Re: Advancing translational research with the Semantic Web

On May 16, 2007, at 3:53 PM, Pat Hayes wrote: Named graphs ARE supported by most triplestores, but they are mostly already reserved for other uses, like the representation of provenance based on the RDF files that the triples were loaded from. Reserved? In what sense? a single URi can ha

Re: Advancing translational research with the Semantic Web

On May 16, 2007, at 3:53 PM, Pat Hayes wrote: Named graphs ARE supported by most triplestores, but they are mostly already reserved for other uses, like the representation of provenance based on the RDF files that the triples were loaded from. Reserved? In what sense? a single URi can have

RE: Advancing translational research with the Semantic Web (Not clear about definition of )

> Let me introduce the relation as an example. >means that contains all of the > participants that make up process . > A concrete example for the use of this property would be > >. [VK] I am not sure if I agree with the semantics of "is_location_of_process" as above. If you stick to

Re: Advancing translational research with the Semantic Web

Matthias wrote: > > The specific difficulties with the location of objects and > > processes are to some degree inherent in the current OWL versions > > of BFO and the Relation Ontology. They make it a bit difficult to > > create statements that relate processes to certain locations and >

Re: Advancing translational research with the Semantic Web

On May 16, 2007, at 12:06 PM, Pat Hayes wrote: What you say ABOUT the statement is up to you, and requires an ontology of statement-making or belief or responsibility. For one suggested approach to all this (which avoids the rather clunky RDF reification mechanism) see http://www.hpl.hp.

Re: Advancing translational research with the Semantic Web

> >>Here Temperature_Feature is a "history" (sensu Hayes) or a >>time-slice. Do I have this correct? [...] >If you want features to be 4-D objects Just for the record, that IS the 'histories' view. That is, 'histories' was the name I used for 4-d objects. Could you please point us to

Re: Advancing translational research with the Semantic Web

On May 22, 2007, at 12:01 AM, Pat Hayes wrote: To encode the temporal structure in OWL takes a little care, but this particular case has been worked out already, and can be handled uniformly in all the cases where it arises. It needs to be handled specially in any case if OWL reasoning is

Re: Advancing translational research with the Semantic Web

On May 18, 2007, at 1:03 PM, [EMAIL PROTECTED] wrote: The specific difficulties with the location of objects and processes are to some degree inherent in the current OWL versions of BFO and the Relation Ontology. They make it a bit difficult to create statements that relate processes to c

Re: Advancing translational research with the Semantic Web

One place to start would be: google: cyc temporal subabstractions http://www.google.com/search?q=cyc+temporal+subabstractions&btnG=Search On May 29, 2007, at 4:59 PM, [EMAIL PROTECTED] wrote: Could you please point us to some literature about the 'histories' view? I remember that Alan Rector

Re: Advancing translational research with the Semantic Web

> >>Here Temperature_Feature is a "history" (sensu Hayes) or a > >>time-slice. Do I have this correct? [...] > >If you want features to be 4-D objects > > Just for the record, that IS the 'histories' view. That is, > 'histories' was the name I used for 4-d objects. Could you please point us t

Re: Advancing translational research with the Semantic Web

On 21 May 2007, at 19:50, Chris Mungall wrote: On May 20, 2007, at 11:49 PM, Alan Rector wrote: Chris On 18 May 2007, at 18:10, Chris Mungall wrote: I'm afraid I'm unclear how to state the OWL n-ary relation pattern(http://www.w3.org/TR/swbp-n-aryRelations) where I really need it.

