pronto : Python frontend to 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

Metadata

Release files for pronto 0.1.11

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Built distribution (wheel)

Table of built distributions (wheels) for pronto 0.1.11
File	Interpreter	ABI	Platform	Reset
pronto-0.1.11-py3-none-any.whl 18.5 kB Jul 12, 2016	Python 3	none	any	Details

Release files / pronto-0.1.11-py3-none-any.whl

Download URL	pronto-0.1.11-py3-none-any.whl
Size	18.5 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`1305ca86af9e7ef2fed44271d48d49b5e507bcde9741f0ef0605240c29d71e86`
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Upload date	Jul 12, 2016
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