Gene Expression micropublications

motivation

We aim at providing a clean, simple interface that will be self-intuitive and will allow researchers to submit high-quality scientific findings directly to a well established central repository (WormBase). Data will be publically shared and could be mined alongside data curated from the literature. This will ensure that every piece of federally funded research will be publicly available -including negative findings.

We will pilot the submission focusing initially only on reporter gene fusions -the most common method to detect gene expression in c.elegans (WormBook chapter in preparation), and plan to expand the model to other gene expression localization experiments (e.g. ISH, smFISH, immunohistochemistry). If the model will prove to be successful, we will scale it up to include submission of other scientific findings (laser ablation experiments, rnai experiments..).

guidelines for gene product localization experiments assessed with reporter gene fusions. The guidelines will be modeled after the MISFISHIE (Minimum information specification for in situ Hybridization and immunohistochemistry experiments) guidelines, comply with Wormbase curation standards, and are intended to define a set of minimum information needed to interprete and reproduce an individual experiment aimed to localize the expression of a transcript or a protein.

instructions

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)

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	Gray out for new picture	Required field
Your name	Picture-Contact and Expression-Contact Add a field in Expr_OA with Contact(multiontology on WBPersons) we could dump later on the info in Expr objects in Experiment Author ?Author (already in model)	pic_contact; exp_contact	single ontology	WBPerson ontology	as in picture OA Contact term info e.g.:id : WBPerson1752 name : Hope Dang email : hoped@u.arizona.edu	yes	yes
Your E-mail address	Generate a field in Exp_OA, generate a field in pic_OA	exp_email pic_email need to be created	smalltext	-	-	yes	yes
Co-authors	Picture-Co-author (needs to be created)- Expression- Co-author (needs to be created)	pic_coaut; exp_coaut	multiontolgy	WBPerson ontology	-	yes	no
Choose a species	Expression-Species Picture-Species	exp_species pic_species	ontology	Species ontology	-	yes
Choose an image (jpg format)	Picture-Source	pic_source	Image will be stored in WBPerson folder, pic_source is the jpg file name. the file name should be submission timestamp (human readable).			no	yes
Gene (e.g. daf-16, ZC132.7)	Expression-Gene	exp_gene	ontology on WBGene	gin_tables	as in Expression OA Gene term info e.g.:id :WBGene00007099 locus:trx-2 synonym:B0024.9 synonym:CELE_B0024.9	yes	yes
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	no	one of the certainly/partially/possibly/not/during/subcellular should contain data
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	no	one of the certainly/partially/possibly/not/during/subcellular should contain data
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	no	one of the certainly/partially/possibly/not/during/subcellular should contain data
Expressed during	Expression-Qualifier LS 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	no	one of the certainly/partially/possibly/not/during/subcellular should contain data
Not expressed in (optional)	Expression-Anatomy	exp_anatomy; also mark the exp_qualifier as NOT NB:once we will have the NOTs is the model we need to see how they will dump	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	no	one of the certainly/partially/possibly/not/during/subcellular should contain data
Not expressed during (optional)	Expression-Qualifier LS	exp_qualifierls also mark the exp_qualifier as NOT NB:once we will have the NOTs is the model we need to see how they will dump	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	no	one of the certainly/partially/possibly/not/during/subcellular should contain data
Pattern description	Expression-Pattern; Picture-Description	exp_pattern;pic_description	bigtext	-		no	yes
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....	no	one of the certainly/partially/possibly/not/during/subcellular should contain data
In tissue/cell (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	no	one of the certainly/partially/possibly/not/during/subcellular should contain data
Comments	Expression-Remark; Picture-Remark	exp_remark;pic_remark	bigtext	-		no	-
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)].	yes	transgene OR construct section should have data. try to see if you can grey out construct stuff if transgene is entered
Genotype Summary (e.g.: daf-16::GFP)	Construct-Summary	cns_summary	smalltext	when transfer please put it in square brackets	-	yes	yes if no transgene is selected
Construction Details	Construct-Construction Details	cns_constructionsummary	bigtext	we should put a question mark next to the name to give more info when clicked	-	yes	yes if no transgene is selected
DNA sequence	Construct-DNA	cns_dna	multi-bigtext joined with pipes	-	if the DNA sequence, Reporter and Vector fields are filled in, then the submission should generate a construct object and append the cnstID to the expression pattern object	yes	yes if no transgene is selected
3'UTR	Construct-3UTR	cns_threeutr	multiontology on WBGene	gin_tables	as in Expression OA Gene term info e.g.:id :WBGene00007099 locus:trx-2 synonym:B0024.9 synonym:CELE_B0024.9	yes	no
Reporter	Construct-Reporter	cns_reporter	multiontology	values in cns_reporter-Karen is OK in turning the list into an ontology	-	yes	yes if no transgene is selected
Backbone Vector	Construct-Clone	cns_clone	multiontology	clone tables	as in construct OA clone field: id: D1001 name: "D1001"remark: "C. elegans genomic clone not used in the final reference genome, submitted by The C. elegans Genome Sequencing Consortium."type: "Cosmid"	yes	yes if no transgene is selected
Fusion Type	Construct-Construct Type	cns_constructtype	ontology	right now is not an ontology, Karen said we can turn this in an ontology, too	-	yes	yes if no transgene is selected
Laboratory	Construct-Laboratory	cns_laboratory	multiontology	WB laboratory	as in Construct OA -> laboratory field: id: LK name: "LK" Mail: "Harvey Mudd College, Claremont CA" Representatives: "Jim Manser"Allele_designation: "gs"	yes	yes if no transgene is selected
Public Name (e.g.: PJKL491, pCK6)	Construct-Public Name	cns_publicname	smalltext		-	yes	yes
Construct Comments	Construct-Remark	cns_remark	bigtext	-		yes	no
Associated Transgene	Construct-Used for transgene	cns_assoctransgene	text	-	-	yes	no
Strain	Construct-Strain	cns_strain	text	-	-	yes	no
Coinjected with	Construct-Coinjected with	cns_coinjectedwith	text	-	-	yes	no
Injection Concentration	Construct-Construction Details	cns_constructionsummary	text, will be put after whatever text there is adding pipe	-	-	yes	no
Integrated by	Construct-Integrated by	cns_integrationmethod	ontology	trp_integration_method	-	yes	no
Submit button
Save Button					Save button saves to a file loadable by URL, filename WBPerson+Date, sends email to user with Link. Once link is loaded and either Submitted or Saved again, delete the previous save file. If a deleted file tries to get loaded by URL, say it's been submitted or saved over.
Help Button	will link to the help page	http://www.wormbase.org/tools/support
the fields below are about functionality, not fields that should be on the form
No Dump	Picture-No Dump; Expression-No Dump Construct-No Dump	pic_nodump; exp_nodump; cns_nodump (needs to be created)	all submissions will for now be set as no_dump
Curator	Picture-Curator; Expression-Curator; Construct Curator	pic_curator; exp_curator; cns_curator	Curator will be Daniela for the three WBPerson12028	other
Micropublication	Picture-Micropublication; Expression-Micropublication Construct Micropublication-create a toggle in the three OAa	pic_microp; exp_microp cns_microp	toggle	every submission that comes through the form should have a micropublication tooggle on
Reporter Gene	Expression-Type	exp_exprtype set to Reporter_gene	every submission will have the type set to Reporter_gene
If user fills out the 'new construct' section	populate in Exp_OA the exp_construct field	exp_construct; cns_name	multiontology/text
Picture OA -> Expression pattern field	exp_name; populate in Pic_OA the pic_exprpattern field	exp_name; pic_exprpattern	singleontology/multiontology

