PSI PepcDB

PepcDB | Data Definitions

PepcDB Content Schema Definitions

PepcDB XML Declaration and Root Element

A PepcDB XML file must begin with the XML declaration and unique root element <pepcTargets>.

The end of the XML file must have the corresponding end root element </pepcTargets>.


Examples:

  • <?xml version="1.0" encoding="UTF-8"?>
    <pepcTargets>
  • <?xml version="1.0" encoding="ISO-8859-1"?>
    <pepcTargets>

XML Presentation:

<?xml version="1.0" encoding="UTF-8"?>
<pepcTargets>
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PepcDB Schema Version

Format version identifier (i.e. 9, 9.2, 9.3, 9.3.1, 9.3.2, 9.3.3).

The current version is 9.3.3.


XML Presentation:

<pepcFormatVersion>9.3.3</pepcFormatVersion>
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Site

Acronym of the Structural Biology Center


Examples:

  • JCSG
  • NESG

XML Presentation:

<site>JCSG</site>
<site>NESG</site>
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Contact Information List

All contact information related to this target, target collection, or related experimental trials is listed here and referenced later.


XML Presentation:

<contactInfoList>
  <contactInfo>
    <contactInfoId>c_1</contactInfoId>
      <name>TB Consortium - Database Group</name>
      <address>Room 105, MBI, Los Angeles 90095</address>
      <country>USA</country>
      <email>tbdbteam@mbi.ucla.edu</email>
      <organization>TB Structural Genomics Consortium</organization>
      <lab>Laboratory of David Eisenberg</lab>
      <role>Archiver</role>
    </contactInfo>

    <contactInfo>
      <contactInfoId>c_2</contactInfoId>
      <name>LANL-Protein Production Facility</name>
      <address>Los Alamos, NM 87545</address>
      <country>USA</country>
      <email>ppteam@lanl.gov</email>
      <organization>Los Alamos National Laboratory</organization>
      <lab>Los Alamos National Laboratory</lab>
      <role>Scientist;/role>
    </contactInfo>
</contactInfoList>
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Contact information ID

An identifier for contact information related to a particular target.

The identifier is defined by the depositing center.


Examples:

  • c_1
  • c_2
XML Presentation: 
<contactInfoId>c_1</contactInfoId>
<contactInfoId>c_2</contactInfoId>
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Name

Name of a group, division, or individual researcher who contributed to the target structural analysis.


Examples:

  • TB Consortium - Database Group
  • LANL-Protein Production Facility
XML Presentation: 
<name>TB Consortium - Database Group</name>
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Address

Detailed address of a group, division, or individual researcher who contributed to the target structural analysis.


Examples:

  • Room 105, MBI, Los Angeles 90095
  • Los Alamos, NM 87545
XML Presentation: 
<address>Room 105, MBI, Los Angeles 90095</address>
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Country

ISO-3166-1 Country code


Examples:

  • United States = US
  • United Kingdom = GB
XML Presentation: 
<country>US</country>
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E-mail

Electronic mail address


Example:

  • target-help@sbkb.org
XML Presentation: 
<email>target-help@sbkb.org</email>
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Organization

Name of the Depositing Center


Example:
  • TB Structural Genomics Consortium
XML Presentation: 
<organization>TB Structural Genomics Consortium</organization>
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Laboratory Name

Laboratory name


Examples:

  • Laboratory of David Eisenberg
  • Los Alamos National Laboratory

XML Presentation:

<lab>Laboratory of David Eisenberg</lab>
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Role

Text description of the role of the group or individual for which contact information is provided


Examples:

  • Archiver
  • Scientist

XML Presentation:

<role>Archiver</role>
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Protocol List

A reusable list of protocols which must include a unique identifier and a text section describing the protocol.

The protocol identifier may be any simple code (e.g. 1, 2, clone1, pur_1, etc).

The protocol definition may also optionally include a name and a brief description.

The protocols defined in this list are referenced in describing the experimental trials attempted on each target.


XML Presentation:

<protocolList>
  <protocol>
    <protocolId>pur_1</protocolId>
    <protocolName>Gel filtration 1</protocolName>
    <protocolDescription>
      Gel filtration purification by FPLC from Pharmacia.
    <protocolDescription/>
    <protocolText>
      Protocol text...
    </protocolText>
  </protocol>

  <protocol>
    <protocolId>pur_2</protocolId>
    <protocolName>Cation exchange chromatography 2</protocolName>
    <protocolDescription>
      Cation exchange purification by FPLC from Pharmacia.
    <protocolDescription/>
    <protocolText>
      Protocol text...
    </protocolText>
  </protocol>
</protocolList>
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Protocol ID

A unique protocol identifier is any simple code defined by the depositing center.


