Element <ProteomeXchangeDataset>

Definition:

Top-level element for a ProteomeXchange XML document describing a dataset.

Type:

ProteomeXchangeDatasetType

Attributes:

Attribute Name	Data Type	Use	Definition
formatVersion	versionRegex	required	Version number of this ProteomeXchange XML format.
id	xs:string	required	Unique identifier for this ProteomeXchange XML document.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
CvList	1	1	The list of controlled vocabularies used in the file.
ChangeLog	0	1	The change log message to record what changes and updates were made to this dataset for a revised announcement.
DatasetSummary	1	1	Broad description of the dataset being announced, inlcuding a title, abstract, review level, etc.
DatasetIdentifierList	1	1	The list of identifiers associated with this dataset, not just the PXD identifier, but possibly DOIs and other identifiers.
DatasetOriginList	1	1	The list of the origins of this dataset. This list can link to other ProteomeXchange datasets or other resources. If this dataset contains previously unreported data, then a 'new dataset' annotation should be used.
SpeciesList	1	1	The list of species from which the data has been generated.
InstrumentList	1	1	The list of instruments on which the data generation was performed.
ModificationList	1	1	The list of amino acid mass modifications caused or considered, defined as cvParams.
ContactList	1	1	The list of contacts related to the ProteomeXchange dataset.
PublicationList	1	1	The list of publications from which the dataset was collected or wherein it is published
KeywordList	1	1	Keywords defined by controlled vocabulary or free text categorised by a controlled vocabolary term (e.g. 'journal article keyword', 'submitter keyword' or 'curator keyword').
FullDatasetLinkList	1	1	The list of links to the complete ProteomeXchange dataset.
DatasetFileList	0	1	The list of ALL files comprising this ProteomeXchange submission.
RepositoryRecordList	0	1	The list of records as found in the repository the data was submitted to (for example PRIDE experiment records).
AdditionalInformation	0	1	A place for all additional information that may be added to the broadcast message and that could not be fit into another location. Here should also go references to other ProteomeXchange submissions.

Example Context:

<ProteomeXchangeDataset id="PXD002167" formatVersion="1.3.0" xsi:noNamespaceSchemaLocation="proteomeXchange-1.3.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <CvList>
        <Cv fullName="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="MS"/>
        <Cv fullName="PRIDE" uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo" id="PRIDE"/>
        <Cv fullName="PSI-MOD" uri="http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/PSI-MOD.obo" id="MOD"/>
        <Cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/>
    </CvList>
  ...
</ProteomeXchangeDataset>

Element <AdditionalInformation>

Definition:

A place for all additional information that may be added to the broadcast message and that could not be fit into another location. Here should also go references to other ProteomeXchange submissions.

Type:

AdditionalInformationType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Element <AnnotationList>

Definition:

Any additional annotation of the record/experiment that the submitter/generator of the message deems important enough to announce.

Type:

AdditionalInformationType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Element <ChangeLog>

Definition:

The change log message to record what changes and updates were made to this dataset for a revised announcement.

Type:

ChangeLogType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ChangeLogEntry	1	unbounded	A single change log entry giving providing the date on the change, a new version number of the dataset and a description of the change/update.

Example Context:

<ChangeLog>
    <ChangeLogEntry date="2016-06-08">Updated publication reference for PubMed record(s): 27251877.</ChangeLogEntry>
</ChangeLog>

Element <ChangeLogEntry>

Definition:

A single change log entry giving providing the date on the change, a new version number of the dataset and a description of the change/update.

Type:

ChangeLogEntryType

Attributes:

Attribute Name	Data Type	Use	Definition
date	xs:date	optional	The date of this entry. This is largely handled by the central ProteomeXchange service anyway, and is largly ignored.
version	xs:string	optional	The version number of this document. The first change would be version 2 here. This is largely handled by the central ProteomeXchange service anyway, and is largly ignored.

