Re: BioRDF Telcon

focused on discussing the initial structure. As we discussed in the last biordf call of 2009, it'd be interesting as part of the demo if your iphone app can demontrate that some queries can be performed based on the structure. Please join the next meeting, which will be in two weeks. Cheers

Re: Health Care and Life Sciences SemanticWb on iPhone and iPod touch

Peter, Complete order. Don On Dec 17, 2009, at 5:01 PM, Peter Ansell wrote: 2009/12/18 Donald Doherty : Hi Kei, Great to hear from you and the podcast idea is excellent. I wonder, is there any effort to have semantics attached to the podcasts? That'd be cool to have triples indic

Re: Health Care and Life Sciences SemanticWb on iPhone and iPod touch

thors associated with a particular paper but a big limitation of every endpoint is that it is impossible to reconstruct the order of the authors. (At least I haven't found a way.) Don On Dec 17, 2009, at 3:26 PM, Kei Cheung wrote: Hi Don, Donald Doherty wrote: Scott Marshall suggested t

Re: Health Care and Life Sciences SemanticWb on iPhone and iPod touch

On Dec 14, 2009, at 1:05 PM, Kingsley Idehen wrote: Donald Doherty wrote: Scott Marshall suggested that people on the HCLS list would have fun with my SemanticWb iPhone and iPod touch app (www.actionpotential.com ). It's one of many technologies I play around with to test the pote

Health Care and Life Sciences SemanticWb on iPhone and iPod touch

;ll be happy to talk about lessons learned. Donald Doherty, Ph.D. donald.dohe...@actionpotential.com

Re: LODD Telcon

Thank you Susie for inviting me to present the Brainstage platform to the LODD team! Also, thank you everyone for your excellent questions. Feel free to contact me using my email address listed below. Best wishes, Don Donald Doherty, Ph.D. President and CEO Brainstage, Inc

Re: LODD Telcon

Regrets everyone. I have a conflicting meeting that has popped onto my calendar that I cannot miss. Sorry! Don On Mar 2, 2009, at 3:09 PM, Susie M Stephens wrote: Here's the reminder for Wednesday's LODD telcon. http://esw.w3.org/topic/HCLSIG/LODD Cheers, Susie == Conference Details ==

Re: Remembering Bill Bug in the KB note

On May 29, 2008, at 10:10 PM, Alan Ruttenberg wrote: I wonder if we could include a line remembering Bill Bug in the KB note. Something simple along the lines of "In memory of our friend and colleague William Bug, Ontological Engineer" -Alan +1 ----- Donald Doherty, Ph.

Re: BioRDF Telcon

Regrets. Another meeting popped up that I cannot miss. Don On Feb 28, 2008, at 9:11 PM, Susie M Stephens wrote: Here's the reminder for Monday's BioRDF telcon. EricP will be hosting the call. Cheers, Susie == Conference Details == * Date of Call: Monday March 3, 2008 * Time of Call: 11:

RE: BioRDF Telcon

Regrets. I have a conflicting appointment. Don -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Susie M Stephens Sent: Friday, November 16, 2007 5:26 PM To: public-semweb-lifesci@w3.org Subject: BioRDF Telcon Here's the reminder for Monday's BioRDF call

RE: BioRDF Telcon

Regrets due to attending and presenting at the Society for Neuroscience meeting. I'll be happy to report on the meeting a week from Monday. Don -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Susie M Stephens Sent: Thursday, November 01, 2007 6:16 PM To:

RE: [HCLSIG] Society for Neuroscience Meeting 2007 Poster PDF

Bill, The pdf is still up but the file is huge ~50 Mbytes. You can get it at (watch the upper and lower cases): http://www.brainstage.com/SfNPoster2007.pdf The following ~5.5 Mbyte png file is very readable and much more manageable: http://www.brainstage.com/sfnposter2007.png Ho

[HCLSIG] Correct URL for Society for Neuroscience Meeting 2007 Poster PDF

Sorry everyone. There was a slight typo in my last post...capital "F" rather than "f" :^/ Here's the correct URL and remember, this file is about 50 MBytes: http://www.brainstage.com/SfNPoster2007.pdf Don -- Donald Doherty, Ph.D. Brainstage Research, Inc. www.brains

