Re: PDDI Info Model Task Force - CONTENT Sub-team minutes for 6/30

rting to build artifacts soon and would benefit from the insight of folks who know FHIR well. best, -R On 07/31/2016 09:40 PM, Renato Iannella wrote: On 29 Jul 2016, at 20:00, Richard Boyce <mailto:rd...@pitt.edu>> wrote: * Knowledge Representation Core Considerations:

PDDI Information Model Task Force - Doodle for all team call to discuss progress and medication reconciliation use case

Dear PDDI Task Force Participants and Stakeholders, We are working to schedule an "all team" call to discuss our progress to date on the information model and then spend time discussing our focus use case - medication reconciliation. If you are interested in attending this meeting, would you

PDDI Info Model Task Force - CONTENT Sub-team minutes for 6/30

, Sam Habiel, Richard Boyce, Dan Malone, Elizabeth Garcia, Louisa Zhang Meeting recording: http://goo.gl/1d7uwg Meeting: * Progress on user-centered definitions o User-Centered Definitions <https://docs.google.com/document/d/1MGPXSkRZVXCd8nzhEgHJLLSxYLhcixiNPqnAmty-

PDDI Info Model Task Force - Standard Sub-team minutes for 6/20

Attendance: Mathias Brochhausen, Kim Nolen, Oya Beyan, Clément Goehrs, Michel Dumontier, Richard Boyce, Louisa Zhang, Elizabeth Garcia Meeting recording: http://goo.gl/X4SVzG Meeting: * Update on the PDDIs to focus on o Content team progress on drug-drug interactions o

PDDI Info Model Task Force - Standard Sub-team minutes for 5/26

Beyan, Jodi Schneider, Xia Jing, Michael Miller, Maria Herrero, Michel Dumontier, Oliver He, Daniela Oliveira, Ratnesh Sahay, Richard Boyce, Louisa Zhang, Elizabeth Garcia Meeting recording: http://goo.gl/Nv1Y6l Meeting: * Introductions * Update from the Content sub-team meeting

PDDI Info Model Task Force - Content Sub-team minutes for 5/19

Hi, the minutes and link to meeting recording for the May 19th meeting of the content sub-team of the PDDI Info Model Task Force are pasted below. Kind regards, -R Minutes for 5/19/2016 (Content subgroup) In Attendance: Evan Draper, Brian LeBaron, Richard Boyce, Dan Malone, John

Please complete this Doodle poll for May to August meetings of the Standard sub-team of the PDDI Info Model Task Force

Hi - if you have not already done so, this is a reminder that we need your input on *Standard sub-team* meetings times for the next three months. I will extend the poll until this Friday and then pick a final time. best regards, -Rich -- Dear Colleagues, We need t

Please complete this Doodle poll for May to August meetings of the Standard sub-team of the PDDI Info Model Task Force

Dear Colleagues, We need to set meeting date/times for the *Standard sub-team* for May to August. Would you please complete the following doodle poll by May 9th? http://doodle.com/poll/vprw4ukskkx5cyn2 Thanks! -Rich -- Richard D Boyce, PhD Assistant Professor of Biomedical Informatics Facult

PDDI Info Task Force (Content sub-group) - Minutes/recording for 3/31

Dear Colleagues, Below are pasted the minutes of the Content sub-group for the PDDI DDI Minimum Information Model Task Force [1]. Minutes for 4/29/2016 (Content subgroup) In Attendance : Evan Draper, Lori Idemoto, Brian LeBaron, Sam Habiel, Richard Boyce, Michael Liebman, Dan Malone

PDDI Info Task Force (Standard sub-group) - Minutes/recording for 4/29

, Oliver He, Kim Nolen, Øystein Nytrø, Oya Beyan, Richard Boyce, Mathias Brochhausen, Daniela & Ratnesh Meeting recording: http://goo.gl/UTX6pY Meeting: * Update from the Content subteam o The content workgroup has agreed upon 10 PDDIs to include: https://goo.gl/rY

Reminder - DDI information model task force meetings (content and standards) this afternoon

Dear Colleagues, This is a reminder that the sub-team meetings of the task force for development of a minimum information model for drug-drug interaction evidence and knowledge will occur this afternoon: Standard development sub-team: April 29th (Friday) at 1-2 Eastern Cont