Re: Advancing translational research with the Semantic Web

I think your approach has, to some degree, simulated the role of named graph. The URI of the newly introduced named class can be viewed as a URI of a named graph that includes a group of statements. The difference here is that the uri of your approach refers to an real entity (the protein) and

Re: Advancing translational research with the Semantic Web

The history of computing is the history of "design patterns" at one level that eventually get built into "higher level languages" at the next level of abstraction up. I think I have a less optimistic view of progress in computer science. For example, many of the paradigmatic GoF desig

Re: Advancing translational research with the Semantic Web

On 21 May 2007, at 19:50, Chris Mungall wrote: On May 20, 2007, at 11:49 PM, Alan Rector wrote: Chris On 18 May 2007, at 18:10, Chris Mungall wrote: I'm afraid I'm unclear how to state the OWL n-ary relation pattern (http://www.w3.org/TR/swbp-n-aryRelations) where I really need i

Re: Advancing translational research with the Semantic Web

On May 22, 2007, at 6:11 AM, Marijke Keet wrote: The history of computing is the history of "design patterns" at one level that eventually get built into "higher level languages" at the next level of abstraction up. I think I have a less optimistic view of progress in computer s

Re: Advancing translational research with the Semantic Web

> "MK" == Marijke Keet <[EMAIL PROTECTED]> writes: MK> I like more expressivity as well, but then, I'm not implementing MK> systems where I'd have to wait 'long' for query answers or see MK> my computer hang upon classifying 1 instance in an 50-concept MK> small ontology (with the la

Re: Advancing translational research with the Semantic Web

The history of computing is the history of "design patterns" at one level that eventually get built into "higher level languages" at the next level of abstraction up. I think I have a less optimistic view of progress in computer science. For example, many of the paradigmatic GoF design

Re: Advancing translational research with the Semantic Web

> "PH" == Pat Hayes <[EMAIL PROTECTED]> writes: CM> In all the examples given, the "lifted"[*] n-ary relation was CM> never truly a relation in the first place and always better CM> modeled as a class. It's kind of cheating. >> >> Well, it is kind of cheating, yes, although if it w

Re: Advancing translational research with the Semantic Web

On May 20, 2007, at 11:49 PM, Alan Rector wrote: Chris On 18 May 2007, at 18:10, Chris Mungall wrote: I'm afraid I'm unclear how to state the OWL n-ary relation pattern(http://www.w3.org/TR/swbp-n-aryRelations) where I really need it. In all the examples given, the "lifted"[*] n-ary re

Re: Advancing translational research with the Semantic Web

On May 21, 2007, at 11:24 AM, Pat Hayes wrote: > "CM" == Chris Mungall <[EMAIL PROTECTED]> writes: >> Out of curiosity, can you describe how different or similar this >> is to the result that you can achieve in the N-ary relation >> design pattern for OWL? >> >> Obviously, b

Re: Advancing translational research with the Semantic Web

On May 21, 2007, at 11:24 AM, Pat Hayes wrote: > "CM" == Chris Mungall <[EMAIL PROTECTED]> writes: >> Out of curiosity, can you describe how different or similar this >> is to the result that you can achieve in the N-ary relation >> design pattern for OWL? >> >> Obviously, b

Re: Advancing translational research with the Semantic Web

On May 20, 2007, at 11:49 PM, Alan Rector wrote: Chris On 18 May 2007, at 18:10, Chris Mungall wrote: I'm afraid I'm unclear how to state the OWL n-ary relation pattern (http://www.w3.org/TR/swbp-n-aryRelations) where I really need it. In all the examples given, the "lifted"[*] n-ary

Re: Advancing translational research with the Semantic Web

> "CM" == Chris Mungall <[EMAIL PROTECTED]> writes: >> Out of curiosity, can you describe how different or similar this >> is to the result that you can achieve in the N-ary relation >> design pattern for OWL? >> >> Obviously, building things into the DL is nice, but it's not

Re: Advancing translational research with the Semantic Web

Chris On 18 May 2007, at 18:10, Chris Mungall wrote: I'm afraid I'm unclear how to state the OWL n-ary relation pattern(http://www.w3.org/TR/swbp-n-aryRelations) where I really need it. In all the examples given, the "lifted"[*] n-ary relation was never truly a relation in the first plac

Re: Advancing translational research with the Semantic Web

> "CM" == Chris Mungall <[EMAIL PROTECTED]> writes: >> Out of curiosity, can you describe how different or similar this >> is to the result that you can achieve in the N-ary relation >> design pattern for OWL? >> >> Obviously, building things into the DL is nice, but it's not >