[HCLSIG] Society for Neuroscience Meeting 2007 Poster PDF

Those interested in the high-res pdf of our Neurosciences poster may get all 50 MBytes here: http://www.brainstage.com/SFNPoster2007.pdf Don - Donald Doherty, Ph.D. Founder and Chief Science Officer Brainstage, Inc. <http://www.brainstage.com/> www.brainstage.com &

RE: [HCLS] Demo KB Data Flow Diagram for PubMeSH Graph

arrows more consistent. Are the ovals really needed? For the neuroscience audience, you might want to spell out TTL. Hope it helps, -Kei Donald Doherty, Ph.D. wrote: >I've updated the draft data flow diagram for creating the PubMeSH graph. >So far I haven't shortened the URIs but

[HCLSIG] New draft of Neurosciences 2007 Poster

I've posted a new draft of HCLSIGs Society for Neurosciences 2007 meeting poster at: http://www.brainstage.com/poster_draft.png Don ----- Donald Doherty, Ph.D. Brainstage, Inc. www.brainstage.com <http://www.brainstage.com/> [EMAIL PROTECTED] 412-683-1410

RE: [HCLS] Demo KB Data Flow Diagram for PubMeSH Graph

@w3.org Subject: Re: [HCLS] Demo KB Data Flow Diagram for PubMeSH Graph Don, Thanks for creating the image-- any chance you can reduce the size of this image? Eric On Oct 14, 2007, at 10:03 PM, Donald Doherty, Ph.D. wrote: I've updated the draft data flow diagram for creatin

[HCLS] Demo KB Data Flow Diagram for PubMeSH Graph

I've updated the draft data flow diagram for creating the PubMeSH graph. So far I haven't shortened the URIs but everything else should be correct. Please let me know if it isn't. Draft found at: http://www.brainstage.com/CreateMedlineTriples.jpg Thank you, Don -- Donal

[HCLS] Step-By-Step Explanation of Banff 2007 Demo SPARQL

u SPARQL / OWL / RDF experts out there to jump in and show me where I've gone wrong :^) The page is at: http://esw.w3.org/topic/HCLS/Banff2007Demo/HCLS/Banff2007Demo/StepByStepExpl anationOfDemoSparql Don - Donald Doherty, Ph.D. Brainstage, Inc. www.brainstage.com <http://w

[HCLSIG] Draft of "How To Create the Banff2007 Demo Knowledge Base For Yourself"

A draft of the step-by-step instructions on how to set up the Banff 2007 Demo Knowledge Base is posted to: http://esw.w3.org/topic/HCLS/Banff2007Demo/HCLS/Banff2007Demo/HowToMakeOneFo rYourself My next step is to get it into a more readable format. Don - Donald Doherty, Ph.D

RE: BioRDF Informal F2F

Johnathan, Thank you so much for taking the lead and putting so much time into this extremely important project. So far I haven't been able to contribute but your work is helping me get up to speed on the issues. The entire SW community will benefit from your prodigious effort. Don -Origina

[HCLS] Demo at Neuroscience 2007

s B-H Don ----- Donald Doherty, Ph.D. Brainstage, Inc. www.brainstage.com <http://www.brainstage.com/> [EMAIL PROTECTED] 412-683-1410 This email message is confidential and/or privileged. It is to be used by the intended recipient only. Use of the information contained in this emai

RE: Banff2007Demo data

Alan, We have hired at least one new person to help set up the demo here. We're waiting for our machine (any experience installing/running it on Mac OS X?). Once we get going we'll be happy to help document and provide the documentation to the community. Don -Original Message- From: [EM

RE: [HCLS] Authors on SfN Abstract

mmons, Cambridge, MA; 18Natl. Ctr. for Biomed. Ontology, Stanford Med. Informatics, Stanford, CA; 19Med. Univ. of Vienna, Vienna, Austria; 20Eli Lilly, Indianapolis, IN; 21Hyperphor, Pacifica, CA -Original Message- From: Donald Doherty [mailto:[EMAIL PROTECTED] Sent: Tuesday, May 15, 2007

