- From: Charles Barr <cebarr01@yahoo.com>
- Date: Sun, 11 Jun 2006 07:49:24 -0700 (PDT)
- To: John Rumble <jumbleusa@earthlink.net>, AJ Chen <canovaj@gmail.com>, public-semweb-lifesci@w3.org
John, I would be interested in the papers and presentations that you mention.
I agree this is an important area. The continual updating of MeSH terms (adding 400 new terms per year) reflects the changing knowledge in publications (indexing and retrieval).
What you are talking about is reaching to the earliest stages of problem formulation, as facilitated (or limited) by the language and variables used to express the concepts in experimental studies. This obviously can potentially affect the generation of knowledge.
In retrospect, my first awareness of this arose in the 1987-1990 time period when I was doing early work with the UMLS and concurrently doing meta-analyses of clinical studies of interferon for hepatitis B. It became clear during attempts to synthesize knowledge generated by various trials that they had used incompatible study designs and/or endpoints that limited the ability to pool information.
I believe there is real merit in evaluating the (implicit) ontologies used in formulating and implementing experimental studies (whether they are pre-clinical or clinical). That is the one step towards optimizing the ability for multiple groups to achieve the maximal amount of useful information from a set of research studies. In the pharmaceutical industry we do use formal terminologies (e.g., MedDRA for documenting adverse events). However, to my knowledge, no one has systematically defined the endpoints and covariates for an area of drug development or clinical research in the way which John is describing. This may just reflect the limitations of my awareness, and I would love to hear more about what others have done / are doing.
Charlie
Charlie Barr, MD, MPH
Chair, Clinical Trials Working Group
American Medical Informatics Association
cebarr@att.net
----- Original Message ----
From: John Rumble <jumbleusa@earthlink.net>
To: AJ Chen <canovaj@gmail.com>; public-semweb-lifesci@w3.org
Sent: Friday, June 9, 2006 1:05:25 PM
Subject: Re: scientific publishing task force update
There has been some important work done on this subject over the last 20 years. A. Shoshoni, F. Olken and others wrote some very insightful papers about differentiating between different types of independent variables in an experiment. I have given several talks in recent years about the problem of evolving scientific knowledge and changing scientific language and how that impacts capturing a description of an experiment. I especially have focused on how new knowledge about independent variables is inevitable and how that affects ontology development and data integration efforts. I can send these along to whomever is interested.
John
Dr. John Rumble
Technical Director
Information International Associates
Oak Ridge TN
www.infointl.com
jrumble@iiaweb.com
jumbleusa@earthlink.net
301 963 7903 (Home Office)
301 502 5729 (Cell)
865 298 1251 (Oak Ridge Office)
----- Original Message -----
From: AJ Chen
To: public-semweb-lifesci@w3.org
Sent: Friday, June 09, 2006 1:09 AM
Subject: scientific publishing task force update
I have created a wiki page for the Scientific Publishing task force, please see http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce
The first task is to develop an ontology for self-publishing of experiment. I have proposed a list of objects and properties related to self-publishing experiment. Please download the attached file under Task Status and review the proposal. Your feedback and comments will be greatly appreciated. You may also edit the file directly and email me the edited file.
It's critical to have more talents to engage in the task force and its tasks. Let me know if you are interested in join the task. If you have any new idea for a new task, please make a proposal and share with the group.
