Knowledgebase Reports

ALL of the files (unvetted annotations from Sandrine) are not loaded on any instance

Reports on production Phenoscape KB

This contains consistency-checked and author-checked files (from 'phenex-files'). It is updated irregularly (every 1-3 months). This contains all of the data files found here. It contains the latest public versions of all ontologies at the time the data were loaded, with the exception of PATO (it currently contains an experimental PATO revision), and TAO (it contains an experimental TAO incorporating the new VAO - this will be removed at the next update of this system).

• Date on which these data were loaded
• Count of annotated publications, by higher level taxon
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of all published characters
• Count of all annotated characters
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of all published character states
• Count of all annotated character states
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of publication taxa (OTUs) across all publications
• Count of annotated taxa (valid taxa, i.e. terms in TTO)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of EQ statements curated (state to phenotype links)
• Count of distinct phenotypes used in taxon annotations
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of curated phenotype assertions (taxon-phenotype annotations)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of distinct phenotype assertions (taxon-phenotype annotations)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of annotated genes
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of genotype-phenotype assertions (including morpholinos as genotypes)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of distinct gene-phenotype assertions (implied by genotype/morpholino assertions)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of distinct phenotypes used in gene annotations
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only

Reports on kb-staging

This contains consistency-checked and author-checked files (from 'phenex-files'). It is updated irregularly (every 1-3 months). This contains all of the data files found here. It contains the latest public versions of all ontologies at the time the data were loaded, with the exception of PATO (it currently contains an experimental PATO revision).

• Date on which these data were loaded
• Count of annotated publications, by higher level taxon
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of all published characters
• Count of all annotated characters
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
  • Ostarioclupeomorpha only
• Count of all published character states
• Count of all annotated character states
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
  • Ostarioclupeomorpha only
• Count of publication taxa (OTUs) across all publications
• Count of annotated taxa (valid taxa, i.e. terms in TTO)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
  • Ostarioclupeomorpha only THIS QUERY HAS A BUG (NOT LIMITED TO TAXA WITH PHENOTYPES - IT IS BEING INVESTIGATED!!!
• Count of EQ statements curated (state to phenotype links)
• Count of distinct phenotypes used in taxon annotations
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
  • Ostarioclupeomorpha only
• Count of curated phenotype assertions (taxon-phenotype annotations)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
  • Ostarioclupeomorpha only
• Count of distinct phenotype assertions (taxon-phenotype annotations)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
  • Ostarioclupeomorpha only
• Count of annotated genes
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of genotype-phenotype assertions (including morpholinos as genotypes)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of distinct gene-phenotype assertions (implied by genotype/morpholino assertions)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of distinct phenotypes used in gene annotations
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only

Reports on kb-dev

This database is used for active development and may often be broken. It should usually not be relied upon for everyday use. This contains all of the data files found here. It contains the latest public versions of all ontologies at the time the data were loaded, with the exception of PATO (it currently contains an experimental PATO revision). It will have the tao with the vao ('new tao') for testing.

• Date on which these data were loaded
• Count of annotated publications, by higher level taxon
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of all published characters
• Count of all annotated characters
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of all published character states
• Count of all annotated character states
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of publication taxa (OTUs) across all publications
• Count of annotated taxa (valid taxa, i.e. terms in TTO)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of EQ statements curated (state to phenotype links)
• Count of distinct phenotypes used in taxon annotations
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of curated phenotype assertions (taxon-phenotype annotations)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of distinct phenotype assertions (taxon-phenotype annotations)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of annotated genes
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of genotype-phenotype assertions (including morpholinos as genotypes)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of distinct gene-phenotype assertions (implied by genotype/morpholino assertions)
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only
• Count of distinct phenotypes used in gene annotations
  • pelvic fin and parts only
  • pectoral fin and parts only
  • skeletal system and parts only

kb-old

This database has the old interface - its data are frozen as of May 2010.