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 |