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xref datasets for AGR homolog data #2137

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katewarner opened this issue Jan 30, 2025 · 0 comments
Open

xref datasets for AGR homolog data #2137

katewarner opened this issue Jan 30, 2025 · 0 comments
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@katewarner
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katewarner commented Jan 30, 2025

Related to #2136 xref datasets for new AGR data in protein_homolog_clusters.csv

Source file = ebi/current/uniprot-proteome-$taxa.nt files
Output file =$taxa _protein_xref_alliance_genome_resources.csv
Species datasets = human, rat, mouse, zebrafish, fruitfly, and yeast

The output file should have the following headers:

"id", "xref_key", "xref_id", "xref_label" 

Input file:
AGR xref data for is present in triples within the different taxa's uniprot-proteome-*.nt files e.g.

<http://purl.uniprot.org/uniprot/A0A096MIX7> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://purl.uniprot.org/agr/RGD:1561261> .
<http://purl.uniprot.org/uniprot/A0AQH0> <http://www.w3.org/2000/01/rdf-schema#seeAlso> http://purl.uniprot.org/agr/FB:FBgn0010590
<http://purl.uniprot.org/uniprot/A0A075F5C6> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://purl.uniprot.org/agr/MGI:96238> .

Output files
There should be seven new $taxa _protein_xref_alliance_genome_resources.csv datasets for human, rat, mouse, zebrafish, fruitfly, and yeast

Example output file: human _protein_xref_alliance_genome_resources.csv

id xref_key xref_id xref_label
A0A087WZT3-1 protein_xref_alliance_genome_resources HGNC:53563
Q13490-1 protein_xref_alliance_genome_resources HGNC:590
Q5SWW7-1 protein_xref_alliance_genome_resources HGNC:31008
@katewarner katewarner assigned katewarner and rykahsay and unassigned katewarner Jan 30, 2025
@katewarner katewarner added this to the 2.8 milestone Jan 30, 2025
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