Integrated search

This search service allows you to more quickly find biomolecules and biochemical information archived by BMRB, PDB, EMDB, Swiss-Prot, BMRB-Metabolomics and Ligand Expo. Search results are displayed in entry list by each information resource. If an entity or sequence matches between different databases, a cross-reference is added between the entries. It also annotated by other information resources such as PubMed, IntAct and PubChem.

For keyword search or BLAST sequence search, please select "Everything" or "Sequence" tab respectively.

Omni-box

Auto-complete function implemented in the omni-box makes it easier to construct queries during user input by suggesting terms used in actual data or displaying descriptions of dictionary components such as the categories and the items. In addition, a "clock" button, , on the title bar offers personalized query history storage function, which helps you to remember past queries for comparison and to adjust queries to get better results.

Filters

Search filter is displayed when you click a "caret" button,   , located left side of the omni-box. The search filter allows you to configure the result to be filtered by release date, author name, molecular function, ligand property, and source organism.

Settings

A "cog" icon, , on the tab menu allows you to change various search settings; target databases, hits per page, query settings, BLAST settings and miscellaneous display settings. Some changes will take effect after "OK" button is selected. Please select "Close" button to hide this panel without any changes.

Query syntax

Lucene query syntax parser implemented in the omni-box that enables structured query composition using Boolean operators ("OR", "AND" and "NOT"), query grouping using parentheses to form sub queries, wildcards (either ? or * character in a term), regular expressions surrounded by slashes (e.g. entry.title:/sh[23]/, it is noted that a regular expression query should have a field scope like "entry.title:"), fuzzy queries based on Demerau-Levenshtein distance using a tilde character in term end, proximity query (e.g. "ph domain"~3, which searches for "ph" and "domain" within 3 words.), range queries (e.g. entry.original_release_date:[20010101 TO 20051231]), and the field scope followed by a colon character, which can specify named data item defined by format dictionary such as NMR-STAR dictionary and PDBx/mmCIF dictionary.
A query is broken up into terms, phrases (a group of terms surrounded by double quotes) and operators. Multiple terms and phrases separated by a white space are automatically conjugated by default "AND" operator (see also "Settings" panel above).

Query example

With this query syntax, you can freely combine text query and field scoped query, which plays like quasi-relational search as follows.

1. Single text query

transferase

2. Sequence query

crtlypfsgerhgqglrfaagelitllqvpdggwwegekedglrgwfpasyvqll

3. Wildcard in a phrase

"Forman-Kay, J.*"

4. Text query with search filter on release date

ubiquitin date:[20120101 TO 20161231]

5. Text query with search filter on author name in conjunction with NOT operator

parkinson authors:NOT parkinson

6. Grouping regular expression query and text query with field scope (on entry title)

entry.title:(/sh[23]/ domain)

7. Text query with field scope (on citation journal name)

citaion.journal_abbrev:nature

8. Text query (as a phrase) with field scope (on quantitative data type)

datum.type:"19F chemical shifts"

9. Combination of text query and range query (on entity's formula weight)

sh2 domain entity.formula_weight:[25000 TO 50000]

10. Combination of proximity query and text query with field scope (on kind of data)

"ph domain"~3 data_set.type:heteronucl_T2_relaxation

11. Boolean operator (explicit AND operator)

chem_shift_completeness_list.assigned_residue_coverage:1.000 AND chem_shift_completeness_list.entity_polymer_type:polypeptide(L)

12. Boolean operator (OR operator to include equivalent condition in EMDB)

entity.formula_weight:[50000 TO 100000] OR mwType.content:[0.05 TO 0.1]

13. SARS-CoV-2 entities (strict)

entity_natural_src.ncbi_taxonomy_id:2697049 OR entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id:2697049 OR sciSpeciesType.ncbiTaxId:2697049

14. SARS-CoV-2 entities (alternative)

"Severe acute respiratory syndrome coronavirus 2"

15. SARS-CoV entities (alternative)

"SARS-CoV"

Result panel

Search results are displayed as a list of entry panes by each information resource. Each entry pane has interactive contents representing entry relationship between different databases via citation sharing, sequence homology, protein-protein interaction and identity of chemical compound. By using “Order by ” menu button, you can rearrange the results by various criteria such as relevance to input keywords, release date, accession ID, experimental method, number of citations, title of primary citation, total formula weight, maximum entity’s formula weight, number of related entries, etc. Tabular results, written in CSV, TSV, XML or JSON, are available from “Export as ” menu button. They are suitable format for saving the results or importing into spreadsheet applications or data analysis tools for further data processing.
At first, each entry pane is displayed in collapsed form for summary, detailed dynamic contents will be displayed when it is scrolled to be visible on browser or user hovers on link titled “Detail ”. All contents hit with the input keywords are highlighted. Otherwise, a “Hit context” menu appears in the pane and enables you to identify where the keyword hit in the source XML document that will serve as a clue to improve the original search query.
Except for the link to open interactive contents, there are two types of URL link; (i) URL links referencing original or external resources, and (ii) URL links referring to be keyword for deeper understanding of relevant researches.

