The dictionary tables contained here are much more Sanger orientated. I provide them here as templates which you may wish to alter to suit your own working practices.

Contents

DoTS::GeneInstanceCategory

This is (in theory) how, why and when GeneInstanceCategory's will be created

A gene can be predictied by 3 seperate programs (glimmer, GeneFinder, Phat). Each one will get a GeneInstanceCategory of predicited linking it to the single gene.

A software package can "auto select" one prediction to be The One. Its catergory is changed to "auto select". At this point the "mirror" GeneFeature will be created which is a clone of the auto selected one.

A curator can review the predictions and choose the right one. They set the category of the prediction to "manually selected" and create a new GeneFeature that is a clone of the prediction BUT its boundries maybe modified etc.

<DoTS::GeneInstanceCategory>
  <gene_instance_category_id>1</gene_instance_category_id>
  <name>manually selected</name>
  <description>A user has picked this prediction over the others</description>
</DoTS::GeneInstanceCategory>
//
<DoTS::GeneInstanceCategory>
  <gene_instance_category_id>2</gene_instance_category_id>
  <name>mirror</name>
  <description>The mirror GeneFeature for the Gene</description>
</DoTS::GeneInstanceCategory>
//
<DoTS::GeneInstanceCategory>
  <gene_instance_category_id>3</gene_instance_category_id>
  <name>predicted</name>
  <description>Automatic prediction of a gene</description>
</DoTS::GeneInstanceCategory>
//
<DoTS::GeneInstanceCategory>
  <gene_instance_category_id>4</gene_instance_category_id>
  <name>auto selected</name>
  <description>Software has picked this prediction over the others</description>
</DoTS::GeneInstanceCategory>
//

DoTS::RNAInstanceCategory

<DoTS::RNAInstanceCategory>
  <name>assembly</name>
  <description>Has come from an EST</description>
</DoTS::RNAInstanceCategory>
<DoTS::RNAInstanceCategory>
  <name>predicted</name>
  <description>Predicted from CDS</description>
</DoTS::RNAInstanceCategory>
<DoTS::RNAInstanceCategory>
  <name>mirror</name>
  <description>The mirror RNAFeature for the RNA</description>
</DoTS::RNAInstanceCategory>

DoTS::ProteinInstanceCategory

<DoTS::ProteinInstanceCategory>
  <name>mirror</name>
  <description>The mirror ProteinFeature for the Protein</description>
</DoTS::ProteinInstanceCategory>

SRes::ReviewStatus

Has a person reviewed the data?

<SRes::ReviewStatus>
  <review_status_id>5</review_status_id>
  <name>Unknown</name>
  <description>Review status not known</description>
</SRes::ReviewStatus>

<SRes::ReviewStatus>
  <review_status_id>10</review_status_id>
  <name>Not reviewed</name>
  <description>A human has not yet reviewed this feature</description>
</SRes::ReviewStatus>

<SRes::ReviewStatus>
  <review_status_id>15</review_status_id>
  <name>Annotated</name>
  <description>Annotator/Curator has attached data to this feature</description>
</SRes::ReviewStatus>