GSA Markup Meeting Notes

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Jan 11, 2011, 11am EST/2pm PST

Attended:

  • WormBase(Pasadena): Karen Yook, Daniela Raciti, Chris Grove, Ranjana Kishore (Dallas), Kimberly Van Auken (Princeton)
  • Textpresso(Pasadena): Arun Rangarajan, Michael Mueller
  • SGD: Marek Skrzypek(Mass), Jodi Hirschman(Mass), Eurie Hong(Stanford)

Correct call in info (for future reference): 1-866-528-2256 / Participant code: 714646

Topic: linking GO terms in GENETICS papers; this was brought up by Marek when he noticed that a paper could have benefited from protein complexes being linked to SGD GO pages.

Major issues:

  • The audience for linking needs to be made more clear as this will drive the types of GO links made.
  • GO term stability needs to be taken into account when linking-- what happens when a GO term is made obsolete? Is one ontology or branch of an ontology more stable than another, and how do we handle the ones that are not stable?
  • Linking to AmiGO instead of or even as well as MOD pages-- in the beginning we will only make links to the MOD but we come back to address this after we have determined the overall feasibility of GO term linking.
  • Curator effort--this is going to be initially large, but will decrease over time.

Action Items, over the next few weeks:

  • Arun will create a GSA linking development site that will be used for developing and testing scripts without impacting the live linking pipelines already in place.
  • Kimberly and Ranjana will give Arun entity list sources for all GO ontologies (to be used for both worm and yeast papers).
  • Using already linked GSA papers, Arun will include linking GO terms in abstracts to the linking script.
  • Ranjana will do QC on worm papers for these papers, Eurie/Marek/Jodi will do QC on yeast papers.
  • Kimberly will do manual linking of the abstracts in parallel with the automated scripts recording the time it takes to do the various; while doing this she will also develop an entity list for GO linking.
  • SGD and WB will also compare linking with other text markup projects/tools - gopubmed.org and NCBO annotator