psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] PSI 2018 Spring meeting

[Jones, A. <And...@li...>]

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

[Psidev-ms-dev] correct URL for namespace and QName missing namespace

[Damon B. <dam...@gm...>]

Following the xlmns link within the imzML1.1.0.xsd doesn't go anywhere, the
link needs to be updated.

schema xmlns:dx="http://psi.hupo.org/ms/mzml"

The following generates an error because the type is missing a namespace.

<xs:element name="binary" type="none">

[Psidev-ms-dev] hyperlink to mzML 1.1.0 xsd is broken

[Damon B. <dam...@gm...>]

The hyperlink to "mzml1.1.0.xsd (main schema)" on the PSI webpage
http://psidev.info/mzml_1_0_0%20  is broken.  The hyperlink tries to go to

http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/schema/mzML1.1.0.xsd

but the following error is show in the browser

The psidev project's CVS data is in read-only mode, so the project may have
switched over to another source-code-management system. To check,
visit the Project
Summary Page for psidev <https://sourceforge.net/projects/psidev> and see
if the menubar lists a newer code repository, such as SVN or Git.

The CVS data can be accessed as follows. You can run a per-module CVS
checkout via pserver protocol:
- *cvs -z3 -d:pserver:anonymous@a.cvs.sourceforge.net:/cvsroot/psidev co -P
htdocs*
- *cvs -z3 -d:pserver:anonymous@a.cvs.sourceforge.net:/cvsroot/psidev co -P
ppp*
- *cvs -z3 -d:pserver:anonymous@a.cvs.sourceforge.net:/cvsroot/psidev co -P
psi*
- *cvs -z3 -d:pserver:anonymous@a.cvs.sourceforge.net:/cvsroot/psidev co -P
psi-ms*

You can view a list of files or copy all the CVS repository data via rsync
(the 1st command lists the files, the 2nd copies):
- *rsync -a a.cvs.sourceforge.net::cvsroot/psidev/*
- *rsync -ai a.cvs.sourceforge.net::cvsroot/psidev/ /my/local/dest/dir/*

If you are a project admin for psidev, you can request that this page
redirect to another repo on your project by submitting a support request
<https://sourceforge.net/support>.

[Psidev-ms-dev] New version 4.1.1 of psi-ms.obo

[Mayer, G. <may...@ru...>]

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

[Psidev-ms-dev] Release candidate 4.1.1_rc2 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

[Psidev-ms-dev] ProteomeXchange related terms part 2

[Juan A. V. <ju...@eb...>]

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

[Psidev-ms-dev] Release candidate 4.1.1_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

[Psidev-ms-dev] New version 4.1.0 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

[Psidev-ms-dev] New version 4.0.19 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

Re: [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 4.0.19_rc1 of psi-ms.obo

[Binz Pierre-A. <Pie...@ch...>]

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

[Psidev-ms-dev] Release candidate 4.0.19_rc1 of psi-ms.obo

[Mayer, G. <gm...@eb...>]

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

[Psidev-ms-dev] New version 4.0.18 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

[Psidev-ms-dev] Release candidate 4.0.18_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

[Psidev-ms-dev] revised version R1 of HUPO PSI recommendation document (file format proBAM), 3-weeks public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

meanwhile the authors of the proBAM specification have submitted a revised
version, 

also reacting on the reviewers’ comments.

Attached are the revised specification document and a file with responses to
all

reviewers’ comments.

 

Also, all necessary information can be found on
http://www.psidev.info/proBAM, 

including links to the documents and example files (accommodating all the 

implemented changes suggested by the reviewers).

 

If you want to comment on the revised version, leave a comment on the web
page

http://www.psidev.info/proBAM-in-docproc

or e-mail me until November 15th.

 

  Many thanks for your work

     Martin

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF 0.056 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

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

 



 

Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Donnerstag, 30. März 2017 09:50
An: 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'ps...@eb...'
<ps...@eb...>; 'psi...@eb...' <psi...@eb...>
Betreff: HUPO PSI recommendation document (file format proBAM), 60-days
public review

 

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

http://www.psidev.info for an overview of activities).

 

A recommendation document specifying the proBAM file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBAM-in-docproc

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 31st May 2017).

