Laboratory for Biomedical Language
LABL brings together faculty and students interested in natural language processing in the biomedical domain, in order to share ideas, methods and tools. Methods include information extraction, information retrieval and machine learning. Domains of application include patient care, genomic research, and public health. Monthly meetings provide a forum for discussion of current projects, publications and new opportunities for research.
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List
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Projects
| Name | Description | Purpose | Tools |
|---|---|---|---|
| MedLEE | Medical Language Extraction and Encoding | Extract, structure, and encode clinical information in textual patient reports. | Semantic Grammar, Robust Parsing, Controlled Vocabulary Mapping, Performace Evaluation |
| Geneways | Genetic pathWays | Extraction of information from the research literature to compile and analyze molecular pathways. | POS Tagging, Disambiguation, Semantic Parsing, Knowledge modeling, Visualization |
| PhenoGenes | Phenotype and Genotype relations | Extraction of relations from medical records and literature in order to associate causes and treatment of diseases | Integration of MedLEE and GENIES, representational model of genotypic and phenotypic relations |
| eNote | Electronic capture of clinical Notes | Flexible entry of clinical notes using natural language processing and speech recognition | Document parser (MedLEE), management of semi-structured clinical data (XML), analysis of time expressions, rules for enhancing data entry |
| HINT | Health Information Needs Tailoring | Digital delivery of medical knowledge at the point of care | Knowledge base of clinical information needs, parser for information content (AQUA), XML databases of medical record and literature |
| AQUA | A Query Analyzer | Analysis of information content of biomedical text for information retrieval and related purposes | Machine learning of POS tagging, dependency syntax, and semantic type assignment |
| TaxonGrab | Taxonomy Grabber | Identification of organism names in text | Parsing, named-entity recognition |
Tools &
Resources
National Library of Medicine Indexing Initiative
Language Technology Group
Medical Entities Dictionary
LABL Tools and Resources
Links
Association for Computational Linguistics
BIONLP.ORG - Natural language processing of biology text
Carol Friedman, PhD, Professor
Department of Medical Informatics
Columbia University