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Table 1 Repositories functionality and Bio-GraphIIn requirements.

From: linkedISA: semantic representation of ISA-Tab experimental metadata

  Data Types Format Browsing/ Searching Programmatic submission Programmatic access CRUD operations Community curation RDF
BioSample DB sample info Sample- TAB browse/search X (email submission) REST API X X YES
ArrayExpress/GEO Sequencing MAGE- TAB browse/filter/ search/ advanced search MAGE-TAB spreadsheet / MIAMExpress REST API X X X*
SRA/ENA next generation sequencing SRA-XML browse/text/ sequence/ advance search Webin, REST REST API X X X
PRIDE mass spectrometry PRIDE-ML PRIDE inspector/ PRIDE Biomart X (FTP upload) Java API X X X
BII All ISA-TAB browse/text search/filtering X SOAP web services X X X
Bio-GraphIIn All ISA-TAB browse/filter/ search/ advanced search YES (upload, REST) REST API YES YES YES
  1. *We are referring to the ArrayExpress repository not to the Expression Atlas, which is available in RDF