Phenoscape

scowl

A Scala DSL for programming with the OWL API.

owlery

Owlery is a set of REST web services which allow querying of an OWL reasoner containing a configured set of ontologies.

owlet

A little OWL in SPARQL.

Phenex

Phenex is an application for annotating character matrix files with ontology terms using the Entity-Quality syntax for describing phenotypes.

rphenoscape

R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R.

scate-shortcourse

Package for the "Phylogenetic comparative analysis of integrated anatomical traits" short course

sparql-utils

Scala SPARQL utilities

KB-DataFest-2017

Promoting Phenoscape KB Data Access and Interoperability Codefest, 2017

pheno-repo

Repository of OWL-based phenotypic descriptions

phenoscape-owl-tools

OWL-based reasoning and data processing utilities for assembling the Phenoscape RDF knowledgebase.

taxrank

Taxonomic rank ontology

TraitFest-2023

Main repository for information advertising and documenting the 2023 SCATE TraitFest

phenoscape-data

NeXML data files annotated by Phenoscape curators.

blazegraph-docker

Docker image for running a Blazegraph server

EnviroPackets

exploration of using phenopackets to describe environments

phenoscape-kb-services

Web services application for the Phenoscape RDF knowledgebase.

phenoscape-kb-ui

Phenoscape KB web user interface.

phenoscape.github.com

Phenoscape website

pipeline-tools

Command-line environment needed to build Phenoscape Knowledgebase

teleost-taxonomy-ontology

An ontology covering the taxonomy of teleosts (bony fish). Now superseded by Vertebrate Taxonomy Ontology.

pipeline

Build pipeline for the Phenoscape Knowledgebase

colao

The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.

homology-annotations-demo

Demonstration files for OWL homology models

kb-data-extracts

Queries (primarily in SPARQL) for data extraction from the Phenoscape KB

phenoscape-kb-ingest

Translations of data sources into OWL axioms for import into the Phenoscape Knowlegebase.

phenoscape-kb-web-ui

Redesigned Phenoscape KB web user interface — in development

phenoscape-ontologies

python-owlery-client

Python client library for the Owlery OpenAPI

scate

Project repo for Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution (SCATE)

ubeRsim

R package for computing semantic similarity metrics using online or offline Ubergraph