[Obo-discuss] Importing owl ontologies and BFO under OBO ? Clear distinct namespaces of BFO and Fugo top level classes ?

[Holger S. <hol...@if...>]

Hello everybody,

As I am actually "the guy from the Saarland" who is implementing the 
IFOMIS version of BFO in OWL, I wanted to add some comments too:

- The new implementation tries to follow the published papers on BFO as 
closely as possible, to be as complete as possible and also to be 
ontologically sound. To chieve this goal I had (and still have) 
discussions with my IFOMIS colleagues Andrew Spear and Pierre Grenon as 
well as with Chris Mungall and Alan Ruttenberg. Further comments from 
other people are naturally very welcome too.

- As pointed out in this thread before, proper textual definitions 
and/or description are still missing in the implementation. But they are 
worked on at the moment (with the help of Andrew Spear) and will be 
introduced over the next few weeks. Here also, comments on the 
understandibility of those descriptions will definitely be helpful for 
us and are therefore encouraged.

- The new implementation is already used productively in the modeling of 
an ontology for a European Union project on clinico-genomic trials on 
cancer. From the feedback I got the BFO implementation seems to work and 
make sense in this setting. In view of this I think the implementation 
to be (quite) stable and that only marginal changes will happen before 
the final (non-beta) version. But on the other hand, this also depends 
on further comment I will get.

- Technically seen, there is no direct relation between this new BFO 
implementation and Chris Mungall's: The Saarland one is built anew from 
ground up and hence independent from that existing one. Naturally, on 
the conceptual level there is quite some overlap since both are based on 
the same papers.

- Right now the namespace for BFO is the somewhat clumsy being 
"www.ifomis.uni-saarland.de/bfo": I will try to get the shorter 
"www.ifomis.de/bfo" or "www.ifomis.org/bfo" but if that works out I will 
now very soon. The namespace of BFO will contain "ifomis" as this is the 
actual place of the BFO development and not 
"www.basicformalontology.org" as proposed elsewhere.

Bye,
Holger Stenzhorn



Trish Whetzel schrieb:
> Hi Daniel,
>
>   
>> We would like to submit an owl ontology to OBO. Our msi-nmr.owl file imports 
>> Fugo.owl from a URI (<owl:imports rdf:resource="XXX">, where XXX is a URI 
>> representing a URL).
>>     
> A few questions for clarification - is the plan to have the msi-nmr 
> ontology as a separate ontology from the whole of FuGO during the entire 
> development and production time of FuGO or will the terms be folded into 
> FuGO at some point, i.e. will the msi-nmr ontology be developed in an 
> independent fashion versus the unified method as discussed in general last 
> year at the MGED meeting (note the choice of for any community is up to 
> the community, my question is to get a better understanding of the 
> management process between MSI and FuGO)?
>
> If the independent method is the choice of the MSI community how will 
> overlaps in term needs be handled between msi-nmr and FuGO and other 
> collaborating communities - which ontology will import from the other and 
> more importantly how will term overlaps be identified? Based on others 
> experience, are there other issues that need to be discussed, policies 
> established?
>
>   
>> Now the question arises, how such owl imports will be handled under OBO.
>> The owl ontologies we want to import (BFO for top level classes and FuGO for 
>> the middle layer) do and will adhere to the OBO principles, but are 
>> themselves not yet placed under OBO.
>> When we submit the msi-nmr ontology, are we allowed to import FuGO or BFO and 
>> FuGO? Will the imported ontologies be imported from a URI that is a URL, i.e. 
>> from the web, or from a protege repository file  ( see 
>> http://protege.cim3.net/cgi-bin/wiki.pl?OWL_Imports_Repositories ) 
>> proliferated with the importing ontology (the latter might be a solution for 
>> the time being when the imported ontologies are not yet stable)?
>>     
> Personally, I am not familiar with this or where the boundary will be 
> between reference ontologies and application ontologies wrt to FuGO 
> depending on how other communities will be using FuGO.
>
> Also, should FuGO itself be submitted to OBO at this time?
>
>   
>> Another problem: Right now FuGO (re)models the BFO top level classes under 
>> its own FuGO-namespace. For the sake of clear modularisation I think FuGO 
>> should import a BFO.owl file instead. I think Chris Mungall has worked on a 
>> BFO.owl (Chris, is there a URL where to import a basic, stable, working 
>> BFO.owl from? I can only find an old version that seems to be broken).
>> In the protege/owl world one would expect FuGO to import the top level 
>> ontology BFO.owl and the msi-nmr.owl would - by importing FuGO - 
>> automatically also import the needed BFO classes.
>>     
> Yes, FuGO does contain the BFO terms under what is technically the FuGO 
> namespace (this is where a language issue comes to play in the 
> development process). We did previously discuss that FuGO will 
> need to import BFO in time, however if the needs of the msi community 
> necessitate that this be done sooner than later that is something that the 
> FuGO developers will need to address. For the most part I assume this 
> will be trivial, however I think that there are some other overlaps of 
> terms between FuGO and BFO that may need to be addressed as well as 
> having a stable representation of BFO in OWL.
>
> WRT to BFO in OWL format, Barry sent around a URL (fugo-devel thread:
> http://tinyurl.com/pzqg6) of SNAP and SPAN which together form BFO (the 
> RO may have been in there as well). My understanding is that the URL that 
> Barry sent around pointed to work done by students and there where some 
> issues with that, minor issues such as typos, somewhat more major in that 
> the terms did not have definitions and other issues that Liju mentioned 
> in general (not sure what those were specifically).
> **Liju did you get a chance to submit your questions to Barry about this 
> work?
> I think that the plan from Barry was to have those issues resolved, 
> however I do not know what the time frame is.
>
> In addition, I believe that Chris Mungall is/was also working on an OWL 
> representation of BFO. I don't know what the exact relationship is between 
> the work of Chris and that from Barry's students.
>
>   
>> I also created a page "Owl ontology imports 
>> <https://www.cbil.upenn.edu/fugowiki/index.php/OntologyImports>" on the 
>> internal FuGO Wiki. So, FuGO-people, feel free to post comments and ideas.
>>     
> Sounds good. If there is anyone that needs a login in order to contribute 
> to the wiki, email me offlist.
>
> Cheers,
> Trish
>
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