Talapady N. Bhat

The Protein Data Bank

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

The Protein Data Bank and the Challenge of Structural Genomics

The PDB has created systems for the processing, exchange, query, and distribution of data that will enable many aspects of high throughput structural genomics.

The Protein Data Bank: unifying the archive

The Protein Data Bank (PDB; http://www.pdb.org/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the progress that has been made in validating all data in the PDB archive and in releasing a uniform archive for the community. We have now produced a collection of mmCIF data files for the PDB archive (ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software.

Thermodynamics of enzyme-catalyzed reactions---a database for quantitative biochemistry

UNLABELLED The Thermodynamics of Enzyme-catalyzed Reactions Database (TECRDB) is a comprehensive collection of thermodynamic data on enzyme-catalyzed reactions. The data, which consist of apparent equilibrium constants and calorimetrically determined molar enthalpies of reaction, are the primary experimental results obtained from thermodynamic studies of biochemical reactions. The results from approximately 1000 published papers containing data on approximately 400 different enzyme-catalyzed reactions constitute the essential information in the database. The information is managed using Oracle and is available on the Web. AVAILABILITY http://xpdb.nist.gov/enzyme_thermodynamics/

The CCPN project: an interim report on a data model for the NMR community.

A recent workshop discusses the progress toward integrating NMR data into a unifying data model.

The PDB data uniformity project

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the data uniformity project that is underway to address the inconsistency in PDB data.

Thermodynamics of Enzyme-Catalyzed Reactions: Part 7—2007 Update

This review serves to update previously published evaluations of equilibrium constants and enthalpy changes for enzyme-catalyzed reactions. For each reaction, the following information is given: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used], the data and their evaluation, and, sometimes, commentary on the data and on any corrections which have been applied to the data or any calculations for which the data have been used. The review contains data from 119 references which have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is also a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.This review serves to update previously published evaluations of equilibrium constants and enthalpy changes for enzyme-catalyzed reactions. For each reaction, the following information is given: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used], the data and their evaluation, and, sometimes, commentary on the data and on any corrections which have been applied to the data or any calculations for which the data have been used. The review contains data from 119 references which have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is also a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.

A framework for scientific data modeling and automated software development

MOTIVATION The lack of standards for storage and exchange of data is a serious hindrance for the large-scale data deposition, data mining and program interoperability that is becoming increasingly important in bioinformatics. The problem lies not only in defining and maintaining the standards, but also in convincing scientists and application programmers with a wide variety of backgrounds and interests to adhere to them. RESULTS We present a UML-based programming framework for the modeling of data and the automated production of software to manipulate that data. Our approach allows one to make an abstract description of the structure of the data used in a particular scientific field and then use it to generate fully functional computer code for data access and input/output routines for data storage, together with accompanying documentation. This code can be generated simultaneously for different programming languages from a single model, together with, for example for format descriptions and I/O libraries XML and various relational databases. The framework is entirely general and could be applied in any subject area. We have used this approach to generate a data exchange standard for structural biology and analysis software for macromolecular NMR spectroscopy. AVAILABILITY The framework is available under the GPL license, the data exchange standard with generated subroutine libraries under the LGPL license. Both may be found at http://www.ccpn.ac.uk; http://sourceforge.net/projects/ccpn CONTACT ccpn@mole.bio.cam.ac.uk.

The Protein Data Bank, 1999–

In 1998, members of the Research Collaboratory for Structural Bioinformatics became the managers of the Protein Data Bank archive. This chapter details the systems used for the deposition, annotation and distribution of the data in the archive. Keywords: databases; nuclear magnetic resonance; NMR; Protein Data Bank; structure validation

New concepts for building vocabulary for cell image ontologies

BackgroundThere are significant challenges associated with the building of ontologies for cell biology experiments including the large numbers of terms and their synonyms. These challenges make it difficult to simultaneously query data from multiple experiments or ontologies. If vocabulary terms were consistently used and reused across and within ontologies, queries would be possible through shared terms. One approach to achieving this is to strictly control the terms used in ontologies in the form of a pre-defined schema, but this approach limits the individual researchers ability to create new terms when needed to describe new experiments.ResultsHere, we propose the use of a limited number of highly reusable common root terms, and rules for an experimentalist to locally expand terms by adding more specific terms under more general root terms to form specific new vocabulary hierarchies that can be used to build ontologies. We illustrate the application of the method to build vocabularies and a prototype database for cell images that uses a visual data-tree of terms to facilitate sophisticated queries based on a experimental parameters. We demonstrate how the terminology might be extended by adding new vocabulary terms into the hierarchy of terms in an evolving process. In this approach, image data and metadata are handled separately, so we also describe a robust file-naming scheme to unambiguously identify image and other files associated with each metadata value. The prototype database http://sbd.nist.gov/ consists of more than 2000 images of cells and benchmark materials, and 163 metadata terms that describe experimental details, including many details about cell culture and handling. Image files of interest can be retrieved, and their data can be compared, by choosing one or more relevant metadata values as search terms. Metadata values for any dataset can be compared with corresponding values of another dataset through logical operations.ConclusionsOrganizing metadata for cell imaging experiments under a framework of rules that include highly reused root terms will facilitate the addition of new terms into a vocabulary hierarchy and encourage the reuse of terms. These vocabulary hierarchies can be converted into XML schema or RDF graphs for displaying and querying, but this is not necessary for using it to annotate cell images. Vocabulary data trees from multiple experiments or laboratories can be aligned at the root terms to facilitate query development. This approach of developing vocabularies is compatible with the major advances in database technology and could be used for building the Semantic Web.