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Library news 2008 winter

Library and Information Newsletter Winter 2008 Content

• • • • • • • • • • • • •

News from Library department Big data in Nature Document Download Manager Endnote outputstyle new and updated Number of NIOO publ. 2008 Citation of NIOO Publications Size of paper and age researcher New Journals New On line resources Database barometer Book acquisitions Tips on how to use NIOO data archive Colophon

Karline Soetaert and Peter Herman, two NIOO-CEME scientist are well known for their workshops in R-programming. They now published a book about it. The R software is open source and can be downloaded by anyone.Together with the book the authors have written an introduction into R, that can be accessed from the Springer website. Interesting also for people from CL and CTE. On loan in all three libraries.

LIBRARY AND INFORMATION SERVICES DEPARTMENT • For general information, please contact our general library mailbox: • Online books by Elsevier (Science Direct) Since November 2008 we have an agreement with Elsevier that we can acquire their books as online books. Up till that date Elsevier wanted us to buy a larger amount of books together, not one by one. That is very unpractical because then we would have to wait before we can have access to the book (until we would have enough titles). From now on we can buy online books one by one at our convenience (and pay later in bulk). • Linkresolver (Linksource) http://infoserver/library/news/lis_news_winter08.cfm (1 of 12) [16-2-2009 9:50:48]

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A "link resolver", or "link-server", parses the elements of an OpenURL and provides links to appropriate services as identified by a library. An OpenURL is a URL that contains metadata. It is a piece of software that takes care of the linking from a database (Web of Science, Google Scholar) to the full text of the article on the publishers site. Our Linkresolver, called LINKSOURCE, is now fully operational. In Web of Science you can find the NIOOLINK button with every article. If we have full text access to this article a click on this button will lead you to the full text at once. If we do not have full text access to this article it will lead you to a request form, with which you can ask for a pdf. The journal titles that we can access full text are controlled by the A-to-Z list. You can find the list on the Ebsco host site. You might want to use the linksolver when you want to handle open URL's (for instance in Zotero or in Endnote) : http://linksource.

Web of Science's links button to full text " " can be found by some articles in Web of Science to which we have full text access. Unfortunately these Full Text buttons do not cover all the journal titles to which we have full text, neither to all the years of a journal title. For example In Web of Science you can see the full text button with the recent articles of Springer titles . But if you jump to theoldest volumes there is no full text button. The NIOOLINK button can lead you then to the full text. SEARCHING AND ALERTING • How to deal with huge quantities of data? BIG DATA: science in the petabyte era. A special feature issue in Nature was published in September 4, 2008. In the Editorial to that edition it says " Researchers need to be obliged to document and manage their data with as much professionalism as they devote to their experiments." An overview of the 10 years of Google and future idea's on seachring and storing data. But also on wikiomics: wiki's in biology research." "Community intelligence is a new concept for biology — and in broader society — and we certainly don't claim to have the final answer," • Open notebook Data on display: Two researchers explain why they're posting their experimental results online by Jean-Claude-Bradley and Cameron Neylon in Nature September 18, 2008. "The basic philosophy of open-notebook science is to have no insider information. Essentially all the information that is available to the [research] group is available to the rest of the world." • Document Download Manager in Science Direct From 1st September, the Document Download Manager will be available on ScienceDirect. It enables you to download multiple pdf files at a time. To be able to work with the Document Download manager you need to have Windows XP (it does not work with Vista). After you performed a search you can select all the pdf's that you wan tot download. Than click on the download PDF's button. The Document Download Manager will open en you can save the pdf's to the destination of your choice.

