Merge pull request #9 from opentargets/return-of-the-uris

Convert mappings back into URIs, normalise and update the script
opentargets · Sep 2, 2022 · f6d3be9 · f6d3be9
2 parents b7f9d73 + 3a464dd
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diff --git a/mappings/disease/README.md b/mappings/disease/README.md
@@ -17,8 +17,26 @@ When amending the file manually, make sure to follow the format:
 
 For introducing the changes, the file could be imported into Google Sheets and exported back as TSV.
 
+### Normalisation script
+
 The maintenance script, `normalise.py`, reads the current manual mappings file (`manual_string.tsv`), performs certain normalisations (such as sorting and duplicate removal), and outputs the updated mappings as `efo/manual_string_NORM.tsv`. This file can then be inspected and moved to replace the original input file. To use the script, install dependencies: `pip install --upgrade pandas ontoma`.
 
+Note that if several records are present for a pair of (PROPERTY_TYPE, SEMANTIC_TAG), only one is kept during the deduplication (the most recent one ty ANNOTATION_DATE). Case normalisation is also done during this process. For example, out of these three lines:
+
+| STUDY    | BIOENTITY | PROPERTY_TYPE | PROPERTY_VALUE      | SEMANTIC_TAG                         | ANNOTATOR   | ANNOTATION_DATE |
+|----------|-----------|---------------|---------------------|--------------------------------------|-------------|-----------------|
+| Genebass |           | disease       | atrial fibrillation | http://www.ebi.ac.uk/efo/EFO_0000275 | Annotator 1 | 2020-02-30      |
+| Genebass |           | disease       | Atrial fibrillation | http://www.ebi.ac.uk/efo/EFO_0000275 | Annotator 2 | 2022-08-16      |
+| ClinVar  |           | disease       | atrial fibrillation | http://www.ebi.ac.uk/efo/EFO_0000275 | Annotator 3 | 2021-06-02      |
+
+Only this one will be kept:
+
+| STUDY    | BIOENTITY | PROPERTY_TYPE | PROPERTY_VALUE      | SEMANTIC_TAG                         | ANNOTATOR   | ANNOTATION_DATE |
+|----------|-----------|---------------|---------------------|--------------------------------------|-------------|-----------------|
+| Genebass |           | disease       | Atrial fibrillation | http://www.ebi.ac.uk/efo/EFO_0000275 | Annotator 2 | 2022-08-16      |
+
+It is assumed that every code which uses the `manual_string.tsv` file will also do case normalisation for comparison. This is already performed in ZOOMA and OnToma.
+
 ## Ontology to ontology
 
 The second file, `manual_xref.tsv`, is currently not used and only exists as a placeholder.