PhD position open

2015-07-03 Thread Mark Wilkinson UPM
ations. If anyone knows of excellent candidates, please send them my way! The candidate will, preferably, have good exposure to linked data/semantic technologies, and must be a competent coder; however there is a lot of flexibility v.v. their educational background. Cheers all! Mark -- Dr

Re: RDF information content and FHIR RDF requirement #14

2015-03-24 Thread Mark Musen
Hi Everyone, We indeed will be moving Protégé 5 to the new OWL API in the next few weeks, which will allow us to serialize in JSON-LD for free. I’ve copied Matthew Horridge on this message, who is the best person to bug about this upgrade ;-) Regards, Mark > On Mar 24, 2015, at 2:13

[CFP, Virtual, Today] Decision Making with Ontologies in IoT 12:30 EST

2015-03-19 Thread Mark Underwood
All other details can be found at http://ontolog-02.cim3.net/wiki/ConferenceCall_2015_03_19 and the main Ontology Summit page at http://ontolog-02.cim3.net/wiki/OntologySummit2015 - Michael Gruninger and Mark Underwood Chairs, Ontology Summit 2015

[bioportal-announce] Letter of support to keep NCBO going!

2015-01-09 Thread Mark Musen
, 2015. Many thanks, Mark --- Mark A. Musen, M.D., Ph.D. Professor of Medicine (Biomedical Informatics) Principal Investigator, the National Center for Biomedical Ontology Director, Stanford Center for Biomedical Informatics Research Stanford

Re: How do you go about versioning ?

2014-09-20 Thread Mark Wilkinson
+1 On 19 September 2014 20:07:52 CEST, Michel Dumontier wrote: >Hi, > I suggest nanopublications to track versioning for assertions > http://www.nanopub.org/guidelines/ > >m. > >On Fri, Sep 19, 2014 at 9:58 AM, Joachim Baran > wrote: >> Hi! >> >> On 19 September 2014 09:45, Andrea Splendiani >

SADI half-day tutorial at ICBO Houston - Oct 6/7

2014-08-15 Thread Mark Wilkinson
) Cheers all! Mark SADI Web Service Design and Publication Tutorial /Presenters: Luke McCarthy (Freelance Programmer & Lead Developer of SADI)/ /Format: Tutorial <http://icbo14.com/types/tutorial/>/ This half­day tutorial will cover the core SADI design patterns, considerations for

[bioportal-announce] New survey for evaluating NCBO technology

2014-08-11 Thread Mark Musen
Dear Colleagues, The National Center for Biomedical Ontology is conducting a new survey to understand better who our users are, what they do with NCBO Technology, and what biomedical and scientific problems they are addressing when using our resources. We ask you to give us 15 minutes of your

Re: NDF-RT and Canada

2013-09-20 Thread Mark
Michel, I love how comprehensive your responses are! I always learn from them and I really should take a lesson from you in this regard vv my own projects! :-) M Michel Dumontier wrote: >Hi Marc, >DrugBank offers mappings to DPD. you can access drugbank data in RDF >with >Bio2RDF. > >bio2r

Re: Data Sharing - a video

2013-05-28 Thread Mark
You will laugh and you will cry. Crying from laughing! Thanks for sharing! M

Wow....

2013-02-05 Thread Mark Wilkinson
I have no words... http://www.freepatentsonline.com/y2013/0030827.html Semantic Interoperability System for Medicinal Information United States Patent Application 20130030827 M -- Dr. Mark D. Wilkinson Isaac Peral Senior Researcher, Biological Informatics Centro de Biotecnología y

Re: Stanford-bound!

2013-01-21 Thread Mark Musen
We are obviously thrilled that Michel will be joining our faculty at Stanford, and we are looking forward to many new opportunities for collaboration with the HCLS community. Mark On Jan 21, 2013, at 11:15 AM, Michel Dumontier wrote: > Dear friends, colleagues and collaborators, > &g

Re: Wiki page on RDF success stories? [was Re: Opening Walled Gardens: RDF / Linked Data as the Universal Exchange Language of Healthcare]

2013-01-15 Thread Mark
Jerven from uniprot has a paper (accepted? Not sure... At least submitted - he sent me the submission) where he details how RDF has made his life much much easier... It may be worth knocking on his door for additional comment at least... M Tom Morris wrote: >On Tue, Jan 15, 2013 at 12:41

RE: Paris this week?

