BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

Whetzel, Patricia L.; Noy, Natalya F.; Shah, Nigam H.; Alexander, Paul R.; Nyulas, Csongor; Tudorache, Tania; Musen, Mark A.

doi:10.1093/nar/gkr469

Cited by 594 publications

(481 citation statements)

References 9 publications

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“…The Annotator processes text submitted by users through a RESTful web interface, uses string-matching to recognize terms from specified biomedical ontologies within the given text, and returns the annotations to the user [15].…”

Section: Methodsmentioning

confidence: 99%

Content Analysis of Reporting Templates and Free-Text Radiology Reports

Hong

Kahn

2013

J Digit Imaging

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The Radiological Society of North America (RSNA) has developed a set of templates for structured reporting of radiology results. To measure how much of the content of conventional narrative ("free-text") reports is covered by the concepts included in the RSNA reporting templates, we selected five reporting templates that represented a variety of imaging modalities and organ systems. From a sample of 8,275 consecutive, de-identified radiology reports from an academic medical center, we identified one corresponding imaging procedure code for each reporting template. The reports were annotated with RadLex and SNOMED CT terms using the BioPortal Annotator web service. The reporting templates we examined accounted for 17 to 49 % of the concepts that actually appeared in a sample of corresponding radiology reports. The findings suggest that the concepts that appear in the reporting templates occur frequently within free-text clinical reports; thus, the templates provide useful coverage of the "domain of discourse" in radiology reports. The techniques used in this study may be helpful to guide the development of reporting templates by identifying concepts that occur frequently in radiology reports, to evaluate the coverage of existing templates, and to establish global benchmarks for reporting templates.

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Section: Methodsmentioning

confidence: 99%

Content Analysis of Reporting Templates and Free-Text Radiology Reports

Hong

Kahn

2013

J Digit Imaging

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“…When a term set is considered organized using one or more of the functions, user's decisions are then approved, or finalized, and an output is generated. OTO can output: (1) csv files pushed to GitHub (https://github.com/ biosemantics/glossaries), (2) zipped files downloadable via the OTO website, and/or (3) term requests sent to ontologies hosted at BioPortal [20].…”

Section: Methodsmentioning

confidence: 99%

OTO: Ontology term organizer

Huang

Macklin

Morris

et al. 2012

Proc of Assoc for Info

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Background: The need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in ontology construction, most software tools for ontology construction are designed for knowledge engineers and not for domain experts to use. The differences in the opinions of different domain experts and in the terminology usages in source literature are rarely addressed by existing software. Methods: OTO software was developed based on the Agile principles. Through iterations of software release and user feedback, new features are added and existing features modified to make the tool more intuitive and efficient to use for small and large data sets. The software is open source and built in Java. Results: Ontology Term Organizer (OTO; http://biosemantics.arizona.edu/OTO/) is a user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users with specific domain knowledge such as biology but not in-depth ontology construction skills. Specifically OTO can be used to establish is_a, part_of, synonym, and order relationships among terms in any domain that reflects the terminology usage in source literature and based on multiple experts' opinions. The organized terms may be fed into formal ontologies to boost their coverage. All datasets organized on OTO are publicly available.

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“…Formal ontologies are a key for the semantic interoperability and integration of data and knowledge from different sources. An ontology may be regarded as "a kind of controlled vocabulary of well-defined terms with specified relationships between those terms, capable of interpretation by both humans and computers" [28]. From a practical point of view, an ontology defines a set of concepts and relations relevant to a domain of interest, along with axioms stating their properties.…”

Section: The Bioket Data Warehousementioning

confidence: 99%

The BioKET Biodiversity Data Warehouse: Data and Knowledge Integration and Extraction

Inthasone

Pasquier

Tettamanzi

et al. 2014

Advances in Intelligent Data Analysis XIII

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Abstract. Biodiversity datasets are generally stored in different formats. This makes it difficult for biologists to combine and integrate them to retrieve useful information for the purpose of, for example, efficiently classify specimens. In this paper, we present BioKET, a data warehouse which is a consolidation of heterogeneous data sources stored in different formats. For the time being, the scopus of BioKET is botanical. We had, among others things, to list all the existing botanical ontologies and relate terms in BioKET with terms in these ontologies. We demonstrate the usefulness of such a resource by applying FIST, a combined biclustering and conceptual association rule extraction method on a dataset extracted from BioKET to analyze the risk status of plants endemic to Laos. Besides, BioKET may be interfaced with other resources, like GeoCAT, to provide a powerful analysis tool for biodiversity data.

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BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

Cited by 594 publications

References 9 publications

Content Analysis of Reporting Templates and Free-Text Radiology Reports

Content Analysis of Reporting Templates and Free-Text Radiology Reports

OTO: Ontology term organizer

The BioKET Biodiversity Data Warehouse: Data and Knowledge Integration and Extraction

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