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Vision: Bench to Bedside

This is a collection of topics and references to those topics that are proposed by the intended participants of the first F2F meeting of the HCLSIG group. It aims to better prepare the participants for the break-out session discussions.

The following table is subjected to change according to the email responses from the HCLSIG Members.

  • ||Topics ||Description ||Interested Participants ||References ||
||||||||||<style="text-align:center;">Ontologies and Knowledge Presentation ||
||bioMedical ontologies || ||Mark Musen ||The National Center for Biomedical Ontology ||
|| Collaborative Ontology Development || Terminological Federation, Group Communication Structures, Social Networks, Meaning Negotiation, Consensus Derivation, Web of Trust, Peer Review, Wikis || Mark Musen, John Madden, Eric Neumann, Vipul Kashyap, Marja-Riitta Koivunen, Vinay Chaudhri, Pat Croke, Alfredo Morales || Annotea social bookmarks and topics? ||
||<style="text-align:left;"|3>scientific literature ||semantics and literature - including semantics of authorship (FOAF?) ||Matt Cockerill || ||
||aggregation of scientific literature ||Jon Wilbanks, Michael Schroeder, Marja-Riitta Koivunen, Vinay Chaudhri || ||
||Knowledge Ecosystems ||Tim Clark || ||
||semantic annotation of unstructured data || ||Davide Zaccagnini, John Madden, Alfredo Morales || ||
||||||||||<style="text-align:center;">Workflow and Pathways ||
||BioPAX pathway knowledge ||BioPAX is a collaborative effort to create a data exchange standard for biological pathway data. It is written in OWL. | Luciano_BioPAX  ||Joanne Luciano, Eric Neumann || www.biopaxwiki.org ||
||Protocolization || Knowledge Merging and Specification, Clinical Process Specification, Intentions, Actions, Outcomes || Tonya Hongsermeier, Sam Brandt, Helen Chen, Vipul Kashyap, Alfredo Morales, Davide Zaccagnini || Adaptive Clinical Protocols and Pathways Subgroup ||
||||||||||<style="text-align:center;">Knowledge Management for Decision Support ||
||knowledge management || semantic models for clinical knowledge e.g., rules, templates, guidelines, etc., use of semantic technologies for knowledge maintenance and update, dependency propagation, provenance || Tonya Hongsermeier, Vipul Kashyap, Alfredo Morales, Eric Neumann, Marja-Riitta Koivunen, Davide Zaccagnini, Helen Chen || ||
||||||||||<style="text-align:center;">Aggregation of Structured Data ||
||bioinformatic databases ||data types and intrinsic semantics, unique identifiers, LSID and metadata ||Eric Neumann ||UniProt rdf ||
||data from OMICS experiments ||gene expression, metabolomics, in vitro studies, preclinical and clinical biomarkers ||Eric Neumann || ||
||||||||||<style="text-align:center;"> Making semantic webs work ||
|| Issue 1: naming || How to overcome age-old problems with naming, synonyms, homonyms, hyponyms etc. ||Robert Stevens, Alfredo Morales || ||
|| Issue 2: annotation / mapping || Mechanisms for annotating large data sets, mapping data into ontologies ||Robert Stevens, Marja-Riitta Koivunen, Davide Zaccagnini || ||
|| Semantic Web Services || Annotating registries of Web Services with biomedical ontologies. Making services easier to find and interoperate || Duncan Hull, Alfredo Morales || BioMOBY, Taverna, OWL-S and the Web Service Modelling Ontology (WSMO) ||