2012-12-03 Thread Mark
I'm at the statistics and computing meeting in Oviedo, then heading to Potsdam day after tomorrow to work for a few days with Tiziana's team on workflow metadata... M "Mead, Charlie (NIH/NCI) [C]" wrote: >Hi Joanne -- > >Unfortunately, I'm in Geneva for the week. > >charlie >__

CfP Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine

2012-06-11 Thread Mark
Alejandro Rodríguez González, PhD (Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA, Spain) Jyotishman Pathak, PhD (Mayo Clinic) Mark Wilkinson, PhD (Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA) Nigam H. Shah, MBBS, PhD (Stanford University) Robert St

Re: Systems Biology / W3C telco - TODAY at 11AM EST

2012-06-06 Thread Mark
Ack! I'm double-booked :-( Sorry Helena! Will the slides/notes be available somewhere? (Michel will probably put his up on Slideshare, right?) Mark On Wed, 06 Jun 2012 13:55:28 +0200, Helena Deus wrote: Dear all, Please join me for the next semantic systems biology telco,

Re: Reminder: SysBio Wednesday 11AM ET / 4PM GMT / 5PM CET

2012-05-24 Thread Mark
7;m speaking out-of-turn, please flame me :-) I can take it! LOL! I just want to see this group succeed, and I am willing to stick my neck out to see if I can help! :-){ ^^^ my neck Best wishes all! Mark

Re: Reminder: SysBio Wednesday 11AM ET / 4PM GMT / 5PM CET

2012-05-22 Thread Mark
Excellent! Looking forward to it! M On Tue, 22 May 2012 15:27:12 +0200, Jun Zhao wrote: Dear all, I am helping Lena to chair tomorrow's call because she is tied up with travel plans. Tomorrow we are planning to learn more about the MAPK pathway by looking into the BioModels database

Re: Combined BioRDF/LODD telcon Monday May 7, 11AM ET / 5PM CET

2012-05-05 Thread Mark
! Once we're "operational" we're going to do some very cool things with the data they're generating! M meg...@fi.upm.es wrote: All; I'm in the process of changing my research group from OEG to Bioinformatics (With Mark Willkinson), both at the UPM, so aplogies f

Re: Minutes from Monday's Linked Life Data (BioRDF / LODD) teleconference

2012-04-27 Thread Mark
Would there be sub-properties of "derived-from": "extracted-from" and "adapted-from"? M On Fri, 27 Apr 2012 10:54:21 +0200, Helen Parkinson wrote: Derived-from can be used to model e.g. DNAs derived from a cell line, a blood derived from a person etc. We will be using this in the Bio

Re: Minutes from Monday's Linked Life Data (BioRDF / LODD) teleconference

2012-04-26 Thread Mark
member at that time but has remained the strongest contender for the job was http://semanticscience.org/resource/is-related-to . -Scott P.S. My sympathy goes out to you Mark as you wait for your WIFI hookup. I guess that you are forced to go to the pub and have a drink in order to get a bit of nor

Re: Minutes from Monday's Linked Life Data (BioRDF / LODD) teleconference

2012-04-26 Thread Mark
ring ontologies!) Jim McCusker wrote: Actually, we've switched over to generating subproperties of sio:has_predicate, so I'm glad you suggested the same thing. Jim On Thu, Apr 26, 2012 at 2:07 PM, Mark wrote: > H... what's the range of that predicate? It's a bit like the

Re: Minutes from Monday's Linked Life Data (BioRDF / LODD) teleconference

2012-04-26 Thread Mark
Fantastic! :-) Jim McCusker wrote: Actually, we've switched over to generating subproperties of sio:has_predicate, so I'm glad you suggested the same thing. Jim On Thu, Apr 26, 2012 at 2:07 PM, Mark wrote: > H... what's the range of that predicate? It's