Re: Advancing translational research with the Semantic Web

Sorry for the delay in replying -- been busy! I can see your point that the design pattern gets more complex when you move to 3 or 4 n-ary relationships. It would be good to have a representation of for n-ary's which is also represented in the logic as opposed to layered on top. Phil >

Re: Advancing translational research with the Semantic Web

Bijan Parsia wrote: On May 16, 2007, at 11:15 AM, Phillip Lord wrote: "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> Just catching up on reading papers :-) EJ> EJ> "It is also useful to know who believes something and EJ> why.

Re: Advancing translational research with the Semantic Web

Chris On 18 May 2007, at 18:10, Chris Mungall wrote: I'm afraid I'm unclear how to state the OWL n-ary relation pattern (http://www.w3.org/TR/swbp-n-aryRelations) where I really need it. In all the examples given, the "lifted"[*] n-ary relation was never truly a relation in the first p

Re: Advancing translational research with the Semantic Web

Chris, Bijan, Pat, All Coming into this late, it seems to me that there are a series of use- cases / requirements / wishes that people are trying to accommodate made worse by real difficulties of the "use vs mention" variety. I think there is a need of a high level document setting out the

Re: Advancing translational research with the Semantic Web

On May 17, 2007, at 8:43 AM, Pat Hayes wrote: On 17 May 2007, at 05:13, Chris Mungall wrote: [snip] The only support I'd want would be some behind-the-scenes optimising away of the fact I have 4n triples when a single 3-ary predicate would do (but hey, again, as it's RDF anyway, I need at

Re: Advancing translational research with the Semantic Web

On May 17, 2007, at 8:43 AM, Pat Hayes wrote: On 17 May 2007, at 05:13, Chris Mungall wrote: [snip] I've never understood why RDF-reification is so loathed. So the syntax is ugly - but I think there may be other reasons RDF/XML hasn't won any beauty contests. They are fairly ugly at the

Re: Advancing translational research with the Semantic Web

On May 18, 2007, at 1:16 AM, Marijke Keet wrote: Staying with article comments but going off topic from this thread, there were two aspects in particular that read oddly and raises more questions than that it provides information. One about the BioRDF, the other the ontology working group

Re: Advancing translational research with the Semantic Web

On May 18, 2007, at 3:40 AM, Phillip Lord wrote: "MK" == Marijke Keet <[EMAIL PROTECTED]> writes: MK> Regarding “reification design patterns” and the reification & MK> OWL (not the thorny logic-based representation of beliefs et MK> al), permit me to mention that support for n-ary re

Re: Advancing translational research with the Semantic Web

> By a reasonable definition of process (following, e.g., the BFO > papers), if a process happens in a location, then each participant is > located in some part of that location. > > In fact, very few such axioms are currently encoded in the BFO and > OBO ontologies The specific diffi

Re: Advancing translational research with the Semantic Web

On May 18, 2007, at 3:06 AM, Eric Jain wrote: Alan Ruttenberg wrote: If you want to say that the protein is found in some tissue, that's what should be said. However, in your email you wrote that the protein is expressed in the tissue. Sorry about that, should run a consistency checker o

RE: Advancing translational research with the Semantic Web

@w3.org Subject: Re: Advancing translational research with the Semantic Web > How would you say e.g. "protein a is expressed in tissue b, according to > source c"? through something like . . . -- Matthias Samwald Yale Center for Medical Informatics, New Haven

Re: Advancing translational research with the Semantic Web

> "MK" == Marijke Keet <[EMAIL PROTECTED]> writes: MK> Regarding “reification design patterns” and the reification & MK> OWL (not the thorny logic-based representation of beliefs et MK> al), permit me to mention that support for n-ary relations MK> ---where n may also be >2--- in desc

Re: Advancing translational research with the Semantic Web

Dear All, Regarding “reification design patterns” and the reification & OWL (not the thorny logic-based representation of beliefs et al), permit me to mention that support for n-ary relations ---where n may also be >2--- in description logics is already possible with DLR [1] and implemented w

