Guidelines on Research Data and Manuscripts
Brain Tumor Research Center
Department of Neurological Surgery
School of Medicine
University of California, San Francisco
§1 Responsibilities of BTRC Principal Investigators
Principal Investigators (PIs) have final responsibility for:
…the validity and quality of the data and manuscripts generated from their laboratories.
…fulfilling BTRC and UCSF research and publication standards, policies, and procedures.
…orienting staff, research fellows, and residents to those standards, policies, and procedures and to the maximum extent possible, seeing to it that they are upheld.
…overseeing the work done by staff, research fellows, and residents, to assure that each has the knowledge, information, and skills necessary to meet BTRC standards.
NOTE: These are developing guidelines, a working document reflecting the standards of the faculty of the BTRC, the Department of Neurological Surgery, and the School of Medicine, University of California, San Francisco. Suggestions for additions or revisions should be directed to the BTRC/IRDM Advisory Committee in care of the address given below.
Developed and written by the BTRC Advisory Committee on Internal Review of Data and Manuscripts (IRDM): Susan Eastwood, ELS(D) Chair; Philip H. Cogen, MD-PhD, John R. Fike, PhD, and Harold Rosegay, PhD-MD, with Michael Berens, PhD. Developed in consultation with Scientific Director Dennis F. Deen, PhD, Director Charles B. Wilson, MD, and the principal investigators of the BTRC.
Copyright 1989 by the University of California, San Francisco. Permission to reproduce these guidelines in whole or in part may be requested from the Brain Tumor Research Center, c/o Department of Neurological Surgery Editorial Office, Box 0926, University of California, San Francisco, San Francisco, CA 94143 [tel: 415/476-3272].
Reprinted with permission from the University of California, San Francisco.
§2 Orientation of BTRC Research Personnel
§2.1 BTRC personnel receive a brochure describing the BTRC research and publication policies and procedures recommended in these guidelines, as well as the School of Medicine, University of California, San Francisco, Guidelines to Promote Ethical Conduct in Research (Appendix A[2.1]), and the Uniform Requirements for Manuscripts Submitted to Biomedical Journals (URM) (Appendix B[2.1]).1
The BTRC brochure includes a directory to sources of information about, e.g., animal care, radioisotope usage, human experimentation requirements, biohazard safety, and statistical support (Appendix C[2.1]).2
§2.2 Fellows and residents beginning work in the BTRC attend an orientation consisting of two 90-minute sessions sponsored by the BTRC. This program provides an overview of the research and publication processes in the BTRC and the resources available to the BTRC research group. Faculty attend the program at least once to familiarize themselves with and provide suggestions related to the information it contains.
§3 Research Data
§3.1 Data Management and Review
In general, two primary forms of data records are maintained in each BTRC laboratory: the methodology notebook and the experimental notebook. Laboratories with several investigators and/or research projects keep a laboratory master log. A data selection file containing data selected for publication and documents related to publication is kept for each paper resulting from a study. BTRC standards for accurate collection and recording of data and for storing data are detailed in §4 of these guidelines.
§3.1.1 The PI has final responsibility for the validity of the data.
§3.1.2 The PI has final responsibility for maintaining methodology notebooks and laboratory master logs relevant to the PI's laboratory and for seeing to it that those books
and all experimental notebooks, data selection files, and related data and records are kept and stored according to BTRC standards.
§3.1.3 The PI has final responsibility for ensuring that data (a) are collected and recorded in the experimental notebook according to BTRC standards and (b) are stored in a comprehensible way for others to have access to them.
§3.1.4 In some laboratories, a "data manager"—at UCSF usually a staff research associate or specialist designated by and responsible to the PI—may maintain methodology notebooks, oversee experimental notebooks, have laboratory management responsibilities, and/or instruct new fellows and residents in laboratory techniques and protocols. In such laboratories, PIs meet with their data manager to review research progress and data at least once each month (see §3.1.6).
