Model changes
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Jump to navigationJump to searchMicropublication in ?Paper class
- Add Micropublication in Type
Type Journal_article #Evidence Review #Evidence Comment #Evidence .... Micropublication #Evidence
- Authors: will be stored in the existing ?Author tag
- Reviewers: Kimberly was proposing to create a ?Reviewer class, similar to ?Authors. This will be beneficial to elevate contributions from the community -for Micropublications but also for concise description contributions/reviews
add Reviewed_by ?Reviewer
- Citation -> the citation will be generated as the other brief citations for papers are generated and will be stored in Brief citation
- Funding -> add a tag: Funding Text
shall we have a more structured schema for funding?
- DOIs will be handled as other Paper DOIs are handled -might be formalized (DB_info as per Raymond's suggestion)
Shall we call the objects WBPaper or WBMicropublication?
Once a Micropub is submitted, in the initial phase a curator will manually generate an object through the paper editior. Moving forward: if/once we will have PMIDs assigned to micropubs, submissions will be ingested directly through the general paper pipeline.
Pictures in #Phenotype_info
Model additions will include
Image ?Picture #Evidence Control_strain ?Strain #Evidence Control_strain_genotype #Evidence --> possibly not - need to discuss with Mary Ann about having this info sent to her behind the scenes for strain curation
Full model
?Phenotype_info Paper_evidence ?Paper Person_evidence ?Person Curator_confirmed ?Person Remark ?Text #Evidence Quantity_description ?Text #Evidence Quantity UNIQUE Int UNIQUE Int #Evidence NOT #Evidence Penetrance Incomplete Text #Evidence Low Text #Evidence High Text #Evidence Complete Text #Evidence Range UNIQUE Int UNIQUE Int #Evidence Recessive #Evidence Semi_dominant #Evidence Dominant #Evidence Haplo_insufficient #Evidence Caused_by_gene ?Gene #Evidence Caused_by_other ?Text #Evidence Rescued_by_transgene ?Transgene Variation_effect Gain_of_function_undetermined_type #Evidence Antimorph_gain_of_function #Evidence Dominant_negative_gain_of_function #Evidence Hypermorph_gain_of_function #Evidence Neomorph_gain_of_function #Evidence Loss_of_function_undetermined_extent #Evidence Null #Evidence Predicted_null_via_sequence #Evidence Probable_null_via_phenotype #Evidence Hypomorph_reduction_of_function #Evidence Predicted_hypomorph_via_sequence #Evidence Probable_hypomorph_via_phenotype #Evidence Wild_allele #Evidence Affected_by Molecule ?Molecule #Evidence Pathogen ?Species #Evidence EQ_annotations Anatomy_term ?Anatomy_term ?PATO_term #Evidence Life_stage ?Life_stage ?PATO_term #Evidence GO_term ?GO_term ?PATO_term #Evidence Molecule_affected ?Molecule ?PATO_term #Evidence Temperature_sensitive Heat_sensitive Text #Evidence Cold_sensitive Text #Evidence Maternal UNIQUE Strictly_maternal #Evidence With_maternal_effect #Evidence Paternal #Evidence Phenotype_assay Strain ?Strain #Evidence Treatment ?Text #Evidence Temperature ?Text #Evidence Genotype ?Text #Evidence Ease_of_scoring UNIQUE ES0_Impossible_to_score #Evidence ES1_Very_hard_to_score #Evidence ES2_Difficult_to_score #Evidence ES3_Easy_to_score #Evidence Image ?Picture #Evidence Control_strain ?Strain #Evidence Control_strain_genotype #Evidence
Sample ACeDB format of data using nemametrix tech note from here: http://nemametrix.com/c-elegans-alzheimers-disease-model/
Transgene : "WBTransgene00000415" Phenotype "WBPhenotype:0000019" Curator_confirmed "?" Phenotype "WBPhenotype:0000019" Paper_evidence "?" Phenotype "WBPhenotype:0000019" Remark "Strain CL4176 accumulates amyloid-β1-42 in body wall muscles after shifting from 15o to 25 oC during L4 (Link et al. 2013). 48 h after the upshift, control strain CL802 showed normal EPG activity whereas CL4176 showed an ~25% decrease in pump frequency (A and data not shown), resulting from the increased probability of long inter-pump intervals (B)." Curator_confirmed "?" Phenotype "WBPhenotype:0000019" Remark "Strain CL4176 accumulates amyloid-β1-42 in body wall muscles after shifting from 15o to 25 oC during L4 (Link et al. 2013). 48 h after the upshift, control strain CL802 showed normal EPG activity whereas CL4176 showed an ~25% decrease in pump frequency (A and data not shown), resulting from the increased probability of long inter-pump intervals (B)." Paper_evidence "?" Phenotype "WBPhenotype:0000019" Life_stage "WBls:0000057" "PATO:0000460" Curator_confirmed "?" Phenotype "WBPhenotype:0000019" Life_stage "WBls:0000057" "PATO:0000460" Paper_evidence "?" Phenotype "WBPhenotype:0000019" Genotype "smg-1(cc546) I; dvIs27 X.dvIs27[pAF29(myo-3/Aβ1-42/let UTR)+pRF4(rol-6(su1006))]" Curator_confirmed "?" Phenotype "WBPhenotype:0000019" Genotype "smg-1(cc546) I; dvIs27 X.dvIs27[pAF29(myo-3/Aβ1-42/let UTR)+pRF4(rol-6(su1006))]" Paper_evidence "?" Phenotype "WBPhenotype:0000019" Caused_by_other "Abeta1-42 Beta amyloid peptide" Curator_confirmed "WBPerson712" Phenotype "WBPhenotype:0000019" Caused_by_other "Abeta1-42 Beta amyloid peptide" Paper_evidence "?" Phenotype "WBPhenotype:0000019" Strain "CL4176" Curator_confirmed "WBPerson557" Phenotype "WBPhenotype:0000019" Strain "CL4176" Paper_evidence "?" Phenotype "WBPhenotype:0000019" Picture "WBPictureID" Curator_confirmed "?" Phenotype "WBPhenotype:0000019" Picture "WBPictureID" Paper_evidence"?" Phenotype "WBPhenotype:0000019" Control_strain "CL802" Curator_confirmed "?" Phenotype "WBPhenotype:0000019" Control_strain "CL802" Paper_evidence "?"
There are a number of issues.
- In this case, the phenotype is to a transgene, not a strain. Unless the strain they are featuring is N2 or some wild type isolate, the phenotype will always go to an allele or transgene etc.
- I don't know how to configure the Curator_confirmed tag and the Paper_evidence tag - I think you've already figured this out?
- Each phenotype tag line is duplicated in an annoying way - perhaps we can clean this up
- We will need to add the tag "Picture" and "Control_strain" to the model. There is already a tag in postgres Control_isolate, but it doesn't seem to be in the model, so there is space in postgres already.
- You will need to create a Picture object for each of the images, I don't know if you want to put the picture legend in the Picture object, or if you want it in the Phenotype_info. I guess either would work.
- I will need to create a Control_strain_genotype for postgres. This info should be sent to Mary Ann rather than be dumped, we can see if we can do this with any and all Strain entries in this OA as well as in others.