WO1996006391A2 - Relational database management system for chemical structure storage, searching and retrieval - Google Patents
Relational database management system for chemical structure storage, searching and retrieval Download PDFInfo
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- WO1996006391A2 WO1996006391A2 PCT/US1995/010171 US9510171W WO9606391A2 WO 1996006391 A2 WO1996006391 A2 WO 1996006391A2 US 9510171 W US9510171 W US 9510171W WO 9606391 A2 WO9606391 A2 WO 9606391A2
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
- G16C20/90—Programming languages; Computing architectures; Database systems; Data warehousing
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
- G16C20/40—Searching chemical structures or physicochemical data
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S707/00—Data processing: database and file management or data structures
- Y10S707/912—Applications of a database
- Y10S707/941—Human sciences
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S707/00—Data processing: database and file management or data structures
- Y10S707/953—Organization of data
- Y10S707/954—Relational
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S707/00—Data processing: database and file management or data structures
- Y10S707/99931—Database or file accessing
- Y10S707/99933—Query processing, i.e. searching
Definitions
- the present invention relates to a relational database management system that stores, searches and retrieves chemical structure information quickly and easily.
- RDBMS relational database management systems
- the advantages of integrating chemical structure information into an RDBMS include: a closer integration with other related chemical data, efficiency in both storage and retrieval of chemical structure data, and better access to the chemical structure data by other related applications.
- relational database technology provides an opportunity to transfer a large amount of the database management responsibility from the specialized database systems described above to a standard widely-accepted technology.
- relational technology has typically not been used as the basis for chemical information systems. This is due to the fact that there are problems inherent in any attempt to cast a chemical structure searching system problem into structured query language (SQL)—the standard language of relational databases. These problems include difficulty in storing and representing chemical structures in a database. No chemical information system has yet been implemented using only relational technology as its database component.
- MACCS Molecular Access System
- ISIS Integrated Scientific Information System
- the present invention overcomes the above-listed problems and additionally has the following advantages: (1) development and maintenance costs will be greatly reduced by using a commercial database package. Accordingly, development efforts and benefits can be more effectively directed toward aspects of system design, and improvements in the underlying database technology will be automatically transferred to the chemical information system. This shift of focus away from database development concentrates the development and maintenance efforts on improving the search strategy and the user interface, which are the highly visible aspects of the system; (2) interfacing with other information systems will be simplified since relational databases are already used to store much of the non-structural chemical data used in research and commercial settings; and (3) portability will be much less of a design drawback since the amount of custom programming is minimal and can easily be adapted to numerous types of technology. Therefore, the portability responsibilities are mostly shouldered by the database manufacturer itself, and not by the developer of the chemical storage system.
- the present invention overcomes the shortfalls in the art by developing a chemical structure search system which expands the capabilities of existing systems by capitalizing on the strengths of relational database technology.
- the present invention allows the user to optimally store and search the chemical structure information using various search strategies such as multi-valued atoms, multi-typed bonds, Mar ush searching and various other options in a relational database management system.
- the present invention allows the routine integration of chemical structure data with other related information such as inventory, spectroscopic data and clinical data via standard relational database methods to allow better usage of all types of chemical information in both commercial and research settings.
- this system will also introduce dynamic querying capabilities which will allow the user to be notified of any new chemicals that are entered into the database that are responsive to previously run queries. This provides the functionality of relational views for chemical structure information.
- structure classes can also be implemented which allow the user to store certain types of information about particular types of chemical structures such as steroids. Accordingly, users can later call up this information in a quick and efficient manner without re-entering or performing previously run queries.
- FIG. 1 is a chemical representation of structure 1 (SI) ;
- FIG. 2 is a chemical representation of structure 2 (S2)
- FIG. 3 is the connection table for structure 2 (S2) set forth in FIG. 2.;
- FIG. 4 defines the bonded atom codes to be used in search key and query generation
- FIG. 5 is chemical representation of query 1 (Ql);
- FIG. 6 is a block flow diagram depicting the registration process
- FIG. 7 is a block flow diagram depicting the generation of search keys
- FIG. 8 is a block flow diagram depicting the operation of dynamic queries
- FIG. 9 depicts the hardware configuration of the present invention.
- FIG. 10 depicts the screen for viewing results of queries
- FIG. 11 is a block flow diagram depicting an alternative key generation process.
