NCBO Wiki - User contributions [en]

Minutes from 06/28/07 Conference Call

2007-06-29T07:17:12Z

Aqualung:

Go back to [[CTO:Main Page]]

Telecon, June 28
Present on the call: Christian Cocos, Kerstin Forsberg, Jennifer Fostel, Matthias Samwald, Jim Zheng

Next call July 19, 12 noon EDT.

Topic of discussion: Consortium forming in Austria to secure funding for an ontological representation of clinical trial data consistent with OBI / BFO work.

Matthias gave an introduction and status report of the consortium. It is based in Austria, and eager to work in concert with the OCI and BFO. All on the call were in agreement that is it good to work together. The goal is to have one standard evolved from both (all) efforts that fits the needs of both groups and does not duplicate effort.

The consortium Matthias represents is not the cancergrid project based in the UK. While neither the Austrian consortium nor OCI presently have a direct contact with this group, we aim to understand the alignment of OCI with the cancergrid ontology either during its development or soon after completion. The cancergrid group plans to finish this calendar year and deposit into the OBO Foundry.

Matthias mentioned the experience that some members of the Consortium have with DOLCE. A logical early step will be to compare the alignment of DOLCE and BFO and OBI / OCI, possibly via alignment of a dataset or terms list. The Consortium is more interested in a good collaboration with OCI and alignment with BFO than in using a particular ontology framework. The Austrian consortium does not have a preferred term list at the moment.

The OCI plans are (1) to participate in the OBI Workshop during July 9 – 14 and (2) to continue the process of collecting and grouping terms. It is thought that the OBI and BFO ontologies need more stability before OCI can start to place terms properly. We will focus on clinical research, but include all terms in hand, many of which come from CDISC and RTC schema.

Given the number of efforts towards an ontology for clinical investigations, it is difficult to assess the “right” one. Ideally all would converge. This is one way that OCI and the Austrian consortium could collectively contribute – by understanding DOLCE / BFO / OCI alignment and by collecting, aligning and defining terms from *all* efforts and placing within OCI (or DOLCE) in a manner consistent with BFO.

We have also plans to invite a member of both CDISC and BRIDG to present their projects at an upcoming telecom, and we hope to incorporate terms and solidify a collaboration with both projects.

Minutes from 06/28/07 Conference Call

2007-06-29T07:15:12Z

Aqualung: New page: Telecon, June 28 Present on the call: Christian Cocos, Kerstin Forsberg, Jennifer Fostel, Matthias Samwald, Jim Zheng Next call July 19, 12 noon EDT. Topic of discussion: Consortium fo...

Telecon, June 28
Present on the call: Christian Cocos, Kerstin Forsberg, Jennifer Fostel, Matthias Samwald, Jim Zheng

Next call July 19, 12 noon EDT.

Topic of discussion: Consortium forming in Austria to secure funding for an ontological representation of clinical trial data consistent with OBI / BFO work.

Matthias gave an introduction and status report of the consortium. It is based in Austria, and eager to work in concert with the OCI and BFO. All on the call were in agreement that is it good to work together. The goal is to have one standard evolved from both (all) efforts that fits the needs of both groups and does not duplicate effort.

The consortium Matthias represents is not the cancergrid project based in the UK. While neither the Austrian consortium nor OCI presently have a direct contact with this group, we aim to understand the alignment of OCI with the cancergrid ontology either during its development or soon after completion. The cancergrid group plans to finish this calendar year and deposit into the OBO Foundry.

Matthias mentioned the experience that some members of the Consortium have with DOLCE. A logical early step will be to compare the alignment of DOLCE and BFO and OBI / OCI, possibly via alignment of a dataset or terms list. The Consortium is more interested in a good collaboration with OCI and alignment with BFO than in using a particular ontology framework. The Austrian consortium does not have a preferred term list at the moment.

The OCI plans are (1) to participate in the OBI Workshop during July 9 – 14 and (2) to continue the process of collecting and grouping terms. It is thought that the OBI and BFO ontologies need more stability before OCI can start to place terms properly. We will focus on clinical research, but include all terms in hand, many of which come from CDISC and RTC schema.

Given the number of efforts towards an ontology for clinical investigations, it is difficult to assess the “right” one. Ideally all would converge. This is one way that OCI and the Austrian consortium could collectively contribute – by understanding DOLCE / BFO / OCI alignment and by collecting, aligning and defining terms from *all* efforts and placing within OCI (or DOLCE) in a manner consistent with BFO.

We have also plans to invite a member of both CDISC and BRIDG to present their projects at an upcoming telecom, and we hope to incorporate terms and solidify a collaboration with both projects.

