JP2006085437A - Non-redundant biopolymer database production method and server for retrieval service - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To reduce a database retrieval work time by accessing a searching Web page for each database when desiring to transversely search a biopolymer database and by dispensing with work for repeating retrieval work or work for removing duplication from an acquired retrieval result. <P>SOLUTION: This non-redundant biopolymer database 104 is produced by using correspondence relation of data among the biopolymer databases A, B, C, and the search is performed to the produced non-redundant biopolymer database. <P>COPYRIGHT: (C)2006,JPO&NCIPI

Description

  The present invention relates to a method for efficiently searching data in biopolymer data files such as base sequences and protein sequences.

Numerous biopolymer databases are published on the Internet (eg Baxebanis, AD: Nucl. Acids Res., 28: 1-10, 2000, “Genetics Databases” (Bishop MJ ed.), Academic Press, Cambridge, 1999). Researchers studying molecular biology search these databases to obtain data related to their research. Since a lot of biopolymer data is duplicated between databases, the biopolymer database publishes the correspondence relationship between duplicate data IDs.
Baxebanis, AD: Nucl.Acids Res., 28: 1-10,2000 "Genetics Databases" (Bishop MJ ed.), Academic Press, Cambridge, 1999

  If you want to search across multiple databases, you need to access the search web page for each database, repeat the search for each database, and there are duplicate data between the databases. Since it is necessary to remove duplicates from the search results, it is very troublesome.

  For example, as shown in FIG. 11, when searching across the database 801 and the database 802, the database 801 and the database 802 are searched, and the corresponding relationship 805 is referred to from the obtained search results 803 and 804. Thus, the duplicate data 806 is deleted, and a search result 807 having no duplicate is acquired.

  An object of the present invention is to provide a method for efficiently searching a biopolymer database.

  In the present invention, by utilizing the correspondence relationship between the data in the biopolymer database, duplication of data is removed, a non-redundant biopolymer database is created, and the created non-redundant biopolymer database is used. To search. By this method, it is possible to perform a search equivalent to a search performed on a plurality of biopolymer databases at the same time and obtain a non-redundant search result.

  According to the present invention, when it is desired to search the biopolymer database cross-sectionally, there is no need to access the search Web page of each database, repeat the search operation, and remove the duplication from the acquired search results. Therefore, the database search work time can be shortened.

Hereinafter, an embodiment for carrying out the present invention will be specifically described with reference to the drawings.
FIG. 1 is a schematic diagram showing an example of a search service according to the present invention. The search service center 111 includes a search service server 105 having a storage device 101. The search service server 105 includes a DB data acquisition unit 121, a correspondence relationship acquisition unit 122, a correspondence relationship table creation unit 123, a non-redundant DB creation unit 124, and a search processing unit 125.

  The search service center 111 downloads data of a plurality of external databases A, B, and C having data overlapping between the databases onto the storage device 101 of the search service server 105 in the search service center 111. This process is performed by the DB data acquisition unit 121 of the search service server 105. Also, the correspondence relationship acquisition unit 122 of the search service server 105 acquires information about the correspondence relationship between the data in the database, and passes it to the correspondence table creation unit 123. The correspondence table creation unit 123 creates a correspondence table 130 that represents the correspondence of data that overlaps between databases and stores it in the storage device 101. Thereafter, by using the correspondence table 130 from the downloaded data of the databases A, B, and C, the duplication of data is removed 103 and the non-redundant biopolymer database 104 is constructed. This processing is performed by the non-redundant DB creation unit 124.

  The search service center 111 uses the non-redundant biopolymer database 104 to provide a network 107 to a user (client) who operates a device including the display device 108, the arithmetic device 109, the keyboard 106, and the mouse 110. To provide search services. This search service is performed by the search processing unit 125 of the search service server 105.

  FIG. 2 is a diagram schematically showing data registered in the databases A, B, and C. In the example of FIG. 2, data A1, A4, A5, A7 are registered in the database A, data B2, B4, B6, B7 are registered in the database B, and data C3, C5, C6, C7 are registered in the database C. Is registered.

  A non-redundant biopolymer database creation method according to the present invention will be described with reference to the flowchart of FIG. 3 and the process diagram of FIG.

  First, the DB data acquisition unit 121 of the search service server 105 in the search service center 111 stores a plurality of external biopolymer databases, in this example, the data of the database A, the database B, and the database C on the storage device 101. (S11). Next, the search service server 105 accesses the database A, the database B, and the database C, and the correspondence relationship acquisition unit 122 acquires information about the correspondence relationship between the databases. The biopolymer database has a part describing the correspondence with the data of other biopolymer databases, and the correspondence acquisition unit 122 cuts out the data of the part and passes it to the correspondence table creation unit 123. The correspondence table creation unit 123 organizes the received data, creates the correspondence table 130, and stores it in the storage device 101 (S12).

  FIG. 4 is a schematic diagram of the correspondence table 130 showing the correspondence of data between databases created in this way. In this example, as data correspondence between databases A-B, A4 and B4, A7 and B7, data correspondence between databases B-C, B6 and C6, B7 and C7, and database C-A As data correspondence, it is registered that C5 and A5 and C7 and A7 are equivalent data.

