Last updated: 26th September, 2023
- ‘Organization’ means the Research Organization of Information and Systems.
- ‘Center’ means the Bioinformation and DDBJ Center of the National Institute of Genetics, the Research Organization of Information and Systems.
- ‘unrestricted-access database’ means a database by which center provides data to user without imposing any restriction on its use or distribution.
- ‘controlled-access database’ means a database by which center provides data to user imposing restriction on its use.
- ‘submitted data’ means data that submitter provides to Center.
- ‘provided data’ means data that center provides to user that includes submitted data, data processed from submitted data and data independently collected by Center.
- ‘unrestricted-access data’ means data that Center provides to user from the unrestricted-access database without imposing any restriction on its use.
- ‘controlled-access data’ means data that Center provides to user from the controlled-access database imposing restriction on its use.
- Except when caused by intent or gross negligence of Center, Center shall not be liable for any damage arising from the use of our services, and user shall indemnify and hold harmless Center from any damage. Furthermore, in the event any dispute arises between a user and any other user or between a user and a third party in relation to our services, Center shall assume no responsibility, and user shall indemnify and hold center harmless from such dispute.
- When using our services, it is requested that user displays appropriate credit.
- You shall use each contents of our websites or any information included at your own responsibility.
- Each contents provided on our websites is created based on various information and data that is regarded reliable at the time of the creation. However, we make no warranty in regard to credibility, accuracy, availability or completeness of the contents.
- We will make all reasonable effort to maintain continuity of our online services, however, we may temporarily suspend or discontinue the operation of our services in the case of maintenance, update, or in the event of force majeure, or when necessary. We attempt to notify user in advance of such temporary suspension or discontinuation, however, we accept no responsibility for the consequences of these discontinuities in the service.
- Upon prior notice of a reasonable period of time, we may terminate all or a part of our services after such period of time.
- If the operation of our services is transferred to a third party due to change in the status of the online service operations or other situations, we shall announce the transfer of service on our website. If you do not agree to such transfer, you may stop to using our services. If you use our services after the notification, you are deemed to have agreed to the transfer of our services and any succession of involved rights and obligations.
Use of Web Browsers
- INSDC data may be freely used, redistributed and modified in accordance with the INSDC Policy.
- Japanese Genotype-phenotype Archive (JGA) data shall be used in compliance with the NBDC Human Data Sharing Guidelines.
- AMED Genome group sharing Database (AGD) data shall be used in compliance with the NBDC Human Data Group Sharing Guidelines.
- We endeavor to improve the quality of the data that we provide, however, we shall make no warranty of availability, accuracy, adequacy, credibility or completeness of the data.
- You shall use data that we provide at your own responsibility and shall indemnify and hold harmless Center from any damage (including damage to third parties) arising in connection with the use.
- Data that we provide may subject to rights attributable to a third party, including patent rights, copyrights, other intellectual property rights, biodiversity-related access and benefit-sharing rights. You shall use such data at your own responsibility, and in the case you infringes third party rights, you shall resolve such dispute at your own responsibility and shall indemnify and hold Center harmless.
Data Submission to Databases
Please refer to Data Submission Guideline.
Usage of NIG Supercomputer System
The following acts are prohibited when using our services or any information:
- Any act that infringes the rights of Center or any third party (including but not limited to intellectual property rights or privacy rights), any act that damages the reputation, credibility or property of Center or any third party, or any act that may encourage such acts;
- Any act that offends public order and morals;
- Any act that violates or may violate any laws or regulations;
- Any act that are a risk to the operation of our services or websites, including but not limited to unauthorized access, impersonation, false declarations or notification, mass mailing, sending of inappropriate or offensive content; or
- Any act of storing or distributing any virus-infected files, contaminated files or other files or links to any website that will damage the function of computers of any third party.
If we determine that a user has conducted any of the above acts, we may, without giving any advance notice to such user, suspend the user’s use of our websites or services and suspend user’s account, delete any data that such user is storing in our services, and notify to relevant authorities or disclose the personal information of the user, and we shall not be responsible for any damage that arises to user due to these measures taken by us.
1. Collection of Information
We may collect the following personal information:
Information of Submitter
In regard to data submitted to the databases operated by us or in collaboration with us, we accept data submitted by submitter in accordance with the Data Submission Guideline.
Information of Inquirer
We collect personal information of any person making inquiries (information of inquirer), when the inquirer sends forms or emails to us, including information such as his/her name, email address, name of organization that he/she belongs to.
Information of Applicants
We collect applicant information when the applicant sends information (such as his/her name, email address, name of organization that he/she belongs to or job position) in the application form or email of seminars or events hosted by us.