Conference Call Minutes

2007-06-29T07:14:27Z

Aqualung:

Go back to [[CTO:Main Page]]

* [[Minutes from 06/28/07 Conference Call]]
* [[Minutes from 05/10/07 Conference Call]]
* [[Minutes from 05/03/07 Conference Call]]
* [[Minutes from 04/19/07 Conference Call]]
* [[Minutes from 04/12/07 Conference Call]]

OCI:Main Page

2007-06-28T18:15:20Z

Aqualung: /* Conference Call Information */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* '''Next CIO conference call: Thursday, July 19.'''
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[High-level Concepts v0.2]]
* [[Initial CTO-OBI Mapping]]
* [[CTO Term Compilation (Jennifer)]]
* [[OBI v0.6.6 Schematic]]

==CTO Development Policies==
* [[Ontology Metadata Policy (from OBI)]]
* [[CTO Check-out Procedure Policy]]
* [[CTO Working Group Membership Policy]]

==Publications==

OCI Google group: http://groups.google.com/group/OCInv

OCI Google mailing list: mailto:OCInv@googlegroups.com

OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

OCI:Main Page

2007-06-28T18:14:34Z

Aqualung: /* Conference Call Information */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* Next CIO conference call: Thursday, July 19.
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[High-level Concepts v0.2]]
* [[Initial CTO-OBI Mapping]]
* [[CTO Term Compilation (Jennifer)]]
* [[OBI v0.6.6 Schematic]]

==CTO Development Policies==
* [[Ontology Metadata Policy (from OBI)]]
* [[CTO Check-out Procedure Policy]]
* [[CTO Working Group Membership Policy]]

==Publications==

OCI Google group: http://groups.google.com/group/OCInv

OCI Google mailing list: mailto:OCInv@googlegroups.com

OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

Conference Call Schedule

2007-06-28T17:00:55Z

Aqualung:

Go back to [[CTO:Main Page]]

'''Meeting changes'''
*NO CALL on Thursday, April 26, 2007. Action items to be accomplished via wiki and email.
*NO CALL on Thursday, July 12, 2007 (OBI meeting).

'''Scheduled meetings:'''
*WEEKLY starting April 19 at 9:00am PST, 11:00am CST, noon EST, 6:00pm Germany

*Thursday April 12, 2007 at 9:30 EDT

OCI:Main Page

2007-06-27T19:48:09Z

Aqualung: /* Publications */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[High-level Concepts v0.2]]
* [[Initial CTO-OBI Mapping]]
* [[CTO Term Compilation (Jennifer)]]
* [[OBI v0.6.6 Schematic]]

==CTO Development Policies==
* [[Ontology Metadata Policy (from OBI)]]
* [[CTO Check-out Procedure Policy]]
* [[CTO Working Group Membership Policy]]

==Publications==

OCI Google group: http://groups.google.com/group/OCInv

OCI Google mailing list: mailto:OCInv@googlegroups.com

OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

OCI:Main Page

2007-06-27T19:47:49Z

Aqualung: /* Publications */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Call-in Information]]
* [[Conference Call Agendas]]
* [[Conference Call Minutes]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[High-level Concepts]]
* [[High-level Concepts v0.2]]
* [[Initial CTO-OBI Mapping]]
* [[CTO Term Compilation (Jennifer)]]
* [[OBI v0.6.6 Schematic]]

==CTO Development Policies==
* [[Ontology Metadata Policy (from OBI)]]
* [[CTO Check-out Procedure Policy]]
* [[CTO Working Group Membership Policy]]

==Publications==

OCI Google group: http://groups.google.com/group/OCInv

OCI Google mailing list: mailto:OCInv@googlegroups.com

CTO SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

Minutes from 04/12/07 Conference Call

2007-04-12T16:25:24Z

Aqualung:

'''Attendees:'''

Cristian Cocos, Jim Zheng, Richard Scheuermann, Jamie Lee, Simona Carini, Jennifer Fostel, Barry Smith, Dave Parrish,Wenle Zhao

'''Introductions:'''

Richard – UTSW, Division of Clinical Sciences, Department of Pathology, OBI, ImmPort

Jamie – UTSW, Department of Pathology, GO, OBI, ImmPort

Cristian – EE, CS, philosophy background; ontology building for the ACGTC (Advanced Clinico Genomic Trials on Cancer) Pan-European Consortium; experience building ontologies in Protégé-OWL

Jennifer – computational biology background; building NIHIS database for clinical info; OBI; interest in analogies in different fields and structure of clinical trials and toxicology experiments

