Transgene curation pipeline

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Importing transgenes from textpresso

every day at 4am :

/home/postgres/work/pgpopulation/textpresso/wrapper.sh

call :

/home/postgres/work/pgpopulation/textpresso/transgene/update_textpresso_transgene.pl
/home/postgres/work/pgpopulation/textpresso/antibody/update_textpresso_antibody.pl
/home/postgres/work/pgpopulation/afp_papers/find_passwd_@.pl
/home/postgres/public_html/cgi-bin/data/ccc_gocuration/get_newset.pl

Relevant script now :

/home/postgres/work/pgpopulation/textpresso/transgene/update_textpresso_transgene.pl

gets data from

http://textpresso-dev.caltech.edu/transgene/transgenes_in_regular_papers.out

--kjy 19:35, 24 May 2012 (UTC)

Curating transgenes

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: "

Phenote 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, in some cases use controlled vocabulary
  • "Conflicting mapping info: ..."
  • "Conflicting genotype: ..."
  • "No transgene info in original publication."
  • "Other integration method: ..."
  • "Clone = "
  • "Mapping info: "
• 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?

Transfer from phenote to OA

• Autocomplete
• Multi-ontology
• Big text = free text, editable expanded box
• Selection list
• Selection list multiple list field
• multi-drop down
• Free text, pipe separated values

Tab 1 (Transgene)

• Pgdbid->keep - postgres database ID, autogenerated -> no change

• Curator

• Name->keep free text ->no change

• Synonym->keep -free text, pipe separated values->no change (but moved from tab 2

• Summary ->keep- Big text -> no change

• Driven by Gene->keep -> change to multi-ontology WBGene, I will want to enter gene by public/sequence name, postgres stores WBGeneID, make sure entries are unique

• Reporter Product->keep -multi-drop down list -> no change, but I do need to know where the file is so I can edit it.

• Other Reporter->keep - free text, pipe separated values -> no change

• Gene->keep-> change to multi-ontology WBGene, I will want to enter gene by public/sequence name, postgres stores WBGeneID, make sure entries are unique

• 3' UTR->NEW field -> multi-ontology WBGene

• Rescues ->NEW field -> multi-ontology WBvariation

• Reference->keep-> change to multi-ontology paper, possible to make box expandable?

Tab 2 (Isolation)

• Remark->keep-> Big text, pipe separated values ->no change

• Clone/plasmid->NEW Field-> multi -ontology using Clone list from acedb select a, a->general_remark, a->positive_gene from a in class clone where a->type = "Plasmid" (remove all "sjj_" clones). also see e-mail. (for now this will be a no dump field).

• Coinjection marker ->NEW field text

• Integrated by->keep -multi-drop down list -> no change, but I do need to know where the file is so I can edit it.

• Map->keep-> multi-drop down list -> no change

• Map Paper->keep ->multi-ontology paper

• Map Person->keep->multi-ontology person

• Location->keep-> multi-ontology laboratory

• Strain->keep ->free text, pipe separated values ->no change

Tab 3 (Expression)

• Marker for->keep->free text->no change

• Marker Paper->keep->multi-ontology paper

• Species->keep->no change

• Driven by Construct->keep-> free text->no change

• Movie-> keep->no change

• Picture-> keep->no change

Tab 4 (Postgres)

• Search New Transgene-> keep-> no change

• SQL-> remove

Way in the future

• Genomic Expression->New field - for developing a standardizing transgene expression nomenclature, eventually we will want to fill this by script composition based on other fields (promoters, reporters, clones)