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.

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."

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".

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

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.

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).

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.

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)."

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.

• 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

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.

• 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

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.

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

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.

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.]

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

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

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?

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.

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?

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.

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.

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

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

No Data Available

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

• 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

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

• 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]

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.

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

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.

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

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."

Replace the text above by the text below.

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."

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."

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.

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

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'.

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'.

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

No Data Available

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'.

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

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.

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

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.

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

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.

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.

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.

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

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".

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

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.

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

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.

Remove the inheritance from Identifiable in
Set_of_haplotypes.

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" />

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" />

Suggested solution: Change namespaces in the generated PSM (XML
Schema) to the following:

• http://www.omg.org/spec/PAGE-OM/20081231/snp
• http://www.omg.org/spec/PAGE-OM/20081231/snp2
• http://www.omg.org/spec/PAGE-OM/20081231/fuge
• http://www.omg.org/spec/PAGE-OM/20081231/page
• http://www.omg.org/spec/PAGE-OM/20081231/bref

Change namespaces in the generated PSM (XML
Schema) to the following:

• http://www.omg.org/spec/PAGE-OM/20081231/snp
• http://www.omg.org/spec/PAGE-OM/20081231/snp2
• http://www.omg.org/spec/PAGE-OM/20081231/fuge
• http://www.omg.org/spec/PAGE-OM/20081231/page
• http://www.omg.org/spec/PAGE-OM/20081231/bref

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".

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".

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

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.

Change the following reference to an OMG rooted URL: "For convenience,
the whole PAGE-OM specification can be seen at
http://www.openpml.org/page-om/model/."

Suggested resolution: Change it but not to the OMG rooted URL but to
this one: http://www.pageom.org/models/omg/v_1.0/

Change it but not to the OMG rooted URL but to
this one: http://www.pageom.org/models/omg/v_1.0/