seminars 2004 information class 05/11/04 joan rosell 30.11.2004 class 3 – article writing

Seminars 2004 Information Class 05/11/04

Joan Rosell

30.11.2004

Class 3 – Article Writing


Acknowledgements

Some of the slides are from

Christophe Bengoa & Ciara K. O’ Sullivan

José Luís Toca


Please participate

questions

clarification

anytime

on any subject

Don’t worry about interrupting the class


Today’s focus and expectations

Article Writing

versus

Bycicle Riding


Thus...

Crafting and article is mostly an ART,

in a small part, a SCIENCE.

Our focus today is

the small SCIENCE part


Agenda

1. “Initial barrier” matters (planning)

2. Drafting the article (executing)

3. Today’s homework


We will try to:

Review most important points Review decision criteria (so you know what to

do, when) Provide simple, clear useful take-home

messages on article writing and reviewing Time-proven techniques, rules-of-thumb Provide a glimpse into ethical issues


Outside our scope are...

Questions of style (class 2) Abstract writing (Class 2) Research organization and planning (Classes 1

and 2) Publication strategy Submitting process (Class 4) Reviewing process (Class 4) In-depth discussion on ethics issues


Agenda





I. INITIAL BARRIER MATTERS

decision to write

defining the story

initial author list

choosing the journal

other matters


decision to write

Intellectual property (IP) is first “Patentable” is, if useful and new

Keep secret?

Patent?

Publish in journal?

Must patent* before publishing (EU- EPO)Must patent* before 1 yr from publishing (USPTO)Must patent* in country of invention

*should say: “submit a patent application”, “registrar una solicitud de patente”


decision to write

Often we ask: Do I have enough material to publish? Should I wait?

Rule of thumb: You do if... Your results provide an answer to a well defined and relevant

question Your work has scientific rigor (scientific method):

• Methods and Results have been survived your rigurous criticism• Results have enough critical mass, i.e., they fully support the

conclusions

Note that, Decision to publish comes after understanding the “question” and the

“conclusion” In other words, goes hand-in-hand with “defining your story”


defining the story

Your Story is publishable when: A relevant question/problem statement Your method allows to research this question Results provide an unambiguous answer to the question Conclusions (answer) are supported by your results, and

other published material.

Your decision to write may precede complete termination of the data analysis

Self criticism while executing the research will help you define your story


initial author list

Who should be an author? Satisfy all:

Has made an original contribution to the article Can defend the main thesis of the article

An author may not: Understand all of the details involved in generating the results Have spent a lot of time on it

An author should: Have made a substantial contribution (what is “substantial”?) Approve of the paper’s contents (read and agree) Take resposibility of at least part of the paper’s contents Authorize being included as an author

Coordinator should choose authorship criteria AND apply it equally

Other contributors should be noted in the “Acknowledgements” section


initial author list

Authorship is an ethical matter

credit of authorship carries assumption of responsibility for and accountability of the work being published

See for example,

(UCSD+VCU) Responsible Conduct of Research internet course:

http://ethics.ucsd.edu/courses/integrity/assignments/authorship.html


choosing the journal

This has been reviewed in other classes, however...

Choosing has become an optimization process :

impact factor versus probability of success

• Read the scope of a candidate journal (internet)• Look for similar published papers• Ask people who’ve published there


other matters

When there is a deadline Approach crafting paper as a Project (see class 2) Realize the importance of

• Communication between partners• Getting all partners involved early on• Your leadership in getting everyone to responding

(questions)


Agenda





II. DRAFTING THE ARTICLE

structure of a research article

writing styles (class 1)

what’s in each section (except abstract)

plagiarism

figures

a few computer tools

other recommendations


structure of a research article

• Title

• Authors’ names and

affiliation

• Abstract, keywords

• Introduction (3)

• Material and methods (1)

• Results (2)

• Discussion (3)

• Conclusions (4)

• Acknowledgements

• References

• Annexes

Slide from Christophe Bengoa & Ciara K. O’ Sullivan

Some journals request discussions to be in the same sections as results, or as conclusions


…writing stile

- Title: short and simple- Abstract: past tense and passive voice, concise, no citations,

no tables, no graphics- Introduction: present tense and past tense for literature

review- Methodology: past tense, take care about units, variables (SI)- Results: past tense,- Conclusions & Discussion: present tense (past tense if you

relate to results), allows scientific speculation- References: depends on journal but author/editors must

be included

This slide is from José Luís Toca (Class 1)


title

The title should inform accurately about the content of the manuscript without ambiguities.

