it helps,
> -R
>
> On 10/02/2015 07:37 AM, Andrea Splendiani wrote:
>> Hi,
>>
>> I am wondering if some of you knows of some tool that can translate (a
>> subset) of SQL to SPARQL (perhaps requiring some constraints on the RDF
>> representation).
>
t;>>
>>> Mikel
>>>
>>> 2015-10-02 14:34 GMT+02:00 Richard Boyce :
>>>
>>>> Hi Andrea, I think that D2R Server is very helpful here:
>>>> http://d2rq.org/d2r-server
>>>>
>>>> All can be done with a mapping
:
>>
>>> Hi Andrea, I think that D2R Server is very helpful here:
>>> http://d2rq.org/d2r-server
>>>
>>> All can be done with a mapping file that you configure. The server
>>> provides a SPARQL web query interface (SNORQL) but also can dump to an
Hi,
I am wondering if some of you knows of some tool that can translate (a
subset) of SQL to SPARQL (perhaps requiring some constraints on the RDF
representation).
In principle it should be simple: classes can appear as tables, URIs as
IDs, datatype properties as columns and object properties as F
gh.
best,
Andrea
On Mon, Sep 22, 2014 at 4:26 PM, Stian Soiland-Reyes <
soiland-re...@cs.manchester.ac.uk> wrote:
> On 22 September 2014 14:19, Andrea Splendiani
> wrote:
> > ok, so it seems our representations are pretty much aligned, except for
> the
> > &q
land-Reyes <
soiland-re...@cs.manchester.ac.uk> wrote:
> On 22 September 2014 12:59, Andrea Splendiani
> wrote:
> > Ho,
> > a related question:
> > hasPreviousVersion: what does it have for domain/range ?
> > I would use this relations as a predicate on version
; I would reorder the URI as "http://eample/V2/P1234";. That way you
> make it
> >>> more explicit that you are talking about data set releases, each of
> which is
> >>> defined by its own URI prefix. That way you can have two P1234 residing
> >>>
ooluris/#cooluris
>>>>
>>>>
>>>> Martynas
>>>> graphityhq.com
>>>>
>>>> On Fri, Sep 19, 2014 at 7:14 PM, Joachim Baran
>>>> wrote:
>>>>> Hi!
>>>>>
>>>>> I woul
ix. That way you can have two P1234 residing
>>> side-by-side even though they might be completely different.
>>>
>>> Should the version always be part of an URI? I would say yes -- despite
>>> seeing your argumentation about the temporal interpretation of URIs
Hi,
I knows how nanopubs work.
Let's say the closer thing I can find to what I need is git, just with a
different id policy.
best,
Andrea
Il giorno 21/set/2014, alle ore 22:00, Michel Dumontier
ha scritto:
> Hi Andrea,
> The nanopublication schema is a general mechanism to associate some
> pr
m.
>
> On Fri, Sep 19, 2014 at 9:58 AM, Joachim Baran
> wrote:
>> Hi!
>>
>> On 19 September 2014 09:45, Andrea Splendiani
>> wrote:
>>>
>>> When a concept change meaning, it changes id ;)
>>
>> Aha! I think it might not always change ID! ;)
>>
>> Best wishes,
>>
>> Kim
knowledge to populate.
>
> Does that make sense?
>
> Best wishes,
>
> Kim
>
> On 19 September 2014 09:31, Andrea Splendiani
> wrote:
>
>> Hi, I don't think that would work in general.
>> One of the issues that I have is that, in general, I don'
letely different.
>
> Should the version always be part of an URI? I would say yes -- despite
> seeing your argumentation about the temporal interpretation of URIs that
> you gave.
>
> Kim
>
> On 19 September 2014 08:38, Andrea Splendiani
> wrote:
>
>> Hi,
>
Hi,
I'm posting here a question I have posted in some other forums.
How do you go about versioning ?
I tend to think at the URI as pointing to the endurant, and this
leaves to the "version" the meaning of "what was known/true about an
entity at a given time". The latter is conveniently packed in
ave a problem at
> all. ;)
>
> - Matthias
>
>
> Am 04.08.2014 14:16, schrieb Andrea Splendiani:
>
> Hi,
> I didn't see the BioHackathon ML message. I have just realised my mail
> setup is a bit messed up...
