David Ochoa

`--properties-file` flag not available job classes

2

The flag `--properties-file=PROPERTIES_FILE` from `gcloud dataproc jobs submit pyspark` [[doc](https://cloud.google.com/sdk/gcloud/reference/dataproc/jobs/submit/pyspark#--properties)] does not seem available through the `PySparkJob` [python class](https://github.com/googleapis/python-dataproc/blob/2107cf8bc54096b7bb14b4de38a9abef5eeada59/google/cloud/dataproc_v1/types/jobs.py#L300). This flag is very handy to add properties that depend on...

## ✨ Context We need a mechanism to retrieve Variant Annotation from variants outside GnomAD. After some consideration, we concluded Ensembl VEP is the best stable source to retrieve the...

feat: devcontainer development environment

6

This PR allows to setup a development environment using the devcontainer stragety. [More info...](https://code.visualstudio.com/docs/devcontainers/containers) A few working functionalities: - start the development environment by just clicking a button/badge (in docker...

fix: write mode added to validation steps

3

Add write mode for the 2 datasets written in each of the validation steps

feat: gwas catalog top-hit + study step

3

Step to run the top-hits in isolation of everything else. The `GWASCatalogTopHitIngestionStep` included here was run in dataproc in 17 minutes. Subsequent PRs will handle GWAS Catalog + Summary Statistics...

Unspecific synonym "intrinsic" for MONDO_0001721

1

"intrinsic" is listed as one of the synonyms of `urethral intrinsic sphincter deficiency` (MONDO_0001721) (Causing some issues with text-mining)

Impact of Orphanet subclasses into OpenTargets pipeline

5

As discussed with SPOT team, we have been investigating the impact of EFO3 (OT version) in the calculation of target-disease associations. In order to do identify potential problems, we have...

Missing EFO terms based on COSMIC NCIT terms

2

COSMIC (v90) is currently not able to map 405 NCIt terms to EFO ([attached](https://github.com/EBISPOT/efo/files/4107729/NCIt_codes_not_mapped_to_EFO_COSMIC_v90.tsv.zip)). Using OxO none map to EFO but 188 (out of 405) map with MONDO at distance...