Gather feedback from developers of bioinformatics tools that consume ontology files

[cmungall]

Many developers have written redundant obo parsers in various languages. Due to the details of the spec it is difficult to write a robust parser. OWL is very difficult to work with, many people use the wrong level of abstraction, e.g. XML parsing. obographs is designed with these developers in mind, see https://douroucouli.wordpress.com/2016/10/04/a-developer-friendly-json-exchange-format-for-ontologies/

This meta-ticket is for gathering feedback from knowledgeable bioinformatics coders who have struggled with obo or owl issues

Python

• ontobio http://ontobio.readthedocs.org @cmungall
• https://github.com/dhimmel/obo - Consider using a JSON representation instead of the obo file format dhimmel/obonet#2
• https://github.com/idoerg/Ontology cc @idoerg
• https://github.com/mschubert/python-obo Add links to other parsers in the README mschubert/python-obo#2 cc @mschubert
• https://github.com/tanghaibao/goatools Consider support for obographs json format tanghaibao/goatools#71 cc @tanghaibao
• AGR
• pronto

Perl

• ontoperl http://search.cpan.org/dist/ONTO-PERL/ cc @easr
• bioperl

R

• goTools
• [MANY MORE, TO BE FILLED IN]

Ruby

• obo_parser https://github.com/mjy/obo_parser cc @myj

Java

• ontolib https://github.com/Phenomics/ontolib/ @drseb
• MANY MORE...

C

• genometools by @gordon, see Document typecheck option in gff3validator genometools/genometools#910

[cmungall]

Many consumers such as @dvklopfenstein would like to see how GO looks in this representation.

This permanent URL should be active on monday:
http://purl.obolibrary.org/obo/go/extensions/go-plus.json

The URL is intended to be permanent, but the underlying representation may change.

For an explanation of go-plus see http://geneontology.org/page/download-ontology

[tgbugs]

Another python parser and serializer for the list https://github.com/tgbugs/pyontutils/blob/master/pyontutils/obo_io.py.