View source for HCLS/OntologyTaskForce

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== Mission and Scope ==

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| The mission of the '''Ontology Task Force''' is to facilitate creation, evaluation and maintenance of "core vocabularies and ontologies to support cross-community data integration and collaborative efforts.” [[FootNote([http://www.w3.org/2001/sw/hcls/charter HCLS Charter])]] <br><br><br>Activities will focus on the theme of ''best practices'' in the context of ''well defined use cases'' that are of interest to the broader HCLS community. <br><br><br>Towards this end, this group will collaborate with other task forces within [http://www.w3.org/2001/sw/hcls/ HCLS] and with the [http://bioontology.org/ National Center for Biomedical Ontology (NCBO)].
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== Key Questions ==

* [[/OntologyDefinition|What is an ontology?]]
** NIST, OMG, NCBO, W3C .... any others ...
** [http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2007 NIST Ontology Definitions]
* [[/OntologyScoping|What information should be represented in an ontology?]]
* [[/OntologyRepresentation|How should information be represented in an ontology?]]
* [[/OntologyCreation|How could ontologies be created?]]
* [[/OntologyAccess|How should ontologies be accessed and used?]]
* [[/OntologyMaintenance|How should ontologies be maintained?]]
* [[/OntologyEvaluation|How should ontologies be evaluated?]]

== Active Tasks ==
* [http://esw.w3.org/topic/HCLS/Labels_and_Definitions Harmonization of the representation of labels, descriptions and definitions of entities in biomedical ontologies]
* [http://esw.w3.org/topic/HCLS/HCLSIG_BibliographicInformation Finding a common standard for the representation of bibliographic information]
* [http://esw.w3.org/topic/HCLS/OntologyTaskForce/BFOProcessDefinitionDiscussion Clarification of BFO Process Definition]
* [http://esw.w3.org/topic/HCLS/OntologyTaskForce/BIONTDSEDCM Mapping Clinical Observations across Clinical Practice and Clinical Trials]
* [http://esw.w3.org/topic/HCLS/Evidence A uniforma representation and reasoning approach for Evidence across HCLS]

== Resources ==

* [http://www.berkeleybop.org/ontologies/#mappings Mappings from Gene Ontology to other ontologies]

== Work products ==

Members of the Task Force share the responsibility for [[/DeliverablesMatrix|preparation of deliverables, with the assistance of collaborators]].

* [[/BIONTDSEDCM|Re-use and Cross Mapping of DCM and SDTM Models]]
* [[/W3CNotes|Notes Prepared for W3C]]
* Use Cases
** [[HCLS/ParkinsonUseCase|Parkinson's Disease]]
** [[HCLS/AlzheimersUseCase|Alzheimer's Disease]]
** [[HCLS/IntegratedUseCase|Integration of AD and PD Use Cases with extension to Bedside]]
* Ontology Building Experiences of Various Groups (Use Cases, Gotchas, Questions, Hacks, Solutions)
** [[HCLS/OntologyTaskForce/POMR|Experiences with building the Problem Oriented Medical Record Ontology]]
** [[Media:HCLS$$OntologyTaskForce$CEM.ppt|Clinical Element Models at IHC]]
** [[HCLS/OntologyTaskForce/SWAN|Experiences with building SWAN Ontology]]
** [[HCLS/OntologyTaskForce/ACPP|Experiences with building ACPP Ontology]]
** [[HCLS/OntologyTaskForce/Brainstage|Experiences with building Brainstage Ontology]]
** [[HCLS/OntologyTaskForce/bio-zen-experience|Experiences with building the bio-zen Ontology]]
** Kei - present his work on Neuron DB ontology
* Examples of using Ontologies
** Sub Task 1: Write up U. Manchester examples for using ontologies
     '''Owner:''' Alan Ruttenberg see [[/Ontologization_for_Transitive_Closure_Inferences/Examples|Ontologization for Transitive Closure Inferences ==> Examples]]
* Sub Task 2: Write up L and C examples for ontologization of Snomed
     '''Owner:''' Davide Zaccagnini
* Sub Task 3: Incorporate, align or extend use case based on these examples
     '''Owner:''' Donald Doherty and Kensaku Kawamoto
* Sub Task 4: [[HCLS/OntologyTaskForce/Create_Bridging_Ontology_between_NeuronDB_and_CoCoDat_databases_and_UMLS_Common_Vocabulary|Create Bridging Ontology between NeuronDB and CoCoDat databases and UMLS Common Vocabulary]]
     '''Owner:''' Donald Doherty
* [[HCLS/OntologyTaskForce/SeedOntology|Seed Ontology]]
** [[/DesignIssues|Design Choices and Issues in creating an ontology]]
** [[/SeedOntology/SeedOntologyDetailedFollowup|List of Statements from Research articles and their representation]]
* [[Media:HCLS$$OntologyTaskForce$AmsterdamF2FStatus.ppt|Amsterdam F2F Presentation of Goals, Status and Collaboration Opportunities]]
* [[HCLS/OntologyTaskForce/SampleOntologiesHCLS/OntologyTaskForce/SampleOntologies|Ontology Fragments]]
   '''Coordinator:''' John Madden
* Sub Task 1: Ontologization for Annotation Inferences
     '''Owner:''' Michael Miller
* Sub Task 2: Ontologization for Classification Inferences
* Sub Task 3: [[HCLS/OntologyTaskForce/Ontologization_for_Transitive_Closure_Inferences|Ontologization for Transitive Closure Inferences]]
* Sub Task 4: Ontologization for Change Propagation Inferences
* Sub Task 5: Experimenation with different design patterns
* [[HCLSIG_BioRDF_Subgroup/Tasks|Mappings to BIORDF Data Sources]]
   '''Coordinator:''' Xiaoshu Wang
* Sub Task 1: Rewrite BIORDF queries using Snomed (or any other ontology)
* Sub Task 2: Coordinate with Tonya, Alan and Susie to see which of the BIORDF data sources can address the questions identified in the use case.
     '''Owner:''' Vipul Kashyap
* [[HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices|Best practice descriptions]]
** Sub Task 1: Best practice for Ontology URI specifications
* [[/DemoImplementations|Demonstration implementations of Semantic Web technology in biomedicine]]