> TrOWL I have tried, but I have the impression it do
e:
> http://vip.cs.man.ac.uk:8080/live.html
>
> I have not worked with HPO yet, so those are just some general
> recommendations.
>
> Best,
> Matthias
>
>
>
> Am 04.08.2014 13:53, schrieb Andrea Splendiani:
>
> Hi all,
>>
>> I have stumbled on
I have waited
for days but we are under 1%).
Does anybody have experience in classifying it ?
If classification is unfeasible, than which use cases does the OWL
representation cater to?
best,
Andrea Splendiani
Hi all,
I am in contact with a startup that is building a semantic knowledge base for
nutrition using semantic web technologies.
They may be looking for somebody to take the lead on the knowledge base
construction. They are based in London, UK.
If somebody is interested, please send me an email
roject, for linked data it
> has the benefit of not being to simple that scientific results be linked to
> it. One of the member communities that participated in the development of OBI
> represented the Nutrigenomics community.
>
> References:
>
> scalar measurement datum
> mass measurement datum
> has measurement unit label
> is quality measurement of
> has measurement value
> mass
> mass unit
>
> Modeling biomedical experimental processes with OBI
> http://purl.obolibrary.org/obo/obi.owl
> http://purl.obolibrary.org/obo/iao.owl
> http://obi-ontology.org
> http://obi-ontology.org/page/Consortium
>
> Regards,
> Alan
>
> ps. have you always worn glasses?
>
> >
> > Any hints/opinions ?
> >
> > best,
> > Andrea Splendiani
> >
> >
> >
k it is not
appropriate. having 10g of salt is not the same has saying "ha person has one
and only one head". If it was 11g, it would not change the entity type, really.
Plus not all numbers are integer.
Any hints/opinions ?
best,
Andrea Splendiani
conditions.
best,
Andrea
Il giorno 31/ago/2013, alle ore 15:24, Carole Goble
ha scritto:
> Did you try
> Http://www.openphacts.org
>
> Carole
>
> Sent from my iPhone
>
> On 31 Aug 2013, at 16:03, "Andrea Splendiani"
> wrote:
>
>> Hi,
>>
ch/ResearchAreas/Pharmacogenetics/ucm083378.htm
>
> 2. http://www.w3.org/wiki/HCLSIG/LODD/Data
>
>
>
> On 08/30/2013 07:40 AM, Andrea Splendiani wrote:
>> Hi all,
>>
>> I was looking for a few datasets to download in RDF (Mesh, Drugbank...), but
>>
Hi,
I know Bio2RDF, but I was looking at other resources as well.
For instance I think I have seen at some point some version of Mesh in SKOS,
but I cannot find an active link. In general, I was wondering whether there was
a list of available resources (Bio2RDF and not) which is kept up2date.
b
Hi all,
I was looking for a few datasets to download in RDF (Mesh, Drugbank...), but
when I google for it, I get a lot of indexes/resources (Data.io, w3c wiki,
ckan,...) with broken links.
Is there a directory which is known to be up2date ?
best,
Andrea
012/05/semantic-models-for-cdisc-based.html
>
> Best,
> Kathrin
>
>
>
> Op 7/15/13 1:34 AM, Andrea Splendiani schreef:
>> Hi,
>>
>> I was wondering if somebody could provide some pointer to work going on in
>> an area that is related to clinical trial
el of detail required
"usually" required by clinical trials). The subject itself can be very vast,
but is there a framework which provides at least an upper perspective on how to
model subjects's features, diseases, interventions, samples (also respect to
time) ?
Any pointer is we
Hi all,
sorry for following this a bit lightly.
If you have multiple validation patterns in a dataset you need to be able to
specify what applies to what, otherwise is too weak.
Perhaps it makes more sense to see the problem from the opposite point of view:
This dataset has the URI collection un
Il giorno 29/mag/2013, alle ore 01:27, Alan Ruttenberg
ha scritto:
>
>
> On Tuesday, May 28, 2013, Andrea Splendiani wrote:
> HI,
>
> perhaps a key makes easier to track usage for someone with whom you have
> established a contract (so servers/IPs may vary, but the &qu
HI,
perhaps a key makes easier to track usage for someone with whom you have
established a contract (so servers/IPs may vary, but the "key" recorded is the
same).
