Difference between revisions of "Citace upload report"

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|concise||Concise Description||con_ ||Ranjana Kishore, Kimberly Van Auken||#Genes with Concise_description||||
 
|concise||Concise Description||con_ ||Ranjana Kishore, Kimberly Van Auken||#Genes with Concise_description||||
 
|-
 
|-
−
|construct||Constructs used in various classes||cns_||Karen Yook, Daniela Raciti, Xiaodong Wang||None||||
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|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||
 
|-
 
|-
 
|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||#DO_terms<br>#Gene with Disease_relevance||||
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|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||#Expr_pattern <br>#Gene with Expr_pattern<br>#Papers with Expr_pattern||||
 
|-
 
|-
−
|gene cluster||phylogenetic profile clusters||N/A||Karen||none||||
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|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||#Genes with GO_term<br>Total Gene--GO_term links||||
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|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_||Xiaodong Wang||#interaction?<br>#Interaction with Regulatory<br>#Paper with interaction? <br>#molecule with interaction?||||
 
|-
 
|-
−
|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||||
+
|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||
 
|-
 
|-
 
|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||#Microarray_experiment<br>#expression_clusters<br>#Papers with microarray_experiment <br>#papers with expression clusters||||
 
|-
 
|-
−
|molecule||Drug/Chemical/Small molecule objects ||mop_||Karen Yook ||#Molecules with RNAi<br> #Molecule with Variation<br>#Molecule with Interaction<br>#Molecule with WBProcess||||
+
|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||
 
|-
 
|-
 
|movie||Movies||mov_ ||Daniela Raciti ||none||||
 
|movie||Movies||mov_ ||Daniela Raciti ||none||||
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|person||People||two_||Cecilia||#persons||||
 
|person||People||two_||Cecilia||#persons||||
 
|-
 
|-
−
|phenotype||Annotation of phenotypes to variations, strains, rearrangements, transgenes||app_||Karen Yook||#Variations with Phenotype<br>#Variations with Phenotype_not_observed<br>#Transgenes with Phenotype<br>#Strains with Phenotype<br>#molecules with variation||||
+
|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||
 
|-
 
|-
 
|picture||figures from papers||pic_ ||Daniela Raciti||#pictures||||
 
|picture||figures from papers||pic_ ||Daniela Raciti||#pictures||||
 
|-
 
|-
−
|biological_topic||Topic curation||pro_||Karen Yook||none||||               
+
|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||               
 
|-
 
|-
−
|process_term||Process term creation||prt_ ||Karen Yook||#topics||||                   
+
|process_term||Process term creation||prt_ ||Karen Yook||#topics||see biological topic stats above||                   
 
|-
 
|-
 
|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, Wen Chen ||#RNAi with Phenotype<br>#RNAi with Phenotype_not_observed<br>#papers with rnai||||
 
|-
 
|-
−
|transgene||Transgene object curation||trp_ ||Karen Yook||#transgenes<br>#paper with transgene<br>total paper transgene links||||
+
|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||
 
|}
 
|}

Revision as of 00:01, 13 September 2014


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_ Xiaodong Wang #antibody objects
#Paper-antibody links
anatomy Anatomy terms and function N/A Raymond Lee #anatomy terms
#anatomy function objects
concise Concise Description con_ Ranjana Kishore, Kimberly Van Auken #Genes with Concise_description
construct Constructs used in various classes cns_ Karen Yook, Daniela Raciti, Xiaodong Wang None # total papers curated for construct
#new papers curated for construct
average # constructs curated/new paper
disease Worm models of human disease dis_ Ranjana Kishore #DO_terms
#Gene with Disease_relevance
exprpat Expression pattern of genes exp_ Daniela Raciti #Expr_pattern
#Gene with Expr_pattern
#Papers with Expr_pattern
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
Total Gene--GO_term links
gene regulation Gene regulation grg_ Xiaodong Wang #interaction?
#Interaction with Regulatory
#Paper with interaction?
#molecule with interaction?
gene interaction Genetic and physical interactions int_ Chris Grove, Gary Schindelman, Kimberly Van Auken, Karen Yook # interactions(total?)
#physical interactions
#genetic interactions
#predicted interactions
#papers with interactions		 #new papers curated for genetic interactions
Microarray microarray N/A Wen Chen #Microarray_experiment
#expression_clusters
#Papers with microarray_experiment
#papers with expression clusters
molecule Drug/Chemical/Small molecule objects mop_ Karen Yook #Molecules with RNAi
#Molecule with Variation
#Molecule with Interaction
#Molecule with WBProcess		 # new papers associated with a Molecule
movie Movies mov_ Daniela Raciti none
paper Papers pap_ Kimberly #papers
Total paper--gene links
person People two_ Cecilia #persons
phenotype Annotation of phenotypes to variations, strains, rearrangements, transgenes app_ Karen Yook #total Variations with Phenotype
#total Variations with Phenotype_not_observed
#total Transgenes with Phenotype
#total Strains with Phenotype
#molecules with variation		 # new papers curated for variation phenotype
average# phenotypes/new paper
picture figures from papers pic_ Daniela Raciti #pictures
biological_topic Topic curation pro_ Karen Yook none # total topics
#new topics
#topics with pathway data (data in pathway tag)
# papers associated with all topics
#new papers associated with topic
process_term Process term creation prt_ Karen Yook #topics see biological topic stats above
RNAi RNAi sequence and phenotype curation rna_ Chris Grove, Gary Schindelman, Wen Chen #RNAi with Phenotype
#RNAi with Phenotype_not_observed
#papers with rnai
transgene Transgene object curation trp_ Karen Yook #transgenes
#paper with transgene
total paper transgene links		 # new papers curated for transgenes
average # transgenes/new paper
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