- From: Peter DeVries <pete.devries@gmail.com>
- Date: Thu, 23 Feb 2012 21:14:04 -0500
- To: Alan Ruttenberg <alanruttenberg@gmail.com>
- Cc: public-lod@w3.org
- Message-ID: <CAE0MQeFM1sgYe2AQ+C0WbYAhMqzxzZRJZrXaUpmPHdNGsBVAsg@mail.gmail.com>
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.
The basics are pretty simple. If you use a URI it should behave in a
predictable way. (Vapour Validator)
OBO does not do this in the expected LOD way. This is fine as long as
people don't give others the impression that it does.
I suspect there is a way for OBO to do this without some special "OBO" rule
like their would have been with LSID's
By this I mean each service has to support special logic that recognizes an
OBO URI and handles it differently from all other URI's.
In a sense the http://purl.obolibrary.org/ service creates a URL mapping
not unlike what I proposed earlier.
The problem is that even those mapped URI's do not work in the expected LOD
way.
This is the distinction that I am calling attention to.
At this point in time it appears to be both a real difference and a
significant difference.
Is this the only theoretical way to handle URI's?
No, but if you intent is to create URI's for the LOD then they should
behave in the expected LOD way.
OBO seems to have all sorts of rules on how OBO ontologies should work, why
can't the OBO people respect the LOD best practices when they are in LOD
space?
Or at least admit that there are differences in the way URI's are handled?
Respectfully,
- Pete
On Thu, Feb 23, 2012 at 8:08 PM, Alan Ruttenberg
<alanruttenberg@gmail.com>wrote:
>
>
> On Thu, Feb 23, 2012 at 4:53 PM, Peter DeVries <pete.devries@gmail.com>wrote:
>
>> Hi Alan,
>>
>> *> What does LOD best practices have to say about biology? *
>>
>> 1) I am a biologist. Most of my work has involved developing computer
>> technologies to help solve biological questions.
>>
>> Yet I have seen this argument used before to support the idea that
>> biology is so different than all other areas of knowledge that it needs
>> LSIDS rather than LOD URI's.
>>
>
> I am a technologist too. If you google you will find that I thought that
> was a bad idea and advocated long and hard that it be tossed.
>
>
>>
>> I am concerned that people who are thinking of creating ontologies for
>>>> the LOD will think that they should do this via OBO.
>>>>
>>>
>>>
>>> We don't think good quality information should be authored with a
>>> specific technology in mind, but should be disseminated in as many ways as
>>> possible.
>>>
>>
>> I agree which is why I originally suggested creating some sort of HAO to
>> LOD mapping ontology. At the time you disagreed with me (see thread)
>>
>
> Because a principle of the semantic web is not to create duplicate URIs
> for the same thing.
>
>
>>
>> This idea was based on the paper Juan had recommended. It seems that
>> there have been some changes to OBO since that was written.
>>
>
> OBO is a collaboration of a number of people. That paper represents rather
> older work and doesn't represent the current thinking. We've also got more
> organized in the years since and our our efforts towards being on the web
> are no longer a hobby but adopted policy. The vetted and accepted document
> on part of web practice is http://obofoundry.org/id-policy.shtml. The OBO
> to OWL mapping is under development but will also go through a ratification
> process at some point.
>
>
>> We are very very early in LOD and semantic web. It is presumptuous, IMO,
>> to call any practice in this area a "best practice".
>>
>>>
>> This is the public lod list and they do have best practices
>> documentation, starting with TBL's 4 things.
>>
>
> That's fine. They can call it what they want. It's a big wide web. But I
> don't, and I expect you don't, believe everything you read.
>
>
>> In those cases where there are large data sets marked up via OBO, then
>>>> some of these other solutions are best.
>>>>
>>>
>>> Which other solutions?
>>>
>>
>> By this I mean if all the related entities are OBO than stay in the OBO
>> world.
>>
>
> What OBO world? Moreover some of the OBO ontologies (they are relatively
> independent efforts, after all) have extensive cross references.
> Unfortunately those don't uniformly use URIs to make those references and
> one of the things I have been pushing (probably for a couple of years now)
> is using URIs for all of them. That will eventually happen but since it
> requires work by other people it happens on a pace that is slower than I
> would desired.
