towards a richer set of information to describe our complete genome collection

Telecon: 2007 03 23

From Genomic Standards Consortium

telecons


2 pm GMT, March 23, 2007


Towards FuGE compliance (continuation of telecons on CAMERA requirements)


Expected: all from last call, Allyson Lister

Apologies: MPI Bremen - MetaFunction meeting


AGENDA

  • review of FuGE as appropriate (AJ)
  • brief description of the CISBAN portal - an 'omic repository based on the FuGE-STK

http://elephant.ncl.ac.uk:8081/portal/home.jsp

  • towards a MIGS/MIMS-OM - review of checklist / schema. Please see Allyson's MIGS-FuGE Notes page for a straw man.
  • review of proposed changes for 1.2
  • AOB



Notes:


Present: Aaron, Leonid, Nelson, Kelvin (working on mapping to MIGS inside CAMERA), Allyson, Andy, Norman, Tanya, Dawn


DF: there is a new wiki page, Andy and Allyson have contributed (wiki was having problems today so we circulated the relevant docs)

DF: let's move onto Andy for further background on FuGE

AJ: I can go over the ontology package if people like (agreement to focus on this as we want to finish the XML in the MIGS schema that deals with ontology term capture)

AJ: the doc contains examples of what the XML would look like; there are many ways to represent ontology terms in XML, there is a formal FuGE compliant way of doing this


  • excerpt from Andy's doc:

Example 1 (true FuGE-compliant)

<AtomicValue value="15"> <unit OntologyTerm_ref="ex001:OntologyIndividual0"/> </AtomicValue>

Reference to…

<OntologyIndividual identifier="ex001:OntologyIndividual0" term="hour" termAccession ="UO:0000032" OntologySource_ref="ex001:OntologySource2"/>

with a further reference to ...

< OntologySource= "http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo?view=log" identifier ="ex001:OntologySource1" name="OBO-unit"/>


Followed by discussion of how to represent measurements and AJ confirmed that measurements are done in the measurement package and this example should be changed.


AJ: In FuGE-compliant XML, all CV terms have unique ids are given only once with a reference (at top of bottom of file) - this is FuGE compliant - all under a common root called ontology collection


We need as a group to decide what to add manually to current XML schema, but in the future the schema will be generated from the UML, AJ: it can be customizable


Allyson demonstrated the CISBAN portal

AL: generates FuGE compliant files (no domain-specific extensions yet available)

DF: can we have a copy of the generic FuGE XML doc you just showed us?

AL: here is is: FuGE Core.xml (comes from the FuGE UML which generates the FuGE XML schema - UML requires MagicDraw: http://fuge.sourceforge.net/dev/index.php)


Then we reviewed Allyson's notes of mapping the MIGS checklist to FuGE


  • one issue is that we need an extension for geographic location


  • could generate MIGS specific set of protocols (could use generic, but perhaps not specific enough)


DF: a simple strawman UML and XML schema would really be helpful - how soon could that be developed?


Allyson and Andy discussed how to move forward on a practical and decided to focus on the core aspects of MIGS - could be delivered by next week


Agreed: GSC needs to focus on 1.2 schema (CAMERA requirements) but have set in motion the OM and this can be delivered later which is great

N: confirmed that CAMERA interest is in the schema so they can do the mapping to internal database; they already have an object model


DF: asked if it could be circulated


L: still in internal development


DF: I suggest a timeline for MIGS-OM generation of schema - suggested draft at June 6-8 workshop, write out XSD by September


AJ: could be much sooner as we have practice doing this


Then discussion moved to exchanging data between sources


N: how do you see MIGS related to NCBI

DF: we are working closely with the INSDC - MIGS is an extension of what they capture


N: a vision of shared resources in the future - ability to share and trade data from GSC, CAMERA and NCBI etc would be great


DF: I would suggest a future telecons topic of GenCat and the Genomic database ID mapping project since those are tools for exchanging data


N: we did discuss LSIDs and CAMERA as an LSID authority, is this still of interest?


DF: yes, but not for IDs for projects, but in the context of unique ID's for the 're-usable' parts of MIGS (e.g. BioMaterial as we discussed) -and this would be great


AL: Newcastle has an LSID authority already:

Useful links:

The technical docs say the following about lsids currently (needs to be updated): " Further, although we do have an LSID Resolution Service running via http://elephant.ncl.ac.uk:8081/authority, due to our beta release status, we cannot currently guarantee that the object returned will always return the same thing. Therefore, until we are at our first full, stable, release we will not be fully compliant with the LSID standard. However, you are free to test the LSID server now, together with the DPI. More information on contacting the LSID Resolution Service will be added shortly, together with an example Java class."


AOB

Norman: interested in a sub conference call on terms, hard to get them and with definitions - want to work on the later

N: weren't precise definitions when they were applied

DF: we should get the GSC to make a more co-ordinated effort now that things are really moving ahead in OBI


Actions:

Actions: Aaron and Andy to go over specifics on getting the XML compliant - but not for now, suggested this be a candidate feature for 1.3 FuGE-compliant version

Allyson to work on MIGS OM with Andy - just most core items - first draft of UML and schema by end of next week

CAMERA to post draft docs of schema and word doc to the CAMERA wiki


Dawn and Norman not around next week, the following Friday is holiday in UK for Easter. Decided to have the next telecon in two weeks to discuss updated CAMERA requirements doc - CAMERA to post docs by email for discusion, Tuesday the 10th at 2pm

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