Directory: Popular Listings 

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

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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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

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

dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/package-insert-DDI...

The "PK DDI" corpus is a new corpus of sections from FDA-approved drug  package inserts (PIs) that have been manually annotated for  pharmacokinetic drug-drug interactions by a pharmacist and a drug  information expert. The two annotators reached consensu ...

Category:Human Annotated

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

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

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 ...

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.

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
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

ytex Popular

code.google.com/p/ytex

The Yale cTAKES Extensions (YTEX) is a set of UIMA annotation engines and utilites that complement the Clinical Text Analysis and Knowledge Extraction System (cTAKES). These include: Semantic Search Engine: A web service that enables users to find doc ...

SecTag Popular

SecTag

knowledgemap.mc.vanderbilt.edu/research/content/sectag-taggi...

Clinical notes are often divided into sections, or segments, such as "history of present illness" or "past medical history." These sections often have subsections as well, such as the "cardiovascular exam" section of the "physical exam." One can gain grea ...

Category:Sectionizer

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

mist-deid.sourceforge.net

The MITRE Identification Scrubber Toolkit (MIST) is a suite of tools for identifying and redacting personally identifiable information (PII) in free-text medical records. MIST helps you replace these PII either with obscuring fillers, such as [NAME], or w ...

LingPipe Text Analytics Java API

lingpipe.com

LingPipe is tool kit for processing text using computational linguistics. LingPipe is used to do tasks like: Find the names of people, organizations or locations in news Automatically classify Twitter search results into categories Suggest correct sp ...

Category:Sectionizer

SemRep Popular

SemRep is a program that extracts semantic predications (subject-predicate-object triples) from biomedical free text. Elements of a semantic predications are drawn from the UMLS knowledge sources; the subject and object pair corresponds to UMLS Metathesau ...

biositemaps.ncbcs.org/rds/search.html

The Resource Discovery System (RDS) is a system for discovering research resources.  RDS has many partnerning institutions which to date include the Clinical and Translational Science Award (CTSA) sites, the National Centers for Biomedical Computing Excel ...

Category:Bioinformatics

labda.sintonia.inf.uc3m.es/DrugDDI/DrugNerAr.html

DrugNerAr Corpus: a corpus annotated with drug anaphoras. Text were collected from the Drugbank database. There is no corpus dedicated to the resolution of the anaphoric expressions occurring in drug interaction descriptions in pharmacological documents, ...

Category:Human Annotated