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Make xrefs between Ensembl IDs and Uniprot IDs in STRING ingest #237

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merged 10 commits into from
Jun 18, 2020

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justaddcoffee
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To partially address #235

This PR:

  • downloads mapping between Ensembl IDs and Uniprot IDs
  • makes an xref edge between equivalent Ensembl IDs and Uniprot IDs in STRING edges.tsv
  • makes a node for the Uniprot ID in STRING nodes.tsv
  • also adds a bunch new unit tests to increase test coverage

@justaddcoffee justaddcoffee marked this pull request as draft June 17, 2020 03:45
@justaddcoffee justaddcoffee marked this pull request as ready for review June 17, 2020 03:59
@justaddcoffee justaddcoffee marked this pull request as draft June 17, 2020 04:07
@justaddcoffee justaddcoffee marked this pull request as ready for review June 17, 2020 04:49
@justaddcoffee justaddcoffee marked this pull request as draft June 17, 2020 23:21
@justaddcoffee
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@deepakunni3 please have a look - I think these last few commits give us what we want.

Note that we have both alias (which contains NCBIGenes ids for genes) and xrefs (which contain UniprotKB ids for proteins) - this is what we want right?

id	name	category	description	alias	xrefs	provided_by
ENSEMBL:ENSG00000004059	ARF5	biolink:Gene	ADP ribosylation factor 5	NCBIGene:381		STRING
ENSEMBL:ENSP00000000233		biolink:Protein			UniprotKB:P84085	STRING

@justaddcoffee justaddcoffee marked this pull request as ready for review June 17, 2020 23:50
@deepakunni3 deepakunni3 merged commit e6d1f87 into master Jun 18, 2020
@justaddcoffee justaddcoffee deleted the issue_235_string_id_norm branch June 24, 2020 16:44
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