Clinical &Research Informatics

Sastry, Chandan

Abstract

This project is a core service for the Division of Intramural Research. It focuses on the development of informatics tools to support multiple investigators and a variety of disease areas. The informatics systems and services support NICHD researchers and investigators from other programs at NIDCR, NINR, NIDCR, NIAMS, NIMH, and NIDDK.? ? CLINICAL INFORMATICS? This research area focuses on the development of applications and services in the areas of clinical and translational medicine. Projects completed this year include the following:? a) Clinical Trials Database - a web-based tool for design, collecting, and reporting clinical observations related to natural history and interval-based studies. The total number of protocols supported by the CTDB grew 95, with an expansion of research questions to 35,000. Our software development group completed four major releases that included the following application features: a data coordinating center module for multi-site studies, a Java based web service to connect to the NLM Unified Medical Language System (UMLS) to obtain medical codes (SNOMED and LOINC), and software integration (Oracle 10g, Solaris 10, Java, Tomcat, and Apache).? b) Biorepository Support - We created a Java-based barcode applet to allow PIs to print labels using the CTDB biorepository module completed for clinical sample tracking. The support team initiated a pilot phase for the Sample Tracking Module with multiple PIs at NICHD and NIDCR.? c) Clinical Trial Survey System - This patient survey system was enhanced with three software releases, adding features for skip rules and PDA usage. The total enrollment was increased to 19 protocols.? d) Clinical Datamart - we developed a star schema and reporting structure for research and hospital data integration. This design accomodates for clinical and genomic family history data, and biospecimens. The total number of protocol reports designed to 220. The team developed an integration with Cognos engine for additional reporting functionality and expanded existing CTDB Datamart with additional FACT tables.? e) Clinical Wiki - we continued to advance the use of wiki tools for clinical research. Collaborative web portals were created for the OB/GYN services, pediatric endocrinology, biomedical education, and other DIR labs.? ? BIOLOGICAL VISUALIZATION? This student-led research area focuses on bilogical visualization. It was established this year to provide training opportunities for cross-disciple research in the areas of molecular animation, web programming, microscopy and digital imaging, and medical illustration. The student projects completed included the animation of the Golgi project in collaboration with J. Lippincott-Schwartz, who presented the work at the Golgi conference in Italy. A Golgi rapid prototype three dimensional model was created and accepted into the Golgi Museum in Pavia, Italy. The group redesigned and architected a new DIR Website based on the revised organizational structure of program areas. The team updated and maintained approximately 90 DIR websites, and developed graphic designs and medical illustrations for multiple projects: DIR annual retreat program, the GPP brochure for the Office of Education, DIR Annual Spring Research Festival, ClinicalTrial Tool Kit (CTK) brochure, and NICHD Summer Program t-shirt. The unit established a photography service for lab websites, including the documentation of microscopy techniques and assistance to the Microscopy Imaging Core (MIC) in with igital asset management tools. The team also expanded the science.nichd.nih.gov wiki to 30 projects. This tool allows PIs to create blogs, share documents/data in a secure manner. As part of this project, the group collaborated with the NIH Library to conduct a wiki workshop for NIH Intramural Investigators? ? BIOINFORMATICS? This research area collaborates with investigators to design and develop informatics applications for genomic research. Projects completed this year include the following:? a) GermSAGE - This database and system manages a collection of male germ cell transcriptome information derived from Serial Analysis of Gene Expression (SAGE). The team developed a web-based application with features to view germ cell transcriptome data in the UCSC Genome Browser. Users can also search genes or specify searching criteria based on tag sequence, chromosomal location or tag counts.? b) TransFragMap - Release 1.0 of this software was completed. This system provides a platform for executing bioinformatics scripts to map array data against genomes. ? c) Family History Genomic Tool - the unit developed this web-based system to assist investigators with the collecting disease patterns in patient families. This project involved the design and development of a unique pedigree reporting feature that accommodates multiple family structures. A pilot of the system is in progress with two DIR Investigators.? ? RESEARCH AND MANAGEMENT INFORMATICS? This software engineering core maintains and develops applications to assist investigators with the management of scientific resources and data. Projects completed this year include the following:? a) MTrac - A web-based application that automates the clearance and approval process for manuscripts in the DIR. Seven major production releases were completed and the team provided user training and deployment to 5 DIR programs (PDN, PRAE, CBMP, PMM, and PCRM). The development team also completed a web service feature to connect to NLM Pubmed.? b) Budget and Financial Systems - The unit created custom views for budgets, maintenance, backup, licensing support, user account management, and training for investigators. This included budget spreadsheets for usage during the DIR Budget Program Planning sessions and PI projections? c)Personnel Systems - The team developed reports and maintained the code for staff management. The team also prepared requirements for proposed NIH Educational Tracking System.? d) Administrative Datamart - The unit collected requirements for this proposed business intelligence tool that will allow PIs to analyze data from Personnel, Budget, MTrac and other admin systems. ? e) Software and Data Services - We established site licenses (e.g., EndNote, Reference Manager, Quosa) to assist investigators with publications and authorship. The group also worked with PIs to host applications, images, and files for scientific laboratory projects.