Integrative Bioinformatics

Abstract

Integrative Bioinformatics deals with the development of methods and tools to solve biological problems as well as providing a better understanding or new knowledge about biochemical phenomena by means of data integration and computational experiments [7]. Current high-throughput technologies such as NMR, mass spectrometry, protein/DNA chips, gel electrophoresis data, Yeast Two-Hybrid, QTL mapping, and NGS generate large quantities of high-throughput data. The challenge of Integrative Bioinformatics is to capture, model, simulate, integrate, and analyze this huge amount of data in addition to the data represented by hundreds of biological databases and thousands of scientific journals. The data needs to be integrated and made available in a consistent way to provide new and deeper insights into complex biological systems. Molecular biology produces this volume of data based on high-throughput technologies. One characteristic of this data is exponential growing. Therefore, storing and analysis of this molecular and cellular data essentially uses methods and concepts of Bioinformatics. Currently, there are more than 2,000 database and information systems available via the Internet, which represent this molecular data. Every year new molecular databases and information systems which can be used via the Internet crop up. The classical definition of an information system is based on a database system which represents the data and tools for the user-specific analysis of this data. Today an information system is or can be embedded into the Internet as shown in Fig. 1.1.

WWW-List of Selected Molecular Information Systems

Genes

• EMBL – http://www.ebi.ac.uk/

• The “EMBL Nucleotide Sequence Database” represents all known DNA and RNA sequences.

• GenBank – http://www.ncbi.nih.gov/Genbank/

• NIH genetic sequence database.

• HGMD – http://www.uwcm.ac.uk/medical_genetics/

• HGMD represents the Human Gene Mutation Database.

Proteins and Enzymes

• ENZYME – http://www.expasy.org/enzyme/

• ENZYME is a repository of information relative to the nomenclature of enzymes.

• LIGAND – http://www.genome.ad.jp/ligand/

• The Ligand Chemical Database for Enzyme Reactions is linking chemical and biological aspects of life in the light of enzymatic reactions.

• PDB – http://www.rcsb.org/pdb/

• PDB presents 3D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.

• PIR – http://pir.georgetown.edu/

• This database is a comprehensive, annotated, and nonredundant set of protein sequence databases in which entries are classified into family groups and where alignments of each group are available.

• PROSITE – http://www.expasy.ch/prosite/

• PROSITE is a database of protein families and domains.

• REBASE – http://rebase.neb.com/

• Restriction Enzyme data BASE is a collection of information about restriction enzymes.

• SWISSPROT – http://www.expasy.org/sprot/

• Protein sequence database.

Pathways

• CSNDB – http://geo.nihs.go.jp/

• The Cell Signaling Networks DataBase (CSNDB) is a data and knowledge base for signaling pathways of human cells.

• KEGG – http://www.genome.ad.jp/

• The Kyoto Encyclopedia of Genes and Genomes represents information of pathways that consist of interacting molecules or genes.

Gene Regulation

• TRANSFAC – http://www.biobase.de

• This database presents data about gene regulatory DNA sequences.

• TRRD – http://www.bionet.nsc.ru/

• Transcription Regulatory Regions Database.

Metabolic Diseases

• OMIM – http://www3.ncbi.nlm.nih.gov/

• The Online Mendelian Inheritance in Man database is a catalogue of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues.

• PATHWAY – http://oxmedinfo.jr2.ox.ac.uk/

• PATHWAY is a database of inherited metabolic diseases. The database is divided into two sections: substances and diseases.

• PEDBASE – http://www.icondata.com/health/pedbase/

• PEDBASE is a database of pediatric disorders. Entries are listed alphabetically by disease or condition name.

• RDB – http://www.rarediseases.org/

• The Rare Disease Database is a delivery system for understandable medical information to the public, including patients, families, physicians, medical institutions, and support organizations.