Telecon: 2007 02 28

From Genomic Standards Consortium

February 28, 2007

Proposed Modifications to the MIGSs/MIMS Schema

Agenda:

(1) review of how CAMERA works within the GSC

(2)review of discussion doc of proposed changes

Present: Frank Oliver, Renzo, Thierry, Wolfgang, Norman, Dawn, Saul, Nelson, Sam, Aaron, Leonid

Notes:

-Discussion doc to be posted to the GSC wiki for additional consultation

-CAMERA to solicit feedback from its own community and provide feedback into the Nature Biotech about MIGS

-Discuss CAMERA authorship on MIGS paper, offered by Dawn / GSC

-Mechanism of data capture: discuss GCat at a later date (DF: gave brief update)

-Need to define boundary between MIGS/MIMS and very detailed aspects of data model. Detail perhaps more important to metagenomics than MIGS (e.g. data processing more complex, binning, complex assembly practices). FOG: IMG also making progress in this way. Could be defined based on what we expect the user to give. ALL: There are different categories of users.

-Ontologies: CAMERA: proposed ontology_prop not isolated to Biomaterial; DF: yes we are at the stage of identifying ontologies to use with MIGS (see the checklist, OBI, EO, Units, Disease); CAMERA: have looked at SWEET for habitat; Norman gave background to OBI and Env Ontology; CAMERA: asked to be kept informed about developments. CAMERA: want to be able to add multiple terms to a single node and to allow users to use terms from ontologies that we might not already know about (capture URI etc)

-CAMERA: cross-cutting ideas - need for permanent unique identifiers, standard use of ontologies.

-Phenotype: of interest to CAMERA but not in context of ocean samples (could be removed from mock schema showing proposed list of changes)

-UIDS; UIDs - make elements explicit in schema, raises issue of how to define / assign them (e.g. promotes reuse)

-BioMaterial -> add BioTreatment

-Future Telecon on RSBI I/S/A required, CAMERA: very useful to have started discussions with Norman on this call; multi-omic perspective valuable in understanding how other communities have / are dealing with this issue

-Likewise for MIMS (started discussion of parameters in MIMS, units, etc, not all of MIMS available for CAMERA data)

-DF to revise doc (all on telecom to send her any specific comments related to this discussion by tonight for inclusion) and send on to CAMERA for further revisions

-RSBI telecom - try next Thursday (Susanna will be back then)

-Norman collecting terms for BioMaterial types for OBI; would love definitions: CAMERA doing ocean, soil and air sampling