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    32 repositories

    • data-distillery-api

      Public
      the Data Distillery API
      Shell
      •0•0•0•1•Updated Feb 14, 2025Feb 14, 2025

    • hs-ontology-api

      Public
      Ontology API built on top of the UBKG API and shared by HuBMAP and SenNet projects
      Python
      •0•1•1•2•Updated Feb 14, 2025Feb 14, 2025

    • Guesdt

      Public
      Guesdt (Graphing UMLS Enables Search In Dynamic Trees)
      Dockerfile
      •0•0•1•0•Updated Feb 13, 2025Feb 13, 2025

    • ubkg-api

      Public
      A web service for the Unified Biomedical Knowlege Graph system
      Python
      •
      MIT License
      •0•1•2•2•Updated Feb 13, 2025Feb 13, 2025

    • ubkg-docs

      Public
      Unified Biomedical Knowledge Graph (UBKG) Documentation
      JavaScript
      •
      MIT License
      •1•2•0•0•Updated Feb 11, 2025Feb 11, 2025

    • data-ingest-board

      Public
      The UI App for HuBMAP and Sennet Data Publishing Dashboard
      JavaScript
      •
      MIT License
      •0•1•20•0•Updated Feb 11, 2025Feb 11, 2025

    • hra-notebooks

      Public
      Fun and Interesting Python Notebooks that use the HRA
      Jupyter Notebook
      •
      MIT License
      •2•0•1•0•Updated Feb 7, 2025Feb 7, 2025

    • data-submission-guide

      Public
      A documentation site for the Data Submission Guide used by both HuBMAP and SenNet
      0•1•3•0•Updated Feb 5, 2025Feb 5, 2025

    • ubkg-etl

      Public
      A framework that combines data from the UMLS with assertions from other data sources into a set of CSV files that can be imported into neo4j to build a Unified Biomedical Knowledge Graph (UBKG)
      Python
      •
      MIT License
      •0•3•6•0•Updated Feb 4, 2025Feb 4, 2025

    • dev-assay-class-api

      Public
      A small development RESTful server exposing /assayclasses and /assayclasses/<assay-code>
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • hra-api

      Public
      HRA-API: Human Reference Atlas API
      human-reference-atlas
      Jupyter Notebook
      •
      MIT License
      •0•0•5•0•Updated Feb 3, 2025Feb 3, 2025

    • SimpleKnowledge

      Public
      The SimpleKnowledge property graph editor
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • hra-dashboard-data

      Public
      Gathers data for the HRA Dashboard
      HTML
      •
      MIT License
      •1•1•1•0•Updated Jan 28, 2025Jan 28, 2025

    • hra-pop

      Public
      HRApop
      human-reference-atlas
      JavaScript
      •
      MIT License
      •1•0•45•1•Updated Jan 24, 2025Jan 24, 2025

    • hra-snorql

      Public
      A query interface to explore the HRA SPARQL endpoint
      JavaScript
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Jan 15, 2025Jan 15, 2025

    • uuid-api

      Public
      A restful web service used to create and query UUIDs used across HuBMAP and SenNet
      Python
      •
      MIT License
      •0•2•6•2•Updated Jan 14, 2025Jan 14, 2025

    • hra-apps

      Public
      hra-apps: Applications using the Human Reference Atlas website
      human-reference-atlas
      HTML
      •
      MIT License
      •0•0•8•0•Updated Jan 9, 2025Jan 9, 2025

    • commons

      Public
      The common code supporting the web services in the consortia
      Python
      •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • user-key-value-api

      Public
      A RESTful service for storing values by user and key
      Python
      •
      MIT License
      •0•0•2•0•Updated Jan 7, 2025Jan 7, 2025

    • hra-ubkg-exporter

      Public
      A CLI for exporting a subset of the HRA Knowledge Graph to UBKG format
      human-reference-atlasubkg
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • hra-jupyter-widgets

      Public
      HRA Web Components wrapped as Jupyter Widgets
      Python
      •
      MIT License
      •0•0•1•0•Updated Dec 17, 2024Dec 17, 2024

    • donor-metadata

      Public
      Application used to prepare de-identified and encoded donor metadata to include with tissue samples registered with HuBMAP or SenNet
      apidockerflaskjinja2wtformsblueprints
      Python
      •
      MIT License
      •0•0•1•0•Updated Dec 6, 2024Dec 6, 2024

    • hra-lit

      Public
      HRAlit
      human-reference-atlas
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • elastic-analysis

      Public
      Scripts for analyzing Elastic Search indexes, initially those used for HuBMAP
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • ubkg-neo4j

      Public
      A container implementation to serve the Unified Biomedical Knowledge Graph in Neo4j
      pythonshelldockerneo4j
      Shell
      •
      MIT License
      •0•1•4•0•Updated Aug 29, 2024Aug 29, 2024

    • clt

      Public
      The X Atlas Consortia Command Line Transfer application
      Python
      •0•0•3•0•Updated Jun 28, 2024Jun 28, 2024

    • ubkg-download

      Public
      Download UI/Service used to distribute UBKG databases with required UMLS license validation
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Jun 12, 2024Jun 12, 2024

    • rule-chain-assay-classifier

      Public
      Python
      •0•0•3•0•Updated Apr 11, 2024Apr 11, 2024

    • hra-enrichr-exporter

      Public
      A CLI for exporting a subset of the HRA Knowledge Graph to Enrichr format
      human-reference-atlas
      Shell
      •
      MIT License
      •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • ubkg_cedar

      Public
      Repository of UBKG edge/node files for CEDAR templates
      MIT License
      •0•0•0•0•Updated Nov 10, 2023Nov 10, 2023