# Instructions to Authors

New – Please note that the journal now encourages authors to complete their copyright licence to publish form online

### Submission

Manuscripts must be submitted online. Once you have prepared your manuscript according to the instructions below please visit the online submission web site. Instructions on submitting your manuscript online can be viewed here.

### Aims

The journal will publish:

• Detailed descriptions of databases, and database tools, in the broad arena of biology - authors are strongly encouraged to include a biological discovery or a 'testable' hypothesis in their papers.
• Shorter papers describing significant updates to established databases.
• Objective reviews of complementary and ancillary databases and database tools.
• User tutorials for database tools.
• Methodology and technical notes on database development.
• Improvements to automated prediction and annotation for biomedical datasets.
• Detailed descriptions of the state and updating of the annotation of genomes.
• Descriptions of the development and content of ontologies of relevance to the biomedical community and the tools specific to the use of these ontologies.
• Articles relevant to the annotation process such as standards for curation, annotation best practices, annotation methodologies, the use of automated and semi-automated methods for annotation and the measures for annotation consistency.
• Perspective manuscripts describing novel approaches, technologies, standards, or methods for database and/or annotation explorations including comparisons of state-of-the-art approaches. Perspectives can also include opinion pieces addressing challenges or debates in the field of biological databases and biocuration.
• Brief invited conference reports on topics related to the scope of the journal.

Descriptions of databases and biocuration application and activities in all areas of biology are welcome, including biological chemistry, genomics, proteomics, glycomics, molecular biology, biomedicine, physiology, ecology, botany, zoology, and taxonomy.

### Open Access Licence

DATABASE authors are required to complete an Open Access license agreement which reflects the open access model outlined below. Upon receipt of accepted manuscripts at Oxford Journals authors will be invited to complete an online copyright licence to publish form.
Oxford Open articles are published under Creative Commons licences. Authors publishing in Database can use the following Creative Common licence for their articles:
• Creative Commons Attribution licence (CC BY)

You can pay Open Access charges using our Author Services site. This will enable you to pay online with a credit/debit card, or request an invoice by email or post. The open access charges applicable are:

Regular charge - £800 / $1600 / €1200 Reduced Rate Developing country charge* - £400 /$800 / €600
Free Developing country charge* - £0 / \$0 / €0

Please note that these charges are in addition to any colour charges that may apply.

Orders from the UK will be subject to the current UK VAT charge. For orders from the rest of the European Union, OUP will assume that the service is provided for business purposes. Please provide a VAT number for yourself or your institution, and ensure you account for your own local VAT correctly.

Please see these guidelines for reuse of Oxford Open content.

### Authorship

The authorship of the paper should be confined to those who have made a significant contribution to the design and execution of the work described.

'Umbrella' groups and authorship:
Many large collaborative studies (frequently resistance surveys) are organized under a group name which represents all the participants. All articles must have at least one named individual as author. Authors who wish to acknowledge the umbrella group from which the data originate should first list the author(s) of the article and follow this with 'on behalf of the GROUP NAME'. If necessary the names of the participants may be listed in the Acknowledgements section.

### Previous publication

Submission of a manuscript to DATABASE implies that it reports unpublished work, that it is not under consideration for publication elsewhere and that, if accepted, it will not be published elsewhere in the same form, either in English or in any other language, without the consent of the publisher. Authors should provide the references of similar work that they have already published, or which is currently under consideration by another journal. If the work has previously been presented at a conference, authors should provide details in the covering letter. The journal will consider publication of work that has previously been presented as either a short abstract or poster at a conference, but not as a full paper. If previously published tables, illustrations or one or more blocks of more than 200 words of text are to be included, then the copyright holder's written permission must be obtained. Include copies of any such permission letters with your paper.
Please note that if considered appropriate, plagiarism checking software may be applied to your manuscript during the editorial review process.

### Conflict of interest

At the point of submission, Database policy requires that each author reveal any financial interests or connections, direct or indirect, or other situations that might raise the question of bias in the work reported or the conclusions, implications, or opinions stated - including pertinent commercial or other sources of funding for the individual author(s) or for the associated department(s) or organization(s), personal relationships, or direct academic competition. When considering whether you should declare a conflicting interest or connection please consider the conflict of interest test: Is there any arrangement that would embarrass you or any of your co-authors if it was to emerge after publication and you had not declared it?