I think it's an easy mechanism to pick up: if you want to maximize users...
this is what any web-developer will do without thinking.
Regrets, last minute issues :(
I'll check the docs!
best,
Andrea
Il giorno 12/mag/2013, alle ore 23:24, Health Care Life Sciences
ha scritto:
>
> This event has been changed.
> more details »
> Linked Life Data
> Changed: This meeting will be held using fuze: please join at
> http://fuze.me/
Hi,
Good point.
I personally find strange to deal with sequences in RDF.
On one side, a sequence is a perfect identifier of itself (once if we factor
out experimental errors).
However, identity of sequences doesn't matter much (similarity of sequences is
what counts). So we could have perfect id
Uhm...
I have the impression that is "precisely" identifying something is the issue...
as at the end the point is: "precisely the same according to which criteria?".
We could given get theoretical and argue that you cannot measure the same thing
twice... but that's another story.
I'm confused a
HI,
From what you say, it looks more as if the apple is the same, but perspective
on the apple are different. So same URI and different graphs seem a more clean
approach.
Using different URIs works as well in practice. But I'm a bit confused on how
you make the generalization step. Who is sayin
Interesting discussion,
I would just add a bit (if it was not added in this long email series):
perhaps it is viable to assert owl:sameAs between individuals.
If you identify a person by passport number or tax number, you can collapse all
statements about the two pretty safely (assuming you cons
No Derivative Works — You may not alter, transform, or build upon this work.
Doesn't sound like building on the shoulders of giants, doesn't it?
But the question is: does it refer to an information artifact (e.g. an image)
or its content?
Best,
Andrea
Apologies for typos, Sent from an iPhone
Hi,
RDF/Triplestores and Neo4J can both be used as technologies to represent graph
structures (like p-p interactions). Neo4J may offer a slightly more natural
representation of edge attributes for some, but otherwise they both can "hold
graphs".
Than they are different tools.
If you go for quer
Hi,
Just a quick comment. We used to have a Semantic Web / BioPAX workgroup, which
probably partially overlaps with the intentions of the W3C Sys Bio Group. The
workgroup has been stale for a while, essentially because of a lack of time
from who was supposed to organize it... but we just had so
Dear all,
The National Resource for Network Biology has put together an exciting list
of ideas for google summer of code projects, a few of which are
semantic-web-oriented (http://nrnb.org/gsoc/); We will be co-mentoring Idea
#5 on Visualizing Semantic Data Landscapes using Cytoscape
(http://pinsc
Hi,
probably there is not much difference. But with Semantic Web data, insight into
the structure of data is more of a key, as you don't have "schemas".
If I query a database, I would look at tables to understand a structure. If I
look a at a Semantic Web knowledge base, perhaps visualization is
i know have
> built strong support and applications. elsevier and deri were sponsors
> also.
>
> cheers,
> michael
>
> Michael Miller
> Software Engineer
> Institute for Systems Biology
>
> [1]: http://semtech2011.semanticweb.com/
>
>
>
mantic web technology,
but bear in mind that Watson is more a cleaver example of NLP.
An interesting question, how to make the case for semantic web technology.
On Thu, Dec 22, 2011 at 4:09 PM, Andrea Splendiani (RRes-Roth)
mailto:andrea.splendi...@rothamsted.ac.uk>>
wrote:
Hi Oliver
hing
> more formal.
>
> Best,
>
> - Anita.
>
> Anita de Waard
> Disruptive Technologies Director, Elsevier Labs
> http://elsatglabs.com/labs/anita/
> a.dewa...@elsevier.com
>
>
>
> -Original Message-
> From: Andrea Splendiani (RRes-Roth)
>
Hi Oliver,
I think it's hard to find this form of "breakthrough evidence" and this may
even be counterproductive to convince people.
If you present a high-level, breakthrough result (say, we save lives), than you
leave two open questions:
- how much of this is dependent on the computational supp
#x27;data integration' and the rest is a bit fuzzy, however, in a first
approximation, which is the size of the problem that the Semantic Web is
trying to tackle ?
