Difference between revisions of "Knowledgebase Reports"

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ALL of the files (unvetted annotations from Sandrine) are not loaded on any instance
 
==Reports on production Phenoscape KB==
 
==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 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 [http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/data/phenex-files/ 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 [http://www.duke.edu/~jpb15/quality.obo 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).
  
−
* [http://kb.phenoscape.org/OBD-WS/statistics/consistencyreports/relationalqualitieswithoutrelatedentities Relational qualities without related entities]
+
* [http://kb.phenoscape.org/OBD-WS/timestamp/ Date on which these data were loaded]
−
* [http://kb.phenoscape.org/OBD-WS/statistics/consistencyreports/nonrelationalqualitieswithrelatedentities Monadic qualities with related entities]
+
* [http://kb.phenoscape.org/OBD-WS/report/count/publications Count of annotated publications, by higher level taxon]
−
* [http://kb.phenoscape.org/OBD-WS/statistics/consistencyreports/characterswithonlyoneannotatedstate Characters with only one annotated state]
+
** [http://kb.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.phenoscape.org/OBD-WS/statistics/consistencyreports/characterswithonlyoneoftwopossibleannotations Presence/absence characters without both states]
+
** [http://kb.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.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.phenoscape.org/OBD-WS/report/count/characters/published Count of all published characters]
 +
* [http://kb.phenoscape.org/OBD-WS/report/count/characters/annotated Count of all annotated characters]
 +
** [http://kb.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.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.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.phenoscape.org/OBD-WS/report/count/characterstates/published Count of all published character states]
 +
* [http://kb.phenoscape.org/OBD-WS/report/count/characterstates/annotated Count of all annotated character states]
 +
** [http://kb.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.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.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.phenoscape.org/OBD-WS/report/count/otus/published Count of publication taxa (OTUs) across all publications]
 +
* [http://kb.phenoscape.org/OBD-WS/report/count/taxa/annotated Count of annotated taxa (valid taxa, i.e. terms in TTO)]
 +
** [http://kb.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.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.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.phenoscape.org/OBD-WS/report/count/phenotypes/curated Count of EQ statements curated (state to phenotype links)]
 +
* [http://kb.phenoscape.org/OBD-WS/report/count/phenotypes/annotated Count of distinct phenotypes used in taxon annotations]
 +
** [http://kb.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.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.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.phenoscape.org/OBD-WS/report/count/annotations/taxa/curated Count of curated taxon phenotype annotations]
 +
** [http://kb.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.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.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.phenoscape.org/OBD-WS/report/count/annotations/taxa/distinct Count of distinct taxon phenotype annotations]
 +
** [http://kb.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.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.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.phenoscape.org/OBD-WS/report/count/genes/annotated Count of annotated genes]
 +
** [http://kb.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.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.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.phenoscape.org/OBD-WS/report/count/annotations/genotypes/curated Count of genotype phenotype annotations (including morpholinos as genotypes)]
 +
** [http://kb.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.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.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.phenoscape.org/OBD-WS/report/count/annotations/genes/distinct Count of distinct gene phenotype annotations (these are implied by genotype and morpholino annotations)]
 +
** [http://kb.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.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.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.phenoscape.org/OBD-WS/report/count/phenotypes/genes/annotated Count of distinct phenotypes used in gene annotations]
 +
** [http://kb.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.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.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-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 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 [http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/data/phenex-files/ 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 [http://www.duke.edu/~jpb15/quality.obo experimental PATO revision]).
−
* [http://kb-staging.phenoscape.org/OBD-WS/statistics/consistencyreports/relationalqualitieswithoutrelatedentities Relational qualities without related entities]
 
−
* [http://kb-staging.phenoscape.org/OBD-WS/statistics/consistencyreports/nonrelationalqualitieswithrelatedentities Monadic qualities with related entities]
 
−
* [http://kb-staging.phenoscape.org/OBD-WS/statistics/consistencyreports/characterswithonlyoneannotatedstate Characters with only one annotated state]
 
−
* [http://kb-staging.phenoscape.org/OBD-WS/statistics/consistencyreports/characterswithonlyoneoftwopossibleannotations Presence/absence characters without both states]
 
