Gene Expression micropublications

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Revision as of 23:27, 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

  • name of the submitter -> Autocomplete on WBPerson (shall we give option to request for 1?)
  • e-mail address of the submitter -> free text
  • 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 Term Info
Your name Picture-Contact pic_contact ontology WBPerson ontology id : WBPerson1752

name : Hope Dang email : hoped@u.arizona.edu

Your E-mail address Generate a field in Exp_OA exp_ needs to be created - -
Choose a species Expression-Species Picture-Species exp_species pic_species ontology Species ontology
Choose an image Picture-Source pic_source Image will be stored in WBPerson folder, pic_source is the jpg file name
Gene (e.g. daf-16, ZC132.7) Expression-Gene exp_gene ontology on locus gin_tables
Certainly expressed in (e.g. pharynx, PVM) Expression-Anatomy exp_anatomy Description Text all
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..