Difference between revisions of "Workshop on Clinical Trial Ontology"

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== General Information ==
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== '''General Information''' ==
  
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The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Clinical Trials. The workshop will take place in March 2007; venue to be determined.
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The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Clinical Trials. The workshop will take place on May 16-17, 2007 at the NIH Campus in Bethesda, MD.  
  
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== Aim of the workshop  ==
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The meeting will be divided into two parts. Day 1 will be a public event consisting of presentations and panel discussions on the CTO and cognate initiatives. Day 2 will be a working meeting devoted to intense discussions of mature drafts of the CTO and to the creation of a strategy for its further development and testing.
  
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Ida,
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The work of the NCBO is funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found [http://nihroadmap.nih.gov/bioinformatics here].
  
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I think that the issue of models vs. ontologies is indeed important. Before we can address this issue sensibly, however, I think we need to have some idea of what a clinical trial ontology should be. My ideas (which are still inchoate) are as follows:
+
We are grateful to the National Heart, Lung and Blood Institute for generous support for this meeting.
  
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1. it should fulfil the three requirements you listed already in
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== '''Aim of the Workshop''' ==
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http://smi-web.stanford.edu/pubs/SMI_Reports/SMI-95-0584.pdf, which is to say:
 
  
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(1) fully and faithfully capture trials of any experimental design
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The aim of the workshop is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.
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(2) represent all the concepts [better: contain all the terms] needed for the task of meta-analysis
 
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(3) be in a form to be used for trial bank interoperation, as much as is possible
 
  
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2. it should share an upper level with the FuGO (Functional Genomics Investigation Ontology), which is attempting to create an ontology whose terms can be used in the annotation of experiments of other, though related, sorts (some members of the FuGO Consortium, e.g. Susanna Sansone have an interest also in the clinical trial ontology). See http://fugo.sourceforge.net/
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The Workshop will bring together representatives of all of the major groups involved in clinical trial informatics, design, execution, analysis and standardization, with the goal of achieving a broad consensus on the requirements which the ontology should address and on the most effective means of realizing these requirements. It will address the potential uses of CTO, and methodology for CTO design and development.
  
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3. it should interoperate with a drug (trial) ontology (or perhaps include the latter as a proper part)
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== '''Goals of the Clinical Trial Ontology Initiative''' ==
  
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4. it should interoperate with an epidemiology study ontology
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The proposed CTO should:
  
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5. it should interoperate with a disease ontology and with the other biomedical ontologies currently being developed within the OBO Foundry
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(1) fully and faithfully capture the types of entities and relationships involved in clinical trials of any experimental design
  
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6. it should provide a formal representation of, and definitions for, terms like:  
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(2) comprehend terms like: ''cohort, randomization, placebo, response, efficacy, control, protocol, null hypothesis, confidence interval, finding, biomarker, primary outcome, secondary outcome, intervention group, confounder,'' etc., including also major relevant statistical terms and terms drawn from resources such as the CDISC [http://www.cdisc.org/glossary/clinicalterminologyv4.pdf glossary] and
 +
all terms needed for the task of meta-analysis of clinical trials;
  
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cohort, randomization, placebo, response, efficacy, control, protocol, etc., including also major relevant statistical terms.
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(3) organize these terms in a structured way, providing definitions and logical relations designed to enhance retrieval of, reasoning with, and integration of the data annotated in its terms.
  
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My proposal would be that we focus on 6., since this is already a very considerable challenge. We might then create a small advance team to collect terms and create a preliminary test version. I hope that you will feel free to make alternative proposals, to maximize the usefulness of the end-result from your point of view.
+
(4) support trial bank interoperation
  
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With greetings
+
(5) form an integral part of the more comprehensive framework of the Ontology for Biomedical Investigations [http://obi.sourceforge.net/ OBI], which itself forms part of the [http://obofoundry.org/ OBO Foundry]
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Barry
 
  
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PS Nota bene: I am no fan of HL7 (see http://ontology.buffalo.edu/HL7/doublestandards.pdf). Indeed I think HL7 V3 is in large part responsible for the $30 bn. cost overruns incurred by the still non-functioning UK national health information infrastructure announced just this week. 
+
(6) draw on and seek maximal alignment with existing clinical trial ontologies, including:
  
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At 01:11 AM 6/8/2006, you wrote:
+
-- the [http://smi.stanford.edu/smi-web/research/details.jsp?PubId=1227 Epoch ontology] used by the [http://www.immunetolerance.org Immune Tolerance Network]
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Barry,
 
  
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What are the objectives you envision for this workshop? You may know that
+
-- the [http://rctbank.ucsf.edu/ontology/outline/index.htm RCT Schema] ontology used by the[http://rctbank.ucsf.edu/ Trial Bank Initiative]
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BRIDG is "comprehensive domain analysis model representing
 
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biomedical/clinical research", taking after HL7. We could probably spend the
 
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whole workshop on philosophical discussions of models vs. ontologies (I had
 
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wanted to ask you your views of that at Stanford but didn't get around to
 
−
it). Defining the objectives and anticipated outcomes would be important for
 
−
deciding who should/must attend.
 
