Annotation Conf. Call 2018-03-27: Difference between revisions

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*Dates set for Oct 17-20
*Dates set for Oct 17-20


== HTP Annotation Guidelines ==
== Updates on Projects ==
*Helen has added documentation on the use of HTP evidence codes to the wiki:
*[https://github.com/geneontology/go-annotation/issues/1592  MAPK cascade- Signaling Project]
**[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Guide to GO Evidence Codes]
*[https://github.com/geneontology/go-ontology/projects/9 Extracellular matrix revisions]
**[https://github.com/geneontology/go-annotation/issues/1773 Annotation standards for HTP proteomics experiments]
***How best to capture the combination of a published paper's experiment combined with secondary curator evaluation using some other methodology?  New combinatorial evidence code and paper plus a GO reference?  (This would be a change to our reference practice.)
**[https://github.com/geneontology/go-annotation/issues/1801 Review RCA evidence code] - Please can the groups listed below review their RCA annotations and decide if they'd still like to keep them and if RCA is still the appropriate evidence code?
***TAIR
***MGI
***SGD
***RGD
***CAFA


== Annotation Review ==
== Evidence Codes ==
*Annotation review is being driven by annotation QC and ontology development
=== RCA ===
*Goal here is for correct and consistent annotation
*[https://github.com/geneontology/go-annotation/issues/1801 Review RCA evidence code]
**Prioritize by:
**Thank you to everyone who has reviewed their existing RCA annotations.
***Annotations that are incorrect
**Many RCA annotations were removed, but some groups are keeping annotations from papers that use methodology consistent with the definition of RCA.
***Annotations to terms that are being made obsolete
**Since these annotations come from papers, the originally proposed one-year restriction does not make sense and will not be an annotation rule.
***Annotations to high level terms that are not informative
***Please send Kimberly PMIDs for papers that were kept for use as examples in our evidence code documentation.
***Annotations to grouping terms for which more granular, informative terms exist (maybe weren't found initially or were created after the annotation was made)
**That said, periodic annotation review is always a good idea.
*Tickets are created in the geneontology/go-annotation repo on github
**Remaining groups will be contacted individually.
*Currently, 55 open tickets labeled with Annotation Review in geneontology/go-annotation
*Tickets are assigned to representatives of the annotation groups that need to perform the review
*Once review is done, please remove yourself from the assignee list AND record the action in the accompanying Google spreadsheet linked from the github ticket
*[https://drive.google.com/drive/folders/1FDfp4yXlLZjrcB0NIbsAgUukDWDwhJe_ Spreadsheet on GO Annotation Google drive with specific annotations, suggestions]
** Need a re-review of palate development annotations.
*Tickets for discussion:
**[https://github.com/geneontology/go-annotation/issues/1298 HAMAP:MF_03064 mapping for Q9P6N6]
***General issue here: when should we capture a causal relation? 
**[https://github.com/geneontology/go-annotation/issues/1746 Review annotations to palate development]
*Some older tickets that still need to be addressed:
**[https://github.com/geneontology/go-annotation/issues/1293 Review annotations to mRNA cleavage]


== Annotation Requests ==
== Annotating High Throughput Experiments ==
*There are some tickets in geneontology/go-annotation that are requesting annotation
*[https://github.com/geneontology/go-annotation/issues/1796 Proposal for curating extracellular matrix proteins from proteomics experiments]
*We'd like to assign these to groups
*[https://github.com/geneontology/go-annotation/issues/1885 Review reference guidelines for GAF, GPAD]
**[https://github.com/geneontology/go-annotation/issues/1326 Annotating yeast autophagy regulators in PMID:25660547 ?]
 
== Annotation Survey ==
*We are putting together a survey on annotation practices across the GOC
*Should be ready very soon
*Would like results before the GOC meeting in NY
 
== GO-CAM/Noctua ==
*Next call tomorrow, Wednesday, March 28th at 11:00am EDT (see Google calendar)
 
== Protein Complexes Working Group ==
*Next call on Monday, April 23rd at 1:10pm EDT (see Google calendar)


= Minutes =  
= Minutes =  
*On call:
*On call: Chris, David H., Dustin, Edith, Giulia, Harold, Helen, Jim, Judy, Karen, Kevin M, Kimberly, Li, Midori, Pascale, Paul T, Penelope, Petra, Rachael, Rob, Sabrina, Sage, Stacia, Stan, Suzi A., Suzi L.
 
