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

Discussion:

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

Proposed solution:

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

No Data Available

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

Discussion: will be solved by new conversion software tool

Proposed solution:

not yet

No Data Available

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

Proposed solution:

Add the following to Section 1.5

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

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

Add the following to the Section 6 (References):

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

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

No Data Available

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

Discussion:

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

Proposed solution:

Reject the issue

No Data Available

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

Discussion:

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

Proposed solution:

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

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

No Data Available

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

Discussion:

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

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

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

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

Proposed solution:

none yet

No Data Available

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

Proposed solution:

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

No Data Available

• Section 4.1 - XLM instead of XML,
• Section 2.0 - 'researches' - should be 'researchers' .
• Section 3.1.1 - XSD and model refer to Anatomic_location, the text
  referes to 'Anatomical_location.
• Section 3.14 - twice "information" in the phrase "contain
  information information".

Proposed solution:

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

No Data Available

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

Discussion:

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

Proposed solution:

not yet

No Data Available

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

Proposed solution:

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

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

No Data Available

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

No Data Available

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

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

No Data Available

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

• All the added classes except Bibref_subject and Bibref_description
  inherit from Identifiable and can have additional properties added to
  them using Annotation and Db_xref. These two classes are mere
  groupings of attributes to Bibliographic_reference and can not exist
  independently.

No Data Available

• Value of 'strand' attribute of Reference_genomic_location is now
  expressed as a 'string' rather than an 'integer'. Valid values are
  'forward', 'reverse' and 'unknown'. 'unknown' is default.

No Data Available

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

No Data Available

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

No Data Available

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

No Data Available

• moved attributes 'size' and 'count_unit' from Population to Panel
• made Individual to inherit from Population
• removed association from Individual to Geographic_location and
  Taxon as they are now inherited from Population
• removed associations from Molecular_sample to Panel and
  Individual and replaced them with one association to Population
• Modified the association from Individual to Panel to allow more
  than one Panel

The net result is that Individual can have new attributes

• race
• ethnicity
• primary_language
• language_family
  and it can be associated to more than one Panel

No Data Available

Removed unnecessary multiple inheritances

• Individual and Sequence were inherited explicitly from Identifiable.

No Data Available

Added abstact class Population to have associations visible

No Data Available