All ontology annotations provided by the Planteome project carry an Evidence Code described here. They are used to suggest the type of experiment or method in a broad sense that was used by the researcher/project to infer the ontology-based annotation of gene, protein, transcript, germplasm, QTL, etc.
The codes are listed along with examples (not an exhaustive list) of the kinds of experiments that would fall into each category. For every evidence category, there is a flexibility for the curators to exercise judgement about the quality of the evidence, and how well it supports annotation to a node (term) within each ontology. The distinction between "TAS"and "NAS" is particularly sensitive to interpretation. If you think that we should include other types of methodologies under the sub-categories and expand the framework of evaluation, please feel free to communicate your suggestions to us.
You can also see more information on the Evidence Codes here: Gene Ontology Guide to Evidence Codes and the Evidence Code Decision Tree
Experimental Evidence Codes (wet lab derived)
IEP inferred from expression pattern
- Transcript levels (e.g. northerns, microarray data)
- Protein levels (e.g. western blots)
IDA inferred from direct assay
- Enzyme assays
- In vitro reconstitution (e.g. transcription)
- Immunofluorescence (for specific localization either / both in a tissue type or in a cellular component)
- Cell fractionation (for cellular component)
- Physical interaction / binding assay (sometimes appropriatefor cellular component)
IMP inferred from mutant phenotype
- Any gene mutation / knockout (or deletion) / disruption
- Over expression / ectopic expression of wild-type or mutantgenes
- Anti-sense experiments
- RNAi experiments
- Specific protein inhibitors
IGI inferred from genetic interaction
- Traditional genetic interactions such as suppressors, syntheticlethals, etc.
- Functional and/or genetic complementation
- Rescue experiments
- Inference about one gene drawn from the phenotype of a mutationin a different gene
- Also where a mutation in one gene (gene A) provides informationabout the function, process, or component of another gene (gene B; i.e.annotate gene B using IGI)
IPI inferred from physical interaction
- 2-hybrid interactions or 3-hybrid interactions
- Co-immunoprecipitation, RIA, ELISA
- Cross-linking / Ligand / Ion / protein binding experiments (affinity interaction experiments)
IAGP inferred by association of genotype from phenotype
- Polymorphism or segregation of genetic markers eg. isozymes,RFLPs (Random Fragment Length Polymorphism), RAPDs (Random amplified polymorphicDNA), AFLPs (Amplified Fragment Length Polymorphism), SNPs (Single Nucleotide Polymorphisms), Microsatellite markers or SSR (Simple Sequence Repeats), TD (Transposon Display).
- Polymorphism or segregation of physical markers eg. FISH,centromeric, heterochromatic regions, chromosomal banding patterns.
- Detection of polymorphisms in segregating plant material derived from Bi-parental crosses eg. F2 lines, F3 families, Back cross populations, viz., BC1, BC2 etc.; Doubled Haploid lines (DH), Recombinant Inbred Lines (RIL).
- Detection of polymorphisms in genetic stocks, e.g., Near Isogenic Lines (NIL), Introgression Lines (IL), Radiation Hybrids (RH), Cytogenetic Stocks (CG), i.e., trisomics, aneuploids, etc.
Non-Experimental Evidence Codes (computationally derived)
IC inferred by curator
- To be used for those cases where an annotation is not supported by any evidence, but can be reasonably inferred by a curator from other POC annotations, for which evidence is available
IEA inferred from electronic annotation
- Annotations based on "hits" in sequence similarity searchs,if they have not been reviewed by curators (curator-reviewed hits wouldget ISS)
- Annotations transferred from database records, if not reviewedby curators (curator-reviewed items may use NAS, or the reviewing processmay lead to print references for the annotation)
ISS inferred from sequence or structural similarity
- Sequence similarity (homologue of / most closely related to)
- Recognized domains
- Structural similarity
- Southern blotting (Should not include the mapping studies from IAGP)
Author Statement Evidence Codes
NAS non-traceable author statement
- Database entries that don't cite a peer reviewed paper orarticle (e.g. Plant gene register, SwissProt records, YPD protein reports)
- Statements in papers (abstract, introduction, or discussion)that a curator cannot trace to another publication
TAS traceable author statement
- Anything in a review article where the original experiments are traceable through that article (material from introductions to non-review papers will sometimes meet this standard)
- Anything found in a text book or dictionary; usually textbook material has become common knowledge.