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Links tagged with 'natural language processing'

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Found 17 links

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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.

This content is being maintained by pthompson.

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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.

This content is being maintained by pthompson.

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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

AliasServerDatabase Content

http://cbi.labri.fr/outils/alias/

DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

BioPortalDatabase Content

http://bioportal.bioontology.org

DNA > Annotations
Expression > Transcript Expression Analysis
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools

BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.

This content is being maintained by whetzel.

NAR Web Server Issue 2009NAR Web Server Issue 2011
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tagsbiomedical research controlled vocabulary natural language processing systems integration terminology as topic

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

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

eTBLASTDatabase Content

http://etest.vbi.vt.edu/etblast3/

Literature > Search Tools

eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.

NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence authorship automated pattern recognition bibliographic databases controlled vocabulary database management systems humans informatics medline natural language processing peer review periodicals as topic publications publishing pubmed software design

GPSDBDatabase Content

http://biomint.pharmadm.com/

Literature > Search Tools
Literature > Text Mining and Semantics

Gene and Protein Synonym DataBase (GPSDB) is a collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user-selected terms.

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tagscontrolled vocabulary database management systems documentation information dissemination medline natural language processing protein databases proteins terminology as topic

HUPO Proteomics Standards InitiativeResource Content

http://psidev.sourceforge.net/

Protein > Proteomics

HUPO Proteomics Standards Initiative (PSI) provides data representation standards to facilitate the exchange, comparison and validation of proteomics data.

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tagsbiochemistry database management systems guidelines as topic humans internationality mass spectrometry natural language processing peptide mapping protein binding protein databases protein interaction mapping proteins proteomics reference standards

iHOPTool Content

http://www.ihop-net.org/UniPub/iHOP/

Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.

NAR Web Server Issue 2007
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tagsanimals arabidopsis biology biomedical engineering caenorhabditis elegans computational biology database management systems drosophila melanogaster escherichia coli genes humans mice natural language processing periodicals as topic publications pubmed signal transduction software design zebrafish

KOBASTool Content

http://kobas.cbi.pku.edu.cn

DNA > Annotations
Human Genome > Databases
Protein > Interactions, Pathways, Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

NAR Web Server Issue 2006NAR Web Server Issue 2011
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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

MetaBioMEDatabase Content

http://metasystems.riken.jp/metabiome/

Protein > Databases

MetaBioiME is a web resource to find novel homologs for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and completed bacterial genomes.

This content is being maintained by tdtaylor.

NAR Database Issue 2010
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tagsanimals bacterial genome computational biology genetic databases humans natural language processing nucleic acid databases open reading frames protein databases sequence alignment tertiary protein structure viral genome

Ontology Lookup ServiceTool Content

http://www.ebi.ac.uk/ols

DNA > Annotations
DNA > DNA and Genomic Analysis
Model Organisms > General Resources

The Ontology Lookup Service provides interactive and programmatic interfaces to query and browse a suite of biomedical ontologies and controlled vocabularies. Users can also navigate the relationships between terms and obtain additional metadata and annotations. Improvements in 2010 have made OLS easier to use, capture more annotations from source data and integrate into external applications.

This content is being maintained by rglcote.

NAR Web Server Issue 2008NAR Web Server Issue 2010
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tagscontrolled vocabulary database management systems factual databases natural language processing programming languages proteomics systems integration

ORegAnnoDatabase Content

http://www.oreganno.org/

DNA > Annotations
DNA > Databases
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Human Genome > Annotations
Human Genome > Sequence Polymorphisms

The Open REGulatory ANNOtation database (ORegAnno) is a collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations.

This content is being maintained by obigriffith.

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tagsanimals binding sites database management systems documentation gene expression regulation genetic databases genetic promoter regions genetic variation humans natural language processing nucleic acid databases periodicals as topic protein binding transcription factors transcriptional regulatory elements