Updated October 10, 2014
- 2-hybrid interactions
- Ion/protein binding experiments
Covers physical interactions between the entity of interest and another molecule (such as a protein, ion or complex). IPI can be thought of as a type of IDA, where the actual binding partner or target can be specified, using "with" in the with/from field.
Often it is difficult to tell from the evidence presented in a paper whether an interaction is direct or not. Any in vivo/cell lysate method always has the possibility of a third 'bridge' protein - there are many examples of this happening in, for example, yeast 2-hybrid experiments when yeast proteins have proven essential for interactions between two human proteins to occur. The only methods that show direct evidence of two proteins binding are when the two proteins have been isolated and pre-purified. Ideally, curators should only capture direct interactions however, it is acceptable to curate interactions even if it is not known whether they are direct or not.
Examples where the IPI evidence code should be used:
- Binding assays where it is possible to put an ID corresponding to the specific binding partner that was shown to interact with the entity being annotated should be annotated with the IPI code, not with IDA.
- Annotations to the GO term ‘binding’ (GO:0005488) or ‘protein complex' (GO:0043234), or their child terms, which are supported by the isolation of a complex by co-immunoprecipitation or pull-down assays may use IPI with the ID corresponding to the ‘antibody target' or ‘tagged' subunit in the with/from column.
- The GO term ‘protein binding’ (GO:0005515) should only be used with the evidence code IPI and an identifier in the ‘with’ field. A reciprocal annotation must also be made to indicate the interaction in the opposite direction.
- Annotations to Molecular Functions (except ‘catalytic activity’ GO:0003824 or its child terms, see below) or Biological Processes may be made using IPI and an entry in the ‘with/from’ field in order to indicate the inference that the annotated entity is involved in the process or function because it interacts with another entity that was shown experimentally to be involved in that process or function.
Examples where the IPI evidence code should not be used:
- The GO term ‘protein binding’ (GO:0005515) should not be used to describe an antibody binding to another protein. However, an effect of an antibody on an activity or process can support a function or process annotation, using the IMP code.
- Annotations to the GO term ‘binding’ (GO:0005488), or its child terms, which are supported by binding assays where it is NOT possible to put an ID corresponding to the specific binding partner that was shown to interact with the gene product being annotated should be annotated with the IDA code, not with IPI (see table 1).
- Annotations to the GO term ‘catalytic activity’ (GO:0003824), or its child terms, should not use the IPI evidence code. It is unlikely that enough information can be obtained from a binding interaction to support such an annotation.
Table 1. Example annotation where it is not possible to add the interacting partner.
|MGI:2137706||Actn1||GO:0051015 (actin filament binding)||PMID:15465019||IDA||-|
Usage of the With/From Column for IPI.
All proteins or gene products annotated using the IPI evidence code should include an identifier in the with/from column, identifying the other protein, macromolecule or chemical involved in the interaction. When multiple entries are placed in the with/from field, they are separated by pipes. Consider using IDA when no identifier can be entered in the with/from column.
The exception to this rule is when annotating a macromolecular complex identifier to an equivalent complex GO term, e.g. annotating the IntAct Complex Portal identifier ‘EBI-706546’ (human BCL-2 homodimer) to ‘BCL-2 complex’ (GO:0097148). In this case, it is acceptable to use the IPI evidence code without an entry in the with/from field, since the member subunits of the complex are encoded in the complex identifier.
e.g. In Table 2 the protein kinase CK2 variant 2 complex (EBI_1253636) has been annotated with the GO term “protein kinase CK2 complex”. The complex was identified by co-purification of the subunits, therefore there is no need to indicate the subunits in the With/From field as these are already encoded in the object identifier.
Table 2. Example of an annotation to a complex identifier.
|EBI-1253636||protein kinase CK2 variant 2||GO:0005956 (protein kinase CK2 complex)||PMID:12242279||IPI||-|
Note that when a complex binds, for example, a protein or chemical that is not an integral part of the complex, it is necessary to indicate in the With/From field the entity to which the complex is binding.
Two examples of how the with/from column is used with IPI are shown in Table 3. Abcd3, a mouse protein, is annotated to protein binding ; GO:0005515, based on Liu et al., 1999 (PMID:10551832). The with/from field has the UniProt protein ID of the protein Abcd3 binds to. In the second example Alb, a rat protein, is annotated to drug binding based on Harada et al., 2002 (PMID:12458670). In this case the CHEBI ID (chemical ID) of the drug that Alb binds to is provided in the with/from column.
Table 3. Example annotations that use entries in the with/from field.
|MGI:1349216||Abcd3||GO:0005515 (protein binding)||PMID:10551832||IPI||UniProt:P33897 (human ABCD1)|UniProt:Q61285 (mouse ABCD2)|
|RGD:2085||Alb||GO:0008144 (drug binding)||PMID:12458670||IPI||CHEBI:28939 (N-acetyl-L-cysteine)|
Note: For an interacting protein, a protein ID is recommended in the with/from column for a IPI annotation, but a gene ID may be used if the database does not have identifiers for individual gene products. A gene ID may also be used if the cited reference provides enough information to determine which gene ID should be used, but not enough to establish which protein ID is correct, for example, in cases where there is a one-to-many relationship between a gene and its protein products. Note that there has been some discrepancy between groups as to the use of the with/from column; please see the note on usage of the with/from column for more details.