Subelements:

none

Example Context:

<ChangeLogEntry date="2016-06-08">Updated publication reference for PubMed record(s): 27251877.</ChangeLogEntry>

Element <Contact>

Definition:

Contact person related to the ProteomeXchange dataset.

Type:

ContactType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the contact to be used for referencing within a document.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<Contact id="project_lab_head">
    <cvParam cvRef="MS" accession="MS:1002332" name="lab head"/>
    <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Peter Barr-Gillespie"/>
    <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="gillespp@ohsu.edu"/>
    <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Oregon Hearing Research Center Oregon Health & Science University Portland  OR  97239  USA"/>
</Contact>

cvParam Mapping Rules:

Path /ProteomeXchangeDataset/ContactList/Contact
MAY supply a *child* term of MS:1000585 (contact attribute) one or more times
  e.g.: MS:1000586 (contact name) 
  e.g.: MS:1000587 (contact address) 
  e.g.: MS:1000588 (contact URL) 
  e.g.: MS:1000589 (contact email) 
  e.g.: MS:1000590 (contact affiliation) 
  e.g.: MS:1001267 (software vendor) 
  e.g.: MS:1001268 (programmer) 
  e.g.: MS:1001269 (instrument vendor) 
  e.g.: MS:1001270 (lab personnel) 
  e.g.: MS:1001271 (researcher) 
  et al.
MUST supply term MS:1000590 (contact affiliation) only once
MUST supply term MS:1000586 (contact name) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Xu Jiang"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="mango0414@163.com"/>
<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="PHD candidate"/>
<cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/>
<cvParam cvRef="MS" accession="MS:1002332" name="lab head"/>

Element <ContactList>

Definition:

The list of contacts related to the ProteomeXchange dataset.

Type:

ContactListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Contact	1	unbounded	Contact person related to the ProteomeXchange dataset.

Example Context:

<ContactList>
    <Contact id="project_submitter">
        <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Peter Barr-Gillespie"/>
        <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="gillespp@ohsu.edu"/>
        <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Oregon Hearing Research Center"/>
        <cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/>
    </Contact>
  ...
</ContactList>

Element <Cv>

Definition:

A source controlled vocabulary (CV) from which cvParams will be obtained.

Type:

CvType

Attributes:

Attribute Name	Data Type	Use	Definition
fullName	xs:string	required	The full name of the CV.
id	xs:ID	required	The unique identifier of this CV within the document to be referenced by cvParam elements.
uri	xs:anyURI	required	The URI of the source CV.
version	xs:string	optional	The version of the CV.

Subelements:

none

Example Context:

<Cv fullName="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="MS"/>

Element <CvList>

Definition:

The list of controlled vocabularies used in the file.

Type:

CvListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Cv	1	unbounded	A source controlled vocabulary (CV) from which cvParams will be obtained.

Example Context:

<CvList>
    <Cv fullName="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="MS"/>
    <Cv fullName="PRIDE" uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo" id="PRIDE"/>
    <Cv fullName="PSI-MOD" uri="http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/PSI-MOD.obo" id="MOD"/>
    <Cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/>
</CvList>

Element <cvParam>

Definition:

A single entry from an ontology or a controlled vocabulary.

Type:

CvParamType

Attributes:

Attribute Name	Data Type	Use	Definition
accession	xs:string	required	The accession or ID number of this CV term in the source CV.
cvRef	xs:IDREF	required	A reference to the cv element from which this term originates.
name	xs:string	required	The name of the parameter.
unitAccession	xs:string	optional	An accession number identifying the unit within the OBO foundry Unit CV.
unitCvRef	xs:string	optional	If a unit term is referenced, this attribute MUST refer to the CV 'id' attribute defined in the cvList in this file.
unitName	xs:string	optional	The name of the unit.
value	xs:string	optional	The user-entered value of the parameter.