Examples:

  • clone1
  • pur_1

XML Presentation:

<protocolId>pur_1</protocolId>
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Protocol Name

The protocol name defined by the depositing center.


Examples:

  • Gel filtration 1
  • Cloning

XML Presentation:

<protocolName>Gel filtration 1</protocolName>
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Protocol Description

A brief description of a protocol.


Examples:

  • Gel filtration by FPLC from Pharmacia
  • Cloning into pET expression vector from Stratagene

XML Presentation:

<protocolDescription>Gel filtration by FPLC from Pharmacia</protocolDescription>
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Protocol Text

A detailed description of a protocol.


Example:

XML Presentation:

<protocolText>Protocol text...</protocolText>
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Project Target List

A description of a project target including a list of trials used to produce the protein and solve the structure.

Each project target must begin with the PepcDB target root element <pepcTarget>.

The end of each target must have the corresponding end target root element </pepcTarget>.


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Project Target ID

A unique identifier for a project target sequence defined by each depositing center, but it must be unique within the project target list and consistent across target list updates.


Examples:

  • WR90EC
  • NYSGRC-P007

XML Presentation:

<id>WR90EC</id>
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Project List

List of projects or programs with which target is associated. For example: PSI (Protein Structure Initiative), phase one, phase two, or phase three (PSI:Biology).


XML Presentation: 
<projectList>
  <project>
    <projectName>PSI</projectName>
    <projectId>1</projectId>
  </project>

  <project>
    <projectName>PSI</projectName>
    <projectId>2</projectId>
  </project>

  <project>
    <projectName>PSI</projectName>
    <projectId>Biology</projectId>
  </project>
</projectList>
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Project Name

Abbreviated name of project. Example: PSI (Protein Structure Initiative)


Example:
  • PSI
XML Presentation: 
<projectName>PSI</projectName>
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Project ID

Project identifier. Example: 1, 2, 3, or Biology to identify Protein Structure Initiative (PSI) first, second, or third research phases.


Examples:
  • 1
  • 2
  • 3
  • Biology
XML Presentation: 
<projectId>Biology</projectId>
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Target Category List

Information about the target being associated with a specific category of targets, such as targets that have biomedical significance or targets that are nominated by the scientific community.


XML Presentation: 
<targetCategoryList>
  <targetCategory>
    <targetCategoryName>biomedical</targetCategoryName>
    <remark>any comments about biomedical significance of this target</remark>
  </targetCategory>

  <targetCategory>
    <targetCategoryName>community nominated</targetCategoryName>
    <remark>information about the nominator such as name and affiliation</remark>
  </targetCategory>
</targetCategoryList>
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Target Category Name

Name of target category from enumerated list of defined target categories.


Examples:
  • biomedical
  • community nominated
  • legacy
  • membrane protein
  • metagenomic
  • structural coverage
  • technology development
  • PSI Biology partnership
XML Presentation: 
<targetCategoryName>biomedical</targetCategoryName>
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Target Category Remark

Any additional information related to target being in this particular category. For example, what is target biomedical significance or inforamtion about a person who nominated this target such as name and affiliation.


Example:
  • Studies suggest that this protein is involved in lung cancer.
XML Presentation: 
<remark>
  Studies suggest that this protein is involved in lung cancer.
</remark>
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Target Current Status

The current status of this target from PepcDB defined status codes.


XML Presentation: 
<status>NMR assigned</status>
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Target Stop Details

Information describing the details for stopping work on this target. This includes a code from an enumerated list describing the stage at which work on target was stopped and any additional details.


XML Presentation: 
<targetStopDetails>
  <stopStatus>crystallization failed</stopStatus>
  <remark>possible explanation of crystalization failure</remark>
</targetStopDetails>

<targetStopDetails>
  <stopStatus>other</stopStatus>
  <remark>End of PSI-2</remark>
</targetStopDetails>
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Target Stop Status

The status code describing the stage of work at which this target was terminated.