Re: Minutes from Monday's Linked Life Data (BioRDF / LODD) teleconference

2012-04-26 Thread Mark
H... what's the range of that predicate? It's a bit like the SIO "has attribute", where you need to be sure to explicitly type what's at the other end to do "useful" reasoning. We're just concluding a project where we use species-of-origin to restrict the choices the SHARE query resolver can

Re: Telcon Schedule.... logistics

2012-04-19 Thread Mark
+1 !!! Elgar Pichler wrote: I personally am a fan of Google Calendar, and all the problems described in this thread could be solved with it. Why not Task and HCLS chairs should set up the proper recurring events on Google Calendar.Explicitly set the time zone for those events.Then explicitly

Re: Katy Wolstencroft @ Systems Biology Task Force - Wed 18th April at 11AM EDT - TODAY!

2012-04-19 Thread Mark
On Wed, 18 Apr 2012 16:58:22 +0200, M. Scott Marshall wrote: Regrets. Any chance of a webex recording? +1 M

An interesting article from The Atlantic

2012-04-07 Thread Mark
http://www.theatlantic.com/technology/archive/2012/04/the-problem-with-wikidata/255564/ I'm unsure of the veracity of the problem he is describing, but I do agree with the underlying premise - that there is not "one ontology to rule them all"... (unfortunately, my recent grant reviewers tho

Re: Fwd: Nature Publishing Group Linked Data Platform

2012-04-05 Thread Mark
On Thu, 05 Apr 2012 23:57:14 +0200, RebholzSchuhmann wrote: NPG was also part of the SESL project. So, they are aware of the needs of the Semantic Web Community. I guess the sophisticated approach is for later. :-) Fair enough :-) It gives impetus to the various warehouse projects tha

Re: Fwd: Nature Publishing Group Linked Data Platform

2012-04-05 Thread Mark
That's the most frustrating thing about many "triplification" initiatives... the use of (only) literals for identifiers! :-/ It's like giving the path information for your URL, without giving the domain-name! I don't understand why the Web is so ~intuitive to people now, but the Semantic

Re: Invitation to NCBO User Survey and gift drawing

2012-03-14 Thread Mark Musen
Many thanks to those of you who have already completed the NCBO user survey. If you have not done so yet, please take 15 minutes to complete the survey to help us to improve BioPortal for everyone. We very much appreciate your help. Mark On Mar 6, 2012, at 4:25 PM, Mark Musen wrote

Re: HCLS - visualization task force?

2012-03-14 Thread Mark
ls for SADI/SHARE. Hopefully we'll have something to show everyone in a few days/weeks! Mark

Re: [biohackathon:392] Re: Fwd: HCLS IG Note on mapping and publishing life sciences RDF

2012-03-13 Thread Mark
About the use of a priori , a posteriori - I will mull that over. I was pretty happy with the way it seemed to communicate our thoughts, a little attached actually.. :( I think it might be better as "post facto"...?? M

Invitation to NCBO User Survey and gift drawing

2012-03-07 Thread Mark Musen
helping us to serve the community better. Mark --- Mark A. Musen, M.D., Ph.D. Professor of Medicine (Biomedical Informatics Research) Director, Stanford Center for Biomedical Informatics Research Stanford University 1265 Welch Road, X-215 Stanford, CA

Graduate and PDF openings in biological informatics & semantics

2012-02-08 Thread Mark
Bioinformatics (INB). ...and just imagine... doing linked-data and semantic web research without privacy constraints! ;-) Please send questions, CVs, and expressions of interest to me by email: ma...@illuminae.com Best wishes all! Mark -- Dr. Mark Wilkinson Associate Professor, Medical Ge

Re: Evidence of Significance of Semantic Web for Life Sciences - a couple of more examples

2012-01-26 Thread Mark
at I could dynamically pull-in other arbitrary data from other SW sources and explore it "manually" using biological common-sense). Alice is guessing that we'll have confirmation of the observation in the next couple of months :-) Fingers crossed!! Mark -- Dr. Mark Wilk

Re: TMO @ Bio-IT World

2012-01-26 Thread Mark Wilkinson
On Thu, 26 Jan 2012 14:51:24 -0800, Jim McCusker wrote: and tools like SADI provide discoverability and potential for "linked algorithms" in the cloud. Thanks for that, Jim!!! Mark -- Dr. Mark Wilkinson Associate Professor, Medical Genetics PI Bioinformatics, Institute

