Difference between revisions of "GSA Markup Meeting Notes"
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===Jan 11, 2011, 11am EST/2pm PST=== | ===Jan 11, 2011, 11am EST/2pm PST=== | ||
'''Attended: ''' | '''Attended: ''' | ||
| − | *WormBase(Pasadena): Karen Yook, | + | *WormBase(Pasadena): Karen Yook, Daniela Raciti, Chris Grove, Ranjana Kishore (Dallas), Kimberly Van Auken (Princeton) |
*Textpresso(Pasadena): Arun Rangarajan, Michael Mueller | *Textpresso(Pasadena): Arun Rangarajan, Michael Mueller | ||
*SGD: Marek Skrzypek(Mass), Jodi Hirschman(Mass), Eurie Hong(Stanford) | *SGD: Marek Skrzypek(Mass), Jodi Hirschman(Mass), Eurie Hong(Stanford) | ||
| Line 22: | Line 22: | ||
*Ranjana will do QC on worm papers for these papers, Eurie/Marek/Jodi will do QC on yeast papers. | *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. | *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 - [http://gopubmed.org/web/gopubmed/2?WEB10O00h00100090000 gopubmed.org] and [http://www.bioontology.org/annotator-service NCBO annotator] | ||
Latest revision as of 23:31, 11 January 2011
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
