- From: Alan Ruttenberg <alanruttenberg@gmail.com>
- Date: Thu, 23 Feb 2012 20:38:41 -0500
- To: Peter DeVries <pete.devries@gmail.com>
- Cc: Chris Mungall <cjmungall@lbl.gov>, Juan Sequeda <juanfederico@gmail.com>, public-lod@w3.org, Kingsley Idehen <kidehen@openlinksw.com>, andy_deans@ncsu.edu, Matt Yoder <diapriid@gmail.com>, Nathan Wilson <nwilson@eol.org>, David Patterson <dpatterson@mbl.edu>, Anne Thessen <athessen@mbl.edu>
- Message-ID: <CAFKQJ8m0+QQAUaCt0jWhF-hG2OChbZODtUc0NyGVm9WURwB7Bg@mail.gmail.com>
All right, down to business. On Thu, Feb 23, 2012 at 1:32 PM, Peter DeVries <pete.devries@gmail.com>wrote: > 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 > > ( Additional Information Here http://linkeddata.org/guides-and-tutorials > ) > > Specifically the rule *#3 When someone looks up a URI, provide useful > information, using the standards (RDF*, SPARQL)* > > You can test this by running curl commands like > > curl -H "Accept: application/rdf+xml" > http://purl.obolibrary.org/obo/HAO_0000000 > I get <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <HTML> <HEAD> <TITLE>302 Found</TITLE> </HEAD> <BODY> <H1>Found</H1> The resource requested is available <A HREF=" http://www.berkeleybop.org/ontologies/HAO_0000000">here</A>.<P> </BODY> </HTML> Curl is not following the redirects. With wget it does, but there is still a problem: wget --header "Accept: application/rdf+xml" http://purl.obolibrary.org/obo/HAO_000000 --2012-02-23 20:26:02-- http://purl.obolibrary.org/obo/HAO_000000 Resolving purl.obolibrary.org (purl.obolibrary.org)... 132.174.1.35 Connecting to purl.obolibrary.org (purl.obolibrary.org)|132.174.1.35|:80... connected. HTTP request sent, awaiting response... 302 Moved Temporarily Location: http://www.berkeleybop.org/ontologies/HAO_000000 [following] --2012-02-23 20:26:02-- http://www.berkeleybop.org/ontologies/HAO_000000 Resolving www.berkeleybop.org (www.berkeleybop.org)... 131.243.192.99 Connecting to www.berkeleybop.org (www.berkeleybop.org)|131.243.192.99|:80... connected. HTTP request sent, awaiting response... 303 See Other Location: http://purl.obolibrary.org/obo/HAO/about/HAO_000000 [following] --2012-02-23 20:26:03-- http://purl.obolibrary.org/obo/HAO/about/HAO_000000 Connecting to purl.obolibrary.org (purl.obolibrary.org)|132.174.1.35|:80... connected. HTTP request sent, awaiting response... 302 Moved Temporarily Location: http://api.hymao.org/api/ontology/ontology_class/HAO_000000[following] --2012-02-23 20:26:03-- http://api.hymao.org/api/ontology/ontology_class/HAO_000000 Resolving api.hymao.org (api.hymao.org)... 128.194.196.117 Connecting to api.hymao.org (api.hymao.org)|128.194.196.117|:80... connected. HTTP request sent, awaiting response... 404 Not Found 2012-02-23 20:26:04 ERROR 404: Not Found. The multiple redirects are fine - an artifact of the fact that purl's redirect rules are not expressive enough. But in the end we don't get RDF, which we should, so this is indeed a problem that I'll take up with the HAO developers. They chose to handle the PURLs themselves rather than using ontobee, and I had the understanding that they would do the RDF bit too but something is amiss. 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_0000000 > This is a legacy URI. The OBO to OWL translation is undergoing a disruptive change so that we can deliver a page per term. I'm not sure where you got this URI from. HAO is distributed at http://purl.obolibrary.org/obo/hao.owland I see there only the URI below. > Mapped URI http://purl.obolibrary.org/obo/HAO_0000000 > Mapped by who? > HTML Page http://api.hymao.org/public/ontology_class/show_expanded/4048 > Yes. Now if they followed the protocol that we suggested that page would have page source that is RDF/XML and show html in the browser. I'll ask them about this. Understand that there isn't a boss of OBO, and that the developers had and exercised the choice to have the PURLs redirect to their site. However I believe they want to serve RDF so I'll find out what's up. > > Check in the Vapour Validator http://validator.linkeddata.org/vapour > > For comparison > > URI for the Species Apis