From: Biana: a software framework for compiling biological interactions and analyzing networks
External Database (checked version) | Details |
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General databases (Sequence, identifiers, and cross-reference databases) | |
Uniprot [31] (Release 14.1) | Protein sequence, identifiers and functional information (domain composition, description, function...). Both Swiss-prot (manually curated) and TrEMBL (automatically annotated) can be inserted into BIANA. Protein sequences and multiple attributes are inserted into BIANA. |
GenPept from GenBank [69] (FASTA formatted file) (Release 167) | Protein sequences translated from the GenBank database. GenBank is the NIH genetic sequence database, a collection of all publicly available DNA. Protein sequences and identifiers are inserted into BIANA. |
Non-redundant Blast Database (FASTA formatted file) (August 2008) | BLAST Non-redundant database from NCBI. Non-redundant protein sequence database with entries from GenPept, SwissProt, PIR, PDF, PDB and NCBI RefSeq. Protein sequences and identifiers are inserted into BIANA. |
International Protein Index (IPI) [12] (September 2008) | Integrated database for proteomics experiments. Protein sequences and identifiers for Human, Mouse, Rat, Zebrafish, Arabidosis, Chicken and Cow are inserted into BIANA. |
HUGO Gene Nomenclature Committee (HGNC) (September 2008) | Approved unique gene symbols for each human gene. Cross-references are inserted into BIANA. http://www.genenames.org |
Cluster of Orthologous Genes (COGs) [70] (2003) | Collection of orthologous protein sets for prokaryotes and eukaryotes. Protein identifiers and COG groups are inserted into BIANA. |
Ontologies | |
Gene Ontology (GO) [33] (version 1.2) | The Gene Ontology provides a controlled vocabulary to describe gene and gene product attributes in any organism. It allows to link in BIANA between GO ID and GO name and type. |
PSI-MI obo | Controlled vocabulary and ontology for molecular interactions and their detection methods. Provides the information about and the relation between method ID and method name. http://psidev.info/MI |
NCBI Taxonomy [71] | The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases. It allows to link between taxonomy ID identifier to Taxonomy name attribute. |
Structural Classification of Proteins (SCOP) [34] | Manually curated database with a comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. It has a hierarchical classification of the structural domains. |
Relation databases | |
PSI-MI 2.5 Format [11] | Data exchange format for molecular interactions. The following protein-protein interaction databases can be inserted into BIANA: IntAct [7] (September 2008), DIP [72] (2008.07.08), HPRD [36] (Release 7), BioGrid [6] (v2.0.44), MPACT [73] (April 2007), MINT [5] (2008.05.21) |
Biopax Level 2 Format | Data exchange format for biological pathway data. The following databases can be inserted into BIANA: Reactome [35] (September 2008) |
iRefIndex [19] | A consolidated protein interaction database with provenance. (April 2009) |
Kyoto Encyclopedia of Genes and Genomes (KEGG) [32] | Kegg Ligand (chemical compounds, drugs, glycans and reactions), Kegg genes (genomes, genes and proteins) and Kegg orthology (ortholog annotation) are inserted into BIANA. |
STRING [74] | Database of known and predicted protein interactions. Includes direct (physical) and indirect (functional) associations. |