2015.2.25
Ver. 2.0

Introduction

An enormous amount of human data is being generated as advancements are made in next-generation sequencing and other analytical techniques. Rules and mechanisms are therefore needed for organizing and storing such data and for effectively utilizing them to make progress in the life sciences.
To promote sharing and utilization of human data while considering protection of personal information,
the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST) created a platform for sharing various human-related data and other information (hereinafter, the NBDC Human Database) and developed rules and guidelines (hereinafter, the Guidelines) for operating it.
The Guidelines apply to human data generated using public funds. We have not verified the consistency between the Guidelines and all the other relevant guidelines, policies, and laws. In addition, global trends concerning life science data as well as the attitude of the general public toward scientific data are expected to change. To respond to such changes, we plan to make necessary modifications at appropriate times.

Contact information:

For information on the Guidelines

NBDC Data Sharing Subcommittee Office
http://humandbs.biosciencedbc.jp/en/contact-us

For information on data use or data submission for the NBDC Human Database

NBDC Human Data Review Board Office
http://humandbs.biosciencedbc.jp/en/contact-us

Contents

  1. Principles
  2. Definitions
  3. Acceptable Data
  4. Data Submission to the NBDC Human Database
  5. Using Data in the NBDC Human Database
  6. Procedure for Revising the Guidelines
  7. Other Topics

1. Principles

  1. The NBDC Human Database is administered based on the following principles.
    • Principle 1: Collecting as much human data generated with public funds as possible
    • Principle 2: Sharing collected data with as many users as possible
    • Principle 3: Properly managing data to avoid identification of individuals who provide specimens
  2. The NBDC performs the following in administering the NBDC Human Database.
    1. Maintaining the Guidelines and reexamining them as the need arises
    2. Reviewing applications for data use and data submission
    3. Maintaining means to access data, through website maintenance, etc.

2. Definitions

  1. Human data
    • Data generated as results of studies using human specimens. Such data include genomic and genetic information, clinical information, photographic information, and so on.
  2. Public funds/grants
    • Funds provided by national and local governments, incorporated administrative agencies, and equivalent organizations.
  3. Principal investigator (PI)
    • The investigator responsible for the research project (the investigator who submits a description of the research to the institutional review board (hereinafter, IRB) of his/her affiliated institution and receives its approval, or a research collaborator whose name appears on the application form for ethics review.)
  4. Data submitter
    • A principal investigator (hereinafter, PI), who provides human data to the NBDC Human Database.
  5. Data user
    • The PI who uses human data from the NBDC Human Database, and research collaborators who are members of the institution that the PI belongs to and whose names are listed in the Application Forms (Form 2 / Form 7) as data users completed by the PI.
  6. Open data
    • Data available for use without any access restrictions. Examples include reference data for published papers.
  7. Controlled-Access data
    • Data available for investigators, who have research experience in related studies, can use for their studies after disclosing information on the data users, the purpose of data use, etc.
  8. Data for future release
    • Data that are planned to be released as open data or controlled-access data after the data submitters make their results public by publication of a paper, acquisition of intellectual property rights, etc.
  9. Data before de-identification or without data sharing plan
    • Data that have not been de-identified or are intended for internal use within a project, a group, or a consortium.
  10. Secondary data
    • All data derived from data that are obtained after submitting an application for data use to the NBDC Human Data Review Board.

3. Acceptable Data

Overview of acceptable data

The NBDC Human Database accepts a wide range of human data generated in projects that receive public funds. Because we aim for data utilization among many investigators, we do not accept data that are provided for the purpose of limited sharing among investigators who collaborate in certain research groups or consortiums.

Data are divided into the following four types according to the state of data release and the level of access restriction (see the figure below).

