Difference between revisions of "Gene Expression micropublications"
(→=form) |
|||
Line 7: | Line 7: | ||
===instructions for the form=== | ===instructions for the form=== | ||
− | |||
− | + | 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 | ||
− | + | *Expressed in -> autocomplete on anatomy terms | |
− | *Expressed in | ||
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 | ||
− | * | + | *Subcellular localization -> autocomplete on GO CC |
− | + | *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 | ||
− | |||
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