Re: Advancing translational research with the Semantic Web

Alan Ruttenberg wrote: If you want to say that the protein is found in some tissue, that's what should be said. However, in your email you wrote that the protein is expressed in the tissue. Sorry about that, should run a consistency checker on my outgoing mail :-) If it is know to be found

Re: Advancing translational research with the Semantic Web

Alan Ruttenberg wrote: Not if the classes are given logical expressions, as I did in my example - in that case a reasoner can infer that they are the equivalent, based on their logical definitions. Well, ideally :-) My main concern is that different people will come up with different "desig

Re: Advancing translational research with the Semantic Web

Alan Ruttenberg wrote: There is a subclass of gene expression processes, during each instance of which some instance of protein a is the participant which is "the thing produced", and which is located_in some instance of tissue b. Phew :-) I would then attach, as above, via an annotation p

Re: Advancing translational research with the Semantic Web

Hi Alan, Can you give a little more detail on exactly how the evidence is linked. I realize I can go to the OWL ontologies you and others created for the demo, but I wondered if you could give a quick review of the syntactical constructs you used to represent the evidence here. You say "

Re: Advancing translational research with the Semantic Web

Alan does an excellent job summing up how the issues discussed in this thread will ultimately need to be brought to bear in asserting the details of biological reality in such a way that algorithms will be able to assist us in reliably inferring new, MEANINGFUL relations. As he states, ther

Re: Advancing translational research with the Semantic Web

On May 17, 2007, at 6:34 PM, Eric Jain wrote: There does indeed seem to be an existing has_participant predicate, but is there also a "protein expression process" class? This would seem rather contrived, from a biologists (if not an ontologists) point of view (all we want to say, after all

Re: Advancing translational research with the Semantic Web

On May 17, 2007, at 1:13 PM, Eric Jain wrote: The "protein expression process" class that needs to be introduced here does seem a bit like bending over backwards (I know in other cases such as protein-protein interactions it fits better); also you need to introduce an additional predicate,

Re: Advancing translational research with the Semantic Web

The example isn't necessarily a disagreement. Both could be true. I think these really need to be class statements, in any case, to make any sense. In my representation this is (schematically) Class protein_a_expression_process_located_in_tissue_b subclassOf expression and produced some

Re: Advancing translational research with the Semantic Web

On May 17, 2007, at 11:49 AM, Eric Jain wrote: How would you say e.g. "protein a is expressed in tissue b, according to source c"? For the demo, the way I said such things was like this (OWL available on request) for cellular location: There is a subclass of protein p each instance of whi

Re: Advancing translational research with the Semantic Web

[EMAIL PROTECTED] wrote: The choice of this design pattern is not arbitrary, it is based on the OBO Relation Ontology [1], BFO and the OWL version of the Gene Ontoloy, which are becoming widely accepted. Other foundational ontologies (like DOLCE) have similar relations and entities. In other wor

Re: Advancing translational research with the Semantic Web

On 17 May 2007, at 05:13, Chris Mungall wrote: [snip] I've never understood why RDF-reification is so loathed. So the syntax is ugly - but I think there may be other reasons RDF/XML hasn't won any beauty contests. They are fairly ugly at the model level as well. And there are problems with

Re: Advancing translational research with the Semantic Web

> >. > >. > >. > > The "protein expression process" class that needs to be introduced here > does seem a bit like bending over backwards [...] > also you need to introduce > an > additional predicate, "has_participant". This would certainly work, > however > >from my point of vie

Re: Advancing translational research with the Semantic Web

> That will get you so far, but you have to be VERY > careful. Will other uses of these relations > retain these very refined meanings this > precisely? I guess that can be said about ANY conceivable approach. People that do not care can make mistakes, whatever approach we choose. > Suppo

Re: Advancing translational research with the Semantic Web

[EMAIL PROTECTED] wrote: How would you say e.g. "protein a is expressed in tissue b, according to source c"? through something like . . . The "protein expression process" class that needs to be introduced here does seem a bit like bending over backwards (I know in other cases such