  
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Initial names:
+
(7) rest on a clear understanding of the relation between CTO and related ventures such as an epidemiology study ontology
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BRIDG: Doug Fridsma, Joyce Niland (maybe)
 
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CDISC: Becky Kush
 
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HL7: Lakshmi Grama
 
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caBIG: not sure exactly who would be right
 
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NIH Roadmap: Stuart Speedie (U. Minn), maybe others -- ask Carol Bean
 
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AMIA CT WG: Michael Kahn, Charlie Barr,
 
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AMIA KR WG: not sure who
 
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Columbia has a group on Clinical Trials Informatics that might be relevant
 
  
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As for dates, towards the middle of May is probably best.
+
(8) rest on a clear understanding of the relation between CTO and data-model-oriented initiatives such as CDISC and BRIDG
  
−
Ida
+
(9) be created through an open process, in which all interested parties can be involved.
  
 +
== '''Agenda''' ==
  
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On 6/4/06 6:43 AM, "Smith, Barry" <phismith@buffalo.edu> wrote:
+
'''<big><u>Wednesday, May 16 - Building 45 (Natcher), Balcony A</u></big>'''
  
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> Dear Ida,
+
* 8:00am -- Registration & Continental Breakfast
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> Thanks for this -- it is clear that there is basic agreement as to
 
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> the facts of the matter concerning 'instances': the problem is rather
 
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> terminological. But more on this later.
 
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>
 
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> Concerning clinical trials, do you have specific persons at BRIDG,
 
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> HL7, CDISC, and caBIG, who you think should be involved in this
 
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> meeting? And do you know anyone at the FDA and at the AMIA WG on
 
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> Clinical Trials (or other similar bodies) who might want to be involved?
 
−
>
 
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> As to date, I am thinking of the second half of April or the first
 
−
> half of May, and on the East coast. Do you have preferences within that
 
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> window?
 
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>
 
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> With greetings
 
−
> Barry
 
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>
 
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> At 01:34 AM 6/3/2006, you wrote:
 
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>> Barry,
 
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>>
 
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>> A clinical trial ontology workshop would be very interesting. Other
 
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>> groups working in this area include BRIDG, HL7, CDISC, caBIG, etc as
 
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>> you probably know. It would be great to use such a meeting to work
 
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>> towards a first reference ontology for clinical trials. Do keep me
 
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>> posted on the meeting as it develops.
 
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>>
 
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>> I agree that 'instance' is used in all the ways you suggest. I think
 
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>> the main source of type-instance confusion in cBIO is in the way the
 
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>> bio and medical informatics communities use defintions 2 and 4. I
 
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>> think that in medical informatics, we tend to conflate #2 and #4
 
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>> because we're always thinking of data for a particular patient (or
 
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>> clinical trial) as the most specific information that needs to be
 
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>> captured. So, needing to capture eg Jane's particular oophorectomy,
 
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>> the type may be SURGICAL-INTERVENTION, the sub-type may be
 
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>> OOPHORECTOMY, and the instance JANE'S-OOPHORECTOMY. From the point
 
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>> of view of an ontologist of surgery, however, who doesn't deal with
 
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>> actual cases of oophorectomies, OOPHORECTOMY can well be an
 
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>> instance, with no need to consider or represent particular
 
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>> oophorectomies. In contrast, because many medical informaticians
 
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>> take care of patients, we tend to care about particular
 
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>> oophorectomies and consider those to be the 'instances'. This then
 
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>> causes us to draw the type-instance distinction at a different level
 
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>> of specificity than a pure ontologist of surgery would.
 
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>>
 
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>> In sum, I don't think the naming of meaning #4, or any of the
 
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>> meanings, is the problem, but rather a different conceptualization
 
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>> of how specific/particular a representation has to be. I hope that
 
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>> clarified rather than confused things?  And hard to do this by email!
 
−
>>
 
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>> Do you have a tentative month/days for the workshop?
 
−
>>
 
−
>> Best,
 
−
>> Ida
 
−
>>
 
−
>>
 
−
>> On 5/27/06 2:54 AM, "Smith, Barry" <phismith@buffalo.edu> wrote:
 
−
>>
 
−
>> Dear Ida,
 
−
>> I plan to organize a clinical trials ontology workshop in 2007, as
 
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>> one of the Center's dissemination workshops, and I am hoping very
 
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>> much that you will be involved. Here, to set us going, is my
 
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>> thinking on types vs. instances:
 
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>> The term 'instance' is used in different ways by different communities.
 
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>> 1. In the database world it means, officially, a complete database
 
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>> environment, including software, table structure, etc.; used when
 
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>> administrators need to describe multiple instances of the same database type.
 
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>> 2. However, the term 'instance' is also used loosely in the
 
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>> information modelling world (e.g. by HL7), to mean the data in a
 
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>> database about a specific case or particular (the data about  Jane,
 
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>> the data about Jane's oophorectomy).
 
−
>>
 
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>> 3. Sometimes ontology people use 'instance' to mean 'leaf node' in an is
 
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>> 4. In the philosophical ontology world, however, and increasingly in
 
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>> the GO/OBO world, 'instance' is used to mean: a particular
 
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>> (individual, spatiotemporal, normally observable) entity which
 
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>> instantiates a given type. Thus a particular organism, cell, tumor,
 
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>> pill, surgical intervention, ....
 
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>> Did I miss anything out?
 
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>> I think we need a term to cover meaning 4., though I would be happy
 
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>> to substitute another term for this if one is suggested.
 
