Telecon: 2007 11 30

From Genomic Standards Consortium

Time : 4pm GMT

[edit] Participants:

• Sean Murphy
• Leonid Kagan
• Dawn Field
• Peter Sterk
• Renzo Kottmann
• Tanya Gray

[edit] Notes

[edit] Items for the agenda

Renzo released new version of GCDML release with GML removed for report types

Continued development of gencat. Demo available with latest GCDML schema loaded: http://gensc.org/gencat http://gensc.org/gencat/gcat/reports/create/input Release version next week with subsequent update to genome catalogue

At last telecon, James Cole described need to review EML in relation to GCDML.

GSC workshop

Peter Sterk's data

capture of controlled vocabulary terms

next pre-release of GCDML

[edit] Use of GML

SM - including gml reference in the schema – if you use java tools – it makes the import of the schema much more complicated

LK - i do not think we should go for an alternative to gml format – we can go towards to making it easier to construct by providing a set of recipes, and eventually there will be tools that will let user construct xml

RK – i have provided basic set of gml – also started to document it but not in a cookbook way. can also provide links to java based software

SM – that sounds great. issue is not whether it is simple but how much jungle to machete through to find that it is simple

[edit] GCDML

RM has submitted new version of GCDML including changes to measurement elements.

Will update further to discussions today and publish final pre-release version before workshop before Tuesday.

SM - do we have official versioning for gcdml?

RK - no, not at moment. one of points i want to raise. hard to discuss at telecon. should discuss outside of telecon to agree on best action for versioning.

at the moment that is why i call it a pre-release version

leonid – you can go with subversion version number – integer

renzo – this version is complete with respect to migs/mims compliance. only thing left from my side is that there are some controlled vocabulary terms missing

would like to have action to finish controlled vocabulary so that it can be released in gcdml

dawn – do it on demand. or go get useful set of cv's

at workshop get quick and obvious controlled vocabulary terms

TG - described controlled vocab term capture in gencat with associated review/approval.

SM single main issue we have – how do we describe in sufficient detail the precise way in which our samples have been collection – if sample comes from wood – sunny side facing the sky

on whale fall – physiological part of that – these distinctions are crucial for the researchers

renzo – i completely agree – my motivation to look at eml

eml could provide solution for this detail of origin of describing samples

extent of envo ontology has been developed and be incorporated

options:

• do it completely with ontology
• do it with eml
• or custom solution

renzo – will come up with 3 lines of ideas and send out tuesday

tanya - described idea for how ontology terms could be used in gcdml and still allow schema parser to validate xml instance including term values. input form would provide ontology term lookup using web service. the term would be captured for review/approval together with ontology term identifier. on approval the term would be inserted as an enumeration in the schema. the enumerated element would have a corresponding ontology term identifer attribute to capture identifier in xml instance. requirement that ontology is available via web service. this would address renzo's idea that only most popular ontology terms would be included in the gcdml schema

[edit] GenCat

RK - suggestion to use alternative to table to control input form layout so it is not so wide

TG - CSS is an option - will look into it

[edit] Environmental Markup Language

environmental markup language

TG -- how to review this?

dawn – raise it at first sessions at the workshop

renzo – technically this is nice but they have re-invented the wheel

how should we look at it – look at how to convert gcdml to eml – or integrate eml components into gcdml? for me it is matter of discussion and decision

dawn - a lot of people think it is a competing concern

renzo – i think aim of schemas is different – with eml cannot model migs/mims using eml. no molecular component as far as i can see

dawn – it would be nice to have a gsc faq – one of obvious questions is how does gcdml differ from eml -

sean – natural that our focus is on ecology – but long term industrial and medical communities will be just as or maybe more prominent that ecology

SM -gcdml could be umbrella that subsumes eml in future

[edit] Phage Dataset

peter – will arrange for phage data submitted next week – should have phage data before the meeting

[edit] Actions

Renzo

• prepare cookbook documentation on use of GCDML
• document changes made to GCDML
• prepare brief description of GCDML for proposed GSC newsletter
• update workshop slides with description of GCDML vs EML
• update GCDML schema further to discussions and publish next pre-release version
• ideas to address sean's requirements

Sean

• prepare cookbook documentation on use of GCDML

Dawn

• finalise delegate list for workshop
• write to Matt Kane for request to point use to documentation on EML compliance
• start a GSC FAQ on the wiki

Tanya

• investigate use of CSS to control report input form layout
• send out notice for telecon next week
• release gencat next week
• update genome catalogue with new codebase
• work with peter to upload reports

Peter

• generate GCDML complianet genome reports from dataset next week