- FIG. 12 is a step-by-step generation of a search key for structure SI.
- the present invention makes use of standard relational database technology such as that found in the commercial product Oracle which is marketed by Oracle Corporation as noted above. All references to the retrieval and storage of information will be done in a standard relational database, and will use standard procedures for doing so, including structured query language (SQL) commands.
- SQL structured query language
- the operations and functions of relational databases discussed in this patent application are well known to those of ordinary skill in the database management field. Those operations and functions can be found in numerous texts, including Oracle users' and developers' manuals.
- a typical computer workstation 1 will contain a central processing unit (CPU) 2, and main memory 3, and can be coupled to storage devices 4 such as magnetic disks, an input device such as a keyboard 5 or mouse, and output device such as a computer monitor screen 6 and a printer 7.
- storage devices 4 such as magnetic disks
- an input device such as a keyboard 5 or mouse
- output device such as a computer monitor screen 6 and a printer 7.
- One or more such storage devices may be utilized.
- the preferred embodiment of the relational database management system for storing, searching and retrieving chemical structure utilizes a microprocessor, such as a Microvax 3100 model 900 operating with a VMS 5.5-2 operating system with at least two gigabytes of disk space and at least 32 megabytes of RAM.
- the system can be provided with more memory to speed up throughput access rates.
- the system could also be optionally coupled to a local area network (LAN) or other communications architecture/environment in order to link with other computer workstations and have access to data from other systems.
- relational databases for a chemical structure search system
- connection table For each structure to be registered in the database, a connection table is constructed at step 24. This table stores information about each atom in the structure including its atomic number, the identity of all of the connected atoms, and the type of bond to each of these connected atoms. For example, the connection table for a chemical structure to be added such as structure S2 as depicted in Figure 2 is shown in Figure 3.
- the table depicts the types of links that are stored between any two given atoms in a structure.
- a single bond between two atoms is denoted by a "1” while a double bond is denoted by a "2" and a triple bond is denoted by a "3.”
- This table is stored in a relational table along with its associated registry number in a compressed sparse matrix form.
- the connection table will be used for the Atom by Atom Matching (ABAM) process which is described more fully below.
- the system searches the existing structures to verify that no duplicates exist in the database at step 26. If the structure has already been entered into the system, it will not be entered again.
- N search keys are stored as data in the relational database. Each search key results from a unique numbering of the atoms with a different atom representing the starting point of the key. In effect, N different search keys are stored for each structure of N atoms.
- the string is a representation of the atomic environment of the starting atom.
- the ordering of characters in the string cannot be sensitive to deletion of portions of the structure or query. That is, deletion can remove portions of the string (with subsequent replacement by wildcards in a query) but cannot cause reordering of the remaining characters in the string.
- One such algorithm which builds the string by adding connectivity information using a breadth-first graph traversal is detailed in FIG. 7, and is used in subsequent examples.
- the following process is used to generate a search key.
- the process starts at step 40, and at step 41 all atoms are marked as "unranked” and "unused”.
- the starting atom is marked as "used” and added to the key.
- the starting atom is marked as the current atom.
- the search string would begin with "Br".
- the first code in the key is shown as the atomic symbol; in practice, a one byte code is used for this purpose.
- the Bromine (Br) atom would be marked as "used” and set to the current atom.
- any unused neighbors are examined.
- the Carbon (C ⁇ atom would be unused and accordingly, the system would advance to step 45 where unused neighbors were ordered. Because there is only one neighbor in this portion of the structure, and the ordering is not terminated by an open site at step 46, and there is no open site at the current atom at step 48, the system advances to step 49, where codes for the neighbors, in order, are added to the key and marked as "used".
- the letter key to indicate the single bond to the Carbon (C atom, and the Carbon (C x ) atom will be marked as "used”.
- the system next adds an end-of-atom marker to the key at step
- the system next verifies that ordering was not terminated, and there was no open site at step 53.
- the process continues at step 54 by examining if any atoms in the key are unranked. In this example, the Carbon (C : ) is unranked. Because the key is not too long (i.e., not longer than a predefined length) at step 55, the Carbon
- (C ⁇ ) is chosen as the first unranked atom in step 56.