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WRITING & PUBLISHING • Endnote styles

Recently some new Endnotestyles have been released for the ISME journal and for Estuaries and Coasts. You can copy the Endnotestyles and put them in your styles foler on C:\Program Files\Endnote X\ . Because the Author parsing (Last name precedes First name) in the import from Wiley-Blackwell journals is not correct there is an update Import filter to use for the Wiley-Blackwell Journals. Download the import filter and put it in the Filter folder on C:\Program Files\Endnote X\. When importing from the Wiley platform choose the SAVE option and then import manually into Endnote by choosing the Wiley importfilter. • NIOO publications in 2008

In 2008 189 articles were publshed, which can be found in Web of Science. In our own collection we registered: 224 articles, refereed 5 articles, non refereed 12 articles in books, proceedings etc. 22 reports 3 books, chapters, editing books http://infoserver/library/news/lis_news_winter08.cfm (3 of 12) [16-2-2009 9:50:48]

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5 dissertations See also NIOO Publications New in 2008 or look into the alert from Web of Science CITATION TRACKING • Citations of NIOO publications published in 2007 & 2008

In Web of Science we can find in January 2009:189 articles published in 2008. These 189 articles have been cited 206 times, and from these 189 articles 76 have been cited at least once. Published in 2007 were 214 articles. Together for 2007 & 2008 makes 412 articles. These 412 articles have been cited 919 times. From these 412 articles 249 have cited at least once. The best cited articles for 2007 & 2008 are: Dunfield, PF; Yuryev, A; Senin, P; Smirnova, AV; Stott, MB; Hou, SB; Ly, B; Saw, JH; Zhou, ZM; Ren, Y; Wang, JM; Mountain, BW; Crowe, MA; Weatherby, TM; Bodelier, PLE; Liesack, W; Feng, L; Wang, L; Alam, M. 2007. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. NATURE 450 (7171): 879-U18. Times Cited: 19 Field, D.; Garrity, G.; Gray, T.; Morrison, N.; Selengut, J.; Sterk, P.; Tatusova, T.; Thomson, N.; Allen, M. J.; Angiuoli, S. V.; Ashburner, M.; Axelrod, N.; Baldauf, S.; Ballard, S.; Boore, J.; Cochrane, G.; Cole, J.; Dawyndt, P.; De Vos, P.; dePamphilis, C.; Edwards, R.; Faruque, N.; Feldman, R.; Gilbert, J.; Gilna, P.; Glockner, F. O.; Goldstein, P.; Guralnick, R.; Haft, D.; Hancock, D.; Hermjakob, H.; Hertz-Fowler, C.; Hugenholtz, P.; Joint, I.; Kagan, L.; Kane, M.; Kennedy, J.; Kowalchuk, G.; Kottmann, R.; Kolker, E.; Kravitz, S.; Kyrpides, N.; Leebens-Mack, J.; Lewis, S. E.; Li, K.; Lister, A. L.; Lord, P.; Maltsev, N.; Markowitz, V.; Martiny, J.; Methe, B.; Mizrachi, I.; Moxon, R.; Nelson, K.; Parkhill, J.; Proctor, L.; White, O.; Sansone, S. A.; Spiers, A.; Stevens, R.; Swift, P.; Taylor, C.; Tateno, Y.; Tett, A.; Turner, S.; Ussery, D.; Vaughan, B.; Ward, N.; Whetzel, T.; Gil, I. S.; Wilson, G.; Wipat, A. The minimum information about a genome sequence (MIGS) specification NATURE BIOTECHNOLOGY , 26 (5): 541-547 MAY 2008 Times Cited: 18 Cole, JJ; Prairie, YT; Caraco, NF; McDowell, WH; Tranvik, LJ; Striegl, RG; Duarte, CM; Kortelainen, P; Downing, JA; Middelburg, JJ; Melack, J. 2007. Plumbing the global carbon cycle: Integrating inland waters into the terrestrial carbon budget. ECOSYSTEMS 10 (1): 171-184. Times Cited: 16 • More citations for longer papers

"A longer paper gathers more citations: Brevity is not the secret to scientific success by Philip Ball in Nature September 18, 2008. In an analysis of 30,027 peer-reviewed papers published between 2000 and 2004 in top astronomy journals, astronomer Krzysztof Stanek of Ohio State University in Columbus found that the median number of citations increases with the length of the paper — from just 6 for papers of 2–3 pages to about 50 for 50-page papers.There is, however, a limit to the benefits of size: citations start to tail off when papers reach lengths of 80 pages or so, perhaps because fewer people have the stamina to read them." • More citations for older scientist