The bottom of page is allocated to visualize statistics on the search results. A green button, , next to pagination buttons is a short cut button to the statistics.

Statistics panel

The statistics are represented as the chart displays summarizing the following perspectives: release date, total molecular weights, available data sets (BMRB), completeness of assigned chemical shifts, highest resolution (PDB, EMDB), R-value (PDB), applied experimental methods, applied refinement methods, cited journal names, most frequent keywords and most frequent entry author names, respectively.

BMRB entry page having static URL

BMRB entry page, each having a static URL, for example, https://bmrbj.pdbj.org/bmr/bmr15400. The entry page basically follows the page design of integrated search result except for having an integrated file export menu, "Download ", which allows you to retrieve various derivative data located in BMRB mirror server and BMRBj data server.

Available data sets from the integrated file export menu are as follows. NMR-STAR, AVS validation report, LACS validation report, CSI, CS-Rossetta structures, DSSP, Watson Click basepairs identified by Wattos, back calculated chemical shifts from structure by SHIFTS, SHIFTX, SPARTA, respectively, MolProbity validation report, BLAST sequence alignment output for each entity, timedomain data (FID), they are maintained by BioMagResBank in US; BMRB/XML, BMRB/RDF, BMRB/JSON, timedomain data of metabolomics entry in nmrML format, Completeness of assigned chemical shifts, Protein Blocks structural annotation, and FASTA sequence file, they are maintained by BMRBj, respectively.

What's new?

Added well-defined region plot as the graphical content for NMR combined restraints.

Incorporated AlphaFold Protein Structure Database sequence information as BLAST query results of each BMRB entry.

Added graphical content for chemical shift validation report is available.

Added RCI and derived paramaters (S², NMR RMSD) plots as the graphical content for NMR combined restraints.

Added rotameric state prediction of ILE/LEU/VAL residues by assigned chemical shifts in the graphical content for NMR combined restraints.

Graphical content for NMR combined restraints is available.

Coordinate and restraints files are accessible from entry page.

Added example queries to search SARS-COV-2 entities.

Launch search service enabling SSL.

Fixed order direction turned to default after selection of pagination buttons.

Enhanced search speed and stability. It is possible to sort search results by the number of interacting partner.

Enabled automatic chart display that depends on user's query.

Thumbnail of BMRB-Only entry is displayed, if possible.

Fixed NMR relation parameters were not shown in some entries.

Fixed hang-up issue while sorting the search results.

Fixed pure relational search missed some entries.

Sequence number will appear on sequence characters of entity as well as non-standard residue.

The article about Data-out activity of PDBj-BMRB group has been published in Protein Science.

Table representation of chemical bounds connecting structural portion, entity, is available.

Chart representations of secondary structure code (Protein Blocks as Sequence logo) is available.

Chart representations of secondary structure code (DSSP as Sequence logo) is available.

Chart representations of relative solvent accessible surface area (SASA) is available.

Chart representations of LACS plot for chemical shift validation is available.

Revised auto-complete feature is aware of relational schema and data.

Retrieved field selection and range selection. For example, Entries containing a entity with molecular weight between 50,000 and 100,000 Da.

nmrML documents are accessible from metabolomics entry page.

BMRB/JSON archive is accessible from entry page.

Chart representations about Spectral density values and D-CSA cross correlation relaxation rate are available.

Table representation about pH titration is available. Fitted pH titration curve will be displayed, if possible.

Table representation about Binding constants and Chemical rates are available.

Chart representations about Coupling constants and RDCs are available.

Chart representations about Hydrogen exchange protection factors and Hydrogen exchange rates are available.

Chart representation about Order parameters is available.

Chart representation about T₁/T₂ with band plots stand for NOE value lower than 0.5 is available.

Chart representations about Heteronuclear T₁, Heteronuclear T₂ relaxation, Heteronuclear T_1ρ relaxation and Heteronuclear NOEs are available.

Release date is added in "Entries sharing articles" content.

Deposition code can be used for searching BMRB entry page.

Chart representation about completeness of assigned chemical shifts is available. Assigned chemical shift table for Metabolomics entries are also available.

Fraction of assigned chemical shifts per residues is available under table about completeness of assigned chemical shifts. In addition, you can download assigned chemical shifts in various formats and access sample information.

Experiment information is available as "Experiment performed" context for BMRB and Metabolomics entries. Spectral images for metabolomics entries are also available.

Entry view page is available for Metabolomics entries. e.g. Metabolomics bmse000400 entry

Sorting in reverse order has been implemented and accessible next to "Order by" menu.

Query history has been implemented and accessible from a clock icon on Search panel.

Entry view page is available for BMRB entries. e.g. BMRB 15400 entry

Fully implemented top search v3's functionality.

• Hit contexts with highlight
• Statistics panel
• Exporting search results by CSV, TSV, XML and JSON formats