Information of User
We collect user information (such as his/her name, email address, name of organization that he/she belongs to) when the user applies for our online service user account.
Information of Supercomputer User
We collect user information (such as his/her name, email address, name of organization that he/she belongs to, address, and telephone number) when the user applies for the user account of the supercomputer operated by us.
Access Information to Website
We automatically collect the following information relating to access when a user accesses the website provided by us (hereinafter referred to as ‘our websites’):
- IP address of the access source;
- Domain of the access source;
- Date and time of access;
- Pages and files of the access destination;
- Words used in search engines for the search of our websites;
- Cookie information; and
- Types and versions of the web browser and operating system used by user.
Furthermore, in our websites, we may use ‘Google Analytics’ that is a web access analytics tool provided by Google. In such case, Google may collect access information. In regard to the data collection and process by Google Analytics, please refer to ‘HOW GOOGLE USES INFORMATION FROM SITES OR APPS THAT USE OUR SERVICES’.
2. Usage of Information
We will use collected personal information for the following purposes. If collected information is personal information, such personal information will not be used for any purpose exceeding the scope of the following without the principal’s consent, unless there exists any grounds to permit such use by the Act on the Protection of Personal Information or other laws or regulations.
Information of Submitter
- To create an account;
- To notify account information;
- To indicate the owner of the submitted data;
- To inquire about or to contact user in regard to submitted data;
- To confirm the organization that the submitter belongs to;
- To acquire statistics of the submitted data;
- To notify any important matters concerning submission; and
- To notify any important matters.
Information of Applicants
- To contact applicants about seminars and events;
- To evaluate the details of seminars and events; or
- To conduct surveys regarding seminars and events.
Information of Inquiries
- To handle inquiries.
Information of User
- To make inquiries and to contact user about our services;
- To notify account information;
- To give invitations for study groups, lectures, seminars and other events;
- To handle inquiries from user; and
- To notify important matters.
Information of Supercomputer User
- To issue a user account for supercomputer;
- To notify user account information for supercomputer;
- To make inquiries or to contact supercomputer user about supercomputer;
- To publicize the purpose of use of supercomputer; and
- To notify important matters.
Access Information to Website
- To identify the number of user or number of accesses to our websites or services;
- To improve the contents, structure, system performance or other issues regarding our websites or services;
- To report or publicize the aggregate information regarding the number of user and number of accesses to our websites or services. Such aggregate information may be used to report to any collaborating organizations of Center. Furthermore, information that may identify an individual will not be included in such aggregate information.
Please refer to Google’s web page set forth in 1 above, in regard to use of access information by Google.
3. Provision of Personal Information to a Third Party
We will not provide personal information to any third party, except for the following cases:
- In the case consent of the principal for such provision is obtained;
- Center is permitted to provide personal information in accordance with laws or regulations; or
- Personal information is disclosed or provided in a condition where it is impossible to identify a specific user (such as by statistical data).
We may jointly use submitted data, submitter’s information of controlled-access database, and access statistic of websites with NBDC.
You can disable the cookies through your browser settings. Please refer to the following page for our recommended browsers: Chrome and Firefox. For other browsers, please refer to the help page of each browser.
However, by disabling or deleting cookies, services of our websites and other websites may not function correctly.
Furthermore, in regard to Google Analytics, you can disable usage of data by installing the following add-on in your browser.
Google Analytics Opt-Out Add-On https://tools.google.com/dlpage/gaoptout
5. Visiting an Official Center Page on Third-Party Websites
We use services (such as social media) operated by third parties as tools to better interact with the public. The privacy and security policies of the third-party sites will apply to your activity on those sites.
Please see ‘Bioinformation and DDBJ Center’s Official Sites in Social Media’ in regard to third-party sites used by Center.
The privacy policies for these services are as follows:
- Twitter: https://twitter.com/ja/privacy
- Google and Youtube: https://policies.google.com/privacy?hl=ja
- Github: https://help.github.com/articles/github-privacy-statement/
- Facebook: https://www.facebook.com/msqrd/privacy
6. Security Management of Personal Information
We will take all reasonable organizational and technical security measures to prevent unauthorized use, loss, modification or destruction of personal information provided to us, in accordance with the information security standards established by Center. We will authorize access to personal information only to our employees, agents, contractors and other third parties that have a need to access such information. Such persons that are granted access to personal information will assume confidentiality obligations under an employment contract or other contracts.
7. Preservation Period of Personal Information
We will comply with all applicable laws and regulations, and preserve personal information only as long as necessary to provide our services.
