TheMethodsOntology

Python module and scripts for parsing the ontology (owl file) and searching pubmed articles for methods. under development

MethodsOntology.py

Owl

• Protege output (owl files)
• ._readMethods: Read in methods from ontology (owl) file
• .getMethods: Return list of methods
• ._parseMethods: Returns list of methods with alternate terms

Pubmed

• Methods for working with on and offline pubmed data
• .getXMLText: Get raw text from pubmed xml file. Uses:
• ._recursiveTextExtract: pull text from all xml elements
• .findMethods: Find methods in paper
• .extractMethods: return dictionary ["methodname","sentence it's in!'"]

Example usage

Use theMethodsOntology module to parse pubmed xml

import MethodsOntology as MO

Test xml file

owl = "root-ontology.owl"
article = "pone.0046493.nxml"

Read in ontology

ontology = MO.Owl(owl)

Create Pubmed parser for article

parser = MO.Pubmed(ontology)

Text is also stored in parser object

text = parser.getXMLText(article)

Now find sentences with methods

matches = parser.extractMethods()