Merge branch 'develop' into main

SysBioChalmers · Mar 11, 2023 · 9c87207 · 9c87207
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diff --git a/data/README.md b/data/README.md
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 This directory contains datasets that were used for the generation and curation of Worm-GEM. The files and their contents are briefly summarized below.
 
 
-- `human2WormOrthologs.json`: The human-worm ortholog pairs downloaded from the [Alliance of Genomes Resources](https://www.alliancegenome.org).
+- `human2WormOrthologs.tsv`: The human-worm ortholog pairs downloaded from the [Alliance of Genomes Resources](https://www.alliancegenome.org) using the following code:
+```bash
+curl -X \
+GET "https://www.alliancegenome.org/api/homologs/9606/6239?filter.stringency=stringent&limit=50000&page=1" \
+-H  "accept: application/json" | \
+jq -r \
+'["fromGeneId", "fromSymbol", "toGeneId", "toSymbol", "best", 
+"bestReverse", "methodCount", "totalMethodCount"], (.results[] | 
+[.gene["id"], .gene["symbol"], .homologGene["id"], .homologGene["symbol"], 
+.best, .bestReverse, .methodCount, .totalMethodCount]) 
+| @tsv' > human2WormOrthologs.tsv
+```
 - `wormSpecificMets.tsv` and `wormSpecificRxns.tsv`: The curated metabolic network that is not part of human metabolism but specific to worm.