Obviously, I would be interested in the Life Sciences and Health Care
context.
best,
Andrea Splendiani
Andrea Splendiani
Se
n in a Semantic Web forum. Save
>>> your energies for more productive discussions, such as how to reconcile the
>>> Palestine/Israel conflict.
>>>
>>> Pat Hayes
>>>
>> --
>> Chime Ogbuji
>> Sent with Sparrow
>>
>
>
> IHMC (850)434 8903 or (650)494 3973
> 40 South Alcaniz St. (850)202 4416 office
> Pensacola(850)202 4440 fax
> FL 32502 (850)291 0667 mobile
> phayesAT-SIGNihmc.us http://www.ihmc.us/users/phayes
>
>
>
>
>
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendi...@bbsrc.ac.uk
gt;> Il giorno 21/giu/2011, alle ore 18.46, Helena Deus ha scritto:
>>
>>> Other standards (outside of semantic web) saw the need to rely on
>>> numeric
>> identifiers, even if that created a burden for their users
>>> e.g. in SNOMED Lung = T-28000
>>&g
ery SNOMED with "all the diseases that affect
T-28000".
> But the fact is that despite the inconvenience of having to fetch 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 s
useable APIs/UIs for people.
>
> Best,
>
> m.
>
>
>
>> -Original Message-
>> From: public-semweb-lifesci-requ...@w3.org [mailto:public-semweb-lifesci-
>> requ...@w3.org] On Behalf Of Sivaram Arabandi, MD
>> Sent: Monday, June 20, 2011 6:14 PM
>&g
> m.
>
> From: public-semweb-lifesci-requ...@w3.org
> [mailto:public-semweb-lifesci-requ...@w3.org] On Behalf Of Sivaram Arabandi,
> MD
> Sent: Monday, June 20, 2011 3:56 PM
> To: Chime Ogbuji
> Cc: Andrea Splendiani; Vagnoni,Matthew M; James Malone; HCLS
> Subject:
nsumers of the nuances that make one scenario
more of an issue than another is much more appropriate.
> General observation: This seems like another neat v.s. scruffy thread and
there seem to be many of these playing out in the various semantic web
communities at this time. http-range-14 v.s. ontology-determined meaning of
resources, dereferencability of RDF URIs, etc.
>
> --
> Chime Ogbuji
> Sent with Sparrow
>
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendi...@bbsrc.ac.uk
veryone" speaks English, then which flavour of English
should the names be in? American english or british english? Trash or
Rubbish? ;-)
>
> --
> Helena F. Deus
> Post-Doctoral Researcher at DERI/NUIG
> http://lenadeus.info/
>
Andrea Splendiani
Senior Bioinformatics Scie
gt; On Mon, 20 Jun 2011 12:08:43 -0700, Andrea Splendiani
> wrote:
>
>
>> - in a continuum between web and semantic web, perhaps IDs are not only
>> intended to be 'understood' by machines.
>>
>> Again, I understand the reason for them. But is it worth the r
p ?o
> WHERE {:MRN ?p ?o}
>
> Or they can quickly jump to that concept by referring to the URI. In
TopBraid Composer there is a text box where you can put a URI in and it will
automatically jump to that resource.
>
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendi...@bbsrc.ac.uk
• Posters and demo submission deadline: 31 October 2011
• Communication of acceptance: 7 November 2011
• Camera ready: 21 November 2011
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
note to i...@swat4ls.org, possibly within this or
the next week. We only need a couple of lines on the topic, intended audience
and time needed at this stage.
best,
Andrea Splendiani
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 76313
d, and makes it easier for us to live our academic lives in
> peace :-) (and easier to get money from research-funding agencies)
>
> Mark
>
>
>
>
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendi...@bbsrc.ac.uk
d, and makes it easier for us to live our academic lives in
> peace :-) (and easier to get money from research-funding agencies)
>
> Mark
>
>
>
>
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendi...@bbsrc.ac.uk
x27;s precisely one
of the lines we are trying to open here at OEG-UPM.
