pronto 0.1.2

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

Overview

pronto is a python module to parse, create, browse and export ontologies from some popular formats. For now, obo and owl/xml were added, 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

Currently there are 2 classes which both inherit from Ontology: Obo and OwlXML. To parse the right kind of file you have to use the right class, although that will probably change to the future to provide an unique Ontology class. Right now though you can still use the Ontology class as a base to merge other ontologies into.

Instantiate an obo ontology and getting a term by accession number:

import pronto
ont = pronto.Obo('path/to/file.obo')
term = ont['REF:ACCESSION']

Display an ontology in obo format and in json format:

import pronto
ont = pronto.OwlXML('https://net.path.should/work/too.owl')
print(ont.obo)
print(ont.json)

Merge two ontologies:

import pronto
nmr = pronto.OwlXML('https://raw.githubusercontent.com/nmrML/nmrML/'
                    'master/ontologies/nmrCV.owl')
ms  =    pronto.Obo('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.Obo('path/to/file.obo')
for term in ont:
    if term.children:
        print(term)

Get grandchildrens of an ontology term:

import pronto
ont = pronto.Obo('path/to/file.obo')
print(ont['RF:XXXXXXX'].children.children)

TODO

• redefine OwlXML and Obo as Parsers in pronto.parser, and always use Ontology to open an ontology file.

• properly define Import Warnings whenever an import fails.

• write a proper documentation

• create a proper relationship class

• 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