 

The format represents output from proteogenomic studies,

mapping the MS-based proteomics PSM information to 

the genome. Background: The proBAM format builds upon the structure of the

original SAM/BAM format (http://samtools.github.io/hts-specs/SAMv1.pdf)

by extending it with other mandatory fields to accommodate unique features

on MS-based proteomics peptide-spectrum matches (PSMs) information.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBAM-in-docproc) 

or send them directly to martin.eisenacher: at : rub.de for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

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

 



 

[Psidev-ms-dev] Tool Training for Proteomics in Bochum

[Julian U. <jul...@ru...>]

Dear colleague,
dear member of the proteomics community,

we would like to call your attention to the training course
    "Tool Training for Proteomics“
which we will be hosted on 7th December 2017 at Ruhr-University Bochum
as part of de.NBI (www.denbi.de).

As the number of participants is limited, please register soon at
https://goo.gl/sd7bMc if you are interested.

Further information about the course is also available at
http://www.denbi.de/22-training-cat/training-courses/418-ttp

If you have any questions don’t hesitate to contact us via
bio...@ru...

Please also forward this message to potentially interested colleagues.

Best regards,
    Julian Uszkoreit

-- 
Dr. rer. nat. JULIAN USZKOREIT
PostDoc
Ruhr-Universität Bochum
Medizinisches Proteom-Center
DEPARTMENTS Medical Bioinformatics / Functional Proteomics
Building ZKF 1.054 | Universitätsstr. 150 | D-44801 Bochum
Fon +49 (0)234 32 29275 | Fax +49 (0)234 32 14554
E-Mail jul...@ru...

[Psidev-ms-dev] New version 4.0.17 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

[Psidev-ms-dev] Release candidate 4.0.17_rc2

[mayerg97 <ger...@ru...>]

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/>

[Psidev-ms-dev] EuBIC 2018 developer’s meeting - Meeting registration & program

[EuBIC developer's m. <eu...@gm...>]

*— EuBIC 2018 developer’s meeting —*

Dear colleague,


We are happy to announce that the registration for the EuBIC 2018
developer’s meeting has now been opened. We encourage everyone to register
in a timely manner as the number of participants is limited and to be able
to enjoy the reduced early bird rate.


The meeting’s program has also been finalized, with various interesting
hackathon projects and keynote speakers. Please find more information below
and on the meeting website.


We look forward to meeting you in Ghent!


*Meeting registration*


More information: http://uahost.uantwerpen.be/eubic18/registration.html


Early registration fees:

- General registration: €100

- PhD student at Ghent University: €50


The registration fees cover the following activities and items:

- Meeting attendance

- On-site catering including coffee breaks and lunches

- Opening reception

- Closing lunch


Additionally you can join the social event on Wednesday 10th January for
€10.


*Hackathon projects*

More information: http://uahost.uantwerpen.be/eubic18/hackathon.html


Topics for the hackathon sessions are divided into the (i) quality control,
(ii) workflows, protocols, and guidelines, and (iii) quantification tracks.
You can find more information on the specific topics included in these
three tracks on the meeting’s website.
You can indicate the project to which you want to contribute during the
registration.


*Keynote speakers*


More information: http://uahost.uantwerpen.be/eubic18/keynote.html


The meeting is honored to welcome the following keynote speakers:

- dr. Laurent Gatto, Cambridge University, United Kingdom

- prof. dr. Lukas Käll, KTH Royal Institute of Technology, Sweden

- dr. Frédérique Lisacek, SIB Swiss Institute of Bioinformatics, Switzerland

- prof. dr. Lennart Martens, Ghent University, Belgium


*Other useful information*


Date: January 9-12, 2018

Location: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium

Venue: http://uahost.uantwerpen.be/eubic18/venue.html

Transport: http://uahost.uantwerpen.be/eubic18/transport.html

Accommodation: http://uahost.uantwerpen.be/eubic18/accommodation.html


*Key dates*


November 10, 2017: Early bird meeting registration deadline

December 22, 2017: Late meeting registration deadline

January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent


*More information*


- website: http://uahost.uantwerpen.be/eubic18/

- social media hashtag: #EuBIC18

- conference email: eu...@gm...


*Sponsorship *inquiries are still welcome at eu...@gm....


Supported by FWO Scientific Research Network ‘Novel Knowledge from Public
Life Sciences Data'.

[Psidev-ms-dev] Release candidate 4.0.17_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

[Psidev-ms-dev] New version 4.0.16 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

Re: [Psidev-ms-dev] [Psi-announce] Proteomics Standards Initiative summary article now open access

[Sandra O. <or...@eb...>]

Tweeted from @psicquic, if anyone would like to contribute a retweet.

