Re: How do OBO ontologies work on the LOD?

2012-02-24 Thread Gregg Kellogg
On Feb 24, 2012, at 1:40 PM, Peter DeVries wrote: > Hi Guys, > > Since you are working with Ruby you might want to check out the work of the > ruby-rdf group, > > In my experience they do really good work, > > RDF.rb: Linked Data for Ruby > http://rdf.rubyforge.org/ > https://github.com/bendiken/

Re: How do OBO ontologies work on the LOD?

2012-02-24 Thread Kingsley Idehen
On 2/24/12 10:29 AM, Matt wrote: Hi Pete, Please keep myself and, more importantly Jim (who did the hard work setting things up here) in the loop on these issues. I didn't see anything going on here until the discussion had gone on for some time- there is a very good chance we could have prevent

Re: How do OBO ontologies work on the LOD?

2012-02-23 Thread Alan Ruttenberg
On Thu, Feb 23, 2012 at 9:14 PM, Peter DeVries wrote: > Hi Alan, > > I am not against OBO. > > I am against people giving the impression that if it is an OBO ontology, > it will work as expected by the LOD community. > Circles. > > The basics are pretty simple. If you use a URI it should behave

Re: How do OBO ontologies work on the LOD?

2012-02-23 Thread Peter DeVries
Here is another example. If I take this HAO URI http://purl.obolibrary.org/obo/HAO_512 And plug it into the Sindice Inspector Tool on this page http://sindice.com/ It it interprets it as a web page, not an owl class. If I take the URI as it exists in the ontology http://purl.org/obo/owl/HA

Re: How do OBO ontologies work on the LOD?

2012-02-23 Thread Alan Ruttenberg
Hi Kinglsey, We don't do content negotiation. I've written concerning why, in the past, to some of the W3C groups. I don't like the practice because it muddies up what exactly the URI means. So we use a not uncommon technique of responding to requests uniformly, with RDF/XML, and providing a styl

Re: How do OBO ontologies work on the LOD?

2012-02-23 Thread Kingsley Idehen
On 2/23/12 1:32 PM, Peter DeVries wrote: However, I think testing using the Vapour Validator is easier to understand. This might best be shown in comparison to a LOD OWL class that works correctly, OBO Ontology URI http://purl.org/obo/owl/HAO#HAO_000 Mapped URI http://purl.obolibrary.or

Re: How do OBO ontologies work on the LOD?

2012-02-23 Thread Alan Ruttenberg
On Thu, Feb 23, 2012 at 9:40 AM, Peter DeVries wrote: > Hi Chris, > > http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#5 > > *"On completions this section will define the semantics of the entirety > of OBO via mappings to OWL2. The mappings could also be used to specify a > translatio

Re: How do OBO ontologies work on the LOD?

2012-02-23 Thread Peter DeVries
Hi Chris, *> Sorry, I'm not following. In OBO format you can map OBO-Style IDs to any URI scheme you like. The default is to map to a http://purl.obolibrary.org/obo URI* As it is implemented HAO does not follow best practices as described here: http://www.w3.org/DesignIssues/LinkedData.html ( A

Re: How do OBO ontologies work on the LOD?

2012-02-23 Thread Chris Mungall
On Feb 23, 2012, at 9:40 AM, Peter DeVries wrote: > Hi Chris, > > http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#5 > > "On completions this section will define the semantics of the entirety of OBO > via mappings to OWL2. The mappings could also be used to specify a > translatio

Re: How do OBO ontologies work on the LOD?

2012-02-23 Thread Peter DeVries
Hi Chris, http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#5 *"On completions this section will define the semantics of the entirety of OBO via mappings to OWL2. The mappings could also be used to specify a translation procedure and/or an interface to OWL tools (such as OWL reasoners

Re: How do OBO ontologies work on the LOD?

2012-02-23 Thread Chris Mungall
OBO-Format is a subset of OWL2-DL http://oboformat.org Cheers Chris On Feb 22, 2012, at 9:50 AM, Peter DeVries wrote: > Hi Alan, > > > We use OWL and the Virtuoso endpoint you are using doesn't understand it. > > Isn't it more accurate to say that OBO is not the same as the OWL standards? >

Re: How do OBO ontologies work on the LOD?

