OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

Gene Ontology: tool for the unification of biology

2000 • 38,297 citations

WordNet: An Electronic Lexical Database

2000 • 12,050 citations

Advances in Neural Information Processing Systems 14

2002 • 9,376 citations

WordNet

1998 • 4,491 citations

Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program.

2001 • 1,979 citations

IntAct: an open source molecular interaction database

2003 • 981 citations

Fast Exact Inference with a Factored Model for Natural Language Parsing

2002 • 756 citations

Constructing biological knowledge bases by extracting information from text sources.

1999 • 605 citations

The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text

2003 • 511 citations

ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text

2005 • 474 citations

Formal Ontology in Information Systems

1998 • 466 citations

Association for Computational Linguistics

2006 • 466 citations

Automatic extraction of biological information from scientific text: protein-protein interactions.

1999 • 439 citations

Comparative experiments on learning information extractors for proteins and their interactions

2004 • 427 citations

Content-rich biological network constructed by mining PubMed abstracts

2004 • 346 citations

Overview of BioCreative II gene normalization

2008 • 329 citations

Biomedical Language Processing: What's Beyond PubMed?

2006 • 297 citations

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data

2003 • 287 citations

MINING MEDLINE: ABSTRACTS, SENTENCES, OR PHRASES?

2001 • 246 citations

Discovering patterns to extract protein–protein interactions from full texts

2004 • 240 citations

Manual curation is not sufficient for annotation of genomic databases

2007 • 233 citations

EVENT EXTRACTION FROM BIOMEDICAL PAPERS USING A FULL PARSER

2000 • 228 citations

Protégé-2000: an open-source ontology-development and knowledge-acquisition environment.

2003 • 222 citations

TREC 2004 Genomics Track Overview

2004 • 202 citations

Extraction of protein interaction information from unstructured text using a context-free grammar

2003 • 189 citations

BioRAT: extracting biological information from full-length papers

2004 • 182 citations

Overview of BioCreAtIvE task 1B: normalized gene lists

2005 • 162 citations

Knowtator

2006 • 162 citations

Protein Structures and Information Extraction from Biological Texts: The PASTA System

2002 • 160 citations

BIDIRECTIONAL INCREMENTAL PARSING FOR AUTOMATIC PATHWAY IDENTIFICATION WITH COMBINATORY CATEGORIAL GRAMMAR

2000 • 149 citations

Building an example application with the Unstructured Information Management Architecture

2004 • 149 citations

Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors

2004 • 148 citations

Extraction of regulatory gene/protein networks from Medline

2005 • 144 citations

Direct memory access parsing

1992 • 139 citations

Facts from Text—Is Text Mining Ready to Deliver?

2005 • 138 citations

TREC 2005 Genomics Track Overview.

2005 • 138 citations

Formal Ontology in Information Systems: Proceedings of the 1st International Conference June 6-8, 1998, Trento, Italy

1998 • 123 citations

A shallow parser based on closed-class words to capture relations in biomedical text

2003 • 121 citations

EXTRACTING SEMANTIC PREDICATIONS FROM MEDLINE CITATIONS FOR PHARMACOGENOMICS

2006 • 120 citations

PASBio: predicate-argument structures for event extraction in molecular biology

2004 • 117 citations

Literature mining and database annotation of protein phosphorylation using a rule-based system

2005 • 116 citations

Natural Language Processing: A Historical Review

1994 • 115 citations

Automatic extraction of gene/protein biological functions from biomedical text

2004 • 82 citations

Mining functional information associated with expression arrays

2001 • 82 citations

Beyond the clause: extraction of phosphorylation information from medline abstracts

2005 • 68 citations

Can Bibliographic Pointers for Known Biological Data Be Found Automatically? Protein Interactions as a Case Study

2001 • 68 citations

The (Non)Utility of Predicate-Argument Frequencies for Pronoun Interpretation.

2004 • 67 citations

Semantic relations asserting the etiology of genetic diseases.

2003 • 65 citations

An environment for relation mining over richly annotated corpora: the case of GENIA

2006 • 65 citations

A critical review of PASBio's argument structures for biomedical verbs

2006 • 58 citations

Improving protein function prediction methods with integrated literature data

2008 • 57 citations

Extraction of Transcript Diversity from Scientific Literature

2005 • 52 citations

Phrasal Queries with LingPipe and Lucene: Ad Hoc Genomics Text Retrieval.

2004 • 38 citations

Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease

2006 • 36 citations

On the unification of syntactic annotations under the stanford dependency scheme

2007 • 34 citations

Discovering patterns to extract protein-protein interactions from full biomedical texts

2004 • 19 citations

ASSESSING AND COMBINING RELIABILITY OF PROTEIN INTERACTION SOURCES

2006 • 14 citations

Building embedded conceptual parsers

1994 • 13 citations

Using Natural Language Processing, Locus Link, and the Gene Ontology to Compare OMIM to MEDLINE

2004 • 9 citations

Determining the syntactic structure of medical terms in clinical notes

2007 • 6 citations