What is the relationship between IAO and EDAM?

[cmungall]

The entire contents of EDAM (https://www.ebi.ac.uk/ols/ontologies/edam http://edamontology.org/page) seems in scope for IAO. However, key differences:

• IAO is not actively developed and EDAM is (I assume)
• EDAM is widely used for the tasks it was created for
• EDAM makes more bioinformatician-friendly labels, e.g. format as opposed to data format specification -- IAO doesn't even have synonyms here
• content: the actual relevant sections are fleshed out in EDAM, i.e. IAO doesn't actually have any formats under it, so EDAM is more pragmatic here. Same for operations.

Some of us are sometimes asked for an ontology recommendation for things like bioinformatics topics, data types, formats, operations, etc. EDAM is the best choice here, there are no alternatives.

This may be unsatisfying for some as EDAM is not integrated into OBO in any way. For many tasks - e.g. categorizing topics - this is fine as most use cases just require a terminology and no reasoning.

But I can see cases where it would be useful to have EDAM better integrated with OBO, e.g. for representing and reasoning over bioinformatics data types and operations.

One possibility is that EDAM top level classes could be made subclasses of relevant IAO classes (via a bridge file) and IAO cedes the content under here.

This may require some compromises on IAO's part, e.g. in ontological naming.

Some things in EDAM could be tidied up too. I don't really understand their hierarchy and whether their subClassOf actually means owl subClassOf. E.g. EDAM has JSON as a subClassOf YAML (I assume because every JSON document is expressible as a YAML document), similarly they have manchester syntax as a subClassof RDF which doesn't make much sense. I

[cmungall]

After writing this I forgot that OBO includes SWO http://www.obofoundry.org/ontology/swo.html

It looks like SWO may actually be doing what I suggest! It seems to be a mix of IAO and EDAM....

However, SWO is trailing behind EDAM and has not been updated for a while. I requested a metadata update: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1040

I also just noticed that EDAM is CC-BY-SA. That contraindicates any reuse within OBO :-(

(I am not sure how SWO manages to be CC-BY, see my comments in the linked ticket)

One possibility here is to work with Wikidata, it is CC-0, and has many of the relevant concepts organized ontologically, e.g. multiple sequence alignment: https://www.wikidata.org/wiki/Q1377767

[allysonlister]

FYI - SWO does make use of IAO and EDAM. Jon Ison and I spend some time a few years back (in 2012, see https://softwareontology.wordpress.com/2012/07/25/swo-edam-merge-overview/) mapping SWO to EDAM. However, that work is now out of date and the latest update of SWO that I'm about to start working on may change the nature of that link.

However, there still will be associations among SWO - IAO - EDAM, so you may wish to take a look once I've got the next version of SWO out.

Thanks :) Allyson

[allysonlister]

Just to update this very old ticket, in the end I had to remove the majority of EDAM from SWO. Although Jon had agreed to import SWO in certain areas, as I agreed to import EDAM, the updates to EDAM never happened and as a consequence SWO was unbalanced. So, there are maybe 8-10 classes I have retained so that users don't wonder why they suddenly disappeared, but all hierarchies have been removed.

EDAM also chose to make their own format classes rather than import and extend SWO, so unfortunately I can't forsee any further collaboration unless things change.

There has been further discussion about the licencing (https://github.com/edamontology/edamontology/issues/724) where it seems it shouldn't be a problem, but I am not a lawyer ;-)

Apropos of nothing, I'm nearly finished updating the SWO build to use the ODK, hopefully making it easier for future contributors (OBI was interested a little while back too). It is a lovely ontology that just needs a bit of updating. I particularly think the licencing section is worthwhile, and would like to see someone who is familiar with https://spdx.dev/ investigate alignment with SWO.

Not sure I can contribute further to this ticket, so please do carry on or close if required. Please let me know if you think I can help further though!