8. Rights of the Individual who is the Principal of Personal Information
If we are requested by the individual who is the principal of information to disclose, modify, suspend use, delete or do other similar acts to his/her personal information in accordance with provisions of laws or regulations, we will conduct such acts in accordance with procedures stipulated by the Research Organization of Information and Systems. Please refer to ‘Information Disclosure and Management’ established by the Research Organization of Information and Systems for details.
- The individual has the right to request information in regard to its personal information possessed by us. In accordance with the request from the principal of information, we will deliver to principal, a copy of his/her personal information that we have and any information relating to the preservation period.
- You has the right to request corrections or suspension of use of your personal information possessed by us, however, such rights are available only if there are reasons to request corrections or if such request is granted in accordance with applicable laws or regulations (such as cases where there is violation of laws or regulations in regard to personal information possessed by us).
- No expense will arise from the exercise of the above rights. We will promptly provide information relating to the status of measures taken to address your claims. However, if your claim apparently lacks evidence or is in excess, we may request you reasonable expenses or refuse to respond to your claims.
9. Contact Information
For information regarding handling of personal information, please contact the following:
Address: 1111 Yata, Mishima, Shizuoka 411-8540, Japan Research Organization of Information and Systems National Institute of Genetics Bioinformation and DDBJ Center
Contact Method: By Contact Form
Data Submission Guideline
This is a guideline for submitting data to the databases operated by the Bioinformation and DDBJ Center (hereinafter referred to as ‘Center’), and sets forth the rights of submitters and items to be observed.
Center may correct obvious errors and inconsistencies, convert format or add relevant information to data provided by submitters, for maintaining quality and improving usability of the data. Center must obtain submitter’s permission in cases where it will process data beyond such purpose.
Rights and Duties of Submitter
Excluding the portion modified by Center, the contents and quality of the data are responsibility of the submitters. Submitter can update his/her data. Submitter should answer inquiries from users and person in charge of the database regarding submitted data, and therefore should correctly maintain its registered contact information. If there are any matters that need to be determined by submitters, we will attempt to contact the submitter wherever possible, however, if we decide that it is necessary, we will consult the superior of the organization where submitter belongs to and follow the judgement of the superior. Data must not be submitted without obtaining the permission of the Principal Investigator. When submitting data derived from a human subject, you must comply with the ‘Submission of Research Data from Human Subjects’.
Scientific data provided by submitter to Center’s database will be disclosed to the public in accordance with the Data Release Policy as set forth below, according to the categories of unrestricted-access data or controlled-access data. Center will not assume any responsibility for any damage arising from such disclosure, relating to copyrights, rights to obtain patents or all rights to other intellectual property of third parties (including submitter), and in the case Center incurs any damage, submitter shall compensate such damage of Center.
Data Release Policy
Center discloses data to the public in accordance with the following principles. In cases 2 or 3, it is deemed that submitter’s approval is obtained in advance and therefore data will be released without making any further confirmation to submitter.
- When the submitter requests us to release the data.
- When the accession number corresponding to data is published and is confirmed. ‘Publish’ means to disclose the accession number to an unspecified number of people by announcement through various media such as academic papers (including ‘in press’ articles made public by on-line preview and preprint server), academic meetings, Internet or press reports. It also includes accession numbers cited in published data, such as accession numbers cited by DDBJ/DRA/GEA/BioSample records. It will not include cases when a third party (excluding submitter) publishes another person’s accession number through negligence.
- When the specified hold-date set by submitter arrives.
Fair Use of Submission System
Use of File Upload Area
Submitter’s private area for uploading files for submission to the database is a temporary place for files until such data submission is completed. Because the database itself provides an almost permanent data storage function, we reserve the right to delete any file stored in the private area longer than a half year, while we attempt to inform submitter before deleting the files. We accept no responsibility for the loss of data in the private area regardless of whether such loss occurs through our intention or negligence.
Creation of Submission Account
Usage of Submission Account
- User must comply with the following in order to use the submission account.
- Promptly update user information if user information is altered due to change or personnel relocation of the account user.
- Do not share your account with any other person.
- Properly manage and store the account ID, password and private key under the responsibility of user.
- Promptly notify us when the account is no longer necessary.
- Any act in our services using the account will be deemed to be the act of user that was issued this account.
- Center may implement temporary suspension or permanent suspension of an account if there is unauthorized use of such account.
Provision of User Information to a Third Party
User shall agree that, in the following cases, we will provide necessary user’s information to a third party or parties and take necessary measures.
- If we decide that such provision to a third party is necessary in the course of our operation, while it is difficult or inappropriate to obtain user’s agreement.
- If we decide that user is conducting any of the Prohibited Use stipulated by Center.