Re: FW: A Fresh Look Proposal (HL7)

2011-09-17 Thread Mark
+1 on MUO - we're also using it for our modeling of cardiovascular clinical data, and are very happy with it. We're making MUO units the range of the "has unit" predicate from Michel Dumontier's SIO ontology. Mark On Sat, 17 Sep 2011 19:48:28 -0700, Jim M

Re: A Fresh Look Proposal (HL7)

2011-08-24 Thread Mark
:-) then I stand corrected! Thanks Jim, M On Wed, 24 Aug 2011 09:11:33 -0700, Jim McCusker wrote: That's just flat out wrong. "Diabetes"@en is encoded in English in N3-based languages. Jim On Wed, Aug 24, 2011 at 12:02 PM, Mark wrote: On Wed, 24 Aug 2011 08:48:

Re: A Fresh Look Proposal (HL7)

2011-08-24 Thread Mark
ialization in order to promote internationalization of the knowledge that is being represented... Mark

Re: FW: A Fresh Look Proposal (HL7)

2011-08-21 Thread Mark
I want to print this message on a T-shirt and wear it everywhere I go! Fantastic :-) Well said, Jim! Mark On Sun, 21 Aug 2011 15:12:00 -0700, Jim McCusker wrote: I feel I need to cut to the chase with this one: XML schema cannot validate semantic correctness. It can validate that

This amused me - have a great day everyone!

2011-08-02 Thread Mark
Just a bit of mirth to help you all through the day! http://dilbert.com/dyn/str_strip/0//000/10/2/9000/800/129847/129847.strip.print.gif Best wishes all! Mark -- Mark Wilkinson Associate Professor, Medical Genetics PI Biological Informatics, Institute for Heart

Web Publishing of Scientific Data and Services Training Course - Vancouver, BC

2011-07-14 Thread Mark
letter with: • A short paragraph outlining your relevant experience and learning objectives; • Online resources you are involved in maintaining • Relevant responsibilities and / or publications in a) bioinformatics, b) web services c) semantic technologies; Best regards, Mark Wilkinson, on

Re: Trying to summarise: Semantic free identifiers

2011-06-21 Thread Mark
On Tue, 21 Jun 2011 12:41:12 -0700, Andrea Splendiani wrote: I bet we could make a test and see the correlation between who prefers opaque vs transparent ids, and who prefers OWL-apis vs Jena. :-) I bet you are absolutely correct about that! :-) M

Re: My task from last week: Semantic free identifiers

2011-06-20 Thread Mark
If you want to work with a more sophisticated API - I might suggest the OWL API. It's more powerful, but also more sophisticated +1!! Mark

Re: My task from last week: Semantic free identifiers

2011-06-20 Thread Mark Wilkinson
27;t use language-neutral method names is a compelling one for me. h... I may be moving to the dark side of this discussion! ;-) LOL! M -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Institute for Heart and Lung Health St. Paul's Hospital/UBC Vancouver, BC, Canada

Re: My task from last week: Semantic free identifiers

2011-06-20 Thread Mark Wilkinson
parql-assist-language-neutral-query-composer http://sadiframework.org/content/2010/11/29/sparql-assist-language-neutral-query-composer/ Manuscript available at: http://arxiv.org/abs/1012.1666 Michel & Mark -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics,

Re: My task from last week: Semantic free identifiers

2011-06-20 Thread Mark
hnically-incorrect" global architecture just for the sake of convenience, lets fix it at the level of the SPARQL query writer. $0.02 <-- mark:partOfMine Mark

Re: [linkedlifew3cnote] Re: Linkset Provenance

2011-06-16 Thread Mark
Message- From: Mark Wilkinson [mailto:ma...@illuminae.com] Sent: 16 June 2011 16:18 To: linkedlifedatapracticesn...@googlegroups.com; Helena Deus Cc: Claus Stie Kallesøe; HCLS; Anja Jentzsch Subject: Re: [linkedlifew3cnote] Re: Linkset Provenance < "drugX" rdf:type myshema:dr

