Matthias, Michael,
I think this is a great idea and I would really like to see some
connections emerge between the HCLS web of data and the LOD web of
data. If I can be of any help with some LOD and DBpedia expertise,
just let me know.
Cheers,
Richard
On 15 Feb 2008, at 13:44, Matthias
I added yet another item to the BioRDF Brainstorming document [1]. Here is
the text that can also be found and edited on the Wiki page:
___HCLS KB mapping to the open linked data repositories___
It would be great if two of the largest coherent Semantic Web structures,
namely the HCLS Knowle
I'd agree - I suspect that simply matching terms doesn't help that much
- we'd need to know the context of it, but then it all gets very sticky.
There is some work on mining the Chemistry literature from Cambridge
(UK) - using ? OSCAR/ Sci-ML I think
We've done a little work in the clin
Alan Ruttenberg wrote:
On Feb 12, 2008, at 3:58 PM, Kei Cheung wrote:
Hi Olivier, Alan, et al,
A prototype version of our neuroscience semantic web portal is
accessible at: http://neuroweb3.med.yale.edu
Nice :)
Thanks :-) . There is still a lot of room for improvement.
Bear in mind,
On Feb 12, 2008, at 8:31 PM, Alan Ruttenberg wrote:
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
On Feb 12, 2008, at 3:58 PM, Kei Cheung wrote:
Hi Olivier, Alan, et al,
A prototype version of our neuroscience semantic web portal is
accessible at: http://neuroweb3.med.yale.edu
Nice :)
Bear in mind, this is a working prototype for proof of concept and
it is still under active develo
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
On Feb 12, 2008, at 11:07 PM, Ernest wrote:
Sorry this is probably obvious to everyone but for the query below,
where can we run it? or what can we run it against? I think Kei and
I are unclear if there is a sparql endpoint that we can use or is
there an owl file containing all this data
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
> I also think that the machine-readable representation of facts about
> biology
> should have a higher priortiy than the description of experimental
setups
> and procedures (which is the major goal of OBI and EXPO). People only
have
> limited time and motivation to create machine-readable annotat
> In what I see as the ideal scenario, each text/database entry would
only
> be annotated with the results
OK.
So what we would need is
(1) a tool for getting authors to indicate which bits of the article
actually are their results, and
(2) a way of representing this in RDF. I suppose we're goi
Olivier Bodenreider wrote:
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?
Yes for the
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?
Yes for the dataset we created (has_unique_g
Hi Olivier, Alan, et al,
A prototype version of our neuroscience semantic web portal is
accessible at: http://neuroweb3.med.yale.edu
Bear in mind, this is a working prototype for proof of concept and it is
still under active development. The Web interface has 3 panels: search
panel (on top)
I'd agree that to capture all the publication might be hard, but to only
capture this bit (I suspect the conclusion) wouldn't you need to find the
conclusion, and ignore the rest? Using the abstract only might help, but
not enoughin any case, there are other bits (e.g. which type of
banan
On a broader brainstorming note, it would be nice to have a way of
specifying that a certain dc:Agent thinks that one is a better
annotation than the other also, with the user deciding to trust
certain Agents to give them useful knowledge, or inversely, to not
trust specific Agents who they fi
Dear All,
Just a note on this:
For example, article pmid:123 contains the text
>> "We found that bananas are yellow. This is in conflict with article
>> pmid:456, which states that bananas are pink".
>>
>> Article pmid:123 should only be annotated with
>> "banana has_quality yellow .
>> pmid:12
On 12/02/2008, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>
> > Good point. What I was sort of driving at (and failing) was the context
> > in which the facts are mentioned---are they the aim of the paper,
> > background information, mentioned as results and so forth?
>
> In what I see as the i
> Good point. What I was sort of driving at (and failing) was the context
> in which the facts are mentioned---are they the aim of the paper,
> background information, mentioned as results and so forth?
In what I see as the ideal scenario, each text/database entry would only be
annotated with
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
17 AM
To: Matthias Samwald
Cc: Susie M Stephens; public-semweb-lifesci@w3.org; Holger Stenzhorn
Subject: Re: BioRDF Brainstorming
I cannot make today's call, but I think it essential for any BioRDF
project to consider how to include currently used terminologies such
as those from UM
eric neumann wrote:
I cannot make today's call, but I think it essential for any BioRDF
project to consider how to include currently used terminologies such
as those from UMLS.
I don't know if Olivier Bodenreider has been on any of the calls
recently, but his proposed offer to mint uris fr
Colin Batchelor wrote:
Surely this is better suited to OBI-type annotations than generic OBO
things?
Please describe further how "OBI-type" differs from "OBO-type". OBI is part
of OBO.
Do you mean quantitative information, such as detailed numerical results of
experiments?
OBI-type annota
I cannot make today's call, but I think it essential for any BioRDF
project to consider how to include currently used terminologies such as
those from UMLS.
I don't know if Olivier Bodenreider has been on any of the calls recently,
but his proposed offer to mint uris from CUI (UMLS, MeSH, etc) is s
I have also added several ideas to the wiki page [1]:
* OBO Structured Digital Abstracts
* SIOC for Science
* OntoWiki and Semantic MediaWiki
* HCLS KB Decentralisation
* Define a simplified OWL-to-RDF mapping for a subset of OWL
Cheers,
Matthias Samwald
Semantic Web Company / DERI Galway / Yal
Hi Susie et al.,
Since SenseLab’s Semantic Web development has been a part of the HCLS
activities, I would like to suggest its new development as part of the
future HCLS activities. One suggestion is the extension of “Entrez
Neuron” to become a Semantic Web portal for mashing up neuroscientif
26 matches
Mail list logo
