Mock-ups for GO website

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Electronic annotation

IEAoverview.jpg

This diagram illustrates some of the main ways of making electronic annotation. It should be read from the top down. The diagram shows sequences from UniProt having electronic GO annotation assigned by several computational methods. All of these methods involve use of mapping files. For more information on mappings see http://www.geneontology.org/GO.indices.shtml.

In the case of the Interpro mapping it is possible to assign electronic GO annotation to your sequences based on InterPro domains and a number of other criteria. For example if your sequence has a DNA binding domain then it makes sense to electronically annotate it to the DNA binding function term. For more information on InterPro mapping please see http://gocwiki.geneontology.org/index.php/InterProScan.


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Sending annotations to the consortium

If you are sending annotations to the consortium then please bear these general rules in mind.


Updating the annotations

The gene ontology structure changes over time and so it is essential that annotations should be maintained long term to accommodate these changes. If you are submitting annotations to the Consortium then you should either ensure that your group has funding to maintain the annotations, or that you have made an agreement with another group that they will carry out maintenance.

General principles for sequence ids

  • You must have stable identifiers for your objects.
  • You must provide information on what the object is. For example, is it a protein or nucleotide. It doesn't matter if a nucleotide sequence is a gene, a genome, or an EST as long as you know whether it is nucleotide sequence or a protein.
  • If a sequence identifier has become obsolete then you should be able to track down what has replaced it. What is the mechanism for that?
  • Your database must have an internal rule that object identifiers are never reused.