BioCreAtIvE - Critical Assessment for Information Extraction in Biology
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Bio-NLP tools

  • Abbreviation Server: Biomedical Abbreviation Server. [ PubMed ]
  • AbGene: Downloadable protein tagger.
  • ABNER: Downloadable biomedical entity tagger. [ PubMed ]
  • AcroMed: Database of computer-generated biomedical acronyms.
  • Acromine: an acronym dictionary automatically constructed from the whole of MEDLINE. [ PubMed ]
  • AcroTagger: Tool to tag biomedical abbreviations in text using XML.
  • AliasServer: Protein aliases handler. [ PubMed ]
  • Ali Baba: Tool to parse PubMed abstracts for biological objects and their relations and visualize them through graphical networks.
  • ARGH: Biomedical Acronym Resolving General Heuristics database.
  • ARROWSMITH (at Chicago): Extended MEDLINE search tool.
  • ARROWSMITH (at UIC): Extended MEDLINE search tool.

  • B
  • BioIE: Rule-based system to extract informative sentences. [ PubMed ]
  • BioNE recognizer: Biomedical Named Entity Recognizer.
  • BioRAT: Information extraction tool for biological research. [ PubMed ]
  • BITOLA: interactive literature-based biomedical discovery support system. [ PubMed ]
  • BioMail: Selective dissemination of information (SDI) service for MEDLINE.

  • C
  • CGC: Candidate Gene Capture, web-based tool for finding rat genes relevant to arthritis.
  • Connexor: Machinese Phrase Tagger and Machinese Syntax.
  • Chilibot: Information extraction tool for relationships between genes, proteins and keywords. [ PubMed ]

  • D
  • Document Relationship Extractor: Relationship Extractor for Biomedical Articles (url currently not working!).
  • Dragon: Dragon Plant Explorer, text mining tool for plant related literature. [ PubMed ]

  • E
  • EBIMed: IR and IE systems based on PubMed abstracts to retrieve gene/protein articles and also their GO term, drug and organism co-occurences.
  • EngCG-2: EngCG-2 tagger online.
  • Entrez Programming Utilities: Tools that provide access to Entrez data outside of the regular web query interface
  • eTBLAST: Performs document based similarity searches of PubMed artiles. [ PubMed ]

  • F
  • FigSearch: Classification system of figures based on the corresponding legend texts. [ PubMed ]

  • G
  • GAPSCORE: Protein and gene name (PGN) tagger. [ PubMed ]
  • GDPInfoSearch: Online literature searching tool of literature related to genomics and disease prevention.
  • GeneInfoMiner: Online literature mining tool to provide abstracts based on sequence ID queries. [ PubMed ]
  • GeneScene: Literature mining tool to visualize and navigate gene regulatory pathways. [ PubMed ]
  • GIFT: Gene Interactions Finder in Text, tool for extraction of fly gene interactions. [ PubMed ]
  • GOAnnotator: Protein-GO annotation extraction from literature.
  • GoMiner: tool for biological interpretation of 'omic' data - including data from gene expression microarrays.
  • GoPubMed: tool to explore biomedical literature (PubMed) according to Gene Ontology. [ PubMed ]

  • H
  • HAPI: High-density Array Pattern Interpreter (HAPI), tool to link gene cluster to the literature using keyword hierarchies.
  • HCAD: Database of literature associated breakpoint of human genes. [ PubMed ]
  • HubMed: Alternative interface to the PubMed database with additional options (e.g. visualization of links between articels TouchGraph).

  • I
  • iHOP: information on hyperlinked proteins. [ PubMed ]
  • Infomap: Information mapping search engine.
  • InfoPubMed: extracts protein-protein interactions.
  • iProLINK: Protein literature mining, tagging and annotation extraction tool. [ PubMed ]

  • J
  • JADE: Selective dissemination of information (SDI) service for MEDLINE.
  • Jave MedlineParser: Java-based tool to parse and load Medline into a relational database. [ PubMed ]

  • K
  • KAT: annotate a protein sequence from a set of scientific references. [ PubMed ]
  • KEX: Downloadable protein tagger.
  • KMedDB: Tool which allows PubMed searches for kinetic parameters of enzymes.

