Annotation Conf. Call, May 13, 2014

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Agenda

E2/E3 changes

See SF item.

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.

Multiple with/from fields could only be applied to new annotations, we couldn't retrofit without going back to the papers, whereas we could deepen the protein binding term for old annotations.

If we agree to multiple with/from entries for IPI, it might be worth thinking how we could capture the details of binding partners in a complex though. e.g. If a complex of three proteins was described, could we annotate to a protein complex term and somehow indicate (via part_of or has_part or some other relation) what each component binds? The idea would be to have a way to say, for example, that a gene product is part of a complex and in the context of that complex it has protein kinase binding and calmodulin binding activity while another member of the complex has only calmodulin binding in the context of that complex.

Alzheimer's Disease Annotation Project (Jane/Paola/Sejal)

http://wiki.geneontology.org/index.php/Alzheimer%27s_Disease_Annotation_Project

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