I've been using UBERON for anatomical parts and SIO's attribute/measurement
approach for metabolites, using CHEBI to classify the chemical types. The
sample (urine, for example,
:X a sio:Sample, UBERON:Urine;
sio:hasPart [
a CHEBI:Creatinine;
sio:hasAttribute [
a sio:Concentration;
sio:hasValue 2.
he explanation here:
> http://goo.gl/8PNuAG#heading=h.r5k2cm3j5iua
>
> David Booth
>
> On 05/06/2015 04:27 PM, Jim McCusker wrote:
> > Lists aren't that bad anymore in SPARQL, now that property paths are
> > available:
> http://www.snee.com/bobdc.blog/2014/04/rdf-l
Lists aren't that bad anymore in SPARQL, now that property paths are
available: http://www.snee.com/bobdc.blog/2014/04/rdf-lists-and-sparql.html
Jim
On Wed, May 6, 2015 at 4:25 PM David Booth wrote:
> In defining the RDF representation of FHIR data, we need to maintain
> element ordering in som
On Fri, May 1, 2015 at 6:08 PM Grahame Grieve <
grah...@healthintersections.com.au> wrote:
> Suggestion 2: Recommend RDF as the best available universal information
>> representation
>>
>
> This completely misses the point; for the kind of disagreement that your
> comments seek to address, RDF is
Both OWL and RDFS are abstract models with no particular serialization.
Ontologies are usually serialized as RDF/XML (that's what's in a .owl file,
usually), but can just as easily be serialized to JSON-LD, Turtle, OWL
Abstract Syntax, Manchester Notation, or many others. Generally, RDF/XML
and Tur
Actually, the impact of punning on reasoners is minimal. There are a set of
OWL predicates that assume the resource is a class, everything else assumes
it is an individual.
Jim
On Fri, Mar 6, 2015 at 10:11 AM Lloyd McKenzie wrote:
> Well, the situation we're in is that there is an official URL
This should work:
http://www.sequenceontology.org/miso/release_2.4/term/SO:051
On Tue, Jan 6, 2015 at 5:36 PM Anders Riutta <
anders.riu...@gladstone.ucsf.edu> wrote:
> Hello,
>
> I'm looking for opinions on the best IRI to use when referring to the term
> "probe" to describe the subject matt
FRBR has a partOf relation: http://vocab.org/frbr/core#partOf
It's domain and range are Endeavour, which is defined as "A class whose
members are any of the products of artistic or creative endeavour."
An RDF graph definitely counts (I would use Expression to talk about an
abstract graph, see
htt
, or not.
>>
> I cannot fathom how this could be inferred from the truth value of a bit.
>
>
--
Jim McCusker
Data Scientist
5AM Solutions
jmccus...@5amsolutions.com
http://5amsolutions.com
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu
http://tw.rpi.edu
Apologies for cross-posting:
ICBO 2014 Call for Participation
5th International Conference on Biomedical Ontologies (ICBO 2014)
Houston, Texas
October 6 - 9, 2014
http://icbo14.com
Overview
The biomedical area has seen an explosive growth in data in the last decade
from electronic health reco
*ICBO 2014Call for Early Career Track PapersDue July 15, 2014*An early
career track paper describes mentored work in the field of ontology carried
out by a student (undergraduate and graduate), post-doctoral fellow, or
junior faculty (within 5 years of appointment), who must be the first
author on
n Tue, May 13, 2014 at 7:54 AM, David Booth
> <*da...@dbooth.org*>
> wrote:
> I was at the HL7 meetings last week, and the idea arose of proposing an
> HL7 work group on RDF for Semantic Interoperability. I took the initiative
> to draft a possible charter. I meant to send it out earlier in case folks
> would like to discuss the idea on our 11:00am Eastern HCLS call today.
> Attached is what I've drafted. I'll join the call and see if anyone wants
> to discuss it. Sorry for the late notice.
