PSI TargetDB

Explanation of the TargetDB
Document Type Definition(DTD)

Content:

Center-Specific Target Identifier

A unique identifier for the target sequence defined by each depositing center.

Examples:
  • WR90EC
  • NYSGRC-P007
XML Presentation 
<id>WR90EC</id>
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Laboratory Name

Laboratory name

Examples:
  • Southeast Collaboratory for Structural Genomics
  • National Institute for Medical Research, UK
XML Presentation
<lab>Southeast Collaboratory for Structural Genomics</lab>
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Date of Target Update

Date on which this target information was updated - yyyy-mm-dd

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

The status of the target sequence. One or more descriptive terms shown below.

Examples:
  • Selected
  • Cloned
  • Expressed
  • Soluble
  • Purified
  • Crystallized
  • Diffraction-quality Crystals
  • Diffraction
  • HSQC
  • NMR Assigned
  • Crystal Structure
  • NMR Structure
  • In PDB
  • Work Stopped
  • Test Target
  • Other
XML Presentation 
<status>Selected</status>
<status>Cloned</status>
<status>Expressed</status>
<status>Soluble</status>
<status>Purified</status>
<status>Crystallized</status>
<status>Diffraction</status>
<status>Diffraction-quality Crystals</status>
<status>Crystal Structure</status>
<status>In PDB</status>
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Protein Sequence

The one-letter code sequence for FASTA comparison

Example: 
  • MKTIIALSYIFCLVFAQDLPGNDNNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELV
XML Presentation 
<sequence>MKTIIALSYIFCLVFAQDLPGNDNNSTATLCLGHHAVPNGTLVKTITNDQIEVTNATELV</sequence>
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Protein Name

The name of the protein for the target sequence.

Examples:
  • Glutamate synthase
  • 29-C10
XML Presentation 
<name>Glutamate synthase</name>
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Related 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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Remarks

Additional text details about this target

Example:
  • An important comment about this target.
XML Presentation 
<remark>An important 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:
  • Arabidopsis thaliana
  • Escherichia coli
  • Caenorhabditis elegans
XML Presentation 
<sourceOrganism>Arabidopsis thaliana</sourceOrganism>
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Database References

Describing related information about this target including a database name and an identifier within the database.

XML Presentation 
<databaseRef>
  <databaseName>Genbank</databaseName>
  <databaseId>189676547</databaseId>
</databaseRef>
<databaseRef>
  <databaseName>PDB</databaseName>
  <databaseId>1y63</databaseId>
</databaseRef>
<databaseRef>
  <databaseName>PDB</databaseName>
  <databaseId>2tem</databaseId>
</databaseRef>
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Database Name

The database name

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

The accession code for the named database.

Examples:
  • 189676547
  • 1y63
XML Presentation 
<databaseId>1y63</databaseId>
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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

http://fasta.bioch.virginia.edu/fasta/fasta_list.html.
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XML Format

Example of target entry in XML format.


Example: 
<target>
<id> Pfu-157236-001 </id>
<lab> Southeast Collaboratory for Structural Genomics </lab>
<date> 2001-06-18 </date>
<status> Proposed </status>
<status> Active Target </status>
<sequence>
 MLKIDLSGKLAFTTASSKGIGFGVAKVLAMAGADVIILSRNEENLKKAKEKIKEIADVNVEYIVADLTKKEDLER
 IVEVKNIGDPDIFFYSTGGPKPGYFMEMTMEDWEEAVKLLLYPAVYLTRALVPGMEKKGFGRIIYSTSVAIKEPI
 PNIALSNVVRISLAGLVRTLAKELGPKGITVNGIMPGIIRTDRVIQLAQDKARREGKSLEEALQDYAKPIPLGRL
 GEPEEIGYLVAFLSSELGSYINGAMIPVDGGRLNSVF
</sequence>
<name> putative alcohol dehydrogenase/reductase </name>
</target>

The XML format follows the recommendations of the

International Task Force on Target Tracking.


And follows this XML Format DTD.

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