Inferred from Direct Assay (IDA): Difference between revisions

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== Overview ==
== Overview ==


*The IDA evidence code is used to indicate a direct assay was carried out to determine the function, process, or component indicated by the GO term. Curators therefore need to be careful, because an experiment considered as a direct assay for a term from one ontology may be a different kind of evidence for a term from another of the ontologies. In particular, there are more kinds of direct assays for cellular component than for function or process. For example, a fractionation experiment might provide "direct assay" evidence that a gene product is in the nucleus, but "protein interaction" (IPI) evidence for its function or process.
*The '''IDA''' evidence code is used to indicate a biochemical or cell biological assay was carried out to support annotation of a gene product's molecular function, role in a biological process, or subcellular location.  


*For transfection experiments or other experiments where a gene from one organism or tissue is put into a system that is not its normal environment, the annotator should use the author's intent and interpretation of the experiment as a guide as to whether IMP or IDA is appropriate. When the author is using an expression system as a way to investigate the normal function of a gene product, IDA is appropriate.
*Examples of such assays include:
**Enzyme assays
**In vitro reconstitution
**Immunofluorescence
**Physical interaction/binding assay
 
*For transfection experiments or other experiments where a gene from one organism or tissue is put into a system that is not its normal environment, the curator should use the author's intent and interpretation of the experiment as a guide as to whether '''IDA''' or '''IMP''' is appropriate. When the author is using an expression system as a way to investigate the normal function of a gene product, '''IDA''' is used.


== Examples of IDA usage ==
== Examples of IDA usage ==
=== Enzymatic assay ===
{| class="wikitable" style="text-align:center"
{| border="1" cellpading="2"
|-
! DB Object ID !! DB Object Symbol !! GO ID !! Contributor !! Taxon !! Evidence Code !! PANTHER family !! Reference !! Date
|-
| UniProtKB:Q9GZZ1 || N-alpha-acetyltransferase 50 || GO:0004596 || UniProt || NCBITaxon:9606 || IDA || PANTHER:PTHR23091 || PMID:21900231 || 20170725
|}
*Figure 3 and Table 2 in [https://www.ncbi.nlm.nih.gov/pubmed/?term=21900231 PMID:21900231 Structure of a ternary Naa50p (NAT5/SAN) N-terminal acetyltransferase complex reveals the molecular basis for substrate-specific acetylation.]
=== In vitro reconstitution ===
{| class="wikitable" style="text-align:center"
{| border="1" cellpading="2"
|-
! DB Object ID !! DB Object Symbol !! Qualifier !! GO ID !! Contributor !! Taxon !! Evidence Code !! PANTHER family !! Reference !! Date
|-
| SGD:S000002299 || RNA polymerase II largest subunit B220 || contributes_to || GO:0001055 || SGD || NCBITaxon:559292 || IDA || PANTHER:PTHR19376 || PMID:8288647|SGD_REF:S000073612 || 20130524
|}
*Figure 2 and Figure 4 in [https://www.ncbi.nlm.nih.gov/pubmed/?term=8288647 PMID:8288647, Purified yeast RNA polymerase II reads through intrinsic blocks to elongation in response to the yeast TFIIS analogue, P37.]
=== Immunofluorescence ===
{| class="wikitable" style="text-align:center"
{| border="1" cellpading="2"
|-
! DB Object ID !! DB Object Symbol !! Qualifier !! GO ID !! Contributor !! Taxon !! Evidence Code !! PANTHER family !! Reference !! Date
|-
| RGD:11508551 || Anp32a ||  || GO:0005634 || RGD || NCBITaxon:10116 || IDA ||  || PMID:20617464|RGD:10401131 || 20170210
|}
*Figure 1 in [https://www.ncbi.nlm.nih.gov/pubmed/?term=20617464 PMID:20617464, CXCL12-mediated regulation of ANP32A/Lanp, a component of the inhibitor of histone acetyl transferase (INHAT) complex, in cortical neurons.]
===Physical interaction/binding assay===
*For 'x binding' annotations when the binding partner 'cannot' be captured in the With (or) From column (GAF Column 8) using a unique accession or identifier.  Note, however, that annotations to 'binding' (GO:0005488) or 'protein binding' (GO:0005515) using IDA are not allowed.  In those cases, curators should choose, or request a more specific child term.
{| class="wikitable" style="text-align:center"
{| border="1" cellpading="2"
|-
! DB Object ID !! DB Object Symbol !! GO ID !! DB:Reference !! Evidence Code !! With (or) From
|-
| MGI:2137706 || Actn1 || GO:0051015 (actin filament binding) || PMID:15465019 || IDA || -
|}


*Types of assays that result in use of '''IDA''':
**Enzyme assays
**In vitro reconstitution (e.g. transcription)
**Immunofluorescence (for Cellular Component)
**Cell fractionation (for Cellular Component)
**Physical interaction/binding assay
***For protein complex membership
***For 'x binding' annotations when the binding partner 'cannot' be captured in the With (or) From column (GAF Column 8) using a unique accession or identifier


*Assays describing the isolation of a complex by immunoprecipitation of a tagged subunit should use IDA, not IPI. Thus this type of assay can provide IDA for annotation to a component term for the specific complex because it is a direct assay for a complex.
*Assays describing the isolation of a complex by immunoprecipitation of a tagged subunit should use IDA, not IPI. Thus this type of assay can provide IDA for annotation to a component term for the specific complex because it is a direct assay for a complex.


