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PDBj Mine is a new web interface to PDBj.

PDBj Mine has the following basic features:

  1. PDBj Mine is based on a relational database.
  2. Enhanced keyword search.
  3. Detailed queries using SQL.

PDBj Mine: Design and implementation of relational database interface for Protein Data Bank Japan.
Kinjo AR, Yamashita R, Nakamura H.
Database, 2010:baq021 (2010) PubMed:20798081 DOI:10.1093/database/BAQ021

[The basics]

Using a search box at the top of each PDBj web page, three types of search described below can be done. Just select a search type and input strings, and you will get the corresponding entry or a list of entries with brief summaries.

  • PDB ID or keyword
  • amino acid sequence or nucleic acid sequence
  • author name

Keyword search

You can use boolean operators for keyword search: &, |, and !. The operators have the usual precedence: NOTANDOR.

AND (&) search

If multiple keywords split by and, & or white space are input, you will get a PDB entry list including all the keywords.

e.g.: Searching entries included both "antibody" and "virus"

antibody and virus

You can also describe following form:

antibody virus

OR (|) search

If multiple keywords split by or or | are input, you will get a PDB entry list including more than one keyword.

e.g.: Searching entries included both "erythrocyte" and "leukocyte"

erythrocyte or leukocyte

Negation NOT (!)

If you want to search not including some keywords, add not or ! operator before such keywords.

e.g.: Searching entries including the "hydrolase" keyword but not including the "phosphate" keyword.

hydrolase not phosphate

Sequence search

You can search entries including an amino acid sequence or a nucleic acid sequence. The sequence is to direct with one letter form. More than five residues can be search.

e.g.:

KGFEPLIQFA

author name search

The format of author name is following:Family name+ commna (,) + white space ( ) +Initial of given name+ period (.)

e.g.:

Ito, N.

As only one author assignment is available in the basic search, you may use the advanced search or the sql search for multiple author search.

[Advanced Search]

If you want to find entries that satisfy certain conditions such as resolution, polymer types, annotations, etc., you can use the Advanced Search interface at /advancedSearch where you can specify a variety of conditions.

[SQL Search]

If Advanced Search does not suffice your need, you can resort to SQL Search where you can write fine-grained queries in SQL, the standard query language for relational databases. To use SQL Search, you must be familiar with SQL as well as the structure of PDBML (PDB's canonical XML format). The structure of the relational database underlying PDBj Mine is based on that of PDBML. The hierarchical structure of PDBML is represented as nested sets defined by pointers to each XML element or attribute. Some examples of SQL queries are presented in PDBj Mine:SQL Queries.

For your convenience, the brief_summary table and some helper functions are defined.

The brief_summary table compiles the information needed for Advanced Search.

The xp_category function returns a PDBML category for a given PDB ID.

SELECT * FROM xp_category('1gof', 'entity')

returns the entity category of the entry 1gof as an XML element of the corresponding PDBML file. For more examples, see PDBj Mine:SQL Queries.

[Examples of SQL queries]

See PDBj Mine:SQL Queries.

Examples of SQL queries based on XPath expressions

See Some XPath expressions (for demonstration only) in PDBj Mine:SQL Queries. Note: They can be extremely slow! Please don't use them.

(last edited: 3 months ago)2013-10-31
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