Annotator protocols

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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 in pipeline

PMCID: 4301805
PMID: 25607983
DOI: 10.1371/journal.pone.0116040

[…] biomedical domain., using four established concept recognition systems and a standard method to build a ssc for phenotype-related concepts reaches in the best case a f1-measure of 33% if only ncbo annotator and ctakes are used for annotations. even if four systems are combined, the obtained ssc is limited to mostly annotations of these two concept recognition systems. however, the best […]

Annotator in publications

PMCID: 5700471
PMID: 29250549
DOI: 10.1155/2017/8565739

[…] accession number, and the annotation text (e.g., “[27::42] hp_0000110 ∣ renal dysplasia”)., besides releasing the gsc, the authors performed a comprehensive evaluation of three ner systems: the ncbo annotator [], the obo annotator [], and the bio-lark cr []. bio-lark cr, just like ihp, is a recognition system with the objective of identifying hpo entities, while the ncbo annotator and the obo […]

PMCID: 5635572
PMID: 29017443
DOI: 10.1186/s12859-017-1858-7

[…] informative. therefore, methods generating synonyms with a higher ic score will have a major impact at the concept recognition task and so, document retrieval., the evaluation process used the obo annotator [], a concept recognizer oriented to perform automatic annotation of phenotypes based on the hpo. the following provides a brief overview of how the obo annotator works. first, it splits […]

PMCID: 4301805
PMID: 25607983
DOI: 10.1371/journal.pone.0116040

[…] we investigate the performance of four extant concept recognition tools: the clinical text analysis and knowledge extraction system (ctakes), the national center for biomedical ontology (ncbo) annotator, the biomedical concept annotation system (becas) and metamap. each of the four concept recognition systems is applied to four different corpora: the i2b2 corpus of clinical documents, […]

PMCID: 4433377
PMID: 25336595
DOI: 10.1136/amiajnl-2014-002902

[…] safety profiling of a drug, learning adverse drug–drug interactions, and learning used-to-treat relationships between drugs and indications., materials we first benchmarked the accuracy of the ncbo annotator and reveal in a manually annotated, publically available dataset from the 2008 i2b2 obesity challenge. we then applied the ncbo annotator and reveal to 9 million clinical notes […]

PMCID: 3337270
PMID: 22541596
DOI: 10.1186/2041-1480-3-S1-S5

[…] the gender split is roughly 60% female, 40% male. ages range from 0 to 90 (adjusted to satisfy hipaa requirements), with an average age of 44 and standard deviation of 25., we created a standalone annotator workflow (figure ) based upon the existing national center for biomedical ontology (ncbo) annotator web service [] that annotates clinical text from electronic health record systems […]

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

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