Submit your manuscript using EndNote 5 or higher and save £30 on the standard BioMed Central Article Processing Charge

Advantages of submitting a manuscript formatted with EndNote 5 or higher to BioMed Central

BioMed Central has collaborated closely with ISI ResearchSoft, the makers of EndNote, to make full use of the structured reference information maintained by the latest versions of EndNote.

This means that when an author submits an EndNote 5+ formatted document, BioMed Central is able to automatically extract the structured information within the manuscript's reference list. Therefore, we can automatically process the reference list into our online full-text format, eliminating the possibility of errors creeping in to the final version of your article. This will make preparation of the full-text version of your article faster, and reduce the need for you to check the proofs for errors in the reference list.

The style file for EndNote that conforms to the BioMed Central reference style is freely available to download:

Special offer - save £30 on the BioMed Central Article Processing Charge

Authors whose articles are accepted for publication by BioMed Central are required to pay a £950 (€1215, US$1870) Article Processing Charge to cover the cost of markup, publication and long term online hosting.

As a special offer to authors using EndNote 5 or higher, for a limited period, a £30 discount on the Article Processing Charge will automatically be granted if the article is accepted for publication. For users of previous versions of EndNote, this means that upgrading to the latest version of EndNote could pay for itself after just 2 publications with BioMed Central.

Note that researchers from BioMed Central member organizations do not have to pay any article processing charges (APC) directly and those from supporter member organizations receive a 15% discount on APCs, but we still encourage you to submit a manuscript formatted with EndNote, as this will speed its processing time, and reduce the need for reference proof-reading.

In order to obtain this discount, you should upload the manuscript file containing your EndNote-formatted bibliography as a .doc file. Please ensure you do not convert to another format (eg RTF or PDF). On upload, the discount will be automatically granted and you will receive a confirmation on-screen and by e-mail.

About EndNote

EndNote is the most widely-used bibliographic software package amongst biological and medical researchers. Its features include:

• Easy to use interface for collecting your references and images
• Tight integration with Microsoft Word, including a 'Cite While You Write' toolbar in Word for inserting citations and figures in your manuscript
• Ability to directly query and download references from online databases such as PubMed
• Over 60 built-in BioMed Central article templates for constructing your manuscript
• Automatic formatting of bibliographies into any one of over 1100 standard formats—find new and updated styles at www.endnote.com

• Available for Windows and Mac OS X

  
  

How to obtain the latest version of EndNote

You can purchase EndNote (or upgrade to the latest version) using the links below:

Note: If you select the downloadable version, you will not only save money, but you can start using EndNote today!

Extraction help guide for EndNote users

Help Guide:

Please be aware that this help guide was designed for PC EndNote X and other versions of the software may vary.

Please also be aware that complicated issues may take a long time to fix, and it may be in your interests to simply remove the inserted programming by removing the field codes.
(We have noted where issues may take a long time to fix.)

Please select one of the options below to see our instructions for correcting common extraction problems.

1. One or more references are missing from my extracted reference list.
2. The data within the references are not displayed correctly.
3. I have too many references in my extracted reference list.
4. My references are mixed up/out of sequence.
5. I don't have EndNote, what do I do now?

Please note that we can only advise in cases where the manuscript has been accepted in principle, and is receiving the final formatting requests. If you have not received the e-mail with the subject "Your manuscript is acceptable for publication in principle" please ignore the extracted references until this has been sent to you.

Note also, that this information is specifically relevant to journals that utilise the data from the EndNote reference software.

Authors submitting to:
BMC Biology,
BMC Medicine,
Arthritis Research and Therapy,
Genome Biology,
Neural Development,
Journal of Biology,
Critical Care and
Breast Cancer Research
are advised to remove the field codes prior to submitting their article (these articles are copyedited).

For instructions see Remove field codes.

Step 1. Determine the first reference from the reference list that has not extracted.
Step 2. Find the first time this reference is cited within the manuscript text.
Step 3. Place your mouse cursor over the citation, grey 'highlighting' should appear.
(Ensure that your settings are correct for this. To change to the correct setting please go to Tools> Options> View and select field shading 'when selected')

This is what the grey box should look like [1] within the text.
First, we need to determine if the field code is truncated or not.
Right click your mouse, and select "Toggle field code".

1. All that appears is " { ADDIN EN.CITE } ". The field code is truncated.
2. Upon 'toggling' a list of information appears. There is no truncation.
3. There is no grey 'highlighting', what do I do?

Please note that references that appear in figures or within additional files should be cited in the legend to the corresponding file, and through the EndNote program.

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If all that appears is " { ADDIN EN.CITE } ", the field code has been truncated.

What this means is the document could not handle the volume of information that was inserted within the citation.
This issue is particularly common to Mac users with EndNote version X.
(Correcting this issue can often take a long time. You may instead wish to remove the field codes.)

