InterPro2GO Session October 4th 2011: Difference between revisions
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A face-to-face meeting at the EBI between GOA curators, GO editors and the InterPro curation team, to go through the InterPro 2 GO mapping process, problematic mappings, relationships between GO terms and InterPro domains etc etc... | A face-to-face meeting at the EBI between GOA curators, GO editors and the InterPro curation team, to go through the InterPro 2 GO mapping process, problematic mappings, relationships between GO terms and InterPro domains etc etc... | ||
==Agenda== | ==Agenda== | ||
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## The idea of using blacklists to prevent erroneous mappings to sequences based on InterPro matches | ## The idea of using blacklists to prevent erroneous mappings to sequences based on InterPro matches | ||
### Relating to black-lists, revisit protein-kinase catalytic domain entry (IPR000719), which maps the terms GO:0006468 protein phosphorylation, GO:0004672 protein kinase activity and GO:0005524 ATP binding to ~100K sequences in UniProt. However, among these are members of the tribbles family, which are psuedo-kinases. So are there sensible ways we can handle this kind of situation without sacrificing large numbers of true positive mappings. | ### Relating to black-lists, revisit protein-kinase catalytic domain entry (IPR000719), which maps the terms GO:0006468 protein phosphorylation, GO:0004672 protein kinase activity and GO:0005524 ATP binding to ~100K sequences in UniProt. However, among these are members of the tribbles family, which are psuedo-kinases. So are there sensible ways we can handle this kind of situation without sacrificing large numbers of true positive mappings. | ||
==Problematic InterPro Mappings== | ==Problematic InterPro Mappings== | ||
* IPR000402. ATPase and ATP metabolism terms. | * IPR000402. ATPase and ATP metabolism terms. | ||
==Minutes== | ==Minutes== |
Revision as of 08:28, 23 September 2011
A face-to-face meeting at the EBI between GOA curators, GO editors and the InterPro curation team, to go through the InterPro 2 GO mapping process, problematic mappings, relationships between GO terms and InterPro domains etc etc...
Agenda
- Jane to give an overview of the multi-organism process node (GO:0051704) in GO, and how to use the terms for annotation
- An overview of the Relation Ontology
- Problematic areas of InterPro to cover:
- When to use particular membrane-associated component mappings (see the recent PAINT paper)
- Use of the protein-binding term ('protein binding ; GO:0005515' and 'binding ; GO:0005488' should only be used for annotation when an identifier is present in the with column (cases where the identifier is absent are strippd out of the GOA files): are there more specific terms InterPro can use instead?).
- How to GO map proteins that form complexes (the relationship ontology might help here)
- GO mapping proteins that have different functions according to the component they're present in.
- Component mappings in general (ie, should we be mapping terms based on proteins that are *only* found in a particular location, or do we map proteins that have been observed in that location at some stage?)
- Clarification on how GOA use the 'NOT' qualifier - are there implications that we need to be aware of in InterPro?
- The idea of using blacklists to prevent erroneous mappings to sequences based on InterPro matches
- Relating to black-lists, revisit protein-kinase catalytic domain entry (IPR000719), which maps the terms GO:0006468 protein phosphorylation, GO:0004672 protein kinase activity and GO:0005524 ATP binding to ~100K sequences in UniProt. However, among these are members of the tribbles family, which are psuedo-kinases. So are there sensible ways we can handle this kind of situation without sacrificing large numbers of true positive mappings.
Problematic InterPro Mappings
- IPR000402. ATPase and ATP metabolism terms.
Minutes
Present:
- Jane Lomax (GO)
- Rebecca Foulger (GO)
- Emily Dimmer (GOA)
- Alex Mitchell (InterPro curation co-ordinator)