Subelements:

none

Example Context:

<cvParam cvRef="PRIDE" accession="PRIDE:0000400" name="Reference" value="Krey JF, Drummond M, Foster S, Porsov E, Vijayakumar S, Choi D, Friderici K, Jones SM, Nuttall AL, Barr-Gillespie PG. Annexin A5 is the Most Abundant Membrane-Associated Protein in Stereocilia but is Dispensable for Hair-Bundle Development and Function. Sci Rep. 2016 Jun 2;6:27221"/>

Element <DatasetFile>

Definition:

Description of the source file, including location and type.

Type:

DatasetFileType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the sourceFile to be used for referencing within a document.
name	xs:string	required	Name of the source file, without reference to location (either URI or local path).

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<DatasetFile id="FILE_4" name="OTHER_MIAPE_PXD002167.zip">
    <cvParam cvRef="PRIDE" accession="PRIDE:0000410" name="'Other' type file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/08/PXD002167/OTHER_MIAPE_PXD002167.zip"/>
</DatasetFile>

cvParam Mapping Rules:

Path /ProteomeXchangeDataset/DatasetFileList/DatasetFile
MUST supply a *child* term of PRIDE:0000403 (Associated file URI) one or more times
  e.g.: PRIDE:0000404 (Associated raw file URI) WARNING: Term has no definition!
  e.g.: PRIDE:0000407 (Result file URI) WARNING: Term has no definition!
  e.g.: PRIDE:0000408 (Search engine output file URI) WARNING: Term has no definition!
  e.g.: PRIDE:0000409 (Peak list file URI) WARNING: Term has no definition!
  e.g.: PRIDE:0000410 ('Other' type file URI) WARNING: Term has no definition!
  e.g.: PRIDE:0000448 (Additional associated raw file URI) WARNING: Term has no definition!
  e.g.: PRIDE:0000449 (Gel image file URI) WARNING: Term has no definition!

Example cvParams:

<cvParam cvRef="PRIDE" accession="PRIDE:0000408" name="Search engine output file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003111/MS150057-1.prot.xml"/>
<cvParam cvRef="PRIDE" accession="PRIDE:0000404" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003111/MS150057-KD1.raw"/>
<cvParam cvRef="PRIDE" accession="PRIDE:0000410" name="'Other' type file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/08/PXD002167/OTHER_EXCEL_FINAL.zip"/>
<cvParam cvRef="PRIDE" accession="PRIDE:0000403" name="Associated file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/08/PXD002167/OTHER_FASTA.zip"/>

Element <DatasetFileList>

Definition:

The list of ALL files comprising this ProteomeXchange submission.

Type:

DatasetFileListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
DatasetFile	1	unbounded	Description of the source file, including location and type.

Example Context:

<DatasetFileList>
    <DatasetFile id="FILE_16" name="MS150057-1.prot.xml">
        <cvParam cvRef="PRIDE" accession="PRIDE:0000408" name="Search engine output file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003111/MS150057-1.prot.xml"/>
    </DatasetFile>
    <DatasetFile id="FILE_17" name="MS150057-KD1.raw">
        <cvParam cvRef="PRIDE" accession="PRIDE:0000404" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003111/MS150057-KD1.raw"/>
    </DatasetFile>
  ...
</DatasetFileList>

Element <DatasetIdentifier>

Definition:

An identifier associated with this dataset, defined by CV term.

Type:

DatasetIdentifierType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<DatasetIdentifier>
    <cvParam cvRef="MS" accession="MS:1001919" name="ProteomeXchange accession number" value="PXD003111"/>
</DatasetIdentifier>

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1001919" name="ProteomeXchange accession number" value="PXD003111"/>

Element <DatasetIdentifierList>

Definition:

The list of identifiers associated with this dataset, not just the PXD identifier, but possibly DOIs and other identifiers.

Type:

DatasetIdentifierListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
DatasetIdentifier	1	unbounded	An identifier associated with this dataset, defined by CV term.