§3.1.5 The PI holds scientific meetings with junior investigators, residents, and fellows once each month, at which time the PI reviews the experimental notebooks and related data and records. To fulfill the educational purposes of the BTRC, though, PIs are encouraged to meet more frequently with these personnel, about once a week, particularly on a one-to-one basis (see §3.1.6).
§3.1.6 PIs are encouraged to initial and date the latest page of each experimental notebook reviewed in the event that documentation of these reviews is needed at a later date.
§3.1.7 The BTRC's scientific director (D. Deen) reviews all methodology and experimental notebooks and related data and records at least twice each year.
§3.2 Statistical Design and Analysis
Investigators are encouraged to consult a statistician when designing a study and interpreting statistical data. Statistical support is available through the Northern California Cancer Program, which is willing to review statistical aspects of BTRC protocols.
§3.3 Use of Pooled BTRC Data
An investigator wishing to base a study on pooled computerized BTRC data that was generated by anyone other than him/herself alone must discuss the project with the BTRC's scientific director and the PI who derived the data before work begins to assure proper authorship, acknowledgment, and attribution of ideas and data.
§3.4 Ownership of Data
Methodology and experimental notebooks and related data and records are the property of the University of California. They may not be removed from the BTRC, although investigators may take a photocopy of all or part of them from the BTRC. [Note: When a PI resigns from the University, arrangements can generally be made to transfer ownership appropriately.]
§3.5 Storage of Data
PIs must store all data notebooks and related data and records in the BTRC for 5 years after the date when funding for a study ends. They may then continue to store them in the BTRC or may make arrangements with the office of the BTRC administrative director (M. Barker) to have them moved to the UCSF storage facility at Oyster Point; the BTRC administrative office keeps a record of retrieval information.
§4 Standards for BTRC Databooks
§4.1 Data Notebooks
§4.1.1 Bound Notebooks with Consecutively Numbered Pages. These databooks, with a permanent (sewn) binding, are the hard copy of choice for data recording. Duplicate pages in the notebooks are intended for generating carbon copies.
§4.1.2 Loose-Leaf Binders. These are used instead of bound data notebooks at the PI's discretion, to log all or portions of experimental records or generated data. Each page must be identifiable as consecutive and belonging to a specific experiment according to a system created and followed in the laboratory (e.g., an experiment-identification number followed
by the sequential page number and investigator's or technician's handwritten initials: 1.23MT); the BTRC's administrative director keeps a record of each laboratory's experiment-identification system in order to properly archive and retrieve data. When an experiment is completed, the consecutive pages of data and notes may be inserted into a plastic sleeve(s) for permanent storage in a binder for the one experiment, or in one binder including all experiments for the study.
§4.1.3 Data and Relevant Material That Must Be Stored Separately (e.g., computerized data files, microscope slides): see 4.4.4-4.4.6.
§4.2 Laboratory Master Log
For studies involving several investigators, or for laboratories with several investigators and/or research projects, the PIs keep a master log that serves to catalog the experiments of the whole study or laboratory. This central log, a hardbound databook with consecutively numbered pages, should contain:
the titles of the studies done by everyone in the laboratory,
the investigators' names,
the inclusive dates of the experiments, and
the location of the experimental notebook and any raw data, computer files, or other relevant materials stored separately for each logged experiment.
§4.3 Methodology Notebook
§4.3.1 In each laboratory, certain techniques or protocols are used in common on a daily basis, such as specific cell culturing techniques (e.g., cell transfers, dilutions, cell counting, media preparation), irradiation techniques, tumor implantation procedures, neurologic examinations, animal anesthesia, electrophoresis procedures, and others. Specific details about each of these commonly used methodologies (including the statistical methodologies) are documented and numbered or assigned reference notations that facilitate citation in experimental notebooks. Such documentation serves to standardize all experiments that generate data of the same form and is also instrumental in training new laboratory personnel.
Notebooks have a section for each technique, and each section contains all versions of the technique, each dated for reference.
A "table of contents" to the methodologies is kept at the front of the notebook.
