Re: Anil Sinaci on the SALUS project & EU health records -- RECORDING NOW AVAILABLE

https://support.webex.com/support/documentation/help/index.htm#9401.htm On Sat, Jun 20, 2015 at 6:57 AM Timothy W. Cook wrote: > On Wed, Jun 17, 2015 at 8:24 PM, David Booth wrote: > >> A recording of Anil's presentation is now available: >> https://mit.webex.com/mit/lsr.php?RCID=efbe6daefbc642

Re: License unknown

does happen in our field (see drugbank as a real life example). > Yes. And republishers need to think more carefully about the consequences of republishing copyrightable information without knowing the license terms. -Alan > > > Regards, > Jerven > > > > On Mo

Re: License unknown

icense value true > > Class: ClosedLicenseData > EquivalentClass: hasOpenLicense value false > > It makes the properties more specific, sure, but it's more than enough to > go on in many situations. > > Jim > > > > On Mon, Jun 23, 2014 at 11:08 AM, Joachi

Re: License unknown

On Mon, Jun 23, 2014 at 11:08 AM, Joachim Baran wrote: > > On 23 June 2014 06:37, Alan Ruttenberg wrote: > >> In the case that the license is not asserted it distinguishes the case >> where the publisher has made an affirmative effort to determine what the >> license

Re: License unknown

ightStatus [ owl:onPropery dct:creator . > :untilDateOfDeath [ > "Some restiction to state 75 > years after creators death" > ] > ]. > etc... > > Regards, > Je

Re: License unknown

On Monday, June 23, 2014, Joachim Baran wrote: > > On 22 June 2014 19:30, Alan Ruttenberg > wrote: > >> What do you have against booleans? :) >> > My points were: > >With a boolean solution -- especially when it only denotes whether > license look

Re: License unknown

What do you have against booleans? :) That seems like a sort of "too many notes" comment about Mozart's work, if you can reach far enough to follow the analogy. -Alan On Fri, Jun 20, 2014 at 3:55 PM, Joachim Baran wrote: > I am sure we can work out the exact predicate later. The issue I rai

Re: License unknown

etermine-license "false"^xsd:Boolean but dc:license has a > valid license as value. > > Alasdair, Eric - Is there anything in the proposed solution that > http://www.w3.org/2013/ShEx/Primer cannot catch? > > Jerven - does it handle your objections? > > -Scott &g

Re: License unknown

ere it would be necessary to contact said > organization/institute/etc. to find out about the licensing terms. It would > also give you an indicator whom to contact, because the data set provider > might be not the same as the licensing body. > > Kim > > > > On 18 June 2014

Re: License unknown

ll wrote: > Just a slight tweak to Alan's suggestion (thanks Alan): > :determined-license "true"^xsd:Boolean > > -Scott > > On Wed, Jun 18, 2014 at 2:36 PM, Alan Ruttenberg > wrote: > > I concur. This is clear from the semantics of OWL. Understand the >

Re: License unknown

I concur. This is clear from the semantics of OWL. Understand the difference between integrity constraints and OWL assertions. If you want to say that there was an attempt to find a license and that it couldn't be found, say that. You could do so as an annotation on the axiom, or as a distinct pro

Re: A couple of questions on OWL modeling

On Fri, Nov 22, 2013 at 5:23 AM, Andrea Splendiani < andrea.splendi...@deri.org> wrote: > Hi, > > I am building a "nutritional knowledge base" and I have stumbled about a few things I would like to ask an opinion about, especially from the OWL-savy people. > > The first question is: to model restri

Re: biontology.org Linked Data URIs?

ich we can load into our store and thereafter provide. Make sure to give the targets of these annotations rdfs:labels, so they display something that entices the user to click them... -Alan > best, > Andrea > > Il giorno 28/mag/2013, alle ore 23:51, Alan Ruttenberg < > ala

Re: biontology.org Linked Data URIs?

On May 28, 2013, at 6:23 PM, Kingsley Idehen wrote: > On 5/28/13 5:04 PM, Richard Boyce wrote: >> I think this helps bioportal keep track of usage (to justify its existence) >> and reduce annoying bots. Also, I get updates from bioportal for having >> registered an account. -R > > Bots are an

Re: owl:sameAs - Harmful to provenance?