Example Context:

<DatasetIdentifierList>
    <DatasetIdentifier>
        <cvParam cvRef="MS" accession="MS:1001919" name="ProteomeXchange accession number" value="PXD003111"/>
    </DatasetIdentifier>
</DatasetIdentifierList>

Element <DatasetOrigin>

Definition:

Specifies via CV term whether this is an original dataset or is a re-interpretation of a previous ProteomeXchange dataset.

Type:

DatasetOriginType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<DatasetOrigin>
    <cvParam cvRef="PRIDE" accession="PRIDE:0000402" name="Original data"/>
</DatasetOrigin>

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Example cvParams:

<cvParam cvRef="PRIDE" accession="PRIDE:0000402" name="Original data"/>

The list of the origins of this dataset. This list can link to other ProteomeXchange datasets or other resources. If this dataset contains previously unreported data, then a 'new dataset' annotation should be used.

Type:

DatasetOriginListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
DatasetOrigin	1	1	Specifies via CV term whether this is an original dataset or is a re-interpretation of a previous ProteomeXchange dataset.

Example Context:

<DatasetOriginList>
    <DatasetOrigin>
        <cvParam cvRef="PRIDE" accession="PRIDE:0000402" name="Original data"/>
    </DatasetOrigin>
</DatasetOriginList>

Element <DatasetSummary>

Definition:

Broad description of the dataset being announced, inlcuding a title, abstract, review level, etc.

Type:

DatasetSummaryType

Attributes:

Attribute Name	Data Type	Use	Definition
announceDate	xs:date	required	The date that this announcement was prepared.
hostingRepository	HostingRepositoryType	required	The hosting repository that handled this dataset and that prepared this ProteomeXchange message.
title	xs:string	required	A descriptive title for the dataset.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Description	1	1	A brief description of the dataset, usually about one paragraph long.
ReviewLevel	1	1	Level of review on this dataset/associated paper.
RepositorySupport	1	1	To what extend the data is supported in the hosting repository.

Example Context:

<DatasetSummary announceDate="2016-06-13" hostingRepository="PRIDE" title="Silencing of eIF5B Changes Proteostasis by Providing Negative Feedback on MAPK Signaling">
    <Description>Protein translational machinery is an important component of proteostasis network (PN) that maintains cellular proteostasis and regulates aging and other cellular processes. Ample evidence indicates that inhibition of translation initiation factor activities enhances stress resistance and extends life span in model organisms. Eukaryotic translation initiation factor 5B (eIF5B) is responsible for joining of pre-40S subunits with 60S ribosomal subunits to give a 80S-like complex in protein translational initiation and its silencing may disrupt proteostasis and trigger cellular processes associated with stress responses. In the present work, eIF5B was genetically manipulated in 293T cells. The physiological aspects of eIF5B-knockdown cells (eIF5B-KN) were characterized showing that they grew slower, had a lower level of intracellular reactive oxygen species (ROS), an increased resistance to oxidative stress and an enhanced autophagy. Proteomic analysis showed that silencing of eIF5B resulted in up-regulation of 88 proteins and down-regulation of 130 proteins in eIF5B-KN compared to control cells, which involved in diverse cellular processes including metabolism, RNA processing, and protein metabolism, and DNA synthesis. The autonomous downregulation of the MAPK singnaling pathway was identified that led to the prolonged S-phase cell-cycle arrest and contributed to the slow growth of eIF5B-KN cells. Glutamine transporters were found to be downregulated which enhanced formation of autophagy. Furthermore, eIF5B knockdown compromised the integrity of 28S rRNA and 8.5.8S rRNA that can be rescued via restoring the eIF5B expression level. Taken together, these results demonstrated that eIF5B silencing providesd a negative feedback to down regulate the MAPK signaling pathway which reconstitutesd the proteostasis, resulting in a decrease in cell growth and an enhanced resistance to oxidative stress. Our data provide a useful resource to further biological exploration into functions of protein synthesis in regulation of proteostasis and aging and suggest that eIF5B plays a role in aging process.</Description>
    <ReviewLevel>
        <cvParam cvRef="PRIDE" accession="PRIDE:0000414" name="Peer-reviewed dataset"/>
    </ReviewLevel>
    <RepositorySupport>
        <cvParam cvRef="PRIDE" accession="PRIDE:0000417" name="Unsupported dataset by repository"/>
  ...
</DatasetSummary>

