Summary of the 4th MPDIC Meeting, Kyoto, October 2007
Present: John Hancock, Janan Eppig, Tetsuro Toyoda, Hiroshi Masuya,
Shigeharu Wakana, Christina Chandras, Holger Maier, Steve Brown, Molly
Bogue, Carol Bult, Judith Blake, Elissa Chesler, Paul Schofield.
1 - PPML - It was generally thought that there is a need for a deeper
discussion of this. I re-circulated the schema in my email of November 12th.
In the first instance we would be grateful for any feedback. We will then need
to find an opportunity for a discussion where we can iron out any issues.
Tools to allow creation of PPML files and validate them are also in
development - ideally we would like to be able to demo these as well at a
meeting, but that will depend on the timescale.
A number of additional discussion items came up in relation to procedures.
- How should they be versioned? Is a procedure different if it uses different
parameters (e.g. times between measurements)? Different equipment?
- How should they be validated, e.g. by comparison between centres, as in
EUMORPHIA?
- Should some indication of reproducilbility/ease of use be given?
- It would be important to relate phenotyping procedures to clinical
investigations ontologies [and, more recently, Altman’s “XML-Based
Interchange Format for
Genotype–Phenotype Data”?].
- There is a potential need to link procedures across species
- There would be value in adding a “friendly” clinicial to this group to facilitate
compatibility with what is going on in the human community.
2 - MIMPP (Minimal Information for Mouse Phenotyping Procedures). Too
early to discuss this in detail. The aim of the standard should be to ensure
reproducibility of phenotyping experiments. Will bring it up again in an
appropriate, focussed meeting.
3 - CASIMIR. CASIMIR is committed to supporting developments in many of
the areas of interest to MPDIC. Two particular meetings may be of particular
value - use case meetings which seek to develop. There was also discussion
of a proposed CASIMIR ontology server. It was suggested these resources
might instead be used to improve the OBO server at the EBI. CASIMIR WP4
is likely to sponsor a workshop on using MP and PATO to annotate phenotype
data some time during 2008.
4 - Web site. All are invited to make suggestions.
5 - Paper authorships. Will keep people informed [see recent emails].
6 - Phenotype ontologies. A number of salient areas were discussed:

The nascent trait ontology and how this relates to MP and EQ. PATO
can serve as a logical definition of phenotypes and traits and can link
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trait level and phenotype level formally. [Suggestion: can we work up a
manuscript on this framework, laying down what is needed to formalise
this structure? Perhaps in the OBO Foundry context?]
The relationship between MP and GO Process terms. There is a
general need for more effective cross-talk between ontology
developers in different domains. [This should be an aim of the OBO
Foundry but MPDIC/CASIMIR may be abel to assist]
The need for an assay CV/ontology. This might form part_of the
framework mentioned above - [Procedure: 00001 is_a
Assay_of Trait:00002]]
OMIA (Online Mendelian Inheritance in Animals) [Note: this contains no
mouse data]
Hiroshi’s high level structure for linking from phenotype through to
chromosome. A question that arose was the formalism for describing
phenotypes in this, which of course is a general issue.