Guidelines from Annotation Camp: Difference between revisions

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Downstream Process guidelines
==Downstream Process guidelines==
 
1. Quite often it is the case that the most relevant GO term will not exist. It is desirable to request terms which describe the involvement of a process in another process, if that will give more specificity to the annotation.
For example, to describe a gene product's "intent" to change the "state" of the cell;
• Growth factor BMP2 is instrumental in cardiac cell differentiation
• Following stimulation with BMP2, large numbers of genes are up/down regulated
Requesting the new GO term 'BMP signaling involved in cardiac cell differentiation' may be preferable to annotating to the separate terms 'BMP signaling' and 'cardiac cell differentiation' as it will be clear how the gene product is involved in cardiac cell differentiation. i.e. qualify how the gene product is involved in the downstream process in preference to annotating to the downstream process term.
 
To assist in the creation of these new terms, the AmiGO 'Cross-product Term Request' tool (http://amigo.berkeleybop.org/cgi-bin/amigo/xp_term_request?mode=process) will be useful, when it has been put into production.
 
 
2. For small scale experiments, curators should annotate to the experimental evidence in the paper.
However, curator judgement should be used, taking into account what the curator knows about:
a) the gene product; does it have a central role causing it to affect multiple processes, or does it have few specific targets?
b) the quality of the experimental assays performed in the paper; are they fully explained and the evidence supplied convincing? (See separate guidelines for annotation of high-throughput experiments.)
 
Example 1. Gene product involved in core process.
 
'''a) Yeast RNA polymerase II subunit RPB2'''
• has core function of RNA polymerase activity
• likely to affect large number of processes unrelated to its function
• most curators agree should annotate only to 'transcription'
 
'''b) Yeast spliceosome'''
• in S. cerevisiae several genes are components of spliceosome
• when mutated the strains have defects in translation
• later evidence confirmed the genes' involvement in mRNA splicing, NOT translation
• since most splicing in yeast is to ribosome genes the effect on translation was seen
• so annotations to 'translation' were removed from the spliceosome components
 
 
3.

Revision as of 08:40, 2 July 2010

Downstream Process guidelines

1. Quite often it is the case that the most relevant GO term will not exist. It is desirable to request terms which describe the involvement of a process in another process, if that will give more specificity to the annotation. For example, to describe a gene product's "intent" to change the "state" of the cell; • Growth factor BMP2 is instrumental in cardiac cell differentiation • Following stimulation with BMP2, large numbers of genes are up/down regulated Requesting the new GO term 'BMP signaling involved in cardiac cell differentiation' may be preferable to annotating to the separate terms 'BMP signaling' and 'cardiac cell differentiation' as it will be clear how the gene product is involved in cardiac cell differentiation. i.e. qualify how the gene product is involved in the downstream process in preference to annotating to the downstream process term.

To assist in the creation of these new terms, the AmiGO 'Cross-product Term Request' tool (http://amigo.berkeleybop.org/cgi-bin/amigo/xp_term_request?mode=process) will be useful, when it has been put into production.


2. For small scale experiments, curators should annotate to the experimental evidence in the paper. However, curator judgement should be used, taking into account what the curator knows about: a) the gene product; does it have a central role causing it to affect multiple processes, or does it have few specific targets? b) the quality of the experimental assays performed in the paper; are they fully explained and the evidence supplied convincing? (See separate guidelines for annotation of high-throughput experiments.)

Example 1. Gene product involved in core process.

a) Yeast RNA polymerase II subunit RPB2 • has core function of RNA polymerase activity • likely to affect large number of processes unrelated to its function • most curators agree should annotate only to 'transcription'

b) Yeast spliceosome • in S. cerevisiae several genes are components of spliceosome • when mutated the strains have defects in translation • later evidence confirmed the genes' involvement in mRNA splicing, NOT translation • since most splicing in yeast is to ribosome genes the effect on translation was seen • so annotations to 'translation' were removed from the spliceosome components


3.