Interactions are generated electronically based on the data that we store on complexes and reactions, i.e. the interactions provided by Reactome are not curated and are not experimental data. In addition, the complexes and reactions in species other than human are derived by orthology inference from the correspondinghuman complexes and reactions.

The meaning of "interaction" is quite broad: 2 protein sequences occur in the same complex or they occur in the same reaction.

The 1st line begins with '#' and gives the number of unique interactions, i.e. unique pairs if UniProt accession numbers.

The rest of the file is tab delimited with columns having following meaning/content:

• Protein ID (e.g. UniProt accession) for interactor 1.
• Ensembl gene id(s delimited by '|') for interactor 1. Note that one UniProt entry may be mapped to multiple Ensembl genes.
• Entrez Gene id(s delimited by '|') for interactor 1. Note that one UniProt entry may be mapped to multiple Entrez Gene ids.
• Protein ID (e.g. UniProt accession) for interactor 2.
• Ensembl gene id(s delimited by '|') for interactor 2. Note that one UniProt entry may be mapped to multiple Ensembl genes.
• Entrez Gene id(s delimited by '|') for interactor 2. Note that one UniProt entry may be mapped to multiple Entrez Gene ids.
• Type of interaction, either 'direct_complex', 'indirect_complex', 'reaction' or 'neighbouring_reaction'. Meanings of those below.
• Interaction context. This is the class and internal identifier of Reactome instance via which this interaction happens. For 'neighbouring_reaction' type interaction this contains a pair of class:identifier string separated by ''.
• Comma-delimited list of PubMed identifiers supporting this interaction. For a reaction these are the PMIDs from the Reaction.literatureReference slot (and not from the "second tier" Reaction.summation.literatureReference). For a complex these are from reations which produce the complex. For 'neighbouring_reaction' type interaction this field is empty.

Interaction types

In Reactome, complexes can be arbitrarily nested, i.e., contain subcomplexes. Here we have complex C1 consisting of complexes C2 and C3. C2 consist of molecules A and B. C3 consists of molecules C and D:

           C1 --- C2 --- A
                |      |
                |      |- B
                |
                |- C3 --- C
                |
                |- D
                

Now really to the interaction types:

• direct_complex - interactors are directly in the same complex, i.e. w/o further nested complexes. From the example interactions A B and C are of this type.
• indirect_complex - interactors in different subcomplexes of a complex. From the example above interactions AC, AD, BC and BD are of this type.
• reaction - interactors participate in the same reaction. Only those reactions are reported for which the intreactors are not complexed (with the exception being association dissociation reactions which are reported).
• neighbouring_reaction - interactor participate in 2 "consecutive" reactions, i.e. when one reaction produces a PhysicalEntity which is either an input or a catalyst for another reaction. However, to avoid the "trivial" (i.e. over ATP, ADP etc) interactions, the computation is done using the 'precedingEvent' attribute used to order reactions in a pathway.

The 'direct_complex' type doesn't really mean true pairwise interaction. For example, Reactome's representation of ribosomal S60 subunit consists "directly" of 40+ proteins and has no sub-complexes. Obviously this can hardly mean that each one of those component proteins directly interacts with every other protein. Hence, the 'direct_complex' vs. 'indirect_complex' distinction is quite meaningless.

Other notes:

• If the same interaction (i.e same UniProte accession pair) happens in multiple contexts, each context is reported on a separate row and hence the row number in the file is bigger than the number of unique interactions reported on the 1st line.
• The order of interactors on one line has no meaning (they are just ordered according to the Reactome internal identifier...). Every interaction with context is reported once, i.e. AB is not reported as BA.