−
>> With greetings
 
−
>> Barry
 
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>> At 10:58 PM 5/26/2006, Ida Sim wrote:
 
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>> Chris,
 
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>> Thanks for this. It's great to see the trial bank schema and instance data
 
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>> imported into OBD as a first step.
 
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>> We are indeed interested in a reference ontology for clinical trials but I
 
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>> don't think we've resolved the issue of types vs. instances. This requires
 
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>> much more discussion.
 
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>> Simona Carini has just joined our project and will work with UVic to push
 
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>> the visualization project further along. That will start to provide concrete
 
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>> uses for OBD and we can then work towards some more implementation
 
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>> questions.
 
−
>> Best,
 
−
>> Ida
 
−
>> On 5/24/06 5:14 PM, "chris mungall" <cjm@fruitfly.org> wrote:
 
−
>>>
 
−
>>> Sorry for the lack of subject line in the previous email! I hate it
 
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>>> when people do that. Here it is again, with subject line.
 
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>>>
 
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>>> On May 24, 2006, at 5:06 PM, chris mungall wrote:
 
−
>>>
 
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>>>> I've added a new wiki page:
 
−
>>>>
 
−
>> <http://smi.stanford.edu/projects/cbio/mwiki-internal/index.php/>http://smi.s
 
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>> tanford.edu/projects/cbio/mwiki-internal/index.php/
 
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>>
 
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>>>> Clinical_Trials_in_OBD
 
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>>>>
 
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>>>> This is reachable from the OBD wiki page
 
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>>>>
 
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>>>> The page contains a link to the demo and a discussion of where to go
 
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>>>> next for representing clinical trials in OBD. In particular OBD, will
 
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>>>> require that terms are represented as types and not as instances,
 
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>>>> which will require a shift away from the current trialbank
 
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>>>> representation. From Ida's slides at the last all hands, it seems
 
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>>>> that trialbank may be moving in this way anyway, towards a reference
 
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>>>> ontology for clinical trials?
 
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>>>>
 
−
>>>> Cheers
 
−
>>>> Chris
 
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>>>> --++**==--++**==--++**==--++**==--++**==--++**==--++**==
 
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>>>> cbio-developers mailing list
 
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>>>> cbio-developers@lists.stanford.edu
 
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>>>> https://mailman.stanford.edu/mailman/listinfo/cbio-developers
 
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>>>>
 
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>>>
 
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>
 
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>
 
−
Ref: ontology for clinical trial
 
  
 +
'''Session 1 (Chair: Barry Smith)'''
  
−
Ricardo Pietrobon co-chairs the MSI Ontology Working Group that represents the metabolomics domain in FuGO.
+
* 9:00am -- Carol Bean: ''Introduction''
  
 +
* 9:10am -- Susan Shurin, Deputy Director of the National Heart Lung and Blood Institute: ''Welcome''
  
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Ricardo is Assistant Professor at Duke University and his current work is primarily in clinical and translational research. He uses an ontology to encode randomized trials.
+
* 9:20am -- Werner Ceusters: ''How to Build an Ontology'' [http://ontology.buffalo.edu/07/CTO/ceusters.ppt ppt]
  
 +
* 10:00am -- Discussion
  
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In particular, his group seeks to expand existing ontologies, by including 'quantitative terms' (e.g. such as risk ratio,
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* 10:15am -- Refreshment Break
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confidence intervals, variables) , so that these would work with statistical packages such as R/bioconductor.
 
  
 +
'''Session 2 (Chair: Dave Parrish)'''
  
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Ricardo has also been in contact with Ida Sim.
+
* 10:30am -- Chris Mungall: ''The OBO Foundry'' [http://ontology.buffalo.edu/07/CTO/mungall.ppt ppt]
  
 +
* 11:00am -- Jennifer Fostel: ''The Ontology for Biomedical Investigations'' [http://ontology.buffalo.edu/07/CTO/fostel.ppt ppt]
  
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Therefore, also as MSI Ontology Working Group, we will be very interested to know more about the plans of this ontology for clinical trial and contribute where possible.
+
* 11:30am -- Richard Scheuermann: ''Introducing the Clinical Trial Ontology'' [http://ontology.buffalo.edu/07/CTO/scheuermann.ppt  ppt]
  
−
== Agenda ==
+
* 12:00pm -- Discussion
  
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== Participation ==
+
* 12:30pm -- Lunch Break
−
Requests for participation are welcome. Please send a brief statement of your expertise to [mailto:phismith@buffalo.edu Barry Smith].
 
