Extend UniProt export #173
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@realmarcin to get this over the finish line, I need your help getting a more precise relation between protein and Rhea codes, please see #168 (comment) and help me fill in this chart |
src/pyobo/sources/uniprot/uniprot.py
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| for go_function_ref in _parse_go(go_functions): | ||
| term.append_relationship(enables, go_function_ref) | ||
| for _go_component_ref in _parse_go(go_components): | ||
| pass # TODO what is the right relation? |
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@realmarcin the model you gave didn't make an explicit differentiation between go processes, components, and locations. Can you help me find or a better relation between a protein and a cellular component implied by a GO annotation appearing in its UniProt record?
src/pyobo/sources/uniprot/uniprot.py
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| term.append_relationship( | ||
| # FIXME this needs a different relation, | ||
| # see https://github.com/biopragmatics/pyobo/pull/168#issuecomment-1918680152 | ||
| participates_in, |
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This is also a blocker for the PR
This should cover it but let us know if any more and what you think of the relations: protein -> reaction (participates_in) |
| ) | ||
| BASE_URL = "https://rest.uniprot.org/uniprotkb/stream" | ||
| SEARCH_URL = "https://rest.uniprot.org/uniprotkb/search" | ||
| QUERY = "(*) AND (reviewed:true)" |
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Hi @cthoyt -- thanks for merging the PR, this looks great and satisfies our request!
The only thing I noticed is that you are setting reviewed=True, which will return the SwissProt subset of reviewed annotations. For our purposes we do not use that flag but request all the data including unreviewed. As long as the reviewed is returned than it's very easy to split the data as needed.
The unreviewed annotations are also required to make complete proteomes and satisfy genome function ingest requirements as you would get from other resources.
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in a follow-up PR we can extend this to enable generation of OBO artifacts from arbitrary queries. Would be happy to review an external PR for this, or I will get to it when I have some free time
Closes #172
This PR adds several additional fields to the uniprot export:
ft_binding- binding interactionsxref_proteomes- theuniprot.proteomereference(s?) from which a record is derivedcc_functiona nice high-level description of the function of the proteingoGO terms associated with the protein (from all 3 hierarchies)xref_geneid- NCBI Gene term from which a protein is producedIt also refactors the way the query URLs are constructed to be more easily extensible