Integration of GIS and Remote Sensing – Publish or PerishMichael Schaepman, Jan Clevers, Ron van Lammerenv. 2.3 / June 2007, with contributions from Wouter Gerritsma (WUR Library)

Outline of the Course

Publish and/or Perish? A scientific approach to publishing

Scientific Paper Form Function

Reviewing a Paper Impact References Tools

Assignment

Publish or Perish? Scientific productivity, in the form of intellectual contributions to the advancement of science and ultimately communicated in written form, is commonly considered to be of fundamental importance to scientific career advancement.

Publish or Perish?

However Judging research at its merits is becoming

increasingly important. Or how do you judge ‘soft’ contributions such as

• published software (under OpenSource)• motions submitted to a parliament• participating in the public debate (an interview in 3FM, a

discussion in NOVA, an article in NRC Handelsblad)• impacting on policy makers (drafting the FP7 work

programmes)• producing visualizations (maps, animations, etc.)

The Paper

Scientists regard only one type of communication as acceptable currency for the advancement of scientific knowledge: a "peer-reviewed" paper in a scientific journal. "Peer review" means that, before publication, the paper is evaluated by other scientists, usually people who work in the same area of research and who are able to evaluate the reported techniques, logic, and the relationship to other work in the field.

Peer-reviewed papers always follow a form and do have – within this form – a dedicated function

The Paper – Form

IMRAD – Introduction, Methods, Results, and Discussion

The Paper – IMRAD IPart Function Should Should not

Titletells what the paper is about

Describe contents clearly and precisely; provide keywords

Include wasted words (‘studies on’, investigation of’); use abbreviations and jargon

Abstract

summarizes the results of the paper, and sometimes the interpretation

State main objectives; describe methods; summarize important results; state major conclusions and significance

Be too long (+300 words); include references; include information that is not in the paper

Introduction

sets the framework of the paper: why it is important or interesting

Describe the problem investigated; review and summarize relevant research; briefly describe the experiment or design

Vaguely relate to other work; cite exhaustive lists of references

The Paper – IMRAD IIPart Function Should Should not

Materials and Methods

gives details of materials used and of experimental methods

Explain the scientific procedure you used; describe what materials and equipment you used; explain the steps you took in your experiment

Use presence tense for what you did; use qualitative statements rather than quantitative ones; mix results with prodcedures

Results

reports what the researchers actually found; data may be in graphs, tables, or photographs

Briefly describe experiment without details of the Methods section; report main results, representative (most common) and best case (ideal)

Repeat tabular data of the experiment; include an interpretation and conclusion

Discussion

discusses two sets of issues: (1) the adequacy of the experiments themselves and (2) the relationship of the results to other work in the field

Summarize most important findings; describe and explain agreements, contradictions, and exceptions; suggest implications; extend findings

Be too general; ignore outliers or deviations in your results; speculate on new experiments that cannot be tested in the near future

The Paper – Function of Parts I

Part Function Critical reading Relaxed reading

Titletells what the paper is about

allows decision of whether to read more

allows decision of whether to read more

Authors

tells who did the work and who assumes responsibility for it

not particularly important

important: some authors are consistently interesting, no matter what their subject is

Abstract

summarizes the results of the paper, and sometimes the interpretation

important: most salient facts in one place

not as important as the frame of the paper in the introduction

Introduction

sets the framework of the paper: why it is important or interesting

not important: the reader should be able to place the paper in context

the most important part of the paper

The Paper – Function of Parts IIPart Function Critical reading Relaxed reading

Materials and Methods

gives details of materials used and of experimental methods

worth detailed attention; tells exactly how experiments were done; the place to look for weaknesses in approach

important only when methods are not standard or paper is otherwise unbelievable; usually obscure to someone not working in the field

Results

reports what the researchers actually found; data may be in graphs, tables, or photographs

ultimately the most important section of the paper: "just the facts"

important: a careful reader will evaluate whether the results actually support the stated hypothesis and if they also support alternative views or raise additional questions

