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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.

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Annotator citations


Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules

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 […]


A new synonym substitution method to enrich the human phenotype ontology

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 […]


Generation of Silver Standard Concept Annotations from Biomedical Texts with Special Relevance to Phenotypes

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, […]


Functional evaluation of out of the box text mining tools for data mining tasks

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 […]


Annotation analysis for testing drug safety signals using unstructured 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 […]


Mining the Gene Wiki for functional genomic knowledge

PMCID: 3271090
PMID: 22165947
DOI: 10.1186/1471-2164-12-603

[…] of the community, the challenge of fully structuring the information remains., computational tools for finding ontology terms in text, such as the national center for biomedical ontology's (ncbo) annotator [] and the national library of medicine's metamap [], can help to address the challenge of structuring information presented in natural language. in this article we describe an approach […]

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

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