The specific entries in the methodology notebook are modified as improvements in the procedures are developed. Changes are noted precisely and dated in the methodology notebook.
Outdated or discontinued methods remain in the methodology notebook, with a notation of the precise date the modified or new method(s) went into effect (e.g., so that earlier methods can be readily retrieved for reference in writing a manuscript).
§4.3.2 The methodology notebook is the final and absolute arbitrating reference when questions of technique are raised in the context of the educational and training responsibilities of the BTRC.
§4.4 Experimental Notebook
§4.4.1 The experimental notebook is the vehicle by which the experiment is fully documented.
§4.4.2 The first several pages of the notebook are reserved for a "table of contents," in which are listed, as the study develops, the experiments and the pages on which the data are located.
§4.4.3 The following minimum information is entered for each experiment; PIs are encouraged to make up a "boilerplate" page that can simply be filled in with this information.
Title of study
Date the study starts; date it ends
Associate investigator's name(s) (i.e., research associate specialist and/or postdoctoral fellow, resident, or graduate student)
Brief statement of hypothesis or study goals
Cell line (passage no.)
Animal strain and supplier
Specific animal identification no. (large animals)
Source of analyzed material
Tumor type and passage no.
Drug type (lot no. and/or source), dose(s), dilution(s)
Radiation source and dose
Special reagents (e.g., antibodies, probes)
Cell culture batch/medium
…study-specific treatment groups, projected number of subjects, and all other elements of the study design with reference to specific techniques or protocols from the methodology notebook [refer to each specific protocol or technique by its designation (e.g., number) in the methodology notebook].
…statistical methodology added to or deviating from that in the methodology notebook.
…a "time line" illustrating the sequence of study events (e.g., start, cells added, medium added, …).
Specific notes about special procedures or steps that differ from the techniques specified in the methodology notebook (e.g., changes in incubation time or temperature, concentration of trypsin, tumor cell inoculum, infusion rates, anesthetic procedure). Any variance from the routine procedures recorded in the methodology notebook must be noted in detail [refer to each specific routine protocol or technique by its designation (e.g., number) in the methodology notebook].
Raw data, or explicit instructions for locating the raw data or retrieving them from storage (see 4.4.4). Of particular importance are notations about excluded data or animals, with detailed information about why those data or animals were excluded.
A brief conclusion of the experiment, including a "value judgment" about the validity of the experiment, whether the study needs to be repeated to validate it, what can and cannot be definitively concluded from the data, and other observations. Simple concluding
descriptions such as ''bad study," or "data suspect," are not acceptable. It is essential to document why the study or data were considered suspect. Justifications for positive judgments must similarly be recorded.
§4.4.4 Raw Data. Whenever possible, raw data are stored together with the experimental notebook; e.g., they may be stapled on the duplicate page following the related databook entry, or placed in a plastic sleeve(s) and inserted in the binder. Data too unwieldy to include is listed in the experimental notebook as it is collected, is described sufficiently for recognition, and is annotated with the name of investigator and explicitly where the data can be found (e.g., location of the tape or disc and its identification number). Raw data include, but are not limited to,
handwritten notes on, e.g., cell or colony counts, tumor dimensions, physiologic endpoints, daily observations on animals, or other visually measured data (e.g., CT or NMR tapes) from which observations were made,
photographs, photomicrographs and negatives
spectra, EEG, evoked potential recordings
films, scans, images
slides (e.g., histologic sections)
dated hard copy from computerized data files (see 4.4.5).
§4.4.5 Computerized Data Files. In the data notebook are included dated hard copy from these files or, if this is too unwieldy, dated summaries that describe the files sufficiently to find and recognize them, including the location of the data file and the particular computer disc(s) on which the data are stored.
§4.4.6 Blinded, Cooperative, or Multicenter Studies. Data for blinded or double-blind studies are kept in separate (perhaps smaller), bound notebooks by the respective investigators and are brought together with the experimental notebook(s) as a single unit for storage at the end of the study, when the code is broken. Data management for cooperative or multicenter studies is developed along these guidelines as the need arises.