>
> Zakim (W3C teleconference bridge).
> Dial-In #: *+1.617.761.6200* <%2B1.617.761.6200> (Cambridge, MA)
> VoIP address: *sip:za...@voip.w3.org*
> Participant Access Code: 4257 ("HCLS")
> IRC: *irc.w3.org* <http://irc.w3.org/> port 6665 channel #HCLS
>
> Thanks,
> David
>
>
--
Jim McCusker
Data Scientist
5AM Solutions
jmccus...@5amsolutions.com
http://5amsolutions.com
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu
http://tw.rpi.edu
Dear colleagues,
We have extended the deadline for accepting submission of scientific papers
for the ICBO 2014 Main Conference until *May 15, 2014*.
Please share the announcement.
Best,
Jim McCusker
(on behalf of the organizers
t; innovative semantic web technology with an end user practical focus
> and efficiency in use," explained SWC co-chairs Andreas Harth,
> Karlsruhe Institute of Technology and Sean Bechhofer, University of
> Manchester."
>
>
> Kind Regards,
> Helena
>
> --
>
That makes sense, then.
Jim
On Tue, Sep 10, 2013 at 11:11 AM, Alasdair J G Gray <
alasdair.g...@manchester.ac.uk> wrote:
> Hi Jim,
>
> On 10 Sep 2013, at 16:02, Jim McCusker wrote:
>
> I think Jerven's point is that it's unclear why having additional
> prop
t;> Alasdair
>>
>>
>>
>>
>> Dr Alasdair J G Gray
>> Research Associate
>> alasdair.g...@manchester.ac.uk
>>
>> http://www.cs.man.ac.uk/~graya/
>>
>> Please consider the environment before printing this email.
>>
>>
>>
Ugh, those don't look like they're likely to be linked data, but I guess
I'll go with it for now.
Thanks,
Jim
On Thu, Jul 25, 2013 at 7:11 PM, Joachim Baran wrote:
>
> On 2013-07-25, at 7:02 PM, Jim McCusker wrote:
>
> GO_REF != GO. I don't see anything
GO_REF != GO. I don't see anything in identifiers.org about GO_REF.
Jim
On Thu, Jul 25, 2013 at 6:25 PM, Joachim Baran wrote:
> Hi!
>
> On 2013-07-25, at 5:41 PM, Jim McCusker wrote:
>
> Does anyone know what the URI prefix is for GO_REF? And no,
> http://www.g
Does anyone know what the URI prefix is for GO_REF? And no,
http://www.geneontology.org/cgi-bin/references.cgi doesn't count. :-)
Thanks,
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-4436
, May 28, 2013 at 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
>
>
> On 05/28/2013 04:54 PM, Jim McCusker wr
=.
>> bioontology.org; path=/; HttpOnly
>> Content-Length: 93664
>> Status: 200
>> Vary: Accept-Encoding
>> Connection: close
>> Content-Type: text/html; charset=utf-8
>>
>>
>>
>> --
>>
>> Regards,
>>
>> Kingsley Idehen
>> Founder & CEO
>> OpenLink Software
>> Company Web: http://www.openlinksw.com
>> Personal Weblog:
>> http://www.openlinksw.com/**blog/~kidehen<http://www.openlinksw.com/blog/~kidehen>
>> Twitter/Identi.ca handle: @kidehen
>> Google+ Profile:
>> https://plus.google.com/**112399767740508618350/about<https://plus.google.com/112399767740508618350/about>
>> LinkedIn Profile:
>> http://www.linkedin.com/in/**kidehen<http://www.linkedin.com/in/kidehen>
>>
>>
>>
>>
>>
>>
>
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-4436
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu
http://tw.rpi.edu
es etc.
>
>
>
>
> Thanks.
>
> Regards,
> Amrapali Zaveri
>
> http://aksw.org/AmrapaliZaveri
>
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-4436
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu
http://tw.rpi.edu
)
http://tw.rpi.edu/web/doc/ProvenanceOfHighThroughputBiomedicalExperiments.
