The Data Driving SPARK
Details on the scope and sources of information in Pew’s interactive antibiotic discovery tool
This information is out of date. Effective November 18, 2021, Pew transferred all SPARK data to The University of Queensland’s Community for Open Antimicrobial Drug Discovery (CO-ADD). Please visit spark.co-add.org or contact [email protected].
To maximize the potential benefits of its Shared Platform for Antibiotic Research and Knowledge (SPARK), The Pew Charitable Trusts is working with a team of antibiotic discovery experts to ensure that the uploaded data are relevant, standardized, and of the highest quality.
Information-sharing platforms have played critical roles in spurring treatment breakthroughs for disease areas such as cancers, neglected tropical diseases, and tuberculosis. Pew hopes that SPARK will do the same for the fight against drug-resistant bacteria by enabling researchers to share data, ideas, and insights that could lead to a more robust and sustainable pipeline of antibiotics for generations to come.
Scope and sources of SPARK data
The goal of SPARK is to organize and disseminate data that are relevant to addressing the key scientific barriers to antibiotic discovery and have the potential to enhance scientific understanding of Gram-negative permeability.
Standards for SPARK data
The team of antibiotic discovery experts developed a set of standards to ensure not only the quality and relevance of the SPARK data but also to ensure it can be harmonized in ways that make it easy for scientists to use and share.
The SPARK team will work with data donors to facilitate uploads. Once data are uploaded, technical experts will work with donors to organize and validate the information before it is made publicly available. This process (represented in the “Uploaded” portion of the graphic below) includes confirming the basic integrity and accuracy of the data, and—where applicable—applying a “controlled vocabulary” that allows the data to be characterized in a standardized way that is easily searchable and usable. This is the first step for all data uploaded into SPARK.
Certain data sets with common elements and comparable variables will undergo a second stage of standardization. They will be “curated,” a process through which they will be transformed, or pivoted, into integrated collections of information. This will be done by a scientific curator, following guidelines generated by the SPARK discovery experts under the leadership of Aileen Rubio of Spero Therapeutics and Marc Navre of Collaborative Drug Discovery. This process (represented by the “Curated” portion of the above graphic) will clearly link studies that capture comparable measurements of antimicrobial activity (e.g., MICs, IC50), enabling researchers to more easily draw comparisons among data from different studies.
Together, this two-tiered approach to standardizing SPARK data will help get new information into the platform quickly. It also will allow users to access individual and bridged data sets to facilitate cross-study comparisons that could accelerate discovery efforts.
Allan Coukell directs health programs at The Pew Charitable Trusts, and Joe Thomas is a senior associate with Pew’s antibiotic resistance project.