  1. Open data
  2. Controlled-Access data
  3. Data for future release
  4. Data before de-identification or without data sharing plan

The NBDC Human Database accepts open data, controlled-access data, and data for future release. For all the types of acceptable data, another round of de-identification must be conducted.

dataClassification e

4. Data Submission to the NBDC Human Database

4.1 Rights of the Data Submitters

  1. The data submitters can set data use restrictions that conform to restrictions specified in the informed consent (e.g., limitation on the scope of diseases for data use).
  2. The data submitters are asked to promptly release their data, but can request that the data be designated as data for future release for the purpose of publication of research results, acquisition of intellectual property rights, etc. However, the time until the date of such future release is limited to what is reasonably necessary for such purposes, and concrete details are determined in a consultation with the NBDC Human Data Review Board.

4.2 Responsibilities of Data Submitters

  1. Data submitters must obtain permission from the head of their affiliated organization after the following steps have been taken. (1) Explain the requirements in the list entitled “Examples of Content for Informed Consent Forms” (shown below) to the research participants from whom the human data are collected. (2) Obtain written informed consent from the participants regarding the submission of such data to databases and the sharing of such data by investigators. (3) Obtain the approval of the IRB of the affiliated organization or other relevant institution regarding such data submission and data sharing. However, if the data submission and data sharing were approved after an ethics review conducted at the start of the entire research project, then another review is not required.
  2. When data submitters provide the NBDC with human data collected from specimens (human biological specimens, diagnostic specimens, etc.) that were obtained without prior intention to submit such data to databases (e.g., in cases where the informational material does not refer to data submission or data sharing), the data submitters must obtain permission from the head of their affiliated organization after obtaining the approval of the IRB of the affiliated organization or other relevant institution.
  3. We ask the data submitters to provide the consent form at the time of application for data submission. We then verify the consistency between data use restrictions and the content of these documents. However, the data submitters are responsible for ensuring that data are provided in accordance with the conditions of the consent agreement.
  4. The data submitters must provide data according to the content of the Application Form for Submitting Data to the NBDC.
  5. The data submitters must conduct another round of data de-identification when they provide data to the NBDC.
  6. After designating data as open data, controlled-access data, etc. based on consultation with the NBDC Human Data Review Board, the data submitters must provide the NBDC with both the data and any necessary accompanying data (e.g., metadata that explain the main data, as well as information needed for quality control). Also, the data submitters must assign an appropriate security level (Type I or Type II) to controlled-access data based on consultation with the NBDC Human Data Review Board.
* For the description of the security levels (Type I and Type II), see the NBDC Security Guidelines for Human Data.
Examples of Content for Informed Consent Forms

* Although examples of statements for the informed consent forms are provided below, actual statements are not limited to these.

Required:
  • Data submission to a database and data sharing among investigators

    • Sample statement: Since the data obtained for this study are also important for other studies, they will be submitted to a database and will be shared with many investigators.

Items desirable for inclusion:
  • Description of the NBDC
    • Sample statement: The National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency conducts projects that aim for broad sharing of various research data; manages public databases that store data obtained from various studies including this analysis; and aims for rapid advancement in research. The NBDC manages and releases data following strict guidelines. These guidelines are reviewed at appropriate times according to changes in laws, regulations, government policy, and societal understanding. For details, please see the NBDC website (http://biosciencedbc.jp/en/).
  • The necessity and importance of data sharing
    • Sample statement: The sharing of research data with other investigators through a database can help advance related studies overall and can aid in the development of new technologies. Data sharing can help medical investigators discover previously unknown causes of disease and help them develop new treatments and therapies.
  • Data released to the public
    • Sample statement: Aggregate-level data derived from data taken from many individuals will be released to the public after ensuring their anonymity.
  • Data released with restrictions
    • Sample statement: Individual-level data are not released to the public, but permission to use individual-level data is given to investigators who have received approval after a rigorous review concerning matters such as scientific views and protection of personal information.
  • Impossibility to remove data
    • Sample statement: Some data already released in publications or distributed for approved research use cannot be deleted, even if you withdraw your consent.

