Python frontend to ontologies - a library to parse, create, browse and export ontologies.
Pronto is a python module to parse, create, browse and export ontologies from some popular formats. For now, obo and owl/xml are available, but more formats are to be added in the future (you can even add your own to work with the current API).
Installing with pip is the easiest:
pip install pronto # if you have the admin rights pip install pronto --user # if you want to install it for only one user
If for some reason you do not like pip, you can also clone the repository and install it with the setup script (still requires setuptools):
git clone https://github.com/althonos/pronto cd pronto python3 setup.py install # may also require admin rights
The class Ontology is likely the one you’ll use the most if all you want is to browse ontologies. It can be used to import ontologies in .owl (sometimes seen as .ont) and .obo formats, merge, and export ontologies to a rudimentary obo file.
Instantiate an obo ontology and getting a term by accession number:
import pronto ont = pronto.Ontology('path/to/file.obo') term = ont['REF:ACCESSION']
Display an ontology in obo format and in json format:
import pronto ont = pronto.Ontology('https://net.path.should/work/too.owl') print(ont.obo) print(ont.json)
Merge two ontologies:
import pronto nmr = pronto.Ontology('https://raw.githubusercontent.com/nmrML/nmrML/' 'master/ontologies/nmrCV.owl') ms = pronto.Ontology('http://psidev.cvs.sourceforge.net/viewvc/psidev/psi' '/psi-ms/mzML/controlledVocabulary/psi-ms.obo') ms.merge(nmr) # MS ontology keeps its metadata but now contains NMR terms # as well. assert('NMR:1000004' in ms)
Explore every term of an ontology and print those with children:
import pronto ont = pronto.Ontology('path/to/file.obo') for term in ont: if term.children: print(term)
Get grandchildrens of an ontology term:
import pronto ont = pronto.Ontology('path/to/file.obo') print(ont['RF:XXXXXXX'].children.children)
If you wish to use this library in a scientific publication, please cite it (see the Zenodo record).
Author: Martin Larralde
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