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Knowtator specifications


Unique identifier OMICS_05234
Name Knowtator
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes


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  • person_outline Philip V. Ogren <>

Publication for Knowtator

Knowtator in publications

PMCID: 4427951
PMID: 25943550
DOI: 10.1186/s12911-015-0160-8

[…] against their corresponding prescription lists.figure 1, medication matches and discrepancies between the clinical notes and the prescription lists were double annotated by two annotators using the knowtator plug-in for protégé [,]. both annotators are english speakers (one clinical research nurse and one with an associate of applied science degree in health information science), with at least […]

PMCID: 4331692
PMID: 25810773
DOI: 10.1186/1758-2946-7-S1-S2

[…] we explored alternative ways on how to present the documents to the annotators in a way that is supported by existing annotation tools. in addition to the myminer tool, the systems brat and knowtator were examined []. finally we decided to adapt the annotateit tool [] as the curation application for the construction of the chemdner corpus. it doesn't require local installation […]

PMCID: 4277395
PMID: 25541956
DOI: 10.1371/journal.pone.0115873

[…] 40 notes. once the annotation schema was finalized, batches of approximately 50 notes were chart reviewed. the process for ehr chart review and annotation is shown in . the annotation software knowtator was used to chart review all of the notes. knowtator has a unique advantage over other annotation tools due to its ability to define complex annotation schemas (e.g. schemas […]

PMCID: 4120729
PMID: 25093069
DOI: 10.1186/2041-1480-5-31

[…] the protégé 4.2 (build 276) [], developed and maintained by the national center for biomedical ontology together with its inbuilt hermit 1.3.3 reasoner [] were used to construct the ontology. the knowtator plugin [] was used for manual annotation of abstracts inside the protégé environment. the text-mining tool prominer [] was utilized for named entity recognition of ontology terms in pubmed […]

PMCID: 4288072
PMID: 25600332
DOI: 10.2196/medinform.3022

[…] this collection of 122 narratives is comprised of approximately 23,000 word tokens and the average number of words per narrative is 190.2 (sd 130.3)., the annotation was carried out using knowtator [], a plugin for protégé []. the knowtator interface allows users to define entities that need to be annotated and configure the relationships between them. the 122 annotated narratives […]

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Knowtator institution(s)
Division of Biomedical Informatics, Mayo Clinic, Chinahester, MN, USA

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