>
>
>>
>>>
>>>> If the statements in HAO are incorrect, then they should be corrected.
>> That is one of the principles. On http://obofoundry.org you will find
>> links to all of the ontologies in the set, and there is contact information
>> via which you can send comments about incorrect assertions. I am certain
>> they would be welcomed. If you find otherwise, do let me know.
>>
>>>
>>>
>>>> Multiply that by millions of occurrence records with identification
>>>> annotated with HAOL properties (some properties might not be visible on
>>>> some specimens)
>>>>
>>>> I have my doubts that OBO inferencing will be of much use, compared to
>>>> the findability, queryability and mashability of the LOD approach.
>>>>
>>>
>>> You can have your doubts. Inference may or may not be necessary for
>>> various tasks. I don't see any principled reason by OBO ontology derived
>>> RDF should differ on matters of findability, queryability and mashability
>>> of other work done in LOD.
>>>
>>
>> Yes if they followed LOD best practices.
>>
>
> We're going in circles. I've said it is policy to be on the web and to try
> to play nice with LOD and other clients. Let's work on specifics. The only
> restriction you'll find is that we won't make a changes that compromises
> the other uses.
>
>
>>
>>>
>>>> Especially in this ontology where most of these axioms seem to be about
>>>> the relation of one anatomical part to another.
>>>>
>>>
>>> That's fine. If the facts that HAO aren't useful to you, don't use them.
>>>
>>>
>>>> I can see the utility in asserting that species X has the following
>>>> anatomical characters URI_1, URI_2, URI_3, URI_4
>>>>
>>>> Heavy inferencing is not needed to make that useful, while proper
>>>> dereferencing of the URI's is important.
>>>>
>>>
>>> Both have their place and there are many different uses. So we try to
>>> provide the ability to do both. If you advocate one over the other then I
>>> expect you simply are not aware of these other uses.
>>>
>>
>> This issue is of a ontology designed for one use case but marketed as a
>> solution to another. I am aware of other uses which is why I was somewhat
>> puzzled that there seemed to be no examples of SPARQL queries that would
>> demonstrate how the authors intended for these to be used. They may exist
>> but I have not found them.
>>
>
> We don't think that ontologies should be designed for one use case. We
> think that's terribly inefficient and simply bad design. We try to design
> ontologies that accurately represent the facts and observations and then
> try to make it accessible for people who want to use it for any purpose.
>
>
>> It was while I was exploring creating such examples that I realized that
>> the ontology does not follow LOD best practices. It was not my intent to
>> call out this one ontology but you asked for specific examples. I suspect
>> the mosquito anatomy ontology has similar issues.
>>
>
> I am happy (ecstatic, in fact) when you look at what the content says and
> report back mistakes, confusions, and specific requests on how it can be
> made useful. We'll do our best or try to help. Please do have a look at the
> mosquito anatomy ontology and send the editors your observations (cc me, if
> you don't mind). And please collect your observations on HAO and send them
> as well. You spent some time doing that work and we don't want to see it
> wasted.
>
>
>> Do people really think that when the Beetle people start on their
>>>> vocabulary they should do it in OBO?
>>>>
>>>
>>> Yes. OBO is the largest community of disparate developers of biomedical
>>> ontologies. There is an emphasis on good quality work and a large biologist
>>> community that can and does weigh in on issue that are important for
>>> understanding and correctly representing the data. We (Well, I) don't claim
>>> to have all the answers, but there are a lot of good people, and we are
>>> sharing what we learn as we go on
>>>
>>
>> Again that is fine if their intent is to stay within the OBO world.
>>
>
> I reject this characterization. I've tried to explain what we do, but this
> kind of statement seems unhelpful, unrepresentative of the utility of
> what's been done, and seems to indicate an incomplete understanding of how
> the semantic web is supposed to work.
>
>
>> What I have realized is that there are edges between the OBO world and
>> the LOD world.
>>
>
> Edges are *everywhere*. Do you work with researchers in different
> disciplines? The problems you are identify here are very simply addressed
> because the architecture that OBO and LOD are embedded in was designed to
> make it easier to smooth over edges. They are a piece of cake when compared
> to, e.g. trying to integrate a variety of different kinds of knowledge
> collected by and from a bunch of fishery managers, ecologists,
> climatologists, and fish biologists and make some novel and productive use
> of the combination.