Element <Description>

Definition:	A brief description of the dataset, usually about one paragraph long.
Type:	xs:string
Attributes:	none
Subelements:	none
Example Context:	<Description>Protein translational machinery is an important component of proteostasis network (PN) that maintains cellular proteostasis and regulates aging and other cellular processes. Ample evidence indicates that inhibition of translation initiation factor activities enhances stress resistance and extends life span in model organisms. Eukaryotic translation initiation factor 5B (eIF5B) is responsible for joining of pre-40S subunits with 60S ribosomal subunits to give a 80S-like complex in protein translational initiation and its silencing may disrupt proteostasis and trigger cellular processes associated with stress responses. In the present work, eIF5B was genetically manipulated in 293T cells. The physiological aspects of eIF5B-knockdown cells (eIF5B-KN) were characterized showing that they grew slower, had a lower level of intracellular reactive oxygen species (ROS), an increased resistance to oxidative stress and an enhanced autophagy. Proteomic analysis showed that silencing of eIF5B resulted in up-regulation of 88 proteins and down-regulation of 130 proteins in eIF5B-KN compared to control cells, which involved in diverse cellular processes including metabolism, RNA processing, and protein metabolism, and DNA synthesis. The autonomous downregulation of the MAPK singnaling pathway was identified that led to the prolonged S-phase cell-cycle arrest and contributed to the slow growth of eIF5B-KN cells. Glutamine transporters were found to be downregulated which enhanced formation of autophagy. Furthermore, eIF5B knockdown compromised the integrity of 28S rRNA and 8.5.8S rRNA that can be rescued via restoring the eIF5B expression level. Taken together, these results demonstrated that eIF5B silencing providesd a negative feedback to down regulate the MAPK signaling pathway which reconstitutesd the proteostasis, resulting in a decrease in cell growth and an enhanced resistance to oxidative stress. Our data provide a useful resource to further biological exploration into functions of protein synthesis in regulation of proteostasis and aging and suggest that eIF5B plays a role in aging process.</Description>

Element <FullDatasetLink>

Definition:

A single link to the full dataset.

Type:

FullDatasetLinkType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A single entry from an ontology or a controlled vocabulary.

Example Context:

<FullDatasetLink>
    <cvParam cvRef="PRIDE" accession="PRIDE:0000411" name="Dataset FTP location" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003111"/>
</FullDatasetLink>

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Example cvParams:

<cvParam cvRef="PRIDE" accession="PRIDE:0000411" name="Dataset FTP location" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003111"/>
<cvParam cvRef="MS" accession="MS:1001930" name="PRIDE project URI" value="http://www.ebi.ac.uk/pride/archive/projects/PXD003111"/>

Element <FullDatasetLinkList>

Definition:

The list of links to the complete ProteomeXchange dataset.

Type:

FullDatasetLinkListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
FullDatasetLink	1	unbounded	A single link to the full dataset.

Example Context:

<FullDatasetLinkList>
    <FullDatasetLink>
        <cvParam cvRef="PRIDE" accession="PRIDE:0000411" name="Dataset FTP location" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003111"/>
    </FullDatasetLink>
    <FullDatasetLink>
        <cvParam cvRef="MS" accession="MS:1001930" name="PRIDE project URI" value="http://www.ebi.ac.uk/pride/archive/projects/PXD003111"/>
    </FullDatasetLink>
  ...
</FullDatasetLinkList>

Element <Instrument>

Definition:

Instrument on which the data has been generated.

