With field
Annotations that use certain evidence codes can contain information in the 'with' field (column 8):
Evidence Code | Mandatory or Optional? | Expected values |
---|---|---|
IC | Mandatory | GO identifier |
IPI | Mandatory | Protein, Gene, Chemical identifier |
IGI | Optional | - |
IMP | Optional | Allele |
IGC | Optional | - |
ISS | Mandatory | Protein or Gene identifier |
ISO | Mandatory | - |
ISM | Optional | - |
ISA | Mandatory? | - |
IEA | Mandatory? | Protein identifier, External vocab it. |
Multiple values in the 'with' field
Interpretation of the pipe ('|') separating values:
- Pipes should only be used with the inferred-from-interaction evidence codes, i.e. IGI and IPI.
- With either IPI or IGI, piped 'with' entries indicate that the evidence is actually a 3-way (or 4-way, or n-ary ...) interaction, not just multiple pairwise interactions.
MOD | evidence code using pipe-separated values | Intended Meaning | Additional id delimiters? | |||||
---|---|---|---|---|---|---|---|---|
FlyBase | IC, IPI | Pipe-separated values indicate a multi-way interaction and so all values displayed in one annotation line should always be grouped together | - | |||||
ZFIN | IC, IPI, ISS, ZFIN | Pipe-separated values indicate a multi-way interaction and so all values displayed in one annotation line should always be grouped together. In addition, for IGI evidence in binary interactions, there is the ZDB-GENE ID of the interacting partner, and the ZDB-MRPHLNO ID for the morpholino used to target the gene BEING ANNOTATED | - | |||||
TAIR | IPI, | Pipe-separated values indicate a multi-way interaction and so all values displayed in one annotation line should always be grouped together | - | |||||
WormBase | IPI, ISS, IMP | Pipe-separated values indicate a multi-way interaction and so all values displayed in one annotation line should always be grouped together | - | |||||
MGI | IC, IPI, ISO, IMP | Only display binary interactions for binding, therefore multiple piped values indicate separate binary interactions that can be reinterpreted as multiple independent binding interactions between the gene product identified in column 2, and directly to each of the ids listed in the with. Therefore it would be correct to reinterprete the file so that each vlaue in the 'with' is displayed on a separate annotation line. Currently do use commas in some IMP and IGI annotations, however these will shortly be removed. | - | |||||
SGD | IC, ISA | - | - | dictyBase | IC, IPI, ISS, | Pipe-separated values indicate multiple independent interactions between the gene product identified in column 2, and each of the ids listed in the with. Therefore it would be correct to reinterprete the file so that each vlaue in the 'with' is displayed on a separate annotation line. | - | |
UniProtKB-GOA | Currently only one identifier is included in the with field for each annotation (although we are intending to allow multiple values in the second half of 2011). Only binary binding interactions are displayed. | - | ||||||
RGD | IC, IPI, | |||||||
PomBase | IC, IPI, ISS | |||||||
CGD | IPI,ISS | |||||||
TIGR | ISS, |
Out-of-date documentation on this - should be deleted?