OA forms, tables, scripts, etc
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Revision as of 21:51, 3 October 2013 by Kyook (talk | contribs) (→OA form ontology/autocomplete dependencies and update scripts)
OA form summaries
OA form | Function (Datatype) | Postgres Tables | Dumper Script | Ontologies used | Other dependencies | Curator | Other remarks |
antibody | Antibody objects | /home/acedb/xiaodong/antibody/use_package.pl | Paper Gene Laboratory |
Xiaodong Wang | |||
concise | Concise Description | con_ | /home/acedb/kimberly/citace_upload/concise/wrapper.pl and /home/postgres/work/citace_upload/concise/dump_concise.pl | n/a | n/a | 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 | GO pipeline is currently in flux as we migrate to using Protein2GO | ||||
genereg | Gene regulation | grg_ grg_tables |
/home/postgres/work/citace_upload/gene_regulation/use_package.pl | Paper Interaction RNAi Antibody Transgene Variation Rearrangement Expr_pattern Sentence Gene Molecule Sequence Anatomy Lifestage |
/home/postgres/work/citace_upload/gene_regulation/get_gene_regulation_ace.pm (Required Perl module) |
Xiaodong Wang | |
interaction | Genetic and physical interactions | int_ int_tables |
/home/postgres/work/citace_upload/interaction/use_package.pl | Paper Gene Variation Phenotype Person Laboratory Antibody Rearrangement Transgene RNAi |
/home/acedb/xiaodong/assigning_interaction_ids/assign_interaction_ids.pl Nightly cronjob script to assign Interaction IDs to PGIDs that do not already have one |
Chris Grove, Gary Schindelman, Kimberly Van Auken, Karen Yook | Only one PGID per Interaction object. Some physical interactions are currently in BioGrid and will need to be migrated to postgres. |
molecule | Drug/Chemical/Small molecule objects | mop_ mop_tables |
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 | pro_ pro_tables |
/home/acedb/karen/process/use_process_curation_package.pl | Paper Person Phenotype Gene Molecule Anatomy Lifestage Expression cluster Taxon Picture |
Karen Yook | ||
process term | Creation of process names | prt_ prt_tables |
/home/acedb/karen/process/use_process_package.pl | Paper GO |
Karen Yook | ||
rnai | RNAi phenotype curation | rna_ rna_tables |
/home/postgres/work/citace_upload/rnai/use_package.pl | Paper Lifestage Phenotype Molecule Person Strain Laboratory PCR Product |
/home/postgres/work/citace_upload/rnai/get_rnai_ace.pm (Required Perl module) |
Chris Grove, Gary Schindelman, Wen Chen | Possible to have multiple PGIDs per WBRNAi object |
transgene | Transgene object curation | trp_ trp_tables |
acedb/karen/transgene ./use_package.pl | Gene Paper Laboratory Person |
/postgres/work/pgpopulation/textpresso/transgene/update_textpreso_transgene.pl which makes http://textpresso-dev.caltech.edu/transgene/ /home/citpub/Karen/TgSummary/getNewTg.pl parses results into trp_tables |
Karen Yook |
OA form ontology/autocomplete dependencies and update scripts
Any field within an OA that works by autocomplete is in a postgres table. Many of them are either obo tables or taken from other OA datatype tables. obo tables are obo_data_<datatype>, obo_syn_<datatype> or obo_name_<datatype>. Other OA datatype tables include trp_<tables>, mop_, grg_, abp_. Exceptions are person, paper, gene data as these are not curated through an OA.
Last updated | Ontology/Autocomplete | postres table | Source(s) | Updating scripts | Used in OA |
WBPaper | pap_tables (non OA) | NCBI pap_tables paper editor |
/home/postgres/work/pgpopulation/pap_papers/new_papers/pap_match.pm the paper editor uses this module to look at NCBI to populate pap_tables |
All | |
201309 | Gene | gin_tables (non OA) | genename server (for most info)/WS (for CDS etc) |
WBGene_information_and_status_pipeline | Most |
Person | two_tables (non OA) | cecilia person editor | manual for author, on-the-fly scripts for abstracts | Most | |
201309 | Variation object | obo_name_variation (WBVarID + public name) obo_syn_variation -delete |
variation name server minus junk variations (total_variations.txt -Variation_gene.txt, -dead variation, -gk(6+digits), -deBono alleles) | updateVariationObo addToVariationObo (routines in the generic.cgi) |
Phenotype GeneReg Interaction GO Movie |
201309 | Variation term_info | obo_data_variation | jolene/WS_AQL_queries/Variation_gene.txt (latest release for variation-gene mappings) Variation Name Server (immediate variation updates--no gene mappings |
generic.cgi?updateVariationObo | Phenotype GeneReg Interaction GO Movie |
GO | obo_name_goid and obo_syn_goid | 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 | phenotype_ontology_obo (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 | |||
ChEBI | Molecule | ||||
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 | ||
201309 | 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 | ||||
2011? | Transgene | /home/acedb/jolene/WS_AQL_queries/transgene_summary.txt manual query of latest release for term info in OA changed to retrieve data from trp_tables |
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? | ||
201309 | Rearrangement object | /home/acedb/jolene/WS_AQL_queries/rearr_simple | http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? | Phenotype Interaction | |
201309 | Rearrangement term info | /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 | |||
<2012 | Laboratory | obo_data_laboratory | /home/acedb/cron/populate_gin.pl | Transgene Expression pattern Interaction Phenotype /data1/Users/arunr/Curator_related/Alleles/scripts (for Mary Ann's alleles) | |
201309 | Clone object | /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 Transgene | |
201309 | Clone term info | /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 Transgene | |
201309 | Strain object | /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 Phenotype | |
201309 | Strain term info | /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 Phenotype | |
201309 | Expression_cluster | /home/acedb/jolene/WS_AQL_queries/strains.txt manually queried from latest release change to get from spica /home/citpub/CitaceMirror/citace/ after each upload |
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo? | Process_curation | |
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 |
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