] to: [0..*]>[0..1]
      Genomic_allele-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genomic_allele_population_frequency-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genomic_gene_structure-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genomic_genotype_population_frequency-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genomic_haplotype-Haplotype_derivation_methods / Changed from: [0..*]<[undef..undef] to: [0..*]>[0..1]
      Genomic_haplotype-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genomic_haplotype_population_frequency-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genomic_observation-Genotype_phenotype_correlation_experiment / Changed from: [undef..undef]<[undef..undef] to: [0..*]<[0..1]
      Genomic_reference_allele-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genomic_variation-Ordered_location / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Genomic_variation-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genomic_variation-Reference_genomic_landmark / Changed from: [undef..undef]<[undef..undef] to: [0..1]<[0..1]
      Genomic_variation-Reference_genomic_location / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Genomic_variation-Reference_genomic_location (2) / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genotype_phenotype_correlation_experiment-Genotype_phenotype_correlation_experiment / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Genotype_phenotype_correlation_experiment-Hypothesis / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Genotype_phenotype_correlation_experiment-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Geographic_location-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Haplotype_block-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Haplotype_derivation_methods-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Haplotype_map-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Heterozygosity-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Hypothesis-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Identifiable-Source / Changed from: [undef..undef]>[0..1] to: [0..1]>[0..1]
      Individual-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Journal-Journal_article / Changed from: [1..1]<[undef..undef] to: [1..1]<[0..1]
      Journal-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Latent_genotype-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Lifestyle_feature-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Location-Location / Changed from: [undef..undef]<[0..*] to: [0..1]<[0..*]
      Location-Map / Changed from: [undef..undef]>[undef..undef] to: [0..*]>[0..1]
      Location_on_plate-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Location_on_plate-Plate [wells] / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Melting_temperature-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Molecular_sample-Molecular_sample / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Molecular_sample-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Multi_vartiation_assay-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Multi_vartiation_assay-Variation_assay / Changed from: [undef..undef]<[0..*] to: [0..1]<[0..*]
      Neighbour_variation-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Observable_feature-Observation_method / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Observable_feature_category-Observable_feature_category / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Observable_feature_category-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Observation_method-Observed_value / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Observation_method-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Observed_value-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Observed_value-Time_accuracy / Changed from: [undef..undef]>[0..1] to: [0..1]>[0..1]
      Observed_value-Value / Changed from: [undef..undef]>[1..1] to: [0..1]>[1..1]
      Oligo-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Organization-Page / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
      Page-Panel / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Person / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Phenotype_feature / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Plate / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Reference_genomic_assembly / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Reference_genomic_landmark / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Reference_genomic_location / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Run / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Service / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Source / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Structural_change / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Subject_descriptor / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Taxon / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Transcription_change / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Translation_change / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Page-Variation_assay / Changed from: [undef..undef]>[0..*] to: [0..1]>[0..*]
      Panel-Panel / Changed from: [0..*]<[undef..undef] to: [0..1]<[0..1]
      Patent-Provider / Changed from: [undef..undef]>[undef..undef] to: [0..1]>[0..1]
      Reference_genomic_assembly-Reference_genomic_location / Changed from: [undef..undef]<[0..*] to: [0..1]<[0..*]
      Reference_genomic_landmark-Reference_genomic_location / Changed from: [undef..undef]<[0..*] to: [0..1]<[0..*]
      Unit-Value / Changed from: [0..1]>[undef..undef] to: [0..1]>[0..1]
      Value-Value / Changed from: [0..*]<[undef..undef] to: [0..*]<[0..1]
  • Updated: Fri, 6 Mar 2015 21:47 GMT

abstract Genotype_phenotype_correlation_experiment

  • Key: PAGEOM_-20
  • Legacy Issue Number: 13055
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Genotype_phenotype_correlation_experiment was defined as abstract
    class. This is clearly a mistake.

    Suggested resolution: Change class
    'Genotype_phenotype_correlation_experiment' to a non abstract one
    in the PIM.

  • Reported: PAGE-OM 1.0b2 — Mon, 3 Nov 2008 05:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Change class
    'Genotype_phenotype_correlation_experiment' to a non abstract one
    in the PIM.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

Clarify conformance section

  • Key: PAGEOM_-18
  • Legacy Issue Number: 13012
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    In the Conformance section the following sentence does not make it
    clear whether or not the PSM schemas define the "data exchange format"
    mentioned:

    "Any implementation using or producing given data exchange format is
    considered complying with this specification."

    Suggested resolution: Replace the text above by:

    "Any implementation using or producing data exchange format defined by
    the Platform specific model defined by this specification is
    considered complying with this specification."

