EVA-4237 / Issue 513 : Updates to SOPs

cmat/consequence_prediction/common/biomart.py

@@ -28,7 +28,8 @@ def build_biomart_request_template(key_column, query_columns):
 
     Note `identifier_list` is left to be filled in later, to ensure the identifiers can be chunked appropriately.
     """
-    biomart_request_template = f"""http://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?>
+    # TODO BioMart not available on new Ensembl
+    biomart_request_template = f"""https://jun2026.archive.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?>
     <!DOCTYPE Query>
     <Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6">
         <Dataset name = "hsapiens_gene_ensembl" interface = "default" >

docs/manual-curation/step2-manual-curation.md

@@ -78,7 +78,8 @@ the filtered selection.
         * 2.2.2 Determine if the mapping in "Replacement mapping" is suitable, if not find a new term to use as mapping
     * 2.3 **Exact synonym matches**
         * 2.3.1 Remove "Blank" from "Exact synonym matches" column
-        * 2.3.2 Determine if the mapping is suitable, if not find a new term to use as mapping
+        * 2.3.2 Determine if the mapping is suitable, if not find a new term to use as mapping.
+          See [below](#notes-on-exact-synonym-matches) for more details.
 3. **Low-confidence mappings or unmapped terms**
     * 3.1 Set the "Status" column to only include "Blank" entries
     * 3.2 Look for suitable mappings from the "All other mappings" columns, or perform your own searches
@@ -114,6 +115,20 @@ at the top. Any comments will become available in the "Notes" field within the n
 Comments from previous iterations that need to be kept for subsequent ones should be copy/pasted from the "Notes" to
 the "Comments" cell.
 
+### Notes on exact synonym matches
+
+Terms listed as exact synonyms are not always accurate so they need to be checked one by one.
+
+One case to look for is when the exact match can be imported (yellow cell in the "Exact match" column) but an exact
+synonym match exists and is in EFO already (green cell in the "Exact synonym match" column). Here it is likely that EFO
+has already made the decision to not import the new term. We should double-check that the synonym does mean the same
+thing as the label, and if it does use the existing EFO term with synonym match over the imported exact match.
+
+An example is "multiple myeloma", an exact match for http://purl.obolibrary.org/obo/HP_0006775 which would need
+to be imported. However it is marked as an exact synonym for "plasma cell myeloma" http://purl.obolibrary.org/obo/MONDO_0009693
+which is already in EFO. In this case the synonym is accurate and so should be used directly rather than importing a new
+term.
+
 ### Note on multiple mappings
 
 Sometimes the source string contains two or more traits. In this case it is necessary to map that string to two or more

docs/manual-curation/step3-export-results.md

@@ -21,8 +21,6 @@ nextflow run ${CODE_ROOT}/pipelines/export_curation_spreadsheet.nf \
   -resume
 ```
 
-## Check and correct known problematic mappings
-There is a [spreadsheet](https://docs.google.com/spreadsheets/d/1m4ld3y3Pfust5JSOJOX9ZmImRCKRGi-fGYj_dExoGj8/edit) which was created to track trait-to-ontology mappings which were especially problematic in the past to users of Open Targets platform. Prior to running subsequent steps, make sure that all traits mentioned in that spreadsheet are mapped to the correct ontology terms in `${BATCH_ROOT_BASE}/manual_curation/latest_mappings.tsv`.
 
 ## Submit feedback to EFO
 Tables for IMPORT and NEW terms will be created by curators during [step 2](step2-manual-curation.md).

tests/output_generation/test_consequence_type.py

@@ -44,4 +44,4 @@ def test_repeat_expansion_so_term():
 
 def test_get_so_accession_dict():
     results = get_so_accession_dict(page_size=100)
-    assert len(results) == 232
+    assert len(results) == 237

tests/trait_mapping/test_trait_processing.py

@@ -78,7 +78,6 @@ def test_with_clinvar_xrefs(self):
         trait = Trait('frontotemporal lobar degeneration with tdp43 inclusions, tardbp-related', None, None, xrefs)
         processed_trait = self.run_process_trait(trait)
         assert not processed_trait.is_finished
-        assert len(processed_trait.candidate_mappings) == 2
-        for mapping in processed_trait.candidate_mappings:
-            if isinstance(mapping, ClinVarXrefMapping):
-                assert mapping.uri == xrefs[0]
+        clinvar_xref_candidates = [m for m in processed_trait.candidate_mappings if isinstance(m, ClinVarXrefMapping)]
+        assert len(clinvar_xref_candidates) == 1
+        assert clinvar_xref_candidates[0].uri == xrefs[0]