Bee. Hive a datamining tool at Biovitrum and i. Novacia Mats Dahlberg Research Informatics i. Novacia AB, Sweden Chem. Axon UGM, Budapest June 7 2006
Research Informatics’ Philosophy • All data in Oracle – Safe, pharma industry standard (e. g. many chemical cartridges, Chem. Axon, MDL, Accelrys, . . . ) – ”Data is our asset. Programs come and go. ” • Integration through database layer –. . . but hidden to the users. Multiple front-ends allowed • Applications rapidly adapted to users needs – Close connection developers - users – Workflow support requires full control over the code • Unorthodox solutions are allowed – Sometimes quick and dirty development – Sometimes unstable code (but usually fixed quickly. . . ) – Sometimes non-standard technical platform (e. g. Bee language)
Bee. Hive • Function – Main repository for ALL research data (almost) – Used by all project teams – Technical platform for various modules • Features – Advanced on-the-fly join of DB table – Versatile handling of lists (compounds, batches, projects. . . ) and Queries – Data grouping (”One-line-per-compound”) – Fully customisable through meta-data, easy to add new branches (CBT, ELN stats etc) – Structure searching through Chem. Axon Oracle cartridge – Built on Bee language from Mol. Soft LLC, San Diego • Status – Moved from MDL’s cartridge 2006 – Business critical. Appr 250 users throughout R&D
The heart – just a SQL generator… • Defines column types and cost for all joinable columns • All possible joins are precalculated, travelling salesman problem (more then 300 tables)
Meta data structure • Define entities and clean up the dictionaries – Compound numbers, protein targets, batches, plasmids. . . – One source for every entity possible to validate numbers no misspellings improved data quality • This is the core of integration - not a particular client or system • None of this comes out-of-the-box! Prog 2 Prog 1 Cross database client Example from Biovitrum
Bee. Hive Overview Query builder with structural searching Navigate through all tables Activity, solubility, chemist etc
Query builder • All unique values in drop-down lists • No hard-coded values • Easy to spot errors
Extraction of data for SAR analysis • One compound per line • Average IC 50 and SD values • Hill number from Activity. Base • Structure pop-up window
Systems and applications: Bee. Hive Modules That Uses JChem • CIMS – Chemical Inventory Management System – Keeps track of all chemicals (bottle history, location, risk phrases etc) – Replaced previous MDL system – Fully barcoded (bottles, shelves, people. . . ) – Has improved compliance, reagent availability and speed of inventory work • Reagent Search – ACX database of chemical catalogues from Cambridge. Soft – Cross-linked to CIMS – ”Give me all amines under 250 Dal and show in-house on top of the list”
Reagent searching
Systems and applications: Bee. Hive Modules /cont’d/ • Chem. Spec – – – Registration of all new compounds Structure based logic for new compounds and batches BVT (i. No) number assignment Connection point for analytical data and requests Used by all medicinal and analytical chemists
What is next on the list? • JChem Calculated properties on all molecule databases – p. Ka, log. P, log. D, . . . • Generation of diverse screening sets on the fly (BCUT? ) • . . .
Summary - informatics • • • Data sharing is crucial Excel is not enough! No database no modelling Each organisation must define their meta data You need a database administrator Define the data structure first - applications can be improved gradually
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