Re: Advancing translational research with the Semantic Web

> How would you say e.g. "protein a is expressed in tissue b, according to source c"? through something like . . . OK, but suppose source d disagrees, and says that a is expressed in e. Now you have . . and its all about the same process. What now associates d with e,

Re: Advancing translational research with the Semantic Web

> >Statements about believe, evidence and provenance can be easily >attached to "". Hmm. They could, but that isn't really internally coherent. If this is supposed to be the name of a process, then its doesn't make sense to say that it has a provenance or that it is subject to belief. T

Re: Advancing translational research with the Semantic Web

> >Statements about believe, evidence and provenance can be easily > >attached to "". > > Hmm. They could, but that isn't really internally coherent. If this > is supposed to be the name of a process, then its doesn't make sense > to say that it has a provenance or that it is subject to belief

Re: Advancing translational research with the Semantic Web

> Just catching up on reading papers :-) "It is also useful to know who believes something and why. However, there is no standard way of expressing such information about a statement [...]" Reification? To return to the original questio

Re: Advancing translational research with the Semantic Web

> How would you say e.g. "protein a is expressed in tissue b, according to > source c"? through something like . . . -- Matthias Samwald Yale Center for Medical Informatics, New Haven / Section on Medical Expert and Knowledge-Based Systems, Vienna / http://neuroscientific.net . -

RE: Advancing translational research with the Semantic Web

> How would you say e.g. "protein a is expressed in tissue b, according > to source c"? Wouldn't this be something along the lines of: in Matthias' model-level-reification approach (given that all the prefixes in the

Re: Advancing translational research with the Semantic Web

[EMAIL PROTECTED] wrote: To return to the original question: In many of the biomedical ontologies we are currently using or developing most of the biological relations that matter ARE already reified. For example, most current ontologies would not contain the statement " ", rather they would co

Re: Advancing translational research with the Semantic Web

> Just catching up on reading papers :-) > > > > "It is also useful to know who believes something and why. However, there > is no standard way of expressing such information about a statement [...]" > > Reification? To return to the original

Re: Advancing translational research with the Semantic Web

On 17 May 2007, at 05:13, Chris Mungall wrote: [snip] I've never understood why RDF-reification is so loathed. So the syntax is ugly - but I think there may be other reasons RDF/XML hasn't won any beauty contests. They are fairly ugly at the model level as well. And there are problems wit

Re: Advancing translational research with the Semantic Web

Nice idea for syntax. Jonathan and I will be working on some sort of macro syntax for SPARQL, which would make this and a lot of other queries be a lot nicer to write. The Virtuoso folks are willing to implement a prototype. If it works out then perhaps it can be proposed for SPARQL 2. More

Re: Advancing translational research with the Semantic Web

Alan Ruttenberg wrote: > prefix dc: > prefix sc: > select ?s ?p ?o ?by > from > where > { ?s ?p ?o. >?statement rdf:type rdf:Statement. >?statement rdf:subject ?s. >?

Re: Advancing translational research with the Semantic Web

On May 17, 2007, at 4:58 AM, Eric Jain wrote: 2. tools don't support reification well (just try writing a SPARQL query that queries statements about statements). prefix dc: prefix sc: insert into graph

Re: Advancing translational research with the Semantic Web

Chris Mungall wrote: Provenance is kind of important for science, and it doesn't do it any favours to mix provenance at the document and statement levels +1 I wouldn't mind if the two levels were supported through the same mechanism, however this risks complicating and slowing down things.