Most of information retrieval services, browsers or data bases use titles to elaborate their indexes, so the more accurate and concise the better to its specific dissemination and retrieval.



a title should be....


InformativeSpecificAccurateConcise

Unambiguous


Keywords


Keywords have not to be “empty words” or express generalities.

When selecting keywords, imagine you are searching for your article in some database


introduction

“introduction” is to frame and present the question/s addressed in the research

“Science is the process of coming up with questions, not with answers” –Francesc Giralt, ETSEQ

• Importance of the topic of research

• bibliographic review

• use it to motivate your research objective

• state objective(s)

• include short descrition of the contents of the article (Sometimes)


introduction

• Set the scene: start broad then focus in

• Provide sufficient background and supporting information to make your case

• No need to include everything!!

• Introduce the relevant past work clearly and fairly

• Reference all statements! (see later)

• When an issue is in dispute, give both sides (you can favour one)

• Fully inform the reader of the current state-of-play Slide by Christophe Bengoa & Ciara K. O’ Sullivan


introduction end

• You have described the problem

• You have described the relevant scientific work up to the present

• Now: tell us what your paper will tackle!

• Give the aim of the study and a broad (brief) outline of the approach (eg method used)

• Don‘t give your results here (there is a whole section in the paper for that)!

Slide by Christophe Bengoa & Ciara K. O’ Sullivan


materials and methods

Usually best written first a general section up front is often useful Rule of thumb: those skilled in the art should

have enough information to reproduce your results.

Mention all methods/chemicals/instruments No need for detailed routine procedures Reference previously reported procedures Describe new methods carefully, clearly and

completely

Based on slides by Christophe Bengoa & Ciara K. O’ Sullivan


results

Results are objective information gathered from the research; are not discussion, interpretation, or conclusions

Answers to the objectives Expose the experiences logically sequenced Omit superfluous results, but… Do not remove those that invalidate the initial

hypothesis, or for any reason are unwanted (unethical, unscientific)



tables and figures Results

aim is to communicate to the reader discuss only the main points Don‘t just repeat in the text what is already

clear in the table/figure (dull and insulting!)



discussion

One should address:

a) what do the results mean?DATA INTERPRETATION

b) How do my results compare to previous work? COMPARING TO OTHER WORK

c) Points of speculation SPECULATION



a) DATA INTERPRETATION discussion

Avoid repeating results

Keep within your data!

Don‘t make statements not supported by your data set (or references)

Be rigorous. For ex., common oversights are: Correlation does not imply Causality

if “A implies B”, “No-B implies No-A”; (not “No-A implies No-B”)

Based on slide by Christophe Bengoa & Ciara K. O’ Sullivan


b) COMPARING TO OTHER WORK discussion

Present your data first, then compare with other data*

„Our results on the cyclisation of the brominated derivatives (Table 1) were in general agreement with those reported by Smith and Jones [21]. We can confirm that.................... Some interesting differences, however, were apparent. For example, .......................“

Always give due credit to other researchers – Involve all previous work that is relevant (ethics)


* As a general rule


c) SPECULATION discussion

Definitive statements require water-tight data

But you can also be speculative in parts

You must choose your words accordingly

Allows the author to introduce new unproven ideas which the current study has hinted at

Meant to stimulate discussion and interest in the topic

It doesn‘t matter if it turns out to be wrong!



criticism of others discussion

REAL EXAMPLE- Someone tried to reproduce the experiments of someone else, without success.

They reported:

“the experiments we have conducted under similar conditions to those of John Doe et al show that the regime obtained by these authors, in fact, corresponds to (everyone’s) standard mode and that variable V is not at all as small as indicated in their measurements”

Any thoughts?