Examples:
  • cloning failed
  • sequencing failed
  • expression failed
  • purification failed
  • mass spec failed
  • crystallization failed
  • poor diffraction
  • poor NMR
  • duplicate target found
  • internal duplicate found
  • TargetDB duplicate found
  • PDB duplicate found
  • structure successful
  • other
XML Presentation: 
<stopStatus>expression failed</stopStatus>
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Target Stop Remark

An optional remark explaining the reason of stopping the work on a target.


XML Presentation: 
<remark>
  Degradation of the expressed product
</remark>
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Related Target ID List

The list of target IDs that are related to the project target.


XML Presentation: 
<relatedTargetIdList>
  <relatedTargetId>
    <id>TX1001</id>
     <remark>a similar sequence in mouse</remark>
  </relatedTargetId>

  <relatedTargetId>
    <id>TX900</id>
    <remark>a similar sequence in rat</remark>
  </relatedTargetId>
</relatedTargetIdList>
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Related Target ID

A unique identifier for a target related to the project target.


Example:
  • TX1001
XML Presentation: 
<id>TX1001</id>
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Related Target Remark

Description of the relationship of project target and related target.


Example:
  • a similar sequence in mouse
XML Presentation: 
<remark>a similar sequence in mouse</remark>
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Target Sequence List

A packet of information describing sequences related to the target.

Sequences are described by a one-letter code sequence, by type (i.e. protein, clone, subclone, etc), by chemical type (i.e. protein or dna), and by construct type (i.e. full orf, domain, fragment, etc.).

In defining a target sequence, it is assumed that the sequence will correspond most closely with the sequence of the ultimate structure determination.


XML Presentation: 
<targetSequenceList>
  <targetSequence>
    <oneLetterCode>
      MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
    </oneLetterCode>
    <sequenceType>protein</sequenceType>
    <sequenceChemicalType>protein</sequenceChemicalType>
    <sequenceConstructType>domain</sequenceConstructType>
  </targetSequence>

  <targetSequence>
    <oneLetterCode>
      MLKVNNLSKIWKDFKLKNVSFEIDREYCVILGPSGAGKSVLIKCIAGILKPDSGRIIL
    </oneLetterCode>
    <sequenceType>protein</sequenceType>
    <sequenceChemicalType>protein</sequenceChemicalType>
    <sequenceConstructType>domain</sequenceConstructType>
  </targetSequence> 
</targetSequenceList>
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Target Sequence Code

The one-letter code sequence for FASTA comparison.


Example:
  • MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
XML Presentation: 
<oneLetterCode>
  MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
</oneLetterCode>
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Target Sequence Type

The type of sequence specified.


Examples:
  • protein
  • experimental protein
  • predicted protein
  • predicted dna
  • clone
  • subclone
XML Presentation: 
<sequenceType>protein</sequenceType>
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Target Sequence Chemical Type

Chemical classification of sequence specified.


Examples:
  • protein
  • dna
XML Presentation: 
<sequenceChemicalType>protein</sequenceChemicalType>
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Target Sequence Construct Type

The construct type for this sequence.


Examples:
  • full ORF
  • domain
  • fragment
XML Presentation: 
<sequenceConstructType>full ORF</sequenceConstructType>
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Protein Name

The name of the protein for the target sequence.


Examples:
  • Glutamate synthase
  • 29-C10
XML Presentation: 
<proteinName>Glutamate synthase</proteinName>
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Target URL

Universal resource locator/internet address related to this target.

This can be a link to a project site containing more information about this target, or some other related site address.


Example:
  • http://www.doe-mbi.ucla.edu/TB/PUBLIC/qs/qsearch.php?dowork=Rv2031c
XML Presentation: 
<url>http://www.doe-mbi.ucla.edu/TB/PUBLIC/qs/qsearch.php?dowork=Rv2031c</url>
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Remark

Additional text details about this target.


Example:
  • A remarkably insightful comment about this target.
XML Presentation: 
<remark>A remarkably insightful comment about this target.</remark>
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Source Organism

The scientific name of the source organism for the target sequence following the nomenclature of the NCBI Taxonomy database:

http://www.ncbi.nlm.nih.gov/Taxonomy.


Examples:
  • Mycobacterium tuberculosis
  • Arabidopsis thaliana
  • Escherichia coli
  • Caenorhabditis elegans
XML Presentation: 
<sourceOrganism>Mycobacterium tuberculosis</sourceOrganism>
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Database List

A list describing related information about this target including a database name and an identifier within the database.


