Transgene curation pipeline

From WormBaseWiki
Revision as of 21:30, 26 June 2010 by Kyook (talk | contribs) (Created page with '===Curate with Phenote=== Invoke the phenote transgene configuration interface and access postres go to directory with phenote $./phenote -c worm-transgene.cfg If you wan…')
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigationJump to search

Curate with Phenote

Invoke the phenote transgene configuration interface and access postres

go to directory with phenote
 $./phenote -c worm-transgene.cfg

If you want to see all the current 'new' transgenes picked up by Textpresso, go to Tab 3 and press the "Search New Transgene" retrieve button. This action with retrieve all transgene objects that have data in the Summary or Remark fields. Usually there will be paper object info already since it was entered from the Textpresso search.

Curators should look for information of new transgenes in the paper document provided by Textpresso (main paper or supplementary file).

Sometimes papers do not provide any information on the transgenes, only the name is provided. Then "No transgene info in original publication." should be entered into the Remark field so that it will not be identified as a new transgene again.

Here is the controlled vocabulary for the transgene remark field:

  • Remark "Conflicting mapping info: ..."
  • Remark "Conflicting genotype: ..."
  • Remark "No transgene info in original publication."
  • Remark "Other integration method: ..."
  • Remark "Clone = "
  • Remark "Mapping info: "

transgene.cfg

T= free text M= multiple values, separate values with a pipe(|) S= selection list

Tab 1

  • Pgdbid- postgres database ID, entered automatically when curator enters a new transgene
  • Name(T)-approved name following Lab-prefix (or WBPaperID), Is or Ex, number
  • Summary(T)- genotype, including co-injection marker and relevant information about making the construct, if papers rport conflicting genotypes use Remark field and controlled vocabulary "Conflicting genotype: ...", if no information enter "No transgene info in original publication." in Remark field.
  • Driven by Gene(T,M)- enter WBGeneID used for promoters in every promoter driven construct of the transgene
  • Reporter Product(S,M)- list has common reporter genes, GFP, RFP, LacZ, etc.
  • Other Reporter(T,M)- enter other products encoded as reporters that do not appear in the drop down list
  • Gene(T,M)- enter WBGeneID for protein output of construct, which isn't considered a reporter product
  • Integrated by(S)- choose integration method if known, use 'not integrated' for Ex transgenes, if integration method is not listed, use Remark field and controlled vocabulary: "Other integration method: ..."
  • Strain(T,M)- not used consistently, enter approved strain names for those strains that contain the transgene
  • Map(S,M)- choose LG(s) of integrated array if known, if papers report differing map positions use Remark field and controlled vocabulary "Conflicting mapping info: ..."

Tab 2

  • Map Paper(T,M?)- WBPaperID for paper that reports mapping info
  • Map Person(T,M)- WBPersonID? or Name, person evidence
  • Marker for(T,M)- not used, Wen's expression data
  • Marker Paper(T,M)- WBPaperID, not used, Wen's expression data
  • Reference(T,M)- WBPaperID, generally autofilled by Textpresso cron job script and bulk upload of Ex search script, add new paper if necessary
  • Remark(T,M)- catch all used for clarifying info from other fields, and for entering construct specifics
  • Species(T,M?)- not used?
  • Synonym(T,M)- other names for the transgene or construct
  • Driven by Construct(T,M)- not sure what this is
  • Location(T,M)- Lab designations for people who have the transgene, not sure about this.

Tab 3

  • Movie(T)- used?
  • Picture(T)- used?
  • Search New Transgene(T)- use to retrieve all transgenes that do not have any summary or remark data
  • SQL-use?