Database articles
Database articles should describe
either a new biomedical database or a database that has been substantially changed and improved since it was last described in a journal (for example by an expansion of data to broaden the range of users, or by a major increase in functionality).
The database must be readily accessible and data within the database should be attributed to a source.
Should a description of a database be submitted as a Database article or a Research article?
An article describing a database but also including research that merits publication in its own right should either be submitted as a Research article or should be split into a Research article and a separate Database article.
Availability of database to reviewers and other researchers
The database described in the manuscript must be available for testing by reviewers in a way that preserves their anonymity. If published, the described databases must be accessible by any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement.
We may require an archive copy of the database to be held by BioMed Central as a safeguard
Manuscript sections for Database articles
Manuscripts for Databases submitted to BMC Biology should be divided into the following sections:
The Accession Numbers of any nucleic acid sequences, protein sequences or atomic coordinates cited in the manuscript should be provided, in square brackets and include the corresponding database name; for example, [EMBL:AB026295, EMBL:AC137000, DDBJ:AE000812, GenBank:U49845, PDB:1BFM, Swiss-Prot:Q96KQ7, PIR:S66116].
The databases for which we can provide direct links are: EMBL Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan (DDBJ ), GenBank at the NCBI (GenBank), Protein Data Bank (PDB), Protein Information Resource (PIR) and the Swiss-Prot Protein Database (Swiss-Prot).
Title page
This should list the title of the article and the full names, institutional addresses, and email addresses for all authors must be included on the title page. The corresponding author should also be indicated.
Abstract
This should not exceed 350 words and should be structured into separate sections headed Background, Description, Conclusions). Please do not use abbreviations or references in the abstract.
Background
The background section should be written to be comprehensible to researchers without specialist knowledge in the area concerned. It should clearly describe the perceived need for the database, mentioning forerunners and competitors, and stating its potential value.
Construction and content
The database schema and implementation should be described in this section, together with information on data sources, the informatics of data generation and quality control.
Utility and Discussion
These may be combined into a single section or presented separately. They may also be broken into subsections with short, informative headings. The user interface should be described and a discussion of the intended uses of the database, and the benefits that are envisioned, should be included, together with data on how its performance and functionality compare with and improve on functionally similar existing databases. A case study of the use of the database may be presented. The planned future development of new features, if any, should be mentioned.
Conclusions
This should state clearly the main conclusions of the article and give a clear explanation of the importance and relevance of the database.
Availability and requirements
This should state the web/ftp address at which the database is available and any restrictions to its use by non-academics.
List of abbreviations
If abbreviations are used in the text, either they should be defined in the text where first used, or a list of abbreviations can be
provided, which should precede the authors' contributions and acknowledgements.
Authors' contributions
In order to give appropriate credit to each author of a paper, the individual contributions of authors to the manuscript should be specified in this section.
An "author" is generally considered to be someone who has made substantive intellectual contributions to a published study. To qualify as an author one should 1) have made substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) have been involved in drafting the manuscript or revising it critically for important intellectual content; and 3) have given final approval of the version to be published. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content. Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship.
We suggest the following kind of format (please use initials to refer to each author's contribution):
AB carried out the molecular genetic studies, participated in the sequence alignment and drafted the manuscript. JY carried out the immunoassays. MT participated in the sequence alignment. ES participated in the design of the study and performed the statistical analysis. FG conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.
All contributors who do not meet the criteria for authorship should be listed in an acknowledgements section. Examples of those who might be acknowledged include a person who provided purely technical help, writing assistance, or a department chair who provided only general support.
Authors' information
You may choose to use this section to include any relevant information about the author(s) that may aid the reader’s interpretation of the article, and understand the standpoint of the author(s). This may include details about the authors' qualifications, current positions they hold at institutions or societies, or any other relevant background information. Please refer to authors using their initials. Note this section should not be used to describe any competing interests.
