Controlled Vocabulary and Ontology for Plants

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.

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 NAS, or the reviewing process may lead to print references for the annotation)

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 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 from association between genotype and phenotype(* NEW )

• 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.