, Matthias Samwald wrote:
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
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
Matt Williams writes:
> I'll try and find a paper on the "p-modals" (possible, probable, etc.)
> and ways of combining them tomorrow and put a paragraph on the wiki.
The SEP has something here:
http://plato.stanford.edu/entries/logic-modal/
Colin.
DISCLAIMER:
This communication (including any
On Feb 14, 2008, at 3:36 AM, [EMAIL PROTECTED] wrote:
As for rdf formats and OWL descriptions, I shall have to leave
that to others - I still haven't grokked Alan's banana class
definition yet.
:)
I will follow up with a better explanation given Chris, and now your
complaints.
-Alan
t;
Cc:Matt Williams <[EMAIL PROTECTED]>, Alan Ruttenberg <[EMAIL
PROTECTED]>, public-semweb-lifesci hcls
Subject: Re: Trust in statements (still is BioRDF Brainstorming)
On Feb 13, 2008, at 2:14 PM, M. Scott Marshall wrote:
>
> Dear Matt,
>
> I see '
HI Chris --
You wrote...
I think the only option here is to embrace rdf-reification (and to push for
better syntax, query and tool support).
Would the approach in question 8 of
www.reengineeringllc.com/demo_agents/RDFQueryLangComparison1.agent
be useful ?
We map such queries automatically
On Feb 13, 2008, at 2:14 PM, M. Scott Marshall wrote:
Dear Matt,
I see 'trust' as a 'view' that can be produced by running a filter
over
the data (provenance). The filter would implement my trust policy, or
one of them. In other words, my trust in a given 'agent' can be due to
the fact th
Dear Matt,
I see 'trust' as a 'view' that can be produced by running a filter over
the data (provenance). The filter would implement my trust policy, or
one of them. In other words, my trust in a given 'agent' can be due to
the fact that it produces data using a certain algorithm. I also place a
Dear Alan,
Thank you for making my point much more clearly than I managed. I'm a
little wary of probabilities in situations like the one you describe, as
it always seems a little hard to pin down what is meant by them. At
least with the symbolic approach, you can give a short paragraph saying
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'm personally fond of the symbolic approach - I think it is more
direct and easier to explain what is meant. It's harder to align
people to a numerical system, I would think, and also provides a
false sense of precision. Explanations are easier to understand as
well: "2 sources thought t
> 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
On 13/02/2008, Matt Williams <[EMAIL PROTECTED]> wrote:
> Just a quick note that the 'trust' we place in an agent /could/ be
> described probabilistically, but could also be described logically. I'm
> assuming that the probabilities that the trust annotations are likely to
> subjective probabiliti
Hi Matt --
Another way of increasing the amount of trust is to provide explanations, in
English, automatically derived from the proofs that an agent carries out.
A serendipitous feature is that the explanations start out with headlines,
and then go progressively into finer details. This aspect i
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
Just a quick note that the 'trust' we place in an agent /could/ be
described probabilistically, but could also be described logically. I'm
assuming that the probabilities that the trust annotations are likely to
subjective probabilities (as we're unlikely to have enough data to
generate objec
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
I've created a Wiki page where people can propose projects for BioRDF to
work on until the end of April [1]. It'd be great if you could post any
ideas that you may have.
Cheers,
Susie
[1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Brainstorming
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