This section describes the details of each window used to operate BSCDB.
The main screen is where you enter when you type http://www.glyco.ac.ru/bcsdb/. The red number indicates how many structures are currently present in BCSDB. Four thematic sections stand for the following operations:
This form allows data retrieval using the unique BCSDB identifier (ID). Enter ID or IDs range in a text field (1), separating different IDs or ID ranges with commas, e.g. 1,2. The range is identified by hyphen, e.g. 1-10. The ' Go ' button (2) processes the query. The text field (3) informs the search engine how much result recods should be output per page (the default value is 30).
In most cases users do not know these IDs. The ID search may be usefull for the fast access to the data that have been previously searched for, if the ID was remembered. To make a link to a certain record from a webpage you should use the syntax <A HREF="http://www.glyco.ac.ru/bcsdb/cgi-csdb/search.cgi?db_id={my_ID_here}">{my_link_name_here}</A>
This form is proposed for searches using bibliographic data and keywords as criteria. If search criteria are specified in several sections of this form (e.g. authors and title), the intersection of queries will be returned as a result. The queries are not case-sensetive.
The Authors section lets you input the author name(s) in text field (1). To avoid spelling errors it is recommended to use the author index available from the Index button (2). For the author index window to appear at least two first letters of the author family name should be specified in the field (3). The list is restricted to the author names beginning with the specified character combination. As soon as you click a certain author in this list, one is copied to the bibliographic form. The author field supports query language with term grouping, wildcards and logical operations. Click here to view the details of its syntax. The sample query "Armstrong L" AND (Einstein OR Pauli) will find records related to papers written together by Armstrong L and one or both of two authors: Einstein or Pauli (with any initials).
The Title section lets you define which words should be present in the publication title of records to retrieve. The query language is supported too. You can enter the title criteria in the text field (4). The sample query capsul* OR C?S will find records related to papers containing at least one of the following words in the title: capsule, capsules, capsular, CPS, COS.
If the checkbox (5) 'in abstracts too' is checked the publication abstract will be analyzed for the specified terms together with the title. Please note that not all of the records in BCSDB have publication abstracts typed in.
The Keywords section lets you define which terms should be present in the keyword list, as comes from the paper. The query language is supported. You can enter the keyword criteria in the text field (10). The sample query capsul* OR C?S will find records related to papers containing at least one of the following words in the keyword list: capsule, capsules, capsular, CPS, COS.
If the checkbox (11) 'in title too' is checked the publication title will be analyzed for the specified terms together with the keyword list.
The checkbox (12) filters out records related to papers with no structure elucidation described. Thus, if this checkbox is checked, records related to papers describing some additional actions on the structures elucidated within some other publication will not be returned.
The selector (13) lets you choose the scope of search. If the default value all database is selected the search will be performed in all BCSDB. If there was a previous query within the current browser session the second variant becomes available: results of the previous query. It provides the mechanism for the intersection of queries of different types, e.g. you first search for some substructure and then intersect the results with some bibliographic data by selecting the search scope as results of the previous query. If the previous query was of the same type as current, the new query overrides the previous.
The ' Go ' button (14) processes the query. The text field (15) informs the search engine how much result records should be output per page (the default value is 30).
The query language is supported in the Authors, Title and Keywords fields of the bibliographic search form. Terms can be combined with AND (syntax: blankspace or & or AND) and OR (syntax: | or OR) logical operations. E.g. Term1 AND Term2 finds records containing both Term1 and Term2, while Term1 OR Term2 finds records containing at least one of terms Term1 or Term2. The default operation (Term1 Term2) is AND. The preference of logical operations can be declared by parentheses, e.g. (Term1 OR Term2) AND Term3. Term grouping with parentheses can be nested.
If the term contains blankspaces, i.e. consists of several words that should come together in the specified order, enquote it with double quotes, e.g. "Holst O", "structure elucidation". This is most often used to combine author family name and initials. To widen the search two wildcards can be used: an asterisk (*) for any alphanumeric sequence (including empty) and a question mark (?) for one alphanumeric character. E.g. glyco* will find 'glycoconjugates', 'glycolipids' etc., while glycopolymer? will find 'glycopolymer' and 'glycopolymers'.
