Difference between revisions of "Gene Expression micropublications"

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| |Construct Comments||Construct-Remark||cns_remark||bigtext||-||||yes||no
 
| |Construct Comments||Construct-Remark||cns_remark||bigtext||-||||yes||no
 
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| |Associated Transgene||Construct-Used for transgene||cns_assotransgene||text||-||-||yes||no
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| |Associated Transgene||Construct-Used for transgene||cns_assoctransgene||text||-||-||yes||no
 
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| |Strain||Construct-Strain|| cns_strain||text||-||-||yes||no
 
| |Strain||Construct-Strain|| cns_strain||text||-||-||yes||no
 
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| |Coinjected with ||Construct-Coinjected with|| cns_coinjected_with||text||-||-||yes||no
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| |Coinjected with ||Construct-Coinjected with|| cns_coinjectedwith||text||-||-||yes||no
 
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| |Injection Concentration ||Construct-Construction Details|| cns_constructionsummary||text, will be put after whatever text there is adding pipe||-||-||yes||no
 
| |Injection Concentration ||Construct-Construction Details|| cns_constructionsummary||text, will be put after whatever text there is adding pipe||-||-||yes||no
 
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| |Integrated by||Construct-Integrated by || cns_integration_method||ontology|| trp_integration_method||-||yes||no
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| |Integrated by||Construct-Integrated by || cns_integrationmethod||ontology|| trp_integration_method||-||yes||no
 
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Revision as of 00:58, 3 March 2015

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 date. 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
Comments Expression-Remark; Picture-Remark exp_remark;pic_remark bigtext - no no
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
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 populate in Pic_OA the pic_exprpattern field pic_exprpattern 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
  • 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