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From: Omenn, G. <go...@me...> - 2018-01-31 17:03:42
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Dear Andy, Eric, and Colleagues--
Have a great meeting. You have a good list of worthy topics.
I remain keenly interested in being part of the group, but the dates are infeasible, as I am booked for Chicago for the American Assn for Cancer Research and the American Society for Clinical Investigation/Association of American Physicians meetings back-to-back all week.
We need to figure out how to capture MS findings for proteotypic peptides from additional data resources besides PeptideAtlas for curation and acceptance into neXtProt. I hope your discussion about spectral data library findings will consider the approach of El Guoshy and Yamamoto in the Dec 2017 Journal of Proteome Research 5th annual special issue from the HUPO Human Proteome Project (attached).
Best wishes
Gil
From: <psi...@eb...> on behalf of Andy Jones <And...@li...>
Date: Wednesday, January 31, 2018 at 11:40 AM
To: "'psi...@eb...'" <psi...@eb...>
Cc: "'psi...@li...'" <psi...@li...>, "'psi...@li...'" <psi...@li...>
Subject: [Psi-announce] PSI 2018 Spring meeting
Dear colleagues,
We are pleased to announce that the PSI 2018 Spring meeting is now open for registration (http://www.psidev.info/content/hupo-psi-meeting-2018). PSI2018 will take place April 18-20th 2018 at EMBL, Heidelberg in Germany. The meeting is free of charge for participants (including lunches, refreshments and a workshop dinner).
The main topics for discussion will working on the new spectral library data format, the Universal spectrum ID, PEFF (extended fasta format) and PROXI (web services API). There will be a track focussing on metabolomics (mzTab format), further work on quality control (qcML) and developments in the molecular interactions group including implementations of MI XML 3.0, CausalTab format, and identification of novel interactions in interactomes.
The PSI always welcomes new participants with an interest in getting involved in proteomics data standards. Please feel free to register and come along to see what we are doing, or forward this message on to other colleagues who may be interested.
http://www.psidev.info/content/hupo-psi-meeting-2018
Best wishes
Andy Jones
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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From: Jones, A. <And...@li...> - 2018-01-31 16:40:29
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Dear colleagues, We are pleased to announce that the PSI 2018 Spring meeting is now open for registration (http://www.psidev.info/content/hupo-psi-meeting-2018). PSI2018 will take place April 18-20th 2018 at EMBL, Heidelberg in Germany. The meeting is free of charge for participants (including lunches, refreshments and a workshop dinner). The main topics for discussion will working on the new spectral library data format, the Universal spectrum ID, PEFF (extended fasta format) and PROXI (web services API). There will be a track focussing on metabolomics (mzTab format), further work on quality control (qcML) and developments in the molecular interactions group including implementations of MI XML 3.0, CausalTab format, and identification of novel interactions in interactomes. The PSI always welcomes new participants with an interest in getting involved in proteomics data standards. Please feel free to register and come along to see what we are doing, or forward this message on to other colleagues who may be interested. http://www.psidev.info/content/hupo-psi-meeting-2018 Best wishes Andy Jones |
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From: Mayer, G. <may...@ru...> - 2018-01-19 12:34:20
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Dear proteomics community, the new version 4.1.1 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It adds some new terms from PRIDE CV. New CV terms in version 4.1.1 of psi-ms.obo: ============================================ [Term] id: MS:1002844 name: Experiment additional parameter def: "Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam." [PSI:PI] is_a: MS:1001458 ! spectrum generation information [Term] id: MS:1002845 name: Associated file URI def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002846 name: Associated raw file URI def: "URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002847 name: ProteomeCentral dataset URI def: "URI associated to one PX submission in ProteomeCentral." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002848 name: Result file URI def: "URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002849 name: Search engine output file URI def: "URI of one search engine output file associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002850 name: Peak list file URI def: "URI of one of one search engine output file associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002851 name: Other type file URI def: "URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002852 name: Dataset FTP location def: "FTP location of one entire PX data set." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002853 name: Dataset with no associated published manuscript def: "A dataset which does not have an associated published manuscript." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002854 name: Peer-reviewed dataset def: "Dataset has been peer-reviewed somehow." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002855 name: Non peer-reviewed dataset def: "Dataset that has not been peer-reviewed by any means." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002856 name: Supported dataset by repository def: "The PX dataset is supported by and is available through the submission repository." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002857 name: Unsupported dataset by repository def: "The PX dataset is not fully supported by the submission repository." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002858 name: Dataset with its publication pending def: "A dataset which has an associated manuscript pending for publication." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002859 name: Additional associated raw file URI def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002860 name: Gel image file URI def: "URI of one gel image file associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002861 name: Reprocessed complete dataset def: "All the raw files included in the original dataset (or group of original datasets) have been reanalysed." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002862 name: Reprocessed subset dataset def: "A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002863 name: Data derived from previous dataset def: "One dataset is a reanalysis of previously published data." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002864 name: No PTMs are included in the dataset def: "No post-translational-modifications are been included in the identified peptides of one dataset." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002865 name: Accepted manuscript def: "A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002866 name: Reference def: "Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002867 name: Experimental information has been refined since this experiment was originally made publicly available def: "This means that the experimental information available has been improved, for instance precursor charges were added." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002868 name: Original data def: "One dataset is not a reanalysis of previously published data." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter Changed CV terms in version 4.1.1 of psi-ms.obo: ================================================ ************ No changed terms Best Regards, Gerhard |
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From: mayerg97 <ger...@ru...> - 2018-01-15 13:54:18