>
> Cheers
>
>
> On og., 2011.eko mairen 26a 15:08, Andrea Splendiani wrote:
> Hi,
>
> I see myself as more involved in the next incarnation of the charter ;)
> Unfortunately, today is a travel d
S")
> IRC Channel: irc.w3.org port 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: Eric Prud'hommeaux
> Scribe: TBD
>
> HCLS IG charter/strategy discussion
> --
> -ericP
>
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendi...@bbsrc.ac.uk
o-chair, http://www.w3.org/blog/hcls
> http://staff.science.uva.nl/~marshall
>
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendi...@bbsrc.ac.uk
se (or for endpoint itself if this holds information which is
"coherent" source-wise):
- update frequency
- last update
- data source (type and in case link).
Does anybody have this already ? Opinions ?
best,
Andrea
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematic
Hi,
quick question:
Is anybody aware of PlexDB (plexdb.org) in RDF, or of some ongoing work in
this direction ?
best,
Andrea Splendiani
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendi...@bbsrc.ac.uk
days of associated
> hackathon and tutorials.
>
> Full details on the workshop can be found at: http://swat4ls.org/2010/
>
> --
> M. Scott Marshall, W3C HCLS IG co-chair
> Leiden University Medical Center / University of Amsterdam
> http://staff.science.uva.nl/~marshall
>
A
hackathon and tutorials.
Full details on the workshop can be found at: http://swat4ls.org/2010/
Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendi...@bbsrc.ac.uk
, University of
Amsterdam, The Netherlands
• Andrea Splendiani, Biomathematics and Bioinformatics dept., Rothamsted
Research, UK
Scientific Program committee (more to be confirmed):
• Erick Antezana, Bayer CropScience, Ghent, Belgium
• Pedro Barahona, Department of
Hi,
did anybody have success in installing 4store with some large dataset (like
Uniprot) on it ?
i'm having a range of problems with "big files" (say, more than 4Gb). Mostly
probably coming up from some interaction with the file system or avahi.
ciao,
Andrea
---
Andrea Sp
ing to join the gatherings.
I've added a presentation to the w3c wiki (http://esw.w3.org/Andrea_Splendiani).
ciao,
Andrea
---
Andrea Splendiani
Senior Bioinformatics Scientist
Rothamsted Research, Harpenden, UK
andrea.splendi...@bbsrc.ac.uk
+44(0)1582 763133 ext 2004
Sorry, what's the AAA principle ?
It seems to me ignoring is not a problem. In case, thinking that you don't
ignore anything is against the SemWeb framework.
Ciao,
Andrea
-Original Message-
From: public-semweb-lifesci-requ...@w3.org
[mailto:public-semweb-lifesci-requ...@w3.org] On Beha
Hi,
What is "meaning" for you ?
For what comes to my mind, either you consider an explicit set of statements,
and then this device will be pointless. Or you consider something that carries
some information, and this rule out almost only white noise.
What do you have in mind ?
Ciao,
Andrea
DF/OWL graphs. That is to say, maybe I'm wrong and
> semantics doesn't even come into existence when somebody attributes an
> RDF/XML graph to a document; but rather it only comes into existence when
> somebody queries across (possibly) many graphs of many different pe
y, a Knowledge Management System for the support of
the European Dendritic Cell Immunology Community
Marco Brandizi, Michaela Gündel, Ciro Scognamiglio and Andrea
Splendiani.
Panel discussion:
Theme: TBD
Plus poster sessions (authors of posters are not listed in this call,
but will be liste
I'm afraid I won't be able to attend in person.
If there is a chance for a skype/phone connection, I would be
interested in participating.
best,
Andrea Splendiani
On 20 Oct 2009, at 23:02, Susie Stephens wrote:
As the Bio-Ontologies SIG at ISMB has been running for 11 years,
it
On Oct 20, 2009, at 1:10 PM, Phillip Lord wrote:
It somewhat overlaps with bio-ontologies, though. If people are
keen to
do this, I'd suggest talking to the bio-ontologies organisers
(Nigam is
best point of contact) to see whether something can be done in
common.
Phil
Andrea Splen
The CFP is largely the same as last year's; I expect that it will
be updated in a few days to include the names of the committee
members. The submission deadline is Dec 1st.
