Difference between revisions of "Phenoscape KB"

From phenoscape
(Data sources)
Line 4: Line 4:
  
 
==Data sources==
 
==Data sources==
===Phenoscape===
+
===Comparative data===
 +
====Phenoscape====
 
* [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===
+
 
 +
===Model organism data===
 +
====ZFIN====
 
Gene expression and genetic phenotype annotations for zebrafish (''Danio rerio''). 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
Line 16: Line 19:
 
** http://zfin.org/downloads/phenoGeneClean.txt
 
** http://zfin.org/downloads/phenoGeneClean.txt
  
===MGI===
+
====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 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
Line 25: Line 28:
 
** Custom report provided by Terry Hayamizu. We are working with the Monarch project to establish continually updated downloadable reports.
 
** Custom report provided by Terry Hayamizu. We are working with the Monarch project to establish continually updated downloadable reports.
  
===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 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
 
* Gene identifiers and names
Line 36: Line 39:
 
** A preliminary annotation file has been provided by Xenbase curators. Not yet imported into the KB.
 
** A preliminary annotation file has been provided by Xenbase curators. Not yet imported into the KB.
  
===HPO===
+
====HPO====
 
Genetic phenotype annotations for human (''Homo sapiens''). HPO data downloads can be found at http://www.human-phenotype-ontology.org/contao/index.php/downloads.html.
 
Genetic phenotype annotations for human (''Homo sapiens''). HPO data downloads can be found at http://www.human-phenotype-ontology.org/contao/index.php/downloads.html.
 
* Genetic phenotype annotations
 
* Genetic phenotype annotations

Revision as of 19:45, 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

Comparative data

Phenoscape

Model organism data

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.

HPO

Genetic phenotype annotations for human (Homo sapiens). HPO data downloads can be found at http://www.human-phenotype-ontology.org/contao/index.php/downloads.html.

Ontologies