== GOC Meeting, NYU, New York, NY, May 12-14th ==
*Register and reserve your hotel room before April 6th if staying at the Shelburne NYC
*If you have any issues with reserving a room, please contact Peter D'Eustachio right away
 
== Updates on Projects ==
=== MAPK Signaling ===
*Some ontology updates to how MAPK signaling pathways are named in GO
*Upcoming: annotation review for potentially re-housing annotations according to the new MAPK pathway terms
*Some existing annotations to upstream genes may need to be re-housed
*The MAPK cascade is a signaling cassette or module that begins with MAP4K or MAP3K and ends with MAPK
*How a MAPK cascade relates to a larger signaling pathway or another downstream process, e.g. neurite extension, remains to be determined in both the ontology and GO-CAM models
=== Extracellular Matrix Revisions ===
*All extracellular matrices have at least some protein component
*David and Rachael working on revisions to the ontology
*Some annotation review will likely be coming
*Will be calling on people for help with top level taxonomic groupings
 
== Evidence Codes ==
=== RCA ===
*Most groups have reviewed their RCA annotations and removed many, but some have stayed
*Propose to remove the one-year restriction on RCA annotations that does not seem to have been enacted formally anyway
*We will work with other annotation groups to review their RCA annotations
=== Annotating High Throughput Experiments ===
*We need an evidence code for combinatorial curation using HTP results further validated by other methods
*Can work with ECO to find or create a suitable code
*Reference field will need to clearly indicate the combined curation methodology
**As a first step towards doing this, we need to determine how to indicate the combined references, e.g. a PMID plus a GO_REF that describes the subsequent analysis
**Currently, some groups include redundant, pipe-separated references in the Reference field of the GAF
**Do we need to continue doing this?  Proposal is to include only one, unique ID for each reference and then, if needed, combine a paper reference with a GO_REF
 
== Annotation Survey ==
*We will be sending out an annotation practices survey for groups to fill in
*Survey will go out later this week or early next
*We'd like the results in time for the May GOC meeting in NYC
 




[[Category:Annotation Working Group]]
[[Category:Annotation Working Group]]

Latest revision as of 12:10, 27 March 2018

Agenda

GOC Meeting, NYU, New York, NY, May 12-14th

  • Reminder to register, and reserve your hotel room before April 6th if staying at the Shelburne NYC
  • Logistics
  • Agenda

20th Anniversary GO Meeting, Montreal, CA

  • Dates set for Oct 17-20

Updates on Projects

Evidence Codes

RCA

  • Review RCA evidence code
    • Thank you to everyone who has reviewed their existing RCA annotations.
    • Many RCA annotations were removed, but some groups are keeping annotations from papers that use methodology consistent with the definition of RCA.
    • Since these annotations come from papers, the originally proposed one-year restriction does not make sense and will not be an annotation rule.
      • Please send Kimberly PMIDs for papers that were kept for use as examples in our evidence code documentation.
    • That said, periodic annotation review is always a good idea.
    • Remaining groups will be contacted individually.

Annotating High Throughput Experiments

Annotation Survey

  • We are putting together a survey on annotation practices across the GOC
  • Should be ready very soon
  • Would like results before the GOC meeting in NY

GO-CAM/Noctua

  • Next call tomorrow, Wednesday, March 28th at 11:00am EDT (see Google calendar)

Protein Complexes Working Group

  • Next call on Monday, April 23rd at 1:10pm EDT (see Google calendar)

Minutes

  • On call: Chris, David H., Dustin, Edith, Giulia, Harold, Helen, Jim, Judy, Karen, Kevin M, Kimberly, Li, Midori, Pascale, Paul T, Penelope, Petra, Rachael, Rob, Sabrina, Sage, Stacia, Stan, Suzi A., Suzi L.

GOC Meeting, NYU, New York, NY, May 12-14th

  • Register and reserve your hotel room before April 6th if staying at the Shelburne NYC
  • If you have any issues with reserving a room, please contact Peter D'Eustachio right away

Updates on Projects

MAPK Signaling

  • Some ontology updates to how MAPK signaling pathways are named in GO
  • Upcoming: annotation review for potentially re-housing annotations according to the new MAPK pathway terms
  • Some existing annotations to upstream genes may need to be re-housed
  • The MAPK cascade is a signaling cassette or module that begins with MAP4K or MAP3K and ends with MAPK
  • How a MAPK cascade relates to a larger signaling pathway or another downstream process, e.g. neurite extension, remains to be determined in both the ontology and GO-CAM models

Extracellular Matrix Revisions

  • All extracellular matrices have at least some protein component
  • David and Rachael working on revisions to the ontology
  • Some annotation review will likely be coming
  • Will be calling on people for help with top level taxonomic groupings

Evidence Codes

RCA

  • Most groups have reviewed their RCA annotations and removed many, but some have stayed
  • Propose to remove the one-year restriction on RCA annotations that does not seem to have been enacted formally anyway
  • We will work with other annotation groups to review their RCA annotations

Annotating High Throughput Experiments

  • We need an evidence code for combinatorial curation using HTP results further validated by other methods
  • Can work with ECO to find or create a suitable code
  • Reference field will need to clearly indicate the combined curation methodology
    • As a first step towards doing this, we need to determine how to indicate the combined references, e.g. a PMID plus a GO_REF that describes the subsequent analysis
    • Currently, some groups include redundant, pipe-separated references in the Reference field of the GAF
    • Do we need to continue doing this? Proposal is to include only one, unique ID for each reference and then, if needed, combine a paper reference with a GO_REF

Annotation Survey

  • We will be sending out an annotation practices survey for groups to fill in
  • Survey will go out later this week or early next
  • We'd like the results in time for the May GOC meeting in NYC