OJVR Referee Forms

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Online Journal of Bioinformatics

REFEREE FORM

Please complete and remit to Editorial office, Online Journal of Bioinformatics

Author(s): Maleki-Dizaji S et al
ID Number: (QF2107T)
Title: A systematic approach to understanding E Coli…….and Published Abstracts.

The Editorial board must ensure that the OJB publishes only papers which are scientifically sound. To achieve this objective, the referees are requested to assist the Editors by making an assessment of a paper submitted for publication by:

(a) Writing a report as described in GENERAL STATEMENTS (Below),
(b} Check the boxes shown below under 1. and 2. ( YES or NO) [N.B.A "NO" assessment must be supported by specific comment in the report.
(c) Make a recommendation under 3.

The Editor-in-Chief would appreciate hearing from any referee who feels that he/she will be unable to review a manuscript within four weeks.

1. CRITERIA FOR JUDGEMENT (Mark "Yes" or "No").

General statements

What is this work about? A data driven methodology to identify metabolic pathways and regulons in a set of differentially expressed genes is described. Once

found, they can be used to retrieve abstracts relating to each metabolic pathway. The authors describe the use of a web based program “Taverna” to achieve this.

Does it add any value to current knowledge (in this area of bioinformatics)? The current example may add some information relating to E coli responses to oxygen.

The statement that certain aspects of E coli physiology may be revealed that could not be shown by conventional analysis, should be supported by examples.

Is it innovative? The example used herein (oxygen/Ecoli) may be novel, however some of the work has been described previously (ie taverna).

Yes/No answers.

Is the work scientifically sound? Y

Is the work an original contribution Y/N
Are the conclusions justified on the evidence presented?Y
Is the work free of major errors in fact, logic or technique? Y
Is the paper clearly and concisely written? Y
Do you consider that the data provided on the care and use of animals (See Instructions to Contributors) is sufficient to establish that the animals used in the experiments were well looked after, that care was taken to avoid distress, and that there was no unethical use of animals? NA

2. PRESENTATION (Mark "Yes" or "No").

Does the title clearly indicate the content of the paper? Y/N (see below)
Does the abstract convey the essence of the article? Y
Are all the tables essential? Y
Are the figures and drawings of good quality? N (see below)
Are the illustrations necessary for an understanding of the text? Y
Is the labelling adequate? Y

3. RECOMMENDATIONS(Mark one with an X)

Not suitable for publication in the OJB
Reassess after major changes
Reassess after suggested changes
Accept for publication with minor changes X
Accept for publication without changes

4. REPORT : TITLE Does the title need to be that long? Suggestion “Bioinformatic analysis of E Coli response to O2: from raw microarray data to pathways and published abstracts. ABSTRACT:NC, INTRODUCTION: Relative importance of E. Coli and Web services in this scheme is emphasized. Fig 1 boxes will have to be enlarged to view the information inside (unless OJB can do otherwise. METHODS: . The various methods to extract information are appropriately described/referenced especially using the prime example case study. RESULTS: Figure 2 will need improvement as the parts do not appear proportionate for example, part F (pie chart). Parts c, d e and f be shown sequentially and distinctly. DISCUSSION. The statements are justified by the methods and results. Publish with minor changes.

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