4.3 Procedure for Data Submission to NBDC Human Database

  1. The data submitter confirms that the responsibilities listed in Section 4.2 above ('Responsibilities of Data Submitters') are fulfilled.
  2. The data submitter coordinates with the NBDC Human Data Review Board Office with regard to, choosing among open data, controlled-access data, or data for future release and, in the case of data for future release, deciding the timing of the release.
  3. The data submitter applies for data submission, following the application procedure for data submission. At the time of application, a copy of the research proposal (the application form for ethics review in his/her institution), a copy of the ethics review approval notification, and the consent form must be attached. If, however, data submission and data sharing are approved by an ethics review held at the beginning of the entire research project, a document indicating that fact can be used instead of a copy of the approval notification.
  4. The NBDC Human Data Review Board decides whether the data can be accepted.
  5. The submitter prepares the data to be submitted (open data or controlled-access data). At that point another round of de-identification is performed (by, for example, reassigning new identification numbers).
  6. The data submitter sends the data as instructed by the NBDC Human Data Review Board Office.
  7. Changes to data (updating data, switching data categories, etc.) are made as the need arises, based on consultation between the data submitter and the NBDC Human Data Review Board Office.

5. Using Data in the NBDC Human Database

5.1 Eligibility for Data Use

5.1.1 Open Data

Anyone can use open data.

5.1.2 Controlled-Access Data

Only investigators who have research experience in relevant studies (those who work at a university, public research institute, or private-sector company and have experience in conducting relevant studies) can apply for data use as a PI. At the time of application, they must show the publications related to the data that you plan to use, as well as an email address provided by their affiliated institution.

5.2 Rights of Data Users

5.2.1 Open Data
  1. The data user can freely present the result of the study for which data from the NBDC Human Database are used.
  2. The data user can freely acquire intellectual property rights based on the result of the study for which data from the NBDC Human Database are used.
5.2.2 Controlled-Access Data
  1. The data user can freely present the result of the study for which data from the NBDC Human Database are used.
  2. The data user can freely acquire intellectual property rights based on the result of the study for which data from the NBDC Human Database are used.

5.3 Responsibilities of Data Users

5.3.1 Open Data
  1. In using data, the user must take responsibility for and make judgments concerning the quality, content, and scientific validity of the data.
  2. The data user must comply with the following rules.

    Basic rules to be complied with in using data

      • The use of data is limited to the study being undertaken.
      • Identification of individuals is prohibited.
      • Redistribution of data is prohibited.
  3. When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are originally reported, or include in the acknowledgment as follows.

    The data used in this research was originally obtained by AAAA research project/group (led by Prof./Dr. BBBB) and available at the website of the National Bioscience Database Center (NBDC; http://biosciencedbc.jp/en/) of the Japan Science and Technology Agency (JST).

5.3.2 Controlled-Access Data
  1. In using data, the user must take responsibility for and make judgments concerning the quality, content, and scientific validity of the data.
  2. When using controlled-access data contained in the NBDC Human Database, the data user must comply with the “Ethical Guidelines for Human Genome/Gene Analysis Research” in Japan.1 That is, the data user must go through a review by the IRB of his/her affiliated institution or another organization with regard to the use of the NBDC Human Database and obtain approval from the review board. The application form for ethics review (the research proposal) must contain statements that are equivalent to the following.
    Examples of Consent Forms and the Research Proposals:

    * Although a sample statement is provided below, actual statements are not limited to this.

    Items included in the application form for ethics review:
    Required:
    • Data contained in the NBDC Human Database JGAS****/hum**** is used for analysis in this research.

         1 “Ethical Guidelines for Human Genome/Gene Analysis Research” in Japan (tentative translation)
         Section 5: Handling of Specimens and Information
         15. Use of Existing Specimens and Information Held by an External Institution
         (1) The PI with an intention to conduct a study using existing specimens and information provided by an external institution must state in a research proposal the content of such specimens and information and the reasons for using them and must obtain approval from an IRB and permission from the head of the institution where the study is conducted.