On Mon, Apr 8, 2013 at 2:10 PM, Michel Dumontier wrote: > > > > On Mon, Apr 8, 2013 at 1:23 PM, Alan Ruttenberg > wrote: > >> Nicely pointed out, TN. >> >> Thinking about "metadata" as some other category of data is usually a bad >> sign. I&

Re: owl:sameAs - Harmful to provenance?

meth/journal/v9/n7/abs/nmeth.2084.html > > T N Bhat > > -Original Message- > From: Phillip Lord [mailto:phillip.l...@newcastle.ac.uk] > Sent: Monday, April 08, 2013 12:53 PM > To: Oliver Ruebenacker > Cc: David Booth; Pat Hayes; Peter Ansell; Alan Ruttenberg; > publi

Re: owl:sameAs - Harmful to provenance?

Dropping Jim from cc in deference to him finishing his defense. On Wed, Apr 3, 2013 at 9:58 PM, David Booth wrote: > On 04/02/2013 05:02 PM, Alan Ruttenberg wrote: > >> On Tuesday, April 2, 2013, David Booth wrote: >> On 03/27/2013 10:56 PM, Pat Hayes wrote: >>

Re: owl:sameAs - Harmful to provenance?

On Tuesday, April 2, 2013, David Booth wrote: > On 03/27/2013 10:56 PM, Pat Hayes wrote: > >> On Mar 27, 2013, at 7:32 PM, Jim McCusker wrote: >> >>> If only owl:sameAs were used correctly... >>> >> >> Well, I agree that is a problem, but don't draw the conclusion that >> there is something wrong

Re: owl:sameAs - Is it used in a right way?

> > Let's say I have a graph G1 containing two statements s1 and s2. >>> >> Both s1 and s2 contain the same uri u1. Do you think the RDF specs >> allow me to use interpretation I1 for s1 and interpretation I2 for s2? >> > > If you are asking whether the spec tells you how to determine the truth

Re: Observations about facts in genomics

On Thu, Mar 21, 2013 at 10:19 PM, Alan Ruttenberg wrote: > > > On Thu, Mar 21, 2013 at 10:15 PM, Pat Hayes wrote: > >> >> On Mar 21, 2013, at 11:38 PM, Alan Ruttenberg wrote: >> >> > >> > >> > On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansel

Re: Observations about facts in genomics

On Thu, Mar 21, 2013 at 10:15 PM, Pat Hayes wrote: > > On Mar 21, 2013, at 11:38 PM, Alan Ruttenberg wrote: > > > > > > > On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansell > wrote: > > On 22 March 2013 12:05, Alan Ruttenberg > wrote: > > > On Wed, Ma

Re: Observations about facts in genomics

On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansell wrote: > On 22 March 2013 12:05, Alan Ruttenberg wrote: > > On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll > wrote: > >> > >> To me, that seems to lead us back to the earlier discussion (rathole?) > >> abou

Re: Observations about facts in genomics

On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll wrote: > To me, that seems to lead us back to the earlier discussion (rathole?) > about owl:sameAs > Don't think so. It is a simple application of the pattern of having information about something. The statements don't have to be true. > > Yes,

Re: availabilty of dailymed and diseasome

I did not. Thanks! On Tue, Mar 19, 2013 at 3:46 PM, Michel Dumontier < michel.dumont...@gmail.com> wrote: > I think you failed to notice the paging. > > m. > > > On Tue, Mar 19, 2013 at 3:30 PM, Alan Ruttenberg > wrote: > >> The rdfization is pretty thin.

Re: availabilty of dailymed and diseasome

The rdfization is pretty thin. Compare http://omim.org/entry/300377 http://cu.omim.bio2rdf.org/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fomim%3A300377 Is the view I looked at missing some of the attributes? -Alan On Tue, Mar 19, 2013 at 12:06 PM, Michel Dumontier < michel.dumont...@gmail.com> wr

Re: owl:sameAs - Is it used in a right way?

phical literature, or using vague assertions. -Alan > > Jim-qua-hcls-member > > > On Sunday, March 17, 2013, Alan Ruttenberg wrote: > >> Can someone *please* tell me what a context is?? >> >> My null hypothesis is that when someone says "context" they

Re: owl:sameAs - Is it used in a right way?

