How a simple botanist is collecting his readings, revised 6. September 2013Klaus Ammann, Guest ProfessorDelft University of Technology, Netherlands

Literature citation, forSlideshows and Manuscripts

First the simple tricks, no need to go over the Bibliographic programmes, direct access via Google Scholar www.scholar.google.org : Here you do not needaccess through a priviledged IP, see next slide

Just type part of the publication title and add at the beginning the first author name (if necessary) in order to clearly identify your paper

You will get in the majority of the cases the full link to the publication journal website (download the citation there and click at the right to the pdf link)

Often you need a privileged access with a university IP with access to the journals to read the full pdf. In most Universities the library personel can give you the links, and if you work on your private IP from home you can go over the VPN-Service (various programmes available, Universities use often Cisco) to change to the University IP where you work or have worked to get privileged access

Usually, the journal websites automatically recognise privileged IP addresses of theUniversities and grant direct access. The Swiss University Network has access to some 80’000 Journals online for the full texts back to 1996.

IP: http://en.wikipedia.org/wiki/IP_address

An easy way to collect correct citations:

The direct way over Google Scholar

Get Google Scholar, if you do not have yet a direct button:Search for «Google Scholar» in the Google window

Write in the Google search lineAuthor (no first name necessary) and title (often only 5-7 words are enough)

You get usually the bold title and to the right the link to the pdf or html, Sometimes the appropriate link is not on the first line, then scroll down

a klick leading directly to the Journals website, where you can press download citation in Your Endnote or other literature database.Then continue by producing a link to the pdf as described above

This way you can often avoid to use the tedious way over web of science and the journals website searching for the volume etc.

Web of Science, Web of Knowledge

Most Universities and many public institutions have access to the Web of Science overthe privileged IP, where you do your literature research.

The later versions of the WOS have direkt buttons for the full text of the citations found, but again you need to be on the priviliged IP of a public institution (which you need anyway to have access to the Web of Science)You can also get access to the priviledged institutional IP withLogging into the priviledged network by VPN (Virtual Private Networking) see the access through the University of Bern (only for student and staff)http://www.id.unibe.ch/content/services/virtual_private_networking_vpn/auf_einen_blick/index_ger.html

Web of Science, all databases

Web of Science, all databasesAccess only through priviledged IP from Institution participating In the consortium of University libraries. Staff and Students of most European University have access, also from outside with VPN (virtual private networking), see Example of the University of Bern:http://apps.webofknowledge.com/select_databases.do?highlighted_tab=select_databases&product=UA&SID=V1nGOzsBX8TpwOkXN7d&last_prod=WOS&cacheurl=no

Web of Knowledge, analytical tools and websites

Web of Knowledge, additional resources:http://apps.webofknowledge.com/additional_resources.do?highlighted_tab=additional_resources&product=UA&SID=V1nGOzsBX8TpwOkXN7d&cacheurl=no

Web of Knowledge search mode

Main search mode „biofuel AND crops“ in Topichttp://apps.webofknowledge.com/UA_GeneralSearch_input.do?highlighted_tab=UA&product=UA&search_mode=GeneralSearch&SID=V1nGOzsBX8TpwOkXN7d&last_prod=WOS&highlighted_tab=UA&cacheurl=no

Web of Science: Search result: «biofuel and crops» first page2224 references» The list as pdf: Full text window: direct download

Web of Knowledge, results

http://www.ask-force.org/web/Biofuel/Bibliography-Biofuel-Crops-WOS-KA-20130906.pdf

Biofuels AND crops:Window of some reference examples (out of 2224), collected with Web of Science

Biofuel / crops from Web of Science and other Sources klaus.ammann@ips.unibe.ch 20130906 2224 references

Abbadi, A. and G. Leckband (2011), Rapeseed breeding for oil content, quality, and sustainability, European Journal of Lipid Science and Technology, 113, 10, pp. 1198-1206, <Go to ISI>://WOS:000297012300004

Abdelgadir, H. A., S. D. Johnson and J. Van Staden (2009), Promoting branching of a potential biofuel crop Jatropha curcas L. by foliar application of plant growth regulators, Plant Growth Regulation, 58, 3, pp. 287-295, <Go to ISI>://WOS:000266455600008

