Robust partial-parsing through incremental, multi-algorithm processing
Text-based intelligent systems
Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Constructing Biological Knowledge Bases by Extracting Information from Text Sources
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Extracting molecular binding relationships from biomedical text
ANLC '00 Proceedings of the sixth conference on Applied natural language processing
Deterministic parsing of syntactic non-fluencies
ACL '83 Proceedings of the 21st annual meeting on Association for Computational Linguistics
Anaphora for everyone: pronominal anaphora resoluation without a parser
COLING '96 Proceedings of the 16th conference on Computational linguistics - Volume 1
MEDSTRACT: natural language tools for mining the biobibliome
HLT '02 Proceedings of the second international conference on Human Language Technology Research
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data
Journal of Biomedical Informatics
Gene name identification and normalization using a model organism database
Journal of Biomedical Informatics - Special issue: Named entity recognition in biomedicine
Gene name extraction using FlyBase resources
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Journal of Biomedical Informatics
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Postnominal prepositional phrase attachment in proteomics
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Disambiguation of biomedical abbreviations
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Prepositions in applications: A survey and introduction to the special issue
Computational Linguistics
A discriminative alignment model for abbreviation recognition
COLING '08 Proceedings of the 22nd International Conference on Computational Linguistics - Volume 1
Adaptive string similarity metrics for biomedical reference resolution
ISMB '05 Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics
Corpus design for biomedical natural language processing
ISMB '05 Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics
Proceedings of the third international workshop on Data and text mining in bioinformatics
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Postnominal prepositional phrase attachment in proteomics
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Learning biological networks via bootstrapping with optimized go-based gene similarity
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Disambiguation in the biomedical domain: The role of ambiguity type
Journal of Biomedical Informatics
Medstract: the next generation
BioNLP '11 Proceedings of BioNLP 2011 Workshop
Automatic extraction of genomic glossary triggered by query
BioDM'06 Proceedings of the 2006 international conference on Data Mining for Biomedical Applications
IJCNLP'04 Proceedings of the First international joint conference on Natural Language Processing
ISBMDA'05 Proceedings of the 6th International conference on Biological and Medical Data Analysis
Score-Based approach for anaphora resolution in drug-drug interactions documents
NLDB'09 Proceedings of the 14th international conference on Applications of Natural Language to Information Systems
Alignment-HMM-based extraction of abbreviations from biomedical text
BioNLP '12 Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
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The automatic extraction of information from Medline articles and abstracts (commonly referred to now as the biobibliome) promises to play an increasingly critical role in aiding research while speeding up the discovery process. We have been developing robust natural language tools for the automated extraction of structured information from biomedical texts as part of a project we call MEDSTRACT. Here we will describe an architecture for developing databases for domain specific information servers for research and support in the biomedical community. These are currently comprised of the following: a Bio-Relation Server, and the Bio-Acronym server, Acromed, which will include also aliases. Each information server is derived automatically from an integration of diverse components which employ robust natural language processing of Medline text and IE techniques. The front-end consists of conventional search and navigation capabilities, as well as visualization tools that help to navigate the databases and explore the results of a search. It is hoped that this set of applications will allow for quick, structured access to relevant information on individual genes by biologists over the web.