Type:

InstrumentType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the instrument to be used for referencing within a document

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<Instrument id="Instrument_1">
    <cvParam cvRef="MS" accession="MS:1001910" name="LTQ Orbitrap Elite"/>
</Instrument>

cvParam Mapping Rules:

Path /ProteomeXchangeDataset/InstrumentList/Instrument
MAY supply a *child* term of MS:1000496 (instrument attribute) one or more times
  e.g.: MS:1000032 (customization) 
  e.g.: MS:1000236 (transmission) 
  e.g.: MS:1000529 (instrument serial number) 
MUST supply term MS:1000031 (instrument model) or any of its children one or more times
  e.g.: MS:1000139 (4000 QTRAP) 
  e.g.: MS:1000140 (4700 Proteomics Analyzer) 
  e.g.: MS:1000141 (apex IV) 
  e.g.: MS:1000142 (apex Q) 
  e.g.: MS:1000143 (API 150EX) 
  e.g.: MS:1000144 (API 150EX Prep) 
  e.g.: MS:1000145 (API 2000) 
  e.g.: MS:1000146 (API 3000) 
  e.g.: MS:1000147 (API 4000) 
  e.g.: MS:1000148 (autoflex II) 
  et al.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1001911" name="Q Exactive"/>
<cvParam cvRef="MS" accession="MS:1001910" name="LTQ Orbitrap Elite"/>

Element <InstrumentList>

Definition:

The list of instruments on which the data generation was performed.

Type:

InstrumentListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Instrument	1	unbounded	Instrument on which the data has been generated.

Example Context:

<InstrumentList>
    <Instrument id="Instrument_1">
        <cvParam cvRef="MS" accession="MS:1001910" name="LTQ Orbitrap Elite"/>
    </Instrument>
</InstrumentList>

Element <InstrumentRef>

Definition:

Container for a reference to the id of an Instrument within this submission

Type:

RefType

Attributes:

Attribute Name	Data Type	Use	Definition
ref	xs:IDREF	required	A reference to an element with and id in this document.

Subelements:

none

Example Context:

Element <KeywordList>

Definition:

Keywords defined by controlled vocabulary or free text categorised by a controlled vocabolary term (e.g. 'journal article keyword', 'submitter keyword' or 'curator keyword').

Type:

KeywordListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<KeywordList>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="Hair cells, hair bundles, stereocilia, kinocilia, auditory, vestibular"/>
    <cvParam cvRef="MS" accession="MS:1001926" name="curator keyword" value="Biological"/>
</KeywordList>

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="protein synthesis; proteomics; proteostasis; eIF5B; ribosome."/>
<cvParam cvRef="MS" accession="MS:1001926" name="curator keyword" value="Biomedical"/>

Element <ModificationList>

Definition:

The list of amino acid mass modifications caused or considered, defined as cvParams.

Type:

ModificationListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<ModificationList>
    <cvParam cvRef="MOD" accession="MOD:01720" name="TMT6plex-126 reporter+balance reagent acylated residue"/>
    <cvParam cvRef="MOD" accession="MOD:00425" name="monohydroxylated residue"/>
    <cvParam cvRef="MOD" accession="MOD:00397" name="iodoacetamide derivatized residue"/>
</ModificationList>

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Example cvParams:

<cvParam cvRef="MOD" accession="MOD:01720" name="TMT6plex-126 reporter+balance reagent acylated residue"/>
<cvParam cvRef="MOD" accession="MOD:00425" name="monohydroxylated residue"/>
<cvParam cvRef="MOD" accession="MOD:00397" name="iodoacetamide derivatized residue"/>

Element <Publication>

Definition:

Reference to a publication in which the dataset is published.

