SWO, EDAM or something in-between?

[Joe Behling]

The software ontology's latest version was published on February 8 2015

see: https://sourceforge.net/projects/theswo/files/

EDAM Git repository shows 33 commits as of this past Tuesday (Nov 1 2016)

see: https://github.com/edamontology/edamontology/graphs/commit-activity

SWO contains many useful classes (most appear to be automatically derived directly from EDAM) and is aligned with BFO / IAO, but appears to be a dead project.  On the other hand EDAM appears to be an active project but from what I can tell is not integrated with BFO or IAO.

I am curious if contributors and users of IAO and BFO ontologies have thoughts or guidance on where to get classes covering key information processing concepts such as Acession ID's, e.g. see:

GenBank accession - http://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Fdata_2292

-joe

[Barry Smith]

'Accession ID' seems to be a good candidate term for IAO. Can you send your list?
Barry

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[Melanie Courtot]

Hi Joe,

I think something like a GenBank accession would fall under the CRID class in IAO, http://purl.obolibrary.org/obo/IAO_0000578

It may be worth adding a synonym though.

If you have a specific list of terms you'd need you could add a ticket under the tracker at https://github.com/information-artifact-ontology/IAO/issues.

Cheers,

Melanie

[Allyson Lister]

Hi Joe,

(Thanks to Melanie for pointing me in the direction of your email!)

SWO is still active, it's just in the process of moving across to github:

https://github.com/allysonlister/swo

We're making a release, but I'm just having an issue or two with one of the release files, so haven't publicized the move yet - still sorting ourselves out on GH before shutting down the SF project and letting people know about the move.

Those of us who develop it all do it part time, which is why updates aren't happening as regularly as we might like.

Please let me know if you have any questions about SWO, please let me know!

Thanks,
Allyson

[Allyson Lister]

Hi Joe, everyone,

Just to say that, although slightly delayed by Christmas and New Year (and my part-time status!), we've just tagged the 1.6 release of SWO on GitHub. You can find the project here:

https://github.com/allysonlister/swo

Any comments or suggestions most welcome, including if you spot any issues with the tag or the release on GitHub itself, as it's the first time I've done it. Thanks guys!

Allyson :)

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[Joe Behling]

Allyson, thank you!

We've been using SWO with great success now for a month.  I have one major issue / question:

SWO defines the class "software" (http://www.ebi.ac.uk/swo/SWO_0000001) as a subclass of IAO:information content entity (http://purl.obolibrary.org/obo/IAO_0000030)
URI = http://www.ebi.ac.uk/swo/SWO_0000001
def = Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations.


This class seems redundant with IAO:Software (http://purl.obolibrary.org/obo/IAO_0000010)
class hierarchy = information content entity / directive information entity / plan specification / Software
URI = http://purl.obolibrary.org/obo/IAO_0000010
def = Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.

Should SWO:Software be deleted and it's subclasses  moved under IAO:Software to maximize ontology reuse, maintain clean separation between upper / middle / domain ontologies, and to minimize confusion and redundancy?

Note, this is not just a theoretical problem.  It is causing some unintended negative consequences in our data processing pipeline.

Thanks!
-joe

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