Difference between revisions of "Gene Expression micropublications"

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| |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.
 
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Revision as of 20:29, 2 February 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

  • 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 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 in the form, multiontology in the OA because it could store in OA also name of co-authors see below co-authors 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, generate a field in pic_OA exp_email pic_email need to be created - - -
Co-authors? they could go to Picture-Contact-(but after the entry coming from Your Name as the first person entered will be the one after which the folder will be named); Expression- Contact pic_contact; exp_contact multiontolgy WBPerson ontology -
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. the file name should be submission date.
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

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

Not expressed in (optional) Expression-Not in Anatomy generate it exp_not_in_anatomy; generate it 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

Not expressed during (optional) Expression-Not in Life Stage generate it exp_not_in_lifestage generate it 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

Pattern description Expression-Pattern; Picture-Description exp_pattern;pic_description text -
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)].

DNA sequence Construct-DNA cns_dna text - 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
Reporter Construct-Reporter cns_reporter Ontology values in cns_reporter -
Vector Construct-Clone cns_clone ontology clone tables -
Comments Expression-Remark; Picture-Remark exp_remark;pic_remark text -
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
other other other other
other other other other

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