Re: [Obo-relations] ontology of spatial relations

[Chris M. <cj...@be...>]

On Feb 1, 2010, at 1:35 AM, Marijke Keet wrote:

> Hi Alan,
>
> I had a quick look at the spatial ontology (the BSPO.owl), and  
> Melissa Haendel saved it according to the ontology annotations  
> (including adding to it? or main developer?) and Chris uploaded it  
> (or also added to it?)

Some time ago I took the FlyBase "spatial qualifier" ontology and  
generalized it for multiple organisms

> The contents puzzle me; unfortunately, the obofoundry link for more  
> info points to the CARO page, but there is no information on the  
> spatial ontology there. The ontology annotation "based on FBqI" is  
> somewhat cryptic to me. Then, going by the name of the ontology, I  
> presumed the intention is that it is subject domain independent,  
> which raised several questions. Googling for more information (...)  
> before writing a long email, I found this [1] page as well, which  
> says "Description: A small ontology for anatomical spatiol  
> references,", so I will ask first two exploratory questions to  
> better understand the context of the ontology:
> - what do the genidXXX as individuals in the ontology, and DbXrefs?

I presume you are looking at the OWL conversion. These artefacts arise  
from the conversion

> - why does it not include some well-established basic spatial  
> relations, such as those of the RCC (or some mereotopology, or more  
> fancy mereogeometry)?
> More generally: is there any chance that the name of this ontology  
> will be changed to something more appropriate w.r.t. the actual  
> contents and intended purpose(s)?

It probably should be.

> [1] http://bioportal.bioontology.org/ontologies/40827
>
> cheers,
> marijke
>
> C. Maria Keet
> KRDB Research Centre
> Faculty of Computer Science
> Free University of Bozen-Bolzano
> Piazza Domenicani 3
> 39100 Bolzano
> Italy
> tel: +39 04710 16128
> fax: +39 04710 16009
> email: ke...@in...
> web: http://www.inf.unibz.it/krdb/
> home: http://www.meteck.org
> blog: http://keet.wordpress.com
>
> Alan Ruttenberg ha scritto:
>>
>> Hello Meena,
>>
>> Chris Mungall has put out the spatial ontology on the obofoundry site
>> for discussion and review. What would make the most sense would be to
>> have a look at it and see whether it is useful for your work.
>>
>> There are a number of us with such needs. As there isn't any such
>> ontology that is in common use within the foundry, we depend on  
>> people
>> looking at what is there and participating in further development to
>> the extent needed.
>>
>> I too will be needing some number of spatial relations for work I  
>> will
>> be doing on brain anatomy and so I will similarly have a look at
>> Chris' work.
>>
>> In regard to your work on anatomy, I might suggest you have a look at
>> the FMA before you expend too much much work - it is a relatively
>> developed ontology of human anatomy and it would be a shame to do  
>> work
>> that replicates its effort. Once again, to the extent that it meets
>> some but not all of your needs, you might consider collaborating with
>> the FMA developers in order to develop a single ontology that serves
>> everyone better.
>>
>> http://sig.biostr.washington.edu/projects/fm/
>> http://groups.google.com/group/fma-owl-2009
>>
>> -Alan
>>
>>
>> On Fri, Jan 22, 2010 at 5:49 AM, Ms. Meena Kharatmal
>> <me...@hb...> wrote:
>>
>>> Hello,
>>>
>>> I have a query from a collaborator who wish to map a domain of  
>>> biology
>>> with spatial relations. In this regard, we have selected the topic  
>>> of
>>> human anatomy. The main reference for our work is Gray's
>>> Anatomy. Initially we may cover only joints, bones or muscles.
>>>
>>> This is a request to the community to give your opinion especially
>>> regarding the spatial relations and whether there would be any other
>>> domain to map exclusively for the spatial relations.
>>>
>>> I am also referring to the spatial ontology on the obofoundry.org
>>> website to get information.
>>>
>>> Thank you.
>>> Best regards.
>>> Meena.
>>> --
>>> "I link, therefore I am"
>>>  ......................................................
>>>    Meena Kharatmal
>>>      blog   -->  http://okeanos.wordpress.com
>>>      twit   -->  http://twitter.com/meena74
>>>      web    -->  http://www.hbcse.tifr.res.in/~meena
>>>  ......................................................
>>>
>>> ------------------------------------------------------------------------------
>>> Throughout its 18-year history, RSA Conference consistently  
>>> attracts the
>>> world's best and brightest in the field, creating opportunities  
>>> for Conference
>>> attendees to learn about information security's most important  
>>> issues through
>>> interactions with peers, luminaries and emerging and established  
>>> companies.
>>> http://p.sf.net/sfu/rsaconf-dev2dev
>>> _______________________________________________
>>> Obo-relations mailing list
>>> Obo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/obo-relations
>>>
>>>
>>
>> ------------------------------------------------------------------------------
>> The Planet: dedicated and managed hosting, cloud storage, colocation
>> Stay online with enterprise data centers and the best network in  
>> the business
>> Choose flexible plans and management services without long-term  
>> contracts
>> Personal 24x7 support from experience hosting pros just a phone  
>> call away.
>> http://p.sf.net/sfu/theplanet-com
>> _______________________________________________
>> Obo-relations mailing list
>> Obo...@li...
>> https://lists.sourceforge.net/lists/listinfo/obo-relations
>>
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the  
> business
> Choose flexible plans and management services without long-term  
> contracts
> Personal 24x7 support from experience hosting pros just a phone call  
> away.
> http://p.sf.net/sfu/theplanet-com_______________________________________________
> Obo-relations mailing list
> Obo...@li...
> https://lists.sourceforge.net/lists/listinfo/obo-relations