As an integral part of the online submission process, Corresponding authors are required to confirm whether they or their co-authors have any conflicts of interest to declare, and to provide details of these. If the Corresponding author is unable to confirm this information on behalf of all co-authors, the authors in question will then be required to submit a completed conflict of interest form to the Editorial Office. It is the Corresponding author’s responsibility to ensure that all authors adhere to this policy.
If the manuscript is published, Conflict of Interest information will be communicated in a statement in the published pap

### Availability of databases

In line with the expectations and standards of the community, authors are expected to ensure their databases and/or online resources remain available for at least 2 years following publication of their paper in DATABASE.

Databases must be freely available to all via the web, not require any login or registration and not be password-protected.

### Deposition of sequence and structural data

Sequence information, co-ordinates used to create molecular models described in a manuscript, and structural data must be submitted in electronic form, prior to acceptance, to the appropriate database for release no later than the date of publication of the corresponding article in DATABASE. Deposition numbers and/or accession numbers provided by the database should be included in the manuscript and entered into the relevant boxes during online submission or communicated to the Editor handling the manuscript as soon as received. In cases where there may be no appropriate database, authors must make their data available on request. Atomic co-ordinates may be included in the publication as supplementary material. Manuscripts will not be published until DATABASE is in receipt of the deposition number.

For papers reporting novel nucleic acid sequences
Nucleic acid sequence information must be deposited with one of the three major collaborative databases (EMBL/GenBank/DDBJ). For sequences obtained from a public or private web site, it is the author's responsibility to ensure that any sequence used within the manuscript is deposited before publication. It is necessary to submit sequences to one database only since data are exchanged between EMBL, GenBank and DDBJ on a daily basis. New sequence names and their accession numbers should be listed at the beginning of the Methods section to aid searches by readers. In order to allow new methods of data search, DATABASE encourages authors to cite GenBank accession numbers when referring to established sequences within their manuscript.

For papers reporting novel three-dimensional structures
Atomic co-ordinates and the related experimental data (structure factor amplitudes/intensities and/or NMR restraints) must be deposited with a database. Authors must agree to release the atomic coordinates and experimental data when the associated article is published.
The Cambridge Crystallographic Data Centre (CCDC) is appropriate for deposition of data on nucleosides, nucleotides and other small molecules.
A member site of the Worldwide Protein Data Bank: RCSB PDB, MSD-EBI), PDBj , or BMRB is appropriate for deposition of data on proteins determined by X-ray crystallography and for all macromolecules determined by NMR methods.
The Nucleic Acid Database (NDB) is appropriate for atomic co-ordinate and structure factor data for crystal structures of nucleic acids.

For papers reporting novel protein sequences
Protein sequences, which have been determined by direct sequencing of the protein, must be submitted to UniProt (i.e. TrEMBL, Swiss-Prot and PIR) using the interactive submission tool SPIN. Please note that they do not provide accession numbers, IN ADVANCE, for protein sequences that are the result of translation of nucleic acid sequences. These translations will forwarded automatically from the nucleotide sequence databases (EMBL/GebBank/DDBJ) and assigned UniProt accession numbers on incorporation into UniProt. Results from characterization experiments should also be submitted to UniProt: for novel sequences, these should be included with the sequence submission. Existing UniProt entries should also be updated. This can include information such as function, subcellular location, subunit, etc.

For papers reporting new ChIP-Seq data
New ChIP-Seq data must be deposited in GEO, with accession numbers at or before acceptance for publication.

Microarray data
All authors must comply with the 'Minimal Information About a Microarray Experiment' (MIAME) guidelines published by the Microarray Gene Expression Data Society, which can be found at here. NAR also requires submission of microarray data to the GEO or ArrayExpress) databases, with accession numbers at or before acceptance for publication.

Quantitative PCR
Authors are encouraged to follow the 'Minimal Information for Publication of Quantitative Real-Time PCR Experiments' (MIQE) guidelines, if appropriate. The guidelines are published by the Real-Time PCR Data Markup Language Consortium and can be found here

### Material Disclaimer

The opinions expressed in Database are those of the authors and contributors, and do not necessarily reflect those of the editors, the editorial board, Oxford University Press or the organization to which the authors are affiliated.