XML Presentation: 
<databaseRefList>
  <databaseRef>
    <databaseName>TB.proteomic_information</databaseName>
    <databaseId>367989</databaseId>        
  </databaseRef>

  <databaseRef>
    <databaseName>Genbank</databaseName>
    <databaseId>189676547</databaseId>
  </databaseRef>

  <databaseRef>
    <databaseName>PDB</databaseName>
    <databaseId>1A2B</databaseId>
  </databaseRef>
</databaseRefList>
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Database Name

The database name.


Examples:
  • TB.proteomic_information
  • Genbank
  • PDB
XML Presentation: 
<databaseName>TB.proteomic_information</databaseName>
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Database ID

The accession code for the named database.


Examples:
  • 367989
  • 189676547
  • 1A2B
XML Presentation: 
<databaseId>367989</databaseId>
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Contact Information Reference List

A list of contacts responsible for this target identified by referencing the previously defined contact information list.


XML Presentation: 
<contactInfoRefList>
  <contactInfoRef>
    <contactInfoId>c_1</contactInfoId>
  </contactInfoRef>

  <contactInfoRef>
    <contactInfoId>c_2</contactInfoId>
  </contactInfoRef>
</contactInfoRefList>
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Contact Information ID

References previously defined contact IDs from Contact Information List.


Examples:
  • c_1
  • c_2
XML Presentation: 
<contactInfoId>c_1</contactInfoId>
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Trial List

A list of protein production trials attempted for this target.

This list should include both successful and failed trials.

Each trial consists of a description of a set of the sequential tasks employed to produce this target.

A trial includes: lab, date, contact information, experimental sequence data, process status data, and references to the protocols used in the trial.


XML Presentation: 
<trialList>
  <trial>
     <trialId>...</trialId>
     <cloneId>...</cloneId>
     <lab>...</lab>
     <date>...</date>
     <contactInfoRefList>
        <!-- List of Contact References -->
     </contactInfoRefList>
     <status>....</status>
     <statusHistoryList>
         <!-- Status History List -->
     </statusHistoryList>
     <trialSequenceList>
         <!-- List of Trial Sequences -->
     </trialSequenceList>
     <trialProtocolList>
         <!-- List of Trial Protocols -->
     </trialProtocolList>
  </trial>

  <trial>
     <lab>...</lab>
     <date>...</date>
     <contactInfoRefList>
        <!-- List of Contact References -->
     </contactInfoRefList>
     <status>....</status>
     <statusHistoryList>
         <!-- Status History List -->
     </statusHistoryList>
     <trialSequenceList>
         <!-- List of Trial Sequences -->
     </trialSequenceList>
     <trialProtocolList>
         <!-- List of Trial Protocols -->
     </trialProtocolList>
  </trial>
</trialList>
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Trial ID

Optional trial ID defined by the depositing center.


Example:
  • 12345a1BCt1p1_54321_1_63421
XML Presentation: 
<trialId>12345a1BCt1p1_54321_1_63421</trailId>
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Materials Repository Clone ID

Optional clone ID from PSI Materials Repository.

Provide clone ID if a clone (vector plus DNA insert) associated with this experimental trial was deposited to the PSI Material Repository.


Example:
  • 83561
XML Presentation: 
<cloneId>83561</cloneId>
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Trial Date

Date on which this trial information was updated - yyyy-mm-dd.


Example:
  • 2001-02-14
XML Presentation: 
<date>2001-02-14</date>
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Trial Contact Information Reference List

A list of contacts responsible for this trial identified by referencing the previously defined contact information list.


XML Presentation: 
<contactInfoRefList>
  <contactInfoRef>
    <contactInfoId>c_1</contactInfoId>
  </contactInfoRef>

  <contactInfoRef>
    <contactInfoId>c_2</contactInfoId>
  </contactInfoRef>
</contactInfoRefList>
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Trial Contact Information ID

References previously defined contact IDs from Contact Information List.


Examples:
  • c_1
  • c_2
XML Presentation: 
<contactInfoId>c_1</contactInfoId>
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Trial Current Status

The current status of this trial. This should correspond to the last status recoreded in the status history list.


Examples:
  • selected
  • cloned
  • expressed
  • soluble
  • purified
  • mass spec verified
  • crystallized
  • diffraction-quality crystals
  • diffraction
  • native diffraction-data
  • phasing diffraction-data
  • HSQC
  • NMR assigned
  • crystal structure
  • NMR structure
  • in BMRB
  • in PDB
  • work stopped
  • test target
  • other
XML Presentation: 
<status>selected</status>
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Trial Status History List

List of timestamped codes describing critical changes in target status.

