Model changes

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Micropublication 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.