Databases pathways of genomics and proteomics
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The document discusses several databases related to human metabolism and pharmacology. It describes the contents and purpose of each database, including the Human Metabolome Database (HMDB), KEGG, MetaCyc, PubChem, ChEBI, DrugBank, the Therapeutic Target Database (TTD), PharmGKB, and Chemical Entities of Biological Interest (ChEBI). These databases contain chemical, clinical, molecular biology, pathway, and genomic data on human metabolites, drugs, and targets.
Databases pathways of genomics and proteomics
- 2. HMDB The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found (and experimentally verified) in the human body. The database contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. HMDB contains information on more than 6500 metabolites. Additionally, approximately 1500 protein (and DNA) sequences are linked to these metabolite entries. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets.
- 3. The BiGG database is a metabolic reconstruction of human metabolism designed for systems biology simulation and metabolic flux balance modeling. It is a comprehensive literature-based genome- scale metabolic reconstruction that accounts for the functions of 1,496 ORFs, 2,004 proteins, 2,766 metabolites, and 3,311 metabolic and transport reactions. It was assembled from build 35 of the human genome.
- 4. setupX, developed by the Fiehn laboratory at UC Davis, is a web-based metabolomics LIMS. It is XML compatible and built around a relational database management core. It is particularly oriented towards the capture and display of GC-MS metabolomic data through its metabolic annotation database called BinBase. for free download of database and source code
- 5. KEGG (Kyoto Encyclopedia of Genes and Genomes) is one of the most complete and widely used databases containing metabolic pathways (372 reference pathwasy) from a wide variety of organisms (>700). These pathways are hyperlinked to metabolite and protein/enzyme information. Currently KEGG has >15,000 compounds (from animals, plants and bacteria), 7742 drugs (including different salt forms and drug carriers) and nearly 11,000 glycan structures.
- 6. MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,100 pathways from more than 1,500 different organisms. MetaCyc is curated from the scientific experimental literature and contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes.
- 7. humanCyc is a bioinformatics database that describes the human metabolic pathways and the human genome. The current version of HumanCyc was constructed using Build 31 of the human genome. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze.
- 8. PubChem PubChem is a freely available database of chemical structures of small organic molecules and information on their biological activities. It contains structure, nomenclature and calculated physico- chemical data and is linked with NIH PubMed/Entrez information. PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. PubChem has >19 million unique chemical structures.
- 9. ChEBI Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The chemical entities in ChEBI are either products of nature (metabolites) or synthetic products used to intervene in the processes of living organisms (drugs or toxins). ChEBI contains structure and nomenclature information along with hyperlinks to many well-regarded databases. ChEBI uses a carefully developed ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are precisely specified. ChEBI has >15,500 chemical entities in its database.
- 10. Drug bank The DrugBank database is a blended bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4800 drug entries including >1,350 FDA-approved small molecule drugs, 123 FDA- approved biotech (protein/peptide) drugs, 71 nutraceuticals and >3,243 experimental drugs. DrugBank also contains extensive SNP-drug data that is useful for pharmacogenomics studies.
- 11. The Therapeutic Target Database (TTD) is a drug database designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. The database currently contains 1535 targets and 2107 drugs/ligands.
- 12. The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. PharmGKB contains searchable data on genes (>20,000), diseases (>3000), drugs (>2500) and pathways (53). It also has detailed information on 470 genetic variants (SNP data) affecting drug metabolism.
- 13. Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The chemical entities in ChEBI are either products of nature (metabolites) or synthetic products used to intervene in the processes of living organisms (drugs or toxins) ChEBI contains structure and nomenclature information along with hyperlinks to many well-regarded databases. ChEBI uses a carefully developed ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are precisely specified. ChEBI has >15,500 chemical entities in its database.