MicroScope - Tutorial   »   MaGe   »   Gene Annotation Editor   »   Annotation Rules


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Considering the Class field, here are some basic annotation rules:

1 a/b/c: Function experimentally demonstrated in the studied organism/species/genus

  • Gene [optional]
  • Synomyms [optional]
  • Product [mandatory]
  • EC number [optional]
  • MetaCyc Reaction [optional]
  • PubMedId [mandatory]
  • ProductType [mandatory]
  • Localization [optional]
  • BioProcess [optional]
  • Roles [optional]

2a : Function of homologous gene experimentally demonstrated in an other organism

  • Gene [optional]
  • Synomyms [optional]
  • Product [mandatory]
  • EC number [optional]
  • MetaCyc Reaction [optional]
  • PubMedId [mandatory]
  • ProductType [mandatory]
  • Localization [optional]
  • BioProcess [optional]
  • Roles [optional]

2b : Function of strongly homologous gene

  • Gene [optional]
  • Synomyms [optional]
  • Product [mandatory]
  • EC number [optional]
  • MetaCyc Reaction [optional]
  • PubMedId [optional]
  • ProductType [mandatory]
  • Localization [optional]
  • BioProcess [optional]
  • Roles [optional]

3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology

  • Gene [not allowed]
  • Synomyms [not allowed]
  • Product [mandatory]: putative function
  • EC number [optional]
  • MetaCyc Reaction [optional]
  • PubMedId [optional]
  • ProductType [mandatory]: putative function
  • Localization [optional]
  • BioProcess [optional]
  • Roles [optional]

4 : Homologs of previously reported genes of unknown function

  • Gene [not allowed]
  • Synomyms [not allowed]
  • Product [mandatory] : conserved (exported/membrane) protein of unknown function (; [domain description])
  • EC number [not allowed]
  • MetaCyc Reaction [optional]
  • PubMedId [optional]
  • ProductType [mandatory]: unknown
  • Localization [optional]
  • BioProcess [optional]
  • Roles [optional]

5 : No homology to any previously reported sequences

  • Gene [not allowed]
  • Synomyms [not allowed]
  • Product [mandatory]: (exported/membrane) protein of unknown function
  • EC number [not allowed]
  • MetaCyc Reaction [optional]
  • PubMedId [optional]
  • ProductType [mandatory]: unknown
  • Localization [optional]
  • BioProcess [optional]
  • Roles [optional]

6 : Doubtful CDS

  • Gene [not allowed]
  • Synomyms [not allowed]
  • Product [mandatory] : protein of unknown function
  • EC number [not allowed]
  • MetaCyc Reaction [not allowed]
  • PubMedId [optional]
  • ProductType [mandatory]: unknown
  • Localization [not allowed]
  • BioProcess [not allowed]
  • Roles [not allowed]

7 : Gene remnant

  • Gene [not allowed]
  • Synomyms [not allowed]
  • Product [mandatory]: protein name (fragment)
  • EC number [not allowed]
  • MetaCyc Reaction [not allowed]
  • PubMedId [optional]
  • ProductType [mandatory]: unknown
  • Localization [not allowed]
  • BioProcess [not allowed]
  • Roles [not allowed]