§4.4.7 Standards for Keeping Experimental Notebooks
§18.104.22.168 Each entry in the experimental notebook should be able to stand alone, to permit others to replicate the work at any time, whether immediately or even years after it is made.
§22.214.171.124 Experiments are logged in the notebook in chronological sequence.
§126.96.36.199 Data are recorded chronologically as they are collected on consecutive pages of the experimental notebook.
§188.8.131.52 Entries should be organized in such a way that someone not familiar with the specific experiment recorded can retrieve all the pertinent details of the study, from the hypothesis to the published article. Notes entered at the time of the experiment summarizing the goals, details, or problems can be invaluable during subsequent analysis or defense of the results and are therefore encouraged. Optimally, the experimental notebook is a journal of the study.
§184.108.40.206 Databooks are kept only in ink and must contain no erasures or "whited-out" changes.
An entry made by mistake is deleted only by drawing a single line through it, preferably in ink of a different color. The deleted material must remain legible beneath the overstrike. Large blocks or a page to be disregarded are crossed over with an "X" or diagonal line and marked, e.g., "OMIT." The page must remain legible.
The corrected data are written beneath or beside the original entry. The explanation for the alteration is clearly written in close proximity to the alteration—preferably on the same page or on the facing page.
§220.127.116.11 If any changes are ever made in the experimental notebook—including a change in values, correction of a mistake, or like alterations—it is absolutely required that those changes be dated and initialed by the person making the alteration, and a clear explanation noted as to why the alteration was made.
§18.104.22.168 In permanently bound databooks containing duplicate (often perforated) numbered pages, only the original bound-in page is used to record data. The duplicate page is used only for a carbon copy or to paste in auxiliary material, e.g., photographs; it is otherwise simply left blank.
§22.214.171.124 Whether permanently bound or loose-leaf, only databooks with consecutively numbered pages should be used. Pages must never be torn from a databook.
§4.5 Data Selection File
Manuscript preparation involves the selection of specific experimental data from the experimental notebook.
§4.5.1 A data selection file, filed separately from the experimental notebook and clearly cross-referenced to it, is kept for each paper to be submitted for publication.
§4.5.2 The data selection file consists of:
Those data selected for reporting and their analyses (including, e.g., graphic presentations and statistical manipulations). These are photocopied from the original experimental notebook and cross-referenced to that notebook page by page (unless the cross-reference is evident on the photocopy).
The rationale for selecting the specific data used in that particular paper, recorded narratively ("I selected this datum on the basis of X; I excluded this datum on the basis of Y."), including justification
for the selection of specific data to make a curve or other statistical representation.
A document naming the coauthors and detailing their specific contribution(s) to the study (Appendix D[4.5.2]).
A document naming the persons cited in the acknowledgments as contributing to the paper and detailing their specific contribution(s) to the study (Appendix E[4.5.2]).
Any other material considered pertinent to selection of data, to authorship, or to any substantial related matter arising during the development of the paper.
§4.5.3 At the completion of a research project, the data selection file for each paper developed from the project is archived in the BTRC together with the experimental notebook(s) for the project and the photocopies of the relevant material from the methodology notebook(s).
§5.1 The first author of a paper is named, coauthors selected, and order of authorship assigned before a study begins. Although changes may take place, such an initial plan provides a context for the relative responsibilities and expectations of each investigator.
§5.2 Authorship is based on the URM, which makes clear the distinction between an author and a contributor to the paper. Contributors are named and their contribution to the study and/or paper specified in the Acknowledgments section of the paper.
§5.2.1 The senior author is the PI responsible for the validity of the data reported and may or may not be the first author of the paper. If the senior author is not the first author, his or her name appears last in order of authorship.
§5.2.2 The first author is the person who generates the data, collects and/or collates the data for review by coauthors, and writes the first draft of the paper.
§126.96.36.199 The first author is responsible for maintaining and archiving the data selection file (see 4.5).
