Difference between revisions of "Citace upload report"

From WormBaseWiki
Jump to navigationJump to search
 
(8 intermediate revisions by 3 users not shown)
Line 13: Line 13:
 
|'''Data class/type'''||'''Curation focus'''||'''Postgres Tables'''<br>([[all OA tables | oa tables]])||'''Curator'''||'''Current Citace dump stat'''||'''Requested stat(s) for Citace report'''||'''Requested stats for build release'''||
 
|'''Data class/type'''||'''Curation focus'''||'''Postgres Tables'''<br>([[all OA tables | oa tables]])||'''Curator'''||'''Current Citace dump stat'''||'''Requested stat(s) for Citace report'''||'''Requested stats for build release'''||
 
|-
 
|-
−
|antibody||C. elegans antibodies||abp_ ||Xiaodong Wang||#antibody objects<br>#Paper-antibody links||||
+
|Antibody||C. elegans antibodies||abp_ ||Daniela Raciti||find Antibody<br>Paper with Antibody<br>Total Paper--Antibody links||||
 
|-
 
|-
−
|anatomy||Anatomy terms and function||N/A||Raymond Lee||#anatomy terms<br>#anatomy function objects||||
+
|anatomy||Anatomy terms and function||N/A||Raymond Lee||find Anatomy_term<br>find Anatomy_function||||
 
|-
 
|-
−
|concise||Concise Description||con_ ||Ranjana Kishore, Kimberly Van Auken||#Genes with Concise_description||||
+
|concise||Concise Description||con_ ||Ranjana Kishore, Kimberly Van Auken||Gene with Concise_description||Gene with |Automated_description<br>Papers for Concise_description<br>Papers for Automated_description||||
 
|-
 
|-
−
|construct||Constructs used in various classes||cns_||Karen Yook, Daniela Raciti, Xiaodong Wang||None||# total papers curated for construct<br>#new papers curated for construct <br> average # constructs curated/new paper||
+
|construct||Constructs used in various classes||cns_||Daniela Raciti||None||# total papers curated for |construct<br>#new papers curated for construct <br> average # constructs curated/new paper||
 
|-
 
|-
−
|disease||Worm models of human disease||dis_ ||Ranjana Kishore||#DO_terms<br>#Gene with Disease_relevance||||
+
|disease||Worm models of human disease||dis_ ||Ranjana Kishore||find DO_term<br>Gene with Experimental_model<br>Gene with |Disease_relevance||Papers for Gene with Experimental_model<br>Papers for Gene with Disease_relevance||||
 
|-
 
|-
−
|exprpat||Expression pattern of genes||exp_ ||Daniela Raciti||#Expr_pattern <br>#Gene with Expr_pattern<br>#Papers with Expr_pattern||||
+
|exprpat||Expression pattern of genes||exp_ ||Daniela Raciti||find Expr_pattern <br>Gene with Expr_pattern<br>Paper with Expr_pattern||||
 
|-
 
|-
 
|gene cluster||phylogenetic profile clusters||N/A||Karen||none||# gene cluster objects||
 
|gene cluster||phylogenetic profile clusters||N/A||Karen||none||# gene cluster objects||
 
|-
 
|-
−
|go||Gene ontology annotation||||Kimberly Van Auken, Ranjana Kishore||#Genes with GO_term<br>Total Gene--GO_term links||||
+
|go||Gene ontology annotation||||Kimberly Van Auken, Ranjana Kishore||Gene with GO_term<br>Total Gene--GO_term links||||
 
|-
 
|-
−
|gene regulation||Gene regulation||grg_||Xiaodong Wang||#interaction?<br>#Interaction with Regulatory<br>#Paper with interaction? <br>#molecule with interaction?||||
+
|gene regulation||Gene regulation||grg_||Chris Grove||Interaction with Regulatory||||
 
