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PepcDB | PepcDB Schema: clearly explained

Content and Report Formats:

pepcDB Schema version

  • Format version identifier (i.e. 6,7,8,9 or 9.1), the current version is 9.1

XML Presentation: 
<pepcFormatVersion>9.1</pepcFormatVersion>
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Site

  • Name of Structural Genomics Center

To search targets from a single Structural Genomics center, select one of the project sites from the list below.

The NIH Structural Genomics Centers: Other Projects: Asia: Europe: XML Presentation: 
<site>TB</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 defined by each structural genomics center.

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

  • Name of a group, division, or indidual 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 indidual 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

Examples:
  • target-help@rcsb.rutgers.edu
XML Presentation: 
<email>target-help@rcsb.rutgers.edu</email>
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Organization

  • Name of Structural Genomics Center

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

  • 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

  • The protocol unique identifier may be any simple code defined by Strucural Genomics Center.

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

  • The protocol name defined by Strucural Genomics 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.

Examples: 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.

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Project pepcTarget ID

  • A unique identifier for project target sequence defined by each structural genomics center, but it must be unique within the project target list and consistant across target list updates.

Examples:
  • WR90EC
  • NYSGRC-P007
XML Presentation: 
<id>WR90EC</id>
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PSI Project List

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

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

          <project>
              <projectName>PSI</projectName>
              <projectId>2</projectId>
      </project>
</projectList>
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Program Name

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

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

  • Project identifier. Example: 1 or 2 to identify Protein Structure Initiative(PSI) first or second research phase.

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

  • Information about target being assosiated with a specific category of targets such as targets that have biomedical significance or targets that are nominated by 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
  • metagenomic
  • membrane protein
  • legacy
  • structural coverage
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.

Examples:
  • Studies suggest that this protein is involved in lung cancer.
XML Presentation: 
<reamrk>
     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>
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Target Stop Status

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

Examples:
  • expression failed
  • cloning failed
  • purification failed
  • crystallization failed
  • poor diffraction
  • poor NMR
  • duplicate target found
  • internal duplicate found
  • TargetDB duplicate found
  • PDB duplicate found
  • mass spec failed
  • sequencing failed
  • 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: 
<reamrk>
      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.

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

  • Description of the relationship of project target and related target.

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

  • A packet of information describing sequences related to target. Sequences are described by a one-letter code sequence, by type (i.e. protein, clone, subclone, etc), chemical type (i.e. protein or dna) and 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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Sequence Code

  • The one-letter code sequence for FASTA comparison.

Examples: MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV XML Presentation: 
<oneLetterCode>
        MATTLPVQRHPRSLFPEFSELFAAFPSFAGLRPTFDTRLMRLEDEMKEGRYEV
</oneLetterCode>
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Sequence Type

  • The type of sequence specified.

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

  • Chemical classification of sequence data.

Examples:
  • protein
  • dna
XML Presentation: 
<sequenceChemicalType>protein</sequenceChemicalType>
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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.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 should include both successful and failed trials. Each trial consists of a description of a set of the sequence 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 structural genomics center

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

  • Optional clone ID from PlasmID database. Provide clone ID if a clone (vector plus DNA insert) associated with this experimental trial was deposited to PSI Material Repository.

Example:
  • 83561
XML Presentation: 
<cloneId>83561</cloneId>
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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 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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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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Status History List

  • List of timestamped codes describing critical changes in target status. The status history record includes 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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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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Status Date

  • Date of status of a trial

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

  • An optional remark about status history of a trial

XML Presentation: 
<remark>optional remark</remark>
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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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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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Stop Status

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

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

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

Examples: XML Presentation: 
<remark>Degradation of the expressed product</remark>
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Trial Database 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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Database Name

  • The database name

Examples:
  • PDB
XML Presentation: 
<databaseName>PDB</databaseName>
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Database ID

  • The accession code for the named database

Examples:
  • 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.

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

  • The construct type for this trial sequence.

Example:
  • 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 can be accompanied by a type 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
  • 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 name of a procedure which is used to collect the measurements, collected measurements, 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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Measurement List

  • List of measurements collected by this procedure. This includes 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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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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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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Measurement Unit

  • Unit of performed measurement if aplicable.

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

  • Uncertainty of performed measurement if aplicable.

Examples:
  • +/-0.06
XML Presentation: 
<measurementUncertainty>+/-0.06<measurementUncertainty/>
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FASTA Sequence Comparison Details

  • Pearson, W.R. and Lipman, D.J. Improved tools for biological sequence comparison.   PNAS 85:2444-2448(1988)

The E()-value cutoff limits the number of scores and alignments shown based on the expected number of scores. A cutoff value of 2.0 (-E 2.0) will show all library sequences with scores with an expectation value <= 2.0.

For protein searches, matched sequences with E()-values < 0.01 for searches of 10,000 protein sequences are almost always homologous. Frequently sequences with E()-values from 1 - 10 are related as well. However, E()-values also reflect differences between the amino acid composition of the query sequence and that of the "average" database sequence. Thus, when searches are done with query sequences with "biased" amino-acid composition, unrelated sequences may have "significant" scores because of sequence bias.

FASTA is available from ftp://ftp.virginia.edu/pub/fasta/.
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Report Formats

FASTA Format

  • Sequences of selected targets are output in Pearson/FASTA format.

Example: 
>001| Protein Kinase (E.C.2.7.1.37) (cAPK) (Catalytic Subunit)

GNAAAAKKGSEQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYA

MKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFSE

PHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEII

LSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKR

FGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF
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XML Format

  • Features of selected PepcDB entry output in XML format.

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