  
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== Participants (First Tentative List] ==
+
'''Session 3 (Chair: Werner Ceusters)'''
  
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Russ Altman -- Stanford University
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* 1:30pm -- Ida Sim: ''The RCT Schema'' [http://ontology.buffalo.edu/07/CTO/sim.ppt  ppt]
  
−
Ted Grasela -- Cognigen Corporation, Amherst, NY
+
* 2:00pm -- Amar Das: ''Epoch: An Ontological Framework for Clinical Trial Management''
 +
[http://ontology.buffalo.edu/07/CTO/Das.pdf ppt]
  
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Mark Musen -- NCBO, Stanford University
+
* 2:30pm -- Barry Smith: ''The Clinical Trial Ontology: Creating Consensus'' [http://ontology.buffalo.edu/07/CTO/smith.ppt  ppt]
  
−
Fabian Neuhaus -– NCBO, University at Buffalo
+
* 3:30pm -- Refreshment Break
  
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Nigam Shah -– NCBO, Stanford Medical Informatics
+
* 4:00pm -- Discussion Session
  
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Susanna Sansone -- EBI, Hinxton, Cambridge
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* 5:00pm -- Close
  
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Ida Sim -- NCBO, University of San Francisco Medical Center
 
  
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Barry Smith -– NCBO, University at Buffalo
+
'''<big><u>Thursday, May 17 - Building 31, Conference Room 10</u></big>'''
  
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== Venue ==
+
* 8:00am -- Registration & Continental Breakfast
 +
 
 +
'''Session 4 (Moderator: Jennifer Fostel)'''
 +
 
 +
* 9:00am -- Building the Clinical Trial Ontology
 +
 
 +
* 10:30am -- Refreshment Break
 +
 
 +
''' Session 5 (Moderator: Alan Ruttenberg)'''
 +
 
 +
* 11:00am -- Applying the Clinical Trial Ontology
 +
**Norbert Graf: ACGT's Clinical Trial Builder [http://ontology.buffalo.edu/07/CTO/graf.ppt ppt]
 +
 
 +
* 12:30pm -- Lunch Break
 +
 
 +
'''Session 6 (Moderator: Richard Scheuermann)'''
 +
 
 +
* 1:30pm -- The Future of the Clinical Trial Ontology [[Media:CTO_Workshop_Day_2_RS_JL.doc]]
 +
 
 +
* 3:00pm -- Close
 +
 
 +
== '''NIH Security Regulations''' ==
 +
 
 +
All visitor vehicles, including taxicabs, hotel and airport shuttles, delivery trucks and vans will be inspected before being allowed on campus. Visitors will be asked to show a form of government-issued photo identification (driver's license, passport, green card, etc.) and to state the purpose of their visit. Be sure to allow extra time for this vehicle inspection procedure. Employees and visitors should continue to wear their identification prominently at all times while on campus.
 +
 +
Guards will remain at certain buildings to address specific program requirements such as sensitive research and safety concerns. At building entrances where guards are posted:
 +
* Visitors may be required to log in, wear a visitors pass and have an employee escort them through the building.
 +
* Visitors may be required to pass through a metal detector and have bags, backpacks or purses inspected or x-rayed as they enter buildings.
 +
Security staff will be looking for and confiscating any suspicious or potentially dangerous materials. U.S. Code prohibits bringing any dangerous weapons onto Federal property, including anything with a blade longer than 2½ inches. Meeting participants may want to leave extra bags or personal materials at their hotel to minimize the time needed for inspection.
 +
 
 +
All visitors including patients, contractors, vendors and delivery persons must use the following entrances:
 +
 +
<u>Rockville Pike at South Drive</u> (Metro):
 +
* Open 24 hours - Inbound and Outbound traffic
 +
* Open to All Vehicles
 +
* Pedestrian Turnstiles Open for Employees
 +
* Gateway Center at Metro Open for Visitor Registration--this is where visitors check-in with security if they are not driving
 +
 
 +
<u>Old Georgetown Road at Center Drive</u> (This entrance is primarily for commercial vehicles and visitors):
 +
* 6am- 7pm -Inbound and Outbound Traffic
 +
* Open to Employee, Commercial and Visitor Vehicles
 +
* Pedestrian Turnstiles Open for Employees
 +
 +
Please note: Visitor parking is limited at NIH. Visitors are encouraged to use public transportation such as the Metrorail subway system which has a convenient stop (Medical Center) on the NIH campus.
 +
 
 +
Visitors arriving by bus will be dropped off at the NIH/Medical Center Metro stop at Rockville Pike and South Drive. Patients and visitors on official business can then ride the Campus Shuttle to the Clinical Center and other designated shuttle stops on the campus.
 +
 
 +
== '''Participants (Final)''' ==
 +
 
 +
Robert Arp -- NCBO, University at Buffalo
 +
 
 +
Elaine Ayres -- NIH / Clinical Center
 +
 
 +
William Barrick -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH
 +
 
 +
Carol Bean -- National Heart, Lung and Blood Institute (NHLBI) / NIH
 +
 
 +
Maureen Beanan -- National Center for Research Resources (NCRR) / NIH
 +
 
 +
Elmer Bernstam -- University of Texas Health Science Center at Houston
 +
 
 +
Olivier Bodenreider -- National Library of Medicine (NLM) / NIH
 +
 
 +
Olga Brazhnik -- National Center for Research Resources (NCRR) / NIH
 +
 
 +
Constantino Castillo -- The KEVRIC Company, Inc.
 +
 
 +
Werner Ceusters -- Ontology Research Group, University at Buffalo
 +
 
 +
Huey Cheung -- Center for Information Technology (CIT) / NIH
 +
 
 +
Ling Chin -- National Institute on Deafness and Other Communication Disorders (NIDCD) / NIH
 +
 