mellifera > http://lod.taxonconcept.org/ses/z9oqP#Species > > Human Page http://lod.taxonconcept.org/ses/z9oqP.html > > Check the URI using the Vapour Validator > > It is my opinion that this ontology could have been (and could still be > modified to) implemented in a way that followed LOD best practices. > Yes, and it will be modified to provide RDF as I have said. > > My concern is that other groups like the beetle people (Coleopterologists) > etc. would see the HAO ontology and assume that they should also use OBO. > They should ;-) > (The assumption being that most of the use of these vocabularies will be > in relationship to LOD URI's) > I still don't know what a LOD URI is. A URI is a URI. > In other words, if the HAO ontology followed LOD best practices then it > would be a good project to model similar efforts on - but it does not. > You are reading too much into the situation. Either there's a misconfiguration or they haven't implemented yet. Simple as that. > Does this help clarify my concern? > Well, it was a long way round, but I hadn't realized they weren't serving RDF. Note for future - don't get wrapped up (an get me wrapped up ;-) in a big deal about LOD versus OWL. A request to that URI isn't behaving as expected. It can be fixed. It will be fixed. Expect something similar to the RDF at http://www.ontobee.org/browser/rdf.php?o=HAO&iri=http://purl.obolibrary.org/obo/HAO_0000000 I'll follow up privately with the HAO developers cc you. Later, Alan > > Respectfully, > > - Pete > > > On Thu, Feb 23, 2012 at 10:09 AM, Chris Mungall <cjmungall@lbl.gov> wrote: > >> >> 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 >> translation procedure and/or an interface to OWL tools (such as OWL >> reasoners).* >> * >> * >> *The translation is defined using a translation function T which >> translates (a fragment of) OBO into OWL DL. The definition of T is often >> recursive, but it will eventually "ground out" in (a fragment of) OWL DL." >> * >> * >> * >> The fact that OBO can be mapped to a subset of OWL 2 LD is not the same >> as saying it is OWL 2. >> >> >> Yes - OBO Format has a formal semantics that is a subset of OWL2-DL >> >> In any case this is not really relevant, since it does not address my >> main concern. >> * >> * >> That OBO and the OBO ontologies converted to OWL (specifically the >> hymenoptera ontology) do not follow LOD best practices. >> >> >> I'm not aware of the issue - what should we do to improve this? >> >> If there is no intention of using this ontology for LOD applications then >> this is not a problem. >> >> Should I interpret your comment as supporting the idea that those >> interested in creating applications for the LOD should do so by creating >> new OBO ontologies when they could just as easily create new OWL ontologies >> that follow LOD best practices? >> >> >> They could do this, the question of whether they should do this is highly >> dependent on the ontology they're creating. But in general I think most >> people developing a new ontology should use an OWL syntax for the primary >> representation. >> >> If you look at how this project was setup, it seems to me that it would >> have been much more direct and LOD compliant to base their URI's and >> ontology on URI's >> related to URL's like this >> http://api.hymao.org/projects/32/public/ontology_class/show/1033 >> >> Than to a non LOD OBO URI? >> >> >> 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 >> >> Respectfully, >> >> - Pete >> >> On Wed, Feb 22, 2012 at 3:48 PM, Chris Mungall <cjmungall@lbl.gov> wrote: >> >>> >>> 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? i.e. *OBO does not equal OWL.