Difference between revisions of "Gene Expression micropublications"

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===instructions for the form===
 
===instructions for the form===
uP data will be displayed under a separate section on the gene expression page i.e. between Anatomical expression patterns and expression profiling graphs
 
  
they will be automatically assigned a tag i.e. uP
+
Every submission will have automatically assigned a tag i.e. uP
  
 
Submission form should have  
 
Submission form should have  
  
  
 +
*species -> Select your species dropdown on species
 
*Image -> we should allow an upload your image button
 
*Image -> we should allow an upload your image button
 
*Gene -> autocomplete on genes required field
 
*Gene -> autocomplete on genes required field
*Pattern Description -> free text  required field
+
*Expressed in -> autocomplete on anatomy terms
*Expressed in tissue/cell-> autocomplete on anatomy terms
 
 
Toggle certain toggle partial toggle uncertain (one of the 3 should be toggled if field 3 has info)
 
Toggle certain toggle partial toggle uncertain (one of the 3 should be toggled if field 3 has info)
 
*Expressed during -> Autocomplete on Life stages
 
*Expressed during -> Autocomplete on Life stages
*Expressed in organelle -> autocomplete on GO CC
+
*Subcellular localization -> autocomplete on GO CC
3 or 5 -> one of them should contain info -> required
+
*Pattern Description -> free text  required field
 
 
 
*Construct used -> autocomplete on transgenes
 
*Construct used -> autocomplete on transgenes
  and -> sequence, reporter, clone
+
  and -> sequence (free text), reporter (ontology on reporters), clone (ontology on clones)
  
 
on of the 2 should be filled
 
on of the 2 should be filled
  
*non elegans? -> Select your species dropdown on species
 
  
 
Name for the expression pattern -> we can call it Micropub0000001 instead of Expr00001 -> Autogenerated
 
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
 
Can we see Wobr tree in term info? so users can navigate the tree if they need to
 +
 +
 +
{| border="1" cellpadding="2" cellspacing="2" {{table}}
 +
| align="center" style="background:#f0f0f0;"|'''uPtag'''
 +
| align="center" style="background:#f0f0f0;"|'''OA label'''
 +
| align="center" style="background:#f0f0f0;"|'''OA pgtable'''
 +
| align="center" style="background:#f0f0f0;"|'''ontology_type'''
 +
| align="center" style="background:#f0f0f0;"|'''ontology_table'''
 +
| align="center" style="background:#f0f0f0;"|'''cross table population script'''
 +
|-
 +
| style="color: grey;"| pgonly||con_id||not a table||pgid||all*||-||-||-||
 +
|-
 +
| style="color: grey;"| pgonly||con_timestamp||not a table||none||||-||||||
 +
|-
 +
| style="color: grey;"| pgonly||con_curator||dropdown||Curator||all||-||-||-||
 +
|-
 +
| Gene||con_wbgene||ontology||WBGene||all||WBGene||gin_tables||||
 +
|-
 +
| ||con_curhistory||ontology||Curator History||all||Concurhst||||||
 +
|-
 +
| Structured_description||con_desctype||dropdown||Description Type||all||||||||
 +
|-
 +
| ||con_desctext||textarea||Description Text||all||||||||cols_size =90, rows_size=12
 +
|-
 +
| ||con_paper||multiontology||Reference||all||WBPaper||pap_tables||||
 +
|-
 +
| ||con_accession||text||Accession Evidence||all||||||||
 +
|-
 +
| ||con_lastupdate||text||Last Updated||all||||||||
 +
|-
 +
| ||con_comment||bigtext||Comment||all||||||||
 +
|-
 +
| ||con_nodump||toggle||NO DUMP||all||||||||
 +
|-
 +
| ||con_person||multiontology||Person||all||WBPerson||?||||
 +
|-
 +
| ||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

Revision as of 22:32, 22 January 2015

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.

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


uPtag OA label OA pgtable ontology_type ontology_table cross table population script
pgonly con_id not a table pgid all* - - -
pgonly con_timestamp not a table none -
pgonly con_curator dropdown Curator all - - -
Gene con_wbgene ontology WBGene all WBGene gin_tables
con_curhistory ontology Curator History all Concurhst
Structured_description con_desctype dropdown Description Type all
con_desctext textarea Description Text all cols_size =90, rows_size=12
con_paper multiontology Reference all WBPaper pap_tables
con_accession text Accession Evidence all
con_lastupdate text Last Updated all
con_comment bigtext Comment all
con_nodump toggle NO DUMP all
con_person multiontology Person all WBPerson ?
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