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NLP toolkit for those nonsensical ontologies

Home Page: https://sap218.github.io/jabberwocky/

License: MIT License

Python 100.00%

ontology python tfidf jabberwocky synonyms textual-data text-mining grep annotation plotting

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jabberwocky's Issues

work with textual data that is not in JSON format

next step

removing class/synonyms from textual data and then looking at the left-over text

input code over study break to make a start

Note to anyone reading this: the code will probably be really bad. But I'm not an expert. Pls forgive. :-)

declare requirements more formally

I am not that sophisticated of a python developer, but I often see a requirements.txt used to declare requirements.

I did successfully install the software by using the prerequisites command in the README, but breaking these out into a dependencies file would probably be a good idea.

update readme & code to include updated clicks

merge jabberwocky-tests and jabberwocky into one github repo

make a gh-pages with markdown of the README from jabber-test - include new test data!

Supported ontology formats and synonym properties

Can you say which ontology formats are meant to work? I see that the pocket monsters example is in OWL/XML. I tried some other formats with catch (RDF/XML, TTL, OFN) and they all gave the same output. I was kind of surprised, but I guess it's using only the terms in listofwords.txt and not finding synonyms in the ontology? When I run with the OFN format file, I don't see any synonyms in ontology_dict_class_synonyms.json. I think it would be good to document supported ontology formats, especially since OWL/XML is a fairly uncommon format.

Related question: I made my own OWL/XML file with a single term 'eye' and used the annotation property http://www.geneontology.org/formats/oboInOwl#hasExactSynonym to add synonym 'visual organ'. I don't see this being found and added to ontology_dict_class_synonyms.json.

Here is the ontology I used:

<?xml version="1.0"?>
<Ontology xmlns="http://www.w3.org/2002/07/owl#"
     xml:base="http://example.org/ontologies/2020/4/28/untitled-ontology-1490"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     ontologyIRI="http://example.org/ontologies/2020/4/28/untitled-ontology-1490">
    <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/>
    <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
    <Prefix name="xml" IRI="http://www.w3.org/XML/1998/namespace"/>
    <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/>
    <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/>
    <Declaration>
        <Class IRI="/eye"/>
    </Declaration>
    <Declaration>
        <AnnotationProperty IRI="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
    </Declaration>
    <AnnotationAssertion>
        <AnnotationProperty IRI="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
        <IRI>/eye</IRI>
        <Literal>visual organ</Literal>
    </AnnotationAssertion>
    <AnnotationAssertion>
        <AnnotationProperty abbreviatedIRI="rdfs:label"/>
        <IRI>/eye</IRI>
        <Literal>eye</Literal>
    </AnnotationAssertion>
</Ontology>

(this is part of JOSS review openjournals/joss-reviews#2168)

(pyenv) localhost:catch jim (master)$ catch --ontology ../ontology/pocketmonsters.owl --keywords listofwords.txt --textfile blogs_formatted.json --parameter blog_post > catch_output.txt
Traceback (most recent call last):
  File "/Users/jim/Documents/Reviews/JOSS/pyenv/bin/catch", line 11, in <module>
    load_entry_point('jabberwocky==0.5.0.1', 'console_scripts', 'catch')()
  File "/Users/jim/Documents/Reviews/JOSS/pyenv/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/Users/jim/Documents/Reviews/JOSS/pyenv/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/Users/jim/Documents/Reviews/JOSS/pyenv/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/jim/Documents/Reviews/JOSS/pyenv/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/Users/jim/Documents/Reviews/JOSS/pyenv/lib/python3.7/site-packages/jabberwocky-0.5.0.1-py3.7.egg/catch/catch.py", line 426, in main
    search_term_dictionary = ontologyPurl(ontology, keywords)
  File "/Users/jim/Documents/Reviews/JOSS/pyenv/lib/python3.7/site-packages/jabberwocky-0.5.0.1-py3.7.egg/catch/catch.py", line 77, in ontologyPurl
    souped = souping(ontology) # Reading in the ontology file
  File "/Users/jim/Documents/Reviews/JOSS/pyenv/lib/python3.7/site-packages/jabberwocky-0.5.0.1-py3.7.egg/catch/catch.py", line 25, in souping
    soup = BeautifulSoup(contents,'xml')
  File "/Users/jim/Documents/Reviews/JOSS/pyenv/lib/python3.7/site-packages/bs4/__init__.py", line 228, in __init__
    % ",".join(features))
bs4.FeatureNotFound: Couldn't find a tree builder with the features you requested: xml. Do you need to install a parser library?

I'm running in a virtual environment with only the jabberwocky dependencies installed.

(this is part of JOSS review openjournals/joss-reviews#2168)

create documentation for the jabberwocky-tests repo

in relation to openjournals/joss-reviews#2168

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