Difference between revisions of "Phenoscape KB"

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(Data sources)
(Data sources)
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* [https://github.com/phenoscape/phenoscape-data/tree/master/Curation%20Files Evolutionary data matrices annotated by Phenoscape curators]
 
* [https://github.com/phenoscape/phenoscape-data/tree/master/Curation%20Files Evolutionary data matrices annotated by Phenoscape curators]
 
===ZFIN===
 
===ZFIN===
Gene expression and genetic phenotype annotations for zebrafish. ZFIN data downloads can be found at http://zfin.org/downloads.
+
Gene expression and genetic phenotype annotations for zebrafish (''Danio rerio''). ZFIN data downloads can be found at http://zfin.org/downloads.
 
* Gene identifiers and names
 
* Gene identifiers and names
 
** http://zfin.org/downloads/genetic_markers.txt
 
** http://zfin.org/downloads/genetic_markers.txt
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===MGI===
 
===MGI===
Gene expression and genetic phenotype annotations for mouse. MGI data downloads can be found at ftp://ftp.informatics.jax.org/pub/reports/index.html.
+
Gene expression and genetic phenotype annotations for mouse (''Mus musculus''). MGI data downloads can be found at ftp://ftp.informatics.jax.org/pub/reports/index.html.
 
* Gene identifiers and names
 
* Gene identifiers and names
 
** ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.rpt
 
** ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.rpt
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===Xenbase===
 
===Xenbase===
 +
Gene expression and genetic phenotype annotations for frog (''Xenopus laevis'' and ''X. tropicalis''). Xenbase data downloads can be found at ftp://ftp.xenbase.org/pub.
 +
* Gene identifiers and names
 +
** ftp://ftp.xenbase.org/pub/GenePageReports/GenePageGeneralInfo_ManuallyCurated.txt
 +
** ftp://ftp.xenbase.org/pub/GenePageReports/XenbaseGenepageToGeneIdMapping.txt
 +
* Gene expression annotations
 +
** ftp://ftp.xenbase.org/pub/GenePageReports/GeneExpression_laevis.txt
 +
** ftp://ftp.xenbase.org/pub//GenePageReports/GeneExpression_tropicalis.txt
 +
 
===Ontologies===
 
===Ontologies===
  

Revision as of 19:38, 3 May 2013

The Phenoscape Knowledgebase (KB) is an integrated dataset, and software infrastructure and services, bringing together evolutionary data matrices annotated by Phenoscape curators, model organism phenotype and gene expression annotations, and a collection of ontologies providing a common semantic framework. The entire dataset is expressed in the OWL Web Ontology Language, and, when used as a database, stored in an RDF triplestore.

This page describes the in-development version of the KB built on OWL and RDF technologies, not the legacy Phenoscape Knowledgebase built on OBD.

Data sources

Phenoscape

ZFIN

Gene expression and genetic phenotype annotations for zebrafish (Danio rerio). ZFIN data downloads can be found at http://zfin.org/downloads.

MGI

Gene expression and genetic phenotype annotations for mouse (Mus musculus). MGI data downloads can be found at ftp://ftp.informatics.jax.org/pub/reports/index.html.

  • Gene identifiers and names
  • Gene expression annotations
    • Custom report provided by Terry Hayamizu. We are working with the Monarch project to establish continually updated downloadable reports.
  • Genetic phenotype annotations
    • Custom report provided by Terry Hayamizu. We are working with the Monarch project to establish continually updated downloadable reports.

Xenbase

Gene expression and genetic phenotype annotations for frog (Xenopus laevis and X. tropicalis). Xenbase data downloads can be found at ftp://ftp.xenbase.org/pub.

Ontologies