Scientific Cyberinfrastructure Research Program

National Institute Of Environmental Health Sciences

Investigators

Linked publications, trials & patents

Abstract

To accomplish its objectives, the SCI program is divided into key area teams (Key Area Team, KAT) for associated coordination and governance processes that reside within the overall SCI program. Highlights of progress toward objectives and accomplishment of milestones within the current KATs include: 1. Core Key Area (Core): Progress has been made in providing foundational software systems, principally Knime and Posit, in the development of skills for use of core resources, such as use of the NIEHS high performance compute cluster, and in developing stronger connections to OSC for support. 2. Evidence Informatics Key Area (EI): Significant progress has been made in automation and developing improved methods for data extraction, leading to an expansion of these efforts and the implementation of new approaches within DTT. This progress is evidenced by recent publications, software development, and DTT presentations at national and international meetings. Additionally, AI approaches are being explored to further support the workflow. Good strides are being made in increasing standardization and interoperability, conducting impact assessments for DTT, and supporting the development of datasets for models. 3. ToxChem Informatics Key Area (TCI): Progress has been made in optimizing the genomic dose-response modeling pipeline in a manner that addresses the repeatability of findings and mechanistic interpretation. To support genomic dose-response studies, a synthetic data generation app has been created to produce synthetic null studies that can be employed to empirically calculate false discovery rates. The data landscape of the DrugMatrix database has been expanded through large-scale inferential methods for sparse matrix completion, to the extent that it now offers comprehensive expression data (Codelink, Affymetrix, and S1500+/Sciome GENIE) and pathology across 8 tissues. All data from DrugMatrix have been made available through multiple web resources that allow for molecular-to-phenotypic linkage for biomarker identification and mechanistic interpretation. The ChemBioTox resource and associated data mining tools have been developed to allow for exploration of known and predicted toxicological properties of over 1 million chemicals of environmental concern. Under the ToxPipe project, significant progress has been made in training Large Language Models using legacy NTP studies and structured data resources such as ChemBioTox and DrugMatrix. The Integrated Chemical Environment had several feature improvements including but not limited to new data visualizations for Search tool query summary results, new overlays for data comparisons in the In Vitro to In Vivo Extrapolation (IVIVE) tool and improved support for chemical name searching in the ICE REST AP. 4. Data Management Key Area (DM): Progress continues in improving and streamlining data management practices, including development and review of NIH data sharing plans, development of DTT data pipelines that address most DTT data types, development of a data dictionary, and development of an integrated data repository. 5. Knowledge Management Key Area (KM): Progress has been made in annotation, harmonization and integrating data from diverse sources for ICE, the DTT data dictionary, Methods2AOPs, and the Environmental Health Language Collaborative (EHLC). Communication and training for all DTT on internal and external platforms are regularly organized. Progress continues toward tangible components – such as tools, applications, libraries, middleware, databases, data sets, hardware systems, ontologies and terminologies, and related training materials and courses – that are hosted on public websites. Where appropriate, new developments or significant updates are supported by publications (see Bibliography). In addition, a new process for SCI-PMT portfolio strategic planning and coordinated development has been partially implemented and will continue as the new ORBIT system becomes available.