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Dear proteomics community, following are the changes for the release candidate 4.1.1_rc2 of the psi-ms.obo file. It integrates some terms from the PRIDE-CV. New CV terms in version 4.1.1_rc2 of psi-ms.obo: ================================================ [Term] id: MS:1002844 name: Experiment additional parameter def: "Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam." [PSI:PI] is_a: MS:1001458 ! spectrum generation information [Term] id: MS:1002845 name: Associated file URI def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002846 name: Associated raw file URI def: "URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002847 name: ProteomeCentral dataset URI def: "URI associated to one PX submission in ProteomeCentral." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002848 name: Result file URI def: "URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002849 name: Search engine output file URI def: "URI of one search engine output file associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002850 name: Peak list file URI def: "URI of one of one search engine output file associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002851 name: Other type file URI def: "URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002852 name: Dataset FTP location def: "FTP location of one entire PX data set." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002853 name: Dataset with no associated published manuscript def: "A dataset which does not have an associated published manuscript." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002854 name: Peer-reviewed dataset def: "Dataset has been peer-reviewed somehow." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002855 name: Non peer-reviewed dataset def: "Dataset that has not been peer-reviewed by any means." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002856 name: Supported dataset by repository def: "The PX dataset is supported by and is available through the submission repository." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002857 name: Unsupported dataset by repository def: "The PX dataset is not fully supported by the submission repository." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002858 name: Dataset with its publication pending def: "A dataset which has an associated manuscript pending for publication." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002859 name: Additional associated raw file URI def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002860 name: Gel image file URI def: "URI of one gel image file associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002861 name: Reprocessed complete dataset def: "All the raw files included in the original dataset (or group of original datasets) have been reanalysed." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002862 name: Reprocessed subset dataset def: "A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002863 name: Data derived from previous dataset def: "One dataset is a reanalysis of previously published data." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002864 name: No PTMs are included in the dataset def: "No post-translational-modifications are been included in the identified peptides of one dataset." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002865 name: Accepted manuscript def: "A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002866 name: Reference def: "Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002867 name: Experimental information has been refined since this experiment was originally made publicly available def: "This means that the experimental information available has been improved, for instance precursor charges were added." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002868 name: Original data def: "One dataset is not a reanalysis of previously published data." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter Changed CV terms in version 4.1.1_rc2 of psi-ms.obo: ==================================================== ************ No changed terms Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *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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From: Juan A. V. <ju...@eb...> - 2018-01-15 10:01:34
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Hi Gerhard, The other day, I forgot to add these extra terms. Apologies for this, my mistake. Again, thanks a lot in advance. It is really appreciated. Best regards, Juan Antonio First of all, please add two new terms, needed to handle reprocessed datasets in PX: [Term] id: MS: ??? name: Reprocessed complete dataset comment: All the raw files included in the original dataset (or group of original datasets) have been reanalysed. xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: MS: ??? name: Reprocessed subset dataset comment: A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed. xref: value-type:xsd\:string "The allowed value-type for this CV term." And then, please add some extra PX related terms from the PRIDE CV that I did not include in the original e-mail the other day. [Term] id: PRIDE:0000397 name: Data derived from previous dataset comment: One dataset is a reanalysis of previously published data is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000398 name: No PTMs are included in the dataset comment: No post-translational-modifications are been included in the identified peptides of one dataset is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000399 name: Accepted manuscript comment: A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet. is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000400 name: Reference xref: value-type:xsd\:string "The allowed value-type for this CV term." comment: Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet. is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000401 name: Experimental information has been refined since this experiment was originally made publicly available comment: This means that the experimental information available has been improved, for instance precursor charges were added. is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000402 name: Original data comment: One dataset is not a reanalysis of previously published data is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav |
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From: mayerg97 <ger...@ru...> - 2018-01-10 15:04:48
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Dear proteomics community, following are the changes for the release candidate 4.1.1_rc1 of the psi-ms.obo file. It integrates some terms from the PRIDE-CV. New CV terms in version 4.1.1_rc1 of psi-ms.obo: ================================================ [Term] id: MS:1002844 name: Experiment additional parameter def: "Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam." [PSI:PI] is_a: MS:1001458 ! spectrum generation information [Term] id: MS:1002845 name: Associated file URI def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002846 name: Associated raw file URI def: "URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002847 name: ProteomeCentral dataset URI def: "URI associated to one PX submission in ProteomeCentral." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002848 name: Result file URI def: "URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002849 name: Search engine output file URI def: "URI of one search engine output file associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002850 name: Peak list file URI def: "URI of one of one search engine output file associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002851 name: Other type file URI def: "URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002852 name: Dataset FTP location def: "FTP location of one entire PX data set." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002853 name: Dataset with no associated published manuscript def: "A dataset which does not have an associated published manuscript." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002854 name: Peer-reviewed dataset def: "Dataset has been peer-reviewed somehow." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002855 name: Non peer-reviewed dataset def: "Dataset that has not been peer-reviewed by any means." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002856 name: Supported dataset by repository def: "The PX dataset is supported by and is available through the submission repository." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002857 name: Unsupported dataset by repository def: "The PX dataset is not fully supported by the submission repository." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002858 name: Dataset with its publication pending def: "A dataset which has an associated manuscript pending for publication." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002859 name: Additional associated raw file URI def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI [Term] id: MS:1002860 name: Gel image file URI def: "URI of one gel image file associated to one PX submission." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002845 ! Associated file URI Changed CV terms in version 4.1.1_rc1 of psi-ms.obo: ==================================================== ************ No changed terms Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *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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From: Juan A. V. <ju...@eb...> - 2018-01-09 15:32:26
