This panel will discuss tools and resources to support text mining and literature mining for medical applications, as well as specific examples of the application of ontologies and literature mining to identify diagnostics and therapies for specific diseases. The keynote talks and the panelists’ contributions will exemplify some current efforts in the field of medical and clinical text mining to better understand the current status of technologies and resources.
This panel will provide an opportunity to discuss how community challenge tasks, in the context of the BioCreative Initiative, could promote collaborative research across the biology/bioinformatics and medical text mining communities. Topics to discuss include the relation to ongoing BioCreative tracks (e.g., the chemical/drug extraction track and the toxicogenomics track), as well the relation to other ongoing evaluations, such as CLEF, TREC and i2b2.
Chairs: Martin Krallinger, Lynette Hirschman, Rezarta Islamaj
Laura I. Furlong
Institute for Genome Sciences, University of Maryland
Dr. Lynn Schriml is an Assistant Professor at the Institute for Genome Sciences, University of Maryland School of Medicine in the Department of Epidemiology and Public Health. Dr. Schriml is the President of the Genomic Standards Consortium, PI of the Human Disease Ontology project and PI of the Alfred P. Sloan Foundation funded MIxS extension for the built environment project. Dr. Schriml’s research is focused on the development and implementation of bioinformatics tools, metadata standards and ontologies for human diseases and microbial genomes towards gaining a broader understanding of the relationship between infectious pathogens, their genomic sequence and associated disease.
Laura I. Furlong
GRIB – IMIM
Laura I. Furlong is head of the Integrative Biomedical Informatics Group, which belongs to the Research Programme on Biomedical Informatics (IMIM-UPF). She has a broad expertise covering molecular biology, computational systems biology and text mining. Her current research is in the area of network medicine approaches to study disease comorbidities, text mining methods to identify disease genes from the literature, and the development of knowledge resources to support translational research, including the databases DisGeNET and PsyGeNET.
University of Manchester / NaCTeM
Dr. Sophia Ananiadou is Professor in Computer Science at the School of Computer Science, the University of Manchester and Director of National Centre for Text Mining (NaCTeM). She has directed NaCTeM to be currently a sustainable biomedical text mining centre, carrying out novel, world-leading research on TM that then informs our provision of services, tools, resources and TM infrastructure, to a variety of users from systems biology, medicine and bioinformatics. Research she has led includes automatic extraction of biomedical entities and their interactions, event extraction and epistemic knowledge extraction; the development of large-scale terminological resources (BioLexicon); the PathText system linking models with evidence derived from TM. She has also focused on the development of an interoperable text mining platform, Argo, which supports both text mining processing, and annotations for curation.
Fraunhofer Institute SCAI
Dr. Juliane Fluck is the head of the text mining group at the Fraunhofer Institute SCAI, Sankt Augustin, Germany. Her research is focused on information extraction, on development of dictionary and ontology resources as well as on the generation of annotated corpora in various biological and medical applications. In the area of neurodegenerative diseases, she participates in the construction of disease-specific taxonomies. Information extraction solutions developed in her group support the construction of mechanistic disease networks in the IMI projects AETIONOMY and EAD. In German projects such as cloud4health, Dr Fluck leads medical report mining activities. She advocates for evaluation standards and participates regularly in evaluation assessments like BioCreAtIvE, i2b2 and the TREC Chemistry and TREC Medical Tracks. In 2011, Dr. Fluck co- organised the TREC Chemistry TREC Track. Currently, she co-organises the BioCreative BEL Track.