Technology: Data Annotation
NCBO aids investigators in biomedical research by developing open source tools to enhance access to and analysis of biomedical data and knowledge. BioPortal – a Web-based application and sharing biomedical ontologies – is just one of many tools that NCBO offers.
Tools
NCBO Annotator
Annotate your own textual biomedical data with biomedical ontology terms
Annotate your own textual biomedical data with biomedical ontology terms
Annotation Summarizer
Prototype in Research - Analyze datasets in term of their annotations
Prototype in Research - Analyze datasets in term of their annotations
BioLit
BioLit extracts database identifiers and rich metadata from open access articles
BioLit extracts database identifiers and rich metadata from open access articles
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cTAKES
Annotate your clinical text with clinical named entities – drugs, diseases/disorders, signs/symptoms, anatomic sites and procedures -- plus attributes such as SNOMED CT or RxNORM code, negation, context (family history of, history of, probable), and drug dosage, route, etc.
Annotate your clinical text with clinical named entities – drugs, diseases/disorders, signs/symptoms, anatomic sites and procedures -- plus attributes such as SNOMED CT or RxNORM code, negation, context (family history of, history of, probable), and drug dosage, route, etc.
ECG-Gadget
Integrates ECG storage & analysis workflows with ECG visualization/annotation
Integrates ECG storage & analysis workflows with ECG visualization/annotation
ISAcreator
Enables users to structure experimental metadata (stand-alone Java application)
Enables users to structure experimental metadata (stand-alone Java application)
Jinx
Volume Segmentation and annotation toll for 3D data sets
Volume Segmentation and annotation toll for 3D data sets
Kino Faceted Indexing and Search Engine
Kino is a faceted indexing and search system, integrated with NCBO. Kino support tools such as the Firefox browser plugin allows biologists to annotate Web documents with NCBO Ontology terms and submit them to a Kino repository.
Kino is a faceted indexing and search system, integrated with NCBO. Kino support tools such as the Firefox browser plugin allows biologists to annotate Web documents with NCBO Ontology terms and submit them to a Kino repository.
Lexicon Builder
Prototype in Research - Build custom lexicons from BioPortal ontologies
Prototype in Research - Build custom lexicons from BioPortal ontologies
ODIE
Toolkit for using ontologies to extract information form free-text clinical documents and using free-text clinical documents to enrich existing ontologies
Toolkit for using ontologies to extract information form free-text clinical documents and using free-text clinical documents to enrich existing ontologies
Ontology Recommender
Recommends ontologies to use for annotation based on descriptions of you datasets
Recommends ontologies to use for annotation based on descriptions of you datasets
OntoMaton
OntoMaton, a tool which allows users to search for ontology terms and tag free text right in Google Spreadsheets.
OntoMaton, a tool which allows users to search for ontology terms and tag free text right in Google Spreadsheets.
OPTIMA: Tool for Automated Ontology Alignment
Optima is a general-purpose tool for aligning ontologies that automatically identifies and matches relevant concepts between ontologies
Optima is a general-purpose tool for aligning ontologies that automatically identifies and matches relevant concepts between ontologies
Terminizer
Assisted detection of ontological terms in free text
Assisted detection of ontological terms in free text
Web Services
NCBO Annotator
Annotate your own textual biomedical data with biomedical ontology terms
Annotate your own textual biomedical data with biomedical ontology terms
Ontology Recommender
Recommends ontologies to use for annotation based on descriptions of you datasets
Recommends ontologies to use for annotation based on descriptions of you datasets
Reflect
Literature annotation service that recognized proteins and small molecules mentioned in a web page, and links them to information - rich summaries
Literature annotation service that recognized proteins and small molecules mentioned in a web page, and links them to information - rich summaries
Terminizer
Assisted detection of ontological terms in free text
Assisted detection of ontological terms in free text