Difference between revisions of "OA forms, tables, scripts, etc"

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|Person || || ||All?
 
|Person || || ||All?
 
|-
 
|-
−
|Variation ||Variation Name Server||/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl ||Phenotype<br> GO<br> Interaction
+
|Variation ||/home/acedb/jolene/WS_AQL_queries/Variation_gene.txt queried from the latest release for variation-gene mappings and http://www.sanger.ac.uk/cgi-bin/Projects/C_elegans/nameserver_json.pl?domain=Variation -Variation Name Server for immediate variation updates (no gene mappings)||http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo ||Phenotype<br> GO<br> Interaction
 
|-
 
|-
−
|GO || || ||Process<br> GO<br> Expression
+
|GO ||http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo||/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl||Process<br> GO<br> Expression
 
|-  
 
|-  
−
|Phenotype||phenotype.obo || ||Phenotype<br> Interaction<br> Process
+
|Phenotype||http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi (from CVS on spica?)||/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl||Phenotype<br> Interaction<br> Process
 
|-  
 
|-  
 
|Molecule||molecule.obo from mop tables? || ||Phenotype<br> Process<br> Gene regulation, RNAi<br>
 
|Molecule||molecule.obo from mop tables? || ||Phenotype<br> Process<br> Gene regulation, RNAi<br>
 
|-
 
|-
−
|Anatomy||WBbt.obo || ||Phenotype<br>Process<br>Expression
+
|Anatomy||https://github.com/raymond91125/Wao/raw/master/WBbt.obo||/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl ||Phenotype<br> Process<br> Expression
 
|-
 
|-
−
|Lifestage||worm_development.obo || ||Phenotype<br>Process<br>Expression
+
|Lifestage||https://raw.github.com/draciti/Life-stage-obo/master/worm_development.obo||/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl||Phenotype<br>Process<br>Expression
 
|-
 
|-
−
|Expression cluster||flat file ||manual update to ||Process
+
|Expression cluster||/home/acedb/jolene/WS_AQL_queries/expr_cluster.txt manually queried from latest release ||http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? ||Process
 
|-
 
|-
 
|Taxon||/home/acedb/karen/processOA/wbspecies.txt (manually updated)||/home/acedb/karen/processOA/update_obo_taxon.pl||Process
 
|Taxon||/home/acedb/karen/processOA/wbspecies.txt (manually updated)||/home/acedb/karen/processOA/update_obo_taxon.pl||Process
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|Picture|| || ||Process
 
|Picture|| || ||Process
 
|-
 
|-
−
|Transgene||trp tables||/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl ?||
+
|Transgene||/home/acedb/jolene/WS_AQL_queries/transgene_summary.txt manual query of latest release for term info in OA, trp_transgenes(?) ||http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? ||
 
|-
 
|-
−
|Rearrangements||obo_oa_ontology||/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl ||Phenotype<br>Interaction
+
|Rearrangements||/home/acedb/jolene/WS_AQL_queries/rearr_simple||http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? ||Phenotype<br>Interaction
 
|-
 
|-
 
|Process||prc tables || ||Interaction
 
|Process||prc tables || ||Interaction
 
|-
 
|-
−
|Laboratory||obo_data_laboratory||updated based on the latest release through populate_gin.pl||Transgene<br> Expression Pattern<br>Interaction<br>Phenotype
+
|Laboratory||obo_data_laboratory||/home/acedb/cron/populate_gin.pl||Transgene<br> Expression pattern<br>Interaction<br>Phenotype
 +
|-
 +
|Clone||/home/acedb/jolene/WS_AQL_queries/clone_info.txt manually queried from latest release||http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? ||Expression pattern
 +
|-
 +
|Strain||/home/acedb/jolene/WS_AQL_queries/strains.txt manually queried from latest release||http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? ||Expression pattern
 +
|-
 +
|Chebi||ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo||/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl||Molecule
 +
|-
 +
|Human Disease DO (humando)||https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/HumanDO.obo||/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl||Human disease
 
