2007 GOC Action Items

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Action Items for review at Sept 2007 GOC meeting held at Princeton

From Jan. 2007 GOC meeting held in Cambridge U.K. http://www.geneontology.org/GO.meetings.shtml?all#consort

Details for Princeton meeting on GO 18th Consortium Meeting pages

1. DONE_Action item for Judy – post templates for yearly reports on Wiki [[1]]

2. DONE Action Item (Hub): Make proposals for various displays of reference genome data
See: http://gocwiki.geneontology.org/index.php/AmiGO:_Prototypes#Reference_Genome

3. DONE (in a sense). Action item for John – make it impossible to add non-is_a complete terms in OBO-Edit.
Addressed by having all GO curators apply a verification check. [mah]

4. IN PROGRESS Action item for Michelle – get this info [i.e., on TIGR course attendance and whether any participants use GO afterwards -mah] We just got our Annotation Engine grant funded and as part of that we will be surveying people who attended the classes.

5. DONE! Action item (David & Chris): create a minimum list of information needed to report methods when doing GO analysis for a publication. This isn't my action item, but this is related. I can tidy this up before the meeting....Val http://gocwiki.geneontology.org/index.php/Reviewing_papers I think this item had to do with tool standards, not reviewing papers. Tools_standards
I seem to recall that both tool standards and paper-reviewing standards were deemed desirable (tho the latter may have transpired after the meeting). [mah]

6. Action Item for Suzi and Managers: Proposal for each working group to write down their protocols and currently active projects. Timelines and priorities/roadmap would be useful. Metrics too. Ontology development_DONE

7. DONE! Action Item for Amelia: Post all presentations from the meeting onto the Wiki site.

8. DONE. Action Item: GO-top: Talk with each manager and bring summary reports to the next meeting.

9. DONE Action Item: Jen and Suzi: Evaluate and make recommendations for project tracking software that might help with this.

10. DONE. Action Item for John: Add a term creation date to the .obo file. It didn't get added to the feature request tracker so it was overlooked. Now added:

11. DONE Action Item for Jen: All “sensu XXX” terms will be changed to “sensu the XXX community”. And undone as well, since it was superceded by the decision to remove sensu altogether (see #72 & &73 below)

12. DONE. Action item for Midori and David (from 2): Find a way to communicate responsibilities and availability viz ontology working groups. Devise a systematic way to bring closure to outstanding term request items. We've made some plans, but not yet acted upon.
We have begun implementing our plans (and refining them, as needed); a respectable number of SF items have been assigned, though for others we still need to find expertise. I think of this as an ongoing ontology development effort rather than a discrete one-off action item. [mah]

13. NOT DONE: Action item for AmiGO Working Group (from 4): The AmiGO Working Group will implement a strategy to incorporate and display the contents of the GO references. Request is on the AmiGO tracker (thanks Jane) http://sourceforge.net/tracker/index.php?func=detail&aid=1667315&group_id=36855&atid=494390

14. DONE! Action Item for Content Group (from 5, low priority): Make actin polymerization a function term. [Content group] In progress, may be done by meeting time; see SF 1621572. -- SF:1621572 closed

15. Action Item for GOA (from 1): Talk to Reactome about getting non-TAS evidence. TAS is no longer considered a useful evidence code and will not be used in any consistency measures of reference genome annotation. Since part of the idea of the reference genomes is to provide a source of IEA annotations for other groups, we strongly encourage reference genome annotators to not use TAS, and instead use experimental evidence codes whenever possible. The GO documentation should also state this in a clear fashion. [annotation camp participants]

16. Action Item for Judy, Harold, Amelia, Eurie, John Day-Richter (from 3,4,5): Resolve communication issues around obsoletes.
What has been done: Obsoletes hidden by default in AmiGO; consider and replaced_by tags deployed in gene_ontology_edit.obo; proposals to obsolete announced on GO list in standard format.

17. NOT DONE (more discussion required) Action Item for Chris and Jane (Revisit 7): Remove the word 'activity' from the molecular function terms, and consider renaming the molecular function ontology. [note that later on in the meeting after action item 73 notes state that more discussion on this proposal is needed]

18. [In Progress] Action Item for Jen & Chris (from 8): Assign priorities for contents changes needed to implement sensu plan. Discuss the different aspects of changes to our use of sensu, write documentation on this, and implement the new strategy. This change will then be announced to the community.
Comment: There is more discussion to be had on this and a slot has been assigned for this in the meeting.

19. SOON TO BE DONE! Action Item for Amelia (Revisit 10): The monthly archive of the GO will also include Release Notes. These notes would include the output of the monthly report script, including the relevant SourceForge IDs, as well as human-readable text that summarizes significant additions or changes to the GO file.

