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    62 repositories

    • goldstandard

      Public
      Python
      •1•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • rphenoscape

      Public
      R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R.
      R
      •
      Other
      •4•5•11•1•Updated Oct 11, 2025Oct 11, 2025

    • taxrank

      Public
      Taxonomic rank ontology
      obofoundry
      obofoundry
      Makefile
      •
      Creative Commons Zero v1.0 Universal
      •6•6•3•0•Updated Sep 24, 2025Sep 24, 2025

    • phenoscape-wiki

      Public
      CSS
      •0•0•2•0•Updated May 13, 2025May 13, 2025

    • phenoscape-kb-web-ui

      Public
      Redesigned Phenoscape KB web user interface — in development
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•27•15•Updated Aug 15, 2024Aug 15, 2024

    • phenoscape-kb-services

      Public
      Web services application for the Phenoscape RDF knowledgebase.
      Scala
      •
      MIT License
      •3•2•49•20•Updated Aug 13, 2024Aug 13, 2024

    • owlet

      Public
      A little OWL in SPARQL.
      Scala
      •
      MIT License
      •5•14•2•8•Updated Aug 13, 2024Aug 13, 2024

    • owlery

      Public
      Owlery is a set of REST web services which allow querying of an OWL reasoner containing a configured set of ontologies.
      Scala
      •
      MIT License
      •12•17•8•15•Updated Aug 13, 2024Aug 13, 2024

    • sparql-utils

      Public
      Scala SPARQL utilities
      Scala
      •
      MIT License
      •2•5•0•7•Updated Jul 29, 2024Jul 29, 2024

    • scowl

      Public
      A Scala DSL for programming with the OWL API.
      Scala
      •
      MIT License
      •8•61•5•8•Updated Jul 10, 2024Jul 10, 2024

    • KB-DataFest-2017

      Public
      Promoting Phenoscape KB Data Access and Interoperability Codefest, 2017
      2•3•27•0•Updated Nov 10, 2023Nov 10, 2023

    • pipeline

      Public
      Build pipeline for the Phenoscape Knowledgebase
      Makefile
      •
      MIT License
      •0•0•16•3•Updated Jul 6, 2023Jul 6, 2023

    • phenoscape-owl-tools

      Public
      OWL-based reasoning and data processing utilities for assembling the Phenoscape RDF knowledgebase.
      Scala
      •
      MIT License
      •5•5•8•3•Updated Jul 6, 2023Jul 6, 2023

    • pheno-repo

      Public
      Repository of OWL-based phenotypic descriptions
      Makefile
      •
      Creative Commons Zero v1.0 Universal
      •2•4•0•0•Updated May 8, 2023May 8, 2023

    • colao

      Public
      The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.
      Makefile
      •
      Creative Commons Attribution 4.0 International
      •5•0•0•0•Updated Apr 20, 2023Apr 20, 2023

    • ubeRsim

      Public
      R package for computing semantic similarity metrics using online or offline Ubergraph
      R
      •
      MIT License
      •0•0•1•0•Updated Jan 26, 2023Jan 26, 2023

    • TraitFest-2023

      Public
      Main repository for information advertising and documenting the 2023 SCATE TraitFest
      R
      •
      Creative Commons Zero v1.0 Universal
      •0•3•19•0•Updated Jan 26, 2023Jan 26, 2023

    • scate-shortcourse

      Public
      Package for the "Phylogenetic comparative analysis of integrated anatomical traits" short course
      R
      •
      Creative Commons Zero v1.0 Universal
      •4•5•0•1•Updated Jan 19, 2023Jan 19, 2023

    • pipeline-tools

      Public
      Command-line environment needed to build Phenoscape Knowledgebase
      Dockerfile
      •1•1•1•0•Updated Jul 5, 2022Jul 5, 2022

    • teleost-taxonomy-ontology

      Public
      An ontology covering the taxonomy of teleosts (bony fish). Now superseded by Vertebrate Taxonomy Ontology.
      obofoundry
      obofoundry
      Creative Commons Zero v1.0 Universal
      •1•1•1•0•Updated Apr 19, 2022Apr 19, 2022

    • python-owlery-client

      Public
      Python client library for the Owlery OpenAPI
      Python
      •0•0•0•0•Updated Apr 14, 2022Apr 14, 2022

    • blazegraph-docker

      Public
      Docker image for running a Blazegraph server
      Dockerfile
      •
      MIT License
      •1•1•0•0•Updated Feb 3, 2022Feb 3, 2022

    • phenoscape-data

      Public
      NeXML data files annotated by Phenoscape curators.
      Java
      •0•2•4•0•Updated Jun 11, 2021Jun 11, 2021

    • EnviroPackets

      Public
      exploration of using phenopackets to describe environments
      Shell
      •
      MIT License
      •1•1•6•0•Updated Mar 30, 2021Mar 30, 2021

    • scate

      Public
      Project repo for Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution (SCATE)
      0•0•7•1•Updated Jan 17, 2021Jan 17, 2021

    • Phenex

      Public
      Phenex is an application for annotating character matrix files with ontology terms using the Entity-Quality syntax for describing phenotypes.
      character-matrixontology-annotation
      character-matrixontology-annotation
      Java
      •
      MIT License
      •3•11•38•0•Updated Feb 27, 2020Feb 27, 2020

    • phenoscape.github.com

      Public
      Phenoscape website
      JavaScript
      •0•1•9•0•Updated Jan 3, 2020Jan 3, 2020

    • kb-data-extracts

      Public
      Queries (primarily in SPARQL) for data extraction from the Phenoscape KB
      Shell
      •
      MIT License
      •0•0•2•1•Updated Dec 11, 2019Dec 11, 2019

    • phenoscape-ontologies

      Public
      0•0•1•0•Updated Oct 15, 2019Oct 15, 2019

    • homology-annotations-demo

      Public
      Demonstration files for OWL homology models
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 20, 2019Sep 20, 2019
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