Abdelgadir, H. A., S. D. Johnson and J. Van Staden (2009), Pollinator effectiveness, breeding system, and tests for inbreeding depression in the biofuel seed crop, Jatropha curcas, Journal of Horticultural Science & Biotechnology, 84, 3, pp. 319-324, <Go to ISI>://WOS:000272389300013

Abdelgadir, H. A., S. D. Johnson and J. Van Staden (2012), Pollen viability, pollen germination and pollen tube growth in the biofuel seed crop Jatropha curcas (Euphorbiaceae), South African Journal of Botany, 79, pp. 132-139, <Go to ISI>://WOS:000302978900019

Abrahamson, L. P., D. J. Robison, T. A. Volk, E. H. White, E. F. Neuhauser, W. H. Benjamin and J. M. Peterson (1998), Sustainability and environmental issues associated with willow bioenergy development in New York (USA), Biomass & Bioenergy, 15, 1, pp. 17-22, <Go to ISI>://WOS:000074996000003

Abramson, M., O. Shoseyov and Z. Shani (2010), Plant cell wall reconstruction toward improved lignocellulosic production and processability, Plant Science, 178, 2, pp. 61-72, <Go to ISI>://WOS:000274877700001

Abreu, I. S., C. R. Carvalho, G. M. A. Carvalho and S. Y. Motoike (2011), First karyotype, DNA C-value and AT/GC base composition of macaw palm (Acrocomia aculeata, Arecaceae) - a promising plant for biodiesel production, Australian Journal of Botany, 59, 2, pp. 149-155, <Go to ISI>://WOS:000288863200005

Acaroglu, M. and H. Aydogan (2012), Biofuels energy sources and future of biofuels energy in Turkey, Biomass & Bioenergy, 36, pp. 69-76, <Go to ISI>://WOS:000300469700008

Window example biofuels AND crops, formatted references

Ammann Klaus (20130906), Bibliography Biofuels AND crops: out of Web of Science and other Sources, 2224 references, in: ASK-FORCE, 131, Klaus Ammann, Neuchâtel, http://www.ask-force.org/web/Biofuel/Bibliography-Biofuel-Crops-WOS-KA-0130906.pdf

Endnote 6 directories of .enl databases Klaus Ammann, 2006 (program see www.endnote.org )

Endnote library, part of directory

Endnote library, first page of the libraries of Klaus Ammann 2006Endnote library, details

Endnote library, contents, selection references transgenic Poplars Status 2006

Endnote library, contents, GM poplars

Below: how to find a specific full text reference (formatted out of the Web of science):

Gatehouse, A. M. R., N. Ferry and R. J. M. Raemaekers (2002), The case of the monarch butterfly: a verdict is returned, Trends in Genetics, 18, 5, pp. 249-251, http://www.botanischergarten.ch/Bt/Gatehouse-Case-Monarch-2002.pdf

1) If you do not have priviledged access through an acacemicInstitution IP, then try the trick over google scholar described in the first slides, you often find an open pdf link.

2) if you have such an IP, then you have the Option a) over the journal and download directly the pdf, if this (rarely) does not work, then option b) go over the Web of Science with a search or MUCH quicker over the doi-link of the reference, then the Web of Science shows directly the detailed reference with the full text button, (at least the recent versions are providing this button).

Web of Science: Search result: «biofuel and crops» first page2224 references» The list as pdf: a) Full text window: direct downloadb) Use DOI – link from any citation, go to ISI...but with WOS active

Web of Knowledge, results

http://www.ask-force.org/web/Biofuel/Bibliography-Biofuel-Crops-WOS-KA-20130906.pdf

Pdf document on screen, you need to produce a link to anExternal link, see example www.hostpoint.com and buy spaceFor 50 Gigabyte 14.80.- Fr. per month, get a domain name(example ask-force.org), create an ftp link with password

Load up program Total Commander http://www.ghisler.com/ You must program a connection to ftp to point left side to your host, right side to your hard disk site with the documents you want to transfer to the ftp-hostFollow instructions in Total Commander when not connected over the button «connect to ftp server»

Draw the document name to your right to the ftp server of your hostto the left

Copy-paste the link you have drawn to the ftp-host on the leftftp://server-p009.hostpoint.ch/www/yourdomain.org/web/Bt1/Gatehouse-Case-Monarch-2002.pdf to your endnote list under URLftp://server.....hostpoint.ch/www/yourdomain.org/web/Bt1/Gatehouse-Case-Monarch-2002.pdf (only accessible with your password)Bt1 here the folder you have named for such documents on the host.

