editorial process

The Editorial Process

ThomasLemberger

Scientific publishing

The publication of scientific information is intended to move science forward. More specifically, the act of publishing is a quid pro quo in which authors receive credit and acknowledgment in exchange for disclosure of their scientific findings.Source: “Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences”,.Board on Life Sciences, The National Academies Press (2003)

disclose findings

credit

move science forward

reviewers&

editors

readers

authors

authors

authorsreaders

authorsreaders

reviewers

authorsreaders

reviewerseditors

authorsreaders

reviewerseditors

scientists

move science forward

critical evaluation

critical evaluation

editorial process

The editorial process

editorialrejection

review

reject revise

reject accept

time

EMBO Publications

quality

quality

community

R Aebersold

GM Church

L Hood

E Liu

P Bork

Julie AhringerCharles AuffrayEwan BirneyTom BlundellThomas S. DeisboeckJan EllenbergMichael ElowitzAlan FershtStan FieldsMark GersteinFrank HolstegeSung Hou KimHiroaki KitanoDoron LancetAndrew J. LinkStephen OliverJeremy NicholsonBernhard PalssonRama RanganathanUwe SauerLuis SerranoLucy ShapiroPamela SilverMichael SnyderJanet ThorntonMasaru TomitaMarc VidalHans V. WesterhoffLothar WillmitzerJohn Yates

Senior Editors Advisory Board

EMBO Editor

R Aebersold

GM Church

L Hood

E Liu

P Bork

Julie AhringerCharles AuffrayEwan BirneyTom BlundellThomas S. DeisboeckJan EllenbergMichael ElowitzAlan FershtStan FieldsMark GersteinFrank HolstegeSung Hou KimHiroaki KitanoDoron LancetAndrew J. LinkStephen OliverJeremy NicholsonBernhard PalssonRama RanganathanUwe SauerLuis SerranoLucy ShapiroPamela SilverMichael SnyderJanet ThorntonMasaru TomitaMarc VidalHans V. WesterhoffLothar WillmitzerJohn Yates

Senior Editors Advisory Board

EMBO Editor

Scope & general policies

To review or not to review...

editorialrejection

review

reject revise

reject accept

time

To review or not to review...

EMBO editors read the entire manuscript

Check existing literature

Decision on a balance of multiple factors:• Scope• Conceptual advance• Mechanistic, functional, system-level biological insights• Utility of methods, dataset, resource• Completeness of the analysis

In case of doubt...R Aebersold

GM Church

L Hood

E Liu

P Bork

Julie AhringerCharles AuffrayEwan BirneyTom BlundellThomas S. DeisboeckJan EllenbergMichael ElowitzAlan FershtStan FieldsMark GersteinFrank HolstegeSung Hou KimHiroaki KitanoDoron LancetAndrew J. LinkStephen OliverJeremy NicholsonBernhard PalssonRama RanganathanUwe SauerLuis SerranoLucy ShapiroPamela SilverMichael SnyderJanet ThorntonMasaru TomitaMarc VidalHans V. WesterhoffLothar WillmitzerJohn Yates

Senior Editors Advisory Board

EMBO Editor

To review or not to review...

editorialrejection

review

reject revise

reject accept

time

Initial editorial decision

To review or not to review...

editorialrejection

review

reject revise

reject accept

time

Peer-review

Referees are invited base on:

• Balance of expertise• Reputation as researcher• Reputation as reviewer• No conflict of interest (positive or negative)

3 (4) reviewers / manuscript

Invite, invite, invite...1. Too busy 2. Too busy; Sorry I can't agree to review this time -- I'm currently working on

reviews for Nature Cell Biology and Nature Methods.3. Too busy; Sorry for the delay in responding. I have so many review assignments

at present that are overdue, I just can't take on another (even though this one looks to be of high interest to me). My colleague … would be a good one for this..

4. Travelling; I would love to review this, but unfortunately am busy traveling and with conferences all of July

5. Travelling6. Too busy 7. Too busy; I am unfortunately unable to review the manuscript due to lack of time

in the month ahead. 8. Lack of interest; I am not convinced by those p-values; also what is the control

data set.9. Conflict of interest; I am just beginning a collaborative effort in which X is a

member. It is a borderline conflict, but I think I should probably recuse myself

10. Too busy; Sorry 11. Too busy; Most sorry - we're currently releasing a new central database and

trying to meet the deadline for an invited review for one of your sister journals. So we're totally swamped, and people are soon leaving for summer holidays

12. Conflict of interest 13. Too busy

Top reviewers are very busy...1. Conflict of interest; Thanks for this invitation, but I actually have a similar

paper in the second round of review right now at Nat Biotech!!!!