RE: [HCLS] Authors on SfN Abstract

lands; 13Teranode Corp., Seattle, WA; 14World Wide Web Consortium, Cambridge, MA; 15Sci. Commons, Cambridge, MA; 16Stanford Univ. Med. Ctr., Stanford, CA; 17Med. Univ. of Vienna, Vienna, Austria; 18Eli Lilly, Indianapolis, IN -Original Message- From: Donald Doherty [mailto:[EMAIL PROTECTED]

RE: [HCLS] Authors on SfN Abstract

Would everyone be comfortable if I simply alphabetized the names between first and last author? If not, please give me another idea! :^) Don -Original Message- From: Donald Doherty [mailto:[EMAIL PROTECTED] Sent: Tuesday, May 15, 2007 1:36 PM To: 'public-semweb-lifesci@w

[HCLS] Authors on SfN Abstract

s, IN; 18Stanford Univ. Med. Ctr., Stanford, CA ----- Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.com <http://www.brainstage.com/> [EMAIL PROTECTED] 412-683-1410

RE: [hcls] The Bibliographic Ontology Specification Group

Matthias, I can really appreciate the value in this right now. Thank you for the heads-up! Don -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Monday, May 14, 2007 8:20 PM To: public-semweb-lifesci@w3.org Subject: [hcls] The Bibl

[HCLS] Society for Neuroscience Abstract on Demo

benefit of presenting an abstract is to expose the neuroscience community to the HCLS demo. There will be about 35,000 people attending the meeting. ----- Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.com <http://www.brainstage.com/> [EMAIL PROTECTED] 412-683-1410 This

[HCLS] WWW2007 Demo and Workshop

inspired by the workshop, and especially by the panel discussion, very useful. Best wishes, Don - Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.com <http://www.brainstage.com/> [EMAIL PROTECTED] 412-683-1410 This email message is confidential and/or privileged. It

RE: correction: pending Soc. for Neuro abstract - due: Tues. 5/15 by 5 PM EDT

I'm almost caught up! We do have two days, if I remember correctly, for revisions. So, as long as we get this in we have some time to revise. Is there anyone out there that hasn't been added to the Google Docs and would still like to be? Don -Original Message- From: [EMAIL P

Re: Mashup browser compatibility help requested.

gt; there is someone knowledgeable about such issues I'd appreciate if > you could have a look and see if you can figure out what the problem > is. Also testing on other browsers/OS would be appreciated. > > The URL to test is http://hcls1.csail.mit.edu:8890/map/ > [EMAIL PROTECTED],[

RE: SfN meeting submission

eties (FAONS) > http://www.faons.org/ > > I'm not certain what the deadlines are for the associated meetings. > > Cheers, > Bill > > On May 2, 2007, at 11:51 AM, Donald Doherty wrote: > >> >> Hi Matthias, >> >> That'd be great! SfN abstracts are

RE: ISMB Bio-Ontologies Meeting

Kei, I'm also interested in contributing. I saw a "due Thursday." This Thursday?! Note that Society for Neuroscience abstracts are not published in a journal. The main value as I see it is to get the demo in front of the intended end users (neuroscientists). There are about 35,000 that attend t

RE: SfN meeting submission

Hi Matthias, That'd be great! SfN abstracts are brief (max. 2300 characters including punctuation!) so focusing on the value to neuroscientists sounds like the right course. Abstract may be presented or posters. Slide presentations are kept very brief and there is so much going on most people wo

RE: ISMB Bio-Ontologies Meeting

Hi Kei, The Society for Neuroscience meeting accepts short abstracts which is typically presented as a poster at the meeting. There are no full length papers published from the Neurosciences meeting. Don -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of K

RE: ISMB Bio-Ontologies Meeting [Neurosciences]

This year's Society for Neuroscience meeting abstracts are due May 15th. I'd like to take the lead on submitting an abstract if the team is interested. Don P.S. This year's meeting is November 3-7 in San Diego, California. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTEC

RE: Mapping NeuronDB to MeSH to BAMS

al neuron in SenseLab are mapped to Pyramidal Cells in MeSH). From the semantic web perspective, I think it would be interesting to see how to use things like OWL constructs to establish such mappings (both one-to-one and one-to-many) to facilitate data integration. Cheers, -Kei Donald Doherty w

