BioPAXValidator
From biopax
Contents |
Overview
The BioPAX Validator helps improve BioPAX data quality. It implements and checks many syntax and semantic rules and BioPAX best practices, which in most cases cannot be formally defined neither using OWL constraints nor - a rule definition language. It was started by Pathway Commons team in 11/2008; and here are initial requirements and design.
BioPAX Rules
Availability
- Bundled releases at http://www.biopax.org/downloads/validator/
- Online version (the latest stable) is at http://www.biopax.org/biopax-validator/
- Validator 2.x and 3x sources (Maven2 project): http://sourceforge.net/p/biopax/validator
- Validator 1.0 sources (has Ant build script): browse or get sources using 'cvs checkout': http://biopax.cvs.sourceforge.net/viewvc/biopax/validator/
- BioPAX Public Maven SNAPSHOTs repository: http://www.biopax.org/m2repo/snapshots/
- BioPAX Public Maven RELEASEs repository: http://www.biopax.org/m2repo/releases/
- Auto-generated documentation (Maven project site): http://www.biopax.org/m2site/
Software that might be useful for or inspire biological pathway data validation:
- OWL2 Validator: http://owl.cs.manchester.ac.uk/validator/
- PSI-MI 2.5 Validator: http://www.ebi.ac.uk/intact/validator/start.xhtml
- RDF Validator: http://www.w3.org/RDF/Validator/
Contribute!
We can imagine several levels of contribution, depending on how familiar you are with the project and what time and resources you are going to grant. It worth noticing that all the listed below categories and tasks are very important, and those that may seem to be for beginners only or somewhat boring to perform, in fact, are currently of highest priority. So we encourage you to actively participate!
Basic
- either try it online or download the latest version and report problems (using the issue tracker: http://sourceforge.net/p/biopax/_list/tickets)
- grab the sources from the CVS and create more BioPAX rule tests that generate example OWL files (a very important and excellent exercise!) - in the org.biopax.validator.Level3RulesUnitTest or TestContextTest class
- feel free to ask to biopax-discuss@googlegroups.com or at http://groups.google.com/group/biopax-discuss
Intermediate
(one may submit patches or become a BioPAX developer to check-in)
- implement a rule labeled with "*" at the BioPAXRules page
- help debug/test/tune
- make web service accept/send zipped BioPAX data
Advanced
- improve auto-fix and normalization
- make it asynchronous, multi-threaded (why?..)
- getting rid of AspectJ LTW?.. [- LTW is not required anymore when the validator is used as java library, but it will ignore all issues that occur in the BioPAX reader while converting from RDF]
- integration with visualization and modelling tools
- add advanced rules that may require using external tools (e.g., check organism, check that sequence match the xref, etc...)
Milestones
| biopax-validator v1.0 alpha | 20-Apr-09 | [done] |
| biopax-validator beta | 07-May-09 | [done] |
| Trying at IOB | May-09 | Toronto-Bangalore |
| XML configuration for the DB synonyms in Xrefs; limit DB usage (allow/deny) | May-09 | [done] |
| New features: FIXIT behavior, errors threshold, and warnings | Jun-09 | [done] |
| Web service and Web site (draft) | Jun-09 | [done] |
| biopax-validator v1.0 beta 2 | Aug-09 | [done] |
| Re-design: simpleIO instead JenaIO; errors - only via AOP; simpler interfaces; a basis for the future multi-thread validation | Jul-Aug | [done] |
| Implementing rules | Aug-Oct-09 | |
| Present the validator at the BioPAX meeting | Nov-09 | [done] NYC USA |
| Assembly or convert BioPAX models online | Collaborate with ChiBE | |
| Begin v2.0 development | Dec-09 | [done] biopax hg (Mercurial) repository; fix/normalization behavior, maven2 |
| Basic CV rule change: do not use the Generic Schema Validator module, nor Ontology Manager; use OLS directly | Dec-09 | [done] |
| BioPAX Validator 1.0 Release | 31-Dec-09 | [done] v1.0.6 is the last 1.x one |
| BioPAX Validator 2.0 | 2010 | [done] normalization, error threshold, new web look, etc... http://www.biopax.org/validator |
| BioPAX Validator 2.0.0 Release | by April-23 (HARMONY) | improved error messages, normalization and auto-fix, ontology manager configuration, docs/examples |
| BioPAX Validator 2.1.0 Release | by end of May 2012 (HARMONY meeting) | add categories, review rules and messages, improve normalizer, upgrade ontology manager, paxtools, and other dependencies, etc. |
| BioPAX Validator 3.0.0 Release | January 2013 | [done] "notstrict" validation profile added; improved auto-fix and normalization; improved console app; improved web style, etc. |
| BioPAX Validator 3.0.1 Release | April 2013 | TODO: fix bugs; improve validating of multiple large files (from a directory) |
| BioPAX Validator 4 | 2013 - 2014 | TODO: JSON support and more web services; optionally, use of a (Pathway Commons) data warehouse and other external resources to, e.g., suggest/fix CV terms, infer some BioPAX properties, check using isoform sequences and identifier vertions, etc... |