Acknowledgements
Please acknowledge anyone who contributed towards the study by making substantial contributions to conception, design, acquisition of data, or analysis and interpretation of data, or who was
involved in drafting the manuscript or revising it critically for important intellectual content, but who does not meet the criteria for authorship.
Please also include their source(s) of funding. Please also acknowledge anyone who contributed materials essential for the study.
Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements.
Please list the source(s) of funding for the study, for each author, and for the manuscript preparation in the acknowledgements section. Authors must describe the role of the funding body, if any, in study design; in the collection, analysis, and interpretation of data; in the writing of the manuscript; and in the decision to submit the manuscript for publication.
References
All references must be numbered consecutively, in square brackets, in the order in which they are cited in the text, followed by any in tables or legends. Reference citations should not appear in titles or headings. Each reference must have an individual reference number. Please avoid excessive referencing. If automatic numbering systems are used, the reference numbers must be finalized and the bibliography must be fully formatted before submission.
Only articles and abstracts that have been published or are in press, or are available through public e-print/preprint servers, may be cited; unpublished abstracts, unpublished data and personal communications should not be included in the reference list, but may be included in the text. Notes/footnotes are not allowed. Obtaining permission to quote personal communications and unpublished data from the cited author(s) is the responsibility of the author. Journal abbreviations follow Index Medicus/MEDLINE. Citations in the reference list should contain all named authors, regardless of how many there are.
Examples of the BMC Biology reference style are shown below. Please take care to follow the reference style precisely; references not in the correct style may be retyped, necessitating tedious proofreading.
Links
Web links and URLs should be included in the reference list. They should be provided in full, including both the title of the site and the URL, in the following format:
The Mouse Tumor Biology Database [http://tumor.informatics.jax.org/mtbwi/index.do]
BMC Biology reference style
Style files are available for use with popular bibliographic management software:
Article within a journal
1. Koonin EV, Altschul SF, Bork P: BRCA1 protein products: functional motifs. Nat Genet 1996, 13:266-267.
Article within a journal supplement
2. Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I: Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins 1999, 43(Suppl 3):149-170.
In press article
3. Kharitonov SA, Barnes PJ: Clinical aspects of exhaled nitric oxide. Eur Respir J, in press.
Published abstract
4. Zvaifler NJ, Burger JA, Marinova-Mutafchieva L, Taylor P, Maini RN: Mesenchymal cells, stromal derived factor-1 and rheumatoid arthritis [abstract]. Arthritis Rheum 1999, 42:s250.
Article within conference proceedings
5. Jones X: Zeolites and synthetic mechanisms. In Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore. Edited by Smith Y. Stoneham: Butterworth-Heinemann; 1996:16-27.
Book chapter, or article within a book
6. Schnepf E: From prey via endosymbiont to plastids: comparative studies in dinoflagellates. In Origins of Plastids. Volume 2. 2nd edition. Edited by Lewin RA. New York: Chapman and Hall; 1993:53-76.
Whole issue of journal
7. Ponder B, Johnston S, Chodosh L (Eds): Innovative oncology. In Breast Cancer Res 1998, 10:1-72.
Whole conference proceedings
8. Smith Y (Ed): Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore. Stoneham: Butterworth-Heinemann; 1996.
Complete book
9. Margulis L: Origin of Eukaryotic Cells. New Haven: Yale University Press; 1970.
Monograph or book in a series
10. Hunninghake GW, Gadek JE: The alveolar macrophage. In Cultured Human Cells and Tissues. Edited by Harris TJR. New York: Academic Press; 1995:54-56. [Stoner G (Series Editor): Methods and Perspectives in Cell Biology, vol 1.]
Book with institutional author
11. Advisory Committee on Genetic Modification: Annual Report. London; 1999.
PhD thesis
12. Kohavi R: Wrappers for performance enhancement and oblivious decision graphs. PhD thesis. Stanford University, Computer Science Department; 1995.
Link / URL
13. The Mouse Tumor Biology Database [http://tumor.informatics.jax.org/mtbwi/index.do]
Instructions for BMC Biology authors