I look forward to another great collection of SIG meetings! Thanks,
Hershel
--
Hershel Safer
e: hsa...@alum.mi
nice to
have a citation to convince others, too. Do you know any?
Thanks!
Take care
Oliver
---
Andrea Splendiani
Senior Bioinformatics Scientist
Rothamsted Research, Harpenden, UK
andrea.splendi...@bbsrc.ac.uk
+44(0)1582 763133 ext 2004
I was wondering who was attending and if something was organized.
best,
Andrea Splendiani
---
Andrea Splendiani
Senior Bioinformatics Scientist
Rothamsted Research, Harpenden, UK
andrea.splendi...@bbsrc.ac.uk
+44(0)1582 763133 ext 2004
, Scotland, United Kingdom
* Adrian Paschke, Corporate Semantic Web, Freie Universitaet
Berlin, Germany
* Paolo Romano, Bioinformatics, National Cancer Research
Institute, Genova, Italy
* Andrea Splendiani, Biomathematics and Bioinformatics dept.,
Rothamsted Research, UK
***More
, Freie Universitaet
Berlin, Germany
* Paolo Romano, Bioinformatics, National Cancer Research
Institute, Genova, Italy
* Andrea Splendiani, Biomathematics and Bioinformatics dept.,
Rothamsted Research, UK
***More information
* http://www.swat4ls.org/2009/
* http://swat4ls.blogspot.com
behalf of Alan
Ruttenberg
Sent: Mon 6/22/2009 18:24
To: Matthias Samwald
Cc: Hilmar Lapp; eric neumann; Andrea Splendiani; w3c semweb HCLS
Subject: Re: Any meeting at ISMB ?
Should work for me. Skype/email is best for details as we get
closer.-Alan
On Mon, Jun 22, 2009 at 9:43 AM, Matthias S
Looks good to me...
Ciao,
Andrea
-Original Message-
From: Matthias Samwald [mailto:samw...@gmx.at]
Sent: 22 June 2009 14:44
To: Alan Ruttenberg; Hilmar Lapp
Cc: eric neumann; andrea splendiani (RRes-Roth); w3c semweb HCLS
Subject: Re: Any meeting at ISMB ?
If there is still interest in
at are not registered
for the main ISMB conference? I, for example, have only registered
for a SIG meeting (and will already fly back in the afternoon of
June 30).
Cheers,
Matthias
From: eric neumann
Sent: Thursday, June 18, 2009 5:04 PM
To: Andrea Splendiani
Cc: w3c semweb HCLS
Subjec
Hi,
I was wondering is somebody on this list was planning to held some
formal/informal meeting at ISMB/ECCB. Perhaps a BOF ?
ciao,
Andrea
---
Andrea Splendiani
Senior Bioinformatics Scientist
Rothamsted Research, Harpenden, UK
andrea.splendi...@bbsrc.ac.uk
+44(0)1582 763133 ext 2004
l giorno 02/mar/09, alle ore 22:43, Xiaoshu Wang ha scritto:
Andrea Splendiani wrote:
One thing that I think would be very useful, though it poses some
semantic problem... is the possibility to assert equivalence in rdf.
At the moment equivalence can be asserted only in owl (and this
implie
g/NIF/BiomaterialEntities/NIF-Organism.owl
See also:
https://wiki.neuinfo.org/xwiki/bin/view/Main/NIFSTDoverview
http://neuinfo.org
On Feb 25, 2009, at 4:17 PM, andrea splendiani (RRes-Roth) wrote:
Thanks!
It'2 240M, but compressed is only 9.
I wonder whether there is some architecture to tra
I guess this could be a good idea for ontology providers...
ciao,
Andrea
Il giorno 26/feb/09, alle ore 05:38, Lee Feigenbaum ha scritto:
andrea splendiani (RRes-Roth) wrote:
Thanks!
It'2 240M, but compressed is only 9. I wonder whether there is some
architecture to transparently tra
critto:
On Feb 25, 2009, at 4:17 PM, andrea splendiani (RRes-Roth) wrote:
Thanks!
It'2 240M, but compressed is only 9.
