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| PDBj MinePDBj Mine is a new web interface to PDBj that supersedes xPSSS. The basic usage of PDBj Mine is similar to xPSSS. Some differences of PDBj Mine from xPSSS are the following:
The basicsFrom the PDBj top page (http://www.pdbj.org/) or the PDBj Mine page (http://www.pdbj.org/mine/), 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.
Keyword searchYou can use boolean operators for keyword search: AND, OR, and NOT. The operators have the usual precedence: NOT > AND > OR. AND searchIf 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 searchIf multiple keywords split by " 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 " operator before such keywords. e.g.: Searching entries including the "hydrolase" keyword but not including the "phosphate" keyword. hydrolase not phosphate Sequence searchYou 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 searchThe format of author name is following: "Family name" + commna (,) + white space ( ) + "Initial of given name" + period (.) e.g.： Ito, N. If you don't follow this format, such as omitting a white space or a period, the proper result won't returned. As the letters between upper case letters and lower case letters are distinguished. Wrong examples: Ito,N. Ito, N 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 SearchIf you want to find entries that satisfy certain conditions such as resolution, polymer types, annotations, etc., you can use the Advanced Search interface at http://service.pdbj.org/mine/advanced.html where you can specify a variety of conditions. SQL SearchIf 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 queriesExamples of SQL queries based on XPath expressionsSee Some XPath expressions (for demonstration only) in PDBj Mine:SQL Queries. Note: They can be extremely slow! Please don't use them. Comparison between SQL in PDBj Mine and XQuery in xPSSS |