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Replace the text above by the text below.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

Figure 7.5: The description of the Identifiable is not fully correct

  • Key: PAGEOM_-17
  • Legacy Issue Number: 13011
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The description of the Identifiable is not fully correct. It says (by
    the Figure 7.5):

    "All classes in the model inherit from Identifiable. In this way,
    their instances are uniquely identifiable. Any Identifiable instance
    must have either attribute 'id', or attribute 'LSID'. Usually, an 'id'
    is used to identify an instance within a known context, and the 'LSID'
    is used when cross-referencing to a different context. The 'LSID'
    attribute follows syntax as defined in the OMG Life Sciences
    Identifiers specification.

    But the PAGE model does not include any attribute "id".

    Suggested resolution: Replace the text mentioned above by the
    following:

    "All classes in the model inherit from Identifiable. In this way,
    their instances are uniquely identifiable. Any Identifiable instance
    must use its "lsid attribute". For this attribute, it is recommended
    to use the OMG Life Sciences Identifier specification."

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Replace the text mentioned above by the
    following:

    "All classes in the model inherit from Identifiable. In this way,
    their instances are uniquely identifiable. Any Identifiable instance
    must use its "lsid attribute". For this attribute, it is recommended
    to use the OMG Life Sciences Identifier specification."

  • Updated: Fri, 6 Mar 2015 21:47 GMT

PAGE-OM: top level XML tag

  • Key: PAGEOM_-19
  • Legacy Issue Number: 13023
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The PSM (the XML Schema) does not have any top-level tag. Its absence makes it very hard to produce a real-life data in this data exchange format.

    Suggested solution: Add a new file, named all.xsd, that includes (imports) all so far defined xsd files, that defines the top level tag "page", and that also defined a list of tags (from the existing PSM) that can be the direct children of the top-level "page" tag. The list has to be yet defined by the FTF members.

  • Reported: PAGE-OM 1.0b2 — Fri, 31 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Add a new file, named all.xsd, that includes (imports) all so far defined xsd files, that defines the top level tag "page", and that also defined a list of tags (from the existing PSM) that can be the direct children of the top-level "page" tag. The list of children is:

    Algorithm
    Anatomic_location
    Annotation
    Assayed_genomic_genotype
    Association_study
    Band_size
    Bibliographic_reference
    Bibref_description
    CDS
    Conclusion
    Contributor
    Cytogenetic_location
    Cytogenetic_map
    Db_xref
    Environment_feature
    Evidence
    Exon
    Experiment_result
    Frequency_set
    Functional_change
    Gene_based_haplotype
    Genetic_location
    Genetic_map
    Genic_variation
    Genomic_allele
    Genomic_allele_population_frequency
    Genomic_gene_structure
    Genomic_genotype_population_frequency
    Genomic_haplotype
    Genomic_haplotype_population_frequency
    Genomic_reference_allele
    Genomic_variation
    Genotype_phenotype_correlation_experiment
    Geographic_location
    Haplotype_block
    Haplotype_derivation_methods
    Haplotype_map
    Heterozygosity
    Hypothesis
    Individual
    Journal
    Latent_genotype
    Lifestyle_feature
    Location_on_plate
    Melting_temperature
    Molecular_sample
    Multi_vartiation_assay
    Neighbour_variation
    Observable_feature_category
    Observation_method
    Observed_value
    Oligo
    Organization
    Panel
    Person
    Phenotype_feature
    Plate
    Reference_genomic_assembly
    Reference_genomic_landmark
    Reference_genomic_location
    Run
    Service
    Source
    Structural_change
    Subject_descriptor
    Taxon
    Transcription_change
    Translation_change
    Variation_assay

  • Updated: Fri, 6 Mar 2015 21:47 GMT

Add a new inheritance relationship

  • Key: PAGEOM_-16
  • Legacy Issue Number: 13010
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    From the users and scientists points of view, it is thought that there
    is a missing a direct connection between Genomic_allele and
    Genomic_observation. This is very much needed because the Locus
    Specific Databases (LSDBs) and diagnosic labs need direct association
    from allele to abstract observation target.

    Suggested resolution:

    Add a new inheritance relationship: The snp2::Genomic_allele should
    inherit from snp2::Genomic_observation.

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Add a new inheritance relationship: The snp2::Genomic_allele should
    inherit from snp2::Genomic_observation.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

several unsufficient cardinalities should be revised

  • Key: PAGEOM_-15
  • Legacy Issue Number: 13009
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    There are several unsufficient cardinalities (listed below in the
    resolution). They should be revised to serve better their scientific
    purpose.