### General

Papers must be clearly written in English. Papers should be submitted in Word, although we do allow Latex files if necessary.

Authors should avoid the use of language or slang which is not in keeping with the academic and professional style of the Journal. Authors should not also seek to use the Journal as a vehicle for marketing any specific product or service.

Authors should follow the conventions of the CSE Style Manual (Council of Science Editors, Reston, VA, 2006). Chemical Abstracts and its indices should be followed for chemical names. For biochemical terminology the recommendations issued by the IUPAC-IUB Commission on Biochemical Nomenclature, as given in Biochemical Nomenclature and Related Documents, published in 1992 by the Biochemical Society, UK should be followed. For enzymes, the recommended name assigned by the IUPAC-IUB Committee on Biochemical Nomenclature, 1978, as given in Enzyme Nomenclature, published by Academic Press, New York, 1992 should be used. Wherever possible, the recommended SI units should be used. Genotypes should be italicised. Phenotypes should not be italicised. For bacterial agents nomenclature Demerec.

Section headings within the manuscript (e.g. Methods, Discussion, Future directions) are at the authors' discretion.

Please list the Database URL clearly on the line beneath the abstract, in the format: 'Database URL: ......'

### References

These should be cited in the text by sequential number only, in order of appearance, and listed numerically in the References section. Online references should be cited as in example 5, below. Please see examples 6 and 7 for papers that have been published online in more than one version. The initial version of a paper published in this way can be cited by the Digital Object Identifier (doi) but, if available, the reference should also include the citation of the final version. Authors should check all references carefully, and in particular ensure that all references in the Reference section are cited in the text. Note that multiple references or page spans under one number are not allowed. Personal communications, unpublished results, manuscripts submitted or in preparation, statistical packages, computer programs and web sites should be cited in the text only, NOT included in the References section.

All references must be cited in the text and should be denoted using numbers in parentheses before the punctuation., e.g. (1, 3–5). At the start of a sentence the authors can be named, e.g. Shadforth et al. (15)...

Style in the References section should be as follows. Journal names should be abbreviated in the style of Chemical Abstracts. NOTE THAT FULL TITLES OF JOURNAL ARTICLES MUST BE PROVIDED.

1. Schmitt,E., Panvert,M., Blanquet,S. and Mechulam,Y. (1995) Transition state stabilisation by the 'high' motif of class I aminoacyl-tRNA synthetases: the case of Escherichia coli methionyl-tRNA synthetase. Nucleic Acids Res., 23, 4793-4798.

2. Huynh,T.V., Young,R.A. and Davies,R.W. (1988) Constructing and screening cDNA libraries in lambdagt10 and lambdagt11. In Glover,D.M. (ed.), DNA Cloning - A Practical Approach. IRL Press, Oxford, Vol. I, pp. 49-78.

3. Maniatis,T., Fritsch,E.F. and Sambrook,J. (1982) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

4. Burnett,R.C. (1993) EMBL accession no. X52486.

5. Capaldi,S., Getts,R.C. and Jayasena,S.D. (2000) Signal amplification through nucleotide extension and excision on a dendritic DNA platform. Nucleic Acids Res., 28, e21.

6. Qiao,D., Chen,W., Stratagoules,E. and Martinez,J. (March 10, 2000) Bile acid-induced activation of activator protein-1 requires both extracellular signal-regulated kinase and protein kinase C signaling. J. Biol. Chem., 10.1074/jbc.M908890199

7. Qiao,D., Chen,W., Stratagoules,E. and Martinez,J. (2000) Bile acid-induced activation of activator protein-1 requires both extracellular signal-regulated kinase and protein kinase C signaling. J. Biol. Chem., 275, 15090-15098. First published on May 19, 2000, 10.1074/jbc.M908890199

8. Bernhagen,J., Elkine,B., Geiger,G., Tovar,G. and Vitzthum,F. (1999) Patent DE-198198889.2-44; PCT/WO/EP/99/03047.

If there are four or more authors, then use the first three followed by et al.
Papers in preparation or submitted for publication should not be in the reference list.

