Code

Add NCBITaxon synonyms#167

Code

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gaurav wants to merge 41 commits intomasterTranslatorSRI/Babel:masterfrom add-ncbitaxon-synonymsTranslatorSRI/Babel:add-ncbitaxon-synonymsCopy head branch name to clipboard

+308-108

Commits

Commits on Jun 27, 2023

• Adds a shortest_name_length value to the synonyms file.

  gaurav

  committed
  41144a2

• Removed some asserts with brackets because they're tuples.

  Show description for 75bebc1
  gaurav

  committed
  75bebc1

• Replaced pull_via_urllib() with requests.get().

  gaurav

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  e37dd99

• Fixed reference to local_filename.

  gaurav

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  f6c28a3

• Modified icRDF.tsv to be downloaded directly from UberGraph.

  Show description for ad91a1a
  gaurav

  committed
  ad91a1a

• Moved icrdf filename into Snakemake file.

  gaurav

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  38f3e23

• Added icrdf_filename as a required parameter to write_compendium().

  gaurav

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  d33cc6c

• Added icrdf_filename to anatomy.

  gaurav

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  79b6dbe

• Added icrdf_filename to chemicals and diseasephenotype.

  gaurav

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  4173978

• Added icrdf_filename to remaining targets.

  gaurav

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  29ae048

• Fixed reference to icrdf_filename.

  gaurav

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  9ad765a

• Fixed SPARQL queries.

  gaurav

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  9f8006a

• Added UMLS version to config.yaml.

  gaurav

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  cc01243

• Added UMLS download instructions to datacollect Snakemake.

  gaurav

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  918a729

• Explicitly added MRSTY.RRF to write_umls_ids().

  gaurav

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  68fc61a

• Removed UMLS files from README.

  gaurav

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  3cc146d

• Added MRCONSO as explicit input to umls.build_sets().

  gaurav

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  f34677a

• First stab at downloading all the descriptions from UberGraph.

  gaurav

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  e17d2f4

• First stab at writing descriptions.

  gaurav

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  907d5a3

• Make description downloads from Ubergraph optional.

  gaurav

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  88cbad8

• Make synonym files inputs to the final tasks.

  Show description for 4a28cb5
  gaurav

  committed
  4a28cb5

• Fixed some additional references to MacromolecularComplexMixin.

  gaurav

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  5ab247c

• Added push trigger for testing.

  gaurav

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  16fb6c9

• Fixed UMLS path.

  gaurav

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  23a87f9

• Fixed incorrect merge.

  gaurav

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  57196d0

• Fixed input parameter name in Snakemake rule.

  gaurav

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  a46fa55

• Included descriptions in the identifiers structure.

  gaurav

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  cf14247

• Fixed typo in pull_umls().

  gaurav

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  199442c

• Replace ftp:// with identical https:// URL.

  Show description for 7fe5f97
  gaurav

  committed
  7fe5f97

• Replaced other UniProtKB FTP URL with HTTPS URL.

  gaurav

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  0ffa6a8

• Fixed icrdf_filename call to write_compendium() in build_protein_compendia().

  gaurav

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  9ea63db

• Fixed incorrect GitHub action (incorrect commit?).

  gaurav

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  43e9529

• Merge branch 'add-lengths-to-synonym-output' into babel-1.0

  gaurav

  committed
  b220498

• Fixed incorrect order and duplication in datacollect.snakefile.

  Show description for c02a5da
  gaurav

  committed
  c02a5da

• Protected label in case of unlabeled cliques.

  gaurav

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  c9fa420

• Fixed duplications in babel_utils.py.

  gaurav

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  e7e9751

• Removed incorrect merge.

  gaurav

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  2175b1a

• Commented out unnecessary print statement.

  gaurav

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  bd5a420

Commits on Jun 28, 2023

• Removed incorrectly duplicated code.

  gaurav

  committed
  966b971

Commits on Jun 29, 2023

• Increased storage on Babel.

  gaurav

  committed
  85ea210

Commits on Jul 10, 2023

• Added counts for next step.

  gaurav

  committed
  8d364e1