Controlled Vocabulary and Ontology for Plants: Evidence codes for curation of Plant Genome Databases

Evidence codes:

In order to help standardize the way evidence codes are used for curation of the various databases in Gramene (www.gramene.org) eg. Protein, Mutant, QTL, etc. by using the necessary Ontology viz.

GO (Gene Ontology) for describing genes and their products.
TO (Trait Ontology) for description of phenotypic traits related to mutants and QTLs.
PO (Plant Ontology) for describing plant specific morphology, anatomy and development related terms.

The codes are listed along with examples (not exhaustive lists) 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 within each ontology. The distinction between "TAS" and "NAS" is particularly sensitive to interpretation. We will appreciate your feedback, 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 thoughts at gramene@gramene.org.

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 GO annotations, for which evidence is available

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 appropriate for cellular component)

IEA inferred from electronic annotation

Annotations based on "hits" in sequence similarity searchs, if they have not been reviewed by curators (curator-reviewed hits would get ISS)
Annotations transferred from database records, if not reviewed by curators (curator-reviewed items may use RCA, or the reviewing process may lead to print references for the annotation)

RCA inferred from Reviewed Computational Analysis

Predictions based on large-scale experiments (e.g. genome-wide two-hybrid, genome-wide synthetic interactions)
Predictions based on integration of large-scale datasets of several types
Text-based computation (e.g. text mining)
This code is used for annotations based on a non-sequence-based computational method, where the results have been reviewed by an author or a curator. As noted above, IEA should be used for any computational annotations that are not checked for accuracy by a curator (or by the authors of a paper describing such analysis), and sequence comparisons that have been reviewed use ISS. For microarray results alone, IEP is preferred, but RCA is used when microarray results are combined with results of other types of large-scale experiments.

IEP inferred from expression pattern

Transcript levels (e.g. northerns, microarray data)
Protein levels (e.g. western blots)

IMP inferred from mutant phenotype

Any gene mutation / knockout (or deletion) / disruption
Over expression / ectopic expression of wild-type or mutant genes
Anti-sense experiments
RNAi experiments
Specific protein inhibitors

IGI inferred from genetic interaction

Traditional genetic interactions such as suppressors, synthetic lethals, etc.
Functional and/or genetic complementation
Rescue experiments
Inference about one gene drawn from the phenotype of a mutation in a different gene
Also where a mutation in one gene (gene A) provides information about 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-purification
Co-immunoprecipitation, RIA, ELISA
Cross-linking / Ligand / Ion / protein binding experiments (affinity interaction experiments)

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)

IAGP *inferred by association of genotype from phenotype

Polymorphism or segregation of genetic markers eg. isozymes, RFLPs (Random Fragment Length Polymorphism), RAPDs (Random amplified polymorphic DNA), 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.

SM starting material

Used only for making associations to the Gramene taxonomy ontology
Based on source germplasm and/or species from which the samples were isolated or derived.
Samples may include DNA, RNA, protein, markers, genes, QTL, maps (mapsets)

NAS non-traceable author statement

Database entries that don't cite a peer reviewed paper or article (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 text book material has become common knowledge (e.g. "everybody" knows that enolase is a glycolytic enzyme).

NR not recorded

Annotations done before curators began tracking evidence types (appears in SGD and FlyBase annotations).
It should not be used for new annotations--use TAS or NAS.