Monarch Initiative

Model systems are the cornerstone of biomedical research to investigate biological processes, test gene-based disease hypotheses, and develop and test disease treatments. The vast knowledge that we have about model systems can be better utilized if semantically aggregated and made queryable based on any number of facets, such as phenotypic similarity, network analysis, gene expression and function, and genomics. The Monarch Initiative aims to provide easy-to-use tools to navigate this data landscape, services for other resources, and educational outreach regarding the production of structured data for biomedical discovery. Monarch is funded by NIH (NIHGrant # 1R24OD011883-01) and is a collaboration between members at Oregon Health & Science University, Lawrence Berkeley National Laboratory, University of California, San Diego, and University of Pittsburgh.

Data Training

ODG and the OHSU Library will host several working sessions to address reproducibility and research communication. The goal is to promote interaction between information scientists and research scientists to support enhanced awareness of data stewardship. Two sessions will be held including a "Data Management Open House", which was held on Wednesday, 10/09, where aspects of the data-research cycle were addressed, including issues surrounding research reproducibility and scholarly communication of findings. We also discussed how to develop a data management plan. The second session will entail hands on data sessions between individual researchers and OHSU library staff. More information is available here


The CTSAconnect project aims to integrate information about research activities, clinical activities, and scientific resources by creating an Integrated Semantic Framework (ontology). This new framework will facilitate the production and consumption of Linked Open Data (a Semantic Web method of sharing data) about investigators, physicians, biomedical research resources, services, and clinical activities. The goal is to enable software to consume data from multiple sources and allow the broadest possible representation of researchers' and clinicians' activities and research products. Current research tracking and networking systems rely largely on publications, but clinical encounters, reagents, techniques, specimens, model organisms, etc., are equally valuable for representing expertise. CTSAconnect is funded by Booz Allen Hamilton (Grant #CTSA 10-001: 100928SB23) and is a collaboration between members at Oregon Health & Science University, Stony Brook University, Cornell University, Harvard University, University at Buffalo, and the University of Florida, and leverages the work of eagle-i, VIVO, and ShareCenter.

eagle-i Network

eagle-i is a free application that makes it easy to discover biomedical research resources at a growing network of universities; more than 50,000 resources are listed and more are added every week. Resource types include model organisms, reagents, core laboratory services, instrumentation, and biospecimens. eagle-i is funded by Booz Allen Hamilton (Grant # 90177520). The Ontology Development Group is responsible for maintaining the OHSU resource data and underlying ontology, and can assist with data entry for OHSU researchers.

Biospecimen Query

This project explored options for enhancing search capabilities for an existing biospecimen search application. Text processing tools were used to map anatomy, pathology, and disease concepts from existing terminologies and ontologies to pathology reports that are currently represented in an unstructured natural text form. The concepts identified in the text were also organized in a relational structure to enable taxonomic and parthood based searches. This was a small exploratory project with a goal of integrating these capabilities in an ongoing effort to expand and integrate OHSU's biospecimen databases. This work was funded by OHSU's Medical Research Foundation.