National Library of Medicine (NLM) ChemIDplus Database Management and Scientific Support

For NLM’s ChemIDplus Database, Cygnus provides management and scientific support including the survey, identification, retrieval, acquisition, and organization of literature on chemical, physical, and biomedical information support. This project work includes Web site database support and maintenance for the NLM’s ChemIDPlus Database and Drug Portal projects. It also includes abstracting, indexing, and cataloging articles for inclusion in the database; entering chemical structures and biological data records; developing and maintaining informational databases using ORACLE and ISIS; designing and developing Web page content and graphics. Our role in this project is to provide researchers with access to quality and accurate health information to advance medical treatments worldwide. Cygnus successfully created customized solutions to identify, collect, organize, verify authority, and share the data and information needed to maximize our clients’ returns to best serve the broad community of worldwide users. This work has similarities to the Chemical Queries activities and in the capabilities and expectations of other indexing tasks within the current solicitation.

Description

For the past 13 years Cygnus’ has successfully supported the NLM ChemIDplus initiative with a high-level scientific team of multidisciplinary professionals committed to the unique needs of this critical projectCygnus’ ChemIDplus team provides chemical, physical, and biomedical information support and Web site database support for the NLM’s ChemIDPlus Database and Drug Portal projects. These services included editing and entering chemical structures and associated chemical information into an MDL chemical structure database. Cygnus staff members also are responsible for the general maintenance of the ChemIDPlus Oracle data tables, including QC, standardizing and formatting biomedical information associated with the ChemIDPlus chemical compounds. Data parsing assignments for NLM included the conduct of special data manipulation tasks and/or data manipulation components.

This work has included the addition to and maintenance of chemical structures, names, molecular formula, and other associated chemical information tasks for the ChemIDplus database. In parallel with these efforts, Cygnus has also offered Oracle and programming support related to data mining, data parsing, and data entry of the records contained in both the ChemIDplus and Drug Information Portal Web databases. Our team marries exceptional subject matter expertise with extensive experience with the relevant specialized software systems. We have provided monitoring, maintenance, mining, and upgrading of these systems to provide added potential for increased usage.

We routinely assist with registrations of chemical structures, either singly or in batches of up to 10,000 at-a-time, into ISIS chemical databases. Our ChemIDplus project staff, investigates, reports, and standardizes chemical information on structure, salt, purity, origin, stereochemistry, geometric isomerism, systematic name, alternate names, chemical and therapeutic class, QSAR data, and CAS and NSC number. We have more than 12 years of experience recording and standardizing pharmacokinetic, toxicological, and biological information. Cygnus’s ChemIDplus Team has performed the following tasks directly for SIS staff:

  • Analyzing data structures of different data sources and designing various programs (PL/SQL stored procedures/functions, Java, C++, Visual Basic, and Perl programs) to parse and transform desirable drug, chemical, and toxicological data into the ChemIDplus format and standards. Using SQL queries and scripts to retrieve matching data to update the locator field, and retrieve new data to load/update the ChemIDplus system with appropriate source information;
  • Generating files for large batch data loading and updating;
  • Retrieving drug and chemical information including structural information from public resources for loading into the ChemIDplus system;
  • Designing and implementing new data integrity QC/QA rules by developing triggers and stored procedures;
  • Using SQL queries and scripts to validate all new and or updated records;
  • Developing and maintaining informational databases related to NLM topics using Oracle and Accelrys; and
  • Participating in system upgrading/migration and Web site support.
  • Abstracting, evaluation, and assembly of preclinical and supportive biological/chemical data
  • Database design, development, and maintenance of biological and chemical structures database
  • Chemical query flagging, investigation and response services
  • Chemical structure analysis and drawing
  • Literature searches, sourcing identification, quality and authority control
  • Content development, document identification, collection, management, and storage
  • Software and hardware maintenance
  • Computer update support
  • Web page development and maintenance
  • Provide software and hardware maintenance, computer update support, and adequate security provisions to protect the integrity and confidentiality of the data;
  • Capture biological, scientific, and biomedical-related information and chemical structures from public literature, patents, and private government contract laboratories for entry into scientific databases
  • Standardize data entry and databases
  • Input chemical structures, and biological and toxicological data records into database tables for Web site support
  • Create Hviews and forms, and configure remote access files appropriate for data review;
  • Apply QC/QA procedures to guarantee 100% accuracy of all data
  • Develop and maintain informational databases related to NLM topics using Oracle and ISIS.

Solutions

Cygnus staff members also are responsible for the general maintenance of the ChemIDPlus Oracle data tables, including QC, standardizing and formatting biomedical information associated with the ChemIDPlus chemical compounds. Data parsing assignments for NLM included the conduct of special data manipulation tasks and/or data manipulation components.

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