  3. The data user must comply with the following rules.

    Basic rules to be complied with in data use

      • The number of users must be limited. (Access is limited to the PI and research collaborators who are members of the institution that the PI belongs to and whose names are listed in the application for data use (Form 2 / Form 7) submitted to the NBDC.)
      • The purpose of data use must be explicitly stated.
      • The use of data for purposes other than the ones stated in the application is prohibited.
      • The use of data is limited to the study being undertaken.
      • Identification of individuals is prohibited.
      • Redistribution of data is prohibited.
  4. The data user must securely handle data, complying with the NBDC Security Guidelines for Human Data (for Data Users) which is found in a separate document. Attention should be paid to the fact that the security level to be maintained varies for different data.* The data user must accept an audit conducted by the NBDC Human Data Review Board or a third party commissioned by the NBDC with regard to the state of implementation of security measures.

    * Security levels:

    Standard-level (Type I) security is required in principle, but high-level (Type II) security may be required based on consultation between data submitters and the NBDC Human Data Review Board. For details on Type I and Type II security, see the NBDC Security Guidelines for Human Data (for Data Users).

  5. The data user must create a security control system corresponding to each security level (Type I, Type II) and submit Form 5 (Checklist for the NBDC Security Guidelines for Human Data) to the NBDC Human Data Review Board Office in order to confirm that the system conforms to the standards put forth by the NBDC.
  6. Should a security-related incident such as data leakage occur, the data user must immediately disconnect devices from the network and report the incident to the NBDC. The data user then promptly implements post-incident measures, following instructions from the NBDC.
  7. When finished with using data, the data user must delete all data obtained from the NBDC Human Database and report on the use (and deletion) of the data, using Form 3 (Report on the Use (and Deletion) of Controlled-Access Data). With regard to keeping secondary data (e.g., results of calculations based on controlled-access data), see the section on the procedure for using controlled-access data (Section 5.4: Procedure for Data Use; Section 5.4.2: Controlled-Access Data).
  8. When the research results including the data which were downloaded from NHA/JGA, are published or presented somewhere, the data user must refer the papers which are originally reported, or include in the acknowledgment as follows.

    Example of a statement in the acknowledgment section The (or, A part of the) data used for this research was originally obtained by AAAA research project/group (led by Prof./Dr. BBBB) and available at the website of the National Bioscience Database Center (NBDC; http://biosciencedbc.jp/en/) of the Japan Science and Technology Agency (JST).

  9. The data user agrees that the NBDC may publish certain statistical information or information about individual data users when it makes public how the NBDC Human Database is used. Published information on individual data users includes the name of the data set used, the date of application, the user name, the user's affiliated institution, and the starting date of the data use.
  10. The data user agrees that, for the purpose of making public how the NBDC Human Database is used, the NBDC holds information on data usage, including information on the data users that is obtained from the time of application to the time of reporting the end of data use and information gathered at the time of incidents.

If violations of above conditions are found, the NBDC may rescind permission for data use and publish information on the violations on a web page. Also, the above conditions are applied to not only PIs but also research collaborators. The PIs are responsible for their research collaborators' compliance with the Guidelines (this document) and the NBDC Security Guidelines for Human Data (for Data Users).

5.4 Procedure for Data Use

5.4.1 Open Data

The data user can freely use open data, which can be obtained from the website for the NBDC Human Database (http://humandbs.biosciencedbc.jp/en/), as permitted under laws and regulations.

