Harmony'2011 - BioPAX Validation Session

[IgorRodchenkov]

Harmony BioPAX Validation Sessions

Dear BioPAX people who are visiting of following Harmony'11 in New York City,

During the Harmony meeting, if possible, please post/reply to this topic if your message is about BioPAX validation!

There will be two 10-minute pre-hackathon sessions related to BioPAX validation on Wednesday morning, April 20, 2011:

1. between 9:00am and 10:00, it's about validation and:
• rules and best practices overview
• writing rules, rule exchange: discuss other (than wiki or java) ways to define rules, e.g., regexp, SWRL, other rule languages
• equivalence: semantic equivalence vs. syntactic equivalence vs. java object equals vs. URI equals
• how to tell non-generic from generic (when neither element have unification xrefs, nor - any members; shall we have a new isGeneric property)
• whether to support "super rules" that look far beyond the BioPAX data in hands (for an external resource/warehouse); CV rules currently do.

1. after 10:30, it's about the validator (Paxtools API based):
• web and console application
• how to implement and test a rule (design, 'rule' beans and 'error' properties: code, category, behavior/level, messages)
• implement junit tests that also generate example BioPAX files for each rule
  
• how to integrate the validator into another project
• auto-fix and normalization (Normalizer)

- and we encourage you to continue discussing and working in the afternoon and next two days! By the end of Harmony, we are going to have:

• BioPAX Validator 2.0.0 released
• feedback: questions, feature requests, bug reports collected
• validation rules reviewed (or even expressed in a new form)
• fun

BioPAX validation related links:

• http://www.biopax.org/validation
  
• http://www.biopax.org/validator
  
• BioPAX Validation Working Group
  
• Work-in-progress/notes documents
  

We look forward to hear from you soon!

Best regards,

Igor Rodchenkov

UofT, baderlab.org

[B. Arman Aksoy]

Hello,

A couple of memos on the issues raised during this session:

• Customization of the Web-based Validator
  
• Users should be able to select
  
• the categories
  
• the level (error/warning)
• of validator rules to be checked
  
• The customization should be session specific
• The current  error/warning choices for some of the rules should be reviewed (i.e. who watches the watchmen?)
  
• Organization of the rules under a tree (so that users can disable a sub tree of rules)
• Logging errors for later use

More community feedback on the issue is definitely welcome!

Cheers,
-- B. Arman Aksoy

[IgorRodchenkov]

Hi Arman, all!

On Wednesday, April 20, 2011 12:13:50 PM UTC-4, B. Arman Aksoy wrote:

Hello,

A couple of memos on the issues raised during this session:

• Customization of the Web-based Validator
  
• Users should be able to select
  
• the categories
  

good idea, will do! 

• the level (error/warning)

was done 

• of validator rules to be checked
  

disagree (better ignore some results or download and install a "tuned" validator). 

• The customization should be session specific

yes - for level, category, num.of errors, fix/normalize options (no - for the rules's messages and warning/error/ignore mode that, at least for the biopax.org/validator instance are to be set by admin.)  

• The current  error/warning choices for some of the rules should be reviewed (i.e. who watches the watchmen?)
  

yes (and they have been reviewed already several times, and new specific comments are always welcomed) 

• Organization of the rules under a tree (so that users can disable a sub tree of rules)

I'm against user disabling or changing rules behavior (there is a risk to fool yourself), but this suggestion is very interesting! Any ideas how the tree should be organized? E.g., - by category (we have three), BioPAX class, property..? 

• Logging errors for later use

could not understand... sorry ;)

 

More community feedback on the issue is definitely welcome!

Cheers,
-- B. Arman Aksoy

Thanks!

BTW, a couple of rules were "fixed", - thanks for your feedbacks (- Ashok, Suzanna, Kira,..). 

IR.