Re: BioRDF Brainstorming

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

Re: BioRDF Brainstorming

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

Re: BioRDF Brainstorming

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

Re: BioRDF Brainstorming

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

Re: BioRDF Brainstorming

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

Re: Trust in statements (was BioRDF Brainstorming)

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

RE: BioRDF Brainstorming

> 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

RE: RE: BioRDF Brainstorming

> 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

Re: Trust in statements (was BioRDF Brainstorming)

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

Re: Trust in statements (was BioRDF Brainstorming)

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

Re: BioRDF Brainstorming

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

Re: BioRDF Brainstorming

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

Re: BioRDF Brainstorming

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)

Re: BioRDF Brainstorming

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

Re: RE: BioRDF Brainstorming

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

Re: BioRDF Brainstorming

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

Trust in statements (was BioRDF Brainstorming)

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

Re: RE: BioRDF Brainstorming

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

Re: Mammographic ontology

Dear Helen, At the moment we have some structure with a patient, who has one or more studies, each of which has one or more images associated with it. each image has zero or more lesions associated with it. We're working with a dataset of ~400 mammogram reports, and using this as the basis

Re: Mammographic ontology

Matt Can you elaborate on what aspects of mammography you include in your ontology? I am interested in the diagnostic aspect, i.e. image features, patient clinical information and the diagnosis to breast cancer. Kind regards. Helen Matt Williams <[EMAIL PROTECTED]> Sent by: [EMAIL PROT

Mammographic ontology

Dear All, Have just been reading the wiki. I note that there is a section on doing a mammogram as a screening test. I have been doing some work on a mammographic ontology, which we might be able to contribute (need to talk to other authors). Would this be useful? How can I align it with ex

RE: [coi] Some classifications of the entities in patient 1

Thanks, Alan! I have posted your comments on the wiki for easier reference at the following location: http://esw.w3.org/topic/HCLS/ClinicalObservationsInteroperability/rough-discussi on-realist-view Regards, ---Vipul > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PR

Re: [COI] Clinical Observations Interoperability, February 12th, 11:00am - 12:00pm, US EST

Vipul As per my assigned task, I have uploaded RIMOWL ontology, CDA owl file, and a presentation that explains briefly some main constructs of these two files, and how the mock up patient data would look like in a CDA documents thus the rdf triples can be generated automatically from these CDA

[coi] Some classifications of the entities in patient 1

Very rough, for discussion. From the realist point of view. Patient 1 in http://esw.w3.org/topic/HCLS/ ClinicalObservationsInteroperability/MockedUpPatientData dispositions: orthostatic intolerance http://en.wikipedia.org/wiki/ Orthostatic_intolerance dizziness D004244 hypertension D0

Statistical Search on the Semantic Web

M. Scott Marshall wrote: The draft of the HCLS Knowledgebase note can be found at http://www.w3.org/2001/sw/hcls/notes/kb/ this looks like it might be related to the above, and possibly of interest to this group: "Statistical search on the semantic web" Kobayashi N, Toyoda T. Bioinforma

[COI] Clinical Observations Interoperability, February 12th, 11:00am - 12:00pm, US EST

Phone +1 617 761 6200, conference 24668 ("BIONT") IRC irc://irc.w3.org:6665/hcls Browser-based IRC client: http://www.w3.org/2001/01/cgi-irc , OR http://ircatwork.com , Server: irc.w3.org:6665 Channel: #hcls Agenda: 1. R

Synergy; Knowledge-oriented Collaboration assessment and research

SYNERGY (Supporting Highly-adaptive Networked Enterprise Collaboration through Semantically-enabled Knowledge Services) is a new 3 year European-funded Seventh Framework Research Project which commenced on the 1 February 2008. It will research the knowledge sharing and collaboration support nee

Re: RE: BioRDF Brainstorming

> 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

HCLS Knowledgebase doc

Dear All, The draft of the HCLS Knowledgebase note can be found at http://www.w3.org/2001/sw/hcls/notes/kb/ Comments are still being integrated so it is a dynamic document. If you have comments, please mail them to me but make sure to read the Document Scope and Target Audience section first. ht

Re: partial review of SenseLab doc

Just a reminder for the other readers of this mailing list: The SenseLab note can be found at http://www.w3.org/2001/sw/hcls/notes/senselab/ If you have comments, please mail them to me within the next few days. The note should soon be finalized. Cheers, Matthias Samwald