Can someone *please* tell me what a context is?? My null hypothesis is that when someone says "context" they either don't know what they are talking about, or are too lazy to say. Both these cases are deadly for clear communication on the web. -Alan On Sun, Mar 17, 2013 at 6:54 PM, Jim McCusker

Re: owl:sameAs - Is it used in a right way?

Neither of them are clear enough to be sure what they are referring to. They both, in their description, refer to molecules in some places, and packaged therapeutics in others. Their CAS numbers agree (though the wikipedia mentions that it is of the sodium salt), as do their INCHI, though the INCHI

owl:sameAs - Is it used in a right way?

My dad's name is Danny. I've known him a Long time, during which he's changed a lot. Am I supposed to stop calling him dad because he's not precisely the same as he was when I was 10? -Alan On Sunday, March 17, 2013, Erich Gombocz wrote: > Observing this discussions for quite a while, I have to

Re: owl:sameAs - Is it used in a right way?

anction to interpret what I say to be about some other Jonathan Rees, because I wasn't specific enough to narrow down the set of Jonathan Reeses to just one. -Alan On Sunday, March 17, 2013, David Booth wrote: > Hi Alan, > > On 03/16/2013 01:49 PM, Alan Ruttenberg wrote: > >> Davi

Re: owl:sameAs - Is it used in a right way?

David's assertion that a uri can mean different things in different graphs is an opinion that does not concur with either the web specifications nor the goals they were built to satisfy. Caveat emptor. -Alan On Saturday, March 16, 2013, David Booth wrote: > Hi Umutcan, > > You have indeed stumbl

Re: owl:sameAs - Is it used in a right way?

There's another perspective, which is to to distinguish descriptions of things from the things themselves. This works if you can agree on identity of the thing but not necessarily on the way to describe it. As an example, consider the class of cars manufactured by Nissan (call it Cn). If you can ag

Re: [Update] Clinical Pharmacogenomics: RxNorm

Will there be anybody discussing the license issues, which seem to disallow this kind of dissemination? -Alan On Tue, Mar 5, 2013 at 1:31 PM, w3.h...@gmail.com wrote: > Tomorrow's clinical pharmacogenomics call will center around RxNorm. Janos > Hajagos will discuss his approach to converting R

Re: From strings to things: ClinicalTrials.gov

bels in the source data. > > Cheers, > Oktie > > > Oktie Hassanzadeh > ok...@cs.toronto.edu > http://www.cs.toronto.edu/~oktie > > > On Sun, Feb 17, 2013 at 1:48 PM, Alan Ruttenberg > wrote: >> >> Oktie, >> >> One thing

Re: From strings to things: ClinicalTrials.gov

Oktie, One thing I think would be helpful is attending more to using human readable labels for terms. For example, if we browse directly at linkedct.org we see a lot of long strings of numbers. But for most of these there is a reasonable label. For example, under outcomes, the first element is pri

Re: From strings to things: ClinicalTrials.gov

Have you looked at https://www.clinicaltrialsregister.eu as well? We did a little work in our group regarding eligibility criteria, and had the impression that the curation was often substantially more detailed at the EU site. In our limited review, both sites, however, suffered from the inability

Re: Wow....