  
−
==Reports on kb-extra==
+
* [http://kb-staging.phenoscape.org/OBD-WS/timestamp/ Date on which these data were loaded]
−
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.
+
* [http://kb-staging.phenoscape.org/OBD-WS/report/count/publications Count of annotated publications, by higher level taxon]
−
* [http://kb-dev.phenoscape.org:8080/obd-expt/statistics/consistencyreports/relationalqualitieswithoutrelatedentities Relational qualities without related entities]
+
** [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-dev.phenoscape.org:8080/obd-expt/statistics/consistencyreports/nonrelationalqualitieswithrelatedentities Monadic qualities with related entities]
+
** [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-dev.phenoscape.org:8080/obd-expt/statistics/consistencyreports/characterswithonlyoneannotatedstate Characters with only one annotated state]
+
** [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-dev.phenoscape.org:8080/obd-expt/statistics/consistencyreports/characterswithonlyoneoftwopossibleannotations Presence/absence characters without both states]
+
* [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/characters/annotated?query=%7B%22taxon%22%3A%5B%7B%22id%22%3A%22TTO%3A253%22%7D%5D%7D Ostarioclupeomorpha 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/characterstates/annotated?query=%7B%22taxon%22%3A%5B%7B%22id%22%3A%22TTO%3A253%22%7D%5D%7D Ostarioclupeomorpha 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/taxa/annotated?query=%7B%22taxon%22%3A%5B%7B%22id%22%3A%22TTO%3A253%22%7D%5D%7D Ostarioclupeomorpha 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/phenotypes/annotated?query=%7B%22taxon%22%3A%5B%7B%22id%22%3A%22TTO%3A253%22%7D%5D%7D Ostarioclupeomorpha only]
 +
* [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/curated Count of curated 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/curated?query=%7B%22taxon%22%3A%5B%7B%22id%22%3A%22TTO%3A253%22%7D%5D%7D Ostarioclupeomorpha only]
 +
* [http://kb-staging.phenoscape.org/OBD-WS/report/count/annotations/taxa/distinct Count of distinct 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/annotations/taxa/distinct?query=%7B%22taxon%22%3A%5B%7B%22id%22%3A%22TTO%3A253%22%7D%5D%7D Ostarioclupeomorpha 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 annotations (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 annotations (these are implied by genotype and morpholino annotations)]
 +
** [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-dev==
 
==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.
+
This database is used for active development and may often be broken. It should usually not be relied upon for everyday use.
−
* [http://kb-dev.phenoscape.org/OBD-WS/report/count/publication Count of annotated publications, by higher level taxon]
+
This contains all of the data files found [http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/data/phenex-files/ 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 [http://www.duke.edu/~jpb15/quality.obo experimental PATO revision]).  It will have the tao with the vao ('new tao') for testing.
 +
 
 +
* [http://kb-dev.phenoscape.org/OBD-WS/timestamp/ Date on which these data were loaded]
 +
* [http://kb-dev.phenoscape.org/OBD-WS/report/count/publications Count of annotated publications, by higher level taxon]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/characters/published Count of all published characters]
 +
* [http://kb-dev.phenoscape.org/OBD-WS/report/count/characters/annotated Count of all annotated characters]
 +
** [http://kb-dev.phenoscape.org/OBD-WS/report/count/characters/annotated?query=%7B%22phenotype%22%3A%5B%7B%22quality%22%3A%7B%22id%22%3A%22PATO%3A0000462%22%7D%7D%2C%20%7B%22quality%22%3A%7B%22id%22%3A%22PATO%3A0000467%22%7D%7D%5D%2C%20%22match_all_phenotypes%22%3A%20false%7D present or absent quality only]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/characterstates/published Count of all published character states]
 +
* [http://kb-dev.phenoscape.org/OBD-WS/report/count/characterstates/annotated Count of all annotated character states]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/otus/published Count of publication taxa (OTUs) across all publications]
 +
* [http://kb-dev.phenoscape.org/OBD-WS/report/count/taxa/annotated Count of annotated taxa (valid taxa, i.e. terms in TTO)]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/phenotypes/curated Count of EQ statements curated (state to phenotype links)]
 +
* [http://kb-dev.phenoscape.org/OBD-WS/report/count/phenotypes/annotated Count of distinct phenotypes used in taxon annotations]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/annotations/taxa/curated Count of curated taxon phenotype annotations]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/annotations/taxa/distinct Count of distinct taxon phenotype annotations]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/genes/annotated Count of annotated genes]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/annotations/genotypes/curated Count of genotype phenotype annotations (including morpholinos as genotypes)]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/annotations/genes/distinct Count of distinct gene phenotype annotations (these are implied by genotype and morpholino annotations)]
 +
** [http://kb-dev.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-dev.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-dev.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-dev.phenoscape.org/OBD-WS/report/count/phenotypes/genes/annotated Count of distinct phenotypes used in gene annotations]
 +
** [http://kb-dev.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-dev.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-dev.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]
 +
 
 +
==kb-old==
 +
This database has the old interface - its data are frozen as of May 2010.
  
 
[[Category:Curation]]
 
[[Category:Curation]]
 
[[Category:Database]]
 
[[Category:Database]]
 
[[Category:Queries]]
 
[[Category:Queries]]

Latest revision as of 15:32, 3 May 2012

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).

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).

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.

kb-old

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

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