Re: [linkedlifew3cnote] Re: Linkset Provenance

2011-06-16 Thread Mark
On Thu, 16 Jun 2011 09:06:47 -0700, Helena Deus wrote: Great to hear from you. Always nice to hear from you too!! M

Re: [linkedlifew3cnote] Re: Linkset Provenance

2011-06-16 Thread Mark
On Thu, 16 Jun 2011 09:06:47 -0700, Helena Deus wrote: I thought the drugs we two individuals (instances of drugs). < :drugX rdf:type myshema:drug > Here you are saying X is "type drug", asserting that "myschema:drug" is an OWL Class. Therefore... < myschema:drug owl:sameAs

Re: [linkedlifew3cnote] Re: Linkset Provenance

2011-06-16 Thread Mark Wilkinson
< "drugX" rdf:type myshema:drug > and then somewhere else state that < myschema:drug owl:sameAs someother:drug >. I wouldn't advise this - it's an OWL Full construct. You can only use sameAs to merge two *individuals* in OWL DL. Mark -- Dr. Ma

Re: HCLS chartering/next steps Thur 26 May

2011-05-26 Thread Mark
easier for us to live our academic lives in peace :-) (and easier to get money from research-funding agencies) Mark

Re: Relations in RDF

2011-05-04 Thread Mark Wilkinson
/documents/5292/version/1 http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html#7 -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Institute for Heart and Lung Health St. Paul's Hospital/UBC Vancouver, BC, Canada

Re: Relations in RDF

2011-05-04 Thread Mark Wilkinson
querying. Are there any thoughts from the group on this? I have no preconceptions here (I have no reason to disbelieve Alan or the RDF folks) so open to thoughts and suggestions. Cheers, James -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Institute for Hear

Re: An Universal Exchange Language

2010-12-14 Thread Mark
qualified and should apply for the $ - we could make a YouTube video of our application and send it in. People could learn something - and we might get rich. Sent from my iPhone On Dec 14, 2010, at 9:44 PM, Mark wrote: But seriously, Tim, if we were to pursue this problem, we would need so

Re: An Universal Exchange Language

2010-12-14 Thread Mark
But seriously, Tim, if we were to pursue this problem, we would need some form of unambiguous identifier for "things"... and given the distributed nature of the biomedical domain, we'd want to make sure that there was some way of resolving that identifier to obtain metadata about it from a

Re: An Universal Exchange Language

2010-12-14 Thread Mark
anne Luciano wrote: > >> Tim. >> >> It's short for ROTFLOL. >> >> :-) >> >> Connected by MOTOBLUR™ on T-Mobile >> >> -Original message- >> From: Tim Clark >> To: Mark Wilkinson >> Cc: public-semweb-lifesci@w3.org, &

Re: An Universal Exchange Language

2010-12-14 Thread Mark
give me the $40M and I'll tell you all about it! M "Tim Clark" wrote: >Mark, that is very interesting, I was unaware of the new ROTFL >language, please forward details. :-) > >Tim > >On Dec 14, 2010, at 5:01 PM, Mark Wilkinson wrote: > >> On Tue,

Re: An Universal Exchange Language

2010-12-14 Thread Mark Wilkinson
On Tue, 14 Dec 2010 13:54:10 -0800, Matthias Löbe wrote: Any suggestions? ROTFL!! :-) M -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics Faculty of Medicine, UBC Principal Investigator, Bioinformatics Institute for Heart and Lung Health St. Paul's Hospital Vancouve

RE: [TMO] patient record normalization

2010-09-12 Thread Mark Wilkinson
I think there's a delicate balance between doing things "the right way" (whatever we as the "expert community" decides that means for us), and making things overly simplistic such that we then have to bolt-on a more correct solution in the future, potentially over thousands of resources. We (th

Re: [TMO] patient record normalization

2010-09-12 Thread Mark
or :x :has-attribute [ a :systolic-blood-pressure; :has-value 120; :has-unit unit:mPa ] [ a :diastolic-blood-pressure; :has-value 80; :has-unit unit:mPa ] This is how we are modeling clinical data in the SADI project. We've now switched to using Michel's SIO ontology, but we had an i

