Commit a1a5b394 authored by Sudeep Sahadevan's avatar Sudeep Sahadevan

add id to name mapping documentation

parent ee8e71e9
......@@ -26,7 +26,8 @@ python scripts/ot_parser.py -h
```
for a description of available commands and required input files and parameters.
#### Mendelian disease associations
### Mendelian disease associations
Use the subcommand `variant` to parse Mendelian disease associations
```shell
......@@ -57,3 +58,22 @@ python scripts/ot_parser.py variant --in /path/to/20.02_evidence_data.json.gz --
cat mendelian_somatic_mutations.bed mendelian_genetic_association.bed | sort -k 1,1 -k2,2n -k3,3n > mendelian_somatic_mutations_genetic_associations_combined.bed
```
### Parse Experimental factor ontology (EFO) id to name mappings
Use subcommand `obo_id_name` to parse EFO id to name mappings from EFO .obo file
```shell
python scripts/ot_parser.py obo_id_name -h
```
**Additional information**
Experimental factor ontology used in this analysis is version: data-version: 3.17.1
The ontology in .owl format is available from the source [here](http://www.ebi.ac.uk/efo/releases/v3.17.1/efo.owl) and the .obo formatted file is available from [EBISPOT](https://github.com/EBISPOT) github repo [here](https://github.com/EBISPOT/efo/releases/download/v3.17.1/efo.obo). OpenTargets Therapeutic area annotations are missing in the ontology, but available in disease id to name mappings, which can be downloaded from [here](https://storage.googleapis.com/open-targets-data-releases/20.02/output/20.02_disease_list.csv.gz)
**Generate id - name mapping file**
```shell
python scripts/ot_parser.py obo_id_name --efo /path/to/efo.obo --out efo_id_name_map.csv
# download disease id to name file
wget -O - https://storage.googleapis.com/open-targets-data-releases/20.02/output/20.02_disease_list.csv.gz | gunzip -c| perl -pe 's/\"//g'| awk 'BEGIN {FS=",";OFS="\t"}{print $1,$2}' > disease_id_name_map.csv
cat disease_id_name_map.csv efo_id_name_map.csv| sort -u > OpenTargets_id_name_map.csv
```
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