Difference between revisions of "Knowledgebase Reports"
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==Reports on kb-staging== | ==Reports on kb-staging== | ||
This contains files that are going into production database (from 'phenex-files'); some are updated daily by curators. It is updated nightly. | This contains files that are going into production database (from 'phenex-files'); some are updated daily by curators. It is updated nightly. | ||
| − | * [http://kb-staging.phenoscape.org/OBD-WS/ | + | * [http://kb-staging.phenoscape.org/OBD-WS/timestamp/ Date on which these data were loaded] |
| − | * [http://kb-staging.phenoscape.org/OBD-WS/ | + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/publications Count of annotated publications, by higher level taxon] |
| − | * [http://kb-staging.phenoscape.org/OBD-WS/ | + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/publications?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] |
| − | * [http://kb-staging.phenoscape.org/OBD-WS/ | + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/publications?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] |
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/publications?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/characters/published Count of all published characters] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/characters/annotated Count of all annotated characters] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/characters/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/characters/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/characters/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/characterstates/published Count of all published character states] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/characterstates/annotated Count of all annotated character states] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/characterstates/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/characterstates/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/characterstates/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/otus/published Count of publication taxa (OTUs) across all publications] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/taxa/annotated Count of annotated taxa (valid taxa, i.e. terms in TTO)] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/taxa/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/taxa/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/taxa/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/phenotypes/curated Count of EQ statements curated (state to phenotype links)] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/phenotypes/annotated Count of distinct phenotypes used in taxon annotations] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/phenotypes/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/phenotypes/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/phenotypes/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/curated Count of curated phenotype assertions (taxon-phenotype annotations)] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/curated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/curated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/curated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/distinct Count of distinct phenotype assertions (taxon-phenotype annotations)] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/distinct?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/distinct?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/distinct?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/genes/annotated Count of annotated genes] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/genes/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/genes/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/genes/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/genotypes/curated Count of genotype-phenotype assertions (including morpholinos as genotypes)] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/genotypes/curated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/genotypes/curated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/genotypes/curated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/genes/distinct Count of distinct gene-phenotype assertions (implied by genotype assertions)] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/genes/distinct?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/genes/distinct?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/genes/distinct?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
| + | * [http://kb-staging.phenoscape.org/OBD-WS/report/count/phenotypes/genes/annotated Count of distinct phenotypes used in gene annotations] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/phenotypes/genes/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001184%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pelvic fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/phenotypes/genes/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only] | ||
| + | ** [http://kb-staging.phenoscape.org/OBD-WS/report/count/phenotypes/genes/annotated?query=%7B%22phenotype%22%3A%5B%7B%22entity%22%3A%7B%22id%22%3A%22TAO%3A0000434%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D skeletal system and parts only] | ||
==Reports on kb-extra== | ==Reports on kb-extra== | ||
Revision as of 18:43, 14 September 2010
Contents
Reports on production Phenoscape KB
This contains consistency-checked and author-checked files (from 'phenex-files'). It is updated irregularly (every 1-3 months).
- Relational qualities without related entities
- Monadic qualities with related entities
- Characters with only one annotated state
- Presence/absence characters without both states
Reports on kb-staging
This contains files that are going into production database (from 'phenex-files'); some are updated daily by curators. It is updated nightly.
- Date on which these data were loaded
- Count of annotated publications, by higher level taxon
- Count of all published characters
- Count of all annotated characters
- Count of all published character states
- Count of all annotated character states
- Count of publication taxa (OTUs) across all publications
- Count of annotated taxa (valid taxa, i.e. terms in TTO)
- Count of EQ statements curated (state to phenotype links)
- Count of distinct phenotypes used in taxon annotations
- Count of curated phenotype assertions (taxon-phenotype annotations)
- Count of distinct phenotype assertions (taxon-phenotype annotations)
- Count of annotated genes
- Count of genotype-phenotype assertions (including morpholinos as genotypes)
- Count of distinct gene-phenotype assertions (implied by genotype assertions)
- Count of distinct phenotypes used in gene annotations
Reports on kb-extra
This database is equivalent to staging but also includes Sandrine's data files and all incomplete files ('incomplete-files' + 'phenex-files'). It is updated nightly.
- Relational qualities without related entities
- Monadic qualities with related entities
- Characters with only one annotated state
- Presence/absence characters without both states
Reports on kb-dev
This database is used for active development and may often be broken. It should not be relied upon for everyday use.
Currently, this database is equivalent to staging but also includes Sandrine's data files.
- Date on which these data were loaded
- Count of annotated publications, by higher level taxon
- Count of all published characters
- Count of all annotated characters
- Count of all published character states
- Count of all annotated character states
- Count of publication taxa (OTUs) across all publications
- Count of annotated taxa (valid taxa, i.e. terms in TTO)
- Count of EQ statements curated (state to phenotype links)
- Count of distinct phenotypes used in taxon annotations
- Count of curated phenotype assertions (taxon-phenotype annotations)
- Count of distinct phenotype assertions (taxon-phenotype annotations)
- Count of annotated genes
- Count of genotype-phenotype assertions (including morpholinos as genotypes)
- Count of distinct gene-phenotype assertions (implied by genotype assertions)
- Count of distinct phenotypes used in gene annotations
