DTD Tree structure of Protein Sequence Database Markup Language

DTD Tree structure of Protein Sequence Database Markup Language generated using Matra

DTD Name: Protein Sequence Database Markup Language
DTD Location: http://pir.georgetown.edu/pirwww/xml/psdml.dtd [cached copy]
DTD Issue Date: January 25, 2002
DTD Version: version 003 (preliminary version)
DTD Status: preliminary version

DTD-Tree [How to read it?]

ProteinDatabase (id, release?, date?)
|
|- Database?
|
+- ProteinEntry+ (id)
   |
   |- header
   |  |
   |  |- uid
   |  |
   |  |- accession*
   |  |
   |  |- created_date
   |  |
   |  |- seq-rev_date
   |  |
   |  +- txt-rev_date
   |
   |- protein
   |  |
   |  |- name (status?, attribution?)
   |  |
   |  |- alt-name* (status?, attribution?)
   |  |
   |  +- contains* (status?, attribution?)
   |
   |- organism
   |  |
   |  |- source
   |  |
   |  |- common?
   |  |
   |  |- formal
   |  |
   |  |- variety?
   |  |
   |  +- note* (status?, attribution?)
   |
   |- reference*
   |  |
   |  |- refinfo (refid?)
   |  |  |
   |  |  |- authors
   |  |  |  |
   |  |  |  |- author+
   |  |  |  |
   |  |  |  |= anonymous
   |  |  |  |
   |  |  |  +- group?
   |  |  |
   |  |  |- citation (type="journal")
   |  |  |
   |  |  |- volume?
   |  |  |
   |  |  |- month?
   |  |  |
   |  |  |- year
   |  |  |
   |  |  |- pages?
   |  |  |
   |  |  |- title
   |  |  |
   |  |  |- description (status?, attribution?)
   |  |  |
   |  |  +- xrefs?
   |  |     |
   |  |     +- xref+
   |  |        |
   |  |        |- db
   |  |        |
   |  |        +- uid
   |  |
   |  |- contents*
   |  |
   |  |- note* (status?, attribution?)
   |  |
   |  +- accinfo* (link?, label?)
   |     |
   |     |- accession
   |     |
   |     |- status*
   |     |
   |     |- mol-type*
   |     |
   |     |- seq-spec?
   |     |
   |     |- xrefs?  -->
   |     |
   |     |- exp-source?
   |     |
   |     +- note* (status?, attribution?)
   |
   |- comment* (status?, attribution?, link?, label?)
   |  |
   |  +- uid
   |
   |- genetics* (label?)
   |  |
   |  |- gene*
   |  |  |
   |  |  |- db?
   |  |  |
   |  |  +- uid
   |  |
   |  |- xrefs?  -->
   |  |
   |  |- map-position?
   |  |
   |  |- genome?
   |  |
   |  |- mobile-element?
   |  |
   |  |- gene-origin?
   |  |
   |  |- genetic-code?
   |  |
   |  |- start-codon?
   |  |
   |  |- introns?
   |  |
   |  |- intron-status?
   |  |
   |  |- other-product*
   |  |
   |  +- note* (status?, attribution?)
   |
   |- complex* (status?, attribution?, link?, label?)
   |  |
   |  +- uid
   |
   |- function* (label?)
   |  |
   |  |- description? (status?, attribution?)
   |  |
   |  |- pathway* (status?, attribution?)
   |  |
   |  +- note* (status?, attribution?)
   |
   |- classification?
   |  |
   |  +- superfamily+
   |
   |- keywords?
   |  |
   |  +- keyword*
   |
   |- feature* (link?, label?)
   |  |
   |  |- feature-type
   |  |
   |  |- description? (status?, attribution?)
   |  |
   |  |- seq-spec?
   |  |
   |  |- status?
   |  |
   |  +- note? (status?, attribution?)
   |
   |- summary
   |  |
   |  |- length
   |  |
   |  |- type
   |  |
   |  +- status?
   |
   +- sequence

Tree representation of the Protein Sequence Database Markup Language DTD (psdml.dtd) - generated using Matra 0.8.2b (http://matra.sourceforge.net/)

How to read the above tree?

Please check the article How to read the DTD Tree to learn how to read the above dtd tree generated by the Matra DTD Parser.

About PIR

The Protein Information Resource (PIR), located at Georgetown University Medical Center (GUMC), is an integrated public bioinformatics resource that supports genomic and proteomic research and scientific studies.

About Matra

Matra is a java based XML DTD parser utility. It is available from http://matra.sourceforge.net. It is freely available under the open-source MPL 1.1 license.