Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database

<p>Abstract</p> <p>Background</p> <p>In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL.</p> <p>Results</p> <p>To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available.</p> <p>Conclusion</p> <p>This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.</p

Inferring Accountability from Trust Perceptions

International audienceOpaque communications between groups of data processors leave individuals out of touch with the circulation and use of their personal information. Empowering individuals in this regard requires sup-plying them — or auditors on their behalf — with clear data handling guarantees. We introduce an inference model providing individuals with global (organization-wide) accountability guarantees which take into account user expectations and varying levels of usage evidence, such as data handling logs. Our model is implemented in the IDP knowledge base system and demonstrated with the scenario of a surveillance infrastructure used by a railroad company. We show that it is flexible enough to be adapted to any use case involving communicating stakeholders for which a trust hierarchy is defined. Via auditors acting for them, individuals can obtain global accountability guarantees, providing them with a trust-dependent synthesis of declared and proven data handling practices for an entire organization