RDB Query Builder
While the standard quick search only allows filtering on a selection of the metadata, the RDB Query Builder enables more flexible filtering of PDB/chem_comp/BIRD/EMDB entries using all the metadata included within the Mine 2 RDB. Note that for even more advanced queries, the manual SQL interface is still required.
Each of the schemas with in the RDB can be searched (and depending on which schema is selected, either PDB, chem_comp (Chemie) or BIRD search is shown), and some degree of inter-schema linking is also supported for filtering.
Upon loading the RDB Quiry Builder page, an empty filter selection object has already been added. Additional filters can be added by clicking on the "Add filter" button in the menu on the right side. The fitler selection object consists of four menus; Schema, Category, Item and Filter. The Schema menu lists all available schemas (e.g. pdbj for PDB data, cc for chem_comp, etc.). Clicking on a schema will show all available tables (which were generated from the mmCIF categories in the dictionary) within that schema. Clicking on a category, will show all available columns (which were generated from the mmCIF items of the corresponding category) within that table. Finally, the Filter menu shows the available filters available, which depends on the type of the selected item. Available filters are text (for text fields), number (for int/float fields to compare numbers (==, >, <, >=, <= operations)), number-between (for int/float fields, to find numbers within a specific range), contains number (to check whether a specific number is within a list of number elements), contains text (to check whether a specific string of text is within a list of text elements). Clicking on the "Add" button will add the filter to the filter list.
The filters part of the filters list have a similar interface to our CIF Editor. This interface can be used to combine multiple filters (to create complex AND/OR (sub)queries) or remove them.
After adding and arranging the filter, select the search Type in the menu to the right. The Type determines how the results are visualized. General shows the results in the same manner as the manual SQL interface shows its results. The other options show the results similar to the quick search for PDB, Chemie and BIRD. The available options depend on the search query used. After selecting a search Type, clicking on the Search button will show the results page.
Click on the "Show RDB documentation" button to find more information about the available categories (SQL tables) or items (SQL columns). Clicking on the "SQL query search" can be used to perform a manual SQL query (text based). A query can also be partially constructed using the RDB Query Builder, and can then be further modified using the manual SQL search, to make use of functionality only available via the very powerful SQL interface.
Each of the schemas with in the RDB can be searched (and depending on which schema is selected, either PDB, chem_comp (Chemie) or BIRD search is shown), and some degree of inter-schema linking is also supported for filtering.
Upon loading the RDB Quiry Builder page, an empty filter selection object has already been added. Additional filters can be added by clicking on the "Add filter" button in the menu on the right side. The fitler selection object consists of four menus; Schema, Category, Item and Filter. The Schema menu lists all available schemas (e.g. pdbj for PDB data, cc for chem_comp, etc.). Clicking on a schema will show all available tables (which were generated from the mmCIF categories in the dictionary) within that schema. Clicking on a category, will show all available columns (which were generated from the mmCIF items of the corresponding category) within that table. Finally, the Filter menu shows the available filters available, which depends on the type of the selected item. Available filters are text (for text fields), number (for int/float fields to compare numbers (==, >, <, >=, <= operations)), number-between (for int/float fields, to find numbers within a specific range), contains number (to check whether a specific number is within a list of number elements), contains text (to check whether a specific string of text is within a list of text elements). Clicking on the "Add" button will add the filter to the filter list.
The filters part of the filters list have a similar interface to our CIF Editor. This interface can be used to combine multiple filters (to create complex AND/OR (sub)queries) or remove them.
After adding and arranging the filter, select the search Type in the menu to the right. The Type determines how the results are visualized. General shows the results in the same manner as the manual SQL interface shows its results. The other options show the results similar to the quick search for PDB, Chemie and BIRD. The available options depend on the search query used. After selecting a search Type, clicking on the Search button will show the results page.
Click on the "Show RDB documentation" button to find more information about the available categories (SQL tables) or items (SQL columns). Clicking on the "SQL query search" can be used to perform a manual SQL query (text based). A query can also be partially constructed using the RDB Query Builder, and can then be further modified using the manual SQL search, to make use of functionality only available via the very powerful SQL interface.
Created: 2021-04-26 (last edited: more than 1 year ago)
