JP2008097320A - Genetic information management system - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide an annotation imparting work environment to sequence information based on various requests during collaborative work between a plurality of users in fields of research, such as molecular biology handling DNA/RNA/amino-acid sequence. <P>SOLUTION: When a user performs search of sequence information, verification whether the user has the access authority for the sequence information data which is a search object based on a user ID is performed. When it is determined that the user has the access authority, the sequence information data which is the search object is transmitted to a terminal device which the user uses and the sequence information data concerned is displayed on a display etc. of a terminal device. Meanwhile when it is determined that the user does not have the access authority, message data to that effect is transmitted to the terminal device which the user concerned uses. <P>COPYRIGHT: (C)2008,JPO&INPIT

Description

  The present invention relates to a mechanism for managing and displaying DNA / RNA / amino acid sequence / annotation data on a computer terminal.

The types of DNA and RNA amino acid sequence information include not only base and amino acid sequence information, but also gene information, marker information, papers on the sequence, and researcher information.
Gene sequence information includes GenBank (The National Center for Biotechnology Information), DDBJ (DNA Data Bank of Japan), and EMBL (European Molecular Biology).
Sequence information provided in public databases such as Laboratory), researchers added their own analysis results to the sequence information in the public database, researchers themselves made sequence determinations, comments on the sequences, etc. Are annotated (annotated with gene sequences).

  In recent research facilities, computer systems capable of mutual communication via a LAN (Local Area Network) have been introduced. Data sharing among collaborators is often shared on a network such as the LAN. Further, a method of restricting access to data by an access right set in an OS (Operating System) of a computer terminal is common.

  In this way, when working while sharing sequence information among collaborators, there are many cases where data is shared using computer terminals connected to a network such as the Internet or an intranet. There are various forms of joint research work. Therefore, there is a need for a work environment system for annotating sequence information that can flexibly cope with these various work modes.

  For example, a user such as a researcher who uses a gene information management system can edit a data file related to sequence information stored in a shared folder in a computer terminal on a network. The information that the editing work was performed at the time is not recorded. In addition, if you plan to publish gene information data later, but you do not want to publish the gene information data until then, detailed access authority to the data file required when collaborating between users is Not provided. Furthermore, among the plurality of researchers, the same sequence information may be noticed unexpectedly, and there is a possibility that research objects overlap.

  It is an object of the present invention to clarify which annotations are assigned to which sequence information and analysis work is performed, so as to meet various requirements at the time of collaborative work among a plurality of users. It is to provide an annotating work environment for the sequence information.

  In order to achieve the above object, the gene information management system of the present invention is a gene using a computer system in which a database server having a storage means and a terminal device used by a user are connected to be able to communicate with a network. In the information management system, the storage means stores a sequence information database in which sequence information data related to gene sequences is registered, and whether or not access authority is set for each sequence information data, When the sequence information data is retrieved from the terminal device by a user, the database server determines whether to disclose the sequence information data based on the access authority.

  According to the gene information management system of the present invention, in the field of research such as molecular biology dealing with DNA / RNA / amino acid sequences, annotating sequence information in accordance with various demands when collaborating among multiple users. A working environment can be provided.

Hereinafter, an embodiment of a gene information management system according to the present invention will be described.
As shown in FIG. 1, the gene information management system in the present embodiment includes a database server 11 and a plurality of terminal devices 12. The database server 11 and the terminal device 12 are connected to the Internet 13 as a network by ADSL using a public telephone line, an optical fiber, or the like. A client server system is constructed with the database server 11 as a server computer and the terminal device 12 connected to the Internet 13 as a client computer.

  The database server 11 includes a CPU (Central Processing Unit), a RAM (Random Access Memory), a ROM (Read Only Memory), and the like that are connected to each other via a bus. Further, an interface (not shown) for inputting / outputting data to / from the terminal device 12 or the like is also provided. Furthermore, a hard disk 14 which is an internal storage device as storage means is connected.

  The hard disk 14 stores a database related to gene sequence information constructed by the user, an OS (Operating System), and the like. The OS is, for example, a network OS such as NetWare (registered trademark). The OS controls the entire database server 11 as well as the Internet 13.

Next, sequence information data registered in a sequence information database in which information related to gene sequences is stored will be described.
As shown in FIG. 2, the table elements of the array information database include Unique ID 15, access authority 16, data creator 17, array type 18, array definition 19, array 20, and annotation information 21. Each of these table elements constitutes one array information data, and the array information database is composed of a plurality of registered array information data.