§188.8.131.52 If the first author leaves the BTRC before the data selection file is complete, responsibility for maintaining it reverts to the senior author.
§5.2.3 The first and senior authors jointly decide whether or not another participant is to be a coauthor. Other coauthors of the paper are named in the order of the importance of their contribution to the research being reported.
§5.3 Order of authorship may be changed with the agreement of the first author and the senior author and according to URM principles; e.g., if any author recommends that changes of personnel over the course of a study call for revision of the initial authorship. All coauthors must be notified of authorship changes before a paper is submitted for publication.
§5.4 Disputes regarding assignment or order of authorship that cannot be resolved among the authors should be addressed to the scientific director of the BTRC. The BTRC Advisory Committee on Internal Review of Data and Manuscripts (IRDM)3 can be consulted as a resource in resolving such disputes.
§6.1 All coauthors meet at least once to discuss the selected data and the results of the work, and to reach agreement on their conclusions, the general direction of the paper, and the work of others, if any, to be referenced or acknowledged.
§6.1.1 This meeting is usually conducted in person but it may be by conference call or computer communications (e.g., Popnet).
§6.1.2 If these alternatives are unworkable, the senior author telephones the absent coauthor(s) or sends him/her a summary of the coauthors' meeting. In such cases, the resolution of any disagreements on the work among coauthors should be documented in letters that are archived in the data selection file.
§6.2 Coauthors are encouraged to review raw data.
§7 Manuscript Submissions
§7.1 BTRC papers must meet the standards and requirements specified in the URM, except for details of style or format that conflict with the instructions of the journal to which the paper is being submitted.
§7.2 BTRC papers must include a notation of all funding for the work reported. To assure that all relevant sources of funding (e.g., donor gifts as well as grants) are acknowledged, consult the BTRC administrative director (M. Barker).
§7.3 BTRC papers are generally submitted from the Department of Neurological Surgery Editorial Office, which maintains and archives the manuscript file and provides forms needed for documentation.
§7.3.1 The senior author is the editor's principal contact regarding the paper, but the senior author may assign a coauthor (e.g., the first author) to follow the editorial process.
§7.3.2 The senior author may request a minimum review and an estimate of need for further editing of a paper. Minimum review consists of checking the correlation of numbers throughout the paper, reference citations, fulfillment of journal requirements, and the required documentation.
§7.4 An Author's Agreement form (Appendix F[7.4]) containing all coauthors' signatures must accompany every paper submitted from the BTRC. One copy of the form is included in the data selection file and one in the manuscript file. All coauthors must personally sign this form (or a copy, see 7.4.2). Signatures in absentia are never legally acceptable. If an author's whereabouts is unknown, this is noted on the form and in the cover letter to the journal.
§7.4.1 Before the initial submission and any subsequent substantially revised submission (see 7.4.4), the senior author or a designated person (e.g., a coauthor, editor) sends one copy
of the "prefinal" (penultimate) draft of the paper, covered with the Author's Agreement form, to each coauthor in turn for final review; if differences still must be settled among coauthors, the paper goes through another draft.
§7.4.2 When the version of the paper to be published is satisfactory to all coauthors, they sign the Author's Agreement form and return it to the Editorial Office. Authors who have left the BTRC are sent a separate copy of the final manuscript and form, if necessary by courier or fax.
§7.4.3 The paper is submitted after all coauthors' signatures are obtained.
§7.4.4 When, after journal peer review, revision of a paper involves additional or different data, a substantial revision of conclusions, a change in authorship, or a change in order of authorship, the renewed agreement of all coauthors is documented on a new Author's Agreement form. This documentation is not needed if the outcome of the original coauthor meetings has not changed. What constitutes "a substantial revision of conclusions" is at the PI's discretion.