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Hi Gerhard, Could you please add the following CV terms coming from the PRIDE CV to the PSI-MS CV? PRIDE CVs accession numbers would need to be replace by MS accession numbers. These terms were originally created a few years ago (2011) to support the generation of the ProteomeXchange XML message, and at the time, we decided to use the PRIDE CV because PSI-MS did not look suitable at the time. But now that PX has grown, in parallel to the scope of the PSI-MS CV, it is the right time to have those terms in PSI MS as well. Also, they would not be the first ones to be created in the PSI-MS CV related to PX. Thanks a lot in advance, Juan Antonio [Term] id: PRIDE:0000403 name: Associated file URI comment: URI of one external file associated to the PRIDE experiment (maybe through a PX submission). xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000404 name: Associated raw file URI comment: URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000403 ! Associated file URI created_by: jav [Term] id: PRIDE:0000406 name: ProteomeCentral dataset URI def: "URI associated to one PX submission in ProteomeCentral." [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000407 name: Result file URI def: "URI of one file labeled as 'Result', associated to one PX submission." [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000403 ! Associated file URI created_by: jav [Term] id: PRIDE:0000408 name: Search engine output file URI def: "URI of one search engine output file associated to one PX submission." [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000403 ! Associated file URI created_by: jav [Term] id: PRIDE:0000409 name: Peak list file URI def: "URI of one of one search engine output file associated to one PX submission." [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000403 ! Associated file URI created_by: jav [Term] id: PRIDE:0000410 name: 'Other' type file URI def: "URI of one file labeled as 'Other', associated to one PX submission." [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000403 ! Associated file URI created_by: jav [Term] id: PRIDE:0000411 name: Dataset FTP location def: "FTP location of one entire PX data set." [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000412 name: Dataset with no associated published manuscript def: "A dataset which does not have an associated published manuscript." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000414 name: Peer-reviewed dataset def: "Dataset has been peer-reviewed somehow." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000415 name: Non peer-reviewed dataset def: "Dataset that has not been peer-reviewed by any means." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000416 name: Supported dataset by repository def: "The PX dataset is supported by and is available through the submission repository." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000417 name: Unsupported dataset by repository def: "The PX dataset is not fully supported by the submission repository." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter created_by: jav [Term] id: PRIDE:0000432 name: Dataset with its publication pending comment: A dataset which has an associated manuscript pending for publication. is_a: PRIDE:0000006 ! Experiment additional parameter created_by: rw [Term] id: PRIDE:0000448 name: Additional associated raw file URI comment: Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE. xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000403 ! Associated file URI created_by: jav [Term] id: PRIDE:0000449 name: Gel image file URI comment: URI of one gel image file associated to one PX submission. xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PRIDE:0000403 ! Associated file URI created_by: tt |
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From: mayerg97 <ger...@ru...> - 2017-12-22 15:47:00
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Dear proteomics community, sorry, I forgot to add the relationship to the parent 'PEFF CV term' and increased also the version numbering to 4.1.0 The new version 4.1.0 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo Changed CV terms in version 4.1.0 of psi-ms.obo: ================================================ ************ Added relationship: part_of MS:0000000 [Term] id: PEFF:0000001 name: PEFF CV term def: "PSI Extended FASTA Format Controlled Vocabulary term." [PSI:PEFF] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *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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From: mayerg97 <ger...@ru...> - 2017-12-22 13:28:37
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Dear proteomics community, the new version 4.0.19 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains the new terms for the upcoming PEFF standard. New CV terms in version 4.0.19 of psi-ms.obo: ============================================= [Term] id: PEFF:0000001 name: PEFF CV term def: "PSI Extended FASTA Format Controlled Vocabulary term." [PSI:PEFF] [Term] id: PEFF:0000002 name: File Header Section term def: "CV term that may appear in a PEFF File Header Section." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000003 name: Individual Sequence Entries Section term def: "CV term that may appear in a PEFF Individual Entry Section." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000008 name: DbName def: "Sequence Database Name." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000009 name: Prefix def: "Sequence Database Prefix." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000010 name: DbDescription def: "Sequence Database Short description." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000011 name: Decoy def: "Specifies whether the Sequence Database is a Decoy." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:boolean "The allowed value-type for this CV term." [Term] id: PEFF:0000012 name: DbSource def: "Source of the database file." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000013 name: DbVersion def: "Database version (release date) according to database provider." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000014 name: DbDate def: "Database date (release or file date of the source) according to database provider." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term is_obsolete: true [Term] id: PEFF:0000015 name: NumberOfEntries def: "Number of sequence entries in the database." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:integer "The allowed value-type for this CV term." [Term] id: PEFF:0000016 name: Conversion def: "Description of the conversion from original format to this current one." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000017 name: SequenceType def: "Molecular type of the sequences." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002002 ! (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+) [Term] id: PEFF:0000018 name: SpecificKey def: "Db specific information (not included in the current list of allowed keys)." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000019 name: SpecificValue def: "PEFF specific values for a defined key." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000020 name: DatabaseDescription def: "Short Description of the PEFF." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000021 name: GeneralComment def: "PEFF file general comment." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000022 name: ProteoformDb def: "Proteoform database flag." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000023 name: CustomTag def: "A tag (short string) used to categorize a sequence annotation (variant or modification)." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001001 name: DbUniqueId def: "Sequence Database unique identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001002 name: PName def: "Protein Name, description." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001003 name: NcbiTaxId def: "NCBI taxonomy identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:int "The allowed value-type for this CV term." [Term] id: PEFF:0001004 name: TaxName def: "Taxonomy name (latin or common name)." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001005 name: GName def: "Gene name." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001006 name: Length def: "Sequence length." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:int "The allowed value-type for this CV term." [Term] id: PEFF:0001007 name: SV def: "Sequence version." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001008 name: EV def: "Entry version." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001009 name: PE def: "Protein Evidence; A UniprotKB code." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:int "The allowed value-type for this CV term." [Term] id: PEFF:0001010 name: Processed def: "Processed Molecule." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001011 name: Variant def: "DEPRECATED in favor of VariantSimple and VariantComplex. Former definition: Sequence variation (substitution, insertion, deletion)." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001012 name: ModResPsi def: "Modified residue with PSI-MOD identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001013 name: ModRes def: "Modified residue without PSI-MOD identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001014 name: AltAC def: "Alternative Accession Code." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001015 name: SeqStatus def: "Sequence Status. Complete or Fragment." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002003 ! \(Complete|Fragment|[a-z0-9A-Z]+) [Term] id: PEFF:0001016 name: CC def: "Entry associated comment." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001017 name: KW def: "Entry associated keyword(s)." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001018 name: GO def: "Gene Ontology code." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001019 name: XRef def: "Cross-reference to an external resource." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001020 name: Chain def: "Sequence range of active processed polypeptide." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001021 name: Signal def: "Sequence range of signal peptide." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001022 name: Transit def: "Sequence range of transit peptide." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001023 name: Conflict def: "Sequence conflict; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001024 name: Crc64 def: "Sequence checksum in crc64." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001025 name: Domain def: "Sequence range of a domain." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001026 name: ID def: "UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001027 name: ModResUnimod def: "Modified residue with Unimod identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001028 name: VariantSimple def: "Simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001029 name: VariantComplex def: "Simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:1002001 name: \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) def: "Regular expression for PEFF description line value with three components." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002002 name: (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+) def: "Regular expression for the molecular type of the sequences." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002003 name: \(Complete|Fragment|[a-z0-9A-Z]+) def: "Regular expression for the Sequence Status." [PSI:PEFF] is_a: MS:1002479 ! regular expression Best Regards, Merry Christmas and a happy New Year Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *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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From: Binz Pierre-A. <Pie...@ch...> - 2017-12-20 16:08:00
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Hi Gerhard, Many thanks for putting this PEFF CV into PSI-MS. A general comment: we need to add the possibility to have the optional tags in a number of sequence specific terms values. This means that the regexp has to allow the additional |nnnnn string at the end of the alphanumeric string. Change term: [Term] Id: PEFF:1000015 name: SeqStatus def: "Sequence Status. Complete or Fragment." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." -> relationship: has_regexp PEFF:1002003 ! \(Complete|Fragment|[a-z0-9A-Z]+) Add new term: [Term] id: PEFF:1002003 name: (Complete|Fragment|[a-z0-9A-Z]+) def: "Regular expression for the Sequence Status." [PSI:PEFF] is_a: MS:1002479 ! regular expression Cheers Pierre-Alain -----Message d'origine----- De : Mayer, Gerhard [mailto:gm...@eb...] Envoyé : mercredi 20 décembre 2017 14:58 À : psi...@li...; psi...@li...; Mass spectrometry standard development <psi...@li...> Objet : [Psidev-pi-dev] Release candidate 4.0.19_rc1 of psi-ms.obo Dear proteomics community, following are the changes for the release candidate 4.0.19_rc1 of the psi-ms.obo file. It contains the new terms for the upcoming PEFF standard. New CV terms in version 4.0.19_rc1 of psi-ms.obo: ================================================= [Term] id: PEFF:0000001 name: PEFF CV term def: "PSI Extended FASTA Format Controlled Vocabulary term." [PSI:PEFF] [Term] id: PEFF:0000002 name: File Header Section term def: "CV term that may appear in a PEFF File Header Section." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000003 name: Individual Sequence Entries Section term def: "CV term that may appear in a PEFF Individual Entry Section." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000008 name: DbName def: "Sequence Database Name." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000009 name: Prefix def: "Sequence Database Prefix." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000010 name: DbDescription def: "Sequence Database Short description." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000011 name: Decoy def: "Specifies whether the Sequence Database is a Decoy." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:boolean "The allowed value-type for this CV term." [Term] id: PEFF:0000012 name: DbSource def: "Source of the database file." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000013 name: DbVersion def: "Database version (release date) according to database provider." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000014 name: DbDate def: "Database date (release or file date of the source) according to database provider." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term is_obsolete: true [Term] id: PEFF:0000015 name: NumberOfEntries def: "Number of sequence entries in the database." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:integer "The allowed value-type for this CV term." [Term] id: PEFF:0000016 name: Conversion def: "Description of the conversion from original format to this current one." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000017 name: SequenceType def: "Molecular type of the sequences." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002002 ! (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+) [Term] id: PEFF:0000018 name: SpecificKey def: "Db specific information (not included in the current list of allowed keys)." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000019 name: SpecificValue def: "PEFF specific values for a defined key." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000020 name: DatabaseDescription def: "Short Description of the PEFF." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000021 name: GeneralComment def: "PEFF file general comment." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000022 name: ProteoformDb def: "Proteoform database flag." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000023 name: CustomTag def: "A tag (short string) used to categorize a sequence annotation (variant or modification)." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001001 name: DbUniqueId def: "Sequence Database unique identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001002 name: PName def: "Protein Name, description." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001003 name: NcbiTaxId def: "NCBI taxonomy identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:int "The allowed value-type for this CV term." [Term] id: PEFF:0001004 name: TaxName def: "Taxonomy name (latin or common name)." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001005 name: GName def: "Gene name." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001006 name: Length def: "Sequence length." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:int "The allowed value-type for this CV term." [Term] id: PEFF:0001007 name: SV def: "Sequence version." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001008 name: EV def: "Entry version." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001009 name: PE def: "Protein Evidence; A UniprotKB code." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:int "The allowed value-type for this CV term." [Term] id: PEFF:0001010 name: Processed def: "Processed Molecule." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001011 name: Variant def: "DEPRECATED in favor of VariantSimple and VariantComplex. Former definition: Sequence variation (substitution, insertion, deletion)." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001012 name: ModResPsi def: "Modified residue with PSI-MOD identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001013 name: ModRes def: "Modified residue without PSI-MOD identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001014 name: AltAC def: "Alternative Accession Code." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001015 name: SeqStatus def: "Sequence Status. Complete or Fragment." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001016 name: CC def: "Entry associated comment." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001017 name: KW def: "Entry associated keyword(s)." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001018 name: GO def: "Gene Ontology code." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001019 name: XRef def: "Cross-reference to an external resource." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001020 name: Chain def: "Sequence range of active processed polypeptide." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001021 name: Signal def: "Sequence range of signal peptide." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001022 name: Transit def: "Sequence range of transit peptide." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001023 name: Conflict def: "Sequence conflict; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001024 name: Crc64 def: "Sequence checksum in crc64." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001025 name: Domain def: "Sequence range of a domain." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001026 name: ID def: "UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001027 name: ModResUnimod def: "Modified residue with Unimod identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001028 name: VariantSimple def: "Simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001029 name: VariantComplex def: "Simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:1002001 name: \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) def: "Regular expression for PEFF description line value with three components." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002002 name: (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+) def: "Regular expression for the molecular type of the sequences." [PSI:PEFF] is_a: MS:1002479 ! regular expression Changed CV terms in version 4.0.19_rc1 of psi-ms.obo: ===================================================== ************ No changed terms Best Regards, Gerhard |
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From: Mayer, G. <gm...@eb...> - 2017-12-20 13:57:57
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Dear proteomics community, following are the changes for the release candidate 4.0.19_rc1 of the psi-ms.obo file. It contains the new terms for the upcoming PEFF standard. New CV terms in version 4.0.19_rc1 of psi-ms.obo: ================================================= [Term] id: PEFF:0000001 name: PEFF CV term def: "PSI Extended FASTA Format Controlled Vocabulary term." [PSI:PEFF] [Term] id: PEFF:0000002 name: File Header Section term def: "CV term that may appear in a PEFF File Header Section." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000003 name: Individual Sequence Entries Section term def: "CV term that may appear in a PEFF Individual Entry Section." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000008 name: DbName def: "Sequence Database Name." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000009 name: Prefix def: "Sequence Database Prefix." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000010 name: DbDescription def: "Sequence Database Short description." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000011 name: Decoy def: "Specifies whether the Sequence Database is a Decoy." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:boolean "The allowed value-type for this CV term." [Term] id: PEFF:0000012 name: DbSource def: "Source of the database file." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000013 name: DbVersion def: "Database version (release date) according to database provider." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000014 name: DbDate def: "Database date (release or file date of the source) according to database provider." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term is_obsolete: true [Term] id: PEFF:0000015 name: NumberOfEntries def: "Number of sequence entries in the database." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:integer "The allowed value-type for this CV term." [Term] id: PEFF:0000016 name: Conversion def: "Description of the conversion from original format to this current one." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000017 name: SequenceType def: "Molecular type of the sequences." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002002 ! (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+) [Term] id: PEFF:0000018 name: SpecificKey def: "Db specific information (not included in the current list of allowed keys)." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000019 name: SpecificValue def: "PEFF specific values for a defined key." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000020 name: DatabaseDescription def: "Short Description of the PEFF." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000021 name: GeneralComment def: "PEFF file general comment." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000022 name: ProteoformDb def: "Proteoform database flag." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0000023 name: CustomTag def: "A tag (short string) used to categorize a sequence annotation (variant or modification)." [PSI:PEFF] is_a: PEFF:0000002 ! File Header Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001001 name: DbUniqueId def: "Sequence Database unique identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001002 name: PName def: "Protein Name, description." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001003 name: NcbiTaxId def: "NCBI taxonomy identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:int "The allowed value-type for this CV term." [Term] id: PEFF:0001004 name: TaxName def: "Taxonomy name (latin or common name)." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001005 name: GName def: "Gene name." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001006 name: Length def: "Sequence length." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:int "The allowed value-type for this CV term." [Term] id: PEFF:0001007 name: SV def: "Sequence version." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001008 name: EV def: "Entry version." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001009 name: PE def: "Protein Evidence; A UniprotKB code." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:int "The allowed value-type for this CV term." [Term] id: PEFF:0001010 name: Processed def: "Processed Molecule." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001011 name: Variant def: "DEPRECATED in favor of VariantSimple and VariantComplex. Former definition: Sequence variation (substitution, insertion, deletion)." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001012 name: ModResPsi def: "Modified residue with PSI-MOD identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001013 name: ModRes def: "Modified residue without PSI-MOD identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001014 name: AltAC def: "Alternative Accession Code." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001015 name: SeqStatus def: "Sequence Status. Complete or Fragment." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001016 name: CC def: "Entry associated comment." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001017 name: KW def: "Entry associated keyword(s)." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001018 name: GO def: "Gene Ontology code." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001019 name: XRef def: "Cross-reference to an external resource." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001020 name: Chain def: "Sequence range of active processed polypeptide." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001021 name: Signal def: "Sequence range of signal peptide." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001022 name: Transit def: "Sequence range of transit peptide." