Difference between revisions of "Gene Expression micropublications"
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− | + | ==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 | 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? | * 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.. | * can we allow upload of multiple images per submission, if so, can we name them after date, followed by a,b,c.. |
Revision as of 00:46, 24 January 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 | 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 | text | - | |
Submit button | |||||
Save Button | |||||
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..