This form lets you input the fragments of structure and send the queries to the database engine. There are two ways of structural query edition: wizard and expert. These two can be switched one to another by the selector (1). The wizard (default) does not require special knowledge except general nomenclature of carbohydrates and is oriented to visual operations. On the other hand, it has some limitations, i.e. not all the queries that search engine can take in are constructable by the wizard. In both modes the search query appears in the Substructure field (4). In the expert mode this field is directly editable, which implies knowledge of the structure encoding rules. When switching from wizard to expert the current query is preserved. When switching from expert to wizard, the query is re-initialized because not everything that an expert can enter is displayable in the wizard form. You can intersect several structural queries by separating them with blankspace in the expert mode.
The scope section (5) is available in both modes and defines the limitations on the structure type (monomers, oligomers, chemical repeting units, biological repeating units, repeating units of cyclic polymers). All boxes checked mean no limitations.
The wizard form is shown on screenshot. The first step is to select a suitable topology from the drop-down list (2). The wizard supports topologies of up to four residues. The graphic representation of topology (3) is displayed on the right. As soon as topology is selected, the appropriate number of residue sections appear below (it's three on the screenshot).
The residue section header (6) includes the position of this residue in the topology (e.g. Residue A) and a constructed residue name with all configurations and substitutions applied.
The first residue section (residue A) contains a unique field Add substitution (13). If this checkbox is checked, it means the residue is substituted by some other residue (in this or another repeating unit, if polymer) to the position specified in the drop-down list (13). Usually this feature is used to indicate the position of attachment of another repeating unit to the leftmost residue.
Each residue section has four Add qualifier controls (14), that allow specification of up to four monovalent substituents. When checked, drop-down lists (15) and (16) become available to control the monovalents substituents and positions of their attachment, accordingly. E.g. on the screenshot the residue A (Fuc4N) is acetylated at position 4 (at nitrogen).
The selector (18) lets you choose the scope of search. If the default value all database is selected the search will be performed in all BCSDB. If there was a previous query within the current browser session the second variant becomes available: results of the previous query. It provides the mechanism for the intersection of queries of different types, e.g. you first search for some microorganism and then intersect the results with some structural data by selecting the search scope as results of the previous query.
If search exact structure (19) is checked the specified structure is interpreted as the complete molecule, i.e. not a structural fragment. The ' Go! ' button (20) processes the query. The text field (21) informs the search engine how much result records should be output per page (the default value is 30).
Make GLYDE link in the bottom (22) opens a new window with entered structure represented both as BCSDB linear code and GLYDE 1.2 XML code. To read more about GLYDE click here.
This form allows to retrieve records with structures originated from a particular microorganism. The alphabetical lists (1), (2) and (3) provide specification of the genus, specie and strain/serogroup respectively. The default position in each list is Any which means no limitations. The second position sp. in the list of species is used to find microorganisms with genus and strain specified but specie name undefined. As soon as the genus is selected (except Any) the specie and strain lists are updated accordingly. As the strain/serogroup list may be rather long (especially if Any is selected for genus or specie) there is a text field (4) to enter it directly. The default value is * (=no limitations).
The selector (5) lets you choose the scope of search. If the default value all database is selected the search will be performed in all BCSDB. If there was a previous query within the current browser session the second variant becomes available: results of the previous query. It provides the mechanism for the intersection of queries of different types, e.g. you first search for some substructure and then intersect the results with some bacterial origin data by selecting the search scope as results of the previous query. If the previous query was of the same type as current, the new query overrides the previous.
The ' Go ' button (6) processes the query. The text field (7) informs the search engine how much result records should be output per page (the default value is 30).
The link List of microorganisms (8) displays the complete list of microorganisms that are present in BCSDB. The link Lookup in NCBI taxonomy (9) retirves the data from NCBI taxonomy database using the selected genus and species as criteria. The data displayed are: scientific name or the organism, synonimic names, rank and taxonomic lineage.
This form allows to retrieve records containing the specified NMR data as a subspectrum of the NMR spectrum stored inside the record itself. The selector (1) allows the selection of a particular nucleus. The subspectrum to search for should be input in the window (3). You can separate signals with spaces or new line characters, the sorting is not required, allowed characters are numbers and decimal dot.
To compare the spectra the BCSDB engine forms all possible subspectra of the stored NMR spectrum with number of signals equal to that found in the user input, and the best-fitting subspectrum is used to calculate the similarity. Similarity is the inverse of the average difference between closest signals, e.g. 1 means the average difference is 1 ppm, 10 means it is 0.1ppm, 0.1 means it is 10ppm etc. A value of 0 stands for no similarity at all, a value of 1000 is for full similarity (exact match of chemical shifts). The treshold field (2) allows the filtering of records according to similarity. Only those records that possess the similarity higher than this treshold will be returned. Good values for carbons are 1 and above; good values for protons are 5 and above. The output records are sorted according to the similarity in the descending order.