"Age is no barrier for productivity" says Geoff Brumfiel in Nature October 28,2008. He refers to a study from the University of Quebec in Montreal. "Citations, meanwhile, remained stable, suggesting that older researchers were both more prolific and more highly cited than their juniors." In this study Yves Gringas in ArXiv Physics and Society, wanted to find http://infoserver/library/news/lis_news_winter08.cfm (4 of 12) [16-2-2009 9:50:48]

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out if creativity and productivity decrease by age. JOURNALS List of online journals:

New: Annual Review of Marine Science 1.2009 Insect Conservation and Diversity 1.2008 - (comes together with Ecological Entomology) Limnologica 29.1999 -

Changes in JSTOR Archive (now from vol 1 no. 1): AMBIO: A Journal of the Human Environment 29.2000 - & JSTOR online archive 1.1972 - 33.2004 Economic Botany 56.2002 - & JSTOR online archive 1.1947 - 56.2002 Microbial Ecology 33.1997 - & archive 1.1974-32.1996 & JSTOR online archive 1.1974-46.2003 Plant Physiology 101.1993 - & JSTOR online Archive 13.1938 - 139.2005

Changes in subscription/access Nucleic Acids Research 24.1996 -(Open Access) Mycological Research 101.1997 - (Archive from 1997 via ScienceDirect) Journal of the Royal Society, Interface: Physical and Life Sciences 1.2004(free access to back issues 1 year after publication) ON LINE RESOURCES • New titles in the list of on line resources In a tree-like form the university and research groups are presented with their research departments and individual researchers. This is the private initiavtive of Richard Price in an effort to offer the scientific community an easy way to contact each other and stay updated. It serves as a social network site for academics with contacts, news feeds and research interests. You can sign in for yourself and add your profile. Darwin 200 in Nature News In February 2009 the 200th anniversary of Charles Darwin will be celebrated. As an anticipation on this celebrating this Nature News site will " provide continuously updated news, research and analysis on Darwin's life, his science and his legacy, as well as news from the Darwin200 consortium of organizations celebrating this landmark event." news/specials/darwin/index.html • Database barometer

How do search results differ and develop? As a test we will make a search on the topic "biodiversity and climate change" for articles published in 2008. http://infoserver/library/news/lis_news_winter08.cfm (5 of 12) [16-2-2009 9:50:48]

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Database Web of Science Science Direct SpringerLink

Search question TS=(bio diversity AND "climate chang*") Pub.Year=2008 pub-date= 2008 and TITLE-ABSTR-KEY(biodiversity) and TITLE-ABSTR-KEY ("climate chang*") Search For (Boolean) > biodiversity AND "climate change" Publication Date > Greater than Monday, January 01, 2008 Anywhere in the article: biodiversity climate change from 2008 to 2008 biodiversity "climate change" 2008 - 2008 Basic Search: biodiversity AND "climate change" Since 2008 - present

BioOne Google Scholar Scopus (not free acccessible) Pubmed "Biodiversity"[Mesh] AND "Climate"[Mesh] AND ("2008/01/01"[Publication Date] : "2008/12/31"[Publication Date])

results March July 89 159 57 31 *

Oct 254 44

Dec 324 56





141 816 64

250 2910 197

350 4420 228

481 5510 397 169

* ScienceDirect has a change in the date search (?) BOOK ACQUISITIONS IN THE LIBRARY