 +
In Hye Cho -- National Library of Medicine (NLM) / NIH
 +
 
 +
Christopher G. Chute -- NCBO, Mayo Clinic
 +
 
 +
Kevin Clany -- Invitrogen Corp.
 +
 
 +
Christian Cocos -- IFOMIS (Saarbrücken, Germany)
 +
 
 +
Elaine Collier -- National Center for Research Resources (NCRR) / NIH
 +
 
 +
Leo Cousineau -- Information Management Consultants (Reston, VA)
 +
 
 +
Lindsay Cowell -- Duke University Medical Center
 +
 
 +
Amar Das -- Stanford Medical Informatics
 +
 
 +
Kaushal Desai -- AstraZeneca
 +
 
 +
Stephen Dobson -- Pfizer Global Research and Development
 +
 
 +
Liju Fan -- Ontology Workshop, LLC
 +
 
 +
Gabriele Feolo -- National Heart, Lung and Blood Institute (NHLBI) / NIH
 +
 
 +
Kerstin Forsberg -- AstraZeneca
 +
 
 +
Jennifer Fostel -- NIH/NIEHS
 +
 
 +
Douglas Fridsma -- University of Pittsburgh
 +
 
 +
Jane Fun -- Contractor, National Library of Medicine (NLM) / NIH
 +
 
 +
Louis J. Goldberg -- University at Buffalo
 +
 
 +
Peter Good -- National Human Genome Research Institute (NHGRI) / NIH
 +
 
 +
Norbert Graf -- Clinic for Paediatric Oncology and Haematology, Saarland University (Homburg, Germany)
 +
 
 +
Lakshmi M. Grama -- National Cancer Institute (NCI) / NIH
 +
 
 +
Ted Grasela -- Cognigen Corporation (Amherst, NY)
 +
 
 +
Herb Hagler -- University of Texas Southwestern Medical Center
 +
 
 +
Andrea Harabin -- National Heart, Lung and Blood Institute (NHLBI) / NIH
 +
 
 +
William Harlan -- Consultant, National Library of Medicine (NLM) / NIH
 +
 
 +
Steve Harris -- Computing Laboratory, University of Oxford
 +
 
 +
Frank Hartel -- NCI Center for Bioinformatics / NIH
 +
 
 +
Calvin A. Johnson -- Center for Information Technology (CIT) / NIH
 +
 
 +
Heather A. Junkins -- CRIIT & NHLBI / NIH
 +
 
 +
Webster Kelsey -- Dept of Biomedical Informatics, University of Pittsburgh
 +
 
 +
Warren A. Kibbe -- Northwestern University
 +
 
 +
Bron W. Kisler -- Clinical Data Interchange Standards Consortium (CDISC)
 +
 
 +
George A. Komatsoulis -- NCI Center for Bioinformatics / NIH
 +
 
 +
Jennie Larkin -- National Heart, Lung and Blood Institute (NHLBI) / NIH
 +
 
 +
William Lau -- Center for Information Technology (CIT) / NIH
 +
 
 +
Jamie Lee -- University of Texas Southwestern Medical Center at Dallas
 +
 
 +
Natasha Levenkov -- Rockefeller University
 +
 
 +
Yuan Liu -- National Institute of Neurological Diseases and Stroke (NINDS) / NIH
 +
 
 +
Yun Lu -- KAI Research, Inc.
 +
 
 +
Dan Lyman -- Information Management Consultants (Reston, VA)
 +
 
 +
Peter Lyster -- Center for Bioinformatics and Computational Biology, National Institute of General Medical Sciences (NIGMS) / NIH
 +
 
 +
Peter Maccallum -- CRUK Cambridge Research Institute, University of Cambridge
 +
 
 +
Charles Mead -- NCI/NIH, Center for Biomedical Informatics and Information Technology
 +
 
 +
Chris Mungall -- NCBO, Lawrence Berkeley National Laboratory
 +
 
 +
Robert A. Musson -- National Heart, Lung and Blood Institute (NHLBI) / NIH
 +
 
 +
Darren Natale -- Georgetown University Medical Center
 +
 
 +
Fabian Neuhaus -– National Institute of Standards and Technology (NIST)
 +
 
 +
Eric Neumann -- Teranode (Seattle, WA)
 +
 
 +
Eduardo Ortiz -- National Heart, Lung and Blood Institute (NHLBI) / NIH
 +
 
 +
Jeng-Jong Pan -- National Institute on Drug Abuse (NIDA) / NIH
 +
 
 +
Dave Parrish -- Immune Tolerance Network (Pittsburgh, PA)
 +
 
 +
George O. Redmond -- National Cancer Institute (NCI) / NIH
 +
 
 +
Dianne M. Reeves -- National Cancer Institute, Center for Biomedical Informatics and Information Technology (formerly NCICB) / NIH
 +
 
 +
Alan Ruttenberg -- Science Commons (c/o MIT CSAIL)
 +
 
 +
Jody Sachs -- National Center for Research Resources (NCRR) / NIH
 +
 
 +
Michael Sayre -- National Center for Research Resources (NCRR) / NIH
 +
 
 +
Richard Scheuermann -- University of Texas Southwestern Medical Center
 +
 
 +
Susan Shurin -- National Heart, Lung and Blood Institute (NHLBI) / NIH
 +
 
 +
Hua-Chuan Sim -- National Library of Medicine (NLM) / NIH
 +
 
 +
Ida Sim -- Trial Bank, University of California at San Francisco Medical Center
 +
 
