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Search Publications by: Talapady N. Bhat (Fed)

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Displaying 1 - 25 of 26

An Infrastructure for Curating, Querying, and Augmenting Document Data: COVID-19 Case Study

August 8, 2023
Author(s)
Eswaran Subrahmanian, Guillaume Sousa Amaral, Talapady N. Bhat, Mary C. Brady, Kevin G. Brady, Jacob Collard, Sarra Chouder, Philippe Dessauw, Alden A. Dima, John T. Elliott, Walid Keyrouz, Nicolas Lelouche, Benjamin Long, Rachael Sexton, Ram D. Sriram
With the advent of the COVID-19 pandemic, there was the hope that data science approaches could help discover means for understanding, mitigating, and treating the disease. This manifested itself in the creation of the COVID-19 Open Research Dataset (CORD

Making Semantic Structures Explicit: Developing and Evaluating Tools and Techniques to Support Understanding of Large Cybersecurity Corpora

February 4, 2022
Author(s)
Ira Monarch, Jacob Collard, Sangjin Shin, Eswaran Subrahmanian, Talapady N. Bhat, Ram D. Sriram
This report describes the adaptation, composition and use of natural language processing, machine learning and other computational tools to help make implicit informational structures in very large technical corpora explicit. The tools applied to the

Human Mitochondrial Protein Database: A Resource for Human Mitochondrial Proteomics

October 12, 2021
Author(s)
Veerasamy Ravichandran, A S. Khan, Peter E. Barker, G B. Vasquez, S J. Zullo, Talapady N. Bhat, G L. Gilliland
A publicly available web-based resource, the Human Mitochondrial Protein Database (HMPD), has been developed to unify data from a broad collection of related resources that provides information about human nuclear and mitochondrial-encoded proteins. This

Generating Domain Terminologies using Root- and Rule-Based Terms

December 21, 2018
Author(s)
Talapady N. Bhat, John T. Elliott, Ursula R. Kattner, Carelyn E. Campbell, Eswaran Subrahmanian, Ram D. Sriram, Jacob Collard, Monarch Ira
Motivated by the need for exible, intuitive, reusable, and normalized ter- minology for the semantic web, we present a general approach for generat- ing sets of such terminologies from nat- ural language documents. The terms that this approach generates

Strategy for extensible, evolving terminology for the Materials Genome Initiative efforts

July 1, 2015
Author(s)
Talapady N. Bhat, Ursula R. Kattner, Laura Bartolo, Carelyn E. Campbell, John T. Elliott
Intuitive, flexible, and evolving terminology plays a significant role in capitalizing on recommended knowledge representation models for material engineering applications. In this article we present a proposed rules-based approach with initial examples

New Concepts for Building Vocabulary for Cell Image Ontologies

December 21, 2011
Author(s)
Anne L. Plant, John T. Elliott, Talapady N. Bhat
Background: We present an approach to cell image databasing that is compatible with searching across a global federation of independent image databases. The variety of biological experiments and data that practitioners would like to access and share is

A Cross-Referencing Web Resource of Pre-Clinical Data for AIDS

October 16, 2008
Author(s)
Talapady N. Bhat, Anh D. Nguyen, G Noble, L Cooney, M Nasr, A Wlodawer, K Das
Structure-based drug discovery relies on efficient compilation and analysis of chemical, biological, pre-clinical and structural data. Factors such as inconsistent naming standards, publications and private archives with scattered and incomplete data, Web

Chemical Taxonomies and Semantic Web for AIDS Research- an over view

October 16, 2008
Author(s)
Talapady N. Bhat
Chemical structures provide the basis for understanding and rationalizing drug discovery process fro Human diseases. The study of interactions of chemicals with target enzymes such as HIV- protease, an AIDS enzyme, is critical for optimizing drug-discovery

InChI a Structure Based IUPAC Identifier for 3-D Structures of AIDS Inhibitors

October 16, 2008
Author(s)
M D. Prasanna, H Rodriguez, J Vondrasek, A Wlodawer, Talapady N. Bhat
The human immunodeficiency virus encodes an aspartic protease which is responsible for posttranslational proteolytic processing of the gag and gag-pol polyprotein gene products into mature functional proteins. Following these proteolytic activities, the

Thermodynamics of Enzyme Catalyzed Reactions: Part 7 - 2007 Update

October 25, 2007
Author(s)
Robert N. Goldberg, Yadu D. Tewari, Talapady N. Bhat
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

Semantic Web for Chemical Genomics: Need, How To, And Hurdles

July 19, 2006
Author(s)
Talapady N. Bhat
Semantic Web has been often suggested as the information technology solution to the growing problem in managing the millions of data points generated by modern science such as nanotechnology and high through-put screening for drugs. However, the progress

HIV Protease Structural Database

August 1, 2002
Author(s)
Veerasamy Ravichandran, J Vondrasek, G L. Gilliland, Talapady N. Bhat, A Wlodawer
The HIV Protease Database (HIVdb) is a web-based archive for HIV protease structural information. HIVdb contains experimentally determined three-dimensional structures of human immunodeficiency virus type 1 (HIV-1), human immunodeficiency virus type 2 (HIV

The Protein Data Bank (PDB)

June 1, 2002
Author(s)
H M. Berman, T Battistuz, Talapady N. Bhat, W Bluhm, P E. Bourne, K Burkhardt, L Iype, Sanjay Jain, P Fagan, J Marvin, D Padilla, Veerasamy Ravichandran, Barry I. Schneider, N Thanki, H Weissig, J Westbrook, C Zardecki
The Protein Data Bank (PDB) is the single worldwide repository 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

The CCPN Project - An Interim Report on a Data Model for the NMR Community

January 1, 2002
Author(s)
R Fogh, W Boucher, E Laue, J Ionides, W Vranken, P Gliwa, J Thornton, E L. Ulrich, J Linge, Talapady N. Bhat, J Westbrook, H M. Berman, G L. Gilliland, M Habeck, W Rieping, M Nilges, J L. Markley
The Collaborative Computing Project for NMR (CCPN) was originally funded by the Biotechnology and Biological Sciences Research Council (BBSRC) in the UK along the lines of CCP4, a similar project for the X-ray community. It has three main aims: i) to

The Protein Data Bank: Unifying the Archive

January 1, 2002
Author(s)
J Westbrook, Z. Feng, Sanjay Jain, Talapady N. Bhat, N Thanki, Veerasamy Ravichandran, G L. Gilliland, W Bluhm, H Weissig, D S. Greer, P E. Bourne, H M. Berman
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

The PDB Data Uniformity Project

January 1, 2001
Author(s)
Talapady N. Bhat, P E. Bourne, Z. Feng, G L. Gilliland, Sanjay Jain, Veerasamy Ravichandran, B. Schneider, K. Schneider, N Thanki, H Weissig, J Westbrook, H M. Berman
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.

The Protein Data Bank and the Challenge of Structural Genomics

November 1, 2000
Author(s)
H M. Berman, Talapady N. Bhat, P E. Bourne, Z. Feng, G L. Gilliland, H Weissig, J Westbrook
The determination of structures on a genomic scale in a high-throughput mode will have an impact on every aspect of the Protein Data Bank (PDB) - the single archive for all biomacromolecular structural data. Although estimates vary, the PDB could triple in