Promoting Phenoscape KB Data Access and Interoperability Codefest, 2017
A little OWL in SPARQL.
A Scala DSL for programming with the OWL API.
An ontology covering the taxonomy of teleosts (bony fish). Now superseded by Vertebrate Taxonomy Ontology.
Phenoscape KB web user interface.
Phenex is an application for annotating character matrix files with ontology terms using the Entity-Quality syntax for describing phenotypes.
NeXML data files annotated by Phenoscape curators.
Owlery is a set of REST web services which allow querying of an OWL reasoner containing a configured set of ontologies.
OWL-based reasoning and data processing utilities for assembling the Phenoscape RDF knowledgebase.
R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R. To become part of rOpenSci.
Web application for exploring the OBD-based Phenoscape Knowledgebase.
Web services application for the Phenoscape RDF knowledgebase.
Tool for querying a local copy of the Phenoscape KB and generating an inferred presence-absence data matrix, for a given taxon and anatomy specification.
Translations of data sources into OWL axioms for import into the Phenoscape Knowlegebase.
Taxonomic rank ontology
Data visualization for Phenoscape database
The Vertebrate Taxonomy Ontology includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, we also incorporate taxonomic information acro…
Miscellaneous queries which are useful for navigating Phenoscape KB data.
Source for the CharaParser application, which uses natural language processing to propose EQ-based phenotype annotations.
Demonstration code for paper submission to the Bio-ontologies SIG Phenotype Day at ISMB 2014.
Java implementation of the unsupervised bootstrapping algorithm used within the CharaParser application.
Convert a VUE document to an OWL ontology.
Build scripts for generating the Phenoscape RDF knowledgebase.
Reference images for the vertebrate skeleton annotated with Uberon terms.
RDF/XML serialization of the Phenoscape RDF knowledgebase.
Phenoscape data services web application for the legacy OBD-based knowledgebase.