MTP annotations scripts

[atlas4213]

Purpose/implementation Section

Create Open Targets Platform v22.11 Target (core annotations for targets) and Disease/Phenotype (core annotations for diseases and phenotypes) tables to utilize for filtering MTP .v1.2 tables and O API OPC v12 data files.

What scientific question is your analysis addressing?

Creating a disease/phenotype table for use with v12 data files

What was your approach?

Download the files to scratch and then convert them from json to csv. Store the csv files in /home/ubuntu/volume/OpenPedCan-analysis/scratch/mtp-csv folder and then use R to pull out the needed data. Then write that data to a tsv file in ~/volume/OpenPedCan-analysis/analyses/mtp-annotations/results.

What GitHub issue does your pull request address?

A missing table that contains all of the disease and phenotype information for downstream v12 processing

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

~/volume/OpenPedCan-analysis/analyses/mtp-annotations01-mtp-annotations.R
~/volume/OpenPedCan-analysis/analyses/mtp-annotationsrun-mtp-annotations.sh
~/volume/OpenPedCan-analysis/analyses/mtp-annotations/resultsmtp-disease-mapping.tsv
~/volume/OpenPedCan-analysis/analyses/mtp-annotations/resultsmtp-target-mapping.tsv

Is there anything that you want to discuss further?

No

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

Two tables

~/volume/OpenPedCan-analysis/analyses/mtp-annotations/resultsmtp-disease-mapping.tsv
~/volume/OpenPedCan-analysis/analyses/mtp-annotations/resultsmtp-target-mapping.tsv

What is your summary of the results?

Two files that contain the Hugo gene_symbol to Ensemble gene_id to Ensemble transcript_id and EFO to MONDO

Reproducibility Checklist

• [ X] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [ X] This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• [X ] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [ X] The analytical code is documented and contains comments.

[ewafula]

Thank you, @atlas4213, for working on this. I have updated the code to condense and make it generic to allow only version number updates to the module for future releases of MTP Open Targets Platform annotations. I have excluded your EC2 instance-dependent file paths to enable running in the OPC docker container and included a module README.

I have submitted a separate PR that adds dasel file converter OPC Dockerfile.

Please review the changes I have before I can merge. I will also ask @sangeetashukla to review and make sure everything looks ok.

[ewafula]

@sangeetashukla, would you mind reviewing this PR? Once merged, you can use mtp-diseases-mapping.tsv.gz and mtp-targets-mapping.tsv.gz results mapping files to ensure the gene_match and efo-mondo-mapping modules, respectively are up to date with required MTP annotations.