Inferred from Physical Interaction (IPI)
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- The IPI evidence codes is used to annotate 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 a unique accession or identifier in the With (or) From column (Column 8 in the GAF).
- It can be 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 two-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 of IPI usage
- Types of assays that result in use of IPI:
- Two-hybrid interactions
- Ion/protein binding experiments
- 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.
Use of the With/From Field for IPI
- The IPI evidence code requires curators to enter a stable database identifier for the interacting entity in the With/From field of the Gene Association File (GAF).
- Independent interactors may be captured in the With/From field by separating each entry with a pipe.
- If the interaction experiment involves multiple perturbations simultaneously, then the respective interactors are separated with a comma.
- Acceptable types of entries in the With/From field include:
- Protein-containing complexes (for annotations to GO:0044877 (protein-containing complex binding)
Quality Control Checks
- Annotations to 'binding ; GO:0005488' and 'protein binding ; GO:0005515' should be made with IPI and an interactor in the 'with' field
Evidence and Conclusion Ontology
Last reviewed: February 23, 2018