Metabolomics Society - Ontology WG – March 2, 2006 call
ATTENDEES:
Oliver Fiehn, Irena Spasic, Andy Tseng, Daniel Schober, Larisa Soldatova and Susanna-Assunta Sansone. Absents: Philippe Rocca-Serra, Matej Oresic, Martin Scholz, Helen Jenkins, Bertram Ludaescher, Lori Querengasser and Chris Taylor
AGENDA and MINUTES:
a. Review actions from previous call <Feb02-06-OWG-minutes.doc>
- Group calendar is now up and running and all the files have been posted. Public webpages and mailing lists (under the Metabolomics Society main page) are not available yet (see ACTION 1).
- Daniel has started working on the NMR list of terms (see section below).
- Comments of the roadmap have been sent by Irena and Andy. Irena also suggest a new version of the figure one, illustrating the experimental components. Susanna will integrate these and produce a final document asap (see ACTION 2).
- The OWG members have been invited to read, comment and approve the final version (see ACTION 3), so this can be circulated to the other WGs.
- Larissa has sent comments to the < Naming_Conventions_DRAFTv2.doc> and has suggested adding more information on the ‘relationship’. The paper from Barry Smith < Relations in Biological Ontology's> is a useful resource. Daniel will integrate these into the draft, extending it. Barry Smith will also be consulted and asked to comment the proposed conventions (see ACTION 4).
- Use cases and competency questions for the Ontology have not been collected (see ACTION 5).
b. Working on the CVs for the NMR subcomponent.
- Following the steps described in the roadmap (see ‘Phase 1’, section on ‘CVs master list’), Daniel has selected some terms from Helen’s NMR list (from < armet_vocabs.xls>) and is currently reviewing these in the light of the proposed naming conventions. He will post a first draft along with an explanatory document (see ACTION 6).
- This should be considered as a test, to proof that our strategy to build CVs master list for each instrument-specific subcomponents works. All the members have been invited to review and discuss the work (see ACTION 7).
c. Working on the PSI CVs for the MS subcomponent.
- Some of the members of the Metabolomics Society Oversight Committee will meet at the PSI meeting, April 21st in San Francisco and a presentation of the Metabolomics Standards Initiative will be made (by Oliver?). The OWG should provide some comment on the usability of the PSI MS CVs in the metabolomics domain (is the coverage sufficient, what is missing etc.). Oliver will review: 1) the <MS-psi-ont-obo.xls>, an excel spreadsheet formatted version of the PSI MS OBO ontology; and 2) the <GCMS.xls>, Irena’s list of terms and definitions for GC-MS from the Leco manual (see ACTION 8).
d. FuGO and OBO
- At the FuGO workshop, Barry Smith, suggested FuGO should be part of the OBO Core Ontology ( as an ‘Application’ ontology (designed for a specific application, in this case data annotation for reporting, submitting and retrieving information). To be part of OBO, FuGO will need to comply with the ‘OBO Evaluation Criteria’, see <OBO_Evaluation_Criteria_draft>. The communities participating in FuGO have been asked to vote in a teleconference on March 8th. Susanna will report the vote of the OWG to the other FuGO communities.
- The OBO distinguishes a certain collection as core ontologies: those that have been built according to sound ontological principles. The determination of whether or not an ontology will be included in the OBO core set of ontologies will be based upon the degree to which it meets these criteria (see < OBO EVALUATION CRITERIA.doc>).
- The OWG members have been invited vote asap – by Mach 7th- (see ACTION 9). Susanna’s vote is for FuGO to be an OBO Core Ontology.
e. Plans for a face-to-face workshop in May.
- The WG has agreed to organize a 2 days face-to-face workshop at Un of Manchester in May, to prepare for the Metabolomics Society’s meeting in Boston, June. Irena will suggest few dates in May (see ACTION 10).
- The proposed agenda is 1) FuGO overview/discussion and tune the work of the OWG with those of others communities within FuGO, 2) Work on CVs for specific experimental components; 3) Users’ interaction and feedback on CVs. Confirmed participants: Larissa, Chris, Daniel, Philippe, Susanna, Irena and Andy.
- The group will also consider a teleconference with members that cannot attend.
f. Unified Medical Language System (UMLS) collaboration.
- Irena and Daniel have discussed with Olivier Bodenreider (of NLM/UMLS, the issue of supporting the technological side of biomedical research in UMLS. Olivier is very positive and would be happy to include in UMLS this type of terminologies, provided that these are well-maintained sources.
- UMLS comprises various vocabularies and some of them may be reused for the metabolomics ontology (e.g. chemical compounds, metabolites etc.)
- Irena has already used UMLS in her research projects; she will download and query UMLS, existing terminologies, identifying gaps and needs (see ACTION 11).
g. Set our next steps, actions, calls etc...
- Susanna has invited the OWG to cc any communications to all the members.
- The next call is scheduled for March 16th at 5pm Central European Time (UK= 4pm, US= 8am PST, 11am EST).
ACTIONS (P= PENDING)
1-P. (Susanna) Follow up on webpages and mailing list.
2. (Susanna) Finalize roadmap.
3. (All) Read, comment and approve the final version.
4. (Daniel) Extend the naming convention doc.
5. (All) List use cases and competency questions for the Ontology.
6. (Daniel) Circulate initial work on the NMR CVs subcomponents.
7. (All) Respond and send comment on the NMR CVs subcomponents.
8. (Oliver) Review PSI MS CVs and CG-MS terms for Leco manual.
9. (All) Vote for FuGO ‘to be or not to be’ an OBO Core Ontology by March 7th.
10. (Irena) Propose dates in May for a 2 days workshop.
11. (Irena and Daniel) Follow up on UMLS and review current terminologies.