- the process repeats itself starting at step 43 with the Carbon (C atom as the current atom.
- the Carbon (Cj) is marked as the current atom, and the unused neighbors are examined at step 44. Once again, there is only a single bond to a Carbon (C 2 ) atom, and therefore the ordering at step 45 is unnecessary.
- a "c” is added to the key, and at step 51 the end-of-atom marker is added to the key. Accordingly the key now reads "Br c . c .”.
- the first unranked atom in the key (C j ) is chosen, and at step 43, it is set as the current atom.
- the process continues by examining the single bond to the Carbon (CJ emanating from this Carbon (C 3 ) , and accordingly "c” and “ . " are added to the key.
- the key now reads "Br c
- the next unranked atom (Oxygen) is then set as the current atom at step 43.
- an end-of-atom marker is simply added to the key at step SI.
- the process once again repeats with C 4 as the current atom. Because there are no unused neighbors, ".” is appended to the string, and the process stops for this starting atom.
- the final search key would be: "Br c . c . c e . c . . .”.
- the same process is repeated for every starting atom in a given structure. This process is also shown, step-by-step, in FIG. 12. (Steps 57, 58 and 59 in FIG. 7 will be explained in Section V. below. )
- search keys are stored in the database with associated registry numbers which correspond to the registry numbers of the connection tables and associated information. Keys that are duplicated due to symmetry are eliminated at registration time.
- step 80 all bonds in a given structure are marked as "untraversed”.
- a starting atom is chosen, which in this case is the Bromine (Br) atom, at step 81, and added to the key at step 82.
- step 85 the system examines if any untraversed bonds to atoms at the next level exist. In this case, there is an untraversed path to a Carbon (C x ) atom. The system next determines that there is no open site at any atom at this level at step 88 and, if not, continues at step 90, by ordering all untraversed bonds to all atoms at the next level.
- C x Carbon
- the system continues by adding the codes for the ordered paths to the key at step 93. Then, at step 94, the system adds an end-of-level marker to the key. Accordingly, the key now reads "Br c .”, and all bonds that are included in the key are marked as "traversed”.
- step 85 the system determines that there are no untraversed paths to atoms at the next level, and stops at step 87.
- the final key reads: "Br c . c . c e . c .”.
- Additional information about each structure can also be stored in the database, such as registry key or other unique identifier of a structure, name, and formula.
- the user may also define any additional information to store and search using standard RDBMS technology.
- Each of the fragment codes comprising the search keys can be made to occupy a single byte in the database. There are approximately 313 of these fragment types existing in a large sample of structures. One byte allows 256 possibilities, three of which cannot be used. (Byte 0 cannot be used due to its importance in programming, and two bytes used in the relational database management system for its wildcard operation cannot be used, since it is normally difficult to search these characters and use the SQL "Like" operator in the same statement) .
- the remaining bytes can be divided into three groups:
- Each query structure generates one search key for each atom in the structure that could be assigned an unambiguous fragment code.
- the search keys of the query structure are generated by applying exactly the same rules to the query structure as those used to generate the database search key defined in Ill.b. above, with the only exception being treatment of wildcards.
- search keys are generated using one unambiguous set of rules. So long as these rules are applied to the query structure in exactly the same fashion, and since each database structure has a key originating from each of its atoms, the results will be standardized.
- every search key generated for the query must match one or more search keys generated for the database structure. Additionally, if any query search key fails to retrieve the structure, the query cannot be a substructure of that structure.
- the user types in a structure in the same way that new structures are entered, and can indicate where there are wildcards (i.e., no particular atom necessary) and where there are multiple acceptable types of atoms or bonds by indicating the specific atoms and bonds that are acceptable in any given position.
- the query keys are generated in the same manner as the search keys for the structures. Accordingly, any acceptable key generation process may be used. Therefore, when generating a query key for Ql in Figure 5, and using the process shown in Figure 7, the following steps occur.
- the process begins at step 40, and at step 41, all atoms are marked as "unranked” and "unused”. A starting atom is chosen and marked as "used”, and the atom code is added to the key at step 42.
- the Bromine (Br) atom will be the starting atom.
- Bromine (Br) is marked as the current atom, and at step 44, it is determined that there are unused neighbors. The process continues at step 45, with all unused neighbors being ordered.