A Biologist's Guide to Mathematical Modeling in Ecology and Evolution S. P. Otto and T. Day. 2007. CEME 9=0725B. A Practical Guide to Ecological Modelling Using R as a Simulation Platform K. Soetaert and P. M. J. Herman. 2009. CEME 9=0723B. CL OeA 291.CTE Gr 14 # Soetaert # 2009 Aquatic Ecosystems and Development: Comparative Asian Perspectives F. Schiemer, D. Simon, U. Amarasinghe and J. Moreau. 2008. CL OeA 292. Current Status of Eutrophication in the Belgian Coastal Zone V. Rousseau, C. Lancelot and D. Cox. 2008. CEME 9-0724B. De vijver in het stadspark Schothorst te Amersfoort: een fysich, chemisch en biologisch onderzoek van het water en de oevers in de periode 1989-2003 A. H. M. Grimbergen, V. van Laar and G. J. van schijndel. 2008. CL LR 101 d. Diversity of chemoautotrophs using the Calvin Benson-Bassham cycle in intertidal marine sediments: Testing new RubisCO primers D. Vasquez Cardenas. 2008. CEME 5-0319R. http://infoserver/library/news/lis_news_winter08.cfm (6 of 12) [16-2-2009 9:50:48]

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Duurzame schelpdiertransporten: Najaar 2008 data rapport A. Engelberts, P. van Avesaath and H. Hummel. 2008. CEME 8-4659R. Ecologische Atlas Noordzee ten behoeve van gebiedsbescherming H. J. Lindeboom, E. M. Dijkman, O. G. Bos, et al. 2008. CEME 8=0786B. Environmental Microbiology : from genomes to biogeochemistry E. L. Madsen. 2008. CEME 5=0177B. Fisheries management 2. The ecosystem approach to fisheries. 2.1 Best practices in ecosystem modelling for informing an ecosystem approach to fisheries. FAO. 2008. CEME 9-1553R.

Handbook of Alien Species in Europe DAISIE. 2009. CEME 8=0788B. Handbook of Stable Isotope Analytical Techniques Vol. 2 De Groot, Pier A. 2008. CEME 1=0366B. Het macrobenthos van de Roggenplaat in het najaar van 2008 : concept rapportage W. Sistermans, M. A. Bermeijer, E. Hartog, O. J. A. van Hoesel, M. M. Markusse and L. de Witte-Dek. 2008. CEME 8-4660R. Het mosselbestand en het areaal aan mosselbanken op de droogvallende platen in de Waddenzee in het voorjaar van 2008 P. C. Goudswaard, J. M. J. Jansen, C. van Zweeden, J. Kesteloo and M. R. van Stralen. 2008. CEME 8-4655R. http://infoserver/library/news/lis_news_winter08.cfm (7 of 12) [16-2-2009 9:50:48]

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Historische ontwikkeling macrofauna levensgemeenschappen Rijn-Maas-monding: Biesbosch, Hollands Diep, haringvliet, Voordelta vanaf 1960 met het oog op de toekomst: Eindrapport december 2008 S. Wijnhoven and H. Hummel. 2008. CEME 8-4661R. Indicator sysstem for biodiversity in Dutch marine waters II: Ecoprofiles of indicator species for Wadden Sea, North Sea and Delta Area H. W. G. Meesters, R. ter Hofstede, C. M. Deerenberg, et al. 2008. CEME 8-4656R. Interactie tussen protozoa en chemoautotrofe micro-organismen in mariene sedimenten P. De Graag. 2008. CEME 5-0320R. Introduction to Geomicrobiology K. Konhauser. 2007. CEME 5=0176B. Meiobenthology: The Microscopic Motile Fauna of Aquatic Sediments O. Giere. 2009. CEME 8=0787B. Mesheften (Ensis directus), halfgeknotte strandschelpen (Spisula subtruncata) en kokkels (Cerastoderma edule) en otterschelpen (Lutraria lutraria)in de Nederlandse kustwateren in 2008 P. C. Goudswaard, J. J. Kesteloo, K. J. Perdon and J. M. Jansen. 2008. CEME. Microbial Ecology of the Oceans D. L. Kirchman. 2008. CEME 5=0175B. Novel modelling approaches to relate biodiversity of marine sediments to ecosystem functioning: Linking models and experiments with patterns in nature. A CoML-EuroCoML-MarBEF Workshop Amsterdam, 15-17 October 2007 / Editors: M. Vos & C. Heip. M. Vos and C. Heip. 2008. CEME 9-1554R. Physiology and genetics of sulfur-oxidizing bacteria C. G. Friedrich. 1998. CEME 5-0317R. Principles of data management : facilitating information sharing K. Gordon. 2007. CL W 169. Rapportage Project TARRA A. Engelberts and P. van Avesaath. 2006. CEME 8-4657R. Shades of red and green. The colorful diversity and ecology of picocyanobacteria in the Baltic Sea Th Haverkamp. 2008. CEME 5=0178B. The arabidopsis book American Society of Plant Biologists. 2002. perlserv/?request=get-static&name=arabidopsis_ebook http://www. The Prince Edwards Islands : Land-Sea Interactions in a Changing Ecosystem S. L. Chown and P. W. Froneman. 2008. CEME ANT-0735. The R book M. J. Crawley. 2007. CEME 1=0365B.