Thanks,
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-4436
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu
http://tw.rpi.edu
(Sorry about the empty reply to myself)
On Wed, Mar 27, 2013 at 8:30 PM, Jim McCusker wrote:
> On Wed, Mar 27, 2013 at 8:26 PM, Pat Hayes wrote:
>
>> That "option" is already available, if you use owl:sameAs correctly (and
>> do not confuse information about some
On Wed, Mar 27, 2013 at 8:30 PM, Jim McCusker wrote:
> On Wed, Mar 27, 2013 at 8:26 PM, Pat Hayes wrote:
>
>> That "option" is already available, if you use owl:sameAs correctly (and
>> do not confuse information about some thing with meta-information about
&
y owl:sameAs were used correctly...
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-4436
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
Thanks for alerting me to PROV.
>
> - Bob
>
>
>
> On Wed, Mar 27, 2013 at 3:42 PM, Jim McCusker wrote:
>
>> Which is why PROV exists. Now we have a floor to work from. I've already
>> integrated it into a number of projects.
>>
>> Jim
>>
interpretation.
>>
>> OTOH, it *is* useful to apply different intepretations to different
>> graphs,
>> and one reason is that you may be using those graphs for different
>> applications, each app in effect applying its own interpretation. But the
>> fac
der a
> single
> interpretation.
>
> The RDF Semantics spec only tells you how to compute the truth value of one
> pair at a time, but you can certainly apply it to
> as
> many pairs as you want -- in full conformance with
> the intent of the spec. This is the same as
"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 wrote:
>
> If you want to use a common context,
hing.
> Say we have a URI for a person, and to talk about this person when young
> and when old we use two different URIs. But than, when do we stop ? What if
> we have a URI per year ? Per day ? ...
>
> best,
> Andrea
>
> Il giorno 17/mar/2013, alle ore 04:34, Jim McCusker
have the same
>> URI as it does not *precisely *describe the same thing.****
>>
>> ** **
>>
>> Cordially,
>>
>> Erich
>>
>> ** **
>>
>> *From:* Jim McCusker [mailto:mcc...@rpi.edu]
>> *Sent:* Saturday, March 16, 2013 9:35 PM
>>
Booth wrote:
> Hi Jim,
>
>
> On 03/16/2013 12:37 PM, Jim McCusker wrote:
>
>> I'm not terribly interested in a Humpty Dumpty interpretation of the web
>> of data.
>>
>
> Well, you'd better get used to it, because that interpretation is s
assertions
>> in a different graph.
>>
>> I think this is a better strategy than using sameAs. There are a bunch
>> of problems with sameAs, not least of which is that often the assertions
>> are incorrect - they mean something different, Jim's post gives a strat
>
> Of course, it's possible to fiat-define as many modal predicates as you
> want, and to use them to navigate through the jungle; but not to
> automagically reason with them. Fiat predicates like (with domain
> e.g. foaf:Person and range e.g. trix:graph; thank you Jeremy) co
I see "A URI denotes only one resource" as a rule of the game that makes it
far more interesting than if we don't accept that rule. If I find that
someone is violating that rule, I'll kick them out of my game (exclude
their graph).
Jim
On Sat, Mar 16, 2013 at 12:37 PM,
rent graphs, and this can cause
> inconsistencies when graphs are merged, as illustrated in Figure 26:
> http://dbooth.org/2010/**ambiguity/paper.html#**inconsistent-merge<http://dbooth.org/2010/ambiguity/paper.html#inconsistent-merge>
>
> That is precisely why it is helpful to keep diff
gt;>>
>>>> The question is always about: do those URIs denote the same thing? Put
>>>> differently, do the two URIs have a common referent?
>>>>
>>>> ## Turtle ##
>>>>
>>>> <#i> owl:sameAs <#you>.