HCLS March 8 TC Minutes

achine Example OWL for NLP and the Allen Brain Atlas: http://sw.neurocommons.org/2007/annotations.owl http://sw.neurocommons.org/2007/aba.owl - Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.com <http://www.brainstage.com/> [EMAIL PROTECTED] 412-683-1410

RE: cell types, brain regions mentioned in gensat

in NeuroNames - but given the deliberate process that must go into UMLS curation, it is an older version of NN and not one that includes any of the work the NN group has done to integrate rodent terminologies in with those for primate. Cheers, Bill On Mar 2, 2007, at 11:13 AM, Donald Do

RE: cell types, brain regions mentioned in gensat

heung; June Kinoshita; Gwen Wong; Donald Doherty Cc: public-semweb-lifesci@w3.org Subject: cell types, brain regions mentioned in gensat I'm making progress in converting gensat to rdf. For mapping considerations, here is the list of cell types mentioned in gensat, followed by the list of bra

RE: More inspiration for the WWW HCLSIG demo

Here's another. http://www.medstory.com It's being purchased by Microsoft. Don -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of William Bug Sent: Thursday, February 22, 2007 1:46 PM To: William Bug Cc: M. Scott Mar

RE: [HCLSIG] ADDL review - Answer ADDL Questions?

Hi All, Susan Catalano said she'd be happy to join one of the HCLSIG teleconference calls to answer questions about ADDL (if there is still a need). Don - Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.com [EMAIL PROTECTED] 412-683-1410

Re: Martone's Ontology

t; Cheers, > Bill > > On Jan 11, 2007, at 7:43 PM, Kashyap, Vipul wrote: > >> If it makes sense, we could put it on the agenda item for the next >> BIONT Telcon? >> >> >> >> ---Vipul >> >> >> >> From: William Bug [mailto:[EMAIL PROT

[HCLS] Wake-up Call for Dad

baby very soon. Mother is well and we've had a very easy time of it until now but we're in the last week or two... My schedule will be somewhat uncertain over the next few weeks! Best wishes and my apologies again, Don -- Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.

Martone's Ontology

Hi Bill, At Neurosciences Maryann Martone talked about her ontology being nearly ready for public consumption. (I forgot the name of her ontology.) It sounded like it would be very helpful in situations like describing distributions or receptors on a cell, locations of various processes in a ce

RE: NIH Request for Information (RFI): To Solicit Input and Ideas for Roadmap Trans-NIH Strategic Initiatives

Eric,   That’s a great idea. However, I wonder if we can make the November 17th date?   Don   -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Eric Neumann Sent: Tuesday, October 31, 2006 8:23 AM To: W3C HCLSIG Subject: NIH Request for Informat

RE: [BIONT] Teleconference on Tuesday, 5th September 2006

I also don’t have Visio but I found this free download of a Visio Viewer from Microsoft:   http://www.microsoft.com/downloads/details.aspx?FamilyId=3FB3BD5C-FED1-46CF-BD53-DA23635AB2DF&displaylang=en   Nevertheless, I agree with Bill that it would be ideal if the XMI can be posted.  

[HCLS] Bridging Ontology...An Automated Approach?

ld be able to automate an interrogation that may see "axon" in DB1. Or maybe it finds "dendrite"... This is rough but a potential approach to automating the formation of connections? Don - Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.com [EMAIL PROTECTED] 412-478-4552

[HCLS] Circularity of Reasoning

at reasoning/classification agents can provide the mechanism to highlight what is same or different identity. On 31/07/2006, at 12:31 PM, Donald Doherty wrote: > > Eric, > > What you call "covering" below seems particularly important. In my > view, > there c

RE: WWW2006 Life Science mashup demo now accessible

Sean,   I’m getting an error when I enter p53 and click on the Find Proteins button. It says “Failed to get privilege UniversalBrowserRead to open http://sparql.org/sparql, A script from http://thefigtrees.net was denied UniversalBrowserRead privileges.”   I’m using Mozilla Firefox 1.5.

