Artif Intell Med - An ontology-based comparative anatomy information system.


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TRODUCTION: This paper describes the design, implementation, and potential use of a comparative anatomy information system (CAIS) for querying on similarities and differences between homologous anatomical structures across species, the knowledge base it operates upon, the method it uses for determining the answers to the queries, and the user interface it employs to present the results. The relevant informatics contributions of our work include (1) the development and application of the structural difference method, a formalism for symbolically representing anatomical similarities and differences across species; (2) the design of the structure of a mapping between the anatomical models of two different species and its application to information about specific structures in humans, mice, and rats; and (3) the design of the internal syntax and semantics of the query language. These contributions provide the foundation for the development of a working system that allows users to submit queries about the similarities and differences between mouse, rat, and human anatomy; delivers result sets that describe those similarities and differences in symbolic terms; and serves as a prototype for the extension of the knowledge base to any number of species. Additionally, we expanded the domain knowledge by identifying medically relevant structural questions for the human, the mouse, and the rat, and made an initial foray into the validation of the application and its content by means of user questionnaires, software testing, and other feedback.METHODS: The anatomical structures of the species to be compared, as well as the mappings between species, are modeled on templates from the Foundational Model of Anatomy knowledge base, and compared using graph-matching techniques. A graphical user interface allows users to issue queries that retrieve information concerning similarities and differences between structures in the species being examined. Queries from diverse information sources, including domain experts, peer-reviewed articles, and reference books, have been used to test the system and to illustrate its potential use in comparative anatomy studies.RESULTS: 157 test queries were submitted to the CAIS system, and all of them were correctly answered. The interface was evaluated in terms of clarity and ease of use. This testing determined that the application works well, and is fairly intuitive to use, but users want to see more clarification of the meaning of the different types of possible queries. Some of the interface issues will naturally be resolved as we refine our conceptual model to deal with partial and complex homologies in the content.CONCLUSIONS: The CAIS system and its associated methods are expected to be useful to biologists and translational medicine researchers. Possible applications range from supporting theoretical work in clarifying and modeling ontogenetic, physiological, pathological, and evolutionary transformations, to concrete techniques for improving the analysis of genotype-phenotype relationships among various animal models in support of a wide array of clinical and scientific initiatives.

Resumo Limpo

troduct paper describ design implement potenti use compar anatomi inform system cai queri similar differ homolog anatom structur across speci knowledg base oper upon method use determin answer queri user interfac employ present result relev informat contribut work includ develop applic structur differ method formal symbol repres anatom similar differ across speci design structur map anatom model two differ speci applic inform specif structur human mice rat design intern syntax semant queri languag contribut provid foundat develop work system allow user submit queri similar differ mous rat human anatomi deliv result set describ similar differ symbol term serv prototyp extens knowledg base number speci addit expand domain knowledg identifi medic relev structur question human mous rat made initi foray valid applic content mean user questionnair softwar test feedbackmethod anatom structur speci compar well map speci model templat foundat model anatomi knowledg base compar use graphmatch techniqu graphic user interfac allow user issu queri retriev inform concern similar differ structur speci examin queri divers inform sourc includ domain expert peerreview articl refer book use test system illustr potenti use compar anatomi studiesresult test queri submit cai system correct answer interfac evalu term clariti eas use test determin applic work well fair intuit use user want see clarif mean differ type possibl queri interfac issu will natur resolv refin conceptu model deal partial complex homolog contentconclus cai system associ method expect use biologist translat medicin research possibl applic rang support theoret work clarifi model ontogenet physiolog patholog evolutionari transform concret techniqu improv analysi genotypephenotyp relationship among various anim model support wide array clinic scientif initi

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