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©2008 Department of Biomedical Informatics™Center for Clinical and Translational Informatics Inventory of Resources Project aka Inventory Resources Working Group (IRWG – voluntary) & Inventory Resources Project Grp (CTSA Admin Suppl) Michael J. Becich, MD PhD (email@example.com) U Pitt, PI Nancy Whelan (firstname.lastname@example.org) U Pitt Brian Athey, PhD (email@example.com) U Mich Kevin Smith, MS (firstname.lastname@example.org) U Mich Shannon McWeeney (email@example.com) OHSU, IRWG Lead Elmer Bernstam, MD (Elmer.V.Bernstam@uth.tmc.edu) UTHSC Daniel Rubin, MD (firstname.lastname@example.org) Stanford Peter Lyster, PhD (email@example.com) NIH/NIGMS, NCBC Collaborator & all 38 CTSA sites who have volunteered time & energy!!!
©2008 Department of Biomedical Informatics™Center for Clinical and Translational Informatics Biomedical Informatics Resource Inventory Project Specific Aims Specific Aim 1 – “…to develop, rapidly implement and prototype the metadata to allow for query of biomedical informatics resources across the CTSA...” This is version 1 of the software and it is live at http://cpctr.upmc.edu/pls/CTSARI/ApacheXML.TopFrame1 Specific Aim #2 – “…to implement an “open source” ontology (Biomedical Resource Ontology or BRO) that interoperates with other biomedical resource inventories (e.g. Biositemaps and NCBCs)…” This will be version 2 of the biomedical informatics resource inventory and will be deployed Q1 2009 Specific Aim #3 – “…build a technology stack that is scalable for use at other CTSA sites as a local tool as well as serving as a federated tool …” This will be version 3 and is the BHAG or “big enchilada”
©2008 Department of Biomedical Informatics™Center for Clinical and Translational Informatics
©2008 Department of Biomedical Informatics™Center for Clinical and Translational Informatics Biomedical Informatics Resource Inventory Specific Aim 1 – First Prototype/Develop Metadata Have contacted and formed relationships with all 38 sites – major kudos to Nancy Whelan –Developed communications with Biomedical Informatics Core Director and established IRWG Point of Contact (POC) –All 38 POCs have now completed first two objectives First Task – Provide Metadata Annotation on Biomedical Informatics Resources –Helped to define metadata now ready to map to BRO (ontology) Second Task – Provide Feedback on Query Interface –Over 100 hits per day (modest for an “unadvertised site”) Over 75% of hits is from non-edu domains (artificial) Ready for Specific Aim #2
©2008 Department of Biomedical Informatics™Center for Clinical and Translational Informatics Biomedical Informatics Resource Inventory Specific Aim 2 – Ontology Implementation Get full set of annotations on each sites biomedical informatics resources –Nancy Whelan will coordinate with IRWG Points of Contact (POC) –Two sites have already provided a full set of resources Extend BRO (ontology) with IRWG metadata suggestions and do 1 st version implementation (Rubin Stanford and Lyster NIH/NIGMS are key) BRO is an ontologic subdomain of BiositeMaps so the same exercise will be needed for BiositeMaps (ditto above) Will require an implementation of an ontology management system – Protégé Begin query tool improvement process (HCI team U Mich) Goal is to complete this Q1 2009
Specific Aim 2 – Biositemaps editor: Information Model (IM) and Biomedical Resource Ontology (BRO) to improve queryability
©2008 Department of Biomedical Informatics™Center for Clinical and Translational Informatics Biomedical Informatics Resource Inventory Specific Aim 3 – Scalable/Portable Toolkit Development Implement the BRO enabled Inventory in BioSiteMaps in the portlet specification (JSR 168) –U Mich team will be critical to this effort Package the Inventory Resources Toolkit for implementation at other sites Finalize the query tool improvement process (U Mich) Plan to share the inventory resources toolkit with other CTSA efforts: –Candidates include: Translational Workgroup Public Private Partnership Workgroup Clinical Ethics Research Education Workgroup Goal is to complete this Q2 2009
©2008 Department of Biomedical Informatics™Center for Clinical and Translational Informatics Biomedical Resource Ontology http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_displa y_name=Biomedical%20Resource%20Ontology Sitemaps.org: consortium of Microsoft, Google, and Yahoo to improve web searching http://www.sitemaps.org/ The BioMoby initiative has very similar objectives as biositemaps http://biomoby.org/ Cancer Data Standards Repository http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr Society for Neuroscience Database Gateway has experimented with a similar effort http://ndg.sfn.org/ The Neuroscience Information Framework (NIF) initiative has a similar effort http://neurogateway.org/catalog/goto.do;jsessionid=F8D6AC6F12C236FB082879CF 3D24867C?page=.home XML Editors: http://en.wikipedia.org/wiki/Xml_editor, see tools under external links, e.g., the biositemaps.xml which is currently on the NCBC National Center for Integrative Biomedical Informatics (NCIBI) portal (https://portal.ncibi.org/portal) was generated using the tool ‘XMLmind’ http://www.xmlmind.com/xmleditor/ Dinov, ID., Rubin, D., Lorensen, W., Dugan, J., Ma, J., Murphy, S., Kirschner, B., Bug, W., Sherman, M., Floratos, A., Kennedy, D., Jagadish, HV., Schmidt, J., Athey, B., Califano, A., Musen, M., Altman, R., Kikinis, R., Kohane, I., Delp, S., Parker, DS., Toga, AW., (2008) iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources. In review. Bibliography for IRWG – NOTE: Please e-mail me at firstname.lastname@example.org for PDFs
©2008 Department of Biomedical Informatics™Center for Clinical and Translational Informatics End of Talk – e-mail me at email@example.com if you have questions or need clarifications about the discussion. End of Talk – e-mail me at firstname.lastname@example.org if you have questions or need clarifications about the discussion. NOTE: Please e-mail me if you want a copy of this presentation or contact info for more information about IRWG Volunteer of Project Groups – 412-623-3941
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