6
$\begingroup$

I'm looking for a lightweight knowledgebase describing the human body to annotate disease sites. I do not need a great level of detail, I just need a kind of basic organs/sub-organs taxonomy. I checked out the Foundational Model of Anatomy ontology, but it's over-kill for my purposes and really cumbersome (Protege fails when it tries to load FMA.owl).

Is there a simple online knowlegebase available for this?

$\endgroup$
3
  • 1
    $\begingroup$ I did manage to open FMA.owl in Protégé, by the way. It took a while and a considerable amount of CPU and RAM but it did work eventually. $\endgroup$ – terdon Jul 5 '17 at 16:10
  • $\begingroup$ Ok! Probably I have no enough HW resources to load FMA and then extracting a small subset from it. That's the reason why I was looking for something smaller. $\endgroup$ – floatingpurr Jul 5 '17 at 16:13
  • 2
    $\begingroup$ I suggest you post a new question asking how to extract a subset of an existing ontology. Give us a link to FMA, explain what you need (for instance, how deep you want to go in the ontology's branches) and ask for help making a "slim" ontology from it. $\endgroup$ – terdon Jul 5 '17 at 18:15
6
$\begingroup$

I am the developer of Uberon and I would be happy to help you with what you need, either from Uberon, or from the FMA.

You mentioned you need something simpler than FMA. There are a variety of tools for creating custom subsets. Additionally, some ontologies provide ready-made subsets for particular purposes.

For example, we make a subset called 'basic.obo' from Uberon: http://uberon.github.io/downloads.html#subsets

You can examine this directly in either oboedit or Protege5 (note Protege5 parses obo so you don't need to convert).

From your question, you didn't indicate you needed programmatic access, but if you do there are a variety of options, as well as more programmer-friendly JSON exports.

Most ontologies have a number of different options for web-browsing, you can see some of the options for Uberon here: http://obofoundry.org/ontology/uberon.html

You mentioned annotating disease sites. There may be a tools (either desktop or web-based) for helping with this - e.g. providing autocomplete over a desired subset of an ontology.

You may also want to ask your question on a mailing list like obo-discuss. Unfortunately many ontology developers don't read stackexchange, but most are always keen to hear of community requirements, to help them provide better and more useful products.

$\endgroup$
3
$\begingroup$

Search in bioportal: For example: SNOMED, UBERON. Please, note that FMA is also available as RDF, csv , etc...

You could also try to convert FMA to obo and try to open it with OBO-edit

$\endgroup$
3
  • 1
    $\begingroup$ SNOMEDCT seems to be a full ontology for any type of clinical data, not only anatomical (e.g. it includes terms such as "smoker" or "observation") which would make it far more complex than the FMA the OP tried. Likewise, Oberon seems to be a cross-species ontology which, again would be more, not less complex than FMA. If I understand correctly, the OP wants something less complete and less complex than FMA. $\endgroup$ – terdon Jul 5 '17 at 15:44
  • $\begingroup$ Yes @terdon, you are right. I'm looking for something simpler and smaller than FMA. $\endgroup$ – floatingpurr Jul 5 '17 at 16:05
  • $\begingroup$ @Pierre, I'm afraid that Oboedit performs even worse than Protege $\endgroup$ – floatingpurr Jul 5 '17 at 16:06

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.