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Python frontend to ontologies - a library to parse, create, browse and export ontologies.

Project description

Version Py versions Build Status Dev repo Codacy Grade License DOI coverage Documentation Status

Overview

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).

Installation

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

Usage

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)

TODO

  • test with many different ontologies
  • extract data from OwlXML where attributes are ontologic terms
  • extract metadatas from OwlXML
  • add other owl serialized formats
  • (maybe) add serialization to owl

Reference

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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