Don't know if you're all aware of a number of projects which are trying to crowdsource information about prior art or otherwise working in order to help combat such cases: http://www.pubpat.org http://patents.stackexchange.com https://www.eff.org/patent-busting?t=1 http://peertopatent.org http://w

Re: HPO and Gene Ontology Licenses

ho wish to assist with maintenance of the Neurocommons >> endpoints would be welcomed. Once they are reviewed and brought up to date >> on which ontologies they load, the Neurocommons RDF Bundling system will >> provide an addition distribution mechanism for creating mirrors. >> >&g

Re: HPO and Gene Ontology Licenses

On Wed, Aug 8, 2012 at 8:28 PM, Peter Ansell wrote: > On 9 August 2012 00:00, Alan Ruttenberg wrote: >> We have discussed that the OBO Foundry policy is to use CC0 or CC-BY >> and it has been put to the GO that we would like to migrate to that >> license. I don'

Re: HPO and Gene Ontology Licenses

On Wednesday, August 8, 2012, Michel Dumontier wrote: > Hi Alan, > > > On Wed, Aug 8, 2012 at 10:00 AM, Alan Ruttenberg wrote: >> >> We have discussed that the OBO Foundry policy is to use CC0 or CC-BY >> and it has been put to the GO that we would like to migra

Re: HPO and Gene Ontology Licenses

We have discussed that the OBO Foundry policy is to use CC0 or CC-BY and it has been put to the GO that we would like to migrate to that license. I don't know the status of that discussion. That said, I would be strongly discouraging of (but unable to prevent) any "no-blank-node" rendering of GO o

2011 International Conference on Biomedical Ontology, Early Bird Registration ends soon

you there. Regards, Alan Ruttenberg (apologies if you receive this message more than once)

CFP: Learning from our mistakes: Adverse event representation (Extended deadline April 10, 2011)

izing Committee Mélanie Courtot, British Columbia Cancer Research Centre Albert Goldfain, Blue Highway, LLC Yongqun “Oliver” He, University of Michigan Medical School Alan Ruttenberg, University at Buffalo, School of Dental Medicine Program Committee • Olivier Bodenreider, Nat

Re: [BioRDF] Comments from Christoph Grabmuller on BioRDF microarray provenance

> The DO is a OBO Foundry candidate, and there is an official OWL > release [1], so wouldn't that be the authoritative source for URIs? Of > course it's easy to replace the definition_citations, but wouldn't it > be much nicer if the user can just download two 'officially' released > OWL files and

Re: [TMO] patient record normalization

We adopted the two component approach rather than the relation approach. -Alan On Sep 9, 2010, at 4:09 PM, Kerstin Forsberg > wrote: The issue of units for measurements was also discussed (but not solved?) in the IAO (Information Artifact Ontology) group earlier this year, see for example:

Re: Any meeting at ISMB ?

r, perhaps? > > Cheers, > Matthias > > > > - > > From: Alan Ruttenberg > Sent: Friday, June 19, 2009 6:00 AM > To: Hilmar Lapp > Cc: eric neumann ; Andrea Splendiani ; Matthias Samwald ; w3c semweb HCLS > Subject: Re: Any meeting at ISMB ? > > > > > >

Re: Any meeting at ISMB ?

On Thu, Jun 18, 2009 at 1:38 PM, Hilmar Lapp wrote: > > On Jun 18, 2009, at 12:36 PM, eric neumann wrote: > > I'm pretty sure BOFs are open to ISMB registered folks only. That does >> not prevent us from having additional meet ups. >> > > > That depen

Re: Is there an NCBI taxonomy in OWL ?

So I count three different sets of URIs for NCBI taxonomy so far. :( -Alan On Fri, Feb 27, 2009 at 11:37 AM, Chris Mungall wrote: > also.. > > part of the NCBI taxonomy is in NIF Organism: > > http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Organism.owl > > See also: > >  https://wiki.neu

Call for Papers: International Conference on Biomedical Ontology, Buffalo, NY, July 2009

erkeley Labs Yves Lussier, University of Chicago Mark Musen, Stanford University Alan Ruttenberg, Science Commons Susanna-Assunta Sansone, EBI Chris Stoeckert, University of Pennsylvania For further information see http://icbo.buffalo.edu or write to [EMAIL PROTECTED] Participation in this meet

Invitation to attend OWL: Experiences and Directions (OWLED) 2008

e. Thanks to their generosity we will be able to provide some amount of funding support for students who need it. Hope to see you there! Feel free to contact me with any questions you might have. Regards, Alan Ruttenberg, general chair [EMAIL PROTECTED] http://www.webont.org/owled/2008/ Acce