 +
Barry Smith -- NCBO, University at Buffalo
 +
 
 +
Ranjana Srivastava -- Information Management Consultants (Reston, VA)
 +
 
 +
Samson Tu -- Stanford University
 +
 
 +
Suresh Varghese -- Digital Infuzion, Inc.
 +
 
 +
Chunhua Weng -- University of Pittsburgh
 +
 
 +
Rebecca Williams -- National Library of Medicine (NLM) / NIH
 +
 
 +
Ashley Xia -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH
 +
 
 +
Sandhya Xirasagar -- Information Management Consultants (Reston, VA)
 +
 
 +
Alison Yao -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH
 +
 
 +
Zhensheng Zhang -- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) / NIH
 +
 
 +
== '''Venue''' ==
 +
 
 +
Day 1: Balcony A, Building 45 (Natcher), NIH Campus, Bethesda, MD
 +
 
 +
Day 2: Conference Room 10, Building 31, NIH Campus, Bethesda, MD
 +
 
 +
A printable NIH Visitors Map can be found at: [http://parking.nih.gov/documents/visitorAccessMap.pdf NIH Visitors Map]
 +
 
 +
A printable schedule of shuttle service between area hotels and NIH can be found at:  [http://dtts.ors.od.nih.gov/documents/south_hotel_shuttles.pdf NIH Shuttles]
 +
 
 +
== '''Links''' ==
 +
 
 +
[http://www.bioontology.org/ncbo/faces/index.xhtml NCBO Bioportal]
 +
 
 +
[http://obo.sourceforge.net Open Biomedical Ontologies]
 +
 
 +
[http://obofoundry.org OBO Foundry]
 +
 
 +
[http://obi.sourceforge.net Ontology for Biomedical Investigations]
 +
 
 +
[http://rctbank.ucsf.edu/ Trial Bank]
 +
 
 +
[http://protege.stanford.edu/conference/2006/submissions/slides/3.2_Shankar_EpochModels.pdf Epoch Ontology]
 +
 
 +
[http://www.ifomis.uni-saarland.de/wiki/index.php/ACGT The ACGT Project]: Advancing Clinico-Genomic Trials on Cancer
 +
 
 +
[http://www.bioontology.org/wiki/index.php/CTO:Main_Page Clinical Trial Ontology Wiki]
 +
 
 +
[http://esw.w3.org/topic/HCLS/OntologyTaskForce/BIONTDSEDCM HCLS Ontology Task Force]
 +
 
 +
A video introduction to ontologies by Barry Smith is available here:
 +
 
 +
*Realmedia: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm
 +
 
 +
*Mediaplayer: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV
 +
 
 +
The second half of this presentation pertains to the building of the Clinical Trial Ontology.
 +
 
 +
== '''Preliminary Fragment of CTO''' (for illustration purposes only) ==
 +
 
 +
[http://cto.googlecode.com/svn/trunk/CTO.owl Current OWL version]
 +
 
 +
[[Image:CTO.jpg]]

Latest revision as of 10:38, 6 August 2008

General Information

The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Clinical Trials. The workshop will take place on May 16-17, 2007 at the NIH Campus in Bethesda, MD.

The meeting will be divided into two parts. Day 1 will be a public event consisting of presentations and panel discussions on the CTO and cognate initiatives. Day 2 will be a working meeting devoted to intense discussions of mature drafts of the CTO and to the creation of a strategy for its further development and testing.

The work of the NCBO is funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found here.

We are grateful to the National Heart, Lung and Blood Institute for generous support for this meeting.

Aim of the Workshop

The aim of the workshop is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.

The Workshop will bring together representatives of all of the major groups involved in clinical trial informatics, design, execution, analysis and standardization, with the goal of achieving a broad consensus on the requirements which the ontology should address and on the most effective means of realizing these requirements. It will address the potential uses of CTO, and methodology for CTO design and development.

Goals of the Clinical Trial Ontology Initiative

The proposed CTO should:

(1) fully and faithfully capture the types of entities and relationships involved in clinical trials of any experimental design

(2) comprehend terms like: cohort, randomization, placebo, response, efficacy, control, protocol, null hypothesis, confidence interval, finding, biomarker, primary outcome, secondary outcome, intervention group, confounder, etc., including also major relevant statistical terms and terms drawn from resources such as the CDISC glossary and all terms needed for the task of meta-analysis of clinical trials;

(3) organize these terms in a structured way, providing definitions and logical relations designed to enhance retrieval of, reasoning with, and integration of the data annotated in its terms.

(4) support trial bank interoperation

(5) form an integral part of the more comprehensive framework of the Ontology for Biomedical Investigations OBI, which itself forms part of the OBO Foundry

(6) draw on and seek maximal alignment with existing clinical trial ontologies, including:

-- the Epoch ontology used by the Immune Tolerance Network

-- the RCT Schema ontology used by theTrial Bank Initiative

(7) rest on a clear understanding of the relation between CTO and related ventures such as an epidemiology study ontology

(8) rest on a clear understanding of the relation between CTO and data-model-oriented initiatives such as CDISC and BRIDG

(9) be created through an open process, in which all interested parties can be involved.