    Suggested resolution:

    Change cardinality of the association between snp2::Latent_genotype
    and snp2::Latent_genotype_specification from '1 to many' to 'many to
    many'.

    Change cardinality of the association between page::Observed_value and
    page::Experiment_result from 'many to 1' to 'many to many'.

    Change cardinality of the association between
    page::Genotype_phenotype_correlation_experiment and
    page::Experiment_result from '1 to many' to 'many to many'.

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Change cardinality of the association between snp2::Latent_genotype
    and snp2::Latent_genotype_specification from '1 to many' to 'many to
    many'.

    Change cardinality of the association between page::Observed_value and
    page::Experiment_result from 'many to 1' to 'many to many'.

    Change cardinality of the association between
    page::Genotype_phenotype_correlation_experiment and
    page::Experiment_result from '1 to many' to 'many to many'.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

Move association

  • Key: PAGEOM_-13
  • Legacy Issue Number: 13007
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The association between snp2::Frequency and snp2::Panel should be
    elsewhere because the frequency of individuals is needed for somatic
    mutations and copy number variations.

    Suggested resolution: Move the association between snp2::Frequency and
    snp2::Panel to an association between snp2::Frequence and
    snp2::Abstract_observation_target.

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Move the association between snp2::Frequency and
    snp2::Panel to an association between snp2::Frequence and
    snp2::Abstract_observation_target.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

Do not include the XSD stereotypes for the classes in the PIM.

  • Key: PAGEOM_-12
  • Legacy Issue Number: 13006
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The diagrams in the final document should not include the XSD
    stereotypes for the classes in the PIM.

    Suggested resolution: Because the diagrams are generated by the EA
    tool and it may be difficult to force this tool not to display the
    stereotypes, and because the diagrams are only illustrative, this
    issue is rejected

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    No Data Available

  • Updated: Fri, 6 Mar 2015 21:47 GMT

Rename attribute 'sex' in snp2::Individual to 'gender'.

  • Key: PAGEOM_-14
  • Legacy Issue Number: 13008
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    There is a concern about the attribute name 'sex' that does not
    represents completely what the PAGE model expresses.

    Suggested resolution: Rename attribute 'sex' in snp2::Individual to
    'gender'.

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Rename attribute 'sex' in snp2::Individual to
    'gender'.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

remove stereotypes

  • Key: PAGEOM_-11
  • Legacy Issue Number: 13005
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    The PIM (as expressed in the XMI and text descriptions) should not
    include XSD specific stereotypes for the UML classes (with the
    exception of the basic types package, because PAGE-OM uses a subset of
    xsd types for primitive types).

    Suggested resolution: Remove these stereotypes, either by finding the
    appropriate option in the EA tool, or by manual removing them from the
    generated XSD.

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Remove these stereotypes, either by finding the
    appropriate option in the EA tool, or by manual removing them from the
    generated XSD.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

redundant association from Enum to Value.

  • Key: PAGEOM_-10
  • Legacy Issue Number: 13004
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Probably by mistake, there is a redundant association from Enum to
    Value.

    Suggested resolution: Keep the association from Enum to Value, but
    name the association between Value and Value as "hierarchical_value".

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Keep the association from Enum to Value, but
    name the association between Value and Value as "hierarchical_value".

  • Updated: Fri, 6 Mar 2015 21:47 GMT

Rename the association from Consensus_genomic_genotype to Latent_genotype

  • Key: PAGEOM_-7
  • Legacy Issue Number: 13001
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    It is necessary to name the association from
    Consensus_genomic_genotype to Latent_genotype as
    "latent_consensus_genotype" because there is another association using
    already the default name.

    Suggested resolution:

    Rename the association from Consensus_genomic_genotype to
    Latent_genotype.

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Association from Consensus_genomic_genotype to Latent_genotype
    was removed, because it was not needed.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

duplicated attributes and associations

  • Key: PAGEOM_-6
  • Legacy Issue Number: 13000
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    In some classes (listed below in the suggested resolution), there are
    duplicated attributes and duplicated asociation targets in the
    (generated) PSM model (in the XML Schem). It is caused by the problem
    in the tool (EA) when converting into XML Schema the "diamond
    inheritance" in the model.

    Suggested resolution:

    Remove duplicated attributes from PSM (snp.xsd) of the Sequence tag:
    creation_date, delete_date, lsid, modify_date, name.

    Remove duplicated association targets from PSM (snp.xsd) of the

    Remove duplicated attributes from PSM (snp.xsd) of the Residue_Change
    tag: creation_date, delete_date, lsid, modify_date, name.

    Remove duplicated association targets from PSM (snp.xsd) of the
    Residue_Change tag: Annotation, Publication, Db_Xref, Source.

