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NLPReViz Popular

github.com/nlpreviz

NLPReViz is prototype tool to visualize and review the result of using NLP techniques to extract boolean variables from clinical text. Our tool combines multiple visualizations to help the users understand these results and make any necessary corrections ...

Category:Software
CLAMP - Clinical Language Annotation, Modeling and Processing toolkit

clamp.uth.edu

CLAMP is a comprehensive clinical Natural Language Processing (NLP) software that enables recognition and automatic encoding of clinical information in narrative patient reports. It provides not only state-of-the-art NLP components but also a user-friendl ...

Category:Software
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CliNER Popular

CliNER

text-machine.cs.uml.edu/cliner

Open-source natural language processing system for named entity recognition in clinical text of electronic health records. CliNER will identify clinically-relevant entities mentioned in a clinical narrative (such as diseases/disorders, signs/symptoms, med ...

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NDF-RT API Popular

rxnav.nlm.nih.gov/NdfrtAPIs.html#

The NDF-RT API is a web service for accessing the current National Drug File - Reference Terminology (NDF-RT) data set from your program via SOAP/WSDL or through a RESTful interface.  The NDF-RT RESTful web API is a simple web service implemented using HT ...

Category:Bioinformatics

RxNorm API Popular

rxnav.nlm.nih.gov/RxNormAPIs.html#

The RxNorm API is a web service for accessing the current RxNorm data set from your program. Clients can access the web service via SOAP/WSDL or through a RESTful interface. RxNorm provides normalized names for clinical drugs and links its names to many o ...

Category:Bioinformatics

RxNav Popular

rxnav.nlm.nih.gov

RxNav is a browser for several drug information sources, including RxNorm, RxTerms and NDF-RT. RxNav finds drugs in RxNorm from the names and codes in its constituent vocabularies. RxNav displays links from clinical drugs, both branded and generic, to the ...

Category:Bioinformatics

MetaCoDe Popular

www.semantic-valley.org

MetaCoDe is currently being developped. It is another UMLS concepts extractor implemented as a GATE plugin. The purpose is to provide tagging tools available for languages other than English, the ongoing efforts being on French.

RxNorm Popular

www.nlm.nih.gov/research/umls/rxnorm/

RxNorm, a standardized nomenclature for clinical drugs and drug delivery devices, is produced by the National Library of Medicine (NLM). In this context, a clinical drug is a pharmaceutical product given to (or taken by) a patient with a therapeutic or di ...

Category:Structured Data

medlineplus.gov/connect

MedlinePlus Connect allows patient portals and electronic health record (EHR) systems to use existing code sets to link to relevant, authoritative patient health information from MedlinePlus.gov. Matches ICD-9-CM or SNOMED CT CORE Problem List Subset code ...

www.ncbi.nlm.nih.gov/books/NBK25500/

The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). The E-utilities use a fixed URL s ...

Category:Bioinformatics

GENIA Corpus Popular

www.nactem.ac.uk/genia/genia-corpus

Corpus annotation is now a key topic for all areas of natural language processing (NLP) and information extraction (IE) which employ supervised learning. With the explosion of results in molecular-biology there is an increased need for IE to extract knowl ...

Category:Human Annotated

GeneReg Corpus Popular

www.julielab.de/Resources/Corpora/GeneReg.html

The GeneReg corpus consists of 314 Medline abstracts dealing with the regulation of gene expression in the model organism E. coli. The regulation of gene expression can be described as the process that modulates the frequency, rate or extent of gene expre ...

Category:Human Annotated

AIMed Corpora Popular

The AImed corpus consists of 225 Medline abstracts. 200 abstracts describe interactions between human proteins, 25 do not refer to any interaction. There are 4084 protein references and around 1000 tagged interactions in this data set. In this data set th ...

Category:Human Annotated

LLL Corpora Popular

genome.jouy.inra.fr/texte/LLLchallenge

The dataset was prepared for the Genic Interaction Extraction Challenge. Extracting gene interaction means extracting the agent (proteins) and the target (genes) of all couples of genic interactions from sentences.  MIG-INRA has annotated hundreds of such ...

Category:Human Annotated
BioInfer: Bio Information Extraction Resource

mars.cs.utu.fi/BioInfer

Biomedical Information Extraction Resource (BioInfer) is a public resource providing a manually annotated corpus and related resources for information extraction in the biomedical domain. The corpus contains sentences from abstracts of biomedical researc ...

Category:Human Annotated

projects.dbmi.columbia.edu/merki/

MERKI extracts patient medication information from structured and free-text clinical data sources. The extracted medication information can be used for medication reconciliation, harmacovigilance and quality assurance. MERKI outputs medication information ...

NeuroLex - A dynamic lexicon of neuroscience terms

neurolex.org

 The NeuroLex project, supported by the Neuroscience Information Framework project, is a dynamic lexicon of neuroscience terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it. The NeuroLex is being ...

Category:Human Annotated
Neuroscience Information Framework (NIF)

neuinfo.org

Informatics and new web technologies (e.g. ontologies, social networking and community wikis) are becoming increasingly important to biomedical researchers. The sharing of research data and information pertaining to resources (i.e. tools, data, materials ...

Category:Annotation

MsPI Popular

aimed11.unipv.it/MsPI/

MsPI is a software tool for protein identification from PMF data. It can be downloaded freely for non-profit institutions from http://aimed11.unipv.it/MsPI

www2.informatik.hu-berlin.de/~hakenber/corpora/

This corpus originated from the BioCreAtIvE task 1A data set for named entity recognition of gene/protein names. We randomly selected 1000 sentences from this set and added additional annotation for interactions between genes/proteins. 173 sentences conta ...

Category:Human Annotated