To produce a link which is publicly accessible:Replace on endnote citation «ftp://yourserver-.... Hostpoint.ch/www withhttp://www.domain-name.org

The citation will be ready for any endnote purpose: copy paste formated, also working with cite while you write, it will create with your bibliography format a bibliography list at the bottom of your manuscript automatically in some 3000 different formats for virtually all journals

Gatehouse, A. M. R., N. Ferry and R. J. M. Raemaekers (2002), The case of the monarch butterfly: a verdict is returned, Trends in Genetics, 18, 5, pp. 249-251, http://www.ask-force.org/web/Bt1/Gatehouse-Case-Monarch-2002.pdf

If it is not possible to find on Google Scholar or Web of Science a full text link, then you have two possiblities:

1.Go to http://sv2qt7zb3k.search.serialssolutions.com/?paramdict=en-USFollow the instructions when the journal is listed, usually full text linksare available back to 1996, there are numerous exceptions for availabilitiesback to No. 1 volume. It might also lead your search automatically to thebig journal archive Istor, with priviledged IP you have generous access.

1.Go to NEBIS, information and instructions below http://www.nebis.ch/

EBZ Regensburg

Regensburg System since 2012 replaced byNEBIS Netzwerk von Bibliotheken und Informationsstellen in der Schweiz http://www.nebis.ch/

How to access full text samples of journals, (since 2012) NEBIS offers to participants with login some 80’000 journals back to 1996 or earlier

Part of the result of a search for «Trends in Genetics»

Trends in Genetics free for EZB participants

Search entry «Trends in Genetics» then choice either NEBIS or direct access SFX Trends in Genetics free for NEBIS participants with login

Choice of «Trends in Genetics» in NEBISOverview of possibilities and volumes availableUpper part

Choice of «Trends in Genetics» in NEBISOverview of possibilities and volumes availableLower part, all available volumes

Gatehouse The Case of the Monarch butterfly full access with VPN

Gatehouse The Case of the Monarch butterfly full access to pdfWith VPN (Virtual Private Networking) Login NEBIS or SFX, example of IP of University of Bern on Laptop

Gatehouse, A.M.R., Ferry, N., & Raemaekers, R.J.M. (2002)The case of the monarch butterfly: a verdict is returned. Trends in Genetics, 18, 5, pp 249-251 http://www.botanischergarten.ch/Bt/Gatehouse-Case-Monarch-2002.pdf

Gatehouse pdf document

Upload of pdf files to Bern server www.botanischergarten.ch

Upload of pdf files to Bern server

Palm Desktop Memo: list of links, poplar, biofuel,(no more in use)

Palm Desktop links poplar biofuel

Endnote library, contents, section of transgenic Poplars

Endnote library, contents, GM poplars

Manuscript citations with authors in text

Manuscript citations with numbers

Literature alphabetic, with links to pdf

Literature alphabetic, with links to pdf

Literature numbered, without links to pdf

Literature numbered, without links to pdfs

Effects Publication

Ammann, K. (2005), Effects of biotechnology on biodiversity: herbicide-tolerant and insect-resistant GM crops Trends in Biotechnology, 23, 8, pp. 388-394, <Go to ISI>://000231342700005 AND http://www.botanischergarten.ch/TIBTECH/Ammann-TIBTECH-Biodiversity-2005.pdf

Example of a most recent publication:

Ammann Klaus (20130415), Genomic Misconception. A fresh look at the biosafety regulation of transgenic and conventional crops: a plea for a process of agnostic regulation, open source, final version, in: New Biotechnology, 30, 50 and typeset 17pp, Ammann K., Neuchatel, http://www.sciencedirect.com/science/article/pii/S1871678413000605 AND With full text link-references, not for publicationhttp://www.ask-force.org/web/NewBiotech/Genomic-Misconception-20130415-names-links.pdf AND typeset corrected: only publicly available full text linkshttp://www.ask-force.org/web/NewBiotech/Ammann-Genomic-Misconception-corrected-final-20130514.pdf AND German Abstract http://www.ask-force.org/web/NewBiotech/Ammann-German-Abstract-Highlights-20130415.pdf

Recently product oriented regulation has been proposed also by DEFRA from the UKhttp://www.ask-force.org/web/Genomics/Ammann-Progress-in-Genomic-Misconception-View-20130906.pdf

Werner Arber, Nobel Laureate 1978:

Interestingly, naturally occurring molecular evolution,i.e. the spontaneous generation of genetic variants hasbeen seen to follow exactly the same three strategies as those used in genetic engineering14. These three strategies are: (a) small local changes in the nucleotide sequences,(b) internal reshuffling of genomic DNA segments, and(c) acquisition of usually rather small segments of DNA

from another type of organism by horizontal gene transfer.