2. Too busy; I have several other reviews due this month as well as organization for the upcoming XX conference

3. Too busy; Sorry I cannot oblige you this time. I myself have been buried under 5 outstanding reviews over here, and already there is no way I will get all of them done in time. I will suggest some alternates below. Please don't hesitate to try again in the future- this type of article is usually something I would be able to review if I weren't so overwhelmed!

4. Too busy; Sorry I cannot review this article this time. I have just accepted two reviews for Nature Biotech and another for Cell.

5. Too busy; I would like to help out, but unfortunately I am also incapacitated at the moment by NIH grant reviews (I am on a study section that meets next week and I have just spent the entire last week reviewing grants).

6. Too busy; I would love to oblige this time, but I must confess I am already over-committed with outstanding reviews for Science and Genome Research.

8. Accepted

9. Too busy; I'm currently reviewing articles for Nature Cell Bio and (I thought) one for you guys? Let me check my records but I think I have an outstanding one for MSB. If not, I can probably do this if I can have until mid July.

10. Too busy; Sorry I can't agree to review this time -- I'm currently working on reviews for Nature Cell Biology and Nature Methods.

Why should I review?Source: “Peer Review Survey 2009: Preliminary Findings”, Sense About Science

http://www.senseaboutscience.org.uk

16%

33%

34%

30%

46%

85%

69%

72%

90%

n=3597

% agree

To review or not to review...

editorialrejection

review

reject revise

reject accept

time

Post-review decision

• Best reviewers are clear, critical & constructive

• Editor can take some distance with reports to integrate and combine evaluations

• Not always based on a majority call

• Whenever possible, main points are highlighted in decision letter to delineate scope of necessary revisions

Post-revision review

editorialrejection

review

reject revise

reject accept

time

Post-review decision

• Single round of major revision

• Avoid progressive ‘erosion’ of reviewers

• Not always possible to reach perfect unanimity

• Main points addressed?

• If there are new issues after revision, do they arise from new experiments, new analysis, tests?

manuscripts

published paper

author author author author

reader reader reader readerreader

Does all this come for free?

10

1-2

>1000

author

$

author-pay

reader-pay

openaccess

subscriptionThe EMBO Journal

MolecularSystemsBiology

What is a ‘paper’?

• Text: text mining• Figures: visual only• Tables: a minority• Supp Info: large-scale

datasets, instrument output, etc...

1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 430 60 90 120 30 60 90 120 30 60 90 120 30 60 90 120

1 (R)-3-Hydroxybutanoate [b-hydroxybutyrate]0.9574 1.0891 0.8703 0.7733 0.9097 1.1547 0.9083 0.7923 0.9093 1.0285 1.2487 1.1114 1.1175 1.2663 1.3734 1.25072 (S)-Lactate [Lactate] 0.9096 0.7994 0.8136 0.8305 0.8779 0.8053 0.916 1.0573 2.6013 0.951 0.8998 0.8763 1.0782 0.9977 1.0655 0.98163 (S)-Malate [Malate] 0.93 0.9433 0.81 0.7767 0.9188 0.7949 0.9658 1.1197 0.8724 0.9712 0.8807 1.0617 1.089 0.9288 0.9039 0.89684 2-Oxoglutarate/Adipate 0.62 0.5952 0.6096 0.5456 1.0446 1.0669 1.1798 1.1872 0.9437 0.9117 0.7324 0.8566 1.0678 1.0864 1.0169 1.17295 3-Hydroxyanthranilate 1.17 0.7451 0.7431 0.5158 1.5547 1.2 1.384 1.3013 1.6317 1.3148 0.6091 0.8683 2.1286 2.0536 1.5357 2.04646 3-Phospho-D-glycerate0.7042 0.6246 0.7407 1.2203 0.9319 1.0611 0.7628 1.3914 0.9795 1.0205 0.5644 0.5692 0.9426 1.4115 0.7368 0.97617 4-Hydroxy-L-proline 0.9185 1.1692 1.0108 0.68 0.9761 1.1119 0.9031 1.1673 0.7453 0.8162 1.0342 0.7889 0.989 0.9821 1.1157 1.01938 4-Pyridoxate 0.9947 0.8989 0.766 0.8138 1.119 0.9762 0.8452 1.0893 1.7607 1.5726 0.906 1.188 1.3262 1.4823 0.9716 1.0789 Acetylcholine 0.881 1 0.7917 0.7202 0.828 0.9299 0.7707 1.293 0.9406 1.0137 1.0868 1.1416 0.8286 0.8537 0.8412 1.001