- the process continues at step 54 by reviewing the unranked atoms represented in the key.
- the system next verifies that a maximum number of atoms has not been reached (the length of the query key does not exceed a predetermined maximum length), and the first unranked atom (C is chosen at step 56.
- step 43 With the Carbon (Cj) atom being set as a current atom. Again, all unused neighbors are examined at step 44, and ordered at step 45. Because the system has still not encountered an open site, the code for this bond (single bond to a Carbon) is added to the key at step 49, with the end of atom marker added to the key at step 51. The query key now reads "Br c . c .”, and C ⁇ is marked as "ranked”.
- the process next repeats itself with C 2 as the first unranked atom in the key at step 56. Accordingly, C 2 is marked as the current atom at step 43, and at step 44 it is determined that there are still "unused” neighbors. The unused neighbors are attempted to be ordered at step 45.
- the bonds of the neighbors consist of a double bond to an Oxygen (0) denoted by "e”, and a wildcard (*) .
- the ordering is not terminated by the open site at step 46, because open sites only terminate this process at step 46 if the open site does not exist on the current atom.
- the "yes" branch is taken at step 481 and at step 50, codes for the neighbors are added to the key with wildcard symbols around them.
- an end-of-atom marker is added to the key at step 51. Accordingly, the current string reads "Br c . c . % e %"; and the C 2 atom is marked as "ranked.”
- step 53 because an open site was found at the current atom, the system advances to step 57.
- This string is a query key, so a wildcard is added to the end of the key at step 58, and the process is stopped at step 59. Accordingly, the final string reads "Br c . c . % e % . %". The process is then repeated with all other atoms as starting atoms.
- the keys generated for query Ql are: 1 ) Br c . c . % e % . %
- the process illustrated in FIG. 11 can also be used to generate query strings.
- the only notable addition would be that when an open site is encountered at step 83 or 88, a wildcard flag is set at steps 84 or 89, respectively.
- the system advances to step 92, and adds wildcard (%) symbols before and after every code to be added to the string at this step. Additionally, a wildcard (%) symbol is added to the end of the string.
- each of the query keys When a match exists between a query and a given structure, each of the query keys will match one or more of the search keys of the structure. Therefore, any one of the query keys may be used to retrieve a matching structure.
- Statistical information is stored in the database allowing the optimal query key to be used as the primary screen.
- connection table is prepared for the query structure in the same way that it is prepared for the newly registered structures in III.a. above (see
- connection tables are then compared atom by atom, bond by bond. If every atom and bond in the connection table for the query is found in the connection table for the structure, the system returns a match.
- the query is a substructure of the retrieval structure.
- Ql (FIG. 5) is a substructure of SI (FIG. 1) .
- each Ql key matches an SI key (Ql keys 1, 2, 3, 4 match SI keys 1, 2, 3, 4 respectively) .
- the chosen key may retrieve a structure for which the query is not a substructure. For example, Ql key 4 would match S2 key 4 even though Ql is not a substructure of S2. However, the ABAM would eliminate this structure.
- the query along with the matching results and other identifying information (such as owner of query and name of query) , are stored in the relational database for later use and viewing.
- the user may simply then advance through and view all of the structures that are a match in the system which are displayed on a screen, such as that shown in FIG. 10. If no structures match, the system will return a message indicating this.
- the user may also list previously conducted searches, edit previously defined searches, update or refresh previously run searches, view structures in any search, and delete previous searches.
- Identity searching involves finding a particular structure within a set of database structures. This operation is performed by users, and is also needed at the time of registration. Typically, this means finding a structure in the database that matches the query exactly.
- An identity search is a special case of the substructure search outlined above, but having no open sites in the query.
- the default definition limits the matching process to element types and bonding. Users can also specify additional structural information such as charge and mass values. This is performed at atom by atom matching time.
- Chemical name searching has been a problem of special note in the field of chemical information systems. Most chemical names are long and complex strings which are not easily searchable by standard substring searching mechanisms. This problem is compounded by the fact that most chemicals are known by many systematic and/or tradenames.
- Chemical name searching can be accomplished by storing and indexing carefully defined name fragments, as well as indexing the complex strings of the complete chemical names. Searching can be performed on a partial or complete chemical name query using standard relational database technology.
- the query is degenerated into its constituent chemical terms.
