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

[Lennart M. <len...@eb...>]

Hi Marc,


Excellent, that was my best guess at solving the issue as well, but it 
took me some more time to get there :D. We'll make sure to update ASAP.

Fredrik, we'll let you know when there is a new version!

Cheers,

lnnrt.

Marc Sturm wrote:
> 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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