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H2O database system [60] proposes an on-line data reorganization with on-the-fly query compilation.
In the case of materialized data sets, the query compilation defines the SQL path through the schema by choosing the relevant main (or submain) table at run-time based on which table columns are involved in the query.
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Various optimization strategies are provided to cache these query compilations, which might in turn provide more optimal performance.
Combination of JavaScript, PHP and MySQL databases permitted the querying and compilation of results for real-time injection of data (e.g. gene symbol, expression values and respective colouring) into the X3D scenes, a process known as Ajax (Asynchronous JavaScript and XML) and more recently, Ajax3D when combined with X3D.
Moreover, codes from atomistic simulation packages, such as Quantum ESPRESSO [44] and NWChem [45], which are interfaced with AiiDA, can be queried for version, compilation and runtime parameters.
However, it is clear that the compilation of queries to generic expression trees, independent of the data store, takes a toll on performance.
Compilation... compilers?
This is a further explanation of the differing results obtained in published compilations in which different query sequences were used.
The VM also includes an SQL cookbook which is a compilation of example SQL queries that users can use as a starting point for their research studies.
Searching the web pages requires manual compilation and curation for each information query; such methods are not scalable in the face of the continually growing number of available biological parts.
We here present results of a query of several databases combining all three approaches to metabolome compilation (literature, in-silico pathways and experimental data), using oryza sativa as example.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com