Submission of Research Data from Human Subjects
Before Submitting Data
For submitting data obtained from researches using samples derived from human subjects (hereinafter referred to as ‘human data’) to the databases of Bioinformation and DDBJ Center (hereinafter referred to as ‘Center’), it is submitter’s responsibility to ensure that the dignity and right of human subject are protected in accordance with all applicable laws and regulations, guiding principles, guidelines, and policies of submitter’s institution. In principle, make sure to remove any direct personal identifiers of human subjects from your metadata.
When you are submitting human data obtained from researches other than researches falling outside the scope of laws, regulations and guidelines (for example, researches using widely utilized and generally available samples of academically established value (*1)), make sure the followings.
- The research plan describing experimental methods, research targets (for example, diseases and samples), and ways of data publication and sharing, has been approved by the institutional review board and by the head of institution who oversees the research.
- The research plan and the informed consent documents describe that human data are deposited to databases, in addition, when the data are to be deposited as controlled-access data, “the data are to be shared among domestic and international researchers including those belong to private companies, who meet user requirements”, and when the data are to be deposited as unrestricted-access data, “the data are to be published on the Internet in a form that anyone can view and access”.
- Before submitting data, you need to present an application (for data to be submitted) to the Data Access Committee of the Department of NBDC Program (NBDC) of Japan Science and Technology Agency and obtain the Committee’s approval upon review thereby.
*1 HeLa whole genome sequence data should be submitted to the NCBI Database of Genotypes and Phenotypes (dbGaP).
Controlled-Access and Database
Before submitting human data, please consider whether controlled-access is required or not when releasing data, on the basis of explanation and consent terms of informed consents obtained from human subjects.
Submit your data to the controlled-access database ‘Japanese Genotype-phenotype Archive (JGA)’.
Submit your data to unrestricted-access databases DDBJ Sequence Read Archive (DRA), Genomic Expression Archive (GEA), MetaboBank or DDBJ. In principle, you can not submit data corresponding to personal identification code (*2) to unrestricted-access databases. When you want to submit data corresponding to personal identification code to unrestricted-access databases, please contact the NBDC. In principle, it is necessary to obtain consents for unrestricted public disclosure of genome data corresponding to personal identification code through databases.
*2 Please refer to the NBDC FAQs, in regard to personal identification code. Personal identification code is defined in the ‘Guidelines on the Act on the Protection of Personal Information (Volume on General Rules) (Japanese language only)’ of the Personal Information Protection Commission.
- Personal Information Protection Commission, Act on the Protection of Personal Information, Laws and regulations, guidelines etc.
- Ethical Guidelines for Medical and Health Research Involving Human Subjects
- NBDC Human Data Sharing Guidelines
- NBDC Security Guidelines for Human Data
- NBDC Human Database (FAQ)
- Notification for research participants regarding our database activities for human data
Credits for Services and Data Use
When you are using contents, services and data provided in the website of Bioinformation and DDBJ Center (hereinafter referred to as ‘Center’), you must give appropriate credit to Center and the provider of the contents, services and data.
When using any content on our website, you must describe the credit (type of license and copyright owner) for each content as recommended in Creative Commons Attribution 4.0 International License (CC-BY 4.0).
Citation of Bioinformation and DDBJ Center
When citing the Bioinformation and DDBJ Center itself, please cite the latest article for Center’s activities in general.
When you use a specific service provided by us, please cite the original article for each service. If the original article is not available, please cite the URL of each service. If such use is not equivalent to citing an article, please state one of the following example sentences with necessary changes as an acknowledgement.
Japanese: 本研究は、生命情報・DDBJセンターの [データベース、検索・解析サービス名] を利用しました。
English: This research was performed using [database, search or analytical service name] of Bioinformation and DDBJ Center.
If you announce your results obtained from using our supercomputer system, please state one of the following example sentences with necessary changes as an acknowledgement.
English: Computations were partially performed on the NIG Supercomputer at ROIS National Institute of Genetics.
When citing individual data, please cite the accession number of the data and (if necessary) its version. When discussing the individual data in details, it is appropriate to cite the article reporting the data.
Usage of Third Party Data Provided by Bioinformation and DDBJ Center
- NCBI Refseq ddbj.nig.ac.jp/public/mirror_database/refseq/release/README
- PDB ftp.wwpdb.org/pub/pdb/advisory.txt
- UniProt ddbj.nig.ac.jp/public/mirror_database/uniprot/README
- ArrayExpress www.ebi.ac.uk/arrayexpress/about.html
- HINV ddbj.nig.ac.jp/public/mirror_database/hinv/README.txt
- International Genome Sample Resource (IGSR) www.internationalgenome.org/IGSR_disclaimer
Bioinformation and DDBJ Center Official Sites on Social Media
Bioinformation and DDBJ Center’s official sites (accounts) on social media are as follows: