Annotation Conf. Call, May 13, 2014: Difference between revisions

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If we do this, we should consider also the possibility of deepening protein binding annotations to child terms of protein binding. Would we want to do the deepening before or after? In the first case you would gain a more specific GO term, but lose the information on whether a protein binds other proteins simultaneously or not. In the second case, you would keep the simultaneous binding information but lose any more specific binding terms.
If we do this, we should consider also the possibility of deepening protein binding annotations to child terms of protein binding. Would we want to do the deepening before or after? In the first case you would gain a more specific GO term, but lose the information on whether a protein binds other proteins simultaneously or not. In the second case, you would keep the simultaneous binding information but lose any more specific binding terms.
===GOC call on June 18th===
We will have a consortium wide conference call on June 18th for 1.5 hours. Please mark your calendars.
http://gocwiki.geneontology.org/index.php/Manager_7May2014#Minutes


[[Category:Meetings]]
[[Category:Meetings]]

Revision as of 17:49, 9 May 2014

Agenda

E2/E3 changes

Extracellular branch of GO CC (David OS)

I've done some work on fixing a number of issues with the extracellular branch of GO CC. I'd like to get some feedback from annotators on my proposed changes before committing them.

With/from cardinality (Rachael)

Examples of multiple with strings for IPI.

This follows on from the discussion of whether to allow more than one ID in the with/from field for certain evidence codes (see http://wiki.geneontology.org/index.php/Manager_16April2014).

Examples for possible representation of multiple with/from entries in protein binding (IPI) annotations are shown below. Reciprocal annotations are not shown, but they would follow the same format as that shown for each example.

1. There is evidence to say that Protein A binds proteins B and C at the same time (comma separated);

DB Object GO ID Reference With/from
Q03388 VPS72 GO:0005515 PMID:24034246 UniProtKB:Q03940,UniProtKB:Q12464,UniProtKB:P35817,UniProtKB:P60010

(see Complex Portal http://wwwdev.ebi.ac.uk/intact/complex/details/EBI-8790722)

2. There is evidence to say that Protein A binds proteins B and C independently (pipe separated);

DB Object GO ID Reference With/from
Q03940 RVB1 GO:0005515 PMID:24034246 UniProtKB:P80428

3. There is no evidence to say whether Protein A binds proteins B and C at the same time or independently (separate annotations);

DB Object GO ID Reference With/from
P19454 CKA2 GO:0005515 PMID:24034246 UniProtKB:P43639
P19454 CKA2 GO:0005515 PMID:24034246 UniProtKB:P38930

If we do this, we should consider also the possibility of deepening protein binding annotations to child terms of protein binding. Would we want to do the deepening before or after? In the first case you would gain a more specific GO term, but lose the information on whether a protein binds other proteins simultaneously or not. In the second case, you would keep the simultaneous binding information but lose any more specific binding terms.

GOC call on June 18th

We will have a consortium wide conference call on June 18th for 1.5 hours. Please mark your calendars. http://gocwiki.geneontology.org/index.php/Manager_7May2014#Minutes