Discussion

discusses two sets of issues: (1) the adequacy of the experiments themselves and (2) the relationship of the results to other work in the field

not so important: the reader should evaluate the data and place them in context

the best window into the author's context, revealing the level of confidence in the conclusions

Bibliographylists other papers relevant to experiments or conclusions

shows where to find details of methods and context

source of additional information

The Paper - Review

‘Good’ journals are always having two independent reviewers looking at your paper – the published paper is then considered to be ‘peer-reviewed’

A reviewer needs to identify, summarize, and evaluate the ideas and information the author has presented. In other words, you will be examining another person's thoughts on a topic from your point of view.

Your stand must go beyond your “gut reaction” to the work and be based on your knowledge

The goal is to make a few key points about the paper, not to discuss everything the authors write

The Paper – Status

In preparation You are working on the manuscript and have already an idea

where to submit the paper Submitted

You have formally submitted the paper to a review process and the reviewers are being assigned

In review You work on comments of reviewers, knowing that the paper will

finally be accepted Accepted, in print

The paper has formally been accepted by the editor and is awaiting print

On-line, preprint, draft final Almost final versions are available on on-line sites or through

other media Printed

Your paper has appeared in a print medium

The Paper – How good is the contribution?

Impact Factor References/Citations Tools

The Impact Factor

The impact factor is a measure of the frequency with which the “average article” in a journal has been cited in a particular year or period. The annual impact factor is a ratio between citations and recent citable items published. Thus, the impact factor of a journal is calculated by dividing the number of current year citations to the source items published in that journal during the previous two years A = total cites in 2004 B = 2004 cites to articles published in 2002-03 (this is a subset

of A) C = number of articles published in 2002-03 D = B/C = 2004 impact factor

Journal Citation Reports

Impact factor Quality of journals, not

of articles Immediacy Index Cited half life

0 2 4 6 8 10

Years after publication

Cita

tions

/yea

rCited half-life

50% citations 50% citations

31

Immediacy index Window

Impact Factor Window

Citation Tools

Citation products available at WUR (subscription costs, not free) Journal Citation Reports (JCR) Web of Science (WOS) (=Science Citation Index) Essential Science Indicators (ESI)

Scopus (‘Google of literature search’)

Freely available web services Google Scholar (scholar.google.com) Citeseer (citeseer.ist.psu.edu) Smealsearch (smealsearch2.psu.edu)

Impact factor

Measure for the quality of journals“… it is also used for assessment of the quality of

individual papers, scientists and departments. For the latter a scientific basis is lacking, as we will demonstrate in this contribution” (Opthof, 1997)

Opthof, T. (1997). Sense and nonsense about the impact factor. Cardiovascular Research 33(1): 1-7. http://dx.doi.org/10.1016/S0008-6363(96)00215-5

50 % of articles generate nearly 90% af all citations

Seglen, P. O. (1997). Why the impact factor of journals should not be used for evaluating research. BMJ 314(7079): 497-502. http://bmj.bmjjournals.com/cgi/content/full/314/7079/497

Impact Factor – Web of Science

Science Citation Index (SCI) is the gold standard for bibliometrics and scientometrics

Wageningen UR library has a subscription on SCI through Web of Science Limited no. of journals (ca. 8.700) Limited search capabilities Errors in data (~ ca. 5%) No interpretation of results