Arber, W. (2002) Roots, strategies and prospects of functional genomics. Current Science, 83, 7, pp 826-828 http://www.botanischergarten.ch/Mutations/Arber-Comparison-2002.pdf

Arber, W. (2002) Roots, strategies and prospects of functional genomics. Current Science, 83, 7, pp 826-828 http://www.botanischergarten.ch/Mutations/Arber-Comparison-2002.pdf

Arber

However, there is a principal difference between the procedures of genetic engineering and those serving in nature for biological evolution. While the genetic engineer pre-reflects his alteration and verifies its results, nature places its genetic variations more randomly and largely independent of an identified goal.

Arber, W. (2002) Roots, strategies and prospects of functional genomics. Current Science, 83, 7, pp 826-828 http://www.botanischergarten.ch/Mutations/Arber-Comparison-2002.pdf

Arber, W. (2002) Roots, strategies and prospects of functional genomics. Current Science, 83, 7, pp 826-828 http://www.botanischergarten.ch/Mutations/Arber-Comparison-2002.pdf

Arber

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Baudo: comparison in genomic disturbance: GM crops are less disturbed (black dots) than classic breeds

Scatter plot representation of transcriptome comparisons, Baudo et al. 2006transgenic vs. controlendosperm 14 dpa

28 dpa 8 dpg

2 conventionallinesEndosperm14 dpa

28 dpa leaf at 8 dpg

transgenic vs. conventional Endosperm14 dpa

28 dpa leaf at 8 dpg

EU-Project Wider Fields, Ammann-Kovacovsky-2008Huesken, A., Ammann, K., Messeguer, J., Papa, R., Robson, P., Schiemann, J., G., S., Stamp, P., J., S., & Wilhelm, R. (2007)

A major European synthesis of data on pollen and seed mediated gene flow in maize in the SIGMEA project. In GMCC-07, Third International Conference on Coexistence between Genetically Modified (GM) and non-GM based Agricultural Supply Chains, Seville Spainhttp://www..botanischergarten.ch/SIGMEA/Huesken-Synthesis-2007.pdff

Wider Fields

Bilsborrow, P.E., Evans, E.J., Bowman, J., & Bland, B.F. (1998)

Contamination of edible double-low oilseed rape crops via pollen transfer from high erucic cultivars. Journal of the Science of Food and Agriculture, 76, 1, pp 17-22 http://www.botanischergarten.ch/Brassica/Bilsborrow-Contamination-Edible-1998.pdf

A real health problem,But not discussed,Since it does not Concern transgenic crops

Real health problem

Matsuoka, Y., Vigouroux, Y., Goodman, M.M., Sanchez, G.J., Buckler, E., & Doebley, J. (2002)A single domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the National Academy of Sciences of the United States of America, 99, 9, pp 6080-6084 http://www.botanischergarten.ch/Bt/Matsuoka-Single-Domestication-2002.pdf

Phylogenesis Maize and

Teosinte

in the US maize yields have accelerated in the last ten yearsin the US maize yields have accelerated in the last ten years

• actual breeding plus cultural practice gain

Troyer, A.F. (2006)Adaptedness and Heterosis in Corn and Mule Hybrids. Crop Science, 46, 2, pp 528-543 http://crop.scijournals.org/cgi/content/abstract/cropsci;46/2/528 AND http://www.botanischergarten.ch/Bt/Troyer-Adaptedness-Heterosis-2006.pdf

corn yields in France and Italy in the corn yields in France and Italy in the

last 10 years fail to show the same trend last 10 years fail to show the same trend

http://epp.eurostat.ec.europa.eu/portal/page?_pageid=0,1136206,0_45570464&_dad=portal&_schema=PORTAL