Difference between revisions of "Knowledgebase Reports"

From phenoscape
(→‎Reports on kb-dev)
(→‎Reports on kb-dev)
 
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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 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).
 
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).
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** [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%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/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 phenotype assertions (taxon-phenotype annotations)]
+
* [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%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%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/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 phenotype assertions (taxon-phenotype annotations)]
+
* [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%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%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only]
Line 39: Line 40:
 
** [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%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/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 assertions (including morpholinos as genotypes)]
+
* [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%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%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/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 assertions (implied by genotype assertions)]
+
* [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%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%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only]
Line 53: Line 54:
  
 
==Reports on kb-staging==
 
==Reports on kb-staging==
−
kb-staging is currently offline for maintenance.  This will be where old tao (with no vao) will be running (so that Wasila and co. can test old tao against new tao (with vao, in kb-dev))
+
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/timestamp/ Date on which these data were loaded]
 +
* [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/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/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/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 usually not be relied upon for everyday use (however as of Dec 17, 2010, it is the most up-to-date and stable system).
+
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 [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.
 
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.
  
Line 67: Line 123:
 
* [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/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 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%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%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only]
Line 85: Line 142:
 
** [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%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/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 phenotype assertions (taxon-phenotype annotations)]
+
* [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%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%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/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 phenotype assertions (taxon-phenotype annotations)]
+
* [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%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%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only]
Line 97: Line 154:
 
** [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%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/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 assertions (including morpholinos as genotypes)]
+
* [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%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%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/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 assertions (implied by genotype assertions)]
+
* [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%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%3A0001161%22%2C%22including_parts%22%3A%20true%7D%7D%5D%7D pectoral fin and parts only]

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.

Retrieved from "https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Knowledgebase_Reports&oldid=9929"