Table 2.

Comparison of annotations in different formats for causal molecular interactions. Data and metadata types, described in the MI2CAST guidelines, that can currently be annotated and stored in each format are listed with the ontologies and controlled vocabularies used. If there is no specification about ontologies and controlled vocabularies to use, the `+' sign is given, meaning that the format stores explicitly this type of data or metadata. Table inspired from [3].

	SIF	SBML qual	PSI-MITAB2.8	GO-CAM	BEL
Source entity	+	+	UniProtKB, RefSeq, ChEBI, EMBL/DDBJ/GenBank, Entrez Gene, Ensembl, EnsemblGenome	UniProtKB, Model Organism Database (MOD) gene identifier, Protein Ontology	HGNC, ChEBI, RefSeq, Entrez Gene, etc.
Interaction effect	+	+	PSI-MI	RO	BEL term: increases, decreases, etc.
Target entity	+	+	UniProtKB, RefSeq, ChEBI, EMBL/DDBJ/GenBank, EntrezGene, Ensembl, EnsemblGenome	UniProtKB, Model Organism Database (MOD) gene identifier, Protein Ontology	HGNC, ChEBI, RefSeq, etc.
Reference			PMID	PMID or MOD reference	PMID
Evidence			PSI-MI	ECO	ECO
Experimental setup					ECO
Biological mechanism			PSI-MI	combination of biological activity and relationship	GO:BP
Biological activity			GO:MF	GO:MF	BEL term: act((prefix:id), ma(prefix:id)), etc.
Biological type			PSI-MI		BEL term: g(), r(), etc.See documentation.
Biological modification			PSI-MOD	Protein Ontology	BEL term: p(prefix:identifier, pmod(prefix:identifier)), etc.
Taxon entity			NCBI Taxonomy	NCBI Taxonomy	NCBI Taxonomy
Taxon interaction			NCBI Taxonomy		NCBI Taxonomy
Tissue type				Uberon (animals), Plant Ontology, Fungal Anatomy Ontology, MOD-specific ontologies	BRENDA Tissue Ontology
Cell type/Cell line				Cell Ontology, MOD-specific ontologies	BRENDA Tissue Ontology, Cell Ontology, Cell Type Ontology
Cellular compartment		+		GO:CC	GO:CC