Simona – UCSF, Ida Sim’s group; background in clinical trials, nursing, and data management; development of RCT schema

Jim Zheng – Medical University South Carolina; biology/CS background; biostatistics/bioinformatics department; clinical trials data management; interest in developing computational models and ontologies using engineering approaches to to formalize process

Wenle – new to group, Medical University South Carolina; project management for clinical trials

'''Discussion Items:'''

''WG organization''
* Conveyed on wiki
* Agreed on Jennifer and Richard as WG chairs; this can be changed in future based on performance

''Funding issues''
* Anyone who wants to take initiative for grant submission is encouraged
* Barry has pending grant application to develop BOLT (Biomedical Ontologies and Logic something) center which is under review. Proposal is to develop ontologies and there may be funding available for CTO

''WG Roles''
* We should establish responsibilities for different roles (chairs, secretary, developers, etc)
* Jamie is volunteered for secretary role to keep wiki updated and organized
* Wiki – individuals can also add their own stuff freely without going through secretary

''Managing discussion threads''
* Discussions through Email makes more sense since people check often but key points or decisions made during discussions should be posted on the wiki
* Agreed that both Chairs will summarize conclusions of discussions and secretary will compile and post on wiki
* Wiki posting a good idea so people can see the progress being made
* Find a time for weekly calls to review discussions – tentatively 6pm Germany, noon Eastern, 11am Central, 9am Pacific on Thursday. Cristian will check his calendar and free call-in options. Tuesday is the other possible day

''Development and WG policies''
* Metadata policy
** Briefly, when terms are being developed and structured, there should be minimum information included like term name, definition, authorship, updates/changes to terms, etc. All agreed to take a look at draft policies (“stolen” from OBI’s metadata policy) and vote on whether we should adopt these.
**Where would we enter these metadata fields in protégé? OBI is still working this out with Protégé Stanford but in the short term, use Comments field.
* Check-out policy
** Basic idea: whenever you want to modify ontology, make sure no one else is working on it, do your work, then let everyone know that you are done. Also, record a log of the changes. Details on wiki. People should be considerate about check-out/in.
**We agree to adopt this policy and be considerate about check-out lengths of time.
*Membership policy – do we need this? Probably not for now but thing about it

''Relationship between CTO/BFO/OBI''
* We should leverage the work OBI has done and make sure our efforts are parallel to OBI.
* We should develop CTO independently using OBI branch structure as a “template” since there is high-level commonality between CTO and OBI domains. If we see a need for changes in OBI we should collaborate with them to reach an agreement. We should import the “stable” version of OBI especially at the high level.
*We can’t avoid flux within OBI but OBI coordinators are receptive to feedback from the clinical trails perspectives; WG chairs will take role to interface with OBI and make sure they understand that changes in high-level structure will impact development of parallel ontologies

''Scope''
* What is the CTO domain? Issue of clinical trials versus clinical research.
* The assumption is that if we adequately cover clinical trials, we would also cover 90% of the clinical research domain
* It is a good idea to define the scope using a top-down and bottom-up approach?
* We also need to define priorities within the domain
* Keep “CTO” name for time being until scope is more fully defined

''Steps for early development progress''
* Assemble lists of terms to combine different perspectives within CTO domain
* Merge lists of terms to remove redundancy
* Position terms into main branches
* Begin work on definitions for terms
* Please give feedback for these proposed steps and proposed goals before NIH meeting for next week’s conference call

''Other''
* Whenever anything is posted on wiki, please send email to the group.

Workshop on Clinical Trial Ontology

2007-03-22T14:43:00Z

Aqualung: /* Preliminary Fragment of CTO (for illustration purposes only) */

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

== 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.

== 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, experimental design,'' 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;

(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 [http://obi.sourceforge.net/ OBI], which itself forms part of the [http://obofoundry.org/ OBO Foundry]

(6) draw on and seek maximal alignment with existing clinical trial ontologies, including the [http://smi.stanford.edu/smi-web/research/details.jsp?PubId=1227 Epoch ontology] used by the [http://www.immunetolerance.org/ Immune Tolerance Network] and the[http://rctbank.ucsf.edu/ontology/outline/index.htm RCT Schema] ontology used by the[http://rctbank.ucsf.edu/ Trial Bank Initiative]

(7) rest on a clear understanding of the relation between CTO and 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) meet the requirements of the [http://obofoundry.org OBO Foundry], and in particular support an adequate treatment of the distinction between ''types'' (''surgical intervention'', ''tumor'', ''human being'') and ''instances'' (Jane's oophorectomy, John's tumor, Fritz)

== Agenda [Draft] ==

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.