PDDI Info Task Force (Standard sub-group) - Minutes/recording for 3/31

hias Brochhausen, Matthias Thomas Samwald, Richard Boyce, Schneider, Jodi, Xia Jing Meeting recording: http://goo.gl/yx4nn7 Meeting: * Update from the Content subteam o Selected PDDIs and plans for the next couple of months + Noted especially 1) PDDIs

Minutes from the 2/24/16 DDI Information task force discussion (content sub group)

, Evan Draper, John Horn, Oktie Hassanzadeh, Richard Boyce, Sam Habiel Meeting recording: None taken (Rich forgot to start the recording, Sorry!) Meeting: * Brief discussion of progress on the proposed task force activities: 1. Clarify definitions for the seven minimum information items

Re: SQL to RDF access ?

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 RDF file that you load in a separate store. hope it helps, -R On 10/

Call for papers - First International Workshop on Drug Interaction Knowledge Representation (DIKR-2014)

Apologies for cross-posting Please forward this message to colleagues in the areas of interest CALL FOR PAPERS First International Workshop on Drug Interaction Knowledge Representation (DIKR-2014) at the International Conference on Biomedical Ontologies (ICBO 2014) October 6-7, 2014 Houston,

FYI: openFDA

FYI: Some folks might be interested in following the openFDA is a project with the Food and Drug Administration---a project to build modern APIs for easier developer and researcher access to public FDA datasets around adverse events, structured product information, and re

Re: Rebecca Boyles_Introduction

Welcome Rebecca! Do you have information on the regular telecon meeting times for HCLS as a whole and for the sub interest groups? -Rich -- Richard D Boyce, PhD Assistant Professor of Biomedical Informatics Faculty, Center for Pharmaceutical Policy and Prescribing Faculty, Geriatric Pharmaceuti

FYI: open NLM-funded postdoctoral research slots

FYI: The Department of Biomedical Informatics at the University of Pittsburgh has 3 open NLM-funded postdoctoral research slots. Would you please forward this announcement to colleagues and listservs you think appropriate? Thank you for your help, -Rich -- Richard D Boyce, PhD Assistant Profe

Re: NDF-RT and Canada

Hi Marc, Attached is a script that will get all DDIs from NDF-RT using a query to the Bioportal SPARQL endpoint. The data is output to as a dictionary to a Python pickle. wrt mapping, one thing I know about NDF-RT is it uses salt forms as the primary label for many of its drugs so mapping re

Re: Links to downloadable Bio Dataset in RDF ?

Hi Andrea, I maintain a resource of all US drug product labeling called LinkedSPLs . The resource is up to date and contains mappings to bio2rdf, drugbank, NDF-RT, ChEBI, and RxNorm. Drugs with clinical pharmacogenomic statements [1] are included in the FDAPhar

FYI: Dynamic enhancement of drug product labels

FYI: Our paper describing a pilot study of using Linked Data to dynamically enhance drug product labels just became available: http://www.jbiomedsem.com/content/4/1/5 The research described was originally conducted as part of a use case [1] for the former Scientific Discourse task force. This

Re: biontology.org Linked Data URIs?

I think this helps bioportal keep track of usage (to justify its existence) and reduce annoying bots. Also, I get updates from bioportal for having registered an account. -R On 05/28/2013 04:54 PM, Jim McCusker wrote: I can see asking for an API key for working with computational resources (li

Re: availabilty of dailymed and diseasome

annot figure out where it goes. http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/page/structuredProductLabelMetadata/00051a01-1c2e-4abb-b04c-548401f822c6 Except the case I'm missing something, is there a quick way to link them appropriately? Maybe a conversion between mannheim's dailymed

Re: availabilty of dailymed and diseasome

Umatcan, LinkedSPls replaces LODD Dailymed which appears to be no longer maintained. Can't say whats going on with diseaseome. -R On 03/18/2013 07:48 AM, Umutcan Şimşek wrote: After movement of lodd datasets there were some availability issues. Some of them seems resolved but dailymed and dis

Re: PK Ontology

This is relevant, thanks for finding Bob. Lang Li's group has been doing some interesting work. This ontology is a start in the right direction but has some issues (see below). I would certainly be interested in discussing this and related work on a call. As you know, I would like to lead an e

Re: Stanford-bound!

