Re: [Psidev-ms-dev] [Fwd: Re: PRODAC validator not checking polarity location]

[Marc S. <st...@in...>]

Hi all,

the OpenMS validator allows only those terms listed in the mapping file. 
However, terms from unknonwn CVs (those for which no mappnig rule 
exists) are ignored.

Best,
  Marc

> We've covered whether the mapping file should be a whitelist, a 
> blacklist, or a combination on the list at some point. We decided that 
> for the PSI CV it would be a whitelist (i.e. if it's not in the mapping 
> file, it's not allowed) and for everything else it would be a blacklist 
> (i.e. it won't flag terms from other CVs as errors, and presumably those 
> terms will never show up in our mapping file).
>
> -Matt
>
>
> Lennart Martens wrote:
>   
>> Hi Fredrik,
>>
>>
>> There is a fundamental issue behind this I guess, but I'll attempt to 
>> post to the list later on to resolve this.
>>
>> The main question here is whether you assume the mapping file defines 
>> the lower boundary (which is what we do), or whether you assume that 
>> it defines the upper boundary (as the OpenMS people do).
>>
>> Put in other words, we verify that the mzML file has at least what is 
>> mandated in the mapping file, but we allow the use of additional terms 
>> as well. The main reason for this is so anyone with a homegrown, 
>> custom cv can include their own terms and still end up with a valid 
>> document.
>>
>> The OpenMS validator seems to take the opposite approach: if it is not 
>> in the mapping file it should not be there.
>>
>> So the erroneous scan polarity term is found by OpenMS, but ignored by 
>> us; but a file with a custom CV term wil validate for us, but maybe 
>> not for OpenMS.
>>
>> Now, we can nuance the situation - if you allow 'unknown' terms (e.g. 
>> from a proprietary CV), but you do not allow terms that are known to 
>> have another place reserved for them in the mapping file (such as the 
>> scan polarity case). We're looking into developing this in an object 
>> rule to test the concept, and it might well be that OpenMS does things 
>> this way.
>>
>> But I'll also post to the list to get opinions and OpenMS feedback. 
>> But I'll do that tomorrow.
>>
>>
>> Cheers,
>>
>> lnnrt.
>>
>> Fredrik Levander wrote:
>>     
>>> Hi Lennart,
>>>
>>> Matt found a possible problem with the PSI/EBI validator. I thought 
>>> it was us running an old version of the validator on the ProDaC web 
>>> site, but now I tried with the latest jmzml and config files locally, 
>>> and it doesn't complain if
>>>
>>> MS:1000130 - positive scan
>>> is used under scan instead of under spectrum. The openMS validator 
>>> flags this as an error. The test was done with small.pwiz.1.1.mzML. 
>>> Do you have any idea of the reason for this? Maybe the term is 
>>> passing if there are already terms fulfilling the rules for the element?
>>>
>>> Best Regards
>>>
>>> Fredrik
>>>
>>> ------------------------------------------------------------------------
>>>
>>> Subject:
>>> Re: PRODAC validator not checking polarity location
>>> From:
>>> Jari Häkkinen <ja...@th...>
>>> Date:
>>> Fri, 24 Jul 2009 23:26:01 +0200
>>> To:
>>> Matthew Chambers <mat...@va...>
>>>
>>> To:
>>> Matthew Chambers <mat...@va...>
>>> CC:
>>> Fredrik Levander <Fre...@im...>
>>>
>>>
>>> Hi,
>>>
>>> Thanks for the report. Fredrik or me will look at the problem as soon 
>>> as we are back in office.
>>>
>>>
>>> Jari
>>>
>>>
>>> Matthew Chambers wrote:
>>>       
>>>> I recently realized that most pwiz vendor readers were putting 
>>>> polarity in scan instead of spectrum and that this was expressed in 
>>>> files that had been verified by the PRODAC validator. That worries 
>>>> me since there's no telling what other attributes it's not checking. 
>>>> I ran the old file through the OpenMS validator and it did catch the 
>>>> misplaced polarity terms.
>>>>
>>>> Thanks,
>>>> Matt
>>>>         
>
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