Telecon: 2007 03 9 2pm

From Genomic Standards Consortium

March 9, 2007

Agenda,

CAMERA requirements for MIGS/MIMS - discussion with RSBI (http://www.mged.org/Workgroups/rsbi/rsbi.html

Present: Renzo, Thierry, Frank-Oliver, Tanya, Susanna, Phillippe, Dawn,Saul, Nelson, Sam, Aaron, Leonid

Apologies: Norman, Chris

Agenda -contributed by CAMERA

Here's some items that we need to resolve:

Consensus on top-level concepts and their relationships

-Definitions of Biomaterial, Biosource(?), Biomaterial Treatment vs Assay or AssayMaterial, etc

-Relationships between terms to be consistent with RSBI

-Should Assay be a child of Biosample? Leonid's suggestion is to simplify here.

How should users define Habitat type?

-What environment ontology to use?

-Norman, any ETA on the ontology that you are working on?

-If it's at too early of a stage, should we endorse NASA SWEET ontology initially?

Consensus on global, "cross-cutting concerns" such as conventions on the

-use of identifiers

-use of ontologies or controlled vocabularies

-use of units and measurements

-properties of any value (eg. Mean, median, std deviation, min, max of range)

Let's try to work through as many of these items as we can on Friday.

Regards, Nelson

Notes:

-DF: didn't update last document: NA: CAMERA waited until this discussion to carry on, so still time to integrate discussions from both telecons before re-circulating it

-group agreed make to make telecon notes public

-introductions by SS and PRS since new to the telecons

-NA: asked for a background to RSBI

-SS: RSBI isn't interested in terminology, but in modularity of checklists - therefore RSBI came up with calling everything an Investigation - the Study is the 'sample' and the Assay is when it enters the technology; now working within OBI to standardize the terminology for this; SS asked if the I/S/A terms came from MGED; DF explained it came from MIGS having I/S/A and CAMERA data being more complex - need to transform the biosource through filtering; CAMERA went to the CMAP image on the RSBI site; SS: good: PRC: filtering of source should be transformation of biosource

-NA: biosource->biomaterial->biosample; if a treatment is applied it is a biosample; biomaterial was original a container for biosource and biosample

-SS: the CMAP is not a formalized, just a guide

-NA: the CMAP is still helpful, seeing if MIGS has everything

-SS: yes, judging against the CMAP is a good exercise

-L: going back to the MIGS schema; for a metagenomic study there could be any number of biosources

-NA: in MIGS BioMaterial is BioSource; in the future we could use Phillipe's suggestion of BioMaterial as a container for BioSource and BioSample

-NA: what is sample processing

-DF: listed items from checklist on web

-NA: how do we link this information to multiple biosources (could be different)

-DF: assume this is where we use your concept of id's for re-usable aspects of schema (biomaterial, biosource)

-SA: will id's be explicit in the schema?

-NA: yes, we think so, CAMERA to take a stab in new version of schema

-NA: let's move on to global issues: what about the ID's; should we use LSIDs; DF: yes, we suggested this from the beginning; NA: yes CAMERA is trying to use LSIDs; TG: would need our own resolution service; there are other unqiue identifiers that do have this; Tanya provided this URL / info:

-below is a link to the Archival Resource Key (ARK) unique identifier naming scheme that was mentioned in the teleconference as an alternative to LSIDs:

http://www.cdlib.org/inside/diglib/ark/

-The Archival Resource Key (ARK) identifier is a naming scheme for persistent access to digital objects (including images, texts, data sets, and finding aids), currently being tested and implemented by the California Digital Library (CDL) for collections that it manages.

-DF: could CAMERA provide an LSID authority?: NA: could look into it, sure: DF mentioned discussions of DOIs versus LSID have happened at past GSC workshops; agreement: let's go forward if possible

-SS: What about FuGE?

-DF: yes, Allyson Lister will be trying to generate a MIGS-OM based on FuGE (hopefully by the workshop)

-SS: pointed out the FuGE paper in the Nat Biotech consultation (along with the MIGS paper)

-SS: pointed out the RSBI has FuGE case studies, SS circulated the link: http://www.mged.org/Workgroups/rsbi/RSBI_use_case_in_FuGE-July06.doc

-NA: let's talk about how we want to use ontologies

-SAM: ontology_prop should be included across the schema? DF: Yes, as we said, MIGS now has CV or a specific ontology identified for each element; when an existing ontology can be used; a user should be directed to it and the software implementation should grab the metadata behind it automatically, if we allow 'unknown' ontologies (or lists of terms etc) to be made; the ontology_prop item should be similar; Phillipe?

-PRC: yes, good summary, if you have an LSID authority this could be implementated as a service

-SS: FuGE - also contains optional links for ontology properties; NA: are you using identifiers; PRC; yes, but need an authority to make this work; PRC: versioning can be an issue if holding the metadata in annotation files

-NA: there seem to be different types of ontologies; terms versus ranges, PRC: mentioned CNote tool, can combined things like PATO, units, measurements; PRC: one can create statements by linking together strings of terms from different ontologies; FuGE allows this

-Renzo: I want to jump in here: have been looking into GML - flexible way to link to ontologies and dictionaries; deal very precisely with measurements (done in context of extending the geographic portion); could look to this to provide measurements / units; NA: can you follow up with specific suggestions on how we use them? RK: yes, I've already started to prepare a document, I can circulate it soon; will be ISO standard soon, therefore more benefits as well

-RK: yes, the CAMERA proposed extension to MIGS is GML compliant; will put into in the wiki

-RK: the MIMS portion can be GML compliant as well; but we still need to discuss which units / measurements; by implementation we can give freedom back to the users to pick multiple (e.g. jscience library for SI units)

-NA: how to deal with habitat type:

SampleTerms from Renzo: http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/Sample_Terms

new page for CVs and Ontologies http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/CVs_and_Ontologies

-NA: yes, we can post the GOS terms to the web

-DF: Will add "MIGS/MIMS Compliance with other standards" to main page of wiki

Decided:

Telecon: Fridays would be good Future topic: FuGE-OM

Agenda for next week:

-RK: GML

-All: review of the sum CAMERA proposed changes (doc and XML schema) - bring items to completion