The BioPAX Validator Web Service
Check
To validate and, optionally, auto-fix and normalize local or remote BioPAX file(s),
submit a multipart/form-data HTTP POST request to
this URL.
Parameters:
- file (actually, parameter name does not matter here, - simply
submit an array of files) OR url (value: a URL to data in BioPAX format)
- retDesired - output format; values: "html" (default), "xml",
or "owl" (modified BioPAX only, no error messages)
- autofix - false/true; try to fix BioPAX errors automatically
and then normalize (default is "false")
- filter - set log level; values: "WARNING" (default, get both
errors and warnings), "ERROR", and "IGNORE" (no problems at all ;))
- maxErrors - set the max. number of not fixed ERROR type cases
to collect (some, but not all, warning and fixed cases will be also reported);
value: a positive integer; "0" (default) means "unlimited", "1" - fail-fast
mode, i.e., stop after the first serious issue, "10" - collect up to ten error cases, etc.
- profile - use an alternative, pre-configured validation profile;
currently, there is only one value available: "notstrict" (for particular
rules to report 'warning' or nothing instead of 'error' - in the default
configuration)
Output Formats:
- HTML - stand-alone HTML+JavaScript validation results page
to save locally and view off-line
- XML - results in the XML format defined by the
XML schema
- OWL - modified BioPAX L3 data (fixed and normalized)
As an example, there is a BioPAX validator-client library
(it connects to http://www.biopax.org/validator/check); the
source code is here (see test classes there as well).