Phenoscape KB

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

• Evolutionary data matrices annotated by Phenoscape curators

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 identifiers and names
  • http://zfin.org/downloads/genetic_markers.txt
  • http://zfin.org/downloads/aliases.txt
• Gene expression annotations
  • http://zfin.org/downloads/wildtype-expression.txt
• Genetic phenotype annotations
  • http://zfin.org/downloads/phenoGeneClean.txt

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
  • ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.rpt
• 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.

• 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
• Genetic phenotype annotations
  • A preliminary annotation file has been provided by Xenbase curators. Not yet imported into the KB.

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
  • http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/genes_to_phenotype.txt

Ontologies

• Uberon cross-species anatomy ontology, with Phenoscape extensions
  • http://purl.obolibrary.org/obo/uberon/ext.owl
  • Imports http://purl.obolibrary.org/obo/uberon/merged.owl
  • Imports http://purl.obolibrary.org/obo/uberon/references/references.owl
• Zebrafish anatomy
  • http://purl.obolibrary.org/obo/zfa.owl
  • Bridge axioms to Uberon: http://purl.obolibrary.org/obo/uberon/bridge/uberon-ext-bridge-to-zfa.owl
• Mouse annotations provided by Terry directly reference Uberon; no mouse-specific ontologies are used at this time.
• Xenopus anatomy
  • http://purl.obolibrary.org/obo/xao.owl
  • Bridge axioms to Uberon: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-xao.owl
• Human phenotypes
  • http://purl.obolibrary.org/obo/hp.owl
  • Logical definitions for human phenotype classes (FMA + PATO): http://purl.obolibrary.org/obo/hp/hp-equivalence-axioms.obo
    • This file is converted to OWL after introducing a special header, logical-definition-view-relation: involves, which is used by the oboformat converter.
  • Bridge axioms from FMA (human anatomy) to Uberon: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl
  • FMA itself is not used (should it be? are there FMA classes used in the HP definitions that don't have direct mappings in the bridge file?)
• Gene Ontology
  • http://purl.obolibrary.org/obo/go.owl
• Biospatial ontology
  • http://purl.obolibrary.org/obo/bspo.owl
• Phenotypic quality ontology
  • http://purl.obolibrary.org/obo/pato.owl
• Vertebrate taxonomy
  • http://purl.obolibrary.org/obo/vto.owl
  • An individual-based taxonomy is generated from this class hierarchy, and both are loaded into the KB.
• Ontology metadata
  • http://purl.obolibrary.org/obo/iao/ontology-metadata.owl