Scientific Cyberinfrastructure Research Program

National Institute Of Environmental Health Sciences

Investigators

Linked publications, trials & patents

Abstract

Core Key Area 1. Our work provides researchers with computational resources needed for analytical work and tool development. 2. Delivered goals included: a. Deployment of RStudio Connect to support deployment of visual-analytics tools. b. Support for data processing pipelines using Knime software. c. Maintenance of the DNTP sandbox, a resource of deploying scientific tools. d. Obtaining ATO for cloud-deployment of the Dextr systematic review tool. Evidence Informatics Key Area 1. Projects focus on advancing the automation of information retrieval from published literature and supports development of tools and models. 2. Accomplishments include: a. Released beta version of Dextr a web-based data extraction tool with user verification. https://www.niehs.nih.gov/research/atniehs/labs/iha/dextr/index.cfm b. Prototype software to support data extraction from tables. c. Model to identify minimum criteria for high quality developmental studies and automate extraction. d. Initial model developed to support automation of DNTP impact assessment using Dextr. e. Explored alternative approaches to developing training datasets. f. Published systematic evidence map protocol that will use Dextr to identify environmental factors that influence immune response to SARS-CoV-2. Data Management Key Area 1. Working to support the NIH Data management and Sharing (DMS) policy. We have created and developed DMS plan (DMSP) templates for both DNTP program and DNTP project level work and approved 15 project level DMSPs. Some required new DMS pipelines which the CEBS team is designing and developing. 2. Working towards our long-term goal of having interoperable DNTP databases the CEBS team is working to integrate all DNTP data in a central CEBS Data Warehouse (CEBSDWH) aligned with the DNTP Data Dictionary (DDD). We approved the CEBSDWH logical model and DMSPs to update CEBSDWH and the DDD. Knowledge Management Key Area 1. DNTP Data Dictionary (DDD): aligns terminology, metadata and endpoints in DNTP studies https://cebs.niehs.nih.gov/cebs/paper/15466. 2. Systematic Evaluation of the Application of Zebrafish in Toxicology (SEAZIT): provides knowledge on use of Zebrafish in toxicology. 3. Integrated Chemical Environment (ICE): supports data interoperability by bringing together multiple databases and tools (e.g., EPA dashboard, CEBS) https://doi.org/10.1016/j.comtox.2021.100184. 4. Environmental Health Language Collaborative: aims to develop and apply a harmonized language for describing Environmental Health Science research (see https://www.mdpi.com/1660-4601/18/17/8985 for workshops and report). 5. Methods2AOP: newly established international collaboration links methods and specific key events or outcomes in an established adverse outcome pathway (AOP). ToxChem Informatics Key Area 1. BMDExpress: new version released for genomic dose-response modeling and determination biological potency. 2. Toxicoinformatics toolbox: the Tox21 Correlation created to facilitate interpretation and read-across. Tox21 Enricher (http://hurlab.med.und.edu/tox21enricher/) updated. 3. Genomic dose-response study reporting: Nine genomic reports published at NIEHS reports describing in vivo biological potency of aromatic phosphate and PFAS chemical classes. 4. Tox21 Database: relational database using open-source PostgreSQL to host Tox21 quantitative high-throughput screening data (https://rstudio.niehs.nih.gov/tox21_qhts_api/). 5. DrugMatrix and TG-gates integrated data mining: Significant progress made in the creation of applications that present users the associations between different data streams contained in the data sets (e.g., between gene expression changes and pathology). 6. ChemBioTox Database and Chemical Prioritization Tool updated.