Remembering Bill Bug in the KB note

I wonder if we could include a line remembering Bill Bug in the KB note. Something simple along the lines of "In memory of our friend and colleague William Bug, Ontological Engineer" -Alan

Re: Cross Language with topic maps [was Re: ìö‘` : KB note]

On May 29, 2008, at 3:01 PM, Pat Hayes wrote: BTW, one can also (of course) have multiple names for the same entity, and (in OWL Full) link the various names to such things as email messages, comments, etc.. Why the "in OWL Full" qualification here? -Alan

Re: SenseLab note: some updates

ally a fair fight ;-) -Alan On May 13, 2008, at 8:36 AM, Alan Ruttenberg wrote: Knowledge base is generally written as two words. Try a google fight on scholar.google.com. -Alan On May 13, 2008, at 8:31 AM, Matthias Samwald wrote: I have made some small updates to the draft SenseLab convers

Re: SenseLab note: some updates

Knowledge base is generally written as two words. Try a google fight on scholar.google.com. -Alan On May 13, 2008, at 8:31 AM, Matthias Samwald wrote: I have made some small updates to the draft SenseLab conversion document based on feedback from members of the group. See http://www.w3.

Re: GO as RDF properties

Hello Tore, You might consider posing this question to the obo-discuss group, where discussion of the use of GO often occurs, or consider joining the biopax-obo effort - http://groups.google.com/group/biopax-obo - where we are currently working on precisely this sort of problem - represe

Re: [COI] Clinical Observations Interoperability, February 26th, 11:00am - 12:00pm EST

Regrets, I am in +14 hours time zone this week. Looking forward to being back in the game next week, Regards, Alan On Feb 23, 2008, at 11:38 PM, Kashyap, Vipul wrote: Phone +1 617 761 6200, conference 24668 ("BIONT") IRC irc://irc.w3.org:6665/hcls Browser-based IRC client: http://www.w3.

Re: [COI] Clinical Observations Interoperability, February 12th, 11:00am - 12:00pm EST

I'm less than likely to be able to attend in the next two weeks, but Kerstin, Bo, and Holger should be able to update you all on our current status. Enjoy the long weekend, Regards, Alan On Feb 15, 2008, at 9:50 PM, Kashyap, Vipul wrote: Phone +1 617 761 6200, conference 24668 ("BIONT")

HealthCyberMap

Just ran in to this while poking around in Pubmed. Anybody know about it, and care to comment about it's relevance to our work? -Alan A first look at HealthCyberMap medical semantic subject search engine. Boulos MN. School for Health, University of Bath, UK. [EMAIL PROTECTED] HealthCyber

Re: Trust in statements (still is BioRDF Brainstorming)

On Feb 14, 2008, at 3:36 AM, [EMAIL PROTECTED] wrote: As for rdf formats and OWL descriptions, I shall have to leave that to others - I still haven't grokked Alan's banana class definition yet. :) I will follow up with a better explanation given Chris, and now your complaints. -Alan

Re: BioRDF Brainstorming

ntrez gene dataset that Olivier's group had created? Separate email. For educational purposes, perhaps have an option to show the sparql queries you use to retrieve the information and offer a sparql endpoint to let people play with fiddling the queries. Regards, Alan Cheers, -Kei

Re: BioRDF Brainstorming

On Feb 12, 2008, at 3:58 PM, Kei Cheung wrote: Also, I have a question regarding retrieval of entez gene information including gene ids, symbols, and snyonyms. Is such information available from the HCLS KB and/or RDF entrez gene dataset that Olivier's group had created? Here is a query

Re: BioRDF Brainstorming

entrez gene info. The other files are there too - let me know if it isn't clear which you need to do some query. Note the dates of the files - they are not current. We're working on putting in to place a system that keeps our endpoint up to date. Regards, Alan Thanks Ernie Alan

Re: BioRDF Brainstorming

On Feb 12, 2008, at 8:59 AM, Colin Batchelor wrote: How do you propose we cope with hedging, that is "It is not impossible that bananas are green", "Taken together, these results would indicate that bananas are blue" and so forth? This is much more common that the unwary reader might suspect