Re: Advancing translational research with the Semantic Web

On May 16, 2007, at 12:16 PM, Pat Hayes wrote: The association is done by the reification using a URI which is intended to identify the triple. However, there is no 'standard' way to associate a URI with an RDF triple. This is exactly the problem that named graphs were proposed as a way t

Re: Advancing translational research with the Semantic Web

Pat Hayes wrote: Our paper suggests that the URI of the RDF/XML document be used as the name in this case. This works as long as you are consistent about it. ...and as long as the document is always opened from its official location (versa from a local copy), and you keep each item is a sepa

Re: Advancing translational research with the Semantic Web

> I really would suggest the named graphs would be a better underpinning. Unlike reification, they do have a full semantics and a clear deployment model, and they follow in a long tradition of naming document-like semantic entities. And unlike RDF reification, they are not widely loathed,

Re: Advancing translational research with the Semantic Web

g translational research with the Semantic Web I really would suggest the named graphs would be a better underpinning. Unlike reification, they do have a full semantics and a clear deployment model, and they follow in a long tradition of naming document-like semantic entities. And unlike

Re: Advancing translational research with the Semantic Web

CTED]>; "'Pat Hayes'" <[EMAIL PROTECTED]>; <[EMAIL PROTECTED]> Cc: ; <[EMAIL PROTECTED]> Sent: Wednesday, May 16, 2007 10:47 AM Subject: RE: Advancing translational research with the Semantic Web Interesting thread. From the user perspective we still ne

RE: Advancing translational research with the Semantic Web

PROTECTED] >Cc: public-semweb-lifesci@w3.org; [EMAIL PROTECTED] >Subject: Re: Advancing translational research with the Semantic Web > > > > >> I really would suggest the named graphs would be a better >> underpinning. Unlike reification, they do have a full semantic

Re: Advancing translational research with the Semantic Web

> I really would suggest the named graphs would be a better > underpinning. Unlike reification, they do have a full semantics and a > clear deployment model, and they follow in a long tradition of naming > document-like semantic entities. And unlike RDF reification, they are > not widely loa

Re: Advancing translational research with the Semantic Web

> "BP" == Bijan Parsia <[EMAIL PROTECTED]> writes: EJ> Reification? >> >> That's who, not why. BP> No, you can do both with reification. Well, you can do anything with anything:-) >> The Gene Ontologies evidence codes are and references are much >> closer. >> >> Also, I

Re: Advancing translational research with the Semantic Web

> "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> Just catching up on reading papers :-) EJ> EJ> "It is also useful to know who believes something and EJ> why. However, there is no standard way of expressing such EJ> informatio

RE: Advancing translational research with the Semantic Web

... or NamedGraphs as statement annotations. Eriic -Original Message- From: [EMAIL PROTECTED] on behalf of Eric Jain Sent: Wed 5/16/2007 5:17 AM To: public-semweb-lifesci Subject: Re: Advancing translational research with the Semantic Web Just catching up on reading papers :-) <h

Re: Advancing translational research with the Semantic Web

> "BP" == Bijan Parsia <[EMAIL PROTECTED]> writes: EJ> Reification? >> >> That's who, not why. BP> No, you can do both with reification. Well, you can do anything with anything:-) >> The Gene Ontologies evidence codes are and references are much >> closer. >> >> Also, I

Re: Advancing translational research with the Semantic Web

On May 16, 2007, at 6:48 AM, Eric Jain wrote: Phillip Lord wrote: "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> Just catching up on reading papers :-) EJ> EJ> "It is also useful to know who believes something and EJ> why. However, t

Re: Advancing translational research with the Semantic Web

Phillip Lord wrote: "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> Just catching up on reading papers :-) EJ> EJ> "It is also useful to know who believes something and EJ> why. However, there is no standard way of expressing such

Re: Advancing translational research with the Semantic Web

On May 16, 2007, at 11:15 AM, Phillip Lord wrote: "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> Just catching up on reading papers :-) EJ> EJ> "It is also useful to know who believes something and EJ> why. However, there is no s

Re: Advancing translational research with the Semantic Web

> "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> Just catching up on reading papers :-) EJ> EJ> "It is also useful to know who believes something and EJ> why. However, there is no standard way of expressing such EJ> information a

Re: Advancing translational research with the Semantic Web

Just catching up on reading papers :-) "It is also useful to know who believes something and why. However, there is no standard way of expressing such information about a statement [...]" Reification?