Agenda

Wednesday, May 16 - Building 45 (Natcher), Balcony A

  • 8:00am -- Registration & Continental Breakfast

Session 1 (Chair: Barry Smith)

  • 9:00am -- Carol Bean: Introduction
  • 9:10am -- Susan Shurin, Deputy Director of the National Heart Lung and Blood Institute: Welcome
  • 9:20am -- Werner Ceusters: How to Build an Ontology ppt
  • 10:00am -- Discussion
  • 10:15am -- Refreshment Break

Session 2 (Chair: Dave Parrish)

  • 10:30am -- Chris Mungall: The OBO Foundry ppt
  • 11:00am -- Jennifer Fostel: The Ontology for Biomedical Investigations ppt
  • 11:30am -- Richard Scheuermann: Introducing the Clinical Trial Ontology ppt
  • 12:00pm -- Discussion
  • 12:30pm -- Lunch Break

Session 3 (Chair: Werner Ceusters)

  • 1:30pm -- Ida Sim: The RCT Schema ppt
  • 2:00pm -- Amar Das: Epoch: An Ontological Framework for Clinical Trial Management

ppt

  • 2:30pm -- Barry Smith: The Clinical Trial Ontology: Creating Consensus ppt
  • 3:30pm -- Refreshment Break
  • 4:00pm -- Discussion Session
  • 5:00pm -- Close


Thursday, May 17 - Building 31, Conference Room 10

  • 8:00am -- Registration & Continental Breakfast

Session 4 (Moderator: Jennifer Fostel)

  • 9:00am -- Building the Clinical Trial Ontology
  • 10:30am -- Refreshment Break

Session 5 (Moderator: Alan Ruttenberg)

  • 11:00am -- Applying the Clinical Trial Ontology
    • Norbert Graf: ACGT's Clinical Trial Builder ppt
  • 12:30pm -- Lunch Break

Session 6 (Moderator: Richard Scheuermann)

  • 3:00pm -- Close

NIH Security Regulations

All visitor vehicles, including taxicabs, hotel and airport shuttles, delivery trucks and vans will be inspected before being allowed on campus. Visitors will be asked to show a form of government-issued photo identification (driver's license, passport, green card, etc.) and to state the purpose of their visit. Be sure to allow extra time for this vehicle inspection procedure. Employees and visitors should continue to wear their identification prominently at all times while on campus.

Guards will remain at certain buildings to address specific program requirements such as sensitive research and safety concerns. At building entrances where guards are posted:

  • Visitors may be required to log in, wear a visitors pass and have an employee escort them through the building.
  • Visitors may be required to pass through a metal detector and have bags, backpacks or purses inspected or x-rayed as they enter buildings.

Security staff will be looking for and confiscating any suspicious or potentially dangerous materials. U.S. Code prohibits bringing any dangerous weapons onto Federal property, including anything with a blade longer than 2½ inches. Meeting participants may want to leave extra bags or personal materials at their hotel to minimize the time needed for inspection.

All visitors including patients, contractors, vendors and delivery persons must use the following entrances:

Rockville Pike at South Drive (Metro):

  • Open 24 hours - Inbound and Outbound traffic
  • Open to All Vehicles
  • Pedestrian Turnstiles Open for Employees
  • Gateway Center at Metro Open for Visitor Registration--this is where visitors check-in with security if they are not driving

Old Georgetown Road at Center Drive (This entrance is primarily for commercial vehicles and visitors):

  • 6am- 7pm -Inbound and Outbound Traffic
  • Open to Employee, Commercial and Visitor Vehicles
  • Pedestrian Turnstiles Open for Employees

Please note: Visitor parking is limited at NIH. Visitors are encouraged to use public transportation such as the Metrorail subway system which has a convenient stop (Medical Center) on the NIH campus.

Visitors arriving by bus will be dropped off at the NIH/Medical Center Metro stop at Rockville Pike and South Drive. Patients and visitors on official business can then ride the Campus Shuttle to the Clinical Center and other designated shuttle stops on the campus.

Participants (Final)

Robert Arp -- NCBO, University at Buffalo

Elaine Ayres -- NIH / Clinical Center

William Barrick -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH

Carol Bean -- National Heart, Lung and Blood Institute (NHLBI) / NIH

Maureen Beanan -- National Center for Research Resources (NCRR) / NIH

Elmer Bernstam -- University of Texas Health Science Center at Houston

Olivier Bodenreider -- National Library of Medicine (NLM) / NIH

Olga Brazhnik -- National Center for Research Resources (NCRR) / NIH

Constantino Castillo -- The KEVRIC Company, Inc.

Werner Ceusters -- Ontology Research Group, University at Buffalo

Huey Cheung -- Center for Information Technology (CIT) / NIH

Ling Chin -- National Institute on Deafness and Other Communication Disorders (NIDCD) / NIH

In Hye Cho -- National Library of Medicine (NLM) / NIH

Christopher G. Chute -- NCBO, Mayo Clinic

Kevin Clany -- Invitrogen Corp.