== Teleconferences ==

Our weekly teleconference occurs on Tuesdays, from 1600h-1700h GMT (1100h-1200h US Eastern Time).
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| Phone
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| IRC
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| Browser-based IRC client
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Our [[/Telcons|archived teleconference minutes]] are available.

== Active participants ==

The following HCLS members are actively involved in the activities of this task force. (Please feel free to add or remove your name. We've put your names as a [[WikiName]], so it will generate a link to your [[WikiHomePage]].) All HCLS participants are welcome to join in the activity of this task force.

* [[BudakArpinar]]
* [[JohnBarkley]]
* [[BillBug]]
* [[KeiCheung]]
* [[DonaldDoherty]]
* [[VipulKashyap]]
* [[KensakuKawamoto]]
* [[JoanneLuciano]]
* [[JohnMadden]]
* [[MichaelMiller]]
* [[AlanRuttenberg]]
* [[MatthiasSamwald]]
* [[AmitSheth]]
* [[SamirTartir]]
* [[XiaoshuWang]]

== Resources ==

We set up a [http://www.connotea.org/group/W3C%20HCLS%20Ontology%20Task%20Force public Connotea group for the Task Force], where we can maintain references of interest to all. 
 <span style="font-size: smaller"> You can view the page without a Connotea username; to add references you will need to (1) [http://www.connotea.org/register get a Connotea username (free)] and (2) [mailto:john.madden@duke.edu?subject=Add%20me%20to%20the%20Connotea%20group send John an email] with you username so he can add you to the group as a contributor. </span>

Feel free to add to our [[HCLS/OntologyTaskForce/UsefulLinks|useful links]] page.

{| border="1" cellpadding="2" cellspacing="0"
|<#D8D8D8><span style="font-size: smaller">|[[HCLSIG|HCLS Home]]</span>
|<#D8D8D8><span style="font-size: smaller">|[[HCLS/OntologyTaskForce|OTF Home]]</span>
|<#D8D8D8><span style="font-size: smaller">|[http://lists.w3.org/Archives/Public/public-semweb-lifesci/ Discussions]</span>
|<#D8D8D8><span style="font-size: smaller">|[mailto:public-semweb-lifesci@w3.org Post to HCLS listserv]</span>
|<#D8D8D8><span style="font-size: smaller">|[[HCLS/OntologyTaskForce/Telcons|Minutes]]</span>
|<#D8D8D8><span style="font-size: smaller">|[[HCLS/OntologyTaskForce/UsefulLinks|Links]]</span>
|}
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[[Category:Hclsig]]