Type:

PublicationType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the publication to be used for referencing within a document

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<Publication id="PMID27251877">
    <cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="27251877"/>
    <cvParam cvRef="PRIDE" accession="PRIDE:0000400" name="Reference" value="Krey JF, Drummond M, Foster S, Porsov E, Vijayakumar S, Choi D, Friderici K, Jones SM, Nuttall AL, Barr-Gillespie PG. Annexin A5 is the Most Abundant Membrane-Associated Protein in Stereocilia but is Dispensable for Hair-Bundle Development and Function. Sci Rep. 2016 Jun 2;6:27221"/>
</Publication>

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="27274532"/>
<cvParam cvRef="PRIDE" accession="PRIDE:0000400" name="Reference" value="Boggs I, Hine B, Smolenksi G, Hettinga K, Zhang L, Wheeler TT. Proteomics data in support of the quantification of the changes of bovine milk proteins during mammary gland involution. Data Brief. 2016 May 13;8:52-5. eCollection 2016 Sep"/>

Element <PublicationList>

Definition:

The list of publications from which the dataset was collected or wherein it is published

Type:

PublicationListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Publication	1	unbounded	Reference to a publication in which the dataset is published.

Example Context:

<PublicationList>
    <Publication id="PMID27251877">
        <cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="27251877"/>
        <cvParam cvRef="PRIDE" accession="PRIDE:0000400" name="Reference" value="Krey JF, Drummond M, Foster S, Porsov E, Vijayakumar S, Choi D, Friderici K, Jones SM, Nuttall AL, Barr-Gillespie PG. Annexin A5 is the Most Abundant Membrane-Associated Protein in Stereocilia but is Dispensable for Hair-Bundle Development and Function. Sci Rep. 2016 Jun 2;6:27221"/>
    </Publication>
</PublicationList>

Element <PublicationRef>

Definition:

to reference the 'id' of a 'Publication' within this submission

Type:

RefType

Attributes:

Attribute Name	Data Type	Use	Definition
ref	xs:IDREF	required	A reference to an element with and id in this document.

Subelements:

none

Example Context:

Element <RepositoryRecord>

Definition:

A record in the repository the data was submitted to corresponding to this dataset (for an example PRIDE experiment record).

Type:

RepositoryRecordType

Attributes:

Attribute Name	Data Type	Use	Definition
label	xs:string	optional	Short label for the type of repository record.
name	xs:string	required	Short name for the repository record, usually like a sample name.
recordID	xs:string	required	A unique identifier for the record within the repository.
repositoryID	HostingRepositoryType	required	Identifier that uniquely defines the hosting repository which holds the data records.
uri	xs:anyURI	required	URI that links to the repository record.

Subelements:

Subelement Name	maxOccurs	Definition
SourceFileRef	unbounded	to reference the 'id' of a 'DatasetFile' within this submission
PublicationRef	unbounded	to reference the 'id' of a 'Publication' within this submission
InstrumentRef	unbounded	Container for a reference to the id of an Instrument within this submission
SampleList	1	The list of samples that are analyzed in this dataset.
ModificationList	1	The list of amino acid mass modifications caused or considered, defined as cvParams.
AnnotationList	1	Any additional annotation of the record/experiment that the submitter/generator of the message deems important enough to announce.

Example Context:

<RepositoryRecord name="Silencing of eIF5B Changes Proteostasis by Providing Negative Feedback on MAPK Signaling" label="PRIDE project" recordID="PXD003111" repositoryID="PRIDE" uri="http://www.ebi.ac.uk/pride/archive/projects/PXD003111"/>

Element <RepositoryRecordList>

Definition:

The list of records as found in the repository the data was submitted to (for example PRIDE experiment records).

Type:

RepositoryRecordListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
RepositoryRecord	1	unbounded	A record in the repository the data was submitted to corresponding to this dataset (for an example PRIDE experiment record).

Example Context:

<RepositoryRecordList>
    <RepositoryRecord name="Silencing of eIF5B Changes Proteostasis by Providing Negative Feedback on MAPK Signaling" label="PRIDE project" recordID="PXD003111" repositoryID="PRIDE" uri="http://www.ebi.ac.uk/pride/archive/projects/PXD003111"/>
</RepositoryRecordList>

Element <RepositorySupport>

Definition:

To what extend the data is supported in the hosting repository.

Type:

RepositorySupportType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A single entry from an ontology or a controlled vocabulary.