Re: [TMO] patient record normalization

2010-09-10 Thread Mark
As usual, I agree with Scott (this is becoming a habit! LOL! Scott, we should really try to work together more closely!) It speaks to a conversation that I had with my review committee this morning about how The Web was built by simply being completely open. Anyone could (can) publish an

Re: NYT Rare Sharing of Data Leads to Progress on Alzheimer’s Published: August 12, 2010

2010-08-13 Thread Mark Wilkinson
"The key to a collaborative Alzheimer’s project was an ambitious agreement to share all the data, making every single finding public immediately." Amen to that! :-) M -- -- Dr. Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Heart + Lung Institute

Re: Towards ontology metrics to guide the development and assessment of "good" ontologies

2010-07-27 Thread Mark
their own DL ontologies. if any of this is helpful let me know and I'll send you whatever we have :-) Mark -- Mark Wilkinson Assistant Professor, Medical Genetics PI Bioinformatics, Heart + Lung Institute @ St. Paul's Hospital University of British Columbia Vancouver, BC Canada

Re: When does a document acquire (web) semantics?

2010-02-02 Thread Mark Wilkinson
to guide the patient to prefer their physician's interpretation vs that of some other quack with their wacky ontology. I don't see that we have any greater control over the situation than that. M -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics

Re: When does a document acquire (web) semantics?

2010-02-01 Thread Mark Wilkinson
On Mon, 01 Feb 2010 14:16:30 -0800, Jim McCusker wrote: The employer/hospital cannot prohibit someone else's ignorance. sigh... how true!! ;-) Mark -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascula

Re: When does a document acquire (web) semantics?

2010-02-01 Thread Mark Wilkinson
real world. If such a thing exists, sure :-) M -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vanc

Re: When does a document acquire (web) semantics?

2010-02-01 Thread Mark Wilkinson
I love this conversation :-) I have a scrap of paper pinned to the filing cabinet beside my desk that says "The World Is Flat - Mark Wilkinson & Ben Good, in the Pub, May 26, 2006". That was the night that I feel I truly came to understand where the "semantics"

Re: [hcls] The future of Semantic Web / Linked Data R&D; translating research into practical applications (was: Updated wiki page for HCLS Knowledge Base)

2009-10-14 Thread Mark
al challenges related to the topic we are discussing :-) Cheers all! Mark On Wed, 14 Oct 2009 06:55:43 -0700, Matthias Samwald wrote: Hi Mark, Moreover, warehousing in and of itself isn't research, nor is it pushing "the state of the art", I have become a bit weary of t

Re: [hcls] Updated wiki page for HCLS Knowledge Base

2009-10-14 Thread Mark
On Wed, 14 Oct 2009 02:51:07 -0700, Egon Willighagen wrote: Just think of it like this: if you aggregated the data already in the way the scientists wants it, he is no longer doing cutting edge science (it's already been done!). Perfectly stated! :-) Moreover, warehousing in and of itse

Re: [hcls] Updated wiki page for HCLS Knowledge Base

2009-10-13 Thread Mark
, if we all pulled in the same direction, we could make the "Web" aspect of the Semantic Web work better than it currently does... Todays programme was brought to you by the letter W ;-) Cheers all! Mark

Semantic Web jobs at the University of Manchester

2009-07-23 Thread Mark Musen
Posted on behalf of Prof. Alan Rector Research Software Developer (2 posts) School of Computer Science Closing date: 29/07/2009 Reference: EPS/90772 An opportunity has arisen to join a successful academic and industrial partnership at the forefront of semantic technologies and health infor

Re: blog: semantic dissonance in uniprot

2009-03-30 Thread Mark
On Mon, 30 Mar 2009 09:11:48 -0700, Michel_Dumontier wrote: (although it's unclear from your website whether services are *actually* described in an OWL document or they just refer to OWL types). Both/either (assuming that I understood your question) The service interfaces are defined as

Re: blog: semantic dissonance in uniprot

2009-03-30 Thread Mark
world... in SADI/CardioSHARE, ontologies are used for *discovery*, not for a priori modelling. I don't know if this is a *pragmatic* way to look at the Semantic Web, but I've always been an idealist LOL! Wish me luck ;-) Mark