20. Action Item for Karen C. (from 11): Add to the documentation that it is okay to use experimental evidence codes for perfectly identical gene products from different strains of the same species.

21. MOVED to EVIDENCE CODE COMMITTEE: Action Item for Eurie (Revisit 12): No conclusion about how to distinguish large- vs small-scale experiments was reached. People are encouraged to keep thinking about this issue, which clearly needs more discussion.

22. DONE: Action Item for John: Link OBO-Edit docs to geneontology.org from oboedit.org.

23. DONE: Action item for Mike: Change documentation to make clear that annotation file column 1 gives the database from which the identifier in column 2 is drawn, NOT (as it currently says) the id of the submitting authority. [changed DB column definition in http://www.geneontology.org/GO.format.annotation.shtml

24. DONE! Action item for Daniel: Form working group to help groups that are having problems resolving redundancy issues.

25. DONE! Action Item for User Advocacy Group: Make all multi-species files (UniProt & PDB) readily and obviously available on the GO website. Include obvious and prominent documentation explaining that these multi-species files will contain redundancies with the other files, but don't necessarily contain all annotations from other groups.

26. [IN PROGRESS] Action Item for Karen E.(?) & Rex: –Work out kinks in getting this data [i.e., GFF3 files] and make it readily available from the GO site.

27. DONE should be checked by Karen E and Suzanna: Action item (Mike): Add SO ids for allowed objects to documentation. (changed doc to say one of gene (SO:0000704), transcript (SO:0000673), protein (SO:0000358), protein_structure, complex. There does not appear to be a SO term for these two concepts protein_structure or complex)

28. Action item (Suzi, Tanya): Continue developing [protein family-based annotation] tool.

29. Action item (Chris): Do it [i.e., new column in annotation files], add the column and document the formalism.
It's not at all clear why this has my name (and I don't remember); it seems more for the software group and annotators. [mah] DONE/IN PROGRES: See Annotation_Cross_products. Awaiting comments from rest of GOC

30. REJECTED Action Item (Content Working Group): Pick a new name for cellular component. [note, this was superseded later with decision not to change this name – see action items 81 & 82].

31. Action Item (Jane): Keep researching CARO integration.

32. DONE! Action Item (AWG): Explore whether this [Mary's graphs] would be a useful addition to AmiGO 2.0.

33. IN PROGESS... Action Item (AWG): There should be more tracking of what users are doing in the next AmiGO; explore the options. EXPLORING

34. SEE ABOVE Action Item (Seth & AWG): Discussed that these changes should be reflected in AmiGO.

35. Action Item (John & Jane): DONE, in as much as there is now the option to add creation/modification times/users to the GO file, which is the minimum possible version of this action item. Come up with a proposal for a history tracking tool, including timeframe and priority, and send out email.

36. Action item (David, Jane): Organize first training meeting.(postponed due to the amount happening at this meeting)

37. Action Item (Nicole, Jane, John, Mark): IN PROGRESS, system will be presented to group by John & Seth. Create proposal to group for term submission software, including the “minimum standards for each term”.

38. NOT DONE! Action Item (AmiGO Working Group): Change AmiGO to hide (by default) structured comments of certain types. Obsolete comments will not be shown. Structured comments that don’t belong will not be shown. Have option to hide comments. [Requires the different types of comment to be specified]

39. Action Item (Karen E.): Send the information [microarray tool evaluation] to the group

40. IN PROGRESS: Action Item (User Advocacy): Create a Wiki page for each tool on GO tools. GO's official tool recommendations (if we have them) can be posted on the Wiki. Link to a Google user group for tool discussions

41. IN PROGRESS: Action Item (User Advocacy): Publish minimum standards for tools on GO tools. This can just extend the existing questionnaire.

42. ONGOING: Action Item (Everyone): Email suggestions for meetings at which we'll do outreach to Eurie & Jane & Jen.

43. DONE, continuing: Action Item (Everyone): Put meetings on the Google calendar.

44. DONE: Action Item (Eurie & Jane): Create Wiki of meetings gathered from emails.

45. Action Items (Managers): Revisit metrics & priorities.

46. Action Item (Managers): Create structure within working group Wikis to allow people to announce what they are working on.
Ontology development started, and ongoing; as "done" as it can be. [mah]

47. Action Item (Everyone): Create list of projects they are working on, post on Wiki.
Ontology development done. [mah]

48. DONE! Action Item (John): Tell everyone I'm worried that we don't have enough of a plan.

49. DONE! Action Item (Chris, Karen C.): Publish a succinct paragraph explaining why unknowns were removed. Karen C. will write documentation targeting biologists; Chris writes an explanation targeting software engineers. Publish on website, possibly in newsletter, wherever necessary. Was newsletter item (Petra)