§8 Publication of Negative Results, Corrections, Errata, and Retractions
The BTRC supports submission for publication of (a) papers reporting results that disprove or fail to replicate earlier published conclusions, (b) a correction of published work that is scientifically flawed, (c) errata in published reports, and (d) a retraction of any report determined fraudulent (see Appendix G).4
BTRC personnel are responsible for informing their coauthors when a correction or retraction is warranted and for publishing it in the journal that published the paper originally. All coauthors on the original paper should coauthor a retraction together with any other investigator(s) later involved in the work. Conflicts and questions in this regard that cannot be resolved among authors are addressed to the scientific director of the BTRC. The IRDM Committee may be consulted as a resource in resolving such disputes.
§9 Questions of Research or Publication Practice Other Than Authorship
§9.1 BTRC personnel should refer questions or problems about research publication practices to their immediate supervisor and/or PI or, if necessary, to the BTRC scientific director. The IRDM Committee or any of its members may be contacted as a resource for information or consultation.
§9.2 BTRC personnel should refer any allegation of improper practice or misconduct in the performance or publication of research to their immediate supervisor and/or PI or, if necessary, to the BTRC scientific director. The person alleging the claim should be able to support it with documentation. All BTRC personnel involved with such an allegation must observe due process during all phases of inquiry. The IRDM Committee or any of its members individually may be consulted as ombudsmen or as a resource for information or consultation by any member of the BTRC.
§9.3 BTRC personnel should refer any question, problem, or allegation not resolved through the channels just described to the chairman of the Department of Neurological Surgery and thereafter, if necessary, to an appropriately responsible University officer.
BTRC PROTOCOL ON RECORDING DATA AND PREPARING FOR PUBLICATION
_____ Review relevant literature (ongoing)
_____ …read original sources in their entirety
_____ …photocopy references or log complete and accurate citation
_____ Plan experimental study design
_____ …obtain statistical consultation
_____ …review and photocopy relevant sections from the appropriate methodology notebook for reference
_____ In the experimental notebook, initially record
_____ …title of study
_____ …PI's name
_____ …date the study starts (inclusive dates after study ends)
_____ …associate investigator (e.g., SRA, postdoctoral fellow, resident)
_____ …brief statement of hypothesis or study goals
_____ …cell line (passage no.); animal strain and supplier, specific animal i.d. no. (large animals); source of analyzed material; tumor type and passage no.
_____ …drug type (lot no. and/or source) and dose(s); radiation source and dose; special reagents (e.g., antibodies, probes); cell culture batch/medium; serum batch/medium
_____ …experimental design in detail (e.g., treatment groups, projected number of subjects), correlated specifically with the methodology notebook
_____ Perform study, recording
_____ …specific notes regarding special procedures or steps that differ from specific techniques (including statistical) taken from the methodology notebook, record of any variance from usual BTRC procedures in specific correlation with the methodology notebook
_____ …raw data, including handwritten notes on data collection, endpoints, daily observations, location of photomicrographs and negatives, and particularly notations about excluded data or animals, with detailed information on why they were excluded
_____ …a "time line" illustrating the sequence of study events (e.g., start, cells added, medium added, … etc.)
_____ …brief conclusion, including a "value judgment" on the validity of the experiment, whether the study needs to be repeated to validate it, what can and cannot be definitively concluded from the data, and other observations
_____ Analyze data
_____ Meet with all coauthors at least once to discuss the raw and selected data, the results of the work, to agree on conclusions, the general direction of the paper, and work to be referenced in the paper
_____ Create a data selection file …in consultation with coauthors as much as possible
_____ …selected data from the experimental notebook and their analysis, including graphic presentations, statistical manipulations, are archived in a data selection file, clearly cross-referenced to the experimental notebook
_____ Select pertinent references
_____ Select and analyze journal most relevant to the work
_____ Write the paper for the journal chosen
_____ …send a working draft to coauthors
_____ …revise paper until final revisions are complete
_____ …complete and archive documentation in the file
_____ …statement and order of authorship, contributors acknowledged, permission to use "personal communications"
_____ …send paper to Editorial Office for editorial consult
_____ …final draft sent from Editorial Office to all authors together with the Author's Agreement form, which all coauthors must personally sign
_____ …Submit paper to journal together with signed Author's Agreement