Re: blog: semantic dissonance in uniprot

2009-03-25 Thread Mark Wilkinson
On Wed, 25 Mar 2009 12:55:41 -0700, Bijan Parsia wrote: But I can't just pull something useful out of my ass and expect it to come out all rainbows and violets. Believe me, I've *tried*. ;) ahhh... yes the elusive Care-Bear predicates! M -- Mark D Wilkinson, PI Bioi

Re: blog: semantic dissonance in uniprot

2009-03-25 Thread Mark Wilkinson
creating formal ontologies :-) M -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada

Re: blog: semantic dissonance in uniprot

2009-03-25 Thread Mark Wilkinson
elf :-) I just picked the same namespace for point of discussion. M -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St.

Re: blog: semantic dissonance in uniprot

2009-03-25 Thread Mark Wilkinson
; is owl:sameAs "William Jefferson Clinton" (the example from the OWL spec) M -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada

Re: blog: semantic dissonance in uniprot

2009-03-25 Thread Mark Wilkinson
On Wed, 25 Mar 2009 09:25:30 -0700, Mark Wilkinson wrote: I agree - the issue also came up at the BioHackathon last week... basically, as Tom Oinn phrased it, "if you're thinking of using owl:sameAs... don't!" That is the brief form of what he said... the longer s

Re: blog: semantic dissonance in uniprot

2009-03-25 Thread Mark Wilkinson
/purl.uniprot.org/po/0009009 is intended to be a class, or intended to be an instance... since owl:sameAs is only supposed to be used to claim the "identicalness" of two individuals, not an individual to a class... Oh what a tangled "Web" we weave! ;-) M -- Mark

Re: Microsoft Releases Open Tools to Enhance Scientific Research Efforts Building on Science Commons Ontologies

2009-03-16 Thread Mark Musen
NCBO are eager to work with other collaborators who may want to use our ontology-related Web services. We're also eager for feedback on our work. Mark On Mar 16, 2009, at 12:53 AM, "M. Scott Marshall" > wrote: "the release of the Ontology Add-in for Microsoft

Re: C-SHALS 2009

2009-01-23 Thread Mark
Hi Egon There are several Google calendars devoted to Semantic Web activities such as conferences, workshops, etc. Do a quick GC search and pick the ones most relevant to your interests :-) Mark On Fri, 23 Jan 2009 03:08:32 -0800, Egon Willighagen wrote: On Fri, Jan 23, 2009 at

Re: HCLSIG telecon 22 Jan

2009-01-21 Thread Mark
Lucky you! He hasn't helped ME (or my students) resolve it :-) :-) :-) Cheers! M On Wed, 21 Jan 2009 17:30:32 -0800, Kei Cheung wrote: Mark, Eric has already helped me to resolve it. Thanks, -Kei Mark wrote: Odd... it worked for me on my linux machine at work, but it doesn

Re: HCLSIG telecon 22 Jan

2009-01-21 Thread Mark
Odd... it worked for me on my linux machine at work, but it doesn't work for me on my windows machine (Opera browser in both cases) ?? On Wed, 21 Jan 2009 06:32:40 -0800, Kei Cheung wrote: Hi Eric, I don't seem to see the slides at: http://www.w3.org/2009/Talks/0122-federation/ Than

Re: BioGateway

2008-11-04 Thread Mark Musen
host a meeting on URIs for biomedical resources next spring or summer. We hope to have more information on this workshop available in the next few weeks. Regards, Mark

SW mentioned

2008-09-04 Thread Mark Wilkinson
http://www.nature.com/news/2008/080903/full/455008a.html Just a heads-up from yesterday's edition of Nature. The SW is mentioned as one of the technologies-to-watch. I quite liked the concise description of both the pro's and the barriers :-) M -- Mark D Wilkinson, PI Bioi

NCBO releases BioPortal version 2.0 ontology repository

2008-08-21 Thread Mark Musen
, Mark

Re: [Myexperiment-discuss] Re: Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