* >>> >>> - Pete >>> >>> On Wed, Feb 22, 2012 at 9:15 AM, Alan Ruttenberg < >>> alanruttenberg@gmail.com> wrote: >>> >>>> >>>> >>>> On Wed, Feb 22, 2012 at 2:55 AM, Peter DeVries <pete.devries@gmail.com>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/HAO_0001000&sid=1151 >>>>> >>>> >>>> Ok, I see. The problem here is the one I alluded to. We use OWL and the >>>> Virtuoso endpoint you are using doesn't understand it. I am ccing Kingsley >>>> and officially "tsk"ing him. We've known each other long enough that I'd >>>> have hoped he would have got some OWL religion by now. By that I don't mean >>>> doing full reasoning arbitrary combinations of RDF from different sources - >>>> but at least correctly parsing OWL is something I would have hoped be >>>> implemented by now. >>>> >>>> What the HAO should look like in a simple linked data browser (where >>>> some of the 'data' is in the form of OWL class definitions) is something >>>> like this: >>>> >>>> >>>> http://www.ontobee.org/browser/rdf.php?o=HAO&iri=http://purl.obolibrary.org/obo/HAO_0001000 >>>> >>>> Virtuoso knows how to do CBD (in fact ontobee is virtuoso as triple >>>> store too), but the page generator on your endpoint isn't doing it on the >>>> page it generates. Instead it does straight links out and links in. The >>>> links in are from an annotation on the axiom. It would be better there to >>>> not display anything, or to display a note saying there is an annotation >>>> that it can't display, or to properly parse the annotation (which would >>>> require another CBD query starting at the annotation) and display it. >>>> Kingsley, the source for ontobee is available - why not pick it up or use >>>> it as a spec for how to properly display OWL? >>>> >>>> The assertional content is: >>>> >>>> *class: tentorio-antennal muscle * >>>> subClassOf: antennal muscle >>>> subClassOf: attached_to some scape >>>> subClassOf: attached_to some anterior tentorial arm >>>> >>>> The SPARQL queries used to collect the content on the page are >>>> available by a link at the bottom of the page. >>>> >>>> The RDF that is generated can be seen by view source. I can see >>>> desirable improvements, e.g. adding some isDefinedBy links, and including >>>> all the inferrred superclasses, but that's not directly to your question, >>>> and is the sort of thing I mean when I say we will be working further on >>>> the RDF for the terms. >>>> >>>> Doing a GET for application/rdf+xml to the purl will pull in >>>> approximately the same RDF. The HAO folks decided to make their own browser >>>> for their content instead of using ontobee, which is fine. What we've tried >>>> to promote within the OBO community is the use of semweb technology as one >>>> form of dissemination, use of stable URIs as identifiers, and the ability >>>> to provide both human readable pages and machine readable pages. I'll get >>>> to Bernard's email later, but I hope you and he will realize that promoting >>>> and starting to successfully achieve implementation of these values for the >>>> OBO ontologies will yield very good value for the semantic web. There is an >>>> incredible amount of very well curated biological knowledge that is >>>> constantly being generated by that community. >>>> >>>> I was thinking that the character states described in this ontology >>>>> could be attached to species like this. >>>>> >>>>> <http://lod.taxonconcept.org/ses/z9oqP#Species> <somePredicate> >>>>> <someHAOCharacterState> >>>>> >>>> >>>> Are there what you would call character states in the example you gave >>>> above? I understand it as a bit of anatomy knowledge - what part connects >>>> to what. I guess what I need to know is what, if any, assertions would you >>>> make given that you now see what was intended to be seen? Do you need a >>>> flattening predicate (my preference would be to use an annotation property) >>>> that more directly links the species concept to scape and anterior >>>> tentorial arm? What should it be? >>>> >>>> >>>> >>>>> And be properly interpreted on Sig.ma example http://bit.ly/zfbimy >>>>> >>>> >>>> I'll have to look at that later. But I would ask of it and of your >>>> endpoint: Is there some obligation to properly interpret what is stated >>>> according the web standard OWL? Surely the obligation for proper >>>> interpretation needs to be a mutual effort? >>>> >>>> From my point of view I want to make the OBO LOD be useful and I >>>> understand that there are different communities that would use it. I think >>>> we need to be true to the representation we choose - it provides a lot of >>>> benefits for