Please note that active participation in Day 2 of the meeting is restricted. If you wish to be considered for participation, please send a brief statement to [mailto:phismith@buffalo.edu Barry Smith].

Observers will be welcome in both parts of the meeting providing they give prior notice, details concerning which will be provided in due course.

----

'''May 16 Natcher Balcony A'''

8.00am Continental Breakfast

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

10.00am Discussion

10.15am Coffee

10.30am Suzanna Lewis: The OBO Foundry

11.00am Jennifer Fostel: The Ontology for Biomedical Investigations

11.30am Richard Scheuermann: Introducing the Clinical Trial Ontology

12.00 noon Discussion

12.30 Lunch

1.30pm Ida Sim: The RCT Schema

2.00pm Amar Das: Epoch: An Ontological Framework for Clinical Trial Management

2.30pm Panel on the Clinical Trial Ontology and the CDISC/BRIDG Initiatives

3.30pm General Discussion

5.00pm Close

----

'''May 17 Building 31 Conference Room 10'''

8.00am Continental Breakfast

9.00am Session 1: Building the Clinical Trial Ontology

11.00am Session 2: Applying the Clinical Trial Ontology

12.30 noon Lunch

1.30pm Session 3: The Future of the Clinical Trial Ontology

4.00pm Close

== Active Participants ==

'''All participants will be required to register. Registration details will be available in due course.'''

Sivaram Arabandi -- Cleveland Clinic

Charles E. Barr -- AMIA Clinical Trial Working Group

Carol Bean -- NIH/NHLBI

Mathias Brochhausen -- IFOMIS / European Center for Ontological Research, Saarbrücken

Werner Ceusters -- Ontology Research Group, University at Buffalo

Chris Chute -- NCBO, Mayo Clinic, Rochester, MN

Lindsay Cowell -- Duke University

Amar Das -- Stanford Medical Informatics

Kaushal Desai -- AstraZeneca

Liju Fan -- Ontology Workshop, LLC

Kerstin Forsberg -- AstraZeneca

Jennifer Fostel -- NIH/NIEHS

Gilberto Fragoso -- NIH/NCI

Douglas Fridsma -- University of Pittsburgh

Louis J. Goldberg -- University at Buffalo

Federico Goodsaid -- (FDA CDER, Office of Clinical Pharmacology)

Norbert Graf -- [http://acgt.ercim.org/ ACGT], Homburg, Germany

Ted Grasela -- Cognigen Corporation, Amherst, NY

Herb Hagler -- University of Texas Southwestern Medical Center

Steve Harris -- Computing Laboratory, University of Oxford

Tina Hernandez-Boussard -- PharmGKB, Stanford University

Warren A. Kibbe -- Northwestern University

Randy Levin -- CDER

Jamie Lee -- University of Texas Southwestern Medical Center

Suzanna Lewis -- NCBO, Berkeley, CA

Eric Little -- Center for Ontology and Interdisciplinary Studies

Peter Maccallum -- UK CancerGrid, Department of Oncology, University of Cambridge

Charles Mead -- NCI Center for Biomedical Informatics and Information Technology

Chris Mungall -- Howard Hughes Institute, Berkeley, CA

Mark Musen -- NCBO, Stanford University, CA

Fabian Neuhaus -– NCBO, University at Buffalo, NY

Chimezie Ogbuji -- Cleveland Clinic Foundation, OH

Dave Parrish -- Immune Tolerance Network, Pittsburgh, PA

Philippe Rocca-Serra -- EBI, Hinxton, Cambridge

Susanna Sansone -- EBI, Hinxton, Cambridge

Nigam Shah -– NCBO, Stanford Medical Informatics

Richard Scheuermann -- University of Texas Southwestern Medical Center

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

Barry Smith -– NCBO, University at Buffalo, NY

Holger Stenzhorn -- IFOMIS, Saarbrücken

Weida Tong -- Center for Toxicoinformatics, FDA NCTR

Trish Whetzel -- University of Pennsylvania

Samson Tu -- Stanford University

Gabriele Weiler -- Fraunhofer Institute, Sankt Ingbert, Germany

Chunhua Weng -- University of Pittsburgh

== Venue ==

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

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

[http://www.nih.gov/about/visitor/index.htm Travel to NIH Campus]

== 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

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]]

OCI:Main Page

2007-03-22T14:26:11Z

Aqualung: /* Publications */ Updated SVN repository link.