The status history record includes the laboratory name responsible for this trial, an enumerated status state, the date corresponding to the beginning of this status state, and an optional completion date and remark.


XML Presentation: 
<statusHistoryList>
       <statusHistory>
         <lab>Laboratory of David Eisenberg</lab>
         <status>selected</status>
         <date>2001-01-10</date>
         <remark>optional remark</remark>
         <dateComplete>2001-02-14</dateComplete>
         <protocolId>sel_1</protocolId>
       </statusHistory>

       <statusHistory>
         <lab>Laboratory of David Eisenberg</lab>
         <status>cloned</status>
         <date>2001-02-14</date>
         <remark>optional remark</remark>
         <dateComplete>2001-02-16</dateComplete>
         <protocolId>clon_1</protocolId>
       </statusHistory>

       <statusHistory>
         <lab>Laboratory of David Eisenberg</lab>
         <status>expressed</status>
         <date>2001-02-16</date>
         <remark>optional remark</remark>
         <dateComplete>2001-02-24</dateComplete>
         <protocolId>expr_1</protocolId>
       </statusHistory>

       <statusHistory>
         <lab>Laboratory of David Eisenberg</lab>
         <status>soluble</status>
         <date>2001-02-24</date>
         <remark>optional remark</remark>
         <dateComplete>2001-03-01</dateComplete>
       </statusHistory>

       <statusHistory>
         <lab>Laboratory of David Eisenberg</lab>
         <status>purified</status>
         <date>2001-03-01</date>
         </statusHistory><remark>optional remark</remark>
         <dateComplete>2001-03-10</dateComplete>
         <protocolId>pur_1</protocolId>
       </statusHistory>
</statusHistoryList>
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Trial Laboratory Name

Name of laboratory responsible for this trial.


Examples:
  • Laboratory of David Eisenberg
  • Los Alamos National Laboratory
XML Presentation: 
<lab>Laboratory of David Eisenberg</lab>
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Trial Status

Status of a trial associated with a specific date.


Examples:
  • selected
  • cloned
  • expressed
  • soluble
  • purified
  • mass spec verified
  • crystallized
  • diffraction-quality crystals
  • diffraction
  • native diffraction-data
  • phasing diffraction-data
  • HSQC
  • NMR assigned
  • crystal structure
  • NMR structure
  • in BMRB
  • in PDB
  • work stopped
  • test target
  • other
XML Presentation: 
<status>selected</status>
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Trial Status Date

Date of the status of a trial.


Example:
  • 2001-02-14
XML Presentation: 
<date>2001-02-14</date>
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Trial Status Remark

An optional remark about status history of a trial.


XML Presentation: 
<remark>optional remark</remark>
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Trial Status Completion Date

An optional completion date of a trial.


Example:
  • 2001-02-14
XML Presentation: 
<dateComplete>2001-02-14</dateComplete>
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Trial Stop Details

Information describing the details for stopping work on this trial.

This includes a code from an enumerated list describing the stage at which the trial was stopped and any additional details.


XML Presentation: 
<stopDetails>
         <stopStatus>expression failed</stopStatus>
         <remark>Degradation of the expressed product</remark>
</stopDetails>
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Trial Stop Status

The status code describing the stage of work at which this trial was terminated.


Examples:
  • cloning failed
  • sequencing failed
  • expression failed
  • purification failed
  • mass spec failed
  • crystallization failed
  • poor diffraction
  • poor NMR
  • duplicate target found
  • internal duplicate found
  • TargetDB duplicate found
  • PDB duplicate found
  • structure successful
  • other
XML Presentation: 
<stopStatus>expression failed</stopStatus>
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Trial Stop Remark

An optional remark explaining the reason of stopping the work on a trial.


XML Presentation: 
<remark>Degradation of the expressed product</remark>
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Trial Database Reference List

A list describing related information about this trial sequence, including a database name and an identifier within the database.

In the situation when a target is associated with multiple PDB IDs (structures of individual domains, structures with different ligands), this data element can be used to present PDB ID associated with a specific crystallization or NMR experimental trial.

Please note that trial database infromation should be also referenced in the Target Database Reference List


XML Presentation: 
<databaseRefList>
         <databaseRef>
             <databaseName>PDB</databaseName>
             <databaseId>1A2B</databaseId>        
         </databaseRef>
</databaseRefList>
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Trial Database Name

The database name.