RE: URI thoughts

Eric, What you call "covering" below seems particularly important. In my view, there can never be one true ontology, especially in science (unless we're done and have reached complete knowledge...if that's possible). You present an interesting solution... Don Donald Doher

[HCLS] RE: scientific publishing task force update

rototype that is now in debug hell...but that's another story.] Don - Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.com [EMAIL PROTECTED] 412-478-4552 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of kei cheung Sent: Thursd

[BIONT] Bridging Ontology Task

lease provide feedback! Thank you, Don Donald Doherty, Ph.D. Brainstage Research, Inc. 412-478-4552

RE: {Disarmed} Gyri of the human neocortex: an MRI-based analysis of volume and variance -- Kennedy et al. 8 (4): 372 -- Cerebral Cortex

Title: Gyri of the human neocortex: an MRI-based analysis of volume and variance -- Kennedy et al. 8 (4): 372 -- Cerebral Cortex You’re absolutely correct, there needs to be a commonly used ontology but there isn’t and there won’t be until it’s in the public domain. Building one is an enor

RE: BioRDF [Telcon]: slides for the UMLS presentation

m/nbt/journal/v23/n9/full/nbt0905-1095.html Cheers, -Kei Donald Doherty wrote: > Matthew's statement is a truism. > > Even though I'm in private enterprise I feel the patent/copyright/etc. > system is broken and a huge liability for where IP needs to go during > the 21^st c

RE: BioRDF [Telcon]: slides for the UMLS presentation

forward…   Don   Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.com [EMAIL PROTECTED] 412-478-4552   -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Matthew Cockerill Sent: Monday, June 05, 2006 6:05 PM To: public-semweb-lifesci@w3

RE: [BIONT] Senselab project ontologies.

ch is a subdatabase of SenseLab, stores some drug-related information about the Parkinson's Disease (http://senselab.med.yale.edu/BrainPharm/dopamine.asp) if it is also of interest to the group. -Kei Donald Doherty wrote: >Alan, > >It seems that NeurWeb provides a great platform fo

RE: [BIONT] Senselab project ontologies.

http://brainmaps.org and one or more of the sites with details on antibodies, genes, and...? Don - Donald Doherty, Ph.D. Brainstage Research, Inc. www.brainstage.com [EMAIL PROTECTED] 412-478-4552 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Alan Rutte

[HCLSIG] Human Brain Project meeting notes...very cool!

queries like the following:   “Give me all images of medium spiny neuron tract-traces and histology of surrounding regions from the Parkinson’s alpha-synuclein mouse model.”   - Donald Doherty, Ph.D. Brainstage Research, Inc. 412-478-4552    

RE: [BIONT] Teleconference Tuesday and Agenda:

Are the BIONT meeting minutes being posted somewhere? March 14 was the last meeting posted to the BIONT Telcon page (http://esw.w3.org/topic/HCLS/OntologyTaskForce/Telcons).   Don   -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kashyap, Vipul

RE: Parkinson's Use Case

Thank you John! I promise to go Wiki... Don -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of John Madden Sent: Tuesday, March 21, 2006 8:23 PM To: HCLS Cc: Kensaku Kawamoto; Vipul Kashyap, Ph.D. Subject: Parkinson's Use Case Everybody, I put Don Dohert

[BIONT] Parkinson's Disease Use Cases

Here are the first baby steps…   Don   - Donald Doherty, Ph.D. Brainstage Research, Inc. 412-478-4552   Parkinson's Disease Use Cases.doc Description: MS-Word document

[HCLSIG] A Basic Neuroscientist Use Case

e somatosensory (sense of touch) system and I remain in a close working relationship with bench researchers. Attached is a short blurb where I jotted down some of my thoughts. Don - Donald Doherty, Ph.D. Brainstage Research, Inc. 412-478-4552 A Neuroscience Researcher Use Case.pdf Des

Introductions: Donald Doherty, Brainstage Research

Hello all,   My name is Donald Doherty. I’m a neuroscientist (both wet and large scale brain systems simulations) and founder of Brainstage Research, Inc. located in Pittsburgh, PA. We are particularly involved in integrating data and simulations (computational neuroinformatics