  • L
  • LingPipe: suite of NLP tools (in Java) including many features such as named-entity detector, an approximate dictionary match named-entity detector, a heuristic sentence boundary detector, a heuristic within-document coreference resolution engine and a set of tools for MEDLINE data.
  • LitLinker: Tool to find associations (links) between medical terms based on term co-occurrence analysis in MEDLINE.
  • LitMiner: Keyword-based tool to predict relatoinships using statistical co-occurrence analysis. [ PubMed ]

  • M
  • MaSTerClass: Case-based reasoning system developed for term classification. [ PubMed ]
  • MatchMiner: set of tools that enables the user to translate between disparate ids for the same gene. [ PubMed ]
  • MedBlast: NLP based retrieval system to return relevant articles for a given query sequence . [ PubMed ]
  • MedGene: Database which uses disease-gene co-citation matrices derived from PubMed to retrieve gene-disease relationships. [ PubMed ]
  • MEDIE: An intelligent search engine, retrieving biomedical events from Medline. [ REF ]
  • MedMiner: tool to extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query. [ PubMed ]
  • MedPost: Part-of-speech tagger for biomedical literature (Medline citations). [ PubMed ]
  • METIS: Multiple Extraction Techniques for Informative Sentences. [ PubMed ]
  • microGENIE: text mining tool for micro-array experiment analysis.
  • MILANO: text mining tool for Microarray Literature-based Annotation. [ PubMed ]
  • MineBlast: Online literature search tool which retrieves abtracts for query sequences in fasta format. [ PubMed ]
  • MuteXt-GPCR: text mining tool to extract point mutations of GPCR.

  • N
  • NLProt: Protein and gene name (PGN) tagger. [ PubMed ]
  • NucleaRDB: text mining tool to extract point mutations of nuclear hormone receptors. [ PubMed ]

  • P
  • PathBinderH: search biomedical literature specifying biological taxonomy. [ PubMed ]
  • Perl ParseMEDLINE: Perl-based tool to parse and load Medline into a relational database. [ PubMed ]
  • PreBIND: SVM based tool to identify protein-protein interaction relevant literature. [ PubMed ]
  • PubClust: Clustering tool of retrieved PubMed abstracts based on SOM.
  • PubCrawler: Selective dissemination of information (SDI) service for PubMed and GenBank.
  • PubFinder: Article retrieval tool for specific scientific topics. [ PubMed ]
  • PubGene: Text mining tool for analysis of gene expression data. [ PubMed ]
  • PubMatrix: Tool to compare any list of terms against any other list of terms in PubMed. [ PubMed ]

  • T
  • TaxonGrab: To for the extraction of taxonomic names.
  • Textpresso: Information extracting and processing tool for C. elegans literature. [ PubMed ]
  • TerMine: An automatic term recognition tool which employs a domain-independent method C-value and combines linguistic and statistical analyses. [ REF ]

  • W
  • Whatizit: tool to extract the meaning of words given their context in biomedical literature.
  • WikiGene: Wikipedia inspired project to collect community-based data of genes. [ PubMed ]
  • WordSpy: Word-based motif discovery tool. [ PubMed ]

  • X
  • XplorMed: explore bibliographic searches from MEDLINE. [ PubMed ]

  • Y
  • Yapex: Protein and gene name (PGN) tagger. [ PubMed ]

[PubMed] : link to corresponding entry of the PubMed database of biomedical literture.
[PDF] : link to the file of the article in pdf format.
[PS] : link to the file of the article in ps format.
[URL] : link to the commented tool description page.
[BIBTEX] : Link to the reference of the article in bibtex format.
[PUBL] : link to the publisher page.
[ABS] : link to the abstract of this publication.


© by Martin Krallinger 2006