Example:
  • PDB
XML Presentation: 
<databaseName>PDB</databaseName>
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Trial Database ID

The accession code for the named database.


Example:
  • 1A2B
XML Presentation: 
<databaseId>1A2B</databaseId>
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Trial Sequence List

The list of experimental sequences related to this trial.

These may contain deliberate modifications or unanticipated differences from the parent target protein sequence.


XML Presentation: 
<trialSequenceList>
       <trialSequence>
         <oneLetterCode>
            MATTLPPQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
         </oneLetterCode>
         <sequenceChemicalType>protein</sequenceChemicalType>
         <sequenceModifications>valine 7 replaced by proline</sequenceModifications>
         <sequenceDetails>five terminal residues cleaved</sequenceDetails>
       </trialSequence>

       <trialSequence>
         <oneLetterCode>
           MLKVNNLSKIWKDFKLKNVSFEIDREYCVILGPSGAGKSVLIKCIAGILKPDSGRIIL
         </oneLetterCode>
         <sequenceChemicalType>protein</sequenceChemicalType>
         <sequenceModifications>valine 7 replaced by leucine</sequenceModifications>
         <sequenceDetails>five terminal residues cleaved</sequenceDetails>
       </trialSequence>
</trialSequenceList>
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Trial Sequence Code

The one-letter code sequence of a trial.


Example:
  • MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
XML Presentation: 
<oneLetterCode>
        MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
</oneLetterCode>
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Trial Sequence Chemical Type

Chemical classification of trial sequence data.


Examples:
  • protein
  • dna
XML Presentation: 
<sequenceChemicalType>protein</sequenceChemicalType>
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Trial Sequence Construct Type

The construct type for this trial sequence.


Examples:
  • full ORF
  • domain
  • fragment
XML Presentation: 
<sequenceConstructType>fragment</sequenceConstructType>
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Trial Sequence Modifications

Deliberate modifications or other unanticipated changes that may occur in a trial sequence relative to the parent target sequence.


Example:
  • valine 7 replaced by proline
XML Presentation: 
<sequenceModifications>valine 7 replaced by proline</sequenceModifications>
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Trial Sequence Details

Changes that may occur in a trial sequence relative to the parent target sequence.


Example:
  • five terminal residues cleaved
XML Presentation: 
<sequenceDetails>five terminal residues cleaved</sequenceDetails>
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Trial Protocol List

A list of references to protocols defined in the protocol list that describe the tasks applied in this experimental trial.

Each protocol refers to a predefined protocol description and is accompanied by the protocol's type of procedure and optional additional details or customization.

Protocols are referenced by their protocolId as previously defined in the protocol list.


XML Presentation: 
<trialProtocolList>
       <protocolRef>
         <protocolId>pur_1</protocolId>
         <protocolType>purification</protocolType>
         <protocolDetails>
            A cat wisker was added for good luck.
         </protocolDetails>
       </protocolRef>

       <protocolRef>
         <protocolId>pur_2</protocolId>
         <protocolType>purification</protocolType>
         <protocolDetails>
            change in sodium chloride gradient range.
         </protocolDetails>
       </protocolRef>
</trialProtocolList>
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Trial Protocol ID

A reference to a predefined protocol ID from Protocol List.


Examples:
  • clone1
  • pur_1
XML Presentation: 
<protocolId>pur_1</protocolId>
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Trial Protocol Type

Type of procedure descibed in the protocol.


Examples:
  • selection
  • gene synthesis
  • growth
  • PCR
  • cloning
  • expression
  • purification
  • mass spec analysis
  • crystallization
  • NMR
XML Presentation: 
<protocolType>purification</protocolType>
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Trial Protocol Details

Changes that were intoduced into the main protocol which are specific to this trial.


Examples:
  • cloning into different expression vector.
  • change in expression time and/or temperature.
XML Presentation: 
<protocolDetails>cloning into different expression vector..</protocolDetails>
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Trial Measurement List

List of measurements associated with this trial.

This includes the name of a procedure which is used to collect the measurements, collected measurements, a reference to a protocol, and optional details related to the measurements.