Congratulations Michel - this is great news! Stanford BMI made a great choice that I expect will catalyze several high impact innovations in the coming years! -Rich On 01/21/2013 02:15 PM, Michel Dumontier wrote: Dear friends, colleagues and collaborators, I'm thrilled to announce that I'

Re: Ontologies for blood glucose, HbA1C measurements?

, Which ontologies can you recommend to identify different types of medical measurements, such as fasting plasma glucose or HbA1C? Thanks! Take care Oliver -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Faculty, Geriatric Pharmaceutical Outcomes and Gero

Re: Fwd: [Ops-ttf] Fwd: DrugBank not available?

r suggestions. thanks, -Rich Cheers, Peter -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research and Training Program Scholar, Comparative Effectiveness Research Program University of Pittsburgh rd...@pitt.edu

Re: Fwd: [Ops-ttf] Fwd: DrugBank not available?

c Development Center Blog(Turkish): http://blog.umutcansimsek.com LinkedIn: http://www.linkedin.com/pub/umutcan-%C5%9Fim%C5%9Fek/53/199/26a -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research and Training P

Re: [Linked Life Data] RDF Guide draft on W3C website

Figure 2 caption, 'DbPedia' should be 'DBPedia' (it is elsewhere)? cheers, michael Michael Miller Software Engineer Institute for Systems Biology *From:*M. Scott Marshall [mailto:mscottmarsh...@gmail.com <mailto:mscottmarsh...@gmail.com>] *Sent:* Monday, Novemb

Re: EUROPE at 4PM CET!!!: Linked Life Data telco on Emerging Practices Note 11AM ET / *4PM CET* today

.w3.org port 6665 channel #HCLS -- Forwarded message -- From: M. Scott Marshall Date: Mon, Oct 1, 2012 at 3:00 PM Subject: Reminder: Linked Life Data telco on Emerging Practices Note 11AM ET / 5PM CET today To: HCLS , linkedlifedatapracticesn...@googlegroups.com, expression...@

FYI: Graduate and Post Doctoral Fellowships available in Biomedical Informatics

nt of Biomedical Informatics 5607 Baum Boulevard BAUM 423, Room 523 Pittsburgh, PA 15206-3701 412-624-3310|Fax: 412-624-5310 crowle...@upmc.edu www.dbmi.pitt.edu -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Researc

Re: Updated Invitation: Pharmacogenomics for Drug Discovery @ Thu 2012-07-19 11:00 - 12:00 (public-semweb-lifesci@w3.org)

e.com/calendar/event?action=VIEW&eid=dWRsdXAwcDlpcjhvZHBja2RvamdsMW5rMHNfMjAxMjA3MTlUMTUwMDAwWiBwdWJsaWMtc2Vtd2ViLWxpZmVzY2lAdzMub3Jn&tok=MTcjdzMuaGNsc0BnbWFpbC5jb21hZmEzNjhiMjJjYzg1OWE5Y2IzZjcwMmRjYmFmZTU2N2FiMzM0ODNm&ctz=America/New_York&hl=en> Invitation from _Google Cal

Re: rxnorm mappings in LinkedSPLs

Office 715-221-7299 lin.si...@mcrf.mfldclin.edu www.marshfieldclinic.org/birc For scheduling assistance, please contact Crystal Gumz, Administrative Secretary gumz.crys...@mcrf.mfldclin.edu 715-221-6403 *From:*Richard Boyce [mailto:rd...@pitt.edu] *Sent:* Friday, July 06

Re: aTag and conclusion sections from PubMed

that in your write up. -Rich On 06/22/2012 04:36 PM, Matthias Samwald wrote: Also, I would be interested to expand the conclusions section demo, any >way that could be accomplished? -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Faculty, Geriatric Pharmaceutical Outco

aTag and conclusion sections from PubMed

_Subgroup/aTags/datasets>. The science commons still provides a text annotation service that embeds atags <http://whatizit.neurocommons.org/>. Since I didn't start working with this group until 2010 I am still discovering work done by members of the group several years ago! -Rich

Re: Evidence-based healthcare ontology and Cochrane systematic Reviews - A linked data project

air of the Scientific Discourse task force. Please follow up with her regarding giving a talk at a regular teleconference. I will look over your links in detail in a week after some deadlines are met. kind regards, -Rich Richard Boyce, PhD Assistant Professor of Biomedical Informatics Scholar, C

Re: what happened to SWAN rsqualifiers?

