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Index UniProt: Xrefs; namepaces #88

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jvwong opened this issue Oct 20, 2020 · 1 comment
Closed

Index UniProt: Xrefs; namepaces #88

jvwong opened this issue Oct 20, 2020 · 1 comment

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@jvwong
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jvwong commented Oct 20, 2020

Next steps:

Grounding service updates:

1. Reenable Uniprot within the grounding service. [JVW]

2. Add an option to the aggregate search (i.e. `/search`) s.t. namespaces can be blocked (i.e. uniprot namespaces aren't returned to Biofactoid UI).  This can accept an option to set the block list manually, but we will have a default value s.t. uniprot is blocked by default. [MF]

3. In the uniprot importer, the xrefs need to be included in the returned grounding json.  [JVW]

Convertor pipeline: [MCS]

1. Within the PC import, instead of doing a `/search` (today), do a `/get` (e.g. `/get` for `uniprot:P01234`).

2. Now, you have a uniprot grounding.  So, within it, get the NCBI xref.

3. Query `/get` with the NCBI xref.

4. Use the NCBI grounding for the factoid entity in the `association`.

Once done: Run the import on the master.factoid.baderlab.org instance. Merge the data into

Refs: PathwayCommons/factoid#881 (comment)

@maxkfranz
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See (2) in #90

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