Thanks,
AJ
--0-2146377084-1150037364=:53393
Content-Type: text/html; charset=us-ascii
<html><head><style type="text/css"><!-- DIV {margin:0px} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">John, I would be interested in the papers and presentations that you mention. </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">I agree this is an important area. The continual updating of MeSH terms (adding 400 new terms per year) reflects the changing knowledge in publications (indexing and retrieval). </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">What you are talking about is reaching to the earliest stages of problem formulation, as facilitated (or limited) by the language and variables used to express the concepts in experimental studies. This obviously can potentially affect the generation of knowledge. </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">In retrospect, my first awareness of this arose in the 1987-1990 time period when I was doing early work with the UMLS and concurrently doing meta-analyses of clinical studies of interferon for hepatitis B. It became clear during attempts to synthesize knowledge generated by various trials that they had used incompatible study designs and/or endpoints that limited the ability to pool information.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">I believe there is real merit in evaluating the (implicit) ontologies used in formulating and implementing experimental studies (whether they are pre-clinical or clinical). That is the one step towards optimizing the ability for multiple groups to achieve the maximal amount of useful information from a set of research studies. In the pharmaceutical industry we do use formal terminologies (e.g., MedDRA for documenting adverse events). However, to my knowledge, no one has systematically defined the endpoints and covariates for an area of drug development or clinical research in the way which John is describing. This may just reflect the limitations of my awareness, and I would love to hear more about what others have done / are doing.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Charlie </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Charlie Barr, MD, MPH</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Chair, Clinical Trials Working Group</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">American Medical Informatics Association</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"><A href="mailto:cebarr@att.net">cebarr@att.net</A><BR><BR></DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: John Rumble <jumbleusa@earthlink.net><BR>To: AJ Chen <canovaj@gmail.com>; public-semweb-lifesci@w3.org<BR>Sent: Friday, June 9, 2006 1:05:25 PM<BR>Subject: Re: scientific publishing task force update<BR><BR>
<STYLE></STYLE>
<DIV><FONT face=Arial size=2>There has been some important work done on this subject over the last 20 years. A. Shoshoni, F. Olken and others wrote some very insightful papers about differentiating between different types of independent variables in an experiment. I have given several talks in recent years about the problem of evolving scientific knowledge and changing scientific language and how that impacts capturing a description of an experiment. I especially have focused on how new knowledge about independent variables is inevitable and how that affects ontology development and data integration efforts. I can send these along to whomever is interested.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>John </FONT><FONT face=Arial size=2></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Dr. John Rumble<BR>Technical Director<BR>Information International Associates<BR>Oak Ridge TN<BR><A id=bodyLinks href="http://www.infointl.com/" target=_blank rel=nofollow>www.infointl.com</A><BR><A id=bodyLinks href="mailto:jrumble@iiaweb.com" target=_blank rel=nofollow>jrumble@iiaweb.com</A><BR><A id=bodyLinks href="mailto:jumbleusa@earthlink.net" target=_blank rel=nofollow>jumbleusa@earthlink.net</A><BR>301 963 7903 (Home Office)<BR>301 502 5729 (Cell)<BR>865 298 1251 (Oak Ridge Office)</FONT></DIV>
<BLOCKQUOTE style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV style="BACKGROUND: #e4e4e4; FONT: 10pt arial"><B>From:</B> <A id=bodyLinks title=canovaj@gmail.com href="mailto:canovaj@gmail.com" target=_blank rel=nofollow>AJ Chen</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A id=bodyLinks title=public-semweb-lifesci@w3.org href="mailto:public-semweb-lifesci@w3.org" target=_blank rel=nofollow>public-semweb-lifesci@w3.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Friday, June 09, 2006 1:09 AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> scientific publishing task force update</DIV>
<DIV><BR></DIV>I have created a wiki page for the Scientific Publishing task force, please see <A id=bodyLinks href="http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce" target=_blank rel=nofollow>http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce</A><BR><BR>The first task is to develop an ontology for self-publishing of experiment. I have proposed a list of objects and properties related to self-publishing experiment. Please download the attached file under Task Status and review the proposal. Your feedback and comments will be greatly appreciated. You may also edit the file directly and email me the edited file. <BR><BR>It's critical to have more talents to engage in the task force and its tasks. Let me know if you are interested in join the task. If you have any new idea for a new task, please make a proposal and share with the group. <BR><BR>Thanks,<BR>AJ<BR></BLOCKQUOTE></DIV><BR></DIV></div></body></html>
--0-2146377084-1150037364=:53393--
Received on Sunday, 11 June 2006 18:51:43 UTC