Annotator statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Annotator

Tool usage distribution map

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Annotator specifications


Unique identifier OMICS_01172
Name Annotator
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No


This tool is not maintained anymore.

Publication for Annotator

Annotator citations


Semantic annotation in biomedicine: the current landscape

J Biomed Semantics
PMCID: 5610427
PMID: 28938912
DOI: 10.1186/s13326-017-0153-x

[…] l texts is the lack of sufficient context for interpreting the entity mentions []. For instance, Tseytlin et al. [] reported that the largest proportion of annotation errors made by their NOBLE Coder annotator was due to the missing or incomplete context or background knowledge.The collective annotation approach was proposed as a way of dealing with this challenge []. It relies on the global topic […]


NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation

J Biomed Semantics
PMCID: 5463318
PMID: 28592275
DOI: 10.1186/s13326-017-0128-y

[…] recommendation systems suggest ontologies that provide high coverage of the input data. As with the original approach, the new recommendation process is driven by the annotations provided by the NCBO Annotator, but the method used to evaluate the candidate ontologies is different. In the new algorithm, each annotation is assigned a score computed in accordance with the following expression:annotat […]


HealthRecSys: A semantic content based recommender system to complement health videos

BMC Med Inform Decis Mak
PMCID: 5433022
PMID: 28506225
DOI: 10.1186/s12911-017-0431-7
call_split See protocol

[…] Plus links, . Given that the number of SNOMED-CT vocabulary terms is larger than those on MedlinePlus, we anticipated that many results would not have matching terms. Although Bio-ontology offers an Annotator Web service that annotates user-provided text (e.g., journal abstracts) with relevant ontology concepts, this feature was not used for this work.For practical reasons, we ignored isolated te […]


The Interaction Network Ontology supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature

BioData Min
PMCID: 5168857
PMID: 28031747
DOI: 10.1186/s13040-016-0118-0

[…] h the support of ontologies, OLM significantly enhances literature mining performance [–]. For example, the Gene Ontology (GO) has been used in supporting literature mining [, , ]. The NCBO BioPortal Annotator [] is a web service that supports ontology-based tagging that uses Mgrep [] as the concept recognizer tool []. We have effectively applied OLM in mining gene-gene interactions [–, , ]. We ha […]


Bio TDS: bioscience query tool discovery system

Nucleic Acids Res
PMCID: 5210639
PMID: 27924016
DOI: 10.1093/nar/gkw940

[…] To enable accurate searching of the Bio-TDS repository, it is important to have meaningful annotations describing the tools and their features. The Bio-TDS includes an automated annotator called TONER (Tools Name Entity Resolution). TONER uses the National Center for Biomedical Ontology (NCBO) ( online annotation service to provide suggested concep […]


Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records

Sci Rep
PMCID: 4869115
PMID: 27185194
DOI: 10.1038/srep26094
call_split See protocol

[…] noses (ICD-9 codes), medications, procedures, and lab tests, as well as free-text clinical notes recorded before the split-point. All the clinical records were pre-processed using the Open Biomedical Annotator to obtain harmonized codes for procedures and lab tests, normalized medications based on brand name and dosages, and to extract clinical concepts from the free-text notes. In particular, the […]

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Annotator institution(s)
Centre for Biomedical Informatics, Stanford University, Stanford, CA, USA

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