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Update goa.yaml #2448

Merged
merged 4 commits into from
Mar 6, 2025
Merged

Update goa.yaml #2448

merged 4 commits into from
Mar 6, 2025

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pgaudet
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@pgaudet pgaudet commented Mar 4, 2025

Fixed goa-yaml for new organisms

@pgaudet
Update goa.yaml
bff1f95 
Fixed goa-yaml for new organisms
@pgaudet pgaudet requested a review from kltm March 4, 2025 08:22
@pgaudet pgaudet mentioned this pull request Mar 4, 2025
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kltm
kltm requested changes Mar 4, 2025
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@pgaudet This generally looks good, but most additions were inconsistent in the description field. Could you double check these and make sure that the species is consistent through the entire stanza?

metadata/datasets/goa.yaml Outdated
url: https://current.geneontology.org/annotations/goa_virus_bacteria_taxon_11251.gpi.gz
id: goa_virus_bacteria_taxon_10360.gpi
label: "goa_virus_bacteria_gpi4neo taxon_10360"
description: "GPI file for use in NEO for virus and bacteria annotation from EBI Gene Ontology Annotation Database taxon_10254"
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Typo?

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This is right

metadata/datasets/goa.yaml Outdated
url: https://current.geneontology.org/annotations/goa_virus_bacteria_taxon_10335.gpi.gz
id: goa_virus_bacteria_taxon_10299.gpi
label: "goa_virus_bacteria_gpi4neo taxon_10299"
description: "GPI file for use in NEO for virus and bacteria annotation from EBI Gene Ontology Annotation Database taxon_10254"
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Typo?

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No this is right

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10299 vs 10254?

metadata/datasets/goa.yaml Outdated

-
- NCBITaxon:10360
exclude: true
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There seems to be whitespace added around here?

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I dont see that in the file. If you can see it in the original file, would you please remove it?

metadata/datasets/goa.yaml Outdated
url: https://current.geneontology.org/annotations/goa_virus_bacteria_taxon_90371.gpi.gz
id: goa_virus_bacteria_taxon_93061.gpi
label: "goa_virus_bacteria_gpi4neo taxon_93061"
description: "GPI file for use in NEO for virus and bacteria annotation from EBI Gene Ontology Annotation Database taxon_85962"
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Typo?

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No, this is right

metadata/datasets/goa.yaml Outdated
-
id: goa_virus_bacteria_taxon_295027.gpi
label: "goa_virus_bacteria_gpi4neo taxon_295027"
description: "GPI file for use in NEO for virus and bacteria annotation from EBI Gene Ontology Annotation Database taxon_272634"
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Typo?

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This is right

metadata/datasets/goa.yaml Outdated
-
id: goa_virus_bacteria_taxon_301447.gpi
label: "goa_virus_bacteria_gpi4neo taxon_301447"
description: "GPI file for use in NEO for virus and bacteria annotation from EBI Gene Ontology Annotation Database taxon_272634"
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Typo?

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Looks right to me

metadata/datasets/goa.yaml Outdated
-
id: goa_virus_bacteria_taxon_565655.gpi
label: "goa_virus_bacteria_gpi4neo taxon_565655"
description: "GPI file for use in NEO for virus and bacteria annotation from EBI Gene Ontology Annotation Database taxon_419947"
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Typo?

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This is right

metadata/datasets/goa.yaml Outdated
-
id: goa_virus_bacteria_taxon_587200.gpi
label: "goa_virus_bacteria_gpi4neo taxon_587200"
description: "GPI file for use in NEO for virus and bacteria annotation from EBI Gene Ontology Annotation Database taxon_575584"
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Typo?

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this is right

@pgaudet
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pgaudet commented Mar 5, 2025

Hi Seth,

It seems you have questioned all my additions/deletions - but they all look OK to me.

For reference: These were added:
574
10299
10338
10360
93061
295027
301447
565655
587200

These were removed:

253
546
548
550
571
615
1352
1390
11251
35703
36352
128958
286636
367830
416870
529507
941280

The only thing I dont see is the blank line; please remove it if you see it!

Thanks, Pascale

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kltm commented Mar 5, 2025

@pgaudet The label taxons are still often different than the description taxons. I've remarked them as "unresolved".

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kltm reviewed Mar 6, 2025
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Will review my own pass.

metadata/datasets/goa.yaml Outdated
url: https://current.geneontology.org/annotations/goa_virus_bacteria_taxon_615.gpi.gz
id: goa_virus_bacteria_taxon_574.gpi
label: "goa_virus_bacteria_gpi4neo taxon_574"
description: "GPI file for use in NEO for virus and bacteria annotation from EBI Gene Ontology Annotation Database taxon_545"
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This is still a typo?

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574 vs 545

metadata/datasets/goa.yaml Outdated
url: https://current.geneontology.org/annotations/goa_virus_bacteria_taxon_10335.gpi.gz
id: goa_virus_bacteria_taxon_10299.gpi
label: "goa_virus_bacteria_gpi4neo taxon_10299"
description: "GPI file for use in NEO for virus and bacteria annotation from EBI Gene Ontology Annotation Database taxon_10254"
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10299 vs 10254?

kltm
kltm approved these changes Mar 6, 2025
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@pgaudet I did a fix pass and think everything matches now.

@kltm kltm merged commit 7d02b01 into master Mar 6, 2025
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pgaudet commented Mar 6, 2025

Sorry I couldn't follow the diff there. Thanks for fixing!

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