>>>
Indeed, it even frees you up to determine what semantics you need in that
context. A property chain is pretty simple to write...
Jim
On Fri, Mar 15, 2013 at 5:16 PM, Kingsley Idehen wrote:
> On 3/15/13 3:18 PM, Jim McCusker wrote:
>
> This is a useful solution, but doesn't addre
;> Umutcan
>>>>
>>>>
>>>> On 15-03-2013 19:38, Kingsley Idehen wrote:
>>>>
>>>>> On 3/15/13 1:05 PM, Umutcan ŞİMŞEK wrote:
>>>>>
>>>>>> My question is, does LODD use owl:sameAs properly? For instance,
t; >>
> >> That's a relation in the form of a 3-tuple based statement that carries
> entailment consequences for a reasoner that understand the relation
> semantics. Through some "context lenses" the statement above could be
> accurate, in others totally i
les and white papers is very much
> appreciated.
> Many thanks in advance,
> Susanna
>
> --
> Susanna-Assunta Sansone, PhDuk.linkedin.com/in/sasansone
>
> University of Oxford e-Research Centre
> Principal Investigator, Team Leader
> isacommons.org | biosharing.org
>
>
n error, please
> notify the sender immediately by reply e-mail and permanently delete this
> e-mail and any attachments without reading, forwarding or saving them.
> Thank you.
>
>
>
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of M
> ** **
>
> --
>
> Michel Dumontier
>
> Associate Professor of Bioinformatics, Carleton University
>
> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
> Group
>
> http://dumontierlab.com
>
--
Jim McCusker
Progr
ou are not the intended recipient of this
> e-mail, you are prohibited from sharing, copying, or otherwise using or
> disclosing its contents. If you have received this e-mail in error, please
> notify the sender immediately by reply e-mail and permanently delete this
> e-mail and a
Because if it does, then they are effectively equivalent.
Jim
On Wednesday, January 16, 2013, Peter Ansell wrote:
> On 17 January 2013 08:27, Jim McCusker wrote:
>> http://www.hpl.hp.com/techreports/2003/HPL-2003-235R1.html
>
> That algorithm doesn't seem very clean, as it
Peter Ansell wrote:
> On 17 January 2013 06:00, Jim McCusker wrote:
> > If you would like to validate that an RDF graph hasn't changed, you can
> > assert it's graph digest. Any new assertions would change the digest
> hash,
> > invalidating the asserted grap
;Mary is pregnant". It has to be qualified to a particular context
> > or time period, such as "On 1-Jan-2013 Mary's pregnancy test was
> > negative". (Sorry for such an obvious example, but hopefully you see
> > what I mean.)
> >
> > To my mind, monotonicity
uot;
> and "open world" as being more about what you *do* with the data, than
> being about the data itself. If the data is designed to be monotonic,
> then for specific uses you can use closed world reasoning.
>
> With all that said, I'm not certain that I'm really
3.org] *On Behalf Of *R. Cornet
> *Sent:* Wednesday, May 23, 2012 2:26 PM
> *To:* Michel Dumontier; Freimuth, Robert, Ph.D.
>
> *Cc:* Jim McCusker; Aaron Brown; Dan Brickley; Renato Iannella; Lin MD,
> Simon; Matthias Samwald; public-semweb-lifesci@w3.org
> *Subject:* RE: RDF Schema /
all its other siblings. I would be reluctant to do that blindly,
though, as it can often result in modeling errors. For instance, Physicians
are not the same thing as Patients, but a Patient can also be a Physician.
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale
ome, and my cell provider in Spain cut me off from high-speed
> cell access too, due to over-use... So I'm basically dial-up speed on my
> phone... And this little seen isn't great for exploring ontologies!)
>
>
>
>
> Jim McCusker wrote:
>>
>> A
n solution?
>
> Cheers all!
