OA forms, tables, scripts, etc
From WormBaseWiki
Jump to navigationJump to searchOA 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 | Variation Name Server | /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl | Phenotype GO Interaction |
GO | Process GO Expression | ||
Phenotype | phenotype.obo | Phenotype Interaction Process | |
Molecule | molecule.obo from mop tables? | Phenotype Process Gene regulation, RNAi | |
Anatomy | WBbt.obo | Phenotype Process Expression | |
Lifestage | worm_development.obo | Phenotype Process Expression | |
Expression cluster | flat file | manual update to | Process |
Taxon | /home/acedb/karen/processOA/wbspecies.txt (manually updated) | /home/acedb/karen/processOA/update_obo_taxon.pl | Process |
Picture | Process | ||
Transgene | trp tables | /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl ? | |
Rearrangements | obo_oa_ontology | /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl | Phenotype Interaction |
Process | prc tables | Interaction |
Back to Caltech documentation