*Transfections into a cell line, overexpression, or ectopic expression of a gene when the expression system used is considered to be an assay system to address basic, normal functions of gene product even if it would not normally be expressed in that cell type or location. If the experiments were conducted to assess the normal function of the gene and the assay system is believed to reproduce this function, i.e., the authors would consider their experiment to be a direct assay, and not a comparison between various alleles of a gene, then the IDA code should be used.  
*Transfections into a cell line, overexpression, or ectopic expression of a gene when the expression system used is considered to be an assay system to address basic, normal functions of gene product even if it would not normally be expressed in that cell type or location. If the experiments were conducted to assess the normal function of the gene and the assay system is believed to reproduce this function, i.e., the authors would consider their experiment to be a direct assay, and not a comparison between various alleles of a gene, then the IDA code should be used.


== Examples where the IDA evidence code should not be used ==
== Examples where the IDA evidence code should not be used ==
Line 29: Line 73:


== Quality Control Checks ==
== Quality Control Checks ==
*[https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000003.md Annotations to 'binding ; GO:0005488' and 'protein binding ; GO:0005515' should be made with IPI and an interactor in the 'with' field]
*[https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000017.md IDA annotations must not have a With/From entry]


== Evidence and Conclusion Ontology ==
== Evidence and Conclusion Ontology ==
[http://www.evidenceontology.org/term/ECO:0000314/  ECO:0000314 direct assay evidence used in manual assertion]


[http://www.evidenceontology.org/term/ECO:0000314/ ECO:0000314 direct assay evidence used in manual assertion]
== Links ==
[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Curator Guide to GO Evidence Codes]


[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Back to: Guide to GO Evidence Codes]
[http://geneontology.org/page/guide-go-evidence-codes Gene Ontology website GO Evidence Codes list]


== Review Status ==
== Review Status ==


Last reviewed: February 12, 2018
Last reviewed: February 23, 2018


[[Category: Annotation]]
[[Category: Evidence Codes]]
[[Category:Evidence Codes]]

Latest revision as of 11:34, 13 April 2019

Overview

  • The IDA evidence code is used to indicate a biochemical or cell biological assay was carried out to support annotation of a gene product's molecular function, role in a biological process, or subcellular location.
  • Examples of such assays include:
    • Enzyme assays
    • In vitro reconstitution
    • Immunofluorescence
    • Physical interaction/binding assay
  • For transfection experiments or other experiments where a gene from one organism or tissue is put into a system that is not its normal environment, the curator should use the author's intent and interpretation of the experiment as a guide as to whether IDA or IMP is appropriate. When the author is using an expression system as a way to investigate the normal function of a gene product, IDA is used.

Examples of IDA usage

Enzymatic assay

DB Object ID DB Object Symbol GO ID Contributor Taxon Evidence Code PANTHER family Reference Date
UniProtKB:Q9GZZ1 N-alpha-acetyltransferase 50 GO:0004596 UniProt NCBITaxon:9606 IDA PANTHER:PTHR23091 PMID:21900231 20170725


In vitro reconstitution

DB Object ID DB Object Symbol Qualifier GO ID Contributor Taxon Evidence Code PANTHER family Reference Date
SGD:S000002299 RNA polymerase II largest subunit B220 contributes_to GO:0001055 SGD NCBITaxon:559292 IDA PANTHER:PTHR19376 SGD_REF:S000073612 20130524


Immunofluorescence

DB Object ID DB Object Symbol Qualifier GO ID Contributor Taxon Evidence Code PANTHER family Reference Date
RGD:11508551 Anp32a GO:0005634 RGD NCBITaxon:10116 IDA RGD:10401131 20170210


Physical interaction/binding assay

  • For 'x binding' annotations when the binding partner 'cannot' be captured in the With (or) From column (GAF Column 8) using a unique accession or identifier. Note, however, that annotations to 'binding' (GO:0005488) or 'protein binding' (GO:0005515) using IDA are not allowed. In those cases, curators should choose, or request a more specific child term.
DB Object ID DB Object Symbol GO ID DB:Reference Evidence Code With (or) From
MGI:2137706 Actn1 GO:0051015 (actin filament binding) PMID:15465019 IDA -


  • Assays describing the isolation of a complex by immunoprecipitation of a tagged subunit should use IDA, not IPI. Thus this type of assay can provide IDA for annotation to a component term for the specific complex because it is a direct assay for a complex.
  • Transfections into a cell line, overexpression, or ectopic expression of a gene when the expression system used is considered to be an assay system to address basic, normal functions of gene product even if it would not normally be expressed in that cell type or location. If the experiments were conducted to assess the normal function of the gene and the assay system is believed to reproduce this function, i.e., the authors would consider their experiment to be a direct assay, and not a comparison between various alleles of a gene, then the IDA code should be used.

Examples where the IDA evidence code should not be used

  • Binding assays where it is possible to put an ID corresponding to the specific binding partner that was shown to interact directly the gene product being annotated should be annotated with the IPI code, not with IDA.
  • Overexpression experiments used to assess the effects on function or expression of a gene compared to normal should use the IMP evidence code.
  • Transfection into a cell line, overexpression, or ectopic expression of a gene where the effects of various alleles of a gene are compared to each other or to wild-type. For this type of experiment, annotate using IMP.

Quality Control Checks

Evidence and Conclusion Ontology

ECO:0000314 direct assay evidence used in manual assertion

Links

Curator Guide to GO Evidence Codes

Gene Ontology website GO Evidence Codes list

Review Status

Last reviewed: February 23, 2018