Table 2.
Data integration database
| Name | Records | Description | Source |
|---|---|---|---|
| Chemical Entities of Biological Interest (ChEBI) | 38 580 | The database of chemical entities of biological interest | www.ebi.ac.uk/chebi |
| ChEBI ontology | 29 974 | ||
| Enzyme | 5 418 | Enzymes nomencalture | ca.expasy.org/enzyme |
| Gene | 8 927 911 | NCBI gene database | www.ncbi.nlm.nih.gov/gene |
| Functional association data/networks (GeneMania) | 21 084 | Gene associations database | genemania.org |
| GO | 34 940 | Gene ontology database | www.geneontology.org |
| GOA | 11 300 749 | Gene ontology annotation | www.ebi.ac.uk/GOA |
| HUGO Gene nomenclature | 35 795 | Human genes nomenclature | www.genenames.org |
| Human major histocompatibility complex | 6 939 | Human major histocompatibility complex (HLA) sequences | www.ebi.ac.uk/imgt/hla |
| Immunoglobulins and T-cell receptors nucleotide sequences | 156 529 | The international imMunoGeneTics information system | www.imgt.org/GeneInfoServlets/htdocs |
| Interpro | 21 749 | Protein sequence analysis and classification | www.ebi.ac.uk/interpro |
| KEGG module | 196 659 | Collection functional units used for annotation and biological interpretation of sequenced genomes. | www.genome.jp/kegg/module.html |
| KEGG pathway | 262 432 | Pathway maps on the molecular interaction and reaction networks for biological interpretation of higher-level systemic functions. | www.genome.jp/kegg/pathway.html |
| KEGG ligand compound | 34 182 | Database of chemical substances and reactions that are relevant to life. | www.genome.jp/kegg/ligand.htm |
| KEGG ligand enzyme | 6 118 | ||
| KEGG Ligand Glycan | 10 985 | ||
| KEGG Ligand Reaction | 9 400 | ||
| Oxford Human Mouse grid | 17 834 | Laboratory mouse genetic, genomic and biological data resources. | www.informatics.jax.org |
| Pfam-A | 12 273 | Collection of protein families, each represented by multiple sequence alignments and hidden Markov models | pfam.sanger.ac.uk |
| Pfam-B | 233 174 | ||
| Pfam seed | 12 273 | ||
| PRINTS | 2 050 | Protein fingerprints, groups of conserved motifs used to characterize a protein families | bioinf.man.ac.uk/dbbrowser/PRINTS |
| Prosite | 2 247 | Documentation entries describing protein domains, families, functional sites and associated patterns and profiles to identify them. | www.expasy.org/prosite/ |
| Prosite documentation | 1 621 | ||
| REBASE | 5 020 | The restriction enzyme database. | rebase.neb.com/rebase/rebase.html |
| RefSeq | 18 236 994 | Set of reference sequences including genomic, transcript, and protein. | www.ncbi.nlm.nih.gov/refseq/ |
| UniProt/Swiss-Prot | 531 473 | Protein database, manually annotated and reviewed. | www.uniprot.org/ |
| Taxonomy | 817 120 | Classification and nomenclature for all of the organisms in the public sequence databases. | www.ncbi.nlm.nih.gov/taxonomy |
| UniProt/TrEMBL | 16 504 022 | Protein database, automatically annotated and not reviewed. | www.uniprot.org |
| Unigene | 2 652 777 | NCBI database of the transcriptome. | www.ncbi.nlm.nih.gov/unigene |
| Uniprot KB | 17 035 495 | Protein knowledgebase (Swiss-Prot + TrEMBL). | www.uniprot.org |
| Total records | 77 163 817 |