>
> M
>
>
>
> "M. Scott Marshall" wrote:
>>
>> We had an interesting discussion with Jim McCusker about Linked Data /
>> RDF representations of MAGE-TAB and some issues, such as choices of
>> predicates to make describe
l communication.
> Macmillan
> Publishers Limited Registered in England and Wales with registered number
> 785998
> Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS
>
>
>
--
Jim McCusker
Programmer Analyst
Krauthammer Lab
I've also used tools like x2x, x2vnc, and osx2x for a long time, but
they've never been quite as good.
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu
PhD Stu
ral Researcher
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Homepage: http://egonw.github.com/
>> LinkedIn: http://se.linkedin.com/in/egonw
>> Blog: http://chem-bla-ics.blogspot.com/
>> PubList: http://www.citeulike.o
t;
>>
>> Dr Jan Aerts
>> Assistant Professor
>> Faculty of Engineering - ESAT/SCD
>> Kasteelpark Arenberg 10 bus 2446
>> 3001 Leuven-Heverlee
>> Tel: +32 16 321053
>> Fax: +32 16 321970
>>
>
>
>
> --
>
#gid=0
If anyone wants to see the symposium agenda, it's here:
http://www.triconference.com/cloud-computing/
Thanks
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu
PhD S
t; with TMO as a use case :)
>
> m.
>
> PS: Jan 27 is the last day for early registration!
>
> --
> Michel Dumontier
> Associate Professor of Bioinformatics
> Carleton University
> http://dumontierlab.com
>
--
Jim McCusker
Programmer Analyst
And here's the link. :-)
http://www.w3.org/blog/SW/2012/01/11/feedback-welcome-an-overview-of-the-provenance-prov-family-of-specs/
On Wed, Jan 11, 2012 at 3:51 PM, Jim McCusker wrote:
> The Provenance WG has made significant progress on PROV, a family of
> specifications for proven
The Provenance WG has made significant progress on PROV, a family of
specifications for provenance on the web. Paul Groth has put up a blog post
to give an overview, and we'd like your feedback on what's been done so far.
Thanks,
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab,
ort 6665 channel #HCLS (see W3C IRC page for
>
> > details, or see Web IRC), Quick Start: Use
>
> > http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for
>
> > IRC access.
>
> > Duration: ~1 hour
>
> > Convener: Scott Marshall
>
c Ramakrishnan; Jodi Schneider; David Shotton; Kaitlin
>
> Thaney; Karin Verspoor; Lynette Hirschman; Susanna-Assunta Sansone;
>
> Kees van Bochove; Katy Wolstencroft; Jun Zhao; Taylor, Michael (ELS-
>
> OXF)
>
> Subject: SWAN-myExp-OBI-ISA
>
>
>
>
>
>
>> refining what we have. We focused on things we wanted to ask questions
>>> about explicitly based on a set of competency questions we had formed.
>>> It's not perfect but I'm of the school of release early, often, refine.
>>>
>>> Cheers,
>>
onvener: M. Scott Marshall
> Scribe: TBD
>
> Agenda
>
> Microarray, Expression RDF: Proceeding with the W3C note - All
> AOB
>
>
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-633
Message-
>> From: expression...@googlegroups.com
>> [mailto:expression...@googlegroups.com] On Behalf Of Jim McCusker
>> Sent: Monday, October 17, 2011 8:12 AM
>> To: expression...@googlegroups.com
>> Cc: HCLS
>> Subject: Re: BioRDF telcon today (1 hour later) 12PM ET / 6PM
idn't see any notice for one so i assumed not.
>>
>> cheers,
>> michael
>>
>>> -Original Message-
>>> From: expression...@googlegroups.com
>>> [mailto:expression...@googlegroups.com] On Behalf Of Jim McCusker
>>> Sent: Monday, October 1
> Duration: ~1 hour
> Convener: Scott Marshall
> Scribe: TBD
>
> [edit]Agenda
>
> Microarray, Expression RDF: Proceeding with the W3C note - All
> Integrating parts of JBI article into W3C note - Helena
> AOB
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Patho
han the second
> one.)
