Repositories list

• biosamples-v4

  Public
  The source code for the new version of the EMBL-EBI BioSamples database

  Java

  •

  Apache License 2.0

  •9•11•1•4•Updated Nov 29, 2024Nov 29, 2024

• json-schema-store

  Public
  A repository for storing versioned JSON Schema

  Java

  •

  Apache License 2.0

  •2•7•1•18•Updated Nov 28, 2024Nov 28, 2024

• cohort-atlas

  Public
  A browser for discovering cohorts and related resources

  Java

  •0•0•20•3•Updated Sep 26, 2024Sep 26, 2024

• cohort-atlas-web

  Public
  web component of cohort atlas

  TypeScript

  •0•0•0•0•Updated Dec 8, 2023Dec 8, 2023

• java2rdf

  Public
  A simple library to map Java objects and Java beans onto RDF/OWL

  Java

  •

  Other

  •0•3•0•0•Updated Nov 7, 2023Nov 7, 2023

• cohort-atlas-harmonisation

  Public
  Harmonisation module of the cohort atlas

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•1•Updated Sep 5, 2023Sep 5, 2023

• curami-v2

  Public
  curami version 2: curation of BioSamples objects

  JavaScript

  •

  Apache License 2.0

  •0•1•0•8•Updated Feb 15, 2023Feb 15, 2023

• biosamples-scripts

  Public
  Scripts for data manipulation in BioSamples

  Python

  •

  Apache License 2.0

  •1•0•0•3•Updated Dec 8, 2022Dec 8, 2022

• bioschemas_marref_demo

  Public
  A sandbox with example pages from the MarRef database for Bioschemas hackathon purposes

  CSS

  •

  Apache License 2.0

  •0•0•0•8•Updated Dec 8, 2022Dec 8, 2022

• ncbi_amr_table_extractor

  Public
  A web scraper to extract amr data from NCBI website

  Python

  •

  Apache License 2.0

  •0•0•0•3•Updated Dec 8, 2022Dec 8, 2022

• biosamples-presto-connector

  Public
  Presto connector to query BioSamples API

  Java

  •0•0•0•4•Updated Nov 16, 2022Nov 16, 2022

• biosamples-web

  Public
  Updated version of the Biosamples UI to work with a Solr backend

  Java

  •0•0•0•17•Updated Nov 16, 2022Nov 16, 2022

• cli-archetype

  Public archive
  Allows you to define a project that produces the binary for a command-line based application, using the Assembly plug-in.

  Java

  •2•0•0•3•Updated Nov 16, 2022Nov 16, 2022

• myequivalents

  Public archive
  myequivalents is a system to manage cross-references between entities, which is compatible with URIs and the Semantic Web.

  Java

  •

  Other

  •1•2•0•8•Updated Jul 7, 2022Jul 7, 2022

• hca-util

  Public
  CLI tool for file transfer (upload and download) to/from Embassy S3. Forked from https://github.com/ebi-ait/hca-util and adapted for Embassy S3

  Python

  •

  Apache License 2.0

  •2•0•0•0•Updated Dec 14, 2021Dec 14, 2021

• EBIBioSamples.github.io

  Public
  HTML

  •0•0•0•0•Updated Jun 7, 2021Jun 7, 2021

• SolrUTF8DecoderProcessor

  Public
  A processor pluggable into solr core that try to fix UTF8 characters encoding problems

  Java

  •

  Apache License 2.0

  •0•0•0•2•Updated May 12, 2021May 12, 2021

• json-schema-validator

  Public
  Javascript validator for HCA metadata

  JavaScript

  •

  Apache License 2.0

  •6•1•0•0•Updated Apr 23, 2021Apr 23, 2021

• certification-service

  Public
  Certification service for BioSamples samples

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 28, 2019Mar 28, 2019

• certification-pipeline-go-prototype

  Public
  Go

  •

  Apache License 2.0

  •0•0•8•0•Updated Dec 14, 2018Dec 14, 2018

• structured_data

  Public
  A repository for structured data representation in BioSamples

  Python

  •0•0•0•0•Updated Sep 10, 2018Sep 10, 2018

• curami

  Public
  Python

  •

  Apache License 2.0

  •0•2•5•0•Updated Aug 23, 2018Aug 23, 2018

• marref_XML_parser

  Public
  A simple parser for MarRef XML. Hoping to parse the XML records into JSON-LD to the BioSchemas standards.

  Python

  •0•0•0•0•Updated Mar 4, 2018Mar 4, 2018

• metagenomics_profile

  Public
  Python

  •0•0•3•0•Updated Feb 15, 2018Feb 15, 2018

• biosd_model_load

  Public
  Java

  •0•0•0•0•Updated Oct 9, 2017Oct 9, 2017

• solrIndexer

  Public
  EBI BioSamples Solr Indexer

  Java

  •

  Other

  •0•0•0•0•Updated Sep 7, 2017Sep 7, 2017

• sampletab_converters

  Public
  Command line tools to convert various biomedical formats into the SampleTab format, used by the EBI Biosamples Database.

  Java

  •

  Other

  •0•0•0•0•Updated Aug 8, 2017Aug 8, 2017

• EbiGeneralSearch

  Public
  An application to generate the xml specific for the EBI general search interface

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 21, 2017Jun 21, 2017

• sampletab_converters_myequivalents

  Public
  Java

  •0•0•0•0•Updated May 9, 2017May 9, 2017

• sampletab_services

  Public
  various sample tab services

  Java

  •

  Other

  •0•0•0•0•Updated Apr 6, 2017Apr 6, 2017