thanks, -Rich On 05/10/2012 11:04 AM, Paolo Ciccarese wrote: Richard, is this what you were looking for? http://swan.mindinformatics.org/ontologies/1.2/qualifiers.owl Best, Paolo On Thu, May 10, 2012 at 10:47 AM, Richard Boyce <mailto:rd...@pitt.edu>> wrote: SWAN used to have an extensi

what happened to SWAN rsqualifiers?

lar in the other resources on <http://swan.mindinformatics.org/ontologies/1.2/>. Does anyone know what happened? thanks! -Rich -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Scholar, Comparative Effectiveness Research Program University of Pittsburgh rd...@pitt.edu 412-648-6768

pharmacogenomics evidence/clinical relevance schemes (was Re: Minutes from Clinical Decision Support teleconference)

ation." "Overall, the therapeutic recommendations are simplified to allow rapid interpretation by clinicians. They have been adopted from the rating scale for evidence-based therapeutic recommendations on the use of retroviral agents. A: Strong recommendation for the statement B: Mod

Re: Minutes from Clinical Decision Support teleconference

tain SNPs to produce personalized drug advice). Very nice! Many participants are hoping to look deeper into this in a followup call. Cheers, Scott -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Scholar, Comparative Effectiveness Research Program University of Pittsburgh rd...@pitt.edu 412-648-6768

FYI: NLM-funded postdoc positions at U of Pittsburgh DBMI

FYI...know of any post-doctoral trainees interested in positions with us at the University of Pittsburgh School of Medicine, Department of Biomedical Informatics? See attached and below --Rich You can view a description of our training program information via a YouTube video athttp://www.youtube

Re: Evidence of Significance of Semantic Web for Life Sciences

riousworld.org Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677 (The Netherlands) -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Scholar, Comparative Effectiveness Research Program University of Pittsburgh rd...@pit

Re: Evidence of Significance of Semantic Web for Life Sciences

a F. Deus Post-Doctoral Researcher at DERI/NUIG http://lenadeus.info/ -- Helena F. Deus Post-Doctoral Researcher at DERI/NUIG http://lenadeus.info/ -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Scholar, Comparative Effectiveness Research Program University of Pittsburgh rd...@pitt.edu 412-648-6768

LODD telcon on THURSDAY 11/10 at 11AM ET

channel=%23hcls for IRC access. Duration: ~1 hour Convener: M. Scott Marshall Scribe: TBD Agenda Discussion of W3C note on RDF practices Brief update LODD datasets AOB -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Scholar, Comparative Effectiveness Research Program Univers

LODD practice note followup

ence list efficiently. kind regards, -Rich -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Scholar, Comparative Effectiveness Research Program University of Pittsburgh rd...@pitt.edu 412-648-6768

LODD telcon on TUESDAY at 11AM ET / 5PM CET

nel=%23hcls for IRC access. Duration: ~1 hour Convener: M. Scott Marshall Scribe: TBD Agenda Please dial in to Zakim as normal for audio. Click here to see Anja's screen Introductions Discussion of W3C note on RDF practices Brief update LODD datasets AOB -- Richard Boyce, PhD Assistan

Re: TM call

l will feature a presentation by Richard Boyce on the Drug Interaction Knowledge Base followed by some discussion around making a podium submission to AMIA and a general update on progress related to the snp db. Cheers, m. ''' Conference Details''&

Re: Quantified Self -- Amsterdam -- November 26-27

including your name, topic, and any web links that might be useful. Ernesto and I will follow up with some practical information about slides, speaking time, etc. Thank you! Best, Gary -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics Scholar, Comparative Effectiveness Research Program University of Pittsburgh rd...@pitt.edu 412-648-6768

drug-drug interaction scientific discourse

for algorithmic inferences. Would anyone have a suggestion? Thanks in advance, -Rich -- Richard Boyce, PhD Assistant Professor of Biomedical Informatics and Intelligent Systems Scholar, Comparative Effectiveness Research Program University of Pittsburgh rd...@pitt.edu 412-648-6768

FYI: 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2011)

for innovative SW applications or analyses applied to health care delivery CALL FOR PAPERS IMPORTANT DATES Abstract submission deadline: May 23, 2011 11:59pm EST Paper submission deadline: May 30, 2011 11:59pm EST Notification of acceptance: August 1, 2011 11:59pm EST Camera-ready copy due: Aug