Re: Trust in statements (was BioRDF Brainstorming)

I'm personally fond of the symbolic approach - I think it is more direct and easier to explain what is meant. It's harder to align people to a numerical system, I would think, and also provides a false sense of precision. Explanations are easier to understand as well: "2 sources thought t

[coi] Some classifications of the entities in patient 1

Very rough, for discussion. From the realist point of view. Patient 1 in http://esw.w3.org/topic/HCLS/ ClinicalObservationsInteroperability/MockedUpPatientData dispositions: orthostatic intolerance http://en.wikipedia.org/wiki/ Orthostatic_intolerance dizziness D004244 hypertension D0

Re: BioRDF Brainstorming

On Feb 11, 2008, at 3:34 PM, Olivier Bodenreider wrote: eric neumann wrote: I haven't been good at following the calls lately, but still am sympathetic to the endeavor and committed to helping as I can (just not quite efficiently). Starting with MeSH might be a good idea as it it does not h

Re: [COI] Clinical Observations Interoperability, February 5th, 11:00am - 12:00pm EST

etes Patient Data > (A) RDF Representation using POMR and Galen: Vipul > Initial Representation available at: > (B) RDF Represenation using HL7/RIM/CDA: Helen and Dan Russler > (C) SDTM Representation: Jennifer and Rachel > (D) "Realist approach": Alan, Kerstin and Bo > (E) De

Draft minutes from today's BioRDF call

http://www.w3.org/2008/01/07-BioRDF-minutes.html -Alan

Semantic Interoperability in Health Informatics: Lessons Learned - Panel Discussion - Thu 2008-01-10

Begin forwarded message: From: "Peter Yim" <[EMAIL PROTECTED]> Date: December 20, 2007 6:40:59 PM EST To: [EMAIL PROTECTED] Subject: [ontolog-invitation] Semantic Interoperability in Health Informatics: Lessons Learned - Panel Discussion - Thu 2008-01-10 Headlin

Minutes from today's BioRDF call

http://www.w3.org/2007/12/17-BioRDF-minutes.html

Re: Minutes from BioRDF telecon 10-Dec-2007

On Dec 13, 2007, at 9:29 AM, Booth, David (HP Software - Boston) wrote: ACTION: Susie to ping Wright State University (Amit) to see if there database is up and available [recorded in [16]http://www.w3.org/2007/12/10-BioRDF-minutes.html#action02] Sadly, their database is not up and runn

Might be interesting to approach these folks about making their KB available in RDF

Begin forwarded message: From: "New Medicine Oncology KnowledgeBASE" <[EMAIL PROTECTED]> Date: December 12, 2007 5:11:48 PM EST Subject: Anticancer Drugs Targeting the ErbB (EGFr/HEr2) Pathway Generated nearly $5 billion Reply-To: "New Medicine Oncology KnowledgeBASE" <[EMAIL PROTECTED]>

Re: [COI] Clinical Observations Interoperability Telcon December 18, Presentation of HL7/ RIM

Note that while the link says the correct URL, clicking on the link brings you to the wrong one. http://www.whitcongress.com is correct. Best, -Alan On Dec 9, 2007, at 4:35 PM, eric neumann wrote: Vipul, The first link should read: 1. Tim Berners Lee Keynote at the World Healthcare Innova

Updated Senselab files

Based on discussion at the last BioRDF call, and a new export from Luis, I've updated the text version as well. The new files are available at the same locations as previously advertised. MS Access version: http://purl.org/commons/hcls/senselab/ SenseLabPublicSnapshot20071119.zip Tab delim

Re: BioRDF Telcon

Notes in line... On Nov 25, 2007, at 1:31 PM, Susie M Stephens wrote: * Scribe: Jonathan Rees Jonathan is traveling. I don't know if he plans to make the call. * SenseLab Conversion into Access tables - Luis Marenco MS Access version: http://purl.oclc.org/commons/hcls/senselab/ SenseLabPu

Anyone planning to go to ESWC and want to do a HCLS demo?