I wonder whether there is some architecture to transparently transfer
compressed ontologies...
well the obo file is a bit more compact, and the source NCBI file is
post I wrote an extension for arq/sparql returning all the descendants
of a given organism. The data were stored in mysql.
Pierre Lindenbaum
- Message d'origine
De : Andrea Splendiani
À : public-semweb-lifesci hcls
Envoyé le : Mercredi, 25 Février 2009, 20h58mn 55s
Objet : Is ther
Thanks. I've been looking for it, but I was not sure the Taxonomy was
inside... and I was trying with different URIs...
Ciao,
Andrea
-Original Message-
From: Melanie Courtot [mailto:mcour...@gmail.com]
Sent: 25 February 2009 20:29
To: andrea splendiani (RRes-Roth)
Cc: public-s
Thanks!
It'2 240M, but compressed is only 9.
I wonder whether there is some architecture to transparently transfer
compressed ontologies...
Ciao,
Andrea
-Original Message-
From: Chris Mungall [mailto:c...@berkeleybop.org]
Sent: 25 February 2009 20:53
To: andrea splendiani (RRes
ere.
Ciao,
Andrea
-Original Message-
From: Erick Antezana [mailto:er...@psb.ugent.be]
Sent: 25 February 2009 20:51
To: andrea splendiani (RRes-Roth)
Cc: public-semweb-lifesci hcls; Vladimir Mironov; Martin Kuiper
Subject: Re: Is there an NCBI taxonomy in OWL ?
Hi Andrea,
you can fi
t the representation itself.
Does anybody have some hint about where I can fin an OWL version ? Or
even an RDF version ? Even better would a sparql endpoint containing
it...
best,
Andrea Splendiani
s ?
Or is this some area that you think needs more exploration ?
It seems to me that to the question "why did you use this
triplestore ?", the usual answer is "I'e tried a few and this worked".
best,
Andrea Splendiani
ualization tool for ontologies. It also
offers an interactive ontology browsing function (the rdf network can
be interactively expanded) and the possibility to define query as
graph patterns (visually).
best,
Andrea Splendiani
[1] http://www.bioinformatics.org/rdfscape/
[2] http://www.cyt
I have to agree that almost all the semantic websites I've seen, with
huge list of triples, look at best discouraging, at worst impenetrable.
But for a core set of lenses you require some standard, no ?
Do you have some specific use-cases to begin with ?
best,
Andrea
Il giorno 11/ott/07, alle
first.
On Sep 20, 2007, at 10:41 AM, Andrea Splendiani wrote:
my 0.001 cents,
If you look at the other sessions, there's nothing so
technologically oriented. And there's already a session on
ontologies.
Maybe a SIG ? (that by the way seem to be more interesting) with
a foc
onal touch).
Andrea
-------
Andrea Splendiani
post-doc, bootstrep project (www.bootstrep.eu)
UPRES-EA 3888 - Laboratoire d'Informatique Médicale
CHU de Pontchaillou
2, rue Henri Le Guilloux
35033 Rennes - France
Tel : +33 2 99 28 92 45 / +33 2 99 28 42 15 (secr.)
Fax : +33 2 99 28 41 60
Il giorno 10/set/07, alle ore 13:48, Xiaoshu Wang ha scritto:
Andrea Splendiani wrote:
The reason, I guess, that "biopax:AUTHORS", is developed is
because the bioPAX people wants it to be a "format" rather making
it a knowledge.
No... just DC was not so widespread and kno
This is not the point. The idea is that a user of a URIs should
accept a commitment to a shared conceptualizazion.
And strictly speaking... information such as authors don't need to be
"in the ontology"... meaning... are we going to define classes in the
real world depending on authors ? (h
uded... uso of GO terms was) and
properly define the role of ontology, format and so on.
By the way, you may note that a "pathway exchange" language with
"pathway" beining something as metabolic/signalling/interaction...
was clearly a underestimation of the task.
Some of th
thway
names. For this, other reosurces are more appropriate.
A proper pathway reconciliation based on biopax (reconciliation
doens't need to end in sameAs...) should make use of the structure of
pathways (reactions, elements, order...) more than lexical properties
anmd testual description
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