10 ADP 0.7591 0.4903 1.1671 0.9234 1.4236 1.6739 1.179 1.4323 NaN 1.4078 1.1456 1.233 1.0579 1.6281 1.719 1.586811 Allantoin 0.8613 0.579 0.7516 1.1048 1.0581 0.794 1.1549 0.9454 0.884 1.2747 0.9573 1.0904 0.9916 1.0472 0.796 0.784212 AMP 0.9546 0.7611 1.601 NaN 0.976 1.715 0.9143 1.0076 0.2266 1.1613 1.1774 1.2984 1.1439 1.7554 1.5396 1.381313 Anthranilate 2.5362 0.6908 1.1932 0.9469 1.2112 1.3147 1.444 0.9224 1.3132 1.0517 0.7356 1.1523 1.1739 1.5901 0.8758 0.869614 ATP 1.3619 0.4733 1.6667 1.6 1.442 2.029 1.2971 1.5797 0.2087 1.2531 1.3029 0.9585 0.6401 1.2749 1.1682 0.763115 Betaine 0.8775 0.7668 0.8221 0.8281 1.0616 1.0725 1.1486 1.0616 0.8547 1.0068 0.973 1.0372 1.259 1.2518 1.1799 1.122316 Bilirubin 0.35 0.2194 0.4177 0.2968 0.8333 1.1256 1.4155 1.2995 0.6516 0.4121 0.5944 0.4639 2.0476 1.8571 2.4476 1.390517 Choline 1.0227 1.0567 0.9858 1.0255 1.0385 0.9675 1.1538 1.1893 0.756 1.0714 1.0952 1.119 1.2013 1.1782 1.4488 1.46218 cis-Aconitate 0.8673 0.7915 0.7725 0.6588 0.9506 0.8025 0.9198 0.9568 0.9179 0.9627 0.9627 1.1493 0.8095 0.7399 0.7436 0.725319 Citrate/Isocitrate 0.9154 0.7331 0.7262 0.7254 0.933 0.8021 0.9701 1.1443 1.0995 1.0429 1.0995 1.1832 0.8551 0.8696 0.8768 0.884120 Creatine 0.828 1.0276 0.7332 0.6648 1.0336 1.3195 0.9444 0.9909 0.4972 0.6875 0.7955 0.6648 1.0473 1.0675 1.2185 1.158121 Creatinine 0.9214 1.0131 1.0568 0.8996 1.0036 0.8873 0.9636 1.0618 0.8143 1.0179 1.0857 1.0929 1.0617 0.9295 1.0352 1.004422 D-Fructose 6-phosphate/D-Glucose 1-phosphate/alpha-D-Glucose 6-phosphate/D-Fructose 1-phosphate0.9541 0.8936 0.8936 1.1376 0.9047 1.0025 1.0407 1.0635 1.056 0.968 0.7392 1.16 0.8217 1.0853 0.8062 0.852723 D-Glucuronate 1.9293 1.7475 1.548 1.5429 1.0145 0.8365 0.9522 1.178 1.1761 0.9468 1.4899 1.5009 1.16 0.696 1.03 0.98124 D-Ribose 5-phosphate/D-Ribulose 5-phosphate0.8806 0.9457 1.0605 1.0109 0.5219 1.2492 0.8906 0.9546 0.6543 0.6349 0.693 0.6736 0.8127 0.5184 0.4314 0.576425 dUMP 0.4283 0.6549 0.4867 0.9513 1.3873 1.7254 1.4366 1.7254 0.6681 1.1983 0.6121 0.6121 0.5796 1.1837 0.6857 0.738826 Fumarate/Maleate 1.0586 0.943 0.8536 0.7858 0.9925 1.1932 0.9681 1.0544 0.6474 0.8284 1.1825 1.0796 0.9479 0.9023 0.776 0.928427 GDP 0.1755 0.1054 0.2109 0.2367 0.9112 1.5877 0.6902 1.2938 NaN 1.7594 1.4332 1.5187 0.7581 1.2248 1.1426 1.21428 Geranyl diphosphate 0.8532 1.2903 0.9984 0.9371 1.0719 0.8658 0.7828 1.2572 1 1.0888 1.221 1.8223 0.9423 0.8613 1 0.733329 Glucose 0.8889 0.8875 0.9181 0.9069 0.9867 0.9684 1.0466 