2012-02-22 Thread Kingsley Idehen
On 2/22/12 9:15 AM, Alan Ruttenberg wrote: On Wed, Feb 22, 2012 at 2:55 AM, Peter DeVries > wrote: Hi Alan, Here is an example from the Hymenoptera Anatomy Ontology http://obofoundry.org/cgi-bin/detail.cgi?id=hymenoptera_anatomy Example via my

Re: How do OBO ontologies work on the LOD?

2012-02-22 Thread Peter DeVries
Hi Alan, > *We use OWL and the Virtuoso endpoint you are using doesn't understand it. * Isn't it more accurate to say that OBO is not the same as the OWL standards? i.e. *OBO does not equal OWL.* - Pete On Wed, Feb 22, 2012 at 9:15 AM, Alan Ruttenberg wrote: > > > On Wed, Feb 22, 2012 at 2:55

Re: How do OBO ontologies work on the LOD?

2012-02-22 Thread Alan Ruttenberg
On Wed, Feb 22, 2012 at 2:55 AM, Peter DeVries wrote: > Hi Alan, > > Here is an example from the Hymenoptera Anatomy Ontology > > http://obofoundry.org/cgi-bin/detail.cgi?id=hymenoptera_anatomy > > Example via my endpoint > > http://lsd.taxonconcept.org/describe/?url=http://purl.obolibrary.org/obo

Re: How do OBO ontologies work on the LOD?

2012-02-22 Thread Bernard Vatant
Hi all I've been lurking to this conversation for a while, and since Kerstin has put my name on the table, I thought I could just drop in. Seems to me that what Peter tries to achieve regarding linking to OBO ontologies is a real challenge. The logic (please read : "logic" in a loose sense here,

Re: How do OBO ontologies work on the LOD?

2012-02-21 Thread Alan Ruttenberg
On Tue, Feb 21, 2012 at 3:51 PM, Peter DeVries wrote: > Hi Juan, > > Thanks for this. I read the paper. They have an "OWL" version of this OBO > vocabulary but it seems to not be a fully mapped OWL version as described > in your paper. > Which one? > > In this particular use case I was thinking

Re: How do OBO ontologies work on the LOD?

2012-02-21 Thread Alan Ruttenberg
On Mon, Feb 20, 2012 at 8:46 PM, Peter DeVries wrote: > How do OBO type ontologies work in the Linked Open Data cloud. > > One that I recently loaded has a large number of blank nodes. > What did you load, specifically? > It the idea that these will be mapped to LOD URI's? > All OBO terms have

Re: How do OBO ontologies work on the LOD?

2012-02-21 Thread Kerstin Forsberg
Hi Alan and Melaine, I think you could provide some clarity to the discussion below. I spontaneously think about MIREOT - Minimum information to reference an external ontology term http://obi-ontology.org/page/MIREOT And, I also wonder if Bernard Vatant's proposal for 5-stars of link vocabolar

Re: How do OBO ontologies work on the LOD?

2012-02-21 Thread Peter DeVries
Hi Juan, Thanks for this. I read the paper. They have an "OWL" version of this OBO vocabulary but it seems to not be a fully mapped OWL version as described in your paper. In this particular use case I was thinking of applying the terms and properties described by the ontology to my species conce

Re: How do OBO ontologies work on the LOD?

2012-02-21 Thread Juan Sequeda
Peter You may want to take a look at this: http://www.ncbi.nlm.nih.gov/pubmed/21388572 The implementation of the OBO to OWL mapping work is part of official Gene Ontology project. Juan Sequeda +1-575-SEQ-UEDA www.juansequeda.com On Mon, Feb 20, 2012 at 7:46 PM, Peter DeVries wrote: > How do O

How do OBO ontologies work on the LOD?

2012-02-20 Thread Peter DeVries
How do OBO type ontologies work in the Linked Open Data cloud. One that I recently loaded has a large number of blank nodes. It the idea that these will be mapped to LOD URI's? Thanks, - Pete -- Pete DeVries