Annotation Conf. Call, January 24, 2012

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  • 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

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 References like PMID:PMID:14561399', or PMID:unpublished or GOC:unpublished should be filtered out.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)


SGD: Rama, Jodi
EBI: Paola, Emily, Yasmin, Prudence, Becky, Rachael
UCL: Ruth, Varsha
Fly: Susan
MGI: Judy, Li, Mary
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, and agreed the IKR documentation could be used instead of the current version, with however a few exceptions:

  1. One of the requirements for IKR is for an appropriate identifier in the With/from column where a published reference cannot be cited in the annotation.

- 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.

ACTION: potential identifier types to be looked into and discussed in subsequence annotation calls.

- In situations where an annotation is made with IKR from a PMID, filling the with/from column shouldn't be a problem.

ACTION: A modified version of documentation can be added to the main GO website

ACTION: to determine correct placement of the ECO IKR code, so that it is not under phylogenetic evidence.

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. For now we will make flavors of ISC for ISS only.

ACTION: Emily/ Rama will discuss needs with Marcus so he can add it to ECO.

ACTION: Emily to advertise draft of ISC to the GO list, including a 2 week limit for responses so that this evidence code can move forward.

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)