Coverage 1945->

Impact Factor (Example from JCR)Which are the Journals (n=5876/5907/5969/6088) with the highest Impact Factor in Journal 2002 2003 2004 2005Annu Rev Immunol 1- 54.45 1- 52.28 1 – 52.431 2 – 47.400Annu Rev Biochem 2- 36.28 2- 37.64 11 – 31.538 4 – 33.456CA-Cancer J Clin 3- 32.88 7- 33.05 2 – 44.515 1 – 49.794New Engl J Med 4- 31.73 5- 34.83 3 – 38.570 3 – 44.016Nature 5- 30.43 8- 30.97 9 – 32.182 11 – 29.273Science 6- 28.95 11- 29.16 10 – 31.853 6 – 30.972Nat Med 7- 28.74 9- 30.55 12 – 31.223 12 – 28.878Nat Immunol 8- 27.86 12- 28.18 14 – 27.586 14 – 27.011Physiol Rev 3- 36.83 5 – 33.918 13 – 28.721Nat Rev Mol Cell Bio 4- 35.04 6 – 33.170 9 – 29.852Nat Rev Cancer 4 – 36.557 5 – 31.694Rev Mod Phys 7 – 32.771 8 – 30.254

Impact Factor – Example Which are the Remote Sensing Journals

(n=11/11/10) with the highest Impact Factor in

2003 2004 2005Trend

Remote Sens Environ 2.641 1 – 3.185 1 – 2.833 IEEE T Geosci Remote 1.867 3 – 1.467 3 – 1.627 Int J. Remote Sens 0.990 6 – 1.128 7 – 0.925 J Geodesy 0.983 8 – 0.732 4 – 1.205 Photogramm Eng Rem S 0.857 2 – 1.574 5 – 1.000 Can J Remote Sens 0.593 5 – 1.284 8 – 0.862 Photogramm Rec 0.519 9 – 0.615 9 – 0.594 ISPRS J Photogramm 0.472 4 – 1.317 2 – 1.674 Surv Rev 10 – 0.137

Sorry – no Journal Citation Reports on GIS in ISI …http://isi4.isiknowledge.com

Impact Factor – Example

Which are the Geo Journals (n=128/128/129) with the highest Impact Factor?

Journal 2003 2004 2005 Earth-Sci Rev 4.014 2 – 4.543 1 – 4.581 Annu Rev Earth Pl Sci 3.618 1 – 5.188 2 – 4.500 Am J. Sci 3.607 14 – 2.259 17 – 2.170 Global Biogeochem Cy 3.383 5 – 2.864 4 – 3.373 Quaternary Sci Rev 3.181 3 – 3.323 6 – 2.950 Paleoceanography 3.048 4 – 3.018 5 – 3.233 J Geophys Res 2.992 6 – 2.839 7 – 2.784 Geostandard Newslet 3 – 4.200

New developments

The H-Index The h-index is an index that quantifies scientific

productivity of a scientist based on the number of papers published by the scientist and on how often these papers are cited in papers written by other scientists. It can also apply to the productivity of a group of scientists, such as a department or university or country. The index was suggested in 2005 by Jorge E. Hirsch and is sometimes called the Hirsch index or Hirsch number. The h-index is currently not a widely accepted measure of scientific productivity, but only one of a number of possible indices.

Hirsch-Number

References/Citations

References/Citations

A written description of a source of information that enables one to identify and, thereby, search for and locate a cited source. The elements of the description (author, title, etc.) follow a prescribed order and format, as determined by a particular manual of style.

What do I need to know about them? Citations provide the details you need to identify different types of

information resources (e.g., books, articles, laws and regulations, statistical data, web sites, etc.) used in academic writing. They can help you judge the quality of the material you read.

Citations contain the information necessary to locate and obtain sources for your assignments and research papers.

Citations present a clear model for describing any type of information resource. Understanding the basic parts of a citation is essential to using them wherever you find them.

You will need to write citations for the sources you use in your own research.

Pointers Link Lists

http://www.grs.wur.nl/UK/Links/ Software to manage references

EndNote http://www.endnote.com/ http://library.wur.nl/endnote/

Internet sites that allow to search references http://www.sciencedirect.com http://isiknowledge.com http://www.scopus.com http://www.scirus.com http://scholar.google.com http://citeseer.ist.psu.edu http://smealsearch2.psu.edu

Searchable libraries http://library.wur.nl/desktop/ http://www.loc.gov/

Assignment

Follow a full peer-review journal publishing process using our own contributions

Read all the documents involved in the process Set up 4 thematic groups

Writing team (elements of style) Review team (positive critics) Presentation team (informers) Positioning team (science background)

Discuss the processes at a final review meeting

Goals of Assignment

Understand the process of publishing and positioning of papers

Train to read others papers, to try to understand them and do a review.

