Difference between revisions of "Gene Expression micropublications"
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| align="center" style="background:#f0f0f0;"|'''cross table population script''' | | align="center" style="background:#f0f0f0;"|'''cross table population script''' | ||
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− | | || pgonly||con_id||not a table||pgid||all*||-||-||-|| | + | | |Enter your Name| pgonly||con_id||not a table||pgid||all*||-||-||-|| |
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| style="color: grey;"| pgonly||con_timestamp||not a table||none||||-|||||| | | style="color: grey;"| pgonly||con_timestamp||not a table||none||||-|||||| |
Revision as of 23:02, 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| 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