Difference between revisions of "Gene Expression micropublications"
| Line 42: | Line 42: | ||
| |Enter your Name||con_id||not a table||pgid||all*||-||-||-|| | | |Enter your Name||con_id||not a table||pgid||all*||-||-||-|| | ||
|- | |- | ||
| − | | | + | | |Enter a contect E-mail address||con_timestamp||not a table||none||||-|||||| |
|- | |- | ||
| − | | | + | | |Choose a species||con_curator||dropdown||Curator||all||-||-||-|| |
|- | |- | ||
| − | | | + | | |Choose an image||con_wbgene||ontology||WBGene||all||WBGene||gin_tables|||| |
|- | |- | ||
| − | | ||con_curhistory||ontology||Curator History||all||Concurhst|||||| | + | | |Gene expressed|con_curhistory||ontology||Curator History||all||Concurhst|||||| |
|- | |- | ||
| Structured_description||con_desctype||dropdown||Description Type||all|||||||| | | Structured_description||con_desctype||dropdown||Description Type||all|||||||| | ||
|- | |- | ||
| − | | ||con_desctext||textarea||Description Text||all||||||||cols_size =90, rows_size=12 | + | | |Expressed in|con_desctext||textarea||Description Text||all||||||||cols_size =90, rows_size=12 |
|- | |- | ||
| − | | ||con_paper||multiontology||Reference||all||WBPaper||pap_tables|||| | + | | |Expressed during|con_paper||multiontology||Reference||all||WBPaper||pap_tables|||| |
|- | |- | ||
| − | | ||con_accession||text||Accession Evidence||all|||||||| | + | | |Subcellular localization|con_accession||text||Accession Evidence||all|||||||| |
|- | |- | ||
| − | | ||con_lastupdate||text||Last Updated||all|||||||| | + | | |Construct used|con_lastupdate||text||Last Updated||all|||||||| |
|- | |- | ||
| ||con_comment||bigtext||Comment||all|||||||| | | ||con_comment||bigtext||Comment||all|||||||| | ||
Revision as of 23:05, 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. 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 | con_id | not a table | pgid | all* | - | - | - | |
| Enter a contect E-mail address | con_timestamp | not a table | none | - | ||||
| Choose a species | con_curator | dropdown | Curator | all | - | - | - | |
| Choose an image | con_wbgene | ontology | WBGene | all | WBGene | gin_tables | ||
| Gene expressed|con_curhistory | ontology | Curator History | all | Concurhst | ||||
| Structured_description | con_desctype | dropdown | Description Type | all | ||||
| 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 | |||||
| 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