5.4.2 Controlled-Access Data
  1. The data user applies for data use, following the application procedure for data use. If multiple investigators from different organizations conduct a collaborative study, an application for data use must be made for each organization.
  2. After going through a review by the IRB of his/her affiliated institution or another organization with regard to the use of the NBDC Human Database and obtaining approval from the review board, the data user submits, at the time of application, a copy of a notification of permission obtained from the head of his/her affiliated institution. However, if the IRB decides that a review can be waived, the data user submits a document indicating that fact.
  3. At the time of application, the data user submits Form 5 (Checklist for the NBDC Security Guidelines for Human Data) and other information and documents required by the NBDC Human Data Review Board Office.
  4. The NBDC Human Data Review Board decides whether or not to grant access to the controlled-access data.
  5. After the NBDC Human Data Review Board approves the access to the data, information necessary for accessing data is provided. The data user accesses data with that information.
  6. In principle, the data user reports information on data use each year in August, using Form 3 (Report on the Use (and Deletion) of Controlled-Access Data). Also, at the time of the report, the data user resubmits Form 5 (Checklist for the NBDC Security Guidelines for Human Data). However, if the end of August falls within a six-month period beginning on the starting date of the data use, the submission of the reports is unnecessary in that year and the reports may be submitted the following August.
  7. When the data use is finished or if the NBDC Human Data Review Board terminates the data use under Section 5.6 (Termination of Data Use), the data user must promptly delete the data and report his/her data use (and deletion) to the NBDC Human Data Review Board Office, using Form 3 (Report on the Use (and Deletion) of Controlled-Access Data). At the same time, the data user can save secondary data (e.g., results of calculations based on controlled-access data) by applying to the NBDC Human Data Review Board Office for permission to keep the secondary data, using Form 4 (Application for Permission to Keep Secondary Data Derived from Controlled-Access Data) , and by obtaining approval from the NBDC Human Data Review Board.

5.5 Cost of Data Use

If costs are incurred in connection with data use (e.g., in cases where data media are needed for sending data), the data user bears the costs.

5.6 Termination of Data Use

If the data user is suspected of violating a condition listed in Section 5.3 (Responsibilities of Data Users) or the NBDC Security Guidelines for Human Data, the NBDC audits the data user suspected of committing the violation, and the NBDC Human Data Review Board judges, based on the result of the audit, whether misconduct occurred. If it is determined that misconduct occurred, the JST/NBDC will do the following:

        1. Order the data user to stop using the data and revokes the permission to access the data set being used.
        2. Not accept, for a certain period, a new application for data use from the investigator who committed the misconduct. This period is determined by the NBDC Human Data Review Board.
        3. Report the misconduct to the head of the violator's affiliated institution, if necessary.

Depending on the situation, termination of data use may be ordered at the stage when suspicion is raised.

Upon receiving an order to terminate data use, the data user must immediately delete all data that have been obtained and all secondary data. In addition, the data user must promptly report the state of data deletion to the NBDC Human Data Review Board Office, using Form 3 (Report on the Use (and Deletion) of Controlled-Access Data) .

6. Procedure for Revising the Guidelines

6.1 Proposal for Revision

If data submitters, data users, and people who are considering data sharing think that revising parts of the Guidelines will potentially lead to smoother provision or use of human data, they can propose their ideas at the website: http://humandbs.biosciencedbc.jp/en/contact-us. Please provide concrete proposals and refer to the relevant parts of the Guidelines.

6.2 Review of Revision Proposals

Upon receipt of a revision proposal, the NBDC Data Sharing Subcommittee promptly reviews its content and decides whether the proposal is adopted or rejected or should be modified.

6.3 Announcement and Implementation of a Revision

Once the details of a revision are decided, they are promptly announced on our website and will be implemented after a certain period set by the NBDC Data Sharing Subcommittee. It should be noted that the post-revision Guidelines are retroactively applied to those who have already obtained approval for their application for data submission or data use unless they notify the NBDC of their objection.

7. Other Topics

7.1 Disclosure of Information Obtained from Applications for Data Submission and Data Use

From the applications received regarding the NBDC Human Database, the NBDC disclosed some input items on NBDC human database website for which applicants' consent is obtained (including information stated in 5.3.2(9)). The members of the NBDC Human Data Review Board and the staff of the NBDC Human Data Review Board Office must not disclose to a third party any other information on applications than those appear on NBDC human database website.

7.2 Notification of Inaccurate Data

With regard to inaccurate data in the NBDC Human Database that are pointed out by data users, the NBDC Human Data Review Board receives notifications from them and then informs the relevant data submitters of the issue and discusses the response with them. Similar actions are taken in cases where people who gave consent point out a possibility of improperly obtained consent or fabricated consent.

Contact information: http://humandbs.biosciencedbc.jp/en/contact-us

See also:

NBDC Security Guidelines for Human Data (separate document)

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