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I am a newbie in Bioinformatics, I want to extract the GO terms from yeast-cyc, which is items in the Go terms tab of this page https://yeast.biocyc.org/gene?orgid=YEAST&id=G3O-29622#tab=GO , not one page but one database like Saccharomyces cerevisiae S288c.

Is there an API or python lib can help us finish this task? I had found biocyc in pypi, but I did not found Go terms was involved in this API.

If the API is not convinient, can I download some dataset in which my required items is include?

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  • $\begingroup$ Not sure if I've misunderstood, but if you want the GO terms for yeast you can get them from uniprot.org/uniprotkb?query=(taxonomy_id:559292). Using the UniProt system you can then generate an API endpoint URL for your query, e.g. here are the GO terms for all yeast genes: rest.uniprot.org/uniprotkb/… (use wget or cURL to pull the data); does that help? $\endgroup$
    – jared_mamrot
    Sep 4 at 3:18
  • $\begingroup$ Thanks, it is the data I need. $\endgroup$
    – Mountain
    Sep 5 at 4:19
  • $\begingroup$ Great! I'll turn my comment into an answer :) $\endgroup$
    – jared_mamrot
    Sep 5 at 5:00

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You can get the GO terms for yeast from UniProt, e.g. https://uniprot.org/uniprotkb?query=(taxonomy_id:559292).

Using the UniProt website you can generate an API endpoint URL for your query, e.g. here are the GO terms for all yeast genes: https://rest.uniprot.org/uniprotkb/stream?fields=accession%2Cid%2Cprotein_name%2Cgene_names%2Cgo&format=tsv&query=%28%28taxonomy_id%3A559292%29%29

You can download this data using wget or cURL, e.g.

wget -O yeast_go_terms.tsv "https://rest.uniprot.org/uniprotkb/stream?fields=accession%2Cid%2Cprotein_name%2Cgene_names%2Cgo&format=tsv&query=%28%28taxonomy_id%3A559292%29%29"
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