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Treillis de concepts et ontologies pour l'interrogation d'un annuaire de sources de donn\'{e}es biologiques (BioRegistry)

Nizar Messai·Marie-Dominique Devignes·Malika Smaïl-Tabbone·Amedeo Napoli
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Abstract

Bioinformatic data sources available on the web are multiple and heterogenous. The lack of documentation and the difficulty of interaction with these data sources require users competence in both informatics and biological fields for an optimal use of sources contents that remain rather under exploited. In this paper we present an approach based on formal concept analysis to classify and search relevant bioinformatic data sources for a given query. It consists in building the concept lattice from the binary relation between bioinformatic data sources and their associated metadata. The concept built from a given query is then merged into the concept lattice. The result is given by the extraction of the set of sources belonging to the extents of the query concept subsumers in the resulting concept lattice. The sources ranking is given by the concept specificity order in the concept lattice. An improvement of the approach consists in automatic query refinement thanks to domain ontologies. Two forms of refinement are possible by generalisation and by specialisation. ----- Les sources de donn\'{e}es biologiques disponibles sur le web sont multiples et h\'{e}t\'{e}rog\`{e}nes. L'utilisation optimale de ces ressources n\'{e}cessite aujourd'hui de la part des utilisateurs des comp\'{e}tences \`{a} la fois en informatique et en biologie, du fait du manque de documentation et des difficult\'{e}s d'interaction avec les sources de donn\'{e}es. De fait, les contenus de ces ressources restent souvent sous-exploit\'{e}s. Nous pr\'{e}sentons ici une approche bas\'{e}e sur l'analyse de concepts formels, pour organiser et rechercher des sources de donn\'{e}es biologiques pertinentes pour une requ\^{e}te donn\'{e}e. Le travail consiste \`{a} construire un treillis de concepts \`{a} partir des m\'{e}ta-donn\'{e}es associ\'{e}es aux sources. Le concept construit \`{a} partir d'une requ\^{e}te donn\'{e}e est alors int\'{e}gr\'{e} au treillis. La r\'{e}ponse \`{a} la requ\^{e}te est ensuite fournie par l'extraction des sources de donn\'{e}es appartenant aux extensions des concepts subsumant le concept requ\^{e}te dans le treillis. Les sources ainsi retourn\'{e}es peuvent \^{e}tre tri\'{e}es selon l'ordre de sp\'{e}cificit\'{e} des concepts dans le treillis. Une proc\'{e}dure de raffinement de requ\^{e}te, bas\'{e}e sur des ontologies du domaine, permet d'am\'{e}liorer le rappel par g\'{e}n\'{e}ralisation ou par sp\'{e}cialisation

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Nizar Messai, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Amedeo Napoli. 2005-06-06. Treillis de concepts et ontologies pour l'interrogation d'un annuaire de sources de donn\'{e}es biologiques (BioRegistry). https://arxiv.org/abs/cs/0506017

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