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001023 name: Conflict def: "Sequence conflict; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001024 name: Crc64 def: "Sequence checksum in crc64." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001025 name: Domain def: "Sequence range of a domain." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001026 name: ID def: "UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." [Term] id: PEFF:0001027 name: ModResUnimod def: "Modified residue with Unimod identifier." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001028 name: VariantSimple def: "Simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:0001029 name: VariantComplex def: "Simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] is_a: PEFF:0000003 ! Individual Sequence Entries Section term xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) [Term] id: PEFF:1002001 name: \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\) def: "Regular expression for PEFF description line value with three components." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002002 name: (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+) def: "Regular expression for the molecular type of the sequences." [PSI:PEFF] is_a: MS:1002479 ! regular expression Changed CV terms in version 4.0.19_rc1 of psi-ms.obo: ===================================================== ************ No changed terms Best Regards, Gerhard |
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From: mayerg97 <ger...@ru...> - 2017-11-14 14:55:14
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Dear proteomics community, the new version 4.0.18 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains terms for the binary mzMLb format and for describing external references. New CV terms in version 4.0.18 of psi-ms.obo: ============================================= ************ New terms for the binary mzMLb format [Term] id: MS:1002838 name: mzMLb format def: "mzMLb file format, mzML encapsulated within HDF5." [PSI:PI, https://github.com/biospi/mzmlb] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002839 name: Conversion to mzMLb def: "Conversion of a file format to Proteomics Standards Initiative mzMLb file format." [PSI:PI] is_a: MS:1000530 ! file format conversion ************ New terms for data characterizing extrenal references [Term] id: MS:1002840 name: external reference data def: "Data belonging to an external reference." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1002841 name: external HDF5 dataset def: "The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the <binary> section of the BinaryDataArray." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002840 ! external reference data [Term] id: MS:1002842 name: external offset def: "The position in the external data where the array begins." [PSI:PI] xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." relationship: has_units UO:0000189 ! Count is_a: MS:1002840 ! external reference data [Term] id: MS:1002843 name: external array length def: "Describes how many fields an array contains." [PSI:PI] xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." relationship: has_units UO:0000189 ! Count is_a: MS:1002840 ! external reference data Changed CV terms in version 4.0.18 of psi-ms.obo: ================================================= ************ Is now a child of MS:1002840 ! external reference data [Term] id: MS:1000878 name: external reference identifier def: "An identifier/accession number to an external reference database." [PSI:MS] is_a: MS:1002840 ! external reference data ************ Changed is_a: MS:1000878 ! external reference identifier ************ --> is_a: MS:1002840 ! external reference data [Term] id: MS:1001923 name: external reference keyword def: "Free text attribute that can enrich the information about an entity." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002840 ! external reference data Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *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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From: mayerg97 <ger...@ru...> - 2017-11-06 10:12:39
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Dear proteomics community, following are the changes for the release candidate 4.0.18_rc1 of the psi-ms.obo file. It contains terms for the binary mzMLb format and for describing external references. New CV terms in version 4.0.18_rc1 of psi-ms.obo: ================================================= ************ New terms for the binary mzMLb format [Term] id: MS:1002838 name: mzMLb format def: "mzMLb file format, mzML encapsulated within HDF5." [PSI:PI, https://github.com/biospi/mzmlb] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002839 name: Conversion to mzMLb def: "Conversion of a file format to Proteomics Standards Initiative mzMLb file format." [PSI:PI] is_a: MS:1000530 ! file format conversion ************ New terms for data characterizing extrenal references [Term] id: MS:1002840 name: external reference data def: "Data belonging to an external reference." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1002841 name: external HDF5 dataset def: "The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the <binary> section of the BinaryDataArray." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002840 ! external reference data [Term] id: MS:1002842 name: external offset def: "The position in the external data where the array begins." [PSI:PI] xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." relationship: has_units UO:0000189 ! Count is_a: MS:1002840 ! external reference data [Term] id: MS:1002843 name: external array length def: "Describes how many fields an array contains." [PSI:PI] xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." relationship: has_units UO:0000189 ! Count is_a: MS:1002840 ! external reference data Changed CV terms in version 4.0.18_rc1 of psi-ms.obo: ===================================================== ************ Is now a child of MS:1002840 ! external reference data [Term] id: MS:1000878 name: external reference identifier def: "An identifier/accession number to an external reference database." [PSI:MS] is_a: MS:1002840 ! external reference data ************ Changed is_a: MS:1000878 ! external reference identifier ************ --> is_a: MS:1002840 ! external reference data [Term] id: MS:1001923 name: external reference keyword def: "Free text attribute that can enrich the information about an entity." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002840 ! external reference data Best Regards, Gerhard -- *--------------------------------------------------------------------* *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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From: mayerg97 <ger...@ru...> - 2017-10-13 09:37:47
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Dear proteomics community, the new version 4.0.17 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains a new term for the LTQ Orbitrap Classic instrument and two terms for iProX. New CV terms in version 4.0.17 of psi-ms.obo: ============================================= [Term] id: MS:1002835 name: LTQ Orbitrap Classic def: "Thermo Fisher Scientific LTQ Orbitrap Classic." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002836 name: iProX dataset identifier def: "Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1002837 name: iProX dataset URI def: "URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier Best Regards, Gerhard -- *--------------------------------------------------------------------* *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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From: mayerg97 <ger...@ru...> - 2017-10-11 07:56:10
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Dear proteomics community, following are the changes for the release candidate 4.0.17_rc2 of the psi-ms.obo file. It contains a new term for the LTQ Orbitrap Classic instrument and two terms for iProX. New CV terms in version 4.0.17_rc2 of psi-ms.obo: ================================================= [Term] id: MS:1002835 name: LTQ Orbitrap Classic def: "Thermo Fisher Scientific LTQ Orbitrap Classic." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002836 name: iProX dataset identifier def: "Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1002837 name: iProX dataset URI def: "URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier Best Regards, Gerhard -- *--------------------------------------------------------------------* *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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From: mayerg97 <ger...@ru...> - 2017-10-09 12:51:50
