‼️Address BIOINF-2016-1672.R1

[Dr. Juan Miguel Cejuela]

Here are the Associate Editor's comments:

---

Here are the comments of the reviewers:

Reviewer: 1

Comments to the Author

I still think that the authors could had better explained some of the requests made by the reviewers:

• rsids: both reviewers asked for clarification about it, but the authors added an explanation in the "previous corpora" section. This should be in the "Introduction" section, where a detailed and clear description of ALL mutations types should be given.

• I still think that the methods should include a wokflow (a figure), as I asked in my previous review. It is poorly described in the paper only in text format. The workflow should also include which corpus was used for which step of the methods. This is still not clear to me as it is scattered throughout the paper.

• The authors says that they added details on the errors in section 3.4, but there is no such section. It seems it is in section 3.3, but numbers in the answers to the reviewers and in the text do not match: 70% versus 44%.

---

• Wait for Burkhard to confirm and send BIOINF-2016-1672.R2

[Dr. Juan Miguel Cejuela]

Whole decision letter:

From:
[e-mail]
To:
[e-mail]
CC:
[e-mail], [e-mail], [e-mail], [e-mail], [e-mail], [e-mail], [e-mail], [e-mail], [e-mail], [e-mail]
Subject:
BIOINF-2016-1672.R1 - Revision
Body:
23-Dec-2016
Manuscript ID: BIOINF-2016-1672.R1
Title: nala: text mining natural language mutation mentions

Dear Mr. Cejuela,

The reviews of your manuscript are now in hand. Most of the concerns have been addressed but the reviewer felt some were not adequately addressed (see below). I am therefore returning your original manuscript for revision in line with the editorial and reviewer comments which can be found at the foot of this e-mail.

Please submit your revised version through the Author Center by clicking on the purple button 'Click here to Submit a Revision' in the Bioinformatics ScholarOne Manuscripts web site (https://mc.manuscriptcentral.com/bioinformatics).

Please ensure that you use either mandatory template format which can be found at:-
http://www.oxfordjournals.org/bioinformatics/for_authors/submission_online.html

We ask that revisions are submitted within one month. The system will automatically remove the revision option if a revised paper has not been submitted within this time.

To facilitate the production process we ask that you upload the following revised manuscript files at the revision stage:

EITHER: (i) A .doc or .rtf file of the revised manuscript, with all tables, figures, schemes and equations inserted in the document.

OR: (ii) All necessary LaTeX files that will be required by the typesetter (including bioinfo.cls, bib, .bst and .ps files) along with postscript and PDF versions of the complete manuscript.

Please can you mark-up the changes made after revision by using the track changes function or highlighting these in red text.

Please upload your final clean version of supplementary materials with your revised submission. This should be in pdf or Word format, not LaTex.

I would also ask that you prepare an accompanying letter explaining exactly how each of the major points raised by the reviewers was addressed. This can be done either in a file uploaded alongside your revised manuscript as a Response to Reviewers file or through the Author Center where you can enter your responses directly in the appropriate box during the revision submission.

Please note that if you decide that you would like your figures printed in colour a charge of £350 per colour figure applies. If appropriate, you will be invoiced after your paper has been published in the print journal.

As a reminder, please also note the following excess page charges. You will be notified of any excess page charges when you receive your proofs:

For Original articles - £100/$165 per excess page (over 7 published pages)
For Discovery notes - £100/$165 per excess page (over 4 published pages)
For Application notes - £100/$165 per excess page (over 2 published pages)

On behalf of the Executive Editor, I want to thank you for selecting Bioinformatics to present your work.

Best regards,
Alison Hutchins
Bioinformatics

Here are the Associate Editor's comments:

---

Here are the comments of the reviewers:

Reviewer: 1

Comments to the Author

I still think that the authors could had better explained some of the requests made by the reviewers:

• rsids: both reviewers asked for clarification about it, but the authors added an explanation in the "previous corpora" section. This should be in the "Introduction" section, where a detailed and clear description of ALL mutations types should be given.

• I still think that the methods should include a wokflow (a figure), as I asked in my previous review. It is poorly described in the paper only in text format. The workflow should also include which corpus was used for which step of the methods. This is still not clear to me as it is scattered throughout the paper.

• The authors says that they added details on the errors in section 3.4, but there is no such section. It seems it is in section 3.3, but numbers in the answers to the reviewers and in the text do not match: 70% versus 44%.

---

Date Sent:
23-Dec-2016