If there is interest several of us can work together to prepare materials. -Alan Begin forwarded message: Resent-From: [EMAIL PROTECTED] From: Joerg Hoffmann <[EMAIL PROTECTED]> Date: November 7, 2007 2:01:11 PM EST Subject: ESWC 2007 Call for System Demonstrations Archived-At:

Envisioning information

Vipul and I were discussing patient records and I remembered a nice layout of a portion from a medical record that Edward Tufte visualized in his book Envisioning Information. It is on page 56 to 57. Unfortunately I don't know of an online way to view the book, but if you have access to a

Re: BioRDF Telcon

Regrets, I'll be taking a day off tomorrow. Speak to you all next week. Best, Alan On Nov 10, 2007, at 5:14 PM, Susie M Stephens wrote: Here's a reminder about Monday's BioRDF call. Cheers, Susie == Conference Details == * Date of Call: Monday November 12, 2007 * Time of Call: 11:00am

[COI] Following up on your comment re "underlying model" in your reviewing the functional requirements spreadsheet

Hi Kersten, During the COI call this week you made some reference to the "underlying model" being an issue in filling out Vipul's functional requirements spread sheet. Do you think you could say again what the issue was that you were referring to? -Alan

For those interested in user interface in the semweb space

Begin forwarded message: From: Duane Nickull <[EMAIL PROTECTED]> Date: October 25, 2007 5:39:35 AM PDT To: "[ontolog-forum]" <[EMAIL PROTECTED]> Subject: [ontolog-forum] Web 2.0 Design Patterns book with ontology throughout. Reply-To: "[ontolog-forum] " <[EMAIL PROTECTED]> On the subject

ESWC

Anyone planning to attend ESWC? Interest in presenting HCLS stuff there? -Alan Begin forwarded message: Resent-From: [EMAIL PROTECTED] From: Raphaël Troncy <[EMAIL PROTECTED]> Date: October 24, 2007 12:44:22 PM EDT To: destinataires inconnus:;destinataires:; Subject: ESWC 2008 Call for Panel P

[COI] seen on another list: GLIF

http://www.glif.org/glif_main.html Clinical practice guidelines and protocols are being applied in diverse areas including policy development, utilization management, education, reference, clinical decision support, conduct of clinical trials, and workflow facilitation. Many parties are eng

Re: resend -- minutes of the 2007-10-15 BioRDF telecon available

I have made a minor correction, attributing responsibility for the readme on demo licensing issues to Jonathan, rather than me. -Alan On Oct 20, 2007, at 5:51 PM, Olivier Bodenreider wrote: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/ 2007-10-15_Conference_Call

Re: Preliminary Comments on ADNI - LONI

the vast majority of the data lies in MRI/ PET, rather than anything else (MRA, etc.) HTH, Matt Alan Ruttenberg wrote: Ok. From which document did you get the information about the particulars of the schema you mention? -Alan On Oct 15, 2007, at 4:27 AM, Matt Williams wrote: No, I didn&#

Re: Preliminary Comments on ADNI - LONI

ading of the terms of use. Matt Alan Ruttenberg wrote: Did you go through the application for access to get this information? Looks like the terms of use would prohibit our publishing any of the content in a demo. Is that your read too? -Alan On Oct 5, 2007, at 4:22 AM, Matt Williams wrote:

Re: Preliminary Comments on ADNI - LONI

Did you go through the application for access to get this information? Looks like the terms of use would prohibit our publishing any of the content in a demo. Is that your read too? -Alan On Oct 5, 2007, at 4:22 AM, Matt Williams wrote: Dear All, This is to try an sketch the outlines of

Re: RFC 2616 vs. AWWW

On Oct 11, 2007, at 4:19 PM, Pat Hayes wrote: URI1 the first URI endpthe http endpoint identified by URI1 URI2 the URI to which endp redirects URI1 redir the http endpoint identified by URI2 potato the potato which (we all know) URI refers to Then the following should hold, according

Boston area: Friday theory lunch: Towards knowledge-based semantic integration of models

