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Table 3 Default external database parsers provided by BIANA.

From: Biana: a software framework for compiling biological interactions and analyzing networks

External Database
(checked version)
Details
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.
  1. BIANA provides the following parsers for common public biologic databases. Updated database parsers can be uploaded in the project webpage http://sbi.imim.es/web/BIANA.php.