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Links tagged with 'natural language processing'

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Found 13 links

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ACELATool Content

http://www.nactem.ac.uk/acela/ [open in a new window]

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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.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
Accelerating the annotation of sparse named entities by dynamic sentence selection200810
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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/ [open in a new window]

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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.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
Building a high-quality sense inventory for improved abbreviation disambiguation201012
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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/ [open in a new window]

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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.

This content is being maintained by pthompson.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
Building a high-quality sense inventory for improved abbreviation disambiguation201012
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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/ [open in a new window]

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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.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
AliasServer: a web server to handle multiple aliases used to refer to proteins200426
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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

ChilibotTool Content

http://www.chilibot.net/ [open in a new window]

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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.

links directory index: 171
TitlePublication YearGoogle Scholar Citation Count
Content-rich biological network constructed by mining PubMed abstracts2004171
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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 [open in a new window]

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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.

This content is being maintained by pthompson.

links directory index: 29
TitlePublication YearGoogle Scholar Citation Count
Disambiguating the species of biomedical named entities using natural language parsers201029
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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

GPSDBDatabase Content

http://biomint.pharmadm.com/ [open in a new window]

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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.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
GPSDB: a new database for synonyms expansion of gene and protein names200512
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tagscontrolled vocabulary database management systems documentation information dissemination medline natural language processing protein databases proteins terminology as topic

HarvesterTool Content

http://harvester.fzk.de/harvester/ [open in a new window]

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Human Genome > Annotations
Protein > Annotation and Function

Harvester provides fast access to public bioinformatic databases and servers for human proteins. Results are returned as a single HTML page that contains the cached and cross-linked output from the following databases/servers: Uniprot/SWISSprot, ensEMBL, BLAST (NCBI), SOURCE, SMART, STRING, PSORT2, CDART, UniGene and SOSUI.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
'Harvester': a fast meta search engine of human protein resources200435
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tagsdatabase management systems documentation humans natural language processing protein databases proteins systems integration

HUPO Proteomics Standards InitiativeResource Content

http://psidev.sourceforge.net/ [open in a new window]

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Protein > Proteomics

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

links directory index: 516
TitlePublication YearGoogle Scholar Citation Count
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data2004405
The proteomics standards initiative2003111
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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

KOBASTool Content

http://kobas.cbi.pku.edu.cn [open in a new window]

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DNA > Annotations
Human Genome > Databases
Protein > Networks & Interactions, Pathways and 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).

links directory index: 215
TitlePublication YearGoogle Scholar Citation Count
KOBAS server: a web-based platform for automated annotation and pathway identification200675
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary2005140
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/ [open in a new window]

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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.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets201011
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 [open in a new window]

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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.

links directory index: 160
TitlePublication YearGoogle Scholar Citation Count
The Ontology Lookup Service: bigger and better20109
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries200849
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries2006102
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/ [open in a new window]

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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.

links directory index: 145
TitlePublication YearGoogle Scholar Citation Count
ORegAnno: an open-access community-driven resource for regulatory annotation200873
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation200672
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external linksLink on Wikipedia
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

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