The selector (4) lets you choose the scope of search. If the default value all database is selected the search will be performed in all BCSDB. If there was a previous query within the current browser session the second variant becomes available: results of the previous query. It provides the mechanism for the intersection of queries of different types, e.g. you first search for some substructure and then intersect the results with some bacterial origin data by selecting the search scope as results of the previous query. If the previous query was of the same type as current, the new query overrides the previous.
The ' Go ' button (5) processes the query. The text field (6) informs the search engine how much result records should be output per page (the default value is 30).
Any search request leads to a number of records found, which can be displayed in two forms: collapsed (only the structure, bacterial origin and issue data) and expanded (all data). Each record can be switched from the collapsed form to the expanded form and back by one click. The header and footer for the result output page are shown on the right. Red numbers in first two lines (1) represent how many records have been found and how many of them are displayed on this page. The Previous and Next links (2) allow the navigation through the result output pages. There is no Previous link for the first page and no Next link for the last one. The expand all records (or collapse all records, depending on the current state) allow bulk operation over the form of record display.
The footer of the output page (the same screenshot) contains a link to resort the records (3). Possible sort modes are: publication year, journal name, microorganism name (default), structure type. The resorting is applied to all the records returned, not only to those displayed on the current page. Three refine query links (4) allow to you intersect the current results with another query and lead you to the search forms with 'search in previous' option enabled. The link (5) stands for the new query of the same type.
A screenshot on the left is the example of a record in the expanded form. (1) is a number of this record among the records found. (2), (3) and (7) stand for the primamry bibliographic reference attached to this record: author list (2), title of the publication (3) and issue data (7): journal name, volume, subvolume if any, year, page range.
(4) is a pseudo-graphic representation of the structure in SweetDB format (JUPAC 2D). The names of residues that were present in the structural search request are highlighted in bold. (5) is one or several microorganisms (genus, species, strain if full taxonomy is available, a part of this information otherwise) that posessed this structure. NCBI Taxonomy links this data to the NCBI TaxID and displays the corresponding page from the NCBI Taxonomy database.
The fact of this structure having been elucidated within the attached publication is reflected by (8). The web-resource related to the publication is linked to by (9). In most cases it's a reference to the PubMed entry. Other data related to bibliography (publisher, corresponding author email, author affiliations etc.) may be or not be present under (10). Two white boxes display the publication abstract (11) and keywords (12).
Other related information (location of this structure inside the article, structure type - oligo, mono, chemical or biological repeating unit of polymer, chemical formula, aglycon information, trivial name, methods used to elucidate the structure, enzymes that releaze or process the structure, availability of synthetic, biosynthetic, genetic and conformation data in the paper, other comments) may be or not be present under (13).
The related records (14) is a list of links to the BCSDB entries that contain the related structures (from the same publication, or products of degradation, or biochemically related). Other data in this section may include IDs of this structure in other databases, if available. Most of these references came from Carbbank database.
If NMR data are availbale the temperature and solvent information is displayed under NMR conditions (15), followed by the NMR assignment tables (16) for 1H and 13C. The linkage column in these tables indicate the path to the residue from the reducing end or from the rightmost residue in the repeating unit.
BCSDB ID (17) is for your reference, for the fast access to this record in future. Pressing Make GLYDE description (18) will open a child window with both GLYDE 1.2 XML and BCSDB-internal descriptions. To retrieve the data stored in GLYCOSCIENCES database for this structure, use the link Retrieve from GLYCOSCIENCES (19).
This feature exports the BCSDB data to the text format (the same format as of the datafile for submission). The format documentation is available on the file submission page. To perform an export you should specify the range of IDs in a text field (1), separating different IDs or ID ranges with commas, e.g. 1,2. The range is identified by hyphen, e.g. 1-10. To export all the database, specify 1-200000. The 'Export' button (2) processes the query and outputs the exported file to the browser. After this you can select all (Ctrl-A), copy (Ctrl-C) and Paste (Ctrl-V) wherever else.
Users can submit own data to BCSDB in two ways: in a step-by-step form or as a file. The former variant does not require knowledge of the file format while the latter provides better performance, especially when submitting several records.
Each field in submission form is described beside it. The obligatory fields are shown in bold.
Instructions for the preparation of a data file and examples are given below the file submission window.
After submission the data are stored in a special validation pool and become available after the BCSDB administrator checks and approves them.