Annotation Conf. Call, January 24, 2012: Difference between revisions

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===IKR Evidence code===
===IKR Evidence code===
All of us agreed that IKR can be used outside of PAINT annotations. However, one of the requirements for IKR is a protein ID or familyID in the With/from column.  
All of us agreed that IKR can be used outside of PAINT annotations. However, one of the requirements for IKR is a protein ID or familyID in the With/from column.  
1) In situations where a curator is looking at the sequence alignment and is intending to use the proposed GO_REF, it is hard to come up with an ID for the with/from column. Until we come up with ways to represent these cases in the 'with/from' column it would be bad precedence to make annotations with IKR and lift the with/from column requirement. Since these are NOT annotations, we should be able to provide the ID of the proteins where the activity is present so the users (and us) can trace the evidence.
1) In situations where a curator is looking at the sequence alignment and is intending to use the proposed GO_REF, it is hard to come up with an ID for the with/from column. Until we come up with ways to represent these cases in the 'with/from' column it would be bad precedence to make annotations with IKR and lift the with/from column requirement. Since these are NOT annotations, we should be able to provide the ID of the proteins where the activity is present so the users (and us) can trace the evidence.<br>
2) In situations where an annotation is made with IKR from a PMID, filling the with/from column shouldn't be a problem.
2) In situations where an annotation is made with IKR from a PMID, filling the with/from column shouldn't be a problem.<br>
3) We should think about how to provide IDs for families when we situation #1
3) We should think about how to provide IDs for families when we situation #<br>
4) The documentation can be added to the main GO website
4) The documentation can be added to the main GO website<br>


===ISC Evidence code===
===ISC Evidence code===

Revision as of 12:19, 25 January 2012

Agenda

  • Update on communication mechanisms for changes to the GO taxon file. (Jane) postphoned until next call


  • FYI on QC checks. The following QC checks have been incorporated into Mike's filtering script and we are planning to move this to production by Feb 1st.

1) All IC annotations should include a GO id in column 8 (with/from)

2) All IDA annotations should NOT include any id in column 8 (with/from)

3) ND-evidenced Annotations to root nodes only http://geneontology.org/GO.annotation_qc.shtml#GO_AR:0000011

4) ND annotations should NOT have PMID in the reference column

5) References in the GAF -Column 6 should be of the format SGD_REF:S000047763|PMID:2676709. References like PMID:PMID:14561399', or PMID:unpublished or GOC:unpublished should be filtered out.

6) Annotations to GO:0005488, 'binding' should be made with IPI and the interacting partner should be in the 'with' column.

7) Annotations with IPI evidence code made after Jan 1, 2012 that don't have an ID in the 'with' column should be filtered out (grand father old annotations)

Minutes

Present:
SGD: Rama, Jodi
EBI: Paola, Emily, ?
UCL: Ruth, Varsha
Fly: Susan
MGI: Judy, Li
Rat: Stan
USC: Paul
UMD: Marcus
TAIR: DongHui
NextProt: Pascale, ?
Reactome: Peter


IKR Evidence code

All of us agreed that IKR can be used outside of PAINT annotations. However, one of the requirements for IKR is a protein ID or familyID in the With/from column. 1) In situations where a curator is looking at the sequence alignment and is intending to use the proposed GO_REF, it is hard to come up with an ID for the with/from column. Until we come up with ways to represent these cases in the 'with/from' column it would be bad precedence to make annotations with IKR and lift the with/from column requirement. Since these are NOT annotations, we should be able to provide the ID of the proteins where the activity is present so the users (and us) can trace the evidence.
2) In situations where an annotation is made with IKR from a PMID, filling the with/from column shouldn't be a problem.
3) We should think about how to provide IDs for families when we situation #
4) The documentation can be added to the main GO website

ISC Evidence code

  • Paul questioned the need for this evidence code, is it a relevant distinction that we are trying to make with this new code? Is it for the users or for us so we know what the supporting evidence is for an ISS? Can this be taken care of by inter-ontology links? Not always because of taxon constraints. We all came to an agreement that it is okay to move forward with this code. One of us will brief Marcus so he can add it to ECO. For now we will make flavors of ISC for ISS only.

New Evidence for Inferences

Did not get to talk about it. Punted to next meeting.

New QCs to go Live soon

If any of you have any questions please write to go-discuss list (or to Rama/Emily)