Authors are asked to ensure the references to named people and/or organisations are accurate and without libellous implications.

### Crossref Funding Data Registry

In order to meet your funding requirements authors are required to name their funding sources, or state if there are none, during the submission process. For further information on this process or to find out more about the CHORUS initiative please click here.

Details of all funding sources for the work in question should be given in a separate section entitled 'Funding'. This should appear before the 'Acknowledgements' section.

The following rules should be followed:

The sentence should begin: ‘This work was supported by …’

The full official funding agency name should be given, i.e. ‘the National Cancer Institute at the National Institutes of Health’ or simply 'National Institutes of Health' not ‘NCI' (one of the 27 subinstitutions) or 'NCI at NIH’ (full RIN-approved list of UK funding agencies)

Grant numbers should be complete and accurate and provided in brackets as follows: ‘[grant number ABX CDXXXXXX]’

Multiple grant numbers should be separated by a comma as follows: ‘[grant numbers ABX CDXXXXXX, EFX GHXXXXXX]’

Agencies should be separated by a semi-colon (plus ‘and’ before the last funding agency)

Where individuals need to be specified for certain sources of funding the following text should be added after the relevant agency or grant number 'to [author initials]'

An example is given here: ‘This work was supported by the National Institutes of Health [P50 CA098252 and CA118790 to R.B.S.R.]
and the Alcohol & Education Research Council [HFY GR667789].

Oxford Journals will deposit all NIH-funded articles in PubMed? Central. See http://www.oxfordjournals.org/for_authors/repositories.html for details. Authors must ensure that manuscripts are clearly indicated as NIH-funded using the guidelines above.

### Figures

You are required to submit high-resolution images, preferably with your initial submission but no later than revision stage. Electronic images (figures and schemes) must be at a minimum resolution of 600 d.p.i. for line drawings (black and white) and 300 d.p.i. for colour or greyscale. Colour figures must be supplied in CMYK not RGB colours. Please ensure that the prepared electronic image files print at a legible size (with lettering of at least 2 mm).

A number of different file formats are acceptable, including: PowerPoint (.ppt), Tagged Image File Format (.tif), Encapsulated PostScript (.eps), Joint Photographic Experts Group (.jpg), Graphics Interchange Format (.gif), Adobe Illustrator (.ai) (please save your files in Illustrator's EPS format), Portable Network Graphics (.png), Microsoft Word (.doc), Rich Text Format (.rtf), and Excel (.xls) but not Portable Document Format (PDF).
Please ensure that the figure is clearly labelled with its figure number.

Third-Party Content in Open Access papers

If you will be publishing your paper under an Open Access licence but it contains material for which you do not have Open Access re-use permissions, please state this clearly by supplying the following credit line alongside the material:

Title of content
Author, Original publication, year of original publication, by permission of [rights holder]

This image/content is not covered by the terms of the Creative Commons licence of this publication. For permission to reuse, please contact the rights holder.

### Internet screen dumps

Internet screen dumps should be provided electronically as BITMAP, with a minimum acceptable resolution of 300 dpi. Their approximate final positions should be indicated in the margin of the text. Authors should be aware that graphics supplied with low resolution are not guaranteed to reproduce well and should be avoided whenever possible.

### Tables

Tables should be submitted in electronic form, preferably in MS Word or Excel. Tables should be referred to in the text and numbered consecutively. They should be supplied separately from the main body of the text, with their approximate final positions indicated in the text. Each column should have a short heading and, where appropriate, the units should be stated. Table legends should describe the content and should be understood independently from the text. Data columns should be right-hand aligned, or aligned by decimal place, where appropriate; data should be sorted where possible. Footnotes should be included on the same pages as the tables themselves and should be used to explain any abbreviations used in the table and denote them by letter. Footnotes should also be used to quote sources.

### Proofs

All manuscripts will undergo some editorial modification, so it is important to check proofs carefully. PDF page proofs will be sent via e-mail to the corresponding author for checking. To avoid delays in publication, proofs should be checked and returned within 48 hours. Corrections should be returned by annotated PDF, e-mail or fax. Extensive changes to the text may be charged to the author.

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