>
> ** **
>
> - Dave
>
> ** **
>
> ** **
>
> ** **
>
> ** **
>
> *From:* Hau, Dave (NIH/NCI) [E]
> *Sent:* Sunday, September 18, 2011 6:47 PM
> *To:* Kerstin Forsberg
>
> *Cc:* Jim McCusker; conor dowling; public-semweb-lifesci@w3.org
ed* by the XML serialization...
> though I am not in any way a "fan" of this bloated representation.
> Nevertheless, we're not creating a semantic web for Anglophones... we're
> creating it for the world! so... unless I am missing something obvious (and
> I may be!
nly a property
>> of the solution but i don't see how it is a datatype. in programming terms
>> i define a variable to be of a certain datatype:
>>
>>
>>
>> int count = 5
>>
>>
>>
>> what does it mean to say,
>>
>>
>>
>>
t; (molar,
> as in 10 M -> 10 Molar).
> http://en.wikipedia.org/wiki/Molar_concentration
>
> Cheers,
> --
> Helena F. Deus
> Post-Doctoral Researcher at DERI/NUIG
> http://lenadeus.info/
>
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale
centration from its other
building blocks:
http://idi.fundacionctic.org/muo/ucum-instances.html#term_unit_amount-of-substance_mole
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http://krauthammerlab.
that
>> identifier prior to the query, SNOMED is widely used.
>>>
>>> What is so special about semantic web identifiers that they don't need
>>> to
>> follow the same path?
>>
>> Andrea Splendiani
>> Senior Bioinformatics Scientist
>&g
is what MIAMI-like standards are needed for--are you
> actually just looking for a nomenclature to describe this? or do you need
> a metric to evaluate the underlying papers?
>
> cheers,
> michael
>
>> -Original Message-
>> From: Jim McCusker [mailto:james.mc
half Of Chris Baker
>> Sent: Wednesday, May 25, 2011 9:08 AM
>> To: Jim McCusker
>> Cc: w3c semweb HCLS
>> Subject: Re: Minimum information about a mutation
>>
>> Hi Jim,
>>
>> I do not know of a MIAME-like standard for protein mutation impacts.
>
Does anyone know of a MIAME-like standard for what should be included
in a dataset of amino acid-level mutations?
Thanks,
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http
opean Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Cambridge, CB10 1SD,
> United Kingdom
> Tel: + 44 (0) 1223 494 676
> Fax: + 44 (0) 1223 494 468
>
>
>
>
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.m
/or graphs (depending on
the API under discussion). Most of my use cases call for multiple
models, so I'd end up shying away from an API that did away with that.
:-)
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu |
wledge Data into Models
> Center for Cell Analysis and Modeling
> http://www.oliver.curiousworld.org
>
>
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu
et a feel for deployment and use of RDFa, both in the
> present and in our hopes/plans. Whatcha got?
> --
> -ericP
>
>
--
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http://kraut
g of HL7 and ISO 21090. We would
need to show how semweb solutions are a better solution, or how it is tied
too much to healthcare, leaving out life sciences, population science,
chemistry, etc. We don't yet have *a* solution for this, we have several.
:-)
Jim
--
Jim McCusker
Programmer Analys
nter Fax: +44(0)1865 610612
> 7 Keble Road, Oxford skype: susanna-a.sansone
> OX1 3QG, UK uk.linkedin.com/in/sasansone
> -
>
>
>
>
>
--
Jim
--
Jim McCusker
Programmer Analyst
Kr
Apologies for crossposting.
We are pleased to announce that registration for the Third
International Provenance and Annotation Workshop (IPAW2010) is now
available at https://www.cs.rpi.edu/ipaw2010/register.html. The
registration site also includes information to help travel plans.
Please note t
Apologies for cross-posting.