|}
 
|}
  

Revision as of 00:50, 2 February 2013

OA form summaries

OA form Function (Datatype) Postgres Tables Scripts Ontologies used Other dependencies Curator Other remarks
antibody Antibody objects Xiaodong Wang
concise Concise Description Ranjana Kishore, Kimberly Van Auken
disease Worm models of human disease dis_ Ranjana Kishore
exprpat Expression pattern of genes expr_ /home/acedb/draciti/oa_expr_ace_dumper/use_package.pl Paper
Gene
Anatomy
GO
Lifestage
Type
Transgene
Antibody
Clone
Strain
Laboratory
 Daniela Raciti
gene class Concise description of gene classes Gene
Paper		 Karen Yook
go Gene ontology annotation Kimberly Van Auken, Ranjana Kishore
genereg Gene regulation Xiaodong Wang
interaction Genetic and physical interactions int_ Paper
Gene
Variation
Phenotype
Person
Laboratory
Antibody
Rearrangement
Transgene
RNAi
 Chris Grove, Gary Schindelman, Kimberly Van Auken, Karen Yook
molecule Drug/Chemical/Small molecule objects mop_ acedb/karen/Molecule/dump_molecule_ace.pl
acedb/karen/Molecule/database.ace		 Paper
Chebi
 Karen Yook
movie Movies mov_ /home/acedb/draciti/oa_movie_ace_dumper use_movie_package.pl Paper
Expr_pattern
Variation
 Daniela Raciti
phenotype Annotation of phenotypes to variations, strains, rearrangements, transgenes app_
app_tables		 acedb/work/allele_phenotype/use_package.pl
acedb/karen/phenote/paper_object/get_paper_object.pl		 Paper
Person
Variation
Rearrangements
Transgene
Gene
Phenotype
Molecule
Anatomy
Lifestage
Laboratory		 Karen Yook
picture Paper figure pic_ /home/acedb/draciti/oa_picture_ace_dumper/dump_picture_ace.pl Paper
Person
Expr_pattern
Anatomy
GO
Lifestage
Cropped_from
 Daniela Raciti
process Process curation prc_ /home/acedb/karen/process/use_process_curation_package.pl Paper
Person
GO
Phenotype
Gene
Molecule
Anatomy
Lifestage
Expression cluster
Taxon
Picture		 Karen Yook
process term Creation of process names pro_ /home/acedb/karen/process/use_process_package.pl Paper Karen Yook
rnai RNAi phenotype curation Chris Grove, Gary Schindelman, Wen Chen
transgene Transgene object curation trp_
trp_tables		 acedb/karen/transgene ./use_package.pl Gene
Paper
Laboratory
Person		 Karen Yook


OA form ontology/dependency sources

Ontology Source Script updating information from source Used in OA form
Paper paper.obo All
Gene Gene name server All?
Person All?
Variation /home/acedb/jolene/WS_AQL_queries/Variation_gene.txt queried from the latest release for variation-gene mappings and http://www.sanger.ac.uk/cgi-bin/Projects/C_elegans/nameserver_json.pl?domain=Variation -Variation Name Server for immediate variation updates (no gene mappings) http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo Phenotype
GO
Interaction
GO http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl Process
GO
Expression
Phenotype http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi (from CVS on spica?) /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl Phenotype
Interaction
Process
Molecule molecule.obo from mop tables? Phenotype
Process
Gene regulation, RNAi
Anatomy https://github.com/raymond91125/Wao/raw/master/WBbt.obo /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl Phenotype
Process
Expression
Lifestage https://raw.github.com/draciti/Life-stage-obo/master/worm_development.obo /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl Phenotype
Process
Expression
Expression cluster /home/acedb/jolene/WS_AQL_queries/expr_cluster.txt manually queried from latest release http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? Process
Taxon /home/acedb/karen/processOA/wbspecies.txt (manually updated) /home/acedb/karen/processOA/update_obo_taxon.pl Process
Picture Process
Transgene /home/acedb/jolene/WS_AQL_queries/transgene_summary.txt manual query of latest release for term info in OA, trp_transgenes(?) http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo?
Rearrangements /home/acedb/jolene/WS_AQL_queries/rearr_simple http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? Phenotype
Interaction
Process prc tables Interaction
Laboratory obo_data_laboratory /home/acedb/cron/populate_gin.pl Transgene
Expression pattern
Interaction
Phenotype
Clone /home/acedb/jolene/WS_AQL_queries/clone_info.txt manually queried from latest release http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? Expression pattern
Strain /home/acedb/jolene/WS_AQL_queries/strains.txt manually queried from latest release http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? Expression pattern
Chebi ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl Molecule
Human Disease DO (humando) https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/HumanDO.obo /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl Human disease


app_tables


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