XML Presentation: 
<trialMeasurementList>

       <trialMeasurement>

         <measurementProcedure>gel filtration</measurementProcedure>
         <measurementList>
             <measurement>
                   <measurementValue>300.00</measurementValue>
                   <measurementName>molecular weight</measurementName>
                   <measurementUnit>kDa</measurementUnit>
                   <measurementUncertainty>+/- 2.65</measurementUncertainty>
             </measurement>
         </measurementList>
         <protocolId>Pur_1</protocolId>
         <remark>Any important comments about this measurement</remark>

      </trialMeasurement>

      <trialMeasurement>

         <measurementProcedure>Mass spec</measurementProcedure>
         <measurementList>

             <measurement>
                   <measurementValue>S157</measurementValue>
                   <measurementName>phosphorylation</measurementName>
                   <measurementUnit></measurementUnit>
                   <measurementUncertainty></measurementUncertainty>
             </measurement>
             <measurement>
                   <measurementValue>K52</measurementValue>
                   <measurementName>methylation</measurementName>
                   <measurementUnit></measurementUnit>
                   <measurementUncertainty></measurementUncertainty>
             </measurement>
             
         </measurementList>
         <protocolId>MassSpecAnalysis_2</protocolId>
         <remark>Any important comments about this measurement</remark>
       
      </trialMeasurement> 
   
      <trialMeasurement>
         <measurementProcedure>X-ray fluorescence</measurementProcedure>
         <measurementList>

             <measurement>
                   <measurementValue>Magnesium</measurementValue>
                   <measurementName>element analysis</measurementName>
                   <measurementUnit></measurementUnit>
                   <measurementUncertainty></measurementUncertainty>
             </measurement>
             <measurement>
                   <measurementValue>1.05:1</measurementValue>
                   <measurementName>stoichiometry</measurementName>
                   <measurementUnit></measurementUnit>
                   <measurementUncertainty></measurementUncertainty>
             </measurement>
          
         <protocolId></protocolId>
         <remark>Any important comments about this measurement</remark>
      
      </trialMeasurement>

        <trialMeasurement>

         <measurementProcedure>isoelectric focusing</measurementProcedure>
         <measurementList>
             <measurement>
                   <measurementValue>6.5</measurementValue>
                   <measurementName>Isoelectric point</measurementName>
                   <measurementUnit></measurementUnit>
                   <measurementUncertainty>+/- 0.65</measurementUncertainty>
             </measurement>
         </measurementList>
         <protocolId>2Dgel_1</protocolId>
         <remark>Any important comments about this measurement</remark>

      </trialMeasurement>

  </trialMeasurementList>
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Trial Measurement Procedure

Name of an experimental procedure used to collect measurement(s) for this trial.


Examples:
  • Mass spec analysis
  • Gel filtration
  • X-ray fluorescence
  • Isoelectic focusing
XML Presentation: 
<measurementProcedure>Gel filtration</measurementProcedure>
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Procedure Measurement List

List of measurements collected by this procedure.

This includes the name of a measurement, measurement value, unit of measurement, and measurement uncertainty.


XML Presentation: 
<measurementList>
       <measurement>
             <measurementValue>Magnesium</measurementValue>
             <measurementName>element analysis</measurementName>
             <measurementUnit></measurementUnit>
             <measurementUncertainty></measurementUncertainty>
       </measurement>

       <measurement>
             <measurementValue>1.05:1</measurementValue>
             <measurementName>magnesuim stoichiometry</measurementName>
             <measurementUnit></measurementUnit>
             <measurementUncertainty></measurementUncertainty>
       </measurement>
</measurementList>
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Procedure Measurement Name

Name of measurement.


Examples:
  • molecular weight
  • isoelectric point
  • phosphorylation
  • methylation
  • element analysis
  • stoichiometry
XML Presentation: 
<measurementName>isoelectric point</measurementName>
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Procedure Measurement Value

Value of measurement.


Examples:
  • 300.00
  • 6.5
  • S157
  • K50
  • magnesium
  • 1.05:1
XML Presentation: 
<measurementValue>magnesium</measurementValue>
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Procedure Measurement Unit

Unit of performed measurement if applicable.


Examples:
  • kDa
  • um
XML Presentation: 
<measurementUnit>kDa</measurementUnit>
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Procedure Measurement Uncertainty

Uncertainty of performed measurement if applicable.


Example:
  • +/-0.06
XML Presentation: 
<measurementUncertainty>+/-0.06</measurementUncertainty>
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Trial Measurement Remark

An optional remark with any important information about this measurement.


XML Presentation: 
<remark>Any important comments about this measurement</remark>
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