1.0133 2.5 1.0099 0.9929 0.9602 1.0595 1.0455 1.049 1.005330 Glycerol 2.0242 1.1722 1.2281 1.4366 1.6504 1.9336 1.385 1.6637 0.8679 1.0635 0.8045 0.904 1.646 2.0248 1.4596 1.521731 Glycerone phosphate 0.5037 0.3424 0.5955 0.4715 1.0759 1.2828 0.9793 1.1172 0.8256 1.4535 0.7791 1.4244 0.9955 1.009 1.009 0.761332 Glycochenodeoxycholate [GCDCA]0.8671 0.2595 0.4557 0.2637 3.3122 0.6244 0.9463 1.1122 2.5942 3.459 3.3925 1.8359 0.6871 0.6274 0.533 0.443433 Glycocholate [GCA] 0.653 0.4302 0.3969 0.2561 2.9144 0.6898 0.7406 1.0535 1.3495 2.4078 2.2913 1.4466 0.6293 0.6638 0.875 0.7534 GTP 0.1553 NaN NaN NaN 1.7146 0.9281 1.2832 0.8562 NaN NaN NaN NaN 1.5458 1.5915 1.7711 1.316935 Hippurate [Hippuric acid]1.5271 1.5039 1.3023 1.3178 0.8323 0.8925 0.9658 0.9023 1.2768 1.7119 1.7966 2.0169 1.3195 1.5602 2.3496 1.691736 Homogentisate 0.979 0.989 0.8586 1.2044 0.939 0.9685 0.9898 0.9268 0.9858 1.022 1.0129 0.9664 1.0884 0.8858 1.0991 1.008637 Hypoxanthine 0.8892 0.8 0.959 0.853 1.0468 1.0906 0.886 0.9971 0.7113 0.419 0.5528 0.6743 0.8681 0.8364 0.5778 1.097638 IMP 1.4475 0.8011 0.9227 NaN 1.2058 1.1801 1.045 0.8039 NaN NaN NaN NaN 0.8084 1.3484 1.324 1.717839 Inosine 1.2565 1.2823 1.4891 0.7952 0.9226 0.3839 0.3452 0.7679 0.795 0.6765 1.1321 0.9408 1.2161 1.5734 1.6814 2.002840 L-2-Aminoadipate 1.2434 0.9883 1.0223 0.6833 0.738 0.5727 0.6397 0.876 4.4956 0.862 1.1062 0.7292 0.6348 0.2441 0.4492 0.408241 Lactose 0.7654 0.3923 0.6692 0.9577 1.0478 0.9952 0.933 1.067 0.3545 1.6349 1.2963 1.4868 0.8257 1.2599 1.4709 0.969442 L-Alanine [Alanine] 1.1979 1.0417 0.6979 0.8073 0.8344 1.0764 0.8981 1.1975 1.0155 0.7764 0.7733 0.7019 1.0308 0.9384 0.8219 0.856243 L-Arginine [Arginine] 0.9884 0.8763 1.0462 1.0636 1.0337 0.9274 1.1579 1.0263 0.8783 1.1913 1.0783 1.1913 1.065 1.0487 0.931 0.982444 L-Asparagine 0.9509 1.2638 1.0061 0.8282 0.9499 1 0.885 1.1091 0.8879 0.8937 1.0402 1.1207 1.3375 1.1583 1.3875 1.120845 L-Aspartate 0.7892 0.9058 0.8475 0.8744 1.3618 1.1809 0.9699 0.9347 0.6886 0.9561 1.364 1.0219 0.8067 1.0084 1.0448 0.946846 L-Citrulline [Citrulline]1.1478 1.3768 1.1626 1.3005 0.9224 1.0099 0.9076 0.9736 0.8754 0.8408 0.9619 0.9377 0.9633 1.0831 1.0513 1.085647 L-Cysteine 0.953 1.0268 0.906 1.0067 0.8766 1.2143 0.8507 0.9286 0.8814 0.8475 1.2966 0.7195 0.7198 0.6259 0.5638 0.53148 Leucine/Isoleucine 0.8542 0.8333 0.825 0.8083 0.9911 0.9554 1.0446 1 0.976 0.916 0.892 0.892 1.012 0.9701 0.9461 0.922249 L-Glutamate 0.5201 0.718 0.8228 0.7206 1.0726 