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Dear proteomics community, following are the changes for the release candidate 4.0.17_rc1 of the psi-ms.obo file. It contains a new term for the LTQ Orbitrap Classic instrument. New CV terms in version 4.0.17_rc1 of psi-ms.obo: ================================================= [Term] id: MS:1002835 name: LTQ Orbitrap Classic def: "Thermo Fisher Scientific LTQ Orbitrap Classic." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model Best Regards, Gerhard -- *--------------------------------------------------------------------* *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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From: mayerg97 <ger...@ru...> - 2017-10-06 14:44:27
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Dear proteomics community, the new version 4.0.16 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains a new term for ProteomeDiscoverer. New CV terms in version 4.0.16 of psi-ms.obo: ============================================= [Term] id: MS:1002834 name: ProteomeDiscoverer:Delta Score def: "The Delta Score reported by Proteome Discoverer version 2." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic Best Regards, Gerhard -- *--------------------------------------------------------------------* *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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From: mayerg97 <ger...@ru...> - 2017-09-28 20:46:35
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Dear proteomics community, attached there's the release candidate 4.0.16_rc1 of the psi-ms.obo file. It contains a new term for ProteomeDiscoverer. New CV terms in version 4.0.16_rc1 of psi-ms.obo: ================================================= [Term] id: MS:1002834 name: ProteomeDiscoverer:Delta Score def: "The Delta Score reported by Proteome Discoverer version 2." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic Best Regards, Gerhard -- *--------------------------------------------------------------------* *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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From: Eric D. <ede...@sy...> - 2017-09-28 20:20:54
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Hi everyone, in case you have not seen it yet, our latest summary of past, ongoing, and future activities of the Proteomics Standards Initiative is now published and open access at JPR: http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.7b00370 I encourage everyone that hasn’t read it yet to have a look and become more involved in PSI than you have been so far. There are still lots of great projects to work on in order to further the mission of the PSI. And citations of this work when mentioning the PSI would great as well. https://www.ncbi.nlm.nih.gov/pubmed/28849660 Regards, Eric |
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From: mayerg97 <ger...@ru...> - 2017-09-18 10:39:01
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Dear proteomics community, attached there's the new version 4.0.15 of the psi-ms.obo file. It contains new terms for the MetaMorpheus search engine, new terms for the metabolomics software package XCMS, a new term for 'alternating polarity mode'. New CV terms in version 4.0.15 of psi-ms.obo: ============================================= ************ new terms for the MetaMorpheus search engine [Term] id: MS:1002826 name: MetaMorpheus def: "MetaMorpheus search engine." [https://github.com/smith-chem-wisc/MetaMorpheus] is_a: MS:1001456 ! analysis software [Term] id: MS:1002827 name: MetaMorpheus:score def: "MetaMorpheus score for PSMs." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1002828 name: MetaMorpheus:protein score def: "MetaMorpheus score for protein groups." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better ************ new terms for XCMS [Term] id: MS:1002829 name: XCMS:into def: "Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype [Term] id: MS:1002830 name: XCMS:intf def: "Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype [Term] id: MS:1002831 name: XCMS:maxo def: "Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype [Term] id: MS:1002832 name: XCMS:area def: "Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype ************ new term 'alternating polarity mode' [Term] id: MS:1002833 name: alternating polarity mode def: "Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired." [PSI:PI] is_a: MS:1000857 ! run attribute Changed CV terms in version 4.0.15 of psi-ms.obo: ================================================= ************ Changed the definition [Term] id: MS:1000465 name: scan polarity def: "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS] relationship: part_of MS:1000441 ! scan ************ Added synonyms [Term] id: MS:1001309 name: Lys-C def: "Endoproteinase Lys-C." [PSI:PI] synonym: "Trypsin/K" EXACT [] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001335 ! (?<=K)(?!P) Best Regards, Gerhard -- *--------------------------------------------------------------------* *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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From: mayerg97 <ger...@ru...> - 2017-09-15 09:12:52
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Dear proteomics community, attached there's the release candidate 4.0.15_rc3 of the psi-ms.obo file. It contains new terms for the MetaMorpheus search engine, new terms for the metabolomics software package XCMS, a new term for 'alternating polarity mode' and two new cleavage agent terms: New CV terms in version 4.0.15_rc3 of psi-ms.obo: ================================================= ************ new terms for the MetaMorpheus search engine [Term] id: MS:1002826 name: MetaMorpheus def: "MetaMorpheus search engine." [https://github.com/smith-chem-wisc/MetaMorpheus] is_a: MS:1001456 ! analysis software [Term] id: MS:1002827 name: MetaMorpheus:score def: "MetaMorpheus score for PSMs." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1002828 name: MetaMorpheus:protein score def: "MetaMorpheus score for protein groups." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better ************ new terms for XCMS [Term] id: MS:1002829 name: XCMS:into def: "Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype [Term] id: MS:1002830 name: XCMS:intf def: "Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype [Term] id: MS:1002831 name: XCMS:maxo def: "Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype [Term] id: MS:1002832 name: XCMS:area def: "Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype ************ new term 'alternating polarity mode' [Term] id: MS:1002833 name: alternating polarity mode def: "Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired." [PSI:PI] is_a: MS:1000857 ! run attribute ************ new cleavage agent terms [Term] id: MS:1002834 name: (?<=[K])(?\!P) def: "Regular expression for Trypsin/K." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1002835 name: Trypsin/K def: "Cleavage agent Trypsin/K." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1002834 ! (?<=[K])(?\!P) [Term] id: MS:1002836 name: (?<=[R])(?\!P) def: "Regular expression for Trypsin/R." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1002837 name: Trypsin/R def: "Cleavage agent Trypsin/R." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1002834 ! (?<=[R])(?\!P) Changed CV terms in version 4.0.15_rc3 of psi-ms.obo: ===================================================== ************ Changed the definition [Term] id: MS:1000465 name: scan polarity def: "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS] relationship: part_of MS:1000441 ! scan Best Regards, Gerhard -- *--------------------------------------------------------------------* *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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From: mayerg97 <ger...@ru...> - 2017-09-08 13:18:47
