Telecon: 2008 05 08

From Genomic Standards Consortium

This telecon is dedicated to further discuss the integration of Habitat-Lite and GCDML see also Telecon:_2008_05_02.

[edit] Attending:

Lynette Hirschman (MITRE, Boston) Renzo Kottmann (MPI, Bremen) Ryan Farris (RDP, E Lansing)

[edit] Notes:

Renzo gave a quick summary of discussion last week with Scott Mardis (MITRE), Dawn Field and M. Ashburner

Q: Who is using GCDML?

CAMERA - will probably build Java libraries for import, export to and from GCDML -- based on discussion w Sean Murphy and Leonid Kagan -- in Maryland. If they do this, they would probably be willing to make these libraries available.

Ryan: Status of Prototype of survey questions for RDP?

Lynette will look over promised questions and respond.

There are two approaches to implementing Habitat-Lite in GCDML

SAWSDL solution - semantic annotation of XML schema Mapping might not so straightforward on the first look.

Other aspect:

GCDML - incorporate Habitat-Lite as terms in GCDML Right now, there are children under <originalSample/>,including water column, sediment,...

This may (or may not) be consistent with Habitat-Lite (and EnvO) structures. Both GCDML, Habitat-Lite and EnvO are still a bit in flux...

Lynette: for annotation in Habitat-Lite,it would be nice to have LEVELS of annotation top level: air/water/terrestrial + maybe food, organism-associated

next level: specifics of habitat And have all this as a series of drop-down menus for people to choose from (PLUS type in full text)

Could this be accommodated in GCDML?

Renzo: it might be tricky and introduce some inconsistencies. In GCDML - people can annotate both (water column, sediment)

Renzo agrred to make a concrete suggestion

There is now an element called marine, within that - element called sediment and a sibling called water column

Lynette: what is the relation between GCDML and migs/migs check list?

Renzo: A standard XML parser only validates if the constraints of the MIGS/MIMS checklist are preserved. This is one application of GCDML; Another application is to take single elements from GCDML and use it for information exchange, e.g., DNA library element

Next steps:

Lynette will send comments to Jim Cole, Ryan Farris on proposed RDP questionnaire/survey (Done)

Lynette will resolve issues on current version of Habitat-Lite and put version (or pointer to version) on the wiki and let Renzo and others know.

Renzo will be working on GCDML and support for Habitat-Lite possibly next week, if Habitat-Lite is stable.

Lynette will talk to Nikos and Victor re GOLD/IMG and use of Habitat-Lite; possibly also to CAMERA people re their tools for import/export of MIGS/MIMS checklist (and GCDML).