University of Pennsylvania

Biomedical Graduate Studies
Responsible Conduct of Research (RCR) and Scientific Rigor and Reproducibility (SRR)

Acquisition and Management of Data

Preface

The acquisition and management of data are vital to the research record. The acquisition of data begins with the execution of a research plan, which in turn relies on a scientific premise and an experimental design, ideally one that considers variables, statistical power, and an authentication of key biological or chemical resources – in short, the elements of reproducibility. The management of data requires a complete and accurate representation of the data, a full accounting of protocols and the logic underlying them, a means of authenticating results by co-workers and others seeking replication, and a protection of such information from loss and inappropriate intrusion.

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Background

Data are acquired through observation and are recorded initially through hand-entered notations, instrument or computer readouts, and/or images. Records of this nature are referred to as ‘primary’ data. These data can be organized subsequently into formats amenable to analysis and presentation, or ‘secondary’ data.

The effective management of data can be achieved through any number of means. At the heart of any such effort however, and constituting a common element across all disciplines, is the laboratory notebook. The notebook provides a record of primary and secondary data. It can, and should, provide as well a record of collaboration, interpretation, and decisions. It allows authentication of work by outside parties and proves ownership in claims to discovery.

The exact format of record-keeping is left to the discretion of the principal investigator. That said, the following guidelines are offered with the intent to protect the integrity of entries in terms of time, authorship, and content. These recommendations originate, with abridgement, in Scientific Integrity (F.L. Macrina, 4th edition, ASM Press).

Guidelines for bound notebooks:
  • The advantages of bound, page-numbered notebooks versus loose-leaf binders are compelling, especially at the level of authentication.
  • A table of contents is invaluable.
  • Entries should be made in chronological order and dated. No page should be skipped.
  • Entries should be clear and legible. They should be made with permanent non-erasable ink, never in pencil. Lines should be drawn through mistaken entries without making the entries completely illegible; correction fluid should not be used.
  • Entries for any single experiment should include date, purpose, materials, protocol, results, discussion, and next steps.
  • Entries must include primary, unedited data, and should include as well any derived data, tables, calculations, and graphs. With regard to primary data, it is imperative to:
    • Document everything – you cannot remember it all.
    • Document everything ASAP – acts and details kept ‘in your head’ are quickly lost.
    • Document everything whether it’s ‘good’ or ‘bad’, ‘right’ or ‘wrong’. Omitting data is dishonest.
    • If data are discarded in a subsequent analysis, clearly note the reason for it. Not infrequently this will require statistical validation.
  • Entries should be made in such a way as to allow the investigator and other researchers to evaluate them at any point in time, inclusive of how data are used to form decisions regarding next steps and how data are selected for presentation, manuscripts, proposals, etc.
  • If word-processing is used in place of handwritten entries, printouts should be affixed permanently to pages of the notebook. Printouts from other software programs should be treated likewise.
  • Should primary or secondary data not be easily handwritten or affixed, or should inclusion be otherwise difficult or unwieldly, the data can be deposited in files, physical or electronic, but with clear identification in the notebook and an organization that befits the organization of the notebook.
  • Regarding storage and protection:    
    • Notebooks and other records should be kept secure from unauthorized access, theft, and destruction through storage that safeguards access and periodic, securely stored backups.
    • Notebooks should not be removed from the laboratory.
Guidelines for computer-assisted record-keeping or electronic notebooks:
  • An official procedure for the lab’s electronic record-keeping process should be defined and communicated by the principal investigator to all users.
  • The location, organization, and nature of electronic records for each user should be clearly defined.
  • The nature of entries with regard to content, how decisions are made, and how data are selected should conform to those recomended above for bound notebooks.
  • Entries should be write-protected and time-stamped to ensure authenticity.
  • The date and content of primary electronic records should never be altered. Any corrections, addenda, or correspondence relating to primary electronic records must be made separately from these records, again in a write-protected and time-stamped fashion.
  • Access to the stored electronic data of researchers in the lab should be authorized by the principal investigator as needed, with full knowledge of all involved parties.
  • Regarding storage and protection:    
    • Regular (daily) backup of all records should be mandated, and the process and oversight of this should be clearly prescribed and regularly monitored for compliance.
    • Data on laptops, portable hard drives, and other portable media should be encrypted.

The notebook and other records should be retained for a sufficient period of time to allow analysis and repetition by others of published material resulting from those data. In general, five to seven years is specified as the minimum period for retention but this may vary under different circumstances.

 

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Policies and Guidelines

There are no formal policies at Penn covering the types or format of record keeping. The only policy of relevance, which pertains to BGS students directly, is to have lab notebooks inspected at each dissertation committee meeting. This procedure is copied here.

“Approved by Biomedical Advisory Committee, September 15, 2006:

All dissertation level students must bring their lab notebooks to their dissertation committee meetings. If a student has previously met with the dissertation committee, then he or she should bring the notebooks used since the last committee meeting. The dissertation committee should make a point of reviewing notebook data at each meeting. There is no expectation that lab notebooks be reviewed in their entirety. However, the dissertation committee should feel confident that the student's lab data are complete and well managed. Graduate groups may wish to impose additional requirements, such as assigning a particular committee member responsibility for reviewing lab notebooks or arranging for the notebooks to be reviewed in greater detail by a committee member outside of the meetings. In any event, each graduate group’s dissertation committee meeting report forms will be amended so as to document the committee’s review of lab notebooks.”

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Case Studies

Access to case studies requires a PennKey. They are available here.

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Comments/Resources

Two textbooks provide excellent discussions of data acquisition and management. Both are electronically accessible through the Biomedical Library. These are:

Scientific Integrity, F.L. Macrina, 4th ed.
Responsible Conduct of Research, A.E. Shamoo and D.B. Resnick, 3rd ed.

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