2008-08-20 Thread Mark Wilkinson
eb-based workflow authoring and enactment environment, and I know this is something that interests the Taverna, Triana and Kepler teams. -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Pr

Re: PURLs of wisdom

2008-05-30 Thread Mark Wilkinson
I can't help but see a lot of LSID-precedent wisdom in these "Active PURLS"... ;-) 8-) Mark On Fri, 30 May 2008 08:36:48 -0700, eric neumann <[EMAIL PROTECTED]> wrote: While attending Semtech 2008 I was impressed with a number of interesting SW talks. One i

New post-doc position: NCBO

2008-05-29 Thread Mark Musen
UCSF. The Center provides national technological infrastructure to support the creation, dissemination, and management of biomedical information and knowledge in machine-processable form. The laboratory of Dr. Mark Musen, principal investigator of the NCBO, is seeking a highly motivated and

NCBO: New Call for Driving Biological Projects

2008-05-17 Thread Mark Musen
to the Center's technological goals. The deadline for receipt of complete proposals for the next round of DBPs is July 1, 2008. I hope that this opportunity will be of interest to some of you. Please be sure to contact me if I can answer any questions about the NCBO or the DBP program. Regards, Mark Musen

Re: Re: URI note snapshot available

2008-04-28 Thread Mark Wilkinson
ally represents, especially when my agent can't read... Mark On Mon, 28 Apr 2008 08:01:17 -0700, Eric Prud'hommeaux <[EMAIL PROTECTED]> wrote: * Jonathan Rees <[EMAIL PROTECTED]> [2008-04-25 13:08-0400] I've been posting revisions to the URI note to the same

CFP: NCBO Driving Biological Projects

2008-02-26 Thread Mark Musen
#x27;s technological goals. The deadline for receipt of complete proposals is April 1, 2008. I hope that this opportunity will be of interest to some of you. Regards, Mark Musen

Re: URI and Web Architecture Revisited

2007-11-13 Thread Mark Wilkinson
Xiaoshu, This is a beautiful synopsis of the problem - THANK YOU for taking the time to write it up as well as you did! I will be using this in my lectures for sure! :-) What made me chuckle was how similar the DFDF concept is to the LSID concept... except that the LSID doesn't rely on

Re: [Fwd: ISMB 2008 Call for Special Session Proposals + More ISCB Conference News]

2007-09-20 Thread Mark Montgomery
Well, I certainly view ontologies as just one part of the semantic web universe, particularly from the enterprise perspective. .02- MM - Original Message - From: "Andrea Splendiani" <[EMAIL PROTECTED]> To: "Suzanna Lewis" <[EMAIL PROTECTED]> Cc: "Paolo Romano" <[EMAIL PROTECTED]>; "

Re: NCBI Resource Locator

2007-09-10 Thread Mark Wilkinson
... in my mailbox it is the 9th of May, 2006. Maybe someone has a more complete record of the conversation? Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x6212

Economist: The long-promised "semantic" web is starting to take shape

2007-08-29 Thread Mark Montgomery
economist.com/index.html Mark Montgomery CEO, Kyield http://www.kyield.com Managing Partner Initium Venture Capital http://www.initiumcapital.com This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender i

Re: [Fwd: Re: identifier to use]

2007-08-27 Thread Mark Wilkinson
ceptable by most people AND offers the largest potential for success, i.e., improves the quality of science and medicine at a global scale. Remember, before the web took off in the mid-90's, many pointed to the limitations of other hyptext systems to why a global network of docume

MAESTRO Manifesto

2007-08-27 Thread Mark Montgomery
sound architecture http://www.kyield.com/Newsletter/September_2007.htm Mark Montgomery Kyield

Re: [Fwd: Re: identifier to use]

2007-08-26 Thread Mark Wilkinson
it already, such as TDWG, IPNI, uBio, to name a few. I think "consensus" here means "me and the people who agree with me" Mark

Re: Paper: URI Identity Management for Semantic Web Data Integration and Linkage

2007-08-01 Thread Mark Montgomery
Unfortunately, none of these or any other I recall seeing to date favors innovation, but rather reinforces group think. The least empowering to group think and automatic replication of either outdated or false information is random ordering, perhaps, but the combination of all of these won't g

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