The paragraph is internally inconsistent (if variable is different, the mode could not have been the same)

And, let’s look at the strong language:

“the experiments we have conducted under similar conditions to those of John Doe et al show that the regime obtained by these authors, in fact, corresponds to (everyone’s) standard mode and that variable V is not at all as small as indicated in their measurements”



Alternative:

“When trying to reproduce the results reported by John Doe et al. variable V became much greater than had been found by these authors. We conclude that our two regimes are different. Therefore our seemingly identical procedures must differ in some aspect that is critical in determining the regime of operation and remains unclarified”


discussion

Avoid trapping yourself:

Stay away from “it is impossible for … to have gotten their result….”, “it is impossible to …”, “our results represent the optimum best efficiency”

Instead: “we would expect a different result from the one they reported, because….”, “our results represent the best efficiency reported to date.”


conclusions

Summarize the implications of your research findings for policy makers, practitioners, or other researchers

Do not repeat yourself

Mention the limitations, if applicable

Identify potential for future research (as needed)



acknowledgements

• Opportunity to thank those not directly involved in the scientific study, but who have assisted in some way

• Technical support

• Provision/collection of samples

• Providing an analysis or identification

• Providing comments

• Providing money! (funding support)



references

• Reference to source where possible and appropriate

• Don‘t neglect old references

• Remember the primary functions of a reference:

(i) support your statement;

(ii) direct the reader to the source of relevant information



plagiarism

“Plagiarism is intellectual theft. It means use of the intellectual creations of another without proper attribution. Plagiarism may take two main forms, which are clearly related:

1. To steal or pass off as one's own the ideas or words, images, or other creative works of another.

2. To use a creative production without crediting the source, even if only minimal information is available to identify it for citation.

Credit must be given for every direct quotation, for paraphrasing or summarizing a work (in whole, or in part, in one's own words), and for information which is not common knowledge.”

(http://www.editor.uci.edu/catalogue/appx/appx.2.htm)



Figures


•Figure = figure caption+ axes+units+ content

• Figures are preferably to show tendencies more than particular (discrete) data.

• Avoid grids, lines, frames, and legends inside the drawing.

• Avoid figures with only a line.

• Use common symbols, clear and neat within the traces.


log vs liniar Figures

Semi-log (log Y vs X)

- exponential trend

Log-log (Log Y vs Log X)

- potential trend

- when showing many powers of 10

- when showing how two curves approach each other as you “move” along X-axis


some computer tools

Reference Manager software:

EndNote, Procite

Data representation and Statistics:

Excel (Low quality, limited possibilities)

SigmaPlot

Origin

Mathematics and Computation:

Mathematica

MathCad


other recommendations

Prepare a rough outline before writing

Write for others Avoid redundancy and repetition

Realize there is an art to crafting an article which will take some time to master sufficiently (accept other’s criticism’s)

Consider a style corrector (€)

Let a senior colleague review the article before sending it to the editor


copyright law

http://www.keytlaw.com/Copyrights/copyrightlaw.htm

http://www.legaldirectory.ws/Intellectual_Property/Copyright_Law/default.aspx

http://southernlibrarianship.icaap.org/content/v04n01/Diotalevi_r01.htm

http://europa.eu.int/comm/internal_market/copyright/index_en.htm


III. Today’s assignment

1. Read this short story describing a research process:http://www.bakerstreet221b.de/canon/sixn.htm (The 6 napoleons)

2. Go to http://pubs.acs.org/about.html, and find notice to authors for JACS*, needed to write a Communication on the research that is described in the short story.

3. But note that1. not all information in t he story should be used

2. there may be more than one way to defining the scope of the research. The important first thing is to make a decision about the scope, then write the article.

*select “J. Am. Chem. Soc.” Then select “Notice to authors” OR ACS Paragon System


Other supporting material

Rules of Thumb for Writing Research Articles:http://www.itc.nl/library/Papers/hengl_rules.pdf

Concise English grammar:The Elements of Style, by William Strunk Jr., E.B. White, Roger Angell (Pearson Higher Education, 1999)

Patent Help:Patent It Yourself, by David Pressman (Nolo, 2004)

Ethical guidelineshttp://pubs.acs.org/about.html (select Ethical Guidelines, 3 page PFD)Other:The Visual Display of Quantitative Information, by Edward R. Tufte (Graphics Press, 2001)

seminars 2004 information class 05/11/04 joan rosell 30.11.2004 class 3 – article writing

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