With field: Difference between revisions

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!MOD!!evidence code using pipe-separated values!!Intended Meaning!! Additional id delimiters?
!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 || -
| FlyBase || IC, IPI, IGI || 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 || -
| ZFIN || IC, IPI, ISS, IGI ||  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  || -
| 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 || -
| WormBase || IPI, ISS, IMP, IGI|| 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.|| -
| MGI || IC, IPI, ISO, IMP, IGI || 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 || || -
| SGD || IC, ISA, IGI || || -
| -  
| -  
| 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. || -
| dictyBase || IC, IPI, ISS, IGI || 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. || -
| 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,  || ||
| RGD || IC, IPI, IGI || ?||
|-
|-
| PomBase || IC, IPI, ISS || ||
| PomBase || IC, IPI, ISS,IGI || ? ||
|-
|-
| CGD || IPI,ISS || ||
| CGD || IPI, ISS, IGI || ? ||
|-
|-
| TIGR || ISS, || ||
| TIGR || ISS, IGI || ? ||
 
|-   
|-   
|}
|}


[http://geneontology.org/GO.evidence.shtml#withUsage Out-of-date documentation on this] - should be deleted?
[http://geneontology.org/GO.evidence.shtml#withUsage Out-of-date documentation on this] - should be deleted?

Revision as of 10:59, 28 March 2011

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, IGI 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, IGI 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, IGI 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, IGI 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, IGI - - dictyBase IC, IPI, ISS, IGI 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, IGI ?
PomBase IC, IPI, ISS,IGI ?
CGD IPI, ISS, IGI ?
TIGR ISS, IGI ?

Out-of-date documentation on this - should be deleted?