National Cancer Institute Uma Mudunuri ABCC, NCI-Frederick ISRCE Monthly Meeting, Nov 9th 2010 bioDBnet The biological DataBase network

Why Integrate? Tremendous growth in information - GenBank used to be distributed in print - petabytes of data per day Biological databases contain diverse but related data - across species and experimental methods - various data types Obtain new information - specific - otherwise impossible to obtain Translate lab results to clinical knowledge - without learning new technology - focus on science

Goal: Integrate all our databases in a scalable and extensible way with minimum changes to the existing schemas Architecture: 1 st tier(UI)Middle tier 3 rd tier(Db) - PHP- XML - Oracle 11g - HTML- PHP - Perl - AJAX- cron jobs - cron jobs - Javascript Database Integration

XML Mapper Advantages - extremely flexible - can add or remove any database - table schemas can be changed - can choose the table relations to be included or excluded - no strict database naming conventions - can connect data from multiple data warehouses - independent of RDBMS

Database Updates Completely automated through cron check for updates everyday download and parse load to dev production loads over the weekend How we do it maintain directory structures common modules addition of new databases is easy

Integration 179 biological identifiers from 28 biological databases bioDBnet proteomics genomics metabolomics transcriptomics protein disease drug Variation/polymorphism interaction microarray Functional annotation Protein feature taxon pathway gene

biological DataBase network

Current menu db2db –handles database to database conversions dbWalk –walk through your own database path dbReport –reports everything about an ID dbFind –finds the type of an identifier and converts it into one of the connectors

Other Features bioText – text search on Gene, UniProt and GO chrView – visualize data on chromosomes goTree – hierarchical representation of GO orgTaxon – get organism taxon identifiers external and internal links wherever possible extensive notes and examples for all of bioDBnet SOAP web services access to sample code

Advantages dynamic flexible not interfere with updates fast performance cater to different needs batch queries ortholog conversions controlled conversions real-time results with current version data can add/delete databases very easily each database is updated independently 100s of queries in seconds various databases and data types follows multiple paths to retrieve maximum results can define own paths using dbWalk

Future add more databases enhanced results display expand text search data mining literature visualization customization

bioDBnet PIDr. Bob Stephens Database UpdatesAnney Che, Gary Smythers DBADavid Liu, Henri Tuthill SuggestionsDr. Ming Yi, Dr. Natalia Volfvosky bioDBnet: the biological database network Uma Mudunuri, Anney Che, Ming Yi, and Robert M. Stephens Bioinformatics February 15; 25(4):