Sandra


On 28/09/2017 20:49, Eric Deutsch wrote:
>
> 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
>
>
>
> _______________________________________________
> Psi-announce mailing list
> Psi...@eb...
> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

-- 
Sandra Orchard

Protein Function Content Team Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

phone: 01223 494675
fax: 01223 494468
email: or...@eb...

[Psidev-ms-dev] Release candidate 4.0.16_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>

[Psidev-ms-dev] Proteomics Standards Initiative summary article now open access

[Eric D. <ede...@sy...>]

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

[Psidev-ms-dev] REVIEW PHASE ENDS SOON! HUPO PSI recommendation document (file format PSI-MI XML 3.0.0), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

 

The 60-days public comments and external 

review phase for PSI-MI XML 3.0.0 ends soon! (29th September 2017).

 

  Best regards 

    Martin Eisenacher (PSI Editor)

 

 

Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Freitag, 28. Juli 2017 17:10
An: 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'ps...@eb...'
<ps...@eb...>; 'psi...@eb...' <psi...@eb...>
Betreff: HUPO PSI recommendation document (file format PSI-MI XML 3.0.0),
60-days public review

 

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

http://www.psidev.info for an overview of activities).

 

There has been a submission to the PSI Document Process 

by the Molecular Interactions workgroup updating the 

PSI-MI format to version 3.0.0 

(from long-time stable XML 2.5, released 2005).

 

The submission (incl. current version of the specification document) can

be found here:

http://www.psidev.info/PSI-MI-in-docproc

 

After having passed a review of the PSI steering group 

with minor changes, the proposed document version 3.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 29th September 2017).

 

Purpose of the format (excerpt from the spec. doc.):

“The existing XML standard (PSI-MI XML2.5) has proven to be, 

and will continue to be, capable of capturing the vast majority 

of molecular interaction data, which are generated by 

techniques such as protein complementation assays, 

affinity capture, biophysical measurements and enzyme assays. 

However, use cases have arisen which cannot be adequately 

described within this XML schema, for example allosteric 

interactions, abstracted interactions and dynamic interactions. 

In order to meet these specialist use cases, a new version of

the XML format has been developed, PSI-MI XML3.0.”

 

Specification document: attached and at

http://www.psidev.info/PSI-MI-in-docproc

Schema MIF300.xsd:
https://github.com/HUPO-PSI/miXML/blob/master/3.0/src/MIF300.xsd 

Schema documentation (Schema browser):
<https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html>
https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html

Schema documentation and use case examples (as Word docs.): 

See appendix documents

at https://github.com/HUPO-PSI/miXML/tree/master/3.0/pub 

or
<https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0>
https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0

(details of appendices in the spec. doc. and below).

 

 PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/PSI-MI-in-docproc) 

or send them directly to martin.eisenacher: at : rub.de for 

example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

 


1.      Appendices


Example files showing how the schema meets each of the use cases listed in
section 1.3. Note, all examples available in the IntAct database (
<http://www.ebi.ac.uk/intact> www.ebi.ac.uk/intact) unless otherwise stated


1.1         Appendix 1 Schema documentation for MIF300.xsd


1.2         Appendix 2 Example file showing the representation of all
molecular interaction data from a single publication (PMID: 26919541) in
PSI-MI XML3.0 – note, includes use case 1.3k, rewrite of bibliography
section


1.3         Appendix 3 Representation of a negative feature range (use case
1.3a)


1.4         Appendix 4 Representation of the sequence change caused by
introduction of a mutation (use case 1.3b)


1.5         Appendix 5 Representation of multiple feature detection methods
and feature roles (use cases 1.3c, 1.3d)


1.6         Appendix 6 Representation of kinetic parameters added at feature
level (use case 1.3e)


1.7         Appendix 7 Representation of variable conditions (dynamic
interactions) in an experiment (use case 1.3f)


1.8         Appendix 8 Representation of an abstracted interaction, a
manually curated protein complex, in PSI-MI XML3.0 (use case 1.3g)


1.9         Appendix 9 Representation of a cooperative interaction in PSI-MI
XML3.0 (Use case 1.3h)


1.10     Appendix 10 Representation of molecule sets i.e. cases where a
participant may be one of a list of molecules (use case 1.3i)


1.11     Appendix 11 Representation of the systematic capture of the
stoichiometry of molecules within an interaction (use case 1.3j)


 

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

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

 



 

 

[Psidev-ms-dev] New version 4.0.15 of psi-ms.obo

[mayerg97 <ger...@ru...>]

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/>