  FIG. 5 is a diagram showing a specific example of data correspondence between biopolymer databases. FIG. 5 shows the correspondence between the UniGene database and the GenBank database published by NCBI (National Center for Biotechnology Information). The data correspondence between the biopolymer databases is disclosed in such a format. The data is tab-delimited and one line represents one record. The first column 301 represents the UniGene ID, and the fourth column 302 represents the GenBank ID corresponding to the UniGene data. For example, data whose ID is UniGene's Hs.103504 (303) corresponds to data whose ID is AF061055 (304) of GenBank. By extracting these data, it is possible to obtain the data correspondence between the databases.

  The subsequent processing is performed by the non-redundant DB creation unit 124 of the search service server 105. The non-redundant DB creation unit 124 first assigns priorities to the database A, the database B, and the database C based on the input of prioritization instructions from the operator. This priority may be arbitrarily assigned. Here, as shown in FIG. 6, it is assumed that a higher score is assigned to the priority in the order of database A, database B, and database C (step 13). Next, in order from the database with the highest priority (step 14), data having no data correspondence with the database with a higher priority than itself is acquired (step 15). By repeating the processing from step 14 to step 15, the non-redundant DB 104 is created.

  The processing of steps 14 and 15 will be described with reference to FIG. First, as shown in FIG. 7A, data is acquired from the database A having the highest priority score. Since no database has a higher priority than the database A, all data A1, A4, A5 and A7 are acquired from the database A. Next, as shown in FIG. 7B, the process moves to a process of acquiring data from the database B having the second priority score. Since the database B has a lower priority than the database A, the data B 2 and B 6 having no correspondence with the database A are acquired from the database B. For the confirmation of the duplicate data, the correspondence table 130 representing the data correspondence between the databases shown in FIG. 4 is used. Here, the dotted line in FIG. 7 indicates that the data is duplicated. Finally, as shown in FIG. 7C, a process of acquiring data from the database C having the lowest priority is performed. Since the database C has a lower priority than the database A and the database B, the data C3 that does not have a corresponding relationship with the database A and the database B is acquired from the database C. Also at this time, the correspondence table shown in FIG. 4 is used for confirmation of duplicate data. In this way, a non-redundant database 104 having data A1, B2, C3, A4, A5, B6, and A7 is created.

  FIG. 8 is a conceptual diagram of a search for the search service server 105 in the search service center 111. As shown in FIG. 8, the user 906 can search through the network 904 for the non-redundant database 903 created by excluding duplicates from the duplicated databases 901 and 902, so that a search result 905 without duplicates can be obtained. it can. A graphical user interface as shown in FIG. 9 is used to input a search keyword by the user. When the user inputs a keyword 403 to be searched in the text box 401 and presses the search start button 402, the search is started, and data related to the input keyword is displayed as a list as shown in FIG. In the list, a database name 501 from which the data is extracted, a data ID 502, and a data summary 503 are displayed. By clicking on the data ID 502, the details of the data can be displayed.

Schematic which shows the example of the search service by this invention. The figure which shows the example of data of a biopolymer database. The flowchart which shows the flow of the method of producing a nonredundant biopolymer database. The schematic diagram of a correspondence table. The figure which shows the specific example of the correspondence of the data between biopolymer databases. The figure which shows the example of a setting of a priority. The process schematic diagram which shows the creation example of a nonredundant biopolymer database. The conceptual diagram of the search with respect to the server for search services. The figure which shows the example of a keyword input graphical user interface. The figure which shows the example of a search result list display graphical user interface. Explanatory drawing of the conventional search method.

Explanation of symbols

DESCRIPTION OF SYMBOLS 101 ... Memory | storage device, 103 ... Duplication removal work, 104 ... Non-redundant biopolymer database, 105 ... Server for search service, 107 ... Network, 111 ... Search service center, 121 ... DB data acquisition part, 122 ... Correspondence Acquisition unit, 123 ... correspondence table creation unit, 124 ... non-redundant DB creation unit, 125 ... search processing unit, 130 ... correspondence table, 301 ... UniGene ID, 302 ... GenBank ID, 303 ... duplicate UniGene ID, 304 ... Duplicate GenBank ID, 401 ... text box, 402 ... search start button, 403 ... keyword, 501 ... database name from which data was extracted, 502 ... data ID, 503 ... data summary, 903 ... non-redundant biopolymer database , 904 ... Network, 905 ... Search results without duplication

Claims (2)

Storing data in a plurality of biopolymer databases having data overlapping between the databases for each database and storing them in a storage device;
Obtaining information on the correspondence between the databases from the plurality of biopolymer databases, and storing it in a storage device as a correspondence table;
Prioritizing the plurality of biopolymer databases;
For the plurality of biopolymer databases stored in the storage device, in order from the database with the highest priority, data whose correspondence with the data of the database with a higher priority than itself is not registered in the correspondence table is acquired. A method for creating a non-redundant biopolymer database, comprising: repeating the process. DB data acquisition unit that acquires data from a plurality of external biopolymer databases, distinguishes each database and stores it in a storage device,
A correspondence acquisition unit that acquires information on data correspondence between the plurality of biopolymer databases; and
A correspondence table creating unit that organizes the information obtained by the correspondence obtaining unit and creates a correspondence table that represents the correspondence of overlapping data between databases;
A non-redundant DB creating unit that creates a non-redundant biopolymer database by removing duplication of data from a plurality of biopolymer database data stored in the storage device with reference to the correspondence table. Characteristic search service server.

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