This panel will explore crowdsourcing and its applications to biocuration. Panelists will provide examples of how crowdsourcing has been used to solve problems in the biomedical domain (e.g., serious games, community annotations) as well as specific applications such as hybrid curation (combining automated entity tagging with crowdsourced relation annotation). The panel will also explore challenges in the capture and encoding of relevant metadata and the creation of data sets for training and evaluation of machine-learning based systems for biocuration.
Chairs: Kevin B. Cohen, Lynette Hirschman
Karėn Fort, University of Paris-Sorbonne
Lynette Hirschman, MITRE
Stephanie Boue, Philip Morris International
Nikos Kyrpides, Joint Genome Institute
Karėn Fort is Associate Professor at University Paris-Sorbonne, in the STIH (Meaning, Text, Computer Science, History) team. Her primary research interest is manual annotation for NLP, which she extended to crowdsourcing annotation, in particular using Games With A Purpose (GWAPs). She is the co-creator of ZombiLingo, a GWAP for dependency syntax annotation. She is also a member of the French SLAM project and as such she conducted research on the analysis of the discourse of schizophrenic patients using NLP techniques. She is developping a community of researchers concerned by ethics in NLP in France, which she hopes to extend worldwide.
The MITRE Corporation
Lynette Hirschman is Chief Scientist for Biomedical Informatics in the Information Technology Center at MITRE. She is a founding organizer of the BioCreative evaluations (Critical Assessment of Information Extraction in Biology) and has served on the organizing committee for the i2b2 Natural Language Processing Shared Task for Clinical Data for the past four years. Her current research focuses on scalable, cost-effective approaches to curation of biomedical data, the integration of clinical data with genomics and multi-omics data for translational medicine, and on secondary use of clinical data, particularly automated de-identification of unstructured clinical records.
After obtaining an engineering degree in biotechnology, Dr Stéphanie Boué conducted her PhD work at the European Molecular Biology Laboratory (EMBL, Heidelberg, Germany) in the field of bioinformatics and alternative splicing and received her PhD degree from the EMBL and the University of Strasbourg. She pursued postdoctoral training at the Center for Regenerative Medicine in Barcelona (CMRB, Barcelona, Spain) studying embryonic stem cell biology, reprogramming to induced pluripotent stem cells and tissue regeneration. In 2010, she joined Philip Morris International (PMI) R&D department of Biological Systems Research that focuses on product testing using in vitro/in vivo models and systems biology approaches. Stéphanie is involved in the construction of biological network models scripted in Biological Expression Language (BEL) and their computational use for systems toxicology. She is also responsible for the preparation of challenges and resources in the sbv IMPROVER project that aims at harvesting crowdsourcing to verify methods and results in systems biology.
Dr. Nikos Kyrpides
Joint Genome Institute
Dr. Kyrpides is leading the Prokaryotic Super Program at the DOE Joint Genome Institute. He has over 20 years of research experience in sequence analysis, bioinformatics, and microbial genomics and has published over 400 papers in the field. He led the development of several pioneering data managements systems in microbial genomics and metagenomics (including GOLD and IMG), which have several thousand users across the world. Dr. Kyrpides has received a number of awards including the van Niel International Prize for Studies in Bacterial Systematics and he is an elected fellow of the American Academy of Microbiology.