query, consistency checking, etc. But we're also trying to be >>>> polite to others and are open to augmenting it so that it can be of utility >>>> to others. The key is for us to first understand how we should do that, for >>>> you to understand what is currently being said, and when we're done for >>>> your client applications to either represent what we've said too, or learn >>>> how to ignore it. >>>> >>>> -Alan >>>> >>>> ps. For some examples of how using OWL is yielding tangible benefits >>>> you could browse http://groups.google.com/group/fma-owl-2009 >>>> In that effort I'm slowly working through translating a human anatomy >>>> ontology, the FMA, into OWL, and in the process discovering (and having >>>> fixed) thousands of errors. >>>> >>>> >>>>> - Pete >>>>> >>>>> >>>>> On Wed, Feb 22, 2012 at 12:27 AM, Alan Ruttenberg < >>>>> alanruttenberg@gmail.com> wrote: >>>>> >>>>>> >>>>>> >>>>>> On Tue, Feb 21, 2012 at 3:51 PM, Peter DeVries < >>>>>> pete.devries@gmail.com> 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 of applying the terms and >>>>>>> properties described by the ontology to my species concepts. >>>>>>> >>>>>> >>>>>> This is a nice example and should be supported. An immediate >>>>>> suggestion is to send mail to obo-discuss@lists.sourceforge.net as >>>>>> that is where you will find both the developers of the OBO LOD support as >>>>>> well as the biologist community. >>>>>> >>>>>> >>>>>>> >>>>>>> For instance: >>>>>>> >>>>>>> species X has this metabolic pathway. (which would be useful for >>>>>>> finding species with potential drug interactions or other chemical >>>>>>> reactions) >>>>>>> >>>>>> >>>>>> We're in the process of revising BFO and the relations ontology. A >>>>>> draft version is at http://purl.obolibrary.org/obo/bfo.owl >>>>>> >>>>>> In terms of that, your statement might be represented as >>>>>> >>>>>> <species> subclassOf 'has site of' some <metabolic process> >>>>>> if you want to represent that all members of the species have the >>>>>> process >>>>>> >>>>>> or >>>>>> >>>>>> <anonymous instance of species> 'has site of' <anonymous instance of >>>>>> process> >>>>>> >>>>>> e.g. >>>>>> >>>>>> @prefix obo: <http://purl.obolibrary.org/obo/> >>>>>> @prefix hasSiteOf: <http://purl.obolibrary.org/obo/BFO_0000067> >>>>>> >>>>>> _:a rdf:type <species> >>>>>> _:b rdf:type <metabolic process> >>>>>> _:a hasSiteOf: _:b >>>>>> >>>>>> If you want to represent that the process happens in some individuals >>>>>> of this species. >>>>>> >>>>>> In the above I write <species> where you would write the uri of your >>>>>> species class (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9903) , >>>>>> and <metabolic process> where you would write the uri of your process class >>>>>> (e.g. http://purl.obolibrary.org/obo/GO_0030245). >>>>>> >>>>>> >>>>>> >>>>>>> I don't think this use case requires the full OBO relationships, >>>>>>> just a mapping ontology that connects terms and characters to those in the >>>>>>> OBO ontology. >>>>>>> >>>>>> >>>>>> Not sure what you mean by this. >>>>>> >>>>>> >>>>>>> >>>>>>> Doing it this way you might get a species "tagged" with something >>>>>>> that is not appropriate but that could be detected by some service that >>>>>>> analyzes the statements made >>>>>>> in the species concept markup >>>>>>> >>>>>> >>>>>> Example? >>>>>> >>>>>>> . >>>>>>> My guess is that some of the OBO ontologies (if fully entailed) will >>>>>>> not play well on the LOD cloud, but they would play a useful role when >>>>>>> mapped as I described. >>>>>>> >>>>>> >>>>>> Examples would be helpful. But note that it is our intention that we >>>>>> *do* play well on the LOD cloud. However also note, we work in OWL and much >>>>>> of what we say is about types/classes, and many(most?) linked data browsers >>>>>> don't understand or present OWL in a meaninful way. One of the reasons we >>>>>> have developed ontobee is that it is designed to do justice to linked >>>>>> ontology terms that are defined in terms of OWL. So class expressions are >>>>>> not left as messes of bnodes, but instead parsed and displayed as OWL. I'd >>>>>> like to see more