1. There are a group of citations within this highlighted section.
2. An individual citation is being truncated.

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The main reason that a group of references become 'truncated' is that the field code cannot handle the large volume of information that is inserted at this point. The software automatically triggers the truncation to avoid the program crashing.

One quick solution to this issue is to select and insert each reference individually.

If you choose to do this, please ensure that you move your cursor to a position out-with the grey 'highlighted' field code.

(Ensure that your settings are correct to view the shading. To change to the correct setting please go to Tools> Options> View and select field shading 'when selected')

e.g. This text is an example of how to insert citations [1] [Insert next citation here] individually to avoid truncation.
This will result in the citations appearing as [1][2][3][4] etc.
We will correct the aesthetics of the citations for the final production.
Please check when inserting these citations that the field code for each is not truncated.

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If an individual citation is being truncated, you will need to do the following.
(Note that this can be very time consuming and you are advised to simply remove the field codes.)

First, to avoid changing the content of your main library, we advise that you create a new library that is specific to this document. To create the document specific library please do the following
(This will only work if you have the original library on your computer)

1. Open the document.
2. Select from the menu-bar [Tools> EndNote> Export travelling library].
3. Select 'A new EndNote library' from the 'Export library to' pop-up box.
4. Call this new library "ETL" and save it to your desktop.
5. This new library should contain all the citations from your manuscript.

What you should do next is remove any non-valid information from the references within the ETL library (specifically from the references with truncated field codes). Information that often clogs up a field code, and is not relevant to the reference list, includes Keywords, attached PDFs, and abstracts. You should remove as much as possible. (For notes on what information is required for the bibliography, please see the reference styles of BMC Biology instructions for authors)

Once you have removed all non-relevant information from this new library, please follow these steps.

1. Remove the truncated citation from the manuscript (ensure all citations of this reference are removed).
2. Select the citation from your new reduced-content ETL library.
3. Insert this citation in all locations where previous citation existed.
4. Check that the field code is not truncated within this new citation.

If this does not work, please send a copy of your ETL library to references@biomedcentral.com

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If you have toggled the field code and it does not appear to be truncated there are a number of issues that can cause the citation to not be extracted correctly.

Please choose one of the following options

1. The grey field code contains a single reference e.g. [1].
2. The grey field code contains more than one reference e.g. [1, 3-6, 8].

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If a single citation, with a full field code, is not extracting from the manuscript then it is likely that the citation has been removed as a duplicate.

Check to see if the reference has been duplicated elsewhere in the reference list.

1. The reference has been duplicated.
2. The reference is not duplicated.

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Duplicated EndNote citations can be caused by a number of different problems.

You will need to find the origin of the duplication.
1. Check that the reference has not been duplicated in your library.
If it has been, delete the duplicate (make sure that you check the citation details, to ensure that you keep the accurate entry).

Then re-insert your reference within the manuscript.
Re-format your bibliography (you can do this by selecting Tools> EndNote> Format bibliography) and confirm that the duplication has been removed.
(Ensure that you format your bibliography in the BioMed Central style, using the BMC style file).

2. If the reference is not duplicated in your library, has your manuscript been generated with multiple libraries?
If so, then the details of the reference may be different in the different libraries.

Delete all the citations to this reference.
Re-insert from an individual library.
Re-format your bibliography (You can do this by selecting Tools> EndNote> Format bibliography) and confirm that the duplication has been removed.
(Ensure that you format your bibliography in the BioMed Central style, using the BMC style file).

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Our extraction system is very sensitive to duplicated references, and will also sometimes make mistakes.
Unfortunately, every so often it will assume that a reference has been duplicated, even though it has not. This is particularly common if the titles of two articles are identical.
The second reference will be recognised as a duplicate and will not be extracted.

If you believe this is what you are experiencing please contact references@biomedcentral.com.

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First, ensure that you have formatted your bibliography.

You can do this by selecting Tools> EndNote> Format bibliography.
(Ensure that you format your bibliography in the BioMed Central style, using the BMC style file).

If you notice that the reference is removed from the formatted bibliography and the citation, (for example [1-3, 5, 10] is formatted to [1-3, 5]) then the reference has not been inserted into the manuscript correctly.

Please re-insert the reference through EndNote.

Always format your bibliography before resubmitting, to ensure that the data that is displayed is the data that has been inserted.

If upon formatting, the citation remains within the field code, then you should check that your reference is not duplicated elsewhere in the reference list.

1. The reference has been duplicated.
2. The reference is not duplicated.

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If a citation does not have grey highlighting, it is most likely that this reference was inserted manually, rather than through the EndNote software.

If you have the relevant reference within your library, please remove the manually inserted citation (throughout your manuscript if it appears more than once) and insert the citation through your EndNote software.