>
> Let's take a small point that will certainly impact integration in your
> work. HAO is an anatomy ontology. You were speaking in terms of characters.
> How are we to bridge these two perspectives? Should we talk (rdf)
> differently about the same entities, each side doing, effectively,
> redundant work, should we battle it out about whether to call the
> relationship hasCharacter or hasPart? Should we make some effort to get the
> interested parties together to understand each other and build their
> respective resources so that they work for both of them?
>
> Distinctions that are not apparent to many people who intend to
>> participating in the LOD world.
>>
>>>
>>> I have tried to point out where I believe you are wrong, but in the end
>>> it is your choice of whether you are interested in working with anything or
>>> anyone you want. It would be a shame, however, to make such a choice based
>>> on flawed information, and from what I see you don't have a good
>>> understanding of our effort yet.
>>>
>>>
>> I think you have turned the situation around. You are on the public_lod
>> list, perhaps you can better explain what is wrong with the LOD best
>> practices and why OBO people believe they are unnecessary, or seem
>> unfamiliar with them?
>>
>
> Many of the OBO people are biologists. Getting them to work with
> technology is a difficult job - they mostly aren't interested in it unless
> it directly helps them solve a problem they are trying to solve right now.
> There is a division of labor. One of the tasks I work on is bridging the
> work they do with that of those who work on the semantic web. I and a few
> other technology-abled (Chris is one of them) work very hard on various
> sides of the technology/biologist boundary - training biologists (and being
> trained by them) on the one hand, translating to web standards on the
> other, provisioning Sparql endpoints, encouraging people like Allen Xiang
> who develops ontobee to develop software that provides useful information
> in the browser for everyone, and in particular you LOD types ;-)
>
> There's a ton that's good about LOD. Some of the content shared is
> amazingly valuable, and very good quality. It's been a great playground (in
> a good sense) for getting people thinking about and practicing semantic web
> technologies. For some types of information LOD seems an optimal solution.
>
> I list here some issues with LOD that I have, since you have asked. I've
> discussed these on this and other W3C mailing lists in the past. They tend
> to be technical issues about some practices, or about some individual's
> idea of what a practice should be, and always based on the specific
> resource I've looked at more closely. There's really nothing I can say as
> LOD as a whole. I'm not sure there's such a thing as LOD as a whole,
> frankly.
> If someone wants to discuss these further, can you please move it to
> another thread, though?
>
> The biggest defect I've seen in many LOD sources I've had a closer look
> at, is that the web stack isn't leveraged to help in quality assurance, and
> so there is a lot of junk (well, as much junk as there was in previous
> generations of informatics systems, which was a lot. Junk = incorrect,
> inconsistent, or uninterpretable assertions). There's also a lot of cases
> of true bad practices - reminting of URIs for the same resource,
> uncontrolled and incorrect use of owl:sameAs, insufficient documentation of
> what URIs denote, sources that are advertised on the LOD cloud but do not
> respond, or are not open. Some in the community also generate an excess of
> hype, which worries me because I've been through a few cycles of hype and
> bust, and the bust tends to have unfortunately collateral damage.
>
>
>> If there is no intention of using the HAO ontology in the LOD world then
>> these concerns are moot.
>>
>
> OBO ontologies are (generally) not designed to or to not be used in any
> specific application. So I can't evaluate whether the concerns are moot :)
> But some of us think semweb and LOD are useful so we work to make the
> bridge.
>
>
>> My concern has always been that people who don't completely understand
>> the distinction between OBO and LOD OWL
>>
>
> Well, I'm sorry to say that so far I'm still putting you in that class.
>
>
>> are being led to believe that they should base their new LOD projects on
>> the OBO way of doing things rather than following LOD best practices. In
>> other words, they assume that if they create their ontology in OBO it will
>> automatically follow LOD best practices. I believe this was the assumption
>> made by the authors of the HAO ontology.
>>
>
> The people whose projects I work to support usually have a few more words
> of medicine and biology in their descriptions of what they will do. I'm
> pretty sure that the HAO authors (whose authors I talk to) weren't assuming
> anything about LOD. But ask them.