linked data browsers do the same. >>>>>> >>>>>> >>>>>>> Does my interpretation seem appropriate to you or am I missing >>>>>>> something? >>>>>>> >>>>>> >>>>>> I hope you are missing something :) But please elaborate so we can >>>>>> see. >>>>>> >>>>>> >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> - Pete >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Feb 21, 2012 at 9:39 AM, Juan Sequeda < >>>>>>> juanfederico@gmail.com> wrote: >>>>>>> >>>>>>>> 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 < >>>>>>>> pete.devries@gmail.com> 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. >>>>>>>>> >>>>>>>>> It the idea that these will be mapped to LOD URI's? >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> - Pete >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------------------------ >>>>>>>>> Pete DeVries >>>>>>>>> Department of Entomology >>>>>>>>> University of Wisconsin - Madison >>>>>>>>> 445 Russell Laboratories >>>>>>>>> 1630 Linden Drive >>>>>>>>> Madison, WI 53706 >>>>>>>>> Email: pdevries@wisc.edu >>>>>>>>> TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge >>>>>>>>> Bases >>>>>>>>> A Semantic Web, Linked Open Data <http://linkeddata.org/> Project >>>>>>>>> >>>>>>>>> -------------------------------------------------------------------------------------- >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> ------------------------------------------------------------------------------------ >>>>>>> Pete DeVries >>>>>>> Department of Entomology >>>>>>> University of Wisconsin - Madison >>>>>>> 445 Russell Laboratories >>>>>>> 1630 Linden Drive >>>>>>> Madison, WI 53706 >>>>>>> Email: pdevries@wisc.edu >>>>>>> TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge >>>>>>> Bases >>>>>>> A Semantic Web, Linked Open Data <http://linkeddata.org/> Project >>>>>>> >>>>>>> -------------------------------------------------------------------------------------- >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> ------------------------------------------------------------------------------------ >>>>> Pete DeVries >>>>> Department of Entomology >>>>> University of Wisconsin - Madison >>>>> 445 Russell Laboratories >>>>> 1630 Linden Drive >>>>> Madison, WI 53706 >>>>> Email: pdevries@wisc.edu >>>>> TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge >>>>> Bases >>>>> A Semantic Web, Linked Open Data <http://linkeddata.org/> Project >>>>> >>>>> -------------------------------------------------------------------------------------- >>>>> >>>> >>>> >>> >>> >>> -- >>> >>> ------------------------------------------------------------------------------------ >>> Pete DeVries >>> Department of Entomology >>> University of Wisconsin - Madison >>> 445 Russell Laboratories >>> 1630 Linden Drive >>> Madison, WI 53706 >>> Email: pdevries@wisc.edu >>> TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge >>> Bases >>> A Semantic Web, Linked Open Data <http://linkeddata.org/> Project >>> >>> -------------------------------------------------------------------------------------- >>> >>> >>> >> >> >> -- >> >> ------------------------------------------------------------------------------------ >> Pete DeVries >> Department of Entomology >> University of Wisconsin - Madison >> 445 Russell Laboratories >> 1630 Linden Drive >> Madison, WI 53706 >> Email: pdevries@wisc.edu >> TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge >> Bases >> A Semantic Web, Linked Open Data <http://linkeddata.org/> Project >> >> -------------------------------------------------------------------------------------- >> >> >> > > > -- > > ------------------------------------------------------------------------------------ > Pete DeVries > Department of Entomology > University of Wisconsin - Madison > 445 Russell Laboratories > 1630 Linden Drive > Madison, WI 53706 > Email: pdevries@wisc.edu > TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge > Bases > A Semantic Web, Linked Open Data <http://linkeddata.org/> Project > > -------------------------------------------------------------------------------------- >
Received on Friday, 24 February 2012 01:39:43 UTC