functionality

• Once you enter an anatomy or a life stage -or both it will prompt another line to enter more terms. We can set that to 100 entries for the certain and 20 for uncertain and partial and NOT

• functionality for submitting 2 -or more- images. User will fill out all details for submission of picture 1 with annotations, once he will submit he will be asked if wants to submit another image -> says yes -> will bring to a fresh form that will generate a new WBPicture ID, same ExprID (we can show it in a box somewhere on the form), same Construct ID (don't create new data for any of the constructs tables). The following fields will be already filled out according to the previous submission:
  • your name, your e-mail address, co-authors, species, gene, transgene used, DNA sequence, Reporter, Vector and all the construct related fields)
  • the fileds will be grayed out so the uer cannot edit them
  • also make sure that there will be a hidden field which will store the ConstructID
  • subsequent sumbissions (picture 2 on) will not write to any of the construct tables
• Once users enter a value, the WBid will be hidden.

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..
• where to put person objects. Person objects will go to the Picture OA as we need to generate a folder with the images for submission

We will also add person objects to Expr objects to keep track of the authorship of the uP In expression they can be stored in Experiment Author ?Author add a field in Expr_OA called exp_contact multiontology on people

• where to put email. we will put e-mail both in exp_OA AND in pic_OA so if the submitter needs to be contacted will be easy to retrieve the info

form

beta trials

• http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/mpub.cgi
• http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/micropub.cgi