Table 1.
Used resources with the corresponding entity classes as well as the namespace symbols provided within OpenBEL
| Entity class | Resources | OpenBEL namespace |
|---|---|---|
| Human genes/proteins | EntrezGene/Uniprot | HGNC |
| Mouse genes/proteins | EntrezGene/Uniprot | MGI |
| Rat genes/proteins | EntrezGene/Uniprot | RGD |
| Protein family names | OpenBEL | SFAM |
| Protein complex names | OpenBEL | SCOMP |
| Protein complex names | Gene Ontology | GOCC |
| Biological processes | Gene Ontology | GOBP |
| Chemical names | OpenBEL | SCHEM |
| Chemical names | ChEBI | CHEBI |
| Chemical names | ChEMBL | CHEMBL |
| Disease names | MeSH | MESHD |
| Anatomical names | MeSH | MESHAnatomy |
| Cell lines | Cell Line Ontology | CellLine |
| Cell structures | MeSH | CellStructure |
These resources were converted into dictionaries and integrated into the workflow: EntrezGene (http://www.ncbi.nlm.nih.gov/gene), Uniprot (http://www.uniprot.org/), OpenBEL name spaces and annotations (http://resources.belframework.org/belframework/), Gene Ontology (http://www.geneontology.org/), ChEBI (http://www.ebi.ac.uk/chebi/), ChEMBL (https://www.ebi.ac.uk/chembl/), MeSH (http://www.nlm.nih.gov/mesh/), and the Cell Line Ontology (cellontology.org/).