>
>
>> For instance, if the EoL.org were to get into creating ontologies with
>> the intent of participating in the the LOD cloud should those ontologies be
>> based on LOD best practices or OBO best practices?
>>
>
> I've told you already that I think working with others who work on OBO is
> (so to speak) the bee's knees. I don't see LOD and OBO as alternatives.
> They focus on somewhat different things, with LOD being more technology
> focused and OBO more science and ontology focused. So I would tell them to
> work with OBO, that their work will also be available for LOD uses, that
> they can avoid a fair amount of work by using other OBO ontologies and the
> various tools that we've developed. I'd tell them that there's a good
> community of biologists who read the mailing lists and will care what they
> do and offer help and suggestions. I'd tell them that we're working to be
> able to represent lots of different information of biological reference in
> an organized way (e.g. to avoid redundantly building expensive resources)
> and that what we all learn from working together will have impact that
> extends beyond their immediate work.
>
> Best,
> Alan
>
>
>
>> Respectfully,
>>
>> - Pete
>>
>>
>>
>>
>>
>>> Best,
>>> Alan
>>>
>>>
>>>>
>>>> Respectfully,
>>>>
>>>> - Pete
>>>>
>>>> P.S. Kudo's to Sig.ma http://sig.ma/ which which handled a HAOL URI I
>>>> sent to it. But it did stop inferencing after ~1000 with a long way to go.
>>>>
>>>> *All that that is probably needed is for Sig.ma to recognizes
>>>> that it is URI for an anatomical character in the Hymenoptera Ontology
>>>> which has
>>>> a human readable description page at a related url. Also at
>>>> the Hymenoptera ontology has as its subject the order Hymenoptera (an
>>>> Insect Order)
>>>>
>>>>
>>>> On Wed, Feb 22, 2012 at 3:32 PM, Kingsley Idehen <
>>>> kidehen@openlinksw.com> wrote:
>>>>
>>>>> On 2/22/12 3:14 PM, Peter DeVries wrote:
>>>>>
>>>>> Hi Kingsley,
>>>>>
>>>>> I don't know if it is that simple, it might fix the blank nodes on my
>>>>> endpoint.
>>>>>
>>>>> However, the OWL version of the ontology has this
>>>>>
>>>>> http://purl.org/obo/owl/HAO#HAO_0000526 URI
>>>>>
>>>>> Which shows up as in the KB
>>>>> http://purl.obolibrary.org/obo/HAO_0000526 (KB View median ocellus
>>>>> http://bit.ly/wOuYkf )
>>>>>
>>>>> Which resolves on the web to this
>>>>> http://api.hymao.org/public/ontology_class/show_expanded/1779
>>>>>
>>>>> So how will this work in general on the LOD where there seems to be
>>>>> a different set of best practices?
>>>>>
>>>>> What is the best way to add this as a schema to my endpoint?
>>>>>
>>>>> - Pete
>>>>>
>>>>>
>>>>> Pete,
>>>>>
>>>>> You can execute the following via your conductor UI or iSQL:
>>>>>
>>>>> sparql
>>>>> define get:soft "add"
>>>>> INSERT INTO <http://purl.obolibrary.org/obo/hao.owl><http://purl.obolibrary.org/obo/hao.owl>
>>>>> {?s rdfs:isDefinedBy <http://purl.obolibrary.org/obo/hao.owl><http://purl.obolibrary.org/obo/hao.owl>.
>>>>> <http://purl.obolibrary.org/obo/hao.owl><http://purl.obolibrary.org/obo/hao.owl>
>>>>> <http://open.vocab.org/terms/defines><http://open.vocab.org/terms/defines>?s.
>>>>> <http://purl.obolibrary.org/obo/hao.owl><http://purl.obolibrary.org/obo/hao.owl>a owl:Ontology .