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Conference Call-in Information]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[Initial CTO-OBI Mapping]]

==CTO Development Policies==
* [[Ontology Metadata Proposal (from OBI)]]
* [[CTO Check-out Procedure Proposal]]

==Publications==

CTO Google group: http://groups.google.com/group/CTOtlg

CTO Google mailing list: mailto:CTOtlg@googlegroups.com

CTO SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

OCI:Main Page

2007-03-16T13:53:57Z

Aqualung: /* Publications */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Conference Call-in Information]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[Initial CTO-OBI Mapping]]

==CTO Development Policies==
* [[Ontology Metadata Proposal (from OBI)]]
* [[CTO Check-out Procedure Proposal]]

==Publications==

CTO Google group: http://groups.google.com/group/CTOtlg

CTO Google mailing list: mailto:CTOtlg@googlegroups.com

CTO SVN repository: http://acgt.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

OCI:Main Page

2007-03-16T13:23:47Z

Aqualung: /* Publications */ Not sure whether posting links to repositories might count as "publications" though...

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Conference Call-in Information]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[Initial CTO-OBI Mapping]]

==CTO Development Policies==
* [[Ontology Metadata Proposal (from OBI)]]
* [[CTO Check-out Procedure Proposal]]

==Publications==

CTO Google group: http://groups.google.com/group/CTOtlg

CTO Google mailing list: send email to CTOtlg@googlegroups.com

CTO SVN repository: http://acgt.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)

==CTO Wiki information==

OCI:Main Page

2007-03-16T13:15:22Z

Aqualung: /* Publications */

=CTO - Clinical Trials Ontology=

==About CTO==

The goal of the CTO Working Group 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.

==Recent Developments==

==Conference Call Information==
* [[Conference Call Schedule]]
* [[Conference Call-in Information]]
* [[Action Items]]

==Meetings==
* [[Upcoming Meetings]]
* [[Meetings Attended]]

==Communities and Working Group (WG) Participants==
* [[CTO WG Chairs]]
* [[CTO Curators]]
* [[Other members of CTO WG]]

==Draft version of CTO==

==Ontology Development Items==
* [[Design Principles]]
* [[Term Lists]]
* [[Initial CTO-OBI Mapping]]

==CTO Development Policies==
* [[Ontology Metadata Proposal (from OBI)]]
* [[CTO Check-out Procedure Proposal]]

==Publications==

CTO Google group: http://groups.google.com/group/CTOtlg

CTO Google mailing list: send email to CTOtlg@googlegroups.com

==CTO Wiki information==

CTO Check-out Procedure Proposal

2007-03-16T13:04:25Z

Aqualung:

[Adapted from Cristian Cocos (username: Aqualung)] When planning to work on the ontology:

1. Make sure, via Skype, that no one is working on the ontology right now,
so that you can be certain that the ontology you will be downloading is the
latest version.

2. Let everybody know that you will be working on the ontology for a certain amount of time, starting now. (Offline Skype status, or no reply, will be interpreted as "not working on the ontology, go ahead"! Make sure, then, that you are always online when working on the CTO.)

3. Download the latest CTO version using your SVN client.

4. Read the log, just so you know what has happened to the CTO since you last
updated it.

5. Do your work, keeping track religiously of all the changes you make. All of
this will go into the log. Will be making heavy use of abbreviations
(ac=added class, mc=modified class, dc=deleted class etc.). The log should
be as exhaustive as possible.

6. When done, you should save all changes locally, and upload them onto the server.
Make sure you fill out the log when uploading (you will be prompted to do
that at the time of the upload).

7. Let everyone know via Skype that you have just uploaded the latest
version, and that you are done with the CTO for now.

CTO Check-out Procedure Proposal

2007-03-16T12:56:47Z

Aqualung:

[Adapted from Cristian Cocos (username: Aqualung)] When planning on working on the ontology:

1. Make sure, via Skype, that no one is working on the ontology right now,
so that you can be certain that the ontology you will be downloading is the
latest version.

2. Let everybody know that you will be working on the ontology for a certain amount of time, starting now. (Offline Skype status, or no reply, will be interpreted as "not working on the ontology, go ahead"! Make sure, then, that you are always online when working on the CTO.)

3. Download the latest CTO version using your SVN client.

4. Read the log, just so you know what has happened to the CTO since you last
updated it.

5. Do your work, keeping track religiously of all the changes you make. All of
this will go into the log. Will be making heavy use of abbreviations
(ac=added class, mc=modified class, dc=deleted class etc.). The log should
be as exhaustive as possible.

6. When done, you should save all changes locally, and upload them onto the server.
Make sure you fill out the log when uploading (you will be prompted to do
that at the time of the upload).

7. Let everyone know via Skype that you have just uploaded the latest
version, and that you are done with the CTO for now.