- the terms are sorted in ascending order by frequency of occurrence found by looking up the number of compounds having a particular term in a stored table.
- This stored table is created by scanning all names of structures upon registration, and storing frequency information in that table. Thus, this table acts as an index to chemical name fragments.
- the search can be performed by intersecting the resulting SELECT statements or using one to drive a correlated subquery.
- Molecular formula can be done by using standard SQL string search methods on all or part of the formula.
- Key searching lookup by identifier is a standard SQL operation.
- a significant advantage of basing a chemical information system in a relational database is the ease with which the structure data can be combined with related data, resulting in a complete, integrated system. This allows information in other systems to be easily imported and exported into the RDBMS using standard RDBMS functionality.
- a relational table is used to store the set of identifiers during each search of the database. This is implemented by creating a table to store general information about the query (current user, date, query structure, options and search statistics) .
- a related table is created to store the identifiers of those structures matching the query.
- Dynamic queries are analogous to relational views. That is, they allow searches of the database to be stored as objects in the database that are always current.
- the following example will illustrate the type of functionality made possible by dynamic queries.
- the system stores the resulting set of compound identifiers at step 62. As the user examines these compounds, the system flags each compound as having been viewed by the user at step 64. Therefore, the system always knows the search results, and the extent to which the user has reviewed them.
- a user interested in a particular class of structures would perform a search once and designate the search as dynamic. Thereafter, the search will be maintained automatically by the system. In fact, the system would notify the user whenever a new steroid was registered in the system at step 66. This is done by having the system perform all dynamic queries on any newly registered molecule as it is registered into the database at step 68 and notifying the user if a match occurs at step 70. The user could then view the previously unseen results at step 72 without having to repeat the query or view previously seen results. While dynamic queries would not have much importance with relatively static databases, they would have many uses in the system serving a research environment. Heavy use of dynamic queries could require allocation of significant amounts of disk space for storing search results. Additionally, the performance of the registration process could be adversely affected by the presence of a large number of dynamic queries.
- the first quota controls the number of dynamic queries that the user can have active at any one time, which will protect performance at the time of the registration process.
- the second quota will control the total number of structure identifiers that each user has stored by dynamic queries to conserve disk space.
- users would be allowed to disable these quota systems, but this may slow the system during the registration process, or may exhaust disk space for the database.
- a "structure class" is defined to be a set of structure identifiers resulting from a substructure search, a chemical name search, a molecular formula search, or by a combination of these searches.
- Structure classes are an application of dynamic queries used to limit the scope of future searches. For example, the system may maintain a structure class for steroids. When a user performs a search, he or she can designate that the result should be restricted to the members of the steroid class. Accordingly, the user could simply query the database for all steroids that have a particular substructure without drawing the entire steroid ring.
- the first benefit is that queries are simplified, i.e., there is no need to draw complex queries, and the second benefit is that the screening phase need only be applied to those compounds already known to be members of the structure class.
- Dynamic queries and structure classes both exhibit a common benefit—the overhead involved in structure searching is encountered only once (when the dynamic query or structure class is defined) and additional overhead is distributed evenly across subsequent updates to the chemical structure database.
Abstract
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EP95929457A EP0777882A4 (en) | 1994-08-10 | 1995-08-10 | Relational database management system for chemical structure storage, searching and retrieval |
AU33202/95A AU3320295A (en) | 1994-08-10 | 1995-08-10 | Relational database management system for chemical struture storage, searching and retrieval |
JP50813396A JP3193383B2 (en) | 1994-08-10 | 1995-08-10 | A relational database management system for storage and retrieval of chemical structures. |
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US08/288,503 | 1994-08-10 | ||
US08/288,503 US5577239A (en) | 1994-08-10 | 1994-08-10 | Chemical structure storage, searching and retrieval system |
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Also Published As
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JPH10507285A (en) | 1998-07-14 |
JP3193383B2 (en) | 2001-07-30 |
EP0777882A2 (en) | 1997-06-11 |
US5577239A (en) | 1996-11-19 |
AU3320295A (en) | 1996-03-14 |
EP0777882A4 (en) | 1997-12-29 |
US6304869B1 (en) | 2001-10-16 |
WO1996006391A3 (en) | 1996-05-09 |
US5950192A (en) | 1999-09-07 |
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