>>>>> ?s <http://www.w3.org/2007/05/powder-s#describedby><http://www.w3.org/2007/05/powder-s#describedby>
>>>>> <http://purl.obolibrary.org/obo/hao.owl><http://purl.obolibrary.org/obo/hao.owl>
>>>>> }
>>>>> FROM <http://purl.obolibrary.org/obo/hao.owl><http://purl.obolibrary.org/obo/hao.owl>
>>>>> WHERE { optional {?s rdfs:subClassOf ?o}. optional {?s
>>>>> rdfs:subPropertyOf ?o}. optional {?s owl:equivalentClass ?o}. optional {?s
>>>>> owl:equivalentProperty ?o}. optional {?s a ?o}}
>>>>> ;
>>>>>
>>>>> sparql
>>>>> select distinct * from <http://purl.obolibrary.org/obo/hao.owl><http://purl.obolibrary.org/obo/hao.owl>
>>>>> where {?s ?p ?o} ;
>>>>>
>>>>> rdfs_rule_set ('hao-rule', 'http://purl.obolibrary.org/obo/hao.owl') .
>>>>>
>>>>>
>>>>> Once that's done, you have a local version of the ontology that
>>>>> associated with an inference rule. After that, simply refer to the
>>>>> inference rule in your SPARQL queries via its pragma or use the &inf
>>>>> parameter re. faceted browsing URL.
>>>>>
>>>>>
>>>>> Hope this helps? If not, we can move it to the Virtuoso forum and iron
>>>>> things out etc..
>>>>>
>>>>> Kingsley
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Feb 22, 2012 at 1:12 PM, Kingsley Idehen <
>>>>> kidehen@openlinksw.com> wrote:
>>>>>
>>>>>> On 2/22/12 9:15 AM, Alan Ruttenberg 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.
>>>>>>
>>>>>>
>>>>>> Yes, I am an OWL believer!
>>>>>>
>>>>>> Pete: use the ontology in question as the basis for a Virtuoso
>>>>>> Inference rule, then invoke the describe URL with the parameter for
>>>>>> inference context application.
>>>>>>
>>>>>> Example:
>>>>>>
>>>>>> 1.
>>>>>> http://linkeddata.uriburner.com/describe/?url=http%3A%2F%2Fpurl.org%2FNET%2Fgooglevocab%23Product-- no inference context
>>>>>> 2.
>>>>>> http://linkeddata.uriburner.com/describe/?uri=http%3A%2F%2Fpurl.org%2FNET%2Fgooglevocab%23Product&inf=oplweb-- inference context applied
>>>>>> 3.
>>>>>> http://virtuoso.openlinksw.com/presentations/SPARQL_Tutorials/SPARQL_Tutorials_Part_5/SPARQL_Tutorials_Part_5.html#(53)
>>>>>>
>>>>>> 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?
>>>>>>
>>>>>>
>>>>>> Will do.
>>>>>>
>>>>>>
>>>>>>
>>>>>> 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.
>>>>>>
>>>>>> Yep!
>>>>>>
>>>>>> SeeAlso:
>>>>>>
>>>>>> 1. https://plus.google.com/s/inference%20owl%20linked%20data%20idehen-- fuzzy search on G+ posts about virtues of OWL and Inference re. data
>>>>>> quality improvements (note: LOD cloud cache is still undergoing maintenance
>>>>>> re. LOD2 so some live demo links might not work).
>>>>>>
>>>>>>
>>>>>>
>>>>>>> - 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.netas 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
>>>>>>>
>>>>>>> --------------------------------------------------------------------------------------
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Kingsley Idehen
>>>>>> Founder & CEO
>>>>>> OpenLink Software
>>>>>> Company Web: http://www.openlinksw.com
>>>>>> Personal Weblog: http://www.openlinksw.com/blog/~kidehen
>>>>>> Twitter/Identi.ca handle: @kidehen
>>>>>> Google+ Profile: https://plus.google.com/112399767740508618350/about
>>>>>> LinkedIn Profile: http://www.linkedin.com/in/kidehen
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> ------------------------------------------------------------------------------------
>>>>> 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
>>>>>
>>>>> --------------------------------------------------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> Regards,
>>>>>
>>>>> Kingsley Idehen
>>>>> Founder & CEO
>>>>> OpenLink Software
>>>>> Company Web: http://www.openlinksw.com
>>>>> Personal Weblog: http://www.openlinksw.com/blog/~kidehen
>>>>> Twitter/Identi.ca handle: @kidehen
>>>>> Google+ Profile: https://plus.google.com/112399767740508618350/about
>>>>> LinkedIn Profile: http://www.linkedin.com/in/kidehen
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> ------------------------------------------------------------------------------------
>>>> 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 02:14:35 UTC