Comprehensive but simple encoding of bioassays to accelerate translational drug discovery

PROJECT SUMMARY Collaborative Drug DiscoveryIncCDDproposes to extend its innovative software platformBioAssay ExpressBAEversionwhich helps biologists to quickly and easily encode their plain text biological assay protocols into formats suitable for computational processingIn PhaseBCDD will further enhance BAE so that it can markup a bioassay with a comprehensivedetailed set of annotations that completely specifies the protocolstep by stepIn its current state of development in PhaseBAEenables scientists to summarize the English language text that specifies an experimental protocolsupplementing it with machine interpretable descriptorsAt the end of PhaseBBAEwill output a detailed machineinterpretable version that will be completely equivalent toand can optionally substitute forthe traditional English language method descriptionThe enhanced BAEsoftware will enable scientists engaged in early stage drug discovery to efficiently and accurately document experimental procedures and intelligently aggregate datasets across research groupsAn important benefit will be facilitating improved accessuse and reproducibility byflagging differences between closely related assayscorrelating differences in protocols with differences in resultsandimproving the reproducibility of experiments conducted in different laboratoriesto highlight potential causes of divergencesThe project will continue to leverage the related broad initiatives at NIH and elsewhere that are working to promote translational researchgather screening data via open repositoriesand apply sophisticated ontologies to classify these datasetsOur project targets the intersection of these disparate initiatives and unifies them by making their complex standards and guidelines for praxis realistically accessible to researchers who want to focus on their scientific work To encourage adoptionthe software will prioritize intuitive ease of use by scientists who are not informatics expertsharmonize with existing laboratory workflowsminimize the extra effort of annotationintegrate seamlessly into preclinical data management platformsincluding but not limited to CDD s own CDD Vaultand deliver clear and immediate benefits to the user as part of an integrated experienceThis combination of new capabilities and extreme ease of use will accelerate translational drug discovery efforts by empowering software platforms that bridge the divide between biologists and medicinal chemists to apply sophisticated toolslong available on the chemistry sidefor the first time also to the biological sideand thus across both domainsExisting software can already easily connect screening results to chemical structuresThis new platform will further connect these data to the purpose and methodology of the screens PROJECT NARRATIVE The proposed project will create novel computational tools that will help researchers to efficiently and accurately document experimental proceduresthereby facilitating improved accessuse and reproducibility of data and assaysThis fundamental capability ultimately accelerates translating new experimental discoveries into the development of novel and improved drugs against a wide range of diseasesThese tools will particularly benefit networks of researchers working on diseases that leading pharmaceutical companies have largely ignored because they are not perceived as highly profitable opportunitiesdespite the fact that in many cases they afflict millions of people