fix(target): remove deprecated Project Score cross-references#138
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Mirror the pis and pts cleanup: drop the Sanger Project Score fetch tasks from pis.yaml and the matching pre-processing + source entries from pts.yaml. The deprecated resource (cog.sanger.ac.uk/cmp/download/ gene_identifiers_latest.csv.gz + essentiality_matrices.zip) is no longer consumed by the pts target step. The Sanger Cell Model Passport download (model_list_latest.csv.gz, used by the Project Score v2 CRISPR evidence parser) is untouched. Companion PRs: - pts: opentargets/pts#138 - pis: opentargets/pis#201 Refs opentargets/issues#4367
Project Score has been deprecated upstream. Drop the xref pipeline
that emitted {id: SIDG..., source: 'ProjectScore'} entries into the
target dbXrefs field:
- Remove _build_project_scores and its inputs/join from target.py
- Drop the project-scores pre-processing and source entries from
config.yaml
The Project Score v2 CRISPR evidence parser (project_score.py) and
the DepMap-backed target_gene_essentiality step are unaffected.
Refs opentargets/issues#4367
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Summary
Project Score has been deprecated upstream. This drops the xref pipeline that emitted
{id: SIDG..., source: 'ProjectScore'}entries into the targetdbXrefsfield._build_project_scores(and its twoproject-scores/parquet inputs, the join intohgnc_ensembl_go, and thexRefcolumn merged intodbXrefs) fromsrc/pts/pyspark/target.pyproject_scores_*source entries on thetargetpyspark step inconfig.yamlOut of scope (intentionally unaffected):
src/pts/pyspark/project_score.py— Project Score v2 CRISPR evidence parser (separate dataset, still maintained)target_gene_essentialitystep — backed by DepMap, not Project ScoreFollow-up PRs needed:
pis— drop the twocog.sanger.ac.uk/cmp/download/fetches underinput/target/project-scores/orchestration— mirror both changes indags/config/{pis,pts}.yamland remove theproject-scores/entries fromscripts/validate_pts_step.pyRefs opentargets/issues#4367
Test plan
targetparquet to verifydbXrefsno longer containssource: ProjectScoreentriesgene_essentialityoutput is unchanged