In the column of UniqueID15, consecutive numbers in the order of sequence information data added to the sequence information database by the user are described.
In the column of access authority 16, information on whether the sequence information data is to be disclosed, not disclosed, or is being prepared for disclosure is described. For example, 1 is described by the user in the column of the access authority 16 when the sequence information data is disclosed, 2 is displayed when the sequence information data is not disclosed, and 3 is prepared when the sequence information data is prepared. Is done.

When 1 is described in the column of the access authority 16 (public), the sequence information data can be freely browsed by all users who browse the sequence information database. On the other hand, when 2 is described in the column of the access authority 16 (not disclosed), the sequence information data cannot be freely viewed by a user other than the data creator. When 3 is described in the access authority 16 column (under preparation), only the data creator, the array type, and the array definition of the array information data can be freely selected by users other than the data creator. You can browse.

  In the column of data creator 17, the name of the user who created the sequence information data is described. In the column of the sequence type 18, in the case of nucleic acids, mRNA (messenger RNA), cDNA (complementary DNA), cRNA (complementary RNA), etc., in the case of amino acid sequences, the amino acid sequence and the type of sequence information are described. Is done. In the column of the sequence definition 19, information on the types of genes such as the Brca1 gene and the Brca2 gene is described. In the column of the sequence 20, a specific sequence of the gene is described.

In the annotation information 21 column, annotations of gene sequences are described by the creator or the like. Since a plurality of pieces of information such as information on gene functions and related images are described in the annotation information 21 column, an annotation table 22 as shown in FIG. 3 is created for each piece of sequence information data. .
Table elements of the annotation table 22 include ID 23, annotation content 24, annotation grantor 25, creation date 26, and update date 27.

  In the column of ID23, a number consisting of different characters and numbers for each annotation is described. In the annotation content 24 column, information regarding specific annotation content is described. The name of the person who gave the annotation is described in the field of the person giving the annotation 25. The date and time when the annotation information was first created is described in the creation date and time 26 column. In the update date / time field 27, the latest date / time updated after creation is described.

Next, a method for editing the sequence information database and a method for accessing the sequence information database will be described.
The following processing is executed under the control of a control means such as a CPU based on a program stored in the ROM or the like of the database server 11.
As shown in FIG. 4, first, a user ID and a password for logging in to the array information database are input by the user from the terminal device 12 (step S1). If the login is successful, the user can access the sequence information database.

  Next, the user is asked to confirm whether or not to edit the sequence information database (step S2). When the user wishes to edit the sequence information database, a sequence information data creation / update screen is transmitted from the database server 11 to the terminal device 12. The user creates / updates the sequence information data based on the contents displayed on the screen (step S3).

When creating / updating array information data, the user is prompted by the database server 11 to set access authority 16 which is a table element of the array information database. The user sets public, non-disclosure, and public preparation access authority to other users for the sequence information data to be created / updated. Here, when the sequence information data is updated and the access authority so far is changed to another access authority, the database server 11 notifies other users by e-mail or the like. Is done.
When the creation / updating of the sequence information data by the user is completed, the sequence information database is updated by the database server 11 (step S4).

  On the other hand, in step S2, if the user does not wish to edit the sequence information database, the database server 11 causes the terminal device 12 to confirm whether or not the sequence information data is being searched. Is transmitted (step S5). When the user wishes to retrieve the sequence information and executes the sequence information search, the database server 11 confirms whether or not the user has access authority for the sequence information data to be retrieved based on the user ID. Is executed (step S6).

  When it is determined that the user has access authority, the database server 11 transmits the sequence information data to be searched to the terminal device 12 used by the user (step S7), and the sequence information data Is displayed on the display or the like of the terminal device 12 (step S8). When it is determined that the user has no access authority, the database server 11 transmits message data to that effect to the terminal device 12 used by the user, and the message data is displayed on the display of the terminal device 12 or the like. Is displayed.

The embodiment described above may be modified as follows.
The database server 11 and the terminal device 12 may be connected via a LAN.
The configuration of the sequence information database is not limited to the form shown in FIG. 2, and necessary information items may be appropriately added or unnecessary information items may be deleted.

The block diagram of a gene information management system. A surface showing an example of data. Annotation table. The flowchart which shows the flow of creation / update of an arrangement | sequence information database.

Explanation of symbols

11 ... Database server,
12 ... a terminal device,
13 ... Internet as a network,
14: Hard disk as storage means.

Claims (1)

A gene information management system using a computer system in which a database server provided with a storage means and a terminal device used by a user are connected to be able to communicate with a network,
The storage means stores a sequence information database in which sequence information data relating to gene sequences is registered,
Whether or not access authority is set for each array information data, and when the array information data is retrieved from the terminal device by a user, the database server publishes the array information data based on the access authority A gene information management system characterized by determining whether or not to perform.

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