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Make upload script executable and update SOP #494

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apriltuesday merged 2 commits into from
Feb 3, 2026
Merged

Make upload script executable and update SOP #494

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dd37deb
make upload script executable and update SOP
apriltuesday Jan 28, 2026
7ea0277
update command in SOP
apriltuesday Jan 28, 2026
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Empty file modified bin/upload_to_gcloud.py
100644 → 100755
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12 changes: 11 additions & 1 deletion docs/open-targets/generate-evidence-strings.md
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Expand Up @@ -53,6 +53,16 @@ Nevertheless, we also report evidence strings in which ``diseaseFromSourceMappe

## 2. Manual follow-up actions

### Check removed mappings and invalid evidence
The pipeline removes mappings that would violate the current JSON schema, and outputs them to `${BATCH_ROOT}/logs/removed_mappings.tsv`.
Check that this file is empty, or only contains expected mappings (e.g. within the material entity branch of EFO).
This can be confirmed with the Open Targets data team if needed.

Any invalid evidence strings are dropped and output in `${BATCH_ROOT}/evidence/invalid_evidence.json`.
Check that this file is empty, or only contains expected evidence given the current state of development (e.g.
unsupported clinical significance terms or other unsupported features).
Anything unusual should be raised with the Open Targets team so it can be addressed as a priority.

### Update summary metrics
After the evidence strings have been generated, summary metrics need to be updated in the Google Sheets [table](https://docs.google.com/spreadsheets/d/1g_4tHNWP4VIikH7Jb0ui5aNr0PiFgvscZYOe69g191k/) on the “Raw statistics” sheet.

Expand All @@ -63,7 +73,7 @@ The evidence string file (`evidence_strings.json`) must be compressed and upload
To do this, run the following:
```shell
gzip evidence_strings/evidence_strings.json
${CODE_ROOT}/bin/upload_to_gcloud.py --input-file evidence_strings/evidence_strings.json.gz --destination-folder disease-target-evidence
${CODE_ROOT}/env/bin/upload_to_gcloud.py --input-file evidence_strings/evidence_strings.json.gz --destination-folder disease-target-evidence
```

Once the upload is complete, send an email to Open Targets (data [at] opentargets.org) containing the following information from the [metrics spreadsheet](https://docs.google.com/spreadsheets/d/1g_4tHNWP4VIikH7Jb0ui5aNr0PiFgvscZYOe69g191k/):
Expand Down