An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines.
Recent industry-academic partnerships involve collaboration among disciplines, locations, and organizations using publicly funded "open-access" and proprietary commercial data sources. These require the effective integration of chemical and biological information from diverse data sources, which presents key informatics, personnel, and organizational challenges. The BioAssay Research Database (BARD) was conceived to address these challenges and serve as a community-wide resource and intuitive web portal for public-sector chemical-biology data. Its initial focus is to enable scientists to more effectively use the National Institutes of Health Roadmap Molecular Libraries Program (MLP) data generated from the 3-year pilot and 6-year production phases of the Molecular Libraries Probe Production Centers Network (MLPCN), which is currently in its final year. BARD evolves the current data standards through structured assay and result annotations that leverage BioAssay Ontology and other industry-standard ontologies, and a core hierarchy of assay definition terms and data standards defined specifically for small-molecule assay data. We initially focused on migrating the highest-value MLP data into BARD and bringing it up to this new standard. We review the technical and organizational challenges overcome by the interdisciplinary BARD team, veterans of public- and private-sector data-integration projects, who are collaborating to describe (functional specifications), design (technical specifications), and implement this next-generation software solution.
Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Andrea
A
de Souza
Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Joshua A
JA
Bittker
Broad Institute of Harvard and MIT, Cambridge, MA, USA.
David L
DL
Lahr
Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Steve
S
Brudz
Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Simon
S
Chatwin
University of New Mexico Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
Tudor I
TI
Oprea
University of New Mexico Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
Anna
A
Waller
University of New Mexico Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
Jeremy J
JJ
Yang
NIH Center for Advancing Translational Sciences, Rockville, MD, USA.
Noel
N
Southall
NIH Center for Advancing Translational Sciences, Rockville, MD, USA.
Rajarshi
R
Guha
Center for Computational Science, University of Miami, Miami, FL, USA.
Stephan C
SC
Schürer
Center for Computational Science, University of Miami, Miami, FL, USA.
Uma D
UD
Vempati
The Translational Research Institute, The Scripps Research Institute, Jupiter, FL, USA.
Mark R
MR
Southern
The Vanderbilt Specialized Chemistry Center for Accelerated Probe Development, Vanderbilt University Medical Center, Nashville, TN, USA.
Eric S
ES
Dawson
Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Paul A
PA
Clemons
Conrad Prebys Center for Chemical Genomics, Sanford|Burnham Medical Research Institute, La Jolla, CA, USA tchung@sanfordburnham.org.
Thomas D Y
TD
Chung
D022126:Access to Information; D001671:Biochemistry; D002626:Chemistry, Pharmaceutical / Q000379:methods; D003625:Data Collection; D062126:Databases, Chemical; D055808:Drug Discovery; D004345:Drug Industry; D020407:Internet; D009316:National Institutes of Health (U.S.); D054852:Small Molecule Libraries / Q000737:chemistry; D012984:Software; D014481:United States
D054852:Small Molecule Libraries
Chemical biological database standards; visualization; web portal