Gene Expression micropublications

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

mappings

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