Items 50-52 are about the WITH field for the IPI code.
50. Action Item (MGI, SGD): Change all pipes to commas. GOA [DONE] has coped with piped data by expanding them into our database. We do not provide sanity checking on this data and instead prefer to assume this has been done by the original submitter. 51. Action Item (Chris, Ben): Work through any database implications. DONE. No implications

52. Action Item (User Advocacy): Announce in newsletter, “what's new” section of GO site.

53. Action Item (Everyone) – Tell code extension advocates to piss off. Attendees voiced strong opinions against extending evidence codes.

54. DONE? Action Item (John): Email Simon Twigger OBO-Edit Piccolo/GraphViz source code.

55. Action item (Karen C): makes these statements very explicit in the documentation.

56. DONE! Action Item (Rex, Eurie): Create a gene page for each reference gene on Wiki. Use Alex's pages as a template. Link Wiki pages to existing annotations.

57. DONE! Action Item (Everyone): Feel good about WebEx, continue to exploit Tanya's account. Continue to use Ready Conference and Skype. Avoid long-term lock-ins.

58. DONE! Action Item (MGD): Get a WebEx account.

59. DONE Action Item (Jen & John & Tanya): Research commercial version of Skype to possibly replace Ready Conference.

60. Action Item (Evidence Code Working Group): Develop a decision tree for choosing an evidence code. Present results at next consortium meeting. (large scale/small scale, reviewed/un-reviewed. Similarity/not-similarity etc).

61. Action Item (Rex): Assign programmer to check integrity of WITH field for annotations.

62. Action Item (Everyone): Add SwissProt keyword ids to WITH column when appropriate.(MGI-DONE, GOA-DONE, ZFIN-DONE)

63. Action Item (Evidence Code Working Group): Send RCA code back to committee.

64. Action Item (Evidence Code Working Group): Except where contradicted by other action items above, accept recommendations in Evidence Code Proposals Draft.

65. Action Item (everyone): Change unknown manual annotations to ND, use GO ref or internal reference, don't reference the paper. IEAs to the root term are acceptable.(MGI-DONE)

66. Action Item (everyone): When annotating NOT, if no positive annotation can be made, the gene product should ALSO be annotated to the root.

67. Action Item (Committee): Update documentation to reflect previous action item.

68. Action Item (Evidence Code Working Group): Send ND back to committee.

69. Action Item (Reference Genome): Discuss scheduling for a reference genome meeting/annotation camp. DONE

70. [Done] Action Item (Jen, Michelle): Outreach annotation course organization, publicity.

71. Action Item (Everyone): Don't use community-specific (limited to being understood only by that community) terms as the primary term name. Create a community-neutral primary term (structured synonym), and use the community-specific term as an exact synonym. Tag these exact synonyms by community as appropriate. DONE

72. DONE Action Item (Jen): Change all “sensu the XXX community” terms back to "sensu XXX". See #11 and #73

73. [In Progress] Action Item (Ontology Editors, high priority): Accept Chris & Jen's proposal to get rid of sensu terms. The few remaining terms should be called “sensu the XXX community”.
Comment: The few remaining sensu terms are awaiting expert input. They are listed here along with questions for specific people: http://gocwiki.geneontology.org/index.php/Meeting_Notes_3

74. Action Item (Chris, Jane, Harold): Create concrete proposal for linking between all GO ontologies, get relationship ontology up to speed, do pilot project in metabolism.

75. DONE! Action Item (Amelia): Talk to Stanford about monthly archive release notes.

76. Action Item (Suzi): Come up with a structure for reporting our time commitments.

77. DONE: Action Item (GO Top): Get back to Karen C. on proposal to extend evidence code committee.

78. IN PROGRESS: Action Item (User Advocacy): Draft an official GO brochure.

79. NOT DONE, can do this when needed. Action Item (Mike): Create GO banners.

80. [Not Done Yet] Action Item (Jen): Create Wiki page with a checklist of what to bring/do when advocating GO at a meeting.
Comment: This is very straightforward to do and has just got lost in the huge number of other things going on. We can do it soon if it is considered high-priority.

81. Action Item (Everyone): Use the word cellular to refer to things related to a cell but aren't necessarily cells or things contained within a cell. Use the word cell to refer to cells themselves or things contained within a cell. (Change cell signaling to cellular signaling, for example).

82. Action Item (Jane): Tweak cellular component definition to clearly distinguish cellular component from cell part. Insert non-formatted text here