Re: [Psidev-pi-dev] FW: ProteoAnnotator_1_2.mzid

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Hi all,

from the validation side, it makes not much difference, if option 1 or 2 
is choosen,
but option 2 is much clearer to read.

Cheers,
Gerhard

Am 31.01.2017 um 16:20 schrieb Jones, Andy:
>
> Hi all,
>
> The validation of proteogenomics example files has revealed a minor 
> flaw in the proteogenomics specs. We use a MUST rule that says every 
> peptide and protein that is not a decoy must state its genomic 
> location. This doesn’t make sense for two reasons:
>
> -Some peptides may have been  identified but not mappable to a 
> chromosome, due to the approach taken i.e. the protein database and 
> gene models are not consistent for sensible reasons
>
> -As we have done, we have a merged result file from hits to Ensembl 
> and Uniprot (Uniprot hits are not mapped).
>
> Solutions:
>
> 1.Relax the MUST rule, to say that CV terms should be added for all 
> mapped peptides/proteins.
>
> a.Downside: hard to encode this logic in the validator
>
> 2.Introduce another CV term for “unmapped peptide” and “unmapped 
> protein” to cater for this case explicitly.
>
> Option 2 seems more formally sensible, but makes more work for data 
> exporters to add CV terms to every peptide/protein, even if they only 
> intended to map one subset.
>
> If possible, can people give opinions fairly quickly. We now have a 
> time pressure to get MCP paper resubmitted within around 2 weeks 
> otherwise it is a new submission.
>
> Best wishes
>
> Andy
>
> *From:*mayerg97 [mailto:ger...@ru...]
> *Sent:* 26 January 2017 13:33
> *To:* Jones, Andy <jo...@li...>; Ghali, Fawaz 
> <fg...@li...>
> *Subject:* Re: ProteoAnnotator_1_2.mzid
>
> Hi Fawaz and Andy,
>
> e.g.
>
> <DBSequence searchDatabase_ref="SearchDB_1" 
> accession="generic|B_GENSCAN00000004093|" 
> id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
>
> is referenced by
>
>   <PeptideEvidence 
> dBSequence_ref="dbseq_generic|B_GENSCAN00000004093|" 
> peptide_ref="FAALDNEEEDK_" start="241" end="251" pre="K" post="E" 
> isDecoy="false" 
> id="FAALDNEEEDK_generic|B_GENSCAN00000004093|_241_251"></PeptideEvidence>
>
> but this PeptideEvidence is not a decoy and has also no genome mapping 
> information defined,
> but the specification document defines in Figure 5 that the CV terms 
> must be present on every PeptideEvidence, unless ifDecoy="true"
>
> Best wishes,
> Gerhard
>
> Am 26.01.2017 um 13:52 schrieb mayerg97:
>
>     Hi Fawaz and Andy,
>
>     it's because there are DBSequences contained, which have no genome
>     mapping defined, e.g.
>
>       <DBSequence searchDatabase_ref="SearchDB_1"
>     accession="generic|B_GENSCAN00000004093|"
>     id="dbseq_generic|B_GENSCAN00000004093|"></DBSequence>
>       <DBSequence searchDatabase_ref="SearchDB_1"
>     accession="generic|B_GENSCAN00000027223|"
>     id="dbseq_generic|B_GENSCAN00000027223|"></DBSequence>
>       <DBSequence searchDatabase_ref="SearchDB_1"
>     accession="generic|B_GENSCAN00000009965|"
>     id="dbseq_generic|B_GENSCAN00000009965|"></DBSequence>
>       <DBSequence searchDatabase_ref="SearchDB_1"
>     accession="generic|B_GENSCAN00000034417|"
>     id="dbseq_generic|B_GENSCAN00000034417|"></DBSequence>
>
>     If we want to allow here both sequences with and without genome
>     mapping, we can change the
>
>     ProteogenomicsDBSequence_must_rule
>
>     into a SHOULD rule instead.
>
>     Best wishes,
>     Gerhard
>
>     Am 26.01.2017 um 13:14 schrieb Jones, Andy:
>
>         Hi Fawaz,
>
>         I don't see anything wrong with this - Gerhard, do you have any ideas?
>
>         Thanks
>
>         Andy
>
>         -----Original Message-----
>
>         From: Ghali, Fawaz
>
>         Sent: 26 January 2017 11:55
>
>         To: Jones, Andy<jo...@li...> <mailto:jo...@li...>
>
>         Subject: ProteoAnnotator_1_2.mzid
>
>         Hi Andy,
>
>         ProteoAnnotator_1_2.mzid has an error:
>
>         Message 1:
>
>              Rule ID: ProteogenomicsDBSequence_must_rule
>
>              Level: ERROR
>
>              Context(/cvParam/@accession ) in 380 locations
>
>              --> None of the given CvTerms were found at '/MzIdentML/SequenceCollection/DBSequence/cvParam/@accession' because no values were found:
>
>            - The sole term MS:1002637 (chromosome name) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>
>            - The sole term MS:1002638 (chromosome strand) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>
>            - The sole term MS:1002644 (genome reference version) or any of its children. A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
>
>         Example:
>
>            <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000395953|" id="dbseq_generic|A_ENSP00000395953|">
>
>              <cvParam cvRef="PSI-MS" accession="MS:1002637" name="chromosome name" value="11"></cvParam>
>
>              <cvParam cvRef="PSI-MS" accession="MS:1002638" name="chromosome strand" value="+"></cvParam>
>
>              <cvParam cvRef="PSI-MS" accession="MS:1002644" name="genome reference version" value="Homo_sapiens.GRCh38.77.gff3"></cvParam>
>
>            </DBSequence>
>
>         Why it's complaining about the name?
>
>         Best wishes,
>
>         Fawaz
>
>     -- 
>
>     *--------------------------------------------------------------------*
>
>     *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
>     *PhD student*
>
>     *Medizinisches Proteom-Center*
>
>     *DEPARTMENT Medical Bioinformatics*
>
>     *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
>
>     *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554
>
>     *E-mail *ger...@ru... <mailto:ger...@ru...>
>
>     www.medizinisches-proteom-center.de
>     <http://www.medizinisches-proteom-center.de/>
>
> -- 
>
> *--------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *PhD student*
>
> *Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
>
> *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554
>
> *E-mail *ger...@ru... <mailto:ger...@ru...>
>
> www.medizinisches-proteom-center.de 
> <http://www.medizinisches-proteom-center.de/>
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*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>