Christian Cocos -- IFOMIS (Saarbrücken, Germany)

Elaine Collier -- National Center for Research Resources (NCRR) / NIH

Leo Cousineau -- Information Management Consultants (Reston, VA)

Lindsay Cowell -- Duke University Medical Center

Amar Das -- Stanford Medical Informatics

Kaushal Desai -- AstraZeneca

Stephen Dobson -- Pfizer Global Research and Development

Liju Fan -- Ontology Workshop, LLC

Gabriele Feolo -- National Heart, Lung and Blood Institute (NHLBI) / NIH

Kerstin Forsberg -- AstraZeneca

Jennifer Fostel -- NIH/NIEHS

Douglas Fridsma -- University of Pittsburgh

Jane Fun -- Contractor, National Library of Medicine (NLM) / NIH

Louis J. Goldberg -- University at Buffalo

Peter Good -- National Human Genome Research Institute (NHGRI) / NIH

Norbert Graf -- Clinic for Paediatric Oncology and Haematology, Saarland University (Homburg, Germany)

Lakshmi M. Grama -- National Cancer Institute (NCI) / NIH

Ted Grasela -- Cognigen Corporation (Amherst, NY)

Herb Hagler -- University of Texas Southwestern Medical Center

Andrea Harabin -- National Heart, Lung and Blood Institute (NHLBI) / NIH

William Harlan -- Consultant, National Library of Medicine (NLM) / NIH

Steve Harris -- Computing Laboratory, University of Oxford

Frank Hartel -- NCI Center for Bioinformatics / NIH

Calvin A. Johnson -- Center for Information Technology (CIT) / NIH

Heather A. Junkins -- CRIIT & NHLBI / NIH

Webster Kelsey -- Dept of Biomedical Informatics, University of Pittsburgh

Warren A. Kibbe -- Northwestern University

Bron W. Kisler -- Clinical Data Interchange Standards Consortium (CDISC)

George A. Komatsoulis -- NCI Center for Bioinformatics / NIH

Jennie Larkin -- National Heart, Lung and Blood Institute (NHLBI) / NIH

William Lau -- Center for Information Technology (CIT) / NIH

Jamie Lee -- University of Texas Southwestern Medical Center at Dallas

Natasha Levenkov -- Rockefeller University

Yuan Liu -- National Institute of Neurological Diseases and Stroke (NINDS) / NIH

Yun Lu -- KAI Research, Inc.

Dan Lyman -- Information Management Consultants (Reston, VA)

Peter Lyster -- Center for Bioinformatics and Computational Biology, National Institute of General Medical Sciences (NIGMS) / NIH

Peter Maccallum -- CRUK Cambridge Research Institute, University of Cambridge

Charles Mead -- NCI/NIH, Center for Biomedical Informatics and Information Technology

Chris Mungall -- NCBO, Lawrence Berkeley National Laboratory

Robert A. Musson -- National Heart, Lung and Blood Institute (NHLBI) / NIH

Darren Natale -- Georgetown University Medical Center

Fabian Neuhaus -– National Institute of Standards and Technology (NIST)

Eric Neumann -- Teranode (Seattle, WA)

Eduardo Ortiz -- National Heart, Lung and Blood Institute (NHLBI) / NIH

Jeng-Jong Pan -- National Institute on Drug Abuse (NIDA) / NIH

Dave Parrish -- Immune Tolerance Network (Pittsburgh, PA)

George O. Redmond -- National Cancer Institute (NCI) / NIH

Dianne M. Reeves -- National Cancer Institute, Center for Biomedical Informatics and Information Technology (formerly NCICB) / NIH

Alan Ruttenberg -- Science Commons (c/o MIT CSAIL)

Jody Sachs -- National Center for Research Resources (NCRR) / NIH

Michael Sayre -- National Center for Research Resources (NCRR) / NIH

Richard Scheuermann -- University of Texas Southwestern Medical Center

Susan Shurin -- National Heart, Lung and Blood Institute (NHLBI) / NIH

Hua-Chuan Sim -- National Library of Medicine (NLM) / NIH

Ida Sim -- Trial Bank, University of California at San Francisco Medical Center

Barry Smith -- NCBO, University at Buffalo

Ranjana Srivastava -- Information Management Consultants (Reston, VA)

Samson Tu -- Stanford University

Suresh Varghese -- Digital Infuzion, Inc.

Chunhua Weng -- University of Pittsburgh

Rebecca Williams -- National Library of Medicine (NLM) / NIH

Ashley Xia -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH

Sandhya Xirasagar -- Information Management Consultants (Reston, VA)

Alison Yao -- National Institute of Allergy and Infectious Diseases (NIAID) / NIH

Zhensheng Zhang -- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) / NIH

Venue

Day 1: Balcony A, Building 45 (Natcher), NIH Campus, Bethesda, MD

Day 2: Conference Room 10, Building 31, NIH Campus, Bethesda, MD

A printable NIH Visitors Map can be found at: NIH Visitors Map

A printable schedule of shuttle service between area hotels and NIH can be found at: NIH Shuttles

Links

NCBO Bioportal

Open Biomedical Ontologies

OBO Foundry

Ontology for Biomedical Investigations

Trial Bank

Epoch Ontology

The ACGT Project: Advancing Clinico-Genomic Trials on Cancer

Clinical Trial Ontology Wiki

HCLS Ontology Task Force

A video introduction to ontologies by Barry Smith is available here:

  • Realmedia: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm
  • Mediaplayer: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV

The second half of this presentation pertains to the building of the Clinical Trial Ontology.

Preliminary Fragment of CTO (for illustration purposes only)

Current OWL version

CTO.jpg

Retrieved from "https://www.bioontology.org//mediawiki/index.php?title=Workshop_on_Clinical_Trial_Ontology&oldid=7511"