pronto
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althonos
A Python frontend to (Open Biomedical) Ontologies.
Right now the `Ontology.dump()` function only supports OBO and OBO Graph JSON. It would be great if it could dump valid OWL (e.g. in RDF/XML) or another serialization of OWL...
I would like some advice on parsing Orphanet OWL file (new model) where part_of relationship is now represented differently. In the previous version 3.3, part_of relationship is represented with the...
When parsing `cellosaurus.obo` downloaded from [here](https://ftp.expasy.org/databases/cellosaurus/), I get this error.  The error is fixed when I manually remove 1. lines starting with `!` (lines 27-48) 2. line with date...
What is the best way to force pronto to continue in the face of messy/real data? ``` >>> cl = Ontology("http://purl.obolibrary.org/obo/uberon.obo") Traceback (most recent call last): File "", line 1,...
Attempting to parse the `aro.owl` file from the OBO Foundry raises a `ValueError`: ```python >>> pronto.Ontology.from_obo_library("aro.owl") Traceback (most recent call last): File "", line 1, in File "/home/althonos/Code/pronto/pronto/ontology.py", line 206,...
Hi, I've read the documentation quite extensively, yet I haven't found any method or function to delete a term from an ontology. For example: ```python from pronto import Ontology go...
I've been debugging the [CHIRO (CHEBI Integrated Role Ontology)](http://www.obofoundry.org/ontology/chiro.html) OBO export, and it had a few issues. First, I had to manually add some `Typedef` stanzas for its ad-hoc relations....
``` >>> cl = Ontology("http://purl.obolibrary.org/obo/cl.obo") Traceback (most recent call last): File "", line 1, in File "/usr/local/Caskroom/miniconda/base/envs/pangenic/lib/python3.8/site-packages/pronto/ontology.py", line 218, in __init__ cls(self).parse_from(_handle) # type: ignore File "/usr/local/Caskroom/miniconda/base/envs/pangenic/lib/python3.8/site-packages/pronto/parsers/obo.py", line 46, in...
Imagine the following Gene Ontology term like `Term('GO:1902779', name='cellular response to alkane')`. Is there any way to retrieve the URI `http://purl.obolibrary.org/obo/GO_1902779`? For example a `term.uri` property? In my case, I...
Your EncodedFile class’s `readinto` can’t handle if `codecs.StreamRecoder.read` returns a bigger chunk than requested: https://github.com/althonos/pronto/blob/37126293472293b4bb3f406b41198a351fec4542/pronto/utils/io.py#L55-L62 But this can happen: And that’s normal, see the [docs for StreamReader](https://docs.python.org/3/library/codecs.html#codecs.StreamReader) (emphasis mine): >...
