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From: andrewrobertjones <not...@gi...> - 2016-04-26 08:57:10
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Hi @ypriverol These are the start positions within exons. This peptide is mapped across a splice junction, so there is the start point within the first exon, then start position within exon 2. I have added the explanation of the encoding to the spec doc. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-214672102 |
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From: Juan A. V. <not...@gi...> - 2016-04-27 08:40:05
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About the concatenated searches, this is not a unique case for proteogenomics. People can make the same (e.g. organisms that don't have a complete genome sequences, and sequences are merged together from different sources). I don't know if this case was explained before in detail in the specification document, but whatever is decided for proteogenomics should be applicable to these cases as well. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-215012253 |
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From: Juan A. V. <not...@gi...> - 2016-04-27 08:50:14
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Do we need to consider at all that a zero-based coordinate system in used in Bed and BAM files, but not in GFF3/GTF files? I guess it is good to assume that we will use a zero-based coordinate system by default. This should be written in the specification document. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-215014952 |
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From: andrewrobertjones <not...@gi...> - 2016-04-28 14:25:57
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@javizca I would vote for the coordinate system being used in mzIdentML is always zero based. If you writing back to GFF afterwards, you would need to do a conversion. This seems safer than having two ways of doing it, and then assuming a reading software will check this parameter. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-215442939 |
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From: andrewrobertjones <not...@gi...> - 2016-05-10 10:11:46
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These points were provisionally agreed on last call. @germa would you mind updating the mapping and validator. Please email me if anything is unclear. @fghali please can you update our example file before the call tomorrow if possible. 1. Proteogenomics – Agreed to move chromosome name and strand to DBSequence (protein-level), also move Genome reference version to DBSequence; Remove “peptide start position on chromosome” as redundant info, this is not needed for the encoding --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-218115381 |
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From: andrewrobertjones <not...@gi...> - 2016-05-11 15:08:32
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@fghali can you let us know when this has been checked versus example files, then close this issue --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-218488936 |
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From: F. G. <not...@gi...> - 2016-05-12 12:34:56
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I'm getting these errors when trying to validate the file using: mzIdentMLValidator_GUI_v1.4.16-SNAPSHOT
`
Message 1:
Rule ID: PeptideLevelStatsObjectRule
Level: ERROR
Context(/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem )
--> The SpectrumIdentificationItem (id='SIR_3007_SII_2') element at /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem doesn't contain the triplet of terms MS:1002520 (peptide group ID), MS:1002500 (peptide passes threshold) and a child of MS:1002358 (search engine specific score for distinct peptides) required in case of peptide-level scoring
Tip: Add the triplet of terms MS:1002520 (peptide group ID), MS:1002500 (peptide passes threshold) and a child of MS:1002358 (search engine specific score for distinct peptides) to each SpectrumIdentificationItem
Message 2:
Rule ID: SpectrumIdentificationList_must_rule
Level: ERROR
Context(/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/cvParam/@accession' because no values were found:
- Any children term of MS:1002438 (spectrum identification list result details). A single instance of this term can be specified. The matching value has to be the identifier of the term, not its name.
Message 3:
Rule ID: ProteinDetectionList_must_rule
Level: ERROR
Context(/cvParam/@accession ) in 2 locations
--> None of the given CvTerms were found at '/MzIdentML/DataCollection/AnalysisData/ProteinDetectionList/cvParam/@accession' because no values were found:
- The sole term MS:1002404 (count of identified proteins) 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.
`
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From: andrewrobertjones <not...@gi...> - 2016-05-13 14:07:12
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@germa Can you investigate Message 1, I can't obviously spot what is wrong with our file https://github.com/HUPO-PSI/mzIdentML/blob/master/examples/1_2examples/ProteoAnnotator/ProteoAnnotator_1_2.mzid.gz In terms of Message 2, we decided to role back on this rule so it is no longer required, and can be safely deleted from mapping file: Rule ID: SpectrumIdentificationList_must_rule @fghali Message 3 is something for you to fix. MS:1002404 needs to be on the ProteinDetectionList, with a value of the number of PAGs with passThreshold=true. This should be inserted by ProteoGrouper. If you need help with this part of (my) code, let me know --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219052974 |
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From: Gerhard M. <not...@gi...> - 2016-05-13 16:16:14
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Message 1: PeptideLevelStatsObjectRule The reason is that the EBI-OLS changed. I think the validation framework from the EBI, from which our validator inherits is not yet adapted to the new Open Lookup Service. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219089796 |
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From: Juan A. V. <not...@gi...> - 2016-05-13 17:37:00
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Thanks @germa, I had not realised about this. In the last 2 weeks we had to update some of the OLS related libraries that are used in our tools because of this. We need to investigate this in detail. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219109797 |
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From: Yasset Perez-R. <not...@gi...> - 2016-05-13 18:19:33
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@germa we implemented the new ols-client and ols-dialog you can used them. Please they are here: OLS-CLIENT https://github.com/PRIDE-Utilities/ols-client OLS_DIALOG https://github.com/PRIDE-Toolsuite/ols-dialog --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219120848 |
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From: Noemi d. T. A. <not...@gi...> - 2016-05-16 08:54:14
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Hi, Related with OLS too. Max from PSI-MI is updating the ontology-manager to the new version from OLS because it is needed for IntAct. I think it is a dependency for the validator framework too. Previously was hosted in the sourceforge svn with other tools https://sourceforge.net/p/psidev/svn/HEAD/tree/psi/tools/ontology-manager/ We are thinking that if you agree, it can be moved to GitHub under HUPO-PSI and share there our changes because they are common libraries and tools for PSI, however until this moment only the specification documents have been hosted in the organisation. What do you think? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219379176 |
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From: Juan A. V. <not...@gi...> - 2016-05-16 09:00:09
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I think it is perfectly fine --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219380210 |
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From: F. G. <not...@gi...> - 2016-06-01 08:42:52
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Closed #4. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#event-678102993 |
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