<p>You can get the GO terms for yeast from UniProt, e.g. <a href="https://uniprot.org/uniprotkb?query=(taxonomy_id:559292)" rel="nofollow noreferrer">https://uniprot.org/uniprotkb?query=(taxonomy_id:559292)</a>.</p>
<p>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: <a href="https://rest.uniprot.org/uniprotkb/stream?fields=accession%2Cid%2Cprotein_name%2Cgene_names%2Cgo&amp;format=tsv&amp;query=%28%28taxonomy_id%3A559292%29%29" rel="nofollow noreferrer">https://rest.uniprot.org/uniprotkb/stream?fields=accession%2Cid%2Cprotein_name%2Cgene_names%2Cgo&amp;format=tsv&amp;query=%28%28taxonomy_id%3A559292%29%29</a></p>
<p>You can download this data using <code>wget</code> or <code>cURL</code>, e.g.</p>
<pre><code>wget -O yeast_go_terms.tsv &quot;https://rest.uniprot.org/uniprotkb/stream?fields=accession%2Cid%2Cprotein_name%2Cgene_names%2Cgo&amp;format=tsv&amp;query=%28%28taxonomy_id%3A559292%29%29&quot;
</code></pre>

CC BY-SA 4.0
2023-09-05T05:00:12.490Z
2023-09-05T05:00:12.490Z
jared_mamrot
<p>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 <a href="https://yeast.biocyc.org/gene?orgid=YEAST&amp;id=G3O-29622#tab=GO" rel="nofollow noreferrer">https://yeast.biocyc.org/gene?orgid=YEAST&amp;id=G3O-29622#tab=GO</a> , not one page but one database like <em>Saccharomyces cerevisiae S288c</em>.</p>
<p>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.</p>
<p>If the API is not convinient, can I download some dataset in which my required items is include?</p>

CC BY-SA 4.0
2023-09-04T03:18:34.727Z
Not sure if I've misunderstood, but if you want the GO terms for yeast you can get them from https://www.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: https://rest.uniprot.org/uniprotkb/stream?fields=accession%2Cid%2Cprotein_name%2Cgene_names%2Cgo&format=tsv&query=%28%28taxonomy_id%3A559292%29%29 (use `wget` or `cURL` to pull the data); does that help?
jared_mamrot
CC BY-SA 4.0
2023-09-05T04:19:52.513Z
Thanks, it is the data I need.
Mountain
CC BY-SA 4.0
2023-09-05T05:00:29.720Z
Great! I'll turn my comment into an answer :)
jared_mamrot
<python><genomics><public-dataset>
How to access yeast-cyc in a programmatic way to extract the GO terms?
# How to access yeast-cyc in a programmatic way to extract the GO terms?

(Asked by: username_0 on 2023-09-02)

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?

**Tags:** python, genomics, public-dataset
> **Comments:**
> **username_1**: Not sure if I've misunderstood, but if you want the GO terms for yeast you can get them from https://www.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: https://rest.uniprot.org/uniprotkb/stream?fields=accession%2Cid%2Cprotein_name%2Cgene_names%2Cgo&format=tsv&query=%28%28taxonomy_id%3A559292%29%29 (use `wget` or `cURL` to pull the data); does that help?  
> **username_0**: Thanks, it is the data I need.  
> **username_1**: Great! I'll turn my comment into an answer :)  

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## 1 answers

### Answer by username_1 on 2023-09-05. Score: 2 | Accepted answer

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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