System codes
Part of the framework of BridgeDb is the annotation of data sources, which is done by means of SytemCodes (SysCode). These SysCodes are either derived from the full name of a database (for example “En” is the SysCode for Ensembl), or their origin is more historical (for example “Ch” is the Syscode for HMDB, but has an abbreviation related to the word “chemicals”).
Gene resources
| Bc | BioCyc |
| Cc | CCDS |
| Sn | dbSNP |
| Ec | EcoGene |
| Em | EMBL |
| En | Ensembl |
| L | NCBI Gene |
| E | Enzyme Nomenclature |
| F | FlyBase |
| G | GenBank |
| Gw | Gene Wiki |
| EnAt | Gramene Arabidopsis |
| Gg | Gramene Genes DB |
| Gl | Gramene Literature |
| EnZm | Gramene Maize |
| EnOj | Gramene Rice |
| H | HGNC |
| Hac | HGNC Accession number |
| Hg | HomoloGene |
| Ir | IRGSP Gene |
| Kg | KEGG Genes |
| Mg | MaizeGDB |
| M | MGI |
| Mbm | miRBase mature sequence |
| Mb | miRBase Sequence |
| N | NASC Gene |
| Om | OMIM |
| Ob | Oryzabase |
| O | Other |
| Pgg | PharmGKB Gene |
| Pl | PlantGDB |
| Q | RefSeq |
| Rf | Rfam |
| R | RGD |
| Os | Rice Ensembl Gene |
| D | SGD |
| Bsu | SubtiWiki |
| A | TAIR |
| Ti | TIGR |
| Tb | TubercuList |
| Uc | UCSC Genome Browser |
| U | UniGene |
| Wn | Wheat gene names |
| Wg | WikiGenes |
| W | WormBase |
| Z | ZFIN |
Metabolite resources
| Ca | CAS |
| Ce | ChEBI |
| Cs | ChemSpider |
| Cl | ChEMBL compound |
| Dr | DrugBank |
| Ch | HMDB |
| Gpl | Guide to Pharmacology Ligand ID (aka IUPHAR) |
| Ik | InChIKey |
| Ck | KEGG Compound |
| Kd | KEGG Drug |
| Kl | KEGG Glycan |
| Lm | LIPID MAPS |
| Lb | LipidBank |
| Pgd | PharmGKB Drug |
| Cpc | PubChem Compound |
| Cps | PubChem Substance |
| Sl | SwissLipids |
| Td | TTD Drug |
| Wd | Wikidata |
| Wi | Wikipedia |
Protein resources
| Br | BRENDA |
| I | InterPro |
| Ip | IPI |
| Ma | MACiE |
| Np | NCBI Protein |
| Pd | PDB |
| Pf | Pfam |
| Pp | PhosphoSite Protein |
| Res | RESID |
| Sma | SMART |
| Spr | SPRINT |
| Str | STRING |
| Sdb | SubstrateDB |
| Sf | SUPFAM |
| Sw | SWISS-MODEL |
| Tt | TTD Target |
| S | Uniprot-TrEMBL |
| Sp | Uniprot-SwissProt |
Interaction resources
| Bi | BIND |
| Bg | BioGrid |
| Dip | Database of Interacting Proteins |
| Eco | EcoCyc |
| Hp | HPRD |
| Ia | IntAct |
| Md | MatrixDB |
| Mc | MetaCyc |
| Mi | MINT |
| Pi | PINA |
| Rh | Rhea |
| Sk | SPIKE |
| Xm | XMetDb |
Pathway resources
Probe resources
| X | Affy |
| Ag | Agilent |
| Ge | CodeLink |
| Il | Illumina |
| Wr | Wheat gene refs |
Ontology resources
| T | GeneOntology |
| Sbo | Systems Biology Ontology |