<p>Search in <a href="https://bioportal.bioontology.org" rel="nofollow noreferrer">bioportal</a>: For example:  <strong><a href="https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=summary" rel="nofollow noreferrer">SNOMED</a></strong>, <strong><a href="https://bioportal.bioontology.org/ontologies/UBERON?p=summary" rel="nofollow noreferrer">UBERON</a></strong>.
Please, note that <strong><a href="https://bioportal.bioontology.org/ontologies/FMA?p=summary" rel="nofollow noreferrer">FMA</a></strong> is also available as RDF, csv , etc...  </p>

<p>You could also try to convert FMA to obo and try to open it with <a href="http://oboedit.org/" rel="nofollow noreferrer">OBO-edit</a></p>

CC BY-SA 3.0
2017-07-05T15:44:35.793Z
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.
terdon
CC BY-SA 3.0
2017-07-05T16:05:35.083Z
Yes @terdon, you are right. I'm looking for something simpler and smaller than FMA.
floatingpurr
CC BY-SA 3.0
2017-07-05T16:06:06.960Z
@Pierre, I'm afraid that Oboedit performs even worse than Protege
floatingpurr
CC BY-SA 3.0
2017-07-05T15:33:55.510Z
2017-09-12T15:34:33.303Z
2017-09-12T15:34:33.303Z
Pierre
<p>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.</p>

<p>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.</p>

<p>For example, we make a subset called 'basic.obo' from Uberon:
<a href="http://uberon.github.io/downloads.html#subsets" rel="noreferrer">http://uberon.github.io/downloads.html#subsets</a></p>

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

<p>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.</p>

<p>Most ontologies have a number of different options for web-browsing, you can see some of the options for Uberon here:
<a href="http://obofoundry.org/ontology/uberon.html" rel="noreferrer">http://obofoundry.org/ontology/uberon.html</a></p>

<p>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.</p>

<p>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.</p>

CC BY-SA 3.0
2017-08-12T21:00:41.833Z
2017-08-12T21:00:41.833Z
Chris Mungall
<p>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 <a href="http://si.washington.edu/projects/fma" rel="noreferrer"><em>Foundational Model of Anatomy ontology</em></a>, but it's over-kill for my purposes and really cumbersome (Protege fails when it tries to load FMA.owl).</p>

<p>Is there a simple online knowlegebase available for this?</p>

CC BY-SA 3.0
2017-07-05T16:10:13.307Z
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.
terdon
CC BY-SA 3.0
2017-07-05T16:13:52.783Z
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.
floatingpurr
CC BY-SA 3.0
2017-07-05T18:15:39.567Z
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.
terdon
<database><ontology>
Human body sites knowledge base
# Human body sites knowledge base

(Asked by: username_0 on 2017-07-05)

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*](http://si.washington.edu/projects/fma), 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?

**Tags:** database, ontology
> **Comments:**
> **username_1**: 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.  
> **username_0**: 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.  
> **username_1**: 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.  

---

## 2 answers

### Answer by username_3 on 2017-08-12. Score: 6 | Accepted answer

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.


---

### Answer by username_2 on 2017-07-05. Score: 3

Search in [bioportal](https://bioportal.bioontology.org): For example: **[SNOMED](https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=summary)**, **[UBERON](https://bioportal.bioontology.org/ontologies/UBERON?p=summary)**.
Please, note that **[FMA](https://bioportal.bioontology.org/ontologies/FMA?p=summary)** is also available as RDF, csv , etc...

You could also try to convert FMA to obo and try to open it with [OBO-edit](http://oboedit.org/)

> **Comments:**
> **username_1**: 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.  
> **username_0**: Yes @terdon, you are right. I'm looking for something simpler and smaller than FMA.  
> **username_0**: @Pierre, I'm afraid that Oboedit performs even worse than Protege  

---

