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. 2009 Oct;2(5):382-5.
doi: 10.1111/j.1752-8062.2009.00147.x.

Creating an ontology-based human phenotyping system: The Rockefeller University bleeding history experience

Andreas C Mauer  1 , Edward M Barbour, Nickolay A Khazanov, Natasha Levenkova, Shamim A Mollah, Barry S Coller
Affiliations

Creating an ontology-based human phenotyping system: The Rockefeller University bleeding history experience

Andreas C Mauer et al. Clin Transl Sci. 2009 Oct.

Abstract

The lack of standardized methods for human phenotyping is a major obstacle in translational science. We have developed a bleeding history phenotyping system comprising an ontology, a questionnaire, a Web-based phenotype recording instrument (PRI), and a database. The ontology facilitates transparency, collaboration, aggregation of data, and data analysis. The integrated system allows investigators worldwide to use the PRI, add their de-identified data to the database, and query the aggregated data. Thus, this system can increase the power to detect genotype-phenotype-environment relationships and help new investigators begin their studies. We anticipate that this approach may be applicable to other disorders.

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Figures

Figure 1
Figure 1
Creation of the bleeding history phenotyping system. After an extensive literature search and review by experts, a paper‐based bleeding history clinical reminder form was expanded into a comprehensive bleeding history questionnaire (BHQ). The questionnaire was used to derive a bleeding history ontology (BHO) as well as a bleeding history database and a graphical user interface and electronic recording instrument, the phenotype recording instrument (PRI).
Figure 2
Figure 2
Conceptual schematic of the bleeding history application ontology and bleeding history domain ontology. The examples of epistaxis and two associated questions are depicted. By deriving its structure directly from the bleeding history questionnaire, the bleeding history application ontology captures exact question syntax. In contrast, the bleeding history domain ontology is an idealized conceptualization of bleeding events, divorced from the exact syntax of any particular question. The bleeding history application ontology is linked to the bleeding history domain ontology via shared Properties. These Properties, in combination with Classes from either ontology, defi ne Individuals, which is a technical term that should not be confused with a specifi c person.
Figure 3
Figure 3
Phenotype recording instrument.
See this image and copyright information in PMC

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