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. 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

• name of the submitter -> Autocomplete on WBPerson (shall we give option to request for 1?)
• e-mail address of the submitter -> free text
• 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- we have to consider certain/partial/uncertain
• 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	Term Info
Your name	Picture-Contact	pic_contact	ontology	WBPerson ontology	as in picture OA Contact term info e.g.:id : WBPerson1752 name : Hope Dang email : hoped@u.arizona.edu
Your E-mail address	Generate a field in Exp_OA	exp_ needs to be created	-	-	-
Choose a species	Expression-Species Picture-Species	exp_species pic_species	ontology	Species ontology	-
Choose an image (jpg format)	Picture-Source	pic_source	Image will be stored in WBPerson folder, pic_source is the jpg file name
Gene (e.g. daf-16, ZC132.7)	Expression-Gene	exp_gene	ontology on locus	gin_tables	as in Expression OA Gene term info e.g.:id : WBGene00007099 locus : trx-2 synonym : B0024.9 synonym : CELE_B0024.9
Certainly expressed in (e.g. pharynx, PVM)	Expression-Anatomy, Picture-Anatomy_term	exp_anatomy;pic_anat_term; also mark the exp_qualifier as certain	Multiontology	Anatomy ontology Filter out obsolete terms	as in expression OA Anatomy Term term info e.g.:id : WBbt:0003681 name : pharynx def : "the feeding organ, a neuro-muscular pump in the head of the animal, used to ingest food, bacteria suspended in liquid, filter them out, grind them up and transport posteriorly into the instestine." [WB:rynl] comment : LINKOUT::WORMATLAS::n synonym : "esophagus" RELATED [] xref : WBPaper:00038216 is_a : WBbt:0003760 ! organ relationship : part_of WBbt:0005743 ! digestive tract relationship : part_of WBbt:0005748 ! alimentary system
Partially expressed in (e.g. anterior part of the intestine? Choose intestine from the box here)	Expression-Anatomy, Picture-Anatomy_term	exp_anatomy;pic_anat_term; also mark the exp_qualifier as Partial	Multiontology	Anatomy ontology Filter out obsolete terms	as in expression OA Anatomy Term term info e.g.:id : WBbt:0003681 name : pharynx def : "the feeding organ, a neuro-muscular pump in the head of the animal, used to ingest food, bacteria suspended in liquid, filter them out, grind them up and transport posteriorly into the instestine." [WB:rynl] comment : LINKOUT::WORMATLAS::n synonym : "esophagus" RELATED [] xref : WBPaper:00038216 is_a : WBbt:0003760 ! organ relationship : part_of WBbt:0005743 ! digestive tract relationship : part_of WBbt:0005748 ! alimentary system
Possibly expressed in (e.g. expressed in only few transgenic animals?)	Expression-Anatomy, Picture-Anatomy_term	exp_anatomy;pic_anat_term; also mark the exp_qualifier as Uncertain	Multiontology	Anatomy ontology Filter out obsolete terms	as in expression OA Anatomy Term term info e.g.:id : WBbt:0003681 name : pharynx def : "the feeding organ, a neuro-muscular pump in the head of the animal, used to ingest food, bacteria suspended in liquid, filter them out, grind them up and transport posteriorly into the instestine." [WB:rynl] comment : LINKOUT::WORMATLAS::n synonym : "esophagus" RELATED [] xref : WBPaper:00038216 is_a : WBbt:0003760 ! organ relationship : part_of WBbt:0005743 ! digestive tract relationship : part_of WBbt:0005748 ! alimentary system
Expressed during	Expression-Life Stage Picture-Life Stage	exp_qualifierls, pic_lifestage	Multiontology	Life Stage Ontology	as in expression OA Life Stage term info and possibly load an image of the elegans developmental cycle, which I will provide id : WBls:0000045 name : L1-L2d ecdysis Ce def : "The stage during L1-L2d molt, after the brief lethargus period, when an animal sheds off old cuticle." [wb:wjc] relationship : part_of WBls:0000043 ! L1-L2d molt Ce I need to discuss with you because I would like to have the Life stage info paired with Anatomy.i.e. we will have 3 Expressed during box, one next to Certainly expressed in, one next to Partially expressed in, one next to Possibly expressed in
Subcellular localization	Expression-GO Term; Picture-Cellular_component	exp_goid; pic_goid	Multiontology	Subset of GO Ontology (goid) that has cellular_component in the Namespace tag	as in expression OA GO Term info:id : GO:0005634 name : nucleus namespace : cellular_component def : "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated....
Transgene used	Expression-Transgene	exp_transgene	Multiontology	trp_tables	as in expression OA GO Transgene info: name : WBTransgene00000659 trp_publicname : Is34(eEx85) Paper : WBPaper00003958 trp_summary : [(mab-9::GFP + pCes1943)].
Pattern description	Expression-Pattern; Picture-Description	exp_pattern	pic_description	-
Submit button
Save Button
Help Button
	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

discussion points

• shall we allow the submission of other formats other than jpg? If so, can we convert them automatically in jpg here?
• can we allow upload of multiple images per submission, if so, can we name them after date, followed by a,b,c..