Data in SABIO-RK can be accessed via web-based user interfaces and web-services offering the possibility of submitting complex searches by defining various search criteria. Currently SABIO-RK has two different versions of web-based user interface, due to a transition process. The new user interface enables to show the user beforehand how many results can be expected for a given set of search criteria. We have improved the search efficiency and changed from an SQL-based search mechanism to inverted indexing for all data entries.
For programmatic access to the database web services were implemented allowing data access via HTTP requests following a Representational State Transfer (REST) approach.
Creating links to SABIO-RK content
Please use the following URL to link to SABIO-RK:
Upload of data files in EnzymeML format
Data in EnzymeML format can be dircetly uploaded into SABIO-RK database via the "Data Input Interface".
After curation the data are transferred to the public searchable database.
For file upload an account is required, which can be requested here.
Upload can be performed programmatically by sending a multipart request as exemplified for a simple curl statement:
curl -F username=yourUsername -F password=yourPassword -F payload=@/home/user/.../yourEnzymeMLFile.xml http://sabiork.h-its.org/datainput/SBMLUpload/uploadEnzymeML
An EnyzmeML validation template (JSON) specifying mandatory SABIO-RK fields can be accessed here.