wiki:AnnotationRules

Biological Process

Transcription

All fission yeast annotations for RNAi so far should be to the term GO:0031048 chromatin silencing by small RNA Note that in GO this does not have a parent to RNAi, because the RNAi definition is defined more strictly in the original "post-transcriptional" usage http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016246#term=ancchart

Translation

For annotations to translation, it should always be possible to specify "cytoplasmic translation" or "mitochondrial translation"

Splicing

Annotations for GT-AG type splicing via the spliceosome should always be to GO:0045292 nuclear mRNA cis splicing, via spliceosome

Cytokinesis

Annotations for cytokinesis in fission yeast should always be to GO:0033205 cell cycle cytokinesis or one of it's children'

Cell wall organization

Annotations to cell wall organization should always be to Fungal-type cell wall organization or biogenesis or one of its children

Transport /Localization

  • Always check that the transport and localization terms have a "cellular transport" or "cellular localization" parentage
  • Note the distinction between "transport" and "localization" and always use the appropriate branch. Localization is more general and can involve establishment or maintenance at a specific location, transport involves directed movement
  • Note that all transmembrane transporters should have an annotation to the process of transmembrane transport. Note that "nucleocytoplasmic transport" IS NOT "transmembrane transport", as the lipid bilayer is not traversed.
  • check that the appropriate "intracellular" term is used e.g "intracellular protein transport"

DNA replication

Annotations to "canonical DNA replication" should be to "DNA-dependent DNA replication" or one of its children

Metabolic processes

Always check that "metabolic processes" used have a "cellular metabolic/biosynthetic /catabolic process" parentage

Response to Stress

We do not generally annotate directly to response to stress. Usually you would have minimally

  • response to cellular oxidative stress (i.e cellular and compound) OR
  • regulation of a specific process in response to stress i.e. regulation of translation in response to stress

Cell polarity related

When annotation g terms related to cell polarity, for example GO:0007163 establishment or maintenance of cell polarity make sure if you are annotating a process which is involved in the cell shape, or its regulation you select one of the child terms GO:0071963 establishment or maintenance of cell polarity regulating cell shape or its descendents.

Sporulation

use ascospore formation or children

Cellular Component

Chromatin, heterochromatin etc. Because fission yeast has no nuclear envelope breakdown during mitosis, you can always annotate to e.g.

  • heterochromatin -> nuclear heterochomatin
  • chromosome telomeric region -> nuclear chromosome, telomeric region
  • telomeric heterochromatin -> nuclear telomeric heterochromatin
  • unse nuclear/cytoplasmic complex terms
  • Use "membrane" rather than "membrane fraction"
  • etc

Molecular Function

Last modified 9 years ago Last modified on Feb 5, 2012, 3:55:34 PM