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Collection of Bio-NLP, Information Retrieval (IR) and Text Mining online or downloadable tools:
A
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Abbreviation Server:
Biomedical Abbreviation Server.
[
PubMed
]
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AbGene:
Downloadable protein tagger.
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ABNER:
Downloadable biomedical entity tagger.
[
PubMed
]
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AcroMed:
Database of computer-generated biomedical acronyms.
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AcroTagger:
Tool to tag biomedical abbreviations in text using XML.
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AliasServer:
Protein aliases handler.
[
PubMed
]
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ARGH:
Biomedical Acronym Resolving General Heuristics database (link not working now!).
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ARROWSMITH (at Chicago):
Extended MEDLINE search tool.
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ARROWSMITH (at UIC):
Extended MEDLINE search tool.
B
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BioIE:
Rule-based system to extract informative sentences.
[
PubMed
]
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BioNE recognizer:
Biomedical Named Entity Recognizer.
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BioRAT:
Information extraction tool for biological research.
[
PubMed
]
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BITOLA:
interactive literature-based biomedical discovery support system.
[
PubMed
]
-
BioMail:
Selective dissemination of information (SDI) service for MEDLINE.
C
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CGC:
Candidate Gene Capture, web-based tool for finding rat genes relevant to arthritis.
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Connexor:
Machinese Phrase Tagger and Machinese Syntax.
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Chilibot:
Information extraction tool for relationships between genes, proteins and keywords.
[
PubMed
]
D
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Document Relationship Extractor:
Relationship Extractor for Biomedical Articles (url currently not working!).
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Dragon:
Dragon Plant Explorer, text mining tool for plant related literature.
[
PubMed
]
E
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EBIMed:
IR and IE systems based on PubMed abstracts to retrieve gene/protein articles and also their GO term, drug and organism co-occurences.
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EngCG-2:
EngCG-2 tagger online.
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Entrez Programming Utilities:
Tools that provide access to Entrez data outside of the regular web query interface
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eTBLAST:
Performs document based similarity searches of PubMed artiles.
[
PubMed
]
F
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FigSearch:
Classification system of figures based on the corresponding legend texts.
[
PubMed
]
G
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GAPSCORE:
Protein and gene name (PGN) tagger.
[
PubMed
]
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GDPInfoSearch:
Online literature searching tool of literature related to genomics and disease prevention.
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GeneInfoMiner:
Online literature mining tool to provide abstracts based on sequence ID queries.
[
PubMed
]
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GeneScene:
Literature mining tool to visualize and navigate gene regulatory pathways.
[
PubMed
]
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GIFT:
Gene Interactions Finder in Text, tool for extraction of fly gene interactions.
[
PubMed
]
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GOAnnotator:
Protein-GO annotation extraction from literature.
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GoMiner:
tool for biological interpretation of 'omic' data - including data from gene expression
microarrays.
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GoPubMed:
tool to explore biomedical literature (PubMed) according to Gene Ontology.
[
PubMed
]
H
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HAPI:
High-density Array Pattern Interpreter (HAPI), tool to link gene cluster to the
literature using keyword hierarchies.
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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
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iHOP:
information on hyperlinked proteins. [
PubMed
]
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Infomap:
Information mapping search engine.
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iProLINK:
Protein literature mining, tagging and annotation extraction tool.
[
PubMed
]
J
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JADE:
Selective dissemination of information (SDI) service for MEDLINE.
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Jave MedlineParser:
Java-based tool to parse and load Medline into a relational database.
[
PubMed
]
K
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KAT:
annotate a protein sequence from a set of scientific references.
[
PubMed
]
-
KEX:
Downloadable protein tagger.
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KMedDB:
Tool which allows PubMed searches for kinetic parameters of enzymes.
L
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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.
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LitLinker:
Tool to find associations (links) between medical terms based on term co-occurrence analysis in MEDLINE.
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LitMiner:
Keyword-based tool to predict relatoinships using statistical co-occurrence analysis.
[
PubMed
]
M
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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
]
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MedGene:
Database which uses disease-gene co-citation matrices derived from PubMed to retrieve gene-disease relationships.
[
PubMed
]
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MedMiner:
tool to extract and organize relevant sentences in the literature based on a gene,
gene-gene or gene-drug query.
[
PubMed
]
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MedPost:
Part-of-speech tagger for biomedical literature (Medline citations).
[
PubMed
]
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METIS:
Multiple Extraction Techniques for Informative Sentences.
[
PubMed
]
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microGENIE:
text mining tool for micro-array experiment analysis.
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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
]
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MuteXt-GPCR:
text mining tool to extract point mutations of GPCR.
N
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NLProt:
Protein and gene name (PGN) tagger.
[
PubMed
]
-
NucleaRDB:
text mining tool to extract point mutations of nuclear hormone receptors.
[
PubMed
]
P
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PathBinderH:
search biomedical literature specifying biological taxonomy.
[
PubMed
]
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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
]
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PubClust:
Clustering tool of retrieved PubMed abstracts based on SOM.
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PubCrawler:
Selective dissemination of information (SDI) service for PubMed and GenBank.
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PubFinder:
Article retrieval tool for specific scientific topics.
[
PubMed
]
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PubGene:
Text mining tool for analysis of gene expression data.
[
PubMed
]
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PubMatrix:
Tool to compare any list of terms against any other list of terms in PubMed.
[
PubMed
]
T
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TaxonGrab:
To for the extraction of taxonomic names.
-
Textpresso:
Information extracting and processing tool for C. elegans literature.
[
PubMed
]
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
]
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WordSpy:
Word-based motif discovery tool.
[
PubMed
]
X
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XplorMed:
explore bibliographic searches from MEDLINE.
[
PubMed
]
Y
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Yapex:
Protein and gene name (PGN) tagger.
[
PubMed
]
LEGEND:
[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.
TOOL COUNTER: 74
NEW ENTRIES: PubFinder, WikiGene, WordSpy and LitMiner (added Tuesday 17th january 2006).
For a review article on some of the existing tools refer to: M. Krallinger and A. Valencia. Text mining and information retrieval services for Molecular Biology. Genome Biology, 6 (7), 224 (2005).
[
PubMed
][
PDF
]
If your tool is not listed or its URL has changed please contact me: martink@cnb.uam.es
This way you help to improve completeness of this list of text mining
tools for biology and biomedicine. The aim of compiling this collection
of text mining, natural language processing (NLP), information
retrieval (IR) and information extraction (IE) tools for the biomedical and
biology domain is to provide an overview of existing technologies,
compare them, to try them out and improve access to literature-derived
information by researchers.
Most of the existing tools are very recent
developments and thus feedback is especially beneficial to monitor
improvements and point out new demands. I would appreciate any feedback and comments on the listed tools!
Refer to my links section for other useful resources for Bio-NLP.
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