BioTop: An upper domain ontology for the life sciences

Beisswanger, Elena; Schulz, Stefan; Stenzhorn, Holger; Hahn, Udo

doi:10.3233/ao-2008-0057

Cited by 81 publications

(17 citation statements)

References 19 publications

(17 reference statements)

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“…A limited review uncovered wrong and missing occurrences in both ST assignments and hierarchical relationships. Schulz et al 94 provided methods and assessed the alignment of UMLS SN with BioTop 95 , 96 and identified inconsistent multiple ST combinations.…”

Section: Resultsmentioning

confidence: 99%

A review of auditing techniques for the Unified Medical Language System

Zheng

Wei

et al. 2020

Journal of the American Medical Informatics Association

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Objective The study sought to describe the literature related to the development of methods for auditing the Unified Medical Language System (UMLS), with particular attention to identifying errors and inconsistencies of attributes of the concepts in the UMLS Metathesaurus. Materials and Methods We applied the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) approach by searching the MEDLINE database and Google Scholar for studies referencing the UMLS and any of several terms related to auditing, error detection, and quality assurance. A qualitative analysis and summarization of articles that met inclusion criteria were performed. Results Eighty-three studies were reviewed in detail. We first categorized techniques based on various aspects including concepts, concept names, and synonymy (n = 37), semantic type assignments (n = 36), hierarchical relationships (n = 24), lateral relationships (n = 12), ontology enrichment (n = 8), and ontology alignment (n = 18). We also categorized the methods according to their level of automation (ie, automated systematic, automated heuristic, or manual) and the type of knowledge used (ie, intrinsic or extrinsic knowledge). Conclusions This study is a comprehensive review of the published methods for auditing the various conceptual aspects of the UMLS. Categorizing the auditing techniques according to the various aspects will enable the curators of the UMLS as well as researchers comprehensive easy access to this wealth of knowledge (eg, for auditing lateral relationships in the UMLS). We also reviewed ontology enrichment and alignment techniques due to their critical use of and impact on the UMLS.

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Section: Resultsmentioning

confidence: 99%

A review of auditing techniques for the Unified Medical Language System

Zheng

Wei

et al. 2020

Journal of the American Medical Informatics Association

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“…Although in an early development stage, the OntoCheck plugin proved already useful in carrying out pre-release checks for ontologies in different projects [ 9 - 14 ]. It has helped alerting developers on labelling violations and contributed in keeping these ontologies clean from naming errors.…”

Section: Discussionmentioning

confidence: 99%

“…An informal requirement analysis was conducted on the basis of the OBO Foundry naming conventions [ 3 ] and on-going editing work in the different ontology engineering projects the authors were involved in. To test and to quantify OntoChecks capabilities, as well as gather further requirements, we applied the plugin within different projects and investigated the following six ontologies: Biotop [ 9 ], DCO [ 10 ], NTDO [ 11 ], GoodRelations [ 12 ], Vehicle Sales Ontology [ 13 ], and @neurist ontology [ 14 ]. For each, we created, stored and applied a different set of checks.…”

Section: Methodsmentioning

confidence: 99%

OntoCheck: verifying ontology naming conventions and metadata completeness in Protégé 4

et al. 2012

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BackgroundAlthough policy providers have outlined minimal metadata guidelines and naming conventions, ontologies of today still display inter- and intra-ontology heterogeneities in class labelling schemes and metadata completeness. This fact is at least partially due to missing or inappropriate tools. Software support can ease this situation and contribute to overall ontology consistency and quality by helping to enforce such conventions.ObjectiveWe provide a plugin for the Protégé Ontology editor to allow for easy checks on compliance towards ontology naming conventions and metadata completeness, as well as curation in case of found violations.ImplementationIn a requirement analysis, derived from a prior standardization approach carried out within the OBO Foundry, we investigate the needed capabilities for software tools to check, curate and maintain class naming conventions. A Protégé tab plugin was implemented accordingly using the Protégé 4.1 libraries. The plugin was tested on six different ontologies. Based on these test results, the plugin could be refined, also by the integration of new functionalities.ResultsThe new Protégé plugin, OntoCheck, allows for ontology tests to be carried out on OWL ontologies. In particular the OntoCheck plugin helps to clean up an ontology with regard to lexical heterogeneity, i.e. enforcing naming conventions and metadata completeness, meeting most of the requirements outlined for such a tool. Found test violations can be corrected to foster consistency in entity naming and meta-annotation within an artefact. Once specified, check constraints like name patterns can be stored and exchanged for later re-use. Here we describe a first version of the software, illustrate its capabilities and use within running ontology development efforts and briefly outline improvements resulting from its application. Further, we discuss OntoChecks capabilities in the context of related tools and highlight potential future expansions.ConclusionsThe OntoCheck plugin facilitates labelling error detection and curation, contributing to lexical quality assurance in OWL ontologies. Ultimately, we hope this Protégé extension will ease ontology alignments as well as lexical post-processing of annotated data and hence can increase overall secondary data usage by humans and computers.

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“…NTDO [ 8 ] leverages classes and relations provided by the upper level ontology BioTop [ 11 ], specializing it downwards to the required leaf node granularity. Additional classes and relations for representing time intervals and their boundaries were imported from the General Formal Ontology (GFO) [ 12 , 13 ].…”

Section: Methodsmentioning

confidence: 99%

Towards an ontological representation of morbidity and mortality in Description Logics

et al. 2012

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BackgroundDespite the high coverage of biomedical ontologies, very few sound definitions of death can be found. Nevertheless, this concept has its relevance in epidemiology, such as for data integration within mortality notification systems. We here introduce an ontological representation of the complex biological qualities and processes that inhere in organisms transitioning from life to death. We further characterize them by causal processes and their temporal borders.ResultsSeveral representational difficulties were faced, mainly regarding kinds of processes with blurred or fiat borders that change their type in a continuous rather than discrete mode. Examples of such hard to grasp concepts are life, death and its relationships with injuries and diseases. We illustrate an iterative optimization of definitions within four versions of the ontology, so as to stress the typical problems encountered in representing complex biological processes. We point out possible solutions for representing concepts related to biological life cycles, preserving identity of participating individuals, i.e. for a patient in transition from life to death. This solution however required the use of extended description logics not yet supported by tools. We also focus on the interdependencies and need to change further parts if one part is changed.ConclusionThe axiomatic definition of mortality we introduce allows the description of biologic processes related to the transition from healthy to diseased or injured, and up to a final death state. Exploiting such definitions embedded into descriptions of pathogen transmissions by arthropod vectors, the complete sequence of infection and disease processes can be described, starting from the inoculation of a pathogen by a vector, until the death of an individual, preserving the identity of the patient.

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BioTop: An upper domain ontology for the life sciences

Cited by 81 publications

References 19 publications

A review of auditing techniques for the Unified Medical Language System

A review of auditing techniques for the Unified Medical Language System

OntoCheck: verifying ontology naming conventions and metadata completeness in Protégé 4

Towards an ontological representation of morbidity and mortality in Description Logics

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