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#34 FMA ontology problem, default physical location has been deprecated
http://identifiers.org/fma/FMA:67112 redirects to incomplete information at
http://www.ebi.ac.uk/ontology-lookup/?termId=FMA:67112
The secondary location seems more useful:
http://purl.bioontology.org/ontology/FMA_subset/FMA:67112
(shows its place in the hierarchy, lists synonyms, etc.)
I suspect this is because the EBI ontology lookup service is being upgraded, so the old one has been deprecated as stated on their webpage. There is information about the upgrade at http://www.ebi.ac.uk/ols/beta/roadmap.html, but for the time being it may be better to have the bioontology.org resource as be the default.
Discussion
Anonymous
Hi Jon,
Thanks for the continued feedback about our services!
Your bug report touches upon a couple of issues, which I will address, and has prodded me with a timely reminder...
On the selection of resolving locations, we have in essence an algorithm which checks various (stored) information such the uptime of each available URL, as well as weighting in favour of the 'primary' provider of the dataset. This assignment of a 'primary' source is strictly limited to the provider of the data in question. The only way to give preference to OLS would be to assign it as the 'primary', which would not really be appropriate.
It might be of interest for you to know that we are currently undergoing an (extended) testing period of our profile system, where users such as yourself could specify which resolving location they prefer, regardless of whether it is the 'primary' or not. I can send you more information on this separately if you wish. Essentially you would be able to select a list of preferred resolving locations stored in our registry, which would be accessed with a parameter, for example identifiers.org/pubmed/12345?profile=XXX (where XXX is a user defined profile name).
With respect to OLS, I am aware that the new system is now in beta, and that the old system will be retired in March. I had originally intended to switch all our OLS access URLs at that time. Your report, however, led me to re-read that notification, and I realise now that the old system is no longer being updated with ontology terms, so could end up out of synch with other sources. For that reason I have changed the access URL for FMA to use the new OLS system, and will update the remaining OLS URLs soon. This should address your concerns about the lack of information through the old (soon to be retired) OLS URLs. (Note however that in the old interface the information you requested is actually available; the term hierarchy can be viewed if you click the 'browse' button).
Hopefully this addresses your bug report, but please feel free to tell me otherwise!
In either case it has been helpful to me, so thanks again,
cheers,
Nick
Thanks, Nick! This does indeed meet my need, which is to have useful info thrown in the face of anyone who follows a link to an ontological term. It helps win my project team over to the semantically interoperable side 8-)
perfect ;)