1.223 0.924 0.7044 0.3814 0.5746 0.912 0.89 0.7253 1.0988 1.1821 1.120450 L-Glutamine 1.035 1.275 1.39 0.965 1.0135 1.0707 0.9529 1.0572 0.8515 1.1965 1.3843 1.2751 0.9182 0.9364 1.1727 1.227351 L-Histidine [Histidine] 1.0901 0.9518 1.2013 1.2034 1.0471 0.961 1.1266 1.0649 0.804 1.1565 1.1349 1.2968 1.068 1.0536 0.9711 1.078452 L-Homocysteine 0.6415 0.5598 0.6981 0.5535 0.8788 0.9636 0.9212 0.7818 0.6103 0.8639 0.7887 0.723 1.0209 0.9121 1.205 1.129753 L-Kynurenine 0.7545 0.9012 0.8802 0.7605 1.2116 0.9217 1.0696 1.1246 0.9587 0.7345 0.7286 0.708 1.0288 1.0576 1.2446 1.280654 L-Lysine [Lysine] 0.9393 0.8645 0.8738 0.9065 0.9526 0.981 0.9905 1.0616 0.861 0.9035 0.9073 0.8803 1 0.9769 0.9196 0.863455 L-Methionine [Methionine]0.9913 0.9113 0.9099 0.8736 1.031 1.0295 1.118 1.0959 0.8512 0.8833 0.9133 0.8308 1.0077 0.9196 0.9768 0.98356 L-Ornithine [Ornithine]0.9028 0.8259 0.915 0.9251 0.9152 0.8457 0.8891 0.8804 0.6661 0.7195 0.7022 0.7367 0.8656 0.7688 0.8333 0.865657 L-Phenylalanine [Phenylalanine]0.94 0.8825 0.9825 0.9325 0.9667 1.0089 1.0532 1.0399 2.4412 0.9602 0.953 0.9458 1.031 0.9595 0.9167 0.902458 L-Proline 0.9023 0.7895 0.782 0.812 1.011 0.999 1.041 1.021 0.7986 0.8472 0.7917 0.8194 1.0468 1.0064 0.8937 0.850259 L-Serine 0.938 0.8761 0.7072 0.5674 0.9899 1.2487 1 1.2571 0.7781 0.7337 0.7426 0.753 0.9187 0.7978 1.156 1.057160 L-Threonine 0.9954 1.023 0.788 0.7465 0.9423 1.3606 0.9471 1.1298 0.817 0.6949 0.8881 0.6848 0.9796 0.9728 1.1156 1.122461 L-Tryptophan 0.9125 0.86 0.9175 0.8375 0.9581 1.0419 1.0335 0.9777 2.3356 0.9093 0.8095 0.8481 0.8584 0.8097 0.8894 0.734562 L-Tyrosine [Tyrosine] 1.0272 0.8231 0.864 0.7619 1.0144 1.0576 1.0288 1.1079 2.137 0.963 1.0593 0.9667 0.7968 0.732 0.856 0.779263 Methylmalonate 1.0502 0.8566 0.9068 0.9606 0.0513 0.9237 1.0339 1.1653 0.6115 0.8057 0.8503 0.0564 1.2751 1.0409 0.974 0.921964 N-(L-Arginino)succinate0.9228 1.2154 0.9421 0.9035 1.082 1.0656 1.2678 0.9672 0.687 0.8044 0.5819 1.0122 1.4737 1.0186 1.2477 0.5294

Data transparencyFrom bench to website

Data transparencyFrom bench to website

•Data ‘transparency’

•Re-visualization

•Re-analysis

•Data integration

•Data ‘searchability’

•Data ‘transparency’

•Re-visualization

•Re-analysis

•Data integration

•Data ‘searchability’

•Data ‘transparency’

•Re-visualization

•Re-analysis

•Data integration

•Data ‘searchability’

Editor?

excitement

science moves forward

broad

critical

reading

molecular biology

molecular biologysystems