Example Context:

<RepositorySupport>
    <cvParam cvRef="PRIDE" accession="PRIDE:0000417" name="Unsupported dataset by repository"/>
</RepositorySupport>

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Example cvParams:

<cvParam cvRef="PRIDE" accession="PRIDE:0000417" name="Unsupported dataset by repository"/>

Element <ReviewLevel>

Definition:

Level of review on this dataset/associated paper.

Type:

ReviewLevelType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A single entry from an ontology or a controlled vocabulary.

Example Context:

<ReviewLevel>
    <cvParam cvRef="PRIDE" accession="PRIDE:0000414" name="Peer-reviewed dataset"/>
</ReviewLevel>

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Example cvParams:

<cvParam cvRef="PRIDE" accession="PRIDE:0000414" name="Peer-reviewed dataset"/>

Element <Sample>

Definition:

A summary of the sample describtion. This should be a (sub) selection of cvParams used to describe the sample. Minimally this should contain information like species, tissue, etc..., but could also contain sample preparation information.

Type:

SampleType

Attributes:

Attribute Name	Data Type	Use	Definition
name	xs:string	required	Short name for the sample analyzed in this dataset.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Element <SampleList>

Definition:

The list of samples that are analyzed in this dataset.

Type:

SampleListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Sample	1	unbounded	A summary of the sample describtion. This should be a (sub) selection of cvParams used to describe the sample. Minimally this should contain information like species, tissue, etc..., but could also contain sample preparation information.

Example Context:

Element <SourceFileRef>

Definition:

to reference the 'id' of a 'DatasetFile' within this submission

Type:

RefType

Attributes:

Attribute Name	Data Type	Use	Definition
ref	xs:IDREF	required	A reference to an element with and id in this document.

Subelements:

none

Example Context:

Element <Species>

Definition:

The species from which the data has been generated.

Type:

SpeciesType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<Species>
    <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Mus musculus (Mouse)"/>
    <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="10090"/>
</Species>

cvParam Mapping Rules:

WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Homo sapiens (Human)"/>
<cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="9606"/>

Element <SpeciesList>

Definition:

The list of species from which the data has been generated.

Type:

SpeciesListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Species	1	unbounded	The species from which the data has been generated.

Example Context:

<SpeciesList>
    <Species>
        <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Mus musculus (Mouse)"/>
        <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="10090"/>
    </Species>
</SpeciesList>

Element <userParam>

Definition:

A single user-defined parameter.

Type:

UserParamType

Attributes:

Attribute Name	Data Type	Use	Definition
name	xs:string	required	The name of the parameter.
unitAccession	xs:string	optional	An accession number identifying the unit within the OBO foundry Unit CV.
unitCvRef	xs:string	optional	If a unit term is referenced, this attribute MUST refer to the CV 'id' attribute defined in the cvList in this file.
unitName	xs:string	optional	The name of the unit.
value	xs:string	optional	The user-entered value of the parameter.

Subelements:

none

Example Context:

Element <ProteomeXchangeDataset>

Element <AdditionalInformation>

Element <AnnotationList>

Element <ChangeLog>

Element <ChangeLogEntry>

Element <Contact>

Element <ContactList>

Element <Cv>

Element <CvList>

Element <cvParam>

Element <DatasetFile>

Element <DatasetFileList>

Element <DatasetIdentifier>

Element <DatasetIdentifierList>

Element <DatasetOrigin>

Element <DatasetOriginList>

Element <DatasetSummary>

Element <Description>

Element <FullDatasetLink>

Element <FullDatasetLinkList>

Element <Instrument>

Element <InstrumentList>

Element <InstrumentRef>

Element <KeywordList>

Element <ModificationList>

Element <Publication>

Element <PublicationList>

Element <PublicationRef>

Element <RepositoryRecord>

Element <RepositoryRecordList>

Element <RepositorySupport>

Element <ReviewLevel>

Element <Sample>

Element <SampleList>

Element <SourceFileRef>

Element <Species>

Element <SpeciesList>

Element <userParam>