If you do not have the relevant reference within your library, and you cannot find it within your resource databases, you can insert the reference manually within EndNote.

Within EndNote you can select from the menu 'Reference> New Reference'.
It should be noted that incorrect manual insertion of a reference within your database can lead to duplication errors (if you enter the details more than once), display errors (within the extracted references), and a list of other unforeseen complications.

Please enter the least amount of relevant information, and select the relevant article type.
Once your reference has been added to the library, please re-insert it within the manuscript, in the place(s) it appeared before.

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Please select the option that best suits the issues you have encountered.

1. There is a problem with the Author listing
2. The italicisation/bolding/underlining has been removed
3. Data is missing, such as page numbers or the URL

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Any issue regarding the display of information within your article will most likely be caused by the incorrect entry of details into your EndNote library. Please check that the details entered into your library are correct.

See Entering references in the EndNote manual.
The basic rules for entering author names are as follows.

1. Author names should be separated by a hard return, such that each author is represented on a new line

2. Author names should be entered in the following format

3. Corporate authors should be entered as follows (note that a comma should be entered at the end only.)

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Only version X (and subsequent versions) of EndNote can support 'Tags' such as italics within the title field.

Earlier versions of EndNote do not support this information in the extractable content.
Please do not attempt to correct this yourself.

Once the manuscript has been accepted and published in preliminary form, we will send you the full text to quality check before it is published. Please at this point check that the extraction process has not removed any font styles or character effects.

The full text will contain the extracted reference list.

You are advised at this point to highlight any italicisation (or other character manipulation) that has been lost in the extraction process. For further information contact references

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The most common reason for data loss during extraction is related to the 'reference type' option in your EndNote library.

We will only extract the relevant information from each reference type to display in the reference list.

For example if a website, within your library, has been assigned as type "Research article", we will not extract the URL (http://www.website.com) as this data is not recognised as valid within our style guide for displaying "Research articles".
To see what information is required for each reference type, please refer to our instructions for authors reference types of BMC Biology.

Another common reason for data loss during extraction is that the data is not entered into the library correctly in the first place.

Please ensure that, if you are entering data into your EndNote library, you place the data in the most relevant field.
If neither of these options applies in your case, please contact references@biomedcentral.com

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If there are too many references in the extracted reference list, then the most likely problem is that the extra references have been added to the manuscript, and have then not been removed correctly.

To view references that have been inserted into the manuscript, please format your bibliography (you can do this by selecting Tools> EndNote> Format bibliography). Note that you must have your library open to be able to do this.
(Ensure that you format your bibliography in the BioMed Central style, using the BMC style file).

If the reference list is modified, and the new reference list contains the full list of references that have been extracted, you should remove the incorrectly inserted citations.

To delete a citation you should delete the number, and the grey highlighted box ('field code') that it is contained within. e.g. " [24] ". (Ensure that your settings are correct to view field codes. To change to the correct setting please go to Tools> Options> View and select field shading 'when selected')
Ensure that you delete all instances of incorrectly inserted citations throughout your manuscript.

Please note that if you are removing a single citation from within a 'field code' that contains a number of citations (for example deleting citation 4 from [2, 4, 27-30], you should delete the entire field code ( " [2, 4, 27-30] ") and then re-insert only the correct references.

If you have formatted your bibliography, and the changes are not reflected in your reference list, please contact references@biomedcentral.com

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We extract references in ascending numerical sequence, as they appear within the text.

If the citations appear in a different order in the extracted reference list, please firstly format your bibliography (You can do this by selecting Tools> EndNote> Format bibliography).
Note that you must have your library open to be able to do this.
(Ensure that you format your bibliography in the BioMed Central style, using the BMC style file)

If the reference list in the manuscript is changed, and now appears as it does in the extracted reference list, please read through your citations carefully to ensure that the citations are in the correct place and order.

Often a reference has been removed from the grey highlighted citation ('field code') manually, but all the data within this 'field code' is preserved, and therefore extracted.

Please note that if you are removing a single citation from within a 'field code' that contains a number of citations (for example deleting citation 4 from [2, 4, 27-30], you should delete the entire field code ( " [2, 4, 27-30] ") and then re-insert only the correct references.

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If a colleague has entered references into your manuscript using EndNote, and/or the extracted reference list is incorrect/incomplete, we advise that you resubmit your manuscript in Rich Text Format (RTF).

Simply select 'File> Save as' from the menu bar then change the option in the save as type field to 'Rich text format'.

Resubmitting in RTF will bypass the extraction process but should make no difference to the manuscript content.

Please note that by re-submitting in this way you will not be eligible for the discount associated with uploading your manuscript with EndNote inserted references. This discount will be removed and the higher Article Processing Charge will be payable.

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