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Remove duplicated attributes from PSM (snp.xsd) of the Sequence tag:
    creation_date, delete_date, lsid, modify_date, name.

    Remove duplicated attributes from PSM (snp.xsd) of the Residue_Change
    tag: creation_date, delete_date, lsid, modify_date, name.

    Remove duplicated association targets from PSM (snp.xsd) of the
    Residue_Change tag: Annotation, Publication, Db_Xref, Source.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

Rename the association from Multi_variation_assay to Genomic_variation

  • Key: PAGEOM_-9
  • Legacy Issue Number: 13003
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Probably by mistake, there is a redundant association from
    Multi_variation_assay to Genomic_variation.

    Suggested resolution: Rename the association from
    Multi_variation_assay to Genomic_variation. Because it has the same
    semantic as the assotiation from Varriation_assay.

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Remove the association from
    Multi_variation_assay to Genomic_variation. Because it has the same
    semantic as the association from Variation_assay.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

Remove the inheritance from Identifiable in Set_of_haplotypes.

  • Key: PAGEOM_-8
  • Legacy Issue Number: 13002
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Probably by mistake, there is a redundant inheritance from
    Identifiable in Set_of_haplotypes.

    Suggested resolution: Remove the inheritance from Identifiable in
    Set_of_haplotypes.

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Remove the inheritance from Identifiable in
    Set_of_haplotypes.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

change name of some associations

  • Key: PAGEOM_-5
  • Legacy Issue Number: 12999
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    There are associations whose names contain spaces (listed below in the
    suggested resolution). For some tools, it would be better to replace
    them by underscores.

    Suggested resolution:

    Rename association "derived from" (Consensus_genomic_genotype) to
    "derived_from".

    Rename association "is treated as" (Gene_variation) to
    "is_treated_as".

    Rename association "one of" (Genomic_allele) to "one_of".

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    Rename association "derived from" (Consensus_genomic_genotype) to
    "derived_from".

    Rename association "is treated as" (Gene_variation) to
    "is_treated_as".

    Name "one of" (Genomic_allele) to "one_of".

  • Updated: Fri, 6 Mar 2015 21:47 GMT

remove duplicated attributes

  • Key: PAGEOM_-4
  • Legacy Issue Number: 12998
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    Some classes (listed below in the suggested resolution) that inherit
    from Identifiable should not have duplicated attributes (because they
    are redundant).

    Suggested resolution:

    In bref::Bibliographic_reference, remove the second Provider
    association.

    In bref::Journal, remove the 'name' attribute.
    In snp::Organization, remove the 'name' attribute.
    In snp::Map, remove the 'name' attribute

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    In bref::Bibliographic_reference, remove the second Provider
    association.

    In bref::Journal, remove the 'name' attribute.
    In snp::Organization, remove the 'name' attribute.
    In snp::Map, remove the 'name' attribute.

  • Updated: Fri, 6 Mar 2015 21:47 GMT

The PSM namespaces should be rooted on the OMG spec directory URL


reference to an OMG rooted URL


There are missing attributes 'schemaLocation' in the *.xsd files.

  • Key: PAGEOM_-3
  • Legacy Issue Number: 12997
  • Status: closed  
  • Source: Japan Biological Informatics Consortium ( Martin Senger)
  • Summary:

    There are missing (even though optional) attributes 'schemaLocation'
    in the *.xsd files.

    Suggested resolution: In all generated XML Schemata (the PSM model,
    the *.xsd files), add the 'schemaLocation' attribute to the import
    tags. For example:

    <xs:import namespace="http://www.openpml.org/page-om/fuge" schemaLocation="fuge.xsd" />
    <xs:import namespace="http://www.openpml.org/page-om/snp" schemaLocation="snp.xsd" />
    <xs:import namespace="http://www.openpml.org/page-om/snp2" schemaLocation="snp2.xsd" />

  • Reported: PAGE-OM 1.0b2 — Wed, 29 Oct 2008 04:00 GMT
  • Disposition: Resolved — PAGE-OM 1.0
  • Disposition Summary:

    In all generated XML Schemata (the PSM model,
    the *.xsd files), add the 'schemaLocation' attribute to the import
    tags. For example:

    <xs:import namespace="http://www.openpml.org/page-om/fuge" schemaLocation="fuge.xsd" />
    <xs:import namespace="http://www.openpml.org/page-om/snp" schemaLocation="snp.xsd" />
    <xs:import namespace="http://www.openpml.org/page-om/snp2" schemaLocation="snp2.xsd" />

  • Updated: Fri, 6 Mar 2015 21:47 GMT