Difference between revisions of "Gene Expression micropublications"
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| |No Dump||Picture-No Dump; Expression-No Dump||pic_nodump; exp_nodump||all submissions will for now be set as no_dump|||| | | |No Dump||Picture-No Dump; Expression-No Dump||pic_nodump; exp_nodump||all submissions will for now be set as no_dump|||| | ||
|- | |- | ||
− | | ||other|| | + | | |Curator||Picture-Curator; Expression-Curator||pic_curator; exp_curator||Curator will be Daniela for bith expression and picture WBPerson12028||other|| |
+ | |- | ||
+ | | |Micropublication||Picture-Micropublication; Expression-Micropublication -create a toggle in both OA||pic_microp; exp_microp||toggle|||| | ||
|} | |} | ||
Revision as of 22:18, 2 February 2015
Contents
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 | ||||
No Dump | Picture-No Dump; Expression-No Dump | pic_nodump; exp_nodump | all submissions will for now be set as no_dump | ||
Curator | Picture-Curator; Expression-Curator | pic_curator; exp_curator | Curator will be Daniela for bith expression and picture WBPerson12028 | other | |
Micropublication | Picture-Micropublication; Expression-Micropublication -create a toggle in both OA | pic_microp; exp_microp | toggle |
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