QxDB: An open-ended, generic database for quantitative physiology

S. Randall Thomas 1 Benjamin Ribba 2 Philippe Tracqui 3
2 NUMED - Numerical Medicine
Inria Grenoble - Rhône-Alpes, UMPA-ENSL - Unité de Mathématiques Pures et Appliquées
3 DynaCell
TIMC-IMAG - Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525
Abstract : Based on the generic data model of the Quantitative Kidney DataBase, QKDB (http://www.lami.univ-evry.fr/~srthomas/qkdb), we have built an open-source MySQL/PHP/Apache database package, QxDB (http://www.lami.univ-evry/~srthomas/qxdb), that is easily adapted for any research domain. As with QKDB, this package is designed particularly for quantitative results needed for hypothesis-based mathematical models. Since these are typically heterogeneous data-types (transport parameters, times-series, anatomical features, images, ...), a central concern was the ability to easily add new data descriptors. Thus, adaptation to new domains is a simple matter of changing the entries in the DB fields table. Results curated in QxDB are supplemented by comments from the contributing experts, giving their evaluations of experimental techniques, breadth of validity of results, etc. Useful features of the web interface include: 1) three levels of user permissions: simple user, contributor, and administrator; 2) multi-criteria search using dynamic roll-down lists or full-text search; 3) convenient entry of bibliographic references by hand, by file upload (formats EndNote, BibTeX, PubMed XML), or by pubmed id number; 4) provision for simple, online extension of the descriptors lists during data entry; 5) administrator management of users, correction/deletion/update of data records. By providing centralized storage for quantitative parameters from the experimental literature, this resource can serve not only to streamline the development of mathematical models, but will also be valuable for the general research community, in the spirit of the IUPS Physiome.
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https://hal.archives-ouvertes.fr/hal-00339704
Contributor : Frédéric Davesne <>
Submitted on : Tuesday, November 18, 2008 - 3:49:35 PM
Last modification on : Tuesday, November 19, 2019 - 2:31:27 AM

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  • HAL Id : hal-00339704, version 1

Citation

S. Randall Thomas, Benjamin Ribba, Philippe Tracqui. QxDB: An open-ended, generic database for quantitative physiology. Federation of American Societies for Experimental Biology 2006, 2006, San Francisco, United States. pp.Elec. Proc. ⟨hal-00339704⟩

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