Featured Profile for Stanford-NCIBI Collaborations

Nigam Shah, MD, PhD

Dr. Nigam Shah is a Research Scientist at Stanford University’s Center for Biomedical Informatics Research.  His research interests include the “use of bio-ontologies for organizing biomedical information to make it actionable”. “Specifically, I work on developing ontology based approaches to integrate diverse information types available for biological systems.  Currently, we are drowning in information but thirsty for knowledge; ontologies might help fix that.”

Dr. Shah was first made aware of NCIBI and its work at the first National Centers for Biomedical Computing All Hands Meeting in 2006 and subsequent interactions with NCIBI researchers at the first American Medical Informatics Association’s Summit on Translational Bioinformatics.  These interactions and information sharing events led to Dr. Shah’s discovery of the NCIBI developed concept recognition tool, Mgrep.  Mgrep is a tool that maps free text to ontology terms.

Currently, Dr. Shah is using Mgrep “to provide a web service for using ontologies stored in BioPortal for annotating user submitted text over the Web”.  The Annotator Web service, at the National Center for Biomedical Ontology, processes text metadata from diverse sources such as gene expression sets, clinical trial reports, and PubMed abstracts and annotates them with ontology terms.  Dr. Shah has compared Mgrep to another concept recognizer called MetaMap which is produced by the National Library of Medicine.  His analysis, described in a 2009 BMC Bioinformatics article, concluded that Mgrep was superior in speed than MetaMap and is one of the reasons why it is used in their Annotator Web service.  Dr. Shah also describes his work on mapping text annotations of gene expression sets to the Unified Medical Language System (UMLS), specifically Gene Expression Omnibus (GEO) and the Stanford Tissue Microarray Database (TMAD), while using Mgrep in another BMC Bioinformatics article.  Dr. Shah’s future plans with Mgrep include working with Dr. Fan Meng, the primary researcher for Mgrep at NCIBI, “to increase the accuracy of the tool and to apply it for ontology based indexing of several public biomedical data sources”.

Featured Profile for NCI-NCIBI Collaborations

Marci Brandenburg, MS, MSI

As the Biosciences Informationist at the National Cancer Institute –Frederick (NCI-Frederick), Marci uses and runs recurring workshops on MiMI Web, MiMI Cytoscape plug-in, Metscape Cytoscape plug-in, and Gene2MeSH tools. “These tools provide new resources that I can bring to NCI-Frederick researchers and train them on how to use them.” 

Marci began working at NCI-Frederick after obtaining her MSI degree in Library Information Services at the University of Michigan’s School of Information. There she interned with the Health Sciences Libraries (HSL) and collaborated with NCIBI on several projects, such as a gene name curation project. 

From her software training workshops at NCI-Frederick, Marci sends scientists’ feedback and questions to NCIBI developers in Michigan who, in turn, respond to her and make enhancements to the tools. Marci also works with the HSL at the University of Michigan to enhance their teaching curriculum on the NCIBI tools. Her future plans for the NCIBI tools are “to continue training on resources and reach more researchers and to use the tools to potentially do information gathering data analysis for researchers.”