HCLSIG BioRDF Subgroup/Meetings/2006-03-20 Conference Call

Conference Details · Date of Call: Monday March 20, 2006 · Time of Call: 11:00am Eastern Time/16:00 UTC · Dial-In #: +1.617.761.6200 (Cambridge, MA) · Participant Access Code: 246733 ("BIORDF") · Duration: ~1 hour · Convener: Susie Stephens · Scribe: Olivier Bodenreider

Draft Agenda 1. Update on the tasks 2. Update on pathway databases 3. Neuroscience presentations

Meeting Minutes

Attendees: Olivier Bodenreider, Davide Zaccagnini, Alan Ruttenberg, John Barkley, Chris Kabor, Kei Cheung, John Wilbanks, Nikesh Kotecha, Paul Sternberg, Daniel Rubin, Roger Cutler, Tim Clark, Karen Skinner, Susie Stephens

Apologies: Scott Marshall, Joanne Luciano, Dan Gardner

Update on the tasks

Reagents/Antibodies – Alan Ruttenberg See: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Reagents The use case is to help researchers search for antibodies. Alan proposes to scrape information from vendors’ web sites and the Alzforum Antibody Directory. He also suggests extracting antibody information from full-text papers using Textpresso. The output would be a RDF version of the resources, an OWL ontology for the RDF material, as well as preformed SPARQL queries for frequent questions. Current participants include Alan Ruttenberg, Tim Clark, Paul Sternberg, June Kinoshita, Hanqing Xie. The task is recruiting.

SenseLab - Kei Cheung See: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/SenseLab The objective is to investigate the conversion of relational databases into RDF/OWL in the context of SenseLab (neuronal data). Tools explored include D2RQ and the RDF features in Oracle. The idea is to define high-level rules for the conversion. Current participants include Kei Cheung, and Susie Stephens.

Pathway Knowledge Base – Nikesh Kotecha See: http://pkb.stanford.edu/ Pathway information from three major resources (Reactome, BioCyc and KEGG) are represented in BioPAX and stored in RDF. Such a representation allows users to query the three resources simultaneously for a given molecule (e.g., ubiquitin). Some of the issues encountered include name space issues (especially between versions of BioPAX) and performance issues when the knowledge base reaches one million triples.

Neuroscience presentations

NeuroCommons – John Wilbanks See: http://sciencecommons.org/data/neurocommons The objective of the NeuroCommons is to extract information and metadata from the publicly available literature and databases, with a focus on neuroscience (autism and Huntington’s disease in particular). TEMIS (http://www.temis.com/) was selected for the text analysis. After the initial effort, the expectation is that the RDF graph will be maintained collaboratively by users (e.g., post-docs). Within BioRDF, NeuroCommons could focus on antibodies (see Reagents above), e.g., extracting antibodies from the publicly available literature (BMC, PLoS, PubMedCentral). Names used in standard vocabularies (e.g., UMLS) and ongoing projects (e.g., BIRN) could be used as a reference.

MIND – Tim Clark See: http://www.mghmind.org/ Tim presented MIND, the MassGeneral Institute for Neurodegenerative Disease. Their focus is on ALS, Huntington’s, Parkinson’s and Alzheimer’s diseases (in collaboration with the Alzheimer Research Forum http://www.alzforum.org/). One of their projects is SWAN (http://swan.mindinformatics.org/), “a project to develop effective specialist knowledge bases for the Alzheimer Disease research community, using the energy and self-organization of that community enabled by Semantic Web technology”. Their goal of organizing and sharing public resources is close to that of BioRDF. The use case suggested by Tim has to do with the availability of reagents, including antibodies, extracted from experiments described in the literature.

Other issues discussed

The task of creating RDF from unstructured information extracted from free text was originally excluded from BioRDF’s mandate, because the group led by Bob Futrelle was interested in pursuing it, but has become more or less orphan recently. Davide Z. suggested we at BioRDF adopted it and he created the corresponding subtask on our wiki: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Natural_Language_Processing_and_RDF.

Karen Skinner mentioned some resources and workshop of interest to the group: · Neuroscience Database Gateway (http://big.sfn.org/NDG/site/), a web resource developed by the Society for Neuroscience, a repository of experimental data, knowledge bases and tools for neuroscientists. · NIAID Immune Ontology workshop (March 21-22, 2006) in Gaithersburg, MD. The outcome of this meeting should also be interesting to the BioRDF group.