Gene Expression micropublications

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Revision as of 00:27, 23 January 2015 by Draciti (talk | contribs) (→‎mappings)
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motivation

generate a user's submission form for reporter expression data containing enough information so that the experiment can be interpreted and/or repeated by others. The submitted data might result into a uP

form

http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/micropub.cgi

instructions for the form

Every submission will have automatically assigned a tag i.e. uP

Submission form should have


  • species -> Select your species dropdown on species
  • Image -> we should allow an upload your image button
  • Gene -> autocomplete on genes required field
  • Expressed in -> autocomplete on anatomy terms

Toggle certain toggle partial toggle uncertain (one of the 3 should be toggled if field 3 has info)

  • Expressed during -> Autocomplete on Life stages
  • Subcellular localization -> autocomplete on GO CC
  • Pattern Description -> free text required field
  • Construct used -> autocomplete on transgenes
and -> sequence (free text), reporter (ontology on reporters), clone (ontology on clones)

on of the 2 should be filled


Name for the expression pattern -> we can call it Micropub0000001 instead of Expr00001 -> Autogenerated Can we see Wobr tree in term info? so users can navigate the tree if they need to

mappings

uPtag OA label OA pgtable ontology_type ontology_table cross table population script
Enter your Name Picture-Contact pic_contact single ontology WBPerson ontology
Enter a contact E-mail address Generate a field in Expr_OA expr_ needs to be created none
Choose a species Expression-Species Picture-Species exp_species pic_species Curator all
Choose an image Picture-Source pic_source Image will be stored in WBPerson folder, pic_source is the jpg file name all WBGene gin_tables
Gene expressed con_curhistory ontology Curator History all Concurhst
Expressed in con_desctext textarea Description Text all cols_size =90, rows_size=12
Expressed during con_paper multiontology Reference all WBPaper pap_tables
Subcellular localization con_accession text Accession Evidence all
Construct used con_lastupdate text Last Updated all
Pattern description con_comment bigtext Comment all
Submit button con_nodump toggle NO DUMP all
Save Button con_person multiontology Person all WBPerson ?
Help Button con_exprtext text Expression Pattern all
con_rnai text RNAi all
con_microarray text Microarray all

web display

uP data will be displayed under a separate section on the gene expression page i.e. between Anatomical expression patterns and expression profiling graphs

discussion points

  • shall we allow the submission of other formats other than jpg? If so, can we convert them automatically in jpg here?
  • can we allow upload of multiple images per submission, if so, can we name them after date, followed by a,b,c..