|-
 
|-
−
|gene interaction||Genetic and physical interactions||int_ ||Chris Grove, Gary Schindelman, Kimberly Van Auken, Karen Yook||# interactions(total?)<br>#physical interactions<br>#genetic interactions<br>#predicted interactions<br>#papers with interactions||#new papers curated for genetic interactions||
+
|gene interaction||Genetic and physical interactions||int_ ||Chris Grove, Gary Schindelman, Kimberly Van Auken, Karen Yook||find |Interaction<br>Interaction with Physical<br>Interaction with Genetic<br>Interaction with Predicted<br>Paper with Interaction||||
 
|-
 
|-
−
|Microarray||microarray||N/A||Wen Chen||#Microarray_experiment<br>#expression_clusters<br>#Papers with microarray_experiment <br>#papers with expression clusters||||
+
|Microarray||microarray||N/A||Wen Chen||find Microarray_experiment||||
 
|-
 
|-
−
|molecule||Drug/Chemical/Small molecule objects ||mop_||Karen Yook ||#Molecules with RNAi<br> #Molecule with Variation<br>#Molecule with Interaction<br>#Molecule with WBProcess||# new papers associated with a Molecule||
+
|Expression_cluster||Expression Cluster||N/A||Wen Chen||find Expression_cluster||||
 +
|-
 +
|Analysis||Proteomics Analysis||N/A||Wen Chen||find Analysis MassSpec*||||
 +
|-
 +
|molecule||Drug/Chemical/Small molecule objects ||mop_||Karen Yook ||Molecule with RNAi<br>Molecule with Variation<br>Molecule with |Interaction<br>Molecule with WBProcess||||
 
|-
 
|-
 
|movie||Movies||mov_ ||Daniela Raciti ||none||||
 
|movie||Movies||mov_ ||Daniela Raciti ||none||||
 
|-
 
|-
−
|paper||Papers||pap_||Kimberly||#papers<br>Total paper--gene links||||
+
|paper||Papers||pap_||Kimberly||find Paper<br>Total Paper--Gene links||||
 
|-
 
|-
−
|person||People||two_||Cecilia||#persons||||
+
|person||People||two_||Cecilia||find Person||||
 
|-
 
|-
−
|phenotype||Annotation of phenotypes to variations, strains, rearrangements, transgenes||app_||Karen Yook||#total Variations with Phenotype<br>#total Variations with Phenotype_not_observed<br>#total Transgenes with Phenotype<br>#total Strains with Phenotype<br>#molecules with variation||# new papers curated for variation phenotype<br>average# phenotypes/new paper||
+
|phenotype||Annotation of phenotypes to variations, strains, rearrangements, transgenes||app_||Gary Schindelman||Variation with Phenotype<br>Variation |with Phenotype_not_observed<br>Transgene with Phenotype<br>Strain with Phenotype||total paper--variation-phenotype link<br>total |variation-|phenotype link<br>||
 
|-
 
|-
−
|picture||figures from papers||pic_ ||Daniela Raciti||#pictures||||
+
|picture||figures from papers||pic_ ||Daniela Raciti||find Picture||||
 
|-
 
|-
−
|biological_topic||Topic curation||pro_||Karen Yook||none||# total topics<br>#new topics<br>#topics with pathway data (data in pathway tag)<br># papers associated with all topics <br>#new papers associated with topic||               
+
|biological_topic||Topic curation||pro_||Karen Yook||none||total topics--gene links<br>#total topic--pathway links<br># total paper--topic |links||               
 
|-
 
|-
−
|process_term||Process term creation||prt_ ||Karen Yook||#topics||see biological topic stats above||                   
+
|process_term||Process term creation||prt_ ||Karen Yook||find WBProcess||||                   
 
|-
 
|-
−
|RNAi||RNAi sequence and phenotype curation||rna_||Chris Grove, Gary Schindelman, Wen Chen ||#RNAi with Phenotype<br>#RNAi with Phenotype_not_observed<br>#papers with rnai||||
+
|RNAi||RNAi sequence and phenotype curation||rna_||Chris Grove, Gary Schindelman||find RNAi<br>RNAi with Phenotype<br>
 +
|RNAi with Phenotype_not_observed<br>Paper with RNAi||||
 