Thanks to Jeremy Zucker for pointing this out to me. http://vcp.med.harvard.edu/tl-schedule.html HMS, Alpert Building, Room 563 at 12 noon Towards knowledge-based semantic integration of models 12 Oct 2007 Carolyn Talcott Computer Science Lab SRI International Abstract In spite of standards

Re: BioRDF Telcon

What were you looking for that wasn't on [1]? - looks like there's a lot of good stuff there, some of which you wrote. Also, there's the "what goes wrong URI" slides from the URI presentations (you're an author on at least one or two of then :) -Alan On Oct 8, 2007, at 9:44 AM, Jonathan Rees

Re: Using SEER Data

in non-rdf) linking SEER with genomic data, but it's not big enough to make use of this. It may also be that clear demonstration of the utility of this might encourage them to relax the licensing restrictions. I have an idea for a different data set which I will send as a separate emai

Re: Using SEER Data

[cc changed to public-semweb-lifesci] We could distribute a script that does the conversion to RDF so that individuals who wanted to use it could still get it themselves and put it into a local store. There are two possible benefits of working with the data: 1) Learning something from it

Surveillance Epidemiology and End Results (SEER)

At a talk I attended today, this resource of patient cancer diagnoses was mentioned as an example of publicly available clinical data. A quick look over the documentation suggests it might be an interesting project to produce an RDF version of the data set. http://seer.cancer.gov/data/ T

Using Pronto: Breast Cancer Risk Models

Begin forwarded message: From: Kendall Clark <[EMAIL PROTECTED]> Date: October 2, 2007 7:45:49 PM EDT To: [EMAIL PROTECTED] Subject: [Pellet-users] Using Pronto Folks, Using Pronto: Breast Cancer Risk Models http://clarkparsia.com/weblog/2007/10/02/using-pronto/ This is the 2nd in a series

Re: [Semantic_Web] Re: Intelligent Search

Hello ontologyonline (do you have name? :) I did a quick poke and was surprised to see that there seem to be no hits on one of top gene ontology categories, molecular_function[1] Perhaps you could walk through how you use the ontology for search in this case, which could elucidate why we d

Re: I read a challenge. was, Re: [gofriends] GO ontology in OWL format

I've started a page on the wiki to record progress on working through the GO SQL queries that Chris documented. http://esw.w3.org/topic/GoSparqlQueries Nothing but the "what is the nuclear chromosome part of" query there yet, but let's work on doing the rest. -Alan

Re: I read a challenge. was, Re: [gofriends] GO ontology in OWL format

On Sep 14, 2007, at 8:40 AM, Chimezie Ogbuji wrote: On Fri, 2007-09-14 at 05:04 -0400, Alan Ruttenberg wrote: In my opinion SQL (with entailments pre-computed) still turns out to be a far superior choice to existing semantic web technology - I'd be interested to see the SPARQL equivalent

Re: I read a challenge. was, Re: [gofriends] GO ontology in OWL format

Here's my way of looking at this. The information from which the classrelations graph was derived was the original OWL. We'd like a world in which we can query the OWL, with reasoner support, but we don't have that yet. We will at some point. The most common way of doing inference in tri

Re: I read a challenge. was, Re: [gofriends] GO ontology in OWL format

On Sep 14, 2007, at 5:04 AM, Alan Ruttenberg wrote: Get it as RDF Swine mail application. Get it as RDF => http://tinyurl.com/3yyepz -Alan

I read a challenge. was, Re: [gofriends] GO ontology in OWL format

Seen on the gofriends list: On Sep 12, 2007, at 1:20 PM, Chris Mungall wrote: Let me also give you some information on the results of our experiments using OWL and Sesame, as part of a different project outside GO. Triplestores such as Sesame seem to work best when you are storing instanc

Re: [hcls] User interfaces for writing / querying RDF: Leeet

Maybe. You could use the examples on the macros page I pointed to to test your theory. -Alan On Sep 14, 2007, at 3:31 AM, Matthias Samwald wrote: On Thu, 2007-09-13 at 23:53 -0400, Alan Ruttenberg wrote: http://code.google.com/p/owl1-1/wiki/MacrosAndSyntax In other words, instead of

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