Fwd: RDF, Linked Data, Semantic Web, SPARQL, OWL, etc.

Begin forwarded message:

> From: Chris Mungall <cjmungall@lbl.gov>
> Subject: Re: RDF, Linked Data, Semantic Web, SPARQL, OWL, etc.
> Date: May 12, 2013 1:31:25 PM EDT
> To: Todd DeLuca <todddeluca@gmail.com>
> Cc: Suzanna Lewis <suzi@berkeleybop.org>
> 
> Hi Todd,
> 
> See my email below for some answers to your questions.
> 
> Suzi, can you forward the message to the list? I will try and re-sub with my other address (sigh...)
> 
> 
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>> Hello cjmungall@lbl.gov,
>> 
>> We're writing to let you know that the group you tried to contact (orthologs) may not exist, or you may not have permission to post messages to the group. A few more details on why you weren't able to post:
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>> Google Groups
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>> Subject: Re: RDF, Linked Data, Semantic Web, SPARQL, OWL, etc.
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>> From: Chris Mungall <cjmungall@lbl.gov>
>> In-Reply-To: <45283db6-3229-4679-89ce-29525ea3bb39@googlegroups.com>
>> Date: Thu, 9 May 2013 23:02:18 -0700
>> Cc: Frederic Bastian <frederic.bastian@unil.ch>,
>> Jerven Bolleman <jerven.bolleman@isb-sib.ch>
>> Message-Id: <C3E34E75-85EC-42A9-B6E3-8753BEE55B04@lbl.gov>
>> References: <45283db6-3229-4679-89ce-29525ea3bb39@googlegroups.com>
>> To: orthologs@googlegroups.com
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>> 
>> 
>> Hi Todd,
>> 
>> I'll answer your questions out of order.
>> 
>> * Which ontologies already exist?
>> 
>> See the publication "An Ontology to clarify homology-related concepts" by Roux and Robinson-Rechavi, and its associated ontology:
>> http://dx.doi.org/10.1016/j.tig.2009.12.012
>> 
>> This is a broad treatment covering both gross anatomical structures and molecules.
>> 
>> So has a "homology" attribute
>> http://ols.wordvis.com/q=SO:0000857
>> 
>> CDAO may be of interest
>> https://www.nescent.org/wg_evoinfo/CDAO
>> it has "homologous to" ( http://purl.obolibrary.org/obo/CDAO_0000181 ) but no sub-relations.
>> 
>> It wasn't clear to me how to download OGO, it looks like it has a fairly basic notion of orthology.
>> 
>> As far as I can tell, there isn't really an ontology or vocabulary that enumerates the various subtypes of homology, including for example in and out paralogs (together with precise formal definitions). But I'm sure this could be added to an ontology like HOM.
>> 
>> In my view, a truly satisfying representatin would be based on phylogeny, with the ability to infer orthology/paralogy using reasoners (somewhat outside the scope of OWL, but possible with some extensions).
>> 
>> You may have more luck with this question on the obo-discuss list.
>> 
>> * is there an OrthoOWL equivalent to OrthoXML
>> 
>> OrthoXML covers more than just homology relations. E.g. genes, blast scores, taxa. One of the advantages of RDF is that it's easier to mix and match different vocabularies, and that is what I would do here. Use parts of CDAO, HOM, SO, the ontologization of the NCBITaxon ontology, etc.
>> 
>> * Value of representing orthologs as RDF
>> 
>> Compared to what? There are certain benefits, such as easier integration with (some) other data resources, resuing parts of other vocabularies (see above). You may get more religious answers from others.
>> 
>> There are certain unique modeling questions. E.g. do you represent homology relations as predicates (and use reification to record provenance), or turn the predicate into a node in its own right? Fairly geeky stuff I'd be
>