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Dear proteomics community, attached there's the release candidate 4.0.15_rc2 of the psi-ms.obo file. It contains new terms for the MetaMorpheus search engine, new terms for the metabolomics software package XCMS and a new term for 'alternating polarity mode', New CV terms in version 4.0.15_rc2 of psi-ms.obo: ================================================= ************ new terms for the MetaMorpheus search engine [Term] id: MS:1002826 name: MetaMorpheus def: "MetaMorpheus search engine." [https://github.com/smith-chem-wisc/MetaMorpheus] is_a: MS:1001456 ! analysis software [Term] id: MS:1002827 name: MetaMorpheus:score def: "MetaMorpheus score for PSMs." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1002828 name: MetaMorpheus:protein score def: "MetaMorpheus score for protein groups." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better ************ new terms for XCMS [Term] id: MS:1002829 name: XCMS:into def: "Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype [Term] id: MS:1002830 name: XCMS:intf def: "Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype [Term] id: MS:1002831 name: XCMS:maxo def: "Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype [Term] id: MS:1002832 name: XCMS:area def: "Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype ************ new term 'alternating polarity mode' [Term] id: MS:1002833 name: alternating polarity mode def: "Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired." [PSI:PI] is_a: MS:1000857 ! run attribute Changed CV terms in version 4.0.15_rc2 of psi-ms.obo: ===================================================== ************ Changed the definition [Term] id: MS:1000465 name: scan polarity def: "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS] relationship: part_of MS:1000441 ! scan Best Regards, Gerhard -- *--------------------------------------------------------------------* *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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From: mayerg97 <ger...@ru...> - 2017-09-06 09:04:48
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Hello Steffen, would it make sense to make 'alternating polarity scan' a child of 'run attribute'? [Term] id: MS:1002826 name: alternating polarity mode def: "Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired." [PSI:MS] is_a: MS:1000857 ! run attribute Cheers, Gerhard Am 24.08.2017 um 00:16 schrieb sneumann: > > Hi, the reason I brought this up was because ISA-Tab is describing the > content of an mzML file, i.e. an attribute of the |<run>| as such > being positive/negative/alternating. > As indicated in my first comment, "alternating" can't be a scan > attribute, but when I searched our obo for "alternating" that parent > term came up. Maybe that was the reason why alternating was obsoleted: > https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo#L3241 > So a better home for "alternating polarity" could be "MS:1001954 > acquisition parameter" (which currently has no children at all ?!) and > which resides below the |<scanSettings>| of the mzML, > which I think is the closest to describing the instrument method we > can find in mzML. > The mapping file currently does not specify which CV terms can go > below |<scanSettings>|. > I also realised we had obsoleted "ionization mode" > https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo#L111 , > which probably sounded a bad idea as scan attribute, but which might > have been good to keep among the |<scanSettings>|. > > So what about: > > 1. Grammar fix, plus removal of mentioning alternating as scan attribute: > > |[Term] id: MS:1000465 name: scan polarity def: "An acquisition mode to > which specifies whether polarity is negative or positive." [PSI:MS] > relationship: part_of MS:1000441 ! scan | > > 2. still add "alternating", but with different parent than proposed > above: > > |[Term] id: MS:1000XXX name: alternating polarity mode def: "Polarity > of the scans is alternating, i.e. both positive and negative mode > scans are acquired.[PSI:MS] is_a: MS:1000009 ! ionization mode | > > 3. Consider re-adding MS:1000009 ! ionization mode, but now as > acquisition parameter (not sure what it was before): > > |[Term] id: MS:1000009 name: ionization mode def: "Whether positive or > negative ions are selected for analysis by the spectrometer." [PSI:MS] > is_a: MS:1001954 ! acquisition parameter | > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <https://github.com/HUPO-PSI/psi-ms-CV/issues/7#issuecomment-324478232>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ADJPfHFTaplW-9_kaetXCkqBJS5mRqHJks5sbKSrgaJpZM4O_syz>. > -- *--------------------------------------------------------------------* *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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From: Jones, A. <And...@li...> - 2017-08-24 11:45:13
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Here is copied a message I just posted on the mzTab for metabolomics google group. Copied here for information, since proteomics people may be interested in discussions around mzTab development. Best wishes Andy ***** Hi all, For those of you who were not at the EBI the last couple of days, here is a quick summary of what was discussed and decided at the workshop. Longer version of the minutes are here: https://docs.google.com/document/d/1d77BzfyZLCz-5TPiVEun-8G8VBOxGOjkD-HhaqWanz4/edit Outcomes We are working towards an mzTab-M 1.1 release over the next few months, and there is a spec doc in GitHub that is close to release candidate status. In this document, the proteomics aspects have been stripped out, and it has been separated into core and metabolomics parts. At the moment, there is no impetus to move proteomics to 1.1 release, so for now mzTab 1.0 is the stable proteomics standard. When further implementations are developed, then it might be that there is a desire to develop an mzTab-P 1.1 or 1.2 version, to fix bugs etc. Towards release candidate, then release: - We will convert the spec doc to an ascii doc format, which can be rendered for viewing, but can also be picked up by software - Nils is going to work on this. - Nils is going to develop jmzTab and validation - Joel is going to update the Progenesis QI exporter - Steffen has already implemented a draft XCMS to mzTab exporter The overall plan is to produce a release candidate over the next month or so, then look to submit to a document process before the year end. A PSI-like document process will be run, probably under an MSI banner. We will resume fortnightly calls later on in Sept, and will make active use of GitHub issues list. I will also update the existing issues, with things discussed and resolved in the meeting. best wishes Andy |
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From: Eric D. <ede...@sy...> - 2017-08-23 18:00:14
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Hi everyone, I just updated the Hub page with the latest information about Sunday: https://github.com/CompMS/Overview/wiki/HUPO-2017 Please update the Doodle poll with your availability so that we can plan accordingly: http://doodle.com/poll/runkh2uwb5ztnmry We know people are going to be there, please put your name down! Yasset, Yassene, Lennart, Yves, Sue, Sam, David, Nuno, Henry, Hannes, George, Mohammed, Steffen, Sandra, Gerben, everyone else, please respond! Thanks, Eric *From:* Juan Antonio Vizcaino [mailto:ju...@eb...] *Sent:* Monday, August 21, 2017 8:50 AM *To:* 'psi...@li...' ( psi...@li...) <Psi...@li...>; Mass spectrometry standard development <psi...@li...>; co...@go... *Cc:* Lennart Martens <len...@UG...>; Yasset Perez-Riverol < yp...@eb...>; Andy Jones <And...@li...>; Eric Deutsch < ede...@sy...>; Henning Hermjakob <hh...@eb...>; Mathias Walzer <wa...@eb...> *Subject:* Preparations for the Bioinformatics Hub at HUPO 2017 Dear all, In order to make some preparations for the “Bioinformatics Hub” during HUPO 2017 in Dublin, we would need to know who is planning to attend the event. I have created a Doodle poll to record this information. Please select those days where you are planning to go to the event. It does not mean that you will not be there all the time, but at least you are planning to spend some time there: http://doodle.com/poll/runkh2uwb5ztnmry It is important to highlight that for Sunday (September 17th), the event will not take place in the convention center. It will take place in the O’Brien Science Centre on the UCD Campus, as the other events planned for Sunday morning/early afternoon. So, extra arrangements need to be done for that day. We have been asked by the organisers to tell everyone that will be attending the event on Sunday to get registered properly for the "Bioinformatics Hub" (for planning the catering, among other reasons). To register, you need to send an e-mail to: HU...@co... I will also create an issue in the CompMS GitHub page, containing this information. This is the wiki page for the event. The content at this point is what we did in Taiwan last year: https://github.com/CompMS/Overview/wiki/HUPO-2017 Best regards, Juan P.S. Please send this e-mail to anyone that you think would be interested in attending. |
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