The 3rd International Provenance and Annotation Workshop (IPAW'2010)
Troy NY, USA, June 15-16, 2010
http://tw.rpi.edu/ipaw2010
IPAW 2010 Call for Late Breaking Contributions
http://tw.rpi.edu/portal/IPAW2010/cflbc
Overview
Interest in and need
ate the MGED ontology website hosted by
> sourceforge.net. Will try it later and send email if I made it. Sorry
> about it since I will take 2 week vacations from tomorrow.
>
> If you like, you can send me the terms you used and I can check whether
> they are in OBI.
>
>
> Th
the list to me
> or check OBI first and submit needed terms to OBI tracker items directly (
> http://sourceforge.net/tracker/?group_id=177891&atid=886178).
>
> I will post latest mapping file later today and let you know the link.
>
>
> Thanks,
>
> Jie
>
> Jim Mc
properties, please let me know. I can check whether it
> can map to any OBI one.
>
> Thanks,
>
> Jie
>
> Jim McCusker wrote:
>
>> Is this just classes, or are properties mapped as well?
>>
>> Jim
>>
>> On Wed, Mar 24, 2010 at 9:07 PM, >
MO, that came out of an
>>> MGED
>>> effort. OBI is to replace MO.
>>>
>>> cheers,
>>> michael
>>>
>>> Michael Miller
>>> Principal Software Developer
>>> www.teranode.com
>>>
>>>
>>> -Original M
/cgi.w3.org/member-bin/irc/irc.cgi>)
> * Duration: ~1 hour
> * Convener: Sudeshna Das
> * Notes: TDB
>
> [edit<http://esw.w3.org/index.php?title=HCLSIG/SWANSIOC/Meetings/2010-3-22_Conference_Call&action=edit§ion=2>]Proposed
> Agenda
>
> * Discourse+Data
health records (in the U.S.
>> >> 'meaningful use' is about to get nailed down) and they're made for
>> >> the web of data but all we have are soap bubbles, all a drift ...
>> > Is there going to be an RDF model based Linked Data View over this
>
om it, I don't gain the same
kind of state that would be encoded in the graph of the document. I'm
still convinced that there are semantics embedded in sub-symbolic
representations (by sub-symbolic, I simply mean a 1:1 connection
between entity/concept/whatever and the symbol/URI/triple for i
erproperties. The employer/hospital cannot prohibit someone else's
ignorance.
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Const
hrough, for
instance, knowing what actual entities the document refers to. Also, the
additional capabilities listed can provide some of that context on a sliding
scale, by providing that context.
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of M
l/http://espresso.med.yale.edu/~jpm78/tw/E-MEXP-986.rdfversus
http://linkeddata.uriburner.com/about/html/http://espresso.med.yale.edu/~jpm78/tw/E-MEXP-986-mod.rdf.
I can't figure out yet how to get rid of the anchor in the base URI using
Jena, but it seems that "#" should work a
e.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986.rdf
<http://linkeddata.uriburner.com/ode/?uri=http%3A%2F%2Fmagetab2rdf.googlecode.com%2Fsvn%2Ftrunk%2Fmagetab2magerdf%2Fexamples%2FE-MEXP-986.rdf>
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of
b2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986/E-MEXP-986.sdrf.txtas
the SDRF for that accession. Am I missing something?
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http://kraut
ty I can add to it that will tell your
linked data tools that that is the right place to start? I took a look at
the file through Longwell last night and was able to get it to load.
Thanks,
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
re that's the case. See below.
> does XML RDF allow referencing an element that is fully defined
> elsewhere? that would make things a lot clearer and concise.
>
We are already doing that. Take a look at the ProtocolApplication elements,
which do exactly that.
Thanks,
Jim
--
Jim Mc
and
I'm trying to keep second-guessing to a minimum. One thing I hope this tool
exposes is the effects of certain kinds of curation on the available data
structures, and maybe some best practices can come out of it.
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Y
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