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The selective value of bacterial shape K. D. Young. 2006. CEME 5-0317R. Threshold of sediment motion under unidirectional currents M. C. Miller, I. N. McCave and P. D. Komar. 1977. CEME 3-0636R. Tussen aarde en leven : bevat tevens Moleculen uit een ver verleden / J. S. Sinninghe DamstĂŠ J. J. Middelburg. 2006. CEME 3-0636R. Verpreiding van Japanse oesters in het Veerse Meer 2008 P. H. van Avesaath, A. Engelberts, M. Bergmijer, O. A. van Hoesel and H. Hummel. 2008. CEME 8-4662R. Verspreiding van abundante macro-algen in het Veerse Meer 2008 P. Van Avesaath, A. Engelberts, M. Bergmeijer, O. A. van Hoesel and H. Hummel. 2008. CEME 7-1638R. Vijftig jaar visserij en beheer op de Noordzee W. L. T. van Densen and M. J. van Overzee. 2008. CEME 8-4654R. Wavelet methods for time series analysis D. B. Percival and A. T. Walden. 2000. CEME 1=0364B. Wildlife ecology, conservation, and management A. R. E. Sinclair, J. M. Fryxell and G. Caughley. CL OeA 290. Tips on how to use the NIOO Data Archive. â—?

NIOO Data Archive

The NIOO Data and Information Portal is online and can be accessed at The portal gives access to: 1.) Data Information System (search data sets) for SEARCHING to find data sets. This part can be used by everybody, although some datasets may have restriced access.

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2.) Data Archiving System (to archive your data). This part is only for CEME researchers. Researchers from CL and CTE can have access to archive their data later this year. Please note that data sets should be archived after finishing a project or when you leave CEME. Of course you are always welcome to archive during a project. When you want to archive your data, you need to register first. Please visit the following links for more information, or direct access: MANUALS Creating an account for the Data Archiving System, all NIOO employees can register ans apply for an account. Select the appropriate Workspace. you can have a private workspace, and you can access the public workspace of your workgroup Upload file and submit metadata, follow th einsturctions to upload your datafile and to add the necesarry metadata to the file Manual on how to use the Marine Data Archive (MDA) ARCHIVING Data Archiving System (username and password required), after you are granted an account, you can login here The following datatypes can be archived: 1. Biotic data http://infoserver/library/news/lis_news_winter08.cfm (10 of 12) [16-2-2009 9:50:48]

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2. In situ instrument data 3. Lab instrument data 4. Experimental data 5. Geographic data 6. Remote sensing data 7. Images and movies 8. Model data 9. Models 10. Software and scripts

Colophon This newsletter will inform you about new developments in information and information technology (internet, online resources) and on the developments in the NIOO Library and Information department (library acquisitions, licenses, access to online resources). For more information, remarks and/ or suggestions, please contact Marianne van der Heijden. http://infoserver/library/news/lis_news_winter08.cfm (11 of 12) [16-2-2009 9:50:48]

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NIOO Library and Information Newsletter 2008 - 4  

Newsletter from the Library and Information Services Department of the Netherlands Institute of Ecology. News on searching, publishing, cit...

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