Train the authors (and colleagues) to take advice from others

To learn how to write (and how not to write) from others

To spread the scientific content of a paper

The Writing Team

Read the Journal Overview document Read the Instructions for Authors Read the Guidelines for Reviewers Read the final published paper Identify the writing style of the paper Summarize the most important elements of the paper

according to the IMRAD style Prepare a presentation that outlines the structure Comment on how good the paper follows the structure

of IMRAD and the requirements of the journal Draw a conclusion what you think about the style of

the paper

The Review Team

Read the Journal Overview document Read the Instructions for Authors Read the first submission Read the Guidelines for Reviewers Read the comments to authors, and the authors replies Read the final published paper Create a presentation that summarizes the review process

(what happened, how long did it take, were all requests fulfilled)

Comment on how you see the process and what your opinion about the procedures are

Draw a conclusion what you think about this process and give an outlook

The Presentation Team

Read the Journal Overview document Read the Instructions for Authors Read the Guidelines for Reviewers Read the final published paper Review the presentation Search in the scientific literature for more work on

this matter (papers, presentations) Compile a presentation using the existing material

and present the paper the way you think you would present it

Draw a conclusion on the paper and give an outlook for further work

The Positioning Team

Read the Journal Overview document Read the Instructions for Authors Read the Guidelines for Reviewers Read the final published paper Search for all contributions of the authors to the scientific world Try to find all relevant information about the authors Compile a presentation with a scientific overview of all the

contributions of the authors (what have they published so far? Make use of keywords)

Analyze the references of the paper (and group them in categories) Try to identify missing references in two groups (new findings and

missed ones (make sure you respect the publication date of the paper))

Make a judgment on the position of the authors (relevance, position, interest, quality, etc.) and of the paper

The Paper: an example of a form

Hengl, T. and Gould M. (2002) Rules of Thumb for Writing Research Articles, In the public domain: http://www.pfos.hr/~hengl/RT/Hengl_RT_0902.pdf

Two Papers to Review

A. Kötz B, Schaepman M, Morsdorf F, Bowyer P, Itten K, Allgöwer B (2004). Radiative Transfer Modeling within a Heterogeneous Canopy for Estimation of Forest Fire Fuel Properties, Remote Sens. Environ., 92, 332-344.

B. Louwsma J, Zlatanova S, van Lammeren R, van Oosterom P (2006). Specifying and Implementing Constraints in GIS – with Examples from a Geo-Virtual Reality System, GeoInformatica, 10, 529-548.

Available Documents – RSE Journal Description of the journal Remote Sensing of Environment

(RSE) RSE, instructions for authors First version submitted to RSE Guidelines to the RSE reviewers Feedback of the RSE reviewers Comments and actions of authors on feedback RSE reviewers Second version submitted to RSE Comments and actions of authors on feedback RSE reviewers,

2nd round Final version of the RSE submitted paper Revised form 21.5.2003, Accepted 24.5.2004, printed version

(30.8.2004) Lecture about the background of the article: Radiative transfer

modeling within a heterogeneous canopy for estimation of fire fuel properties

Endnote library about spectroscopy of forest

Available Documents – GeIn Journal Description of the GeoInformatica journal (GeIn) Website of the GeoInformatica journal GeIn, instructions for authors First version submitted to GeIn Feedback of the GeIn reviewers Comments and actions of authors on feedback

GeIn reviewers Final version of the GeIn submitted paper Revised form 14.9.2005, Accepted 29.3.2006,

printed version (30.8.2004) Autocarto lecture about the article Zip-file with articles Cockcroft and Dutch GIN

article