|-
 
|-
−
|transgene||Transgene object curation||trp_ ||Karen Yook||#transgenes<br>#paper with transgene<br>total paper transgene links||# new papers curated for transgenes <br>average # transgenes/new paper||
+
|transgene||Transgene object curation||trp_ ||Daniela Raciti||find Transgene<br>Paper with Transgene<br>Total Paper--Transgene links||||
 
|}
 
|}

Latest revision as of 18:13, 6 October 2017


Goals for upload report

  • Summary of the uploaded data classes/objects - this summary should be blind to requests from curators and should alert Caltech to missing data classes or severe changes in numbers of objects within preexisting data classes
  • Summary of curation work - this summary should be curator driven, in some cases the summary will require a more involved aceperl query to get at the actual annotation rather than a straight data class object number.

Issues/Discussion

Data classes/types curated and sent to Hinxton

For each data type, please indicate what information you want to know upon Citace data testing and what information you want to include the report to Hinxton.

Data class/type Curation focus Postgres Tables
( oa tables)		 Curator Current Citace dump stat Requested stat(s) for Citace report Requested stats for build release
Antibody C. elegans antibodies abp_ Daniela Raciti find Antibody
Paper with Antibody
Total Paper--Antibody links
anatomy Anatomy terms and function N/A Raymond Lee find Anatomy_term
find Anatomy_function
concise Concise Description con_ Ranjana Kishore, Kimberly Van Auken Gene with Concise_description Automated_description
Papers for Concise_description
Papers for Automated_description
construct Constructs used in various classes cns_ Daniela Raciti None construct
#new papers curated for construct
average # constructs curated/new paper
disease Worm models of human disease dis_ Ranjana Kishore Disease_relevance Papers for Gene with Experimental_model
Papers for Gene with Disease_relevance
exprpat Expression pattern of genes exp_ Daniela Raciti find Expr_pattern
Gene with Expr_pattern
Paper with Expr_pattern
gene cluster phylogenetic profile clusters N/A Karen none # gene cluster objects
go Gene ontology annotation Kimberly Van Auken, Ranjana Kishore Gene with GO_term
Total Gene--GO_term links
gene regulation Gene regulation grg_ Chris Grove Interaction with Regulatory
gene interaction Genetic and physical interactions int_ Chris Grove, Gary Schindelman, Kimberly Van Auken, Karen Yook Interaction
Interaction with Physical
Interaction with Genetic
Interaction with Predicted
Paper with Interaction
Microarray microarray N/A Wen Chen find Microarray_experiment
Expression_cluster Expression Cluster N/A Wen Chen find Expression_cluster
Analysis Proteomics Analysis N/A Wen Chen find Analysis MassSpec*
molecule Drug/Chemical/Small molecule objects mop_ Karen Yook Interaction
Molecule with WBProcess
movie Movies mov_ Daniela Raciti none
paper Papers pap_ Kimberly find Paper
Total Paper--Gene links
person People two_ Cecilia find Person
phenotype Annotation of phenotypes to variations, strains, rearrangements, transgenes app_ Gary Schindelman with Phenotype_not_observed
Transgene with Phenotype
Strain with Phenotype		 variation-|phenotype link
picture figures from papers pic_ Daniela Raciti find Picture
biological_topic Topic curation pro_ Karen Yook none links
process_term Process term creation prt_ Karen Yook find WBProcess
RNAi RNAi sequence and phenotype curation rna_ Chris Grove, Gary Schindelman find RNAi
RNAi with Phenotype
 RNAi with Phenotype_not_observed
Paper with RNAi
transgene Transgene object curation trp_ Daniela Raciti find Transgene
Paper with Transgene
Total Paper--Transgene links
Retrieved from "https://wiki.wormbase.org/index.php?title=Citace_upload_report&oldid=31811"