Categories to use for bioinformatics topics

[michaelbarton]

What should be the choice of topics for 'the field of research?'
Last year I used the categories from the Bioinformatics journal but this is rather limited.
EDAM seems to be the only actively developed bioinformatics ontology.

http://voxel.dl.sourceforge.net/project/edamontology/EDAM_beta12.obo

Perhaps the top level topic terms could be parsed out of here.

[michaelbarton]

I found that @robsyme has a library for processing .obo files. @robsyme do you think you could illustrate a way to parse out the non-obsolete list of top-level bioinformatics from the above obo file using your library? I think this list could be used in the survey.

[robsyme]

No probs. Do you just want those that are topics (is_a: EDAM:0000003)? If so:

["Nucleic acids",
"Sequence",
"Structure",
"Phylogenetics",
"Microarrays",
"Proteomics",
"Literature and documentation",
"Data handling",
"Sequencing and mapping",
"Classification",
"Ontologies and nomenclature",
"Proteins",
"Pathways, networks and models",
"Laboratory resources",
"Informatics",
"Organism",
"Genomics",
"Genotype and phenotype"]

[robsyme]

#3

[michaelbarton]

Are there sub-level topics below these? I think comparing the topics below this would give an idea of which of the two to use.

[robsyme]

Yeah, the topics are a bit vauge. I'll pull them out when I get home in a
couple of hours. I'll also pull request on the correct branch next time,
sorry.
-r

On 5 Nov 2011 00:21, "Michael Barton" <
reply@reply.github.com>
wrote:

Are there sub-level topics below these? I think comparing the topics below
this would give an idea of which of the two to use.

---

Reply to this email directly or view it on GitHub:

#2 (comment)

[robsyme]

Rather than send a pull request, I've put the topics and sub-topics up at https://gist.github.com/1341255 for discussion and forking. Note that there are topics with no subtopics (Laboratory resources, Classification etc). I suspect that we'll probably want to add items to this list.

[michaelbarton]

Thanks for this Rob. EDAM has just recently released un updated version of the ontology. Could you repeat this parsing with the new ontology, beta13?

http://sourceforge.net/projects/edamontology/files/

[robsyme]

Sorry for the very slow response. The prof has been on my back to get a paper finished. Everything is up at https://gist.github.com/1341255

These are all the is_a relations flowing down from "Topic"

[michaelbarton]

That's great. Thanks for the code too.