> > Text Mining and Semantics

Text Mining and Semantics

Links to tools for more complex searching and for making connections between text and other scientific information. This section focuses specifically on text such as scientific publications, article abstracts, or NCBI GenBank records. It also covers the role of growing field of semantic web content in biological data integration.

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Found 38 links

Displaying 15 links

ACELATool Content

http://www.nactem.ac.uk/acela/

Literature > Text Mining and Semantics

The ACELA (ACcElerated Annotation) tool aims to reduce the human effort required to produce a gold standard corpus of named entity (NE) annotations.

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tagsaccelerated annotation algorithms annotation tool artificial intelligence automated pattern recognition bibliographic databases named entity annotation natural language processing terminology as topic text mining
setsUniversity of Manchester

AcromineTool Content

http://www.nactem.ac.uk/software/acromine/

Literature > Text Mining and Semantics

Acromine is an tool that finds full forms of acronyms that appear in MEDLINE.

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tagsalgorithms automatic acronym expansion bibliographic databases cluster analysis computational biology dictionaries as topic medline natural language processing polymerase chain reaction reproducibility of results statistical models x-ray computed tomography
setsUniversity of Manchester

Acromine DisambiguatorTool Content

http://www.nactem.ac.uk/software/acromine_disambiguation/

Literature > Text Mining and Semantics

Given a biomedical text, Acromine Disambiguator correctly predicts expanded full forms of acronoyms appearing in the text. As acronyms appearing in biomedical texts are often ambiguous, such a disambiguation process is important to ensure the correct interpretation of the text.

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tagsalgorithms automatic acronym disambiguation automatic acronym expansion bibliographic databases cluster analysis computational biology dictionaries as topic medline natural language processing polymerase chain reaction reproducibility of results statistical models x-ray computed tomography
setsUniversity of Manchester

BeeSpace NavigatorTool Content

http://www.beespace.illinois.edu

DNA > Annotations
Literature > Text Mining and Semantics

BeeSpace Navigator is a tool for exploratory analysis of gene function using biological literature. It is an automated version of the curation process to extract gene function.

NAR Web Server Issue 2011
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BioLitTool Content

http://biolit.ucsd.edu

Literature > Text Mining and Semantics

BioLit is a web sever resource that integrates scientific publications with existing biological databases. To perform this link, BioLit searches the full text of the article for metadata such as database identifiers and ontology terms.

NAR Web Server Issue 2008
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tagsfactual databases protein databases pubmed systems integration

bioNMFTool Content

http://bionmf.dacya.ucm.es/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics
Protein > Proteomics

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

NAR Web Server Issue 2008
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tagsalgorithms cluster analysis computational biology gene expression profiling

botXminerDatabase Content

http://botdb.abcc.ncifcrf.gov/

Literature > Search Tools
Literature > Text Mining and Semantics

botXminer is a literature searching tool that allows you to search BotDB. BotDB citations contain only those articles with either \'botulinum\' or \'tetanus\' anywhere in their text. botXminer is an interface to this subset of complete medline xml files loaded into an Oracle XMLDB.

NAR Web Server Issue 2006
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tagsamino acid sequence botulinum toxins database management systems medline molecular sequence data protein databases tetanus toxin

BSQATool Content

http://www.beespace.uiuc.edu/QuestionAnswer

Literature > Text Mining and Semantics
Model Organisms > Fly

BeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.

NAR Web Server Issue 2010
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tagsanimal behavior animals data mining drosophila melanogaster gene expression regulation homeodomain proteins insect genes insects systems integration trans-activators

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

NAR Web Server Issue 2007
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tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

ChilibotTool Content

http://www.chilibot.net/

Literature > Text Mining and Semantics

Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. The results are returned as a graph.

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tagsbiology information services natural language processing protein binding protein databases pubmed software design

CoPubTool Content

http://www.copub.org

Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics

CoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.

NAR Web Server Issue 2008NAR Web Server Issue 2011
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tagsanimals gene expression profiling humans medline mice oligonucleotide array sequence analysis rats

DECATool Content

http://www.nactem.ac.uk/deca_details/start.cgi

Literature > Text Mining and Semantics

DECA is a species disambiguation system for biological named entities. The system will identify protein entities and disambiguate them according to species, by assigning NCBI Taxonomy organism IDs.

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tagsartificial intelligence data mining factual databases named entity recognition natural language processing species disambiguation species specificity terminology as topic text mining

E3MinerTool Content

http://e3miner.biopathway.org

Literature > Text Mining and Semantics

E3Miner is a web-based text mining tool that extracts and incorporates comprehensive knowledge about ubiquitin-protein ligases (E3) with their underlying mechanisms. This tool integrates available E3 data from the published literature as well as from the biological databases.

NAR Web Server Issue 2008
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tagsmedline protein databases ubiquitin-protein ligases

FABLEDatabase Content

http://fable.chop.edu/

Literature > Text Mining and Semantics

Fast Automated Biomedical Literature Extraction (FABLE) mines the  biomedical literature for information about human genes and proteins. User can find articles mentioning a gene of interest (Article Finder), generate a list of genes associated with one or more keywords (Gene Lister), or use a local mirror of the UCSC Genome Browser with a literature track (LitTrack).

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FACTA+Tool Content

http://refine1-nactem.mc.man.ac.uk/facta/

Literature > Text Mining and Semantics

FACTA+ (Finding Associated Concepts with Text Analysis) is a real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed, with additional features to help users to discover and visualize indirect associations between important biomedical concepts such as genes, diseases and chemical compounds.

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tagsdatabase management systems medline term association discovery text mining

Tags associated with subcategory 'Literature/Text Mining and Semantics'

medline pubmed humans algorithms text mining genes natural language processing database management systems animals University of Manchester protein databases factual databases mice computational biology artificial intelligence terminology as topic systems integration gene expression profiling cluster analysis bibliographic databases genetic databases controlled vocabulary rats gene expression regulation mutation pharmaceutical preparations genetic models metabolism ubiquitin-protein ligases bone resorption neural networks (computer) molecular cloning hepatoerythropoietic porphyria osteoporosis inborn genetic diseases human genome pancreatic neoplasms programming languages periodicals as topic zebrafish caenorhabditis elegans software design drosophila melanogaster publications signal transduction escherichia coli biomedical engineering tetanus toxin fuzzy logic bibliography of medicine benchmarking information systems research molecular sequence data botulinum toxins evaluation studies as topic medical subject headings arabidopsis automatic acronym disambiguation term association discovery yeast named entity annotation automatic acronym expansion dictionaries as topic automatic term extraction x-ray computed tomography statistical models polymerase chain reaction reproducibility of results automated pattern recognition annotation tool metabolites full text document retrieval bayesian classifier information extraction dictionary lookup term variation protein gene accelerated annotation named entity recognition biomedical acronym recognition species disambiguation trans-activators insects insect genes homeodomain proteins documentation information dissemination oligonucleotide array sequence analysis disease transcription factors proteins arabidopsis proteins data mining biology arabidopsis agamous protein animal behavior orthology relationships species specificity