Talk:2010 Bar Harbor Agenda: Difference between revisions

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==Minutes==
==Minutes==
-Mindi XX from RGD- taking over Simon's position
-Mindi XX from RGD- taking over Simon's position
-Sven's first GO meeting


===Grant Aims (Suzi)===
===Grant Aims (Suzi)===
Line 20: Line 21:
*All these items available on the wiki. Please use the tracker and add your thoughts.
*All these items available on the wiki. Please use the tracker and add your thoughts.
* We want to build the ontology automatically. CheBI is not requesting terms from us. It is the use of other ontologies to build GO.  
* We want to build the ontology automatically. CheBI is not requesting terms from us. It is the use of other ontologies to build GO.  
* How are we doing? Metrics? are we meeting our goals? If we can provide some sense of completeness, breadth of annotation etc. Scientist who use the GO should provide metrics on how GO worked for us. Some papers say GO is great, some papers use other resources and so on. * Just because the paper used KEGG, doesn't mean they did not like GO. They probably did not get the results they wanted with KEGG. If people are finding GO to be complex, we shd provide cuts of GO (GO-slims). 2 kinds of consumers (MODs and groups like Reactome and then consumers who stay at a distance and plug in their data into GO).
* How are we doing? Metrics? are we meeting our goals? If we can provide some sense of completeness, breadth of annotation etc. Scientist who use the GO should provide metrics on how GO worked for us. Some papers say GO is great, some papers use other resources and so on. * Just because the paper used KEGG, doesn't mean they did not like GO. They probably did not get the results they wanted with KEGG. If people are finding GO to be complex, we shd provide cuts of GO (GO-slims). 2 kinds of consumers (MODs and groups like Reactome and then consumers who stay at a distance and plug in their data into GO). Many people who go away are because they don't find the data in GO (not annotated). Karens comment- user said 'i can't remember if the term is in the MF or BP'.
* Mary-metrics with 'us'. How do we use it (Mods), metrics on how many papers have been curated by the MODs, these metrics are important as well.
* How about we pair up with a specific group (say cancer biologist). Do analysis with them (now and after 3 months)
* if we got more mappings to ext. databases, then users don't have to learn a new system. they could say use just metacyc
* Talk about IEA mappings (parking lot discussion)
* leverage existing tools (PAINT and PANTHR families) and what we have in GO and do a first pass. Get broad coverage. Depth coverage is costly.

Revision as of 11:13, 7 September 2010

Minutes

-Mindi XX from RGD- taking over Simon's position -Sven's first GO meeting

Grant Aims (Suzi)

  • Aim 1:
    • building the ontology- regulates relationship, is_a, connecting to external ontologies (CheBi, Cell ontology)
    • ref. genome- lot of progress
    • general annotation, MODS, WGs coming together, coming up with standards- good progress.

So to some extent our aims will remain the same.

    • How can we get detailed/rich annotations
    • Quality control group
    • rate limiting step- literature curation. Improve on item e. Richness is vague. Elaborate on that item.
  • Aim 2: Ref.genome
    • improve software
  • Aim 3:
  • 2b-Infrastructure to approach these bacterial folks to make annotations. Do we have better relation with JGI now? Suzi- Yes. She has been invited to give a talk. Jonathan Eisen is involved.
  • How to find out who is doing what- lot of c.elegans-pathogens papers. Where do you send the pathogen information? No infrastructure for that. It is not that we are having difficulty identifying genes to annotate.
  • All these items available on the wiki. Please use the tracker and add your thoughts.
  • We want to build the ontology automatically. CheBI is not requesting terms from us. It is the use of other ontologies to build GO.
  • How are we doing? Metrics? are we meeting our goals? If we can provide some sense of completeness, breadth of annotation etc. Scientist who use the GO should provide metrics on how GO worked for us. Some papers say GO is great, some papers use other resources and so on. * Just because the paper used KEGG, doesn't mean they did not like GO. They probably did not get the results they wanted with KEGG. If people are finding GO to be complex, we shd provide cuts of GO (GO-slims). 2 kinds of consumers (MODs and groups like Reactome and then consumers who stay at a distance and plug in their data into GO). Many people who go away are because they don't find the data in GO (not annotated). Karens comment- user said 'i can't remember if the term is in the MF or BP'.
  • Mary-metrics with 'us'. How do we use it (Mods), metrics on how many papers have been curated by the MODs, these metrics are important as well.
  • How about we pair up with a specific group (say cancer biologist). Do analysis with them (now and after 3 months)
  • if we got more mappings to ext. databases, then users don't have to learn a new system. they could say use just metacyc
  • Talk about IEA mappings (parking lot discussion)
  • leverage existing tools (PAINT and PANTHR families) and what we have in GO and do a first pass. Get broad coverage. Depth coverage is costly.
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