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	<title>Comments on: Next Generation Scientific Articles: Reflections on a changing landscape</title>
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	<description>In the spider-web of facts, many a truth is strangled</description>
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		<title>By: Bio-ontologies for everyone with new Microsoft Word Add-in &#8211; Abhishek Tiwari - In the spider-web of facts, many a truth is strangled</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8808</link>
		<dc:creator>Bio-ontologies for everyone with new Microsoft Word Add-in &#8211; Abhishek Tiwari - In the spider-web of facts, many a truth is strangled</dc:creator>
		<pubDate>Thu, 21 Oct 2010 12:16:28 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8808</guid>
		<description>[...] in ontologies and controlled vocabularies. I am sure this tool is going to fuel the debate on the article of the future as like everyone else I think that the next generation of scientific articles will be semantic rich [...]</description>
		<content:encoded><![CDATA[<p>[...] in ontologies and controlled vocabularies. I am sure this tool is going to fuel the debate on the article of the future as like everyone else I think that the next generation of scientific articles will be semantic rich [...]</p>
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		<title>By: buy mirena</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8795</link>
		<dc:creator>buy mirena</dc:creator>
		<pubDate>Thu, 24 Jun 2010 03:24:48 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8795</guid>
		<description>Chemistry is one of the intangibles in a relationship and yet it can make or break it. There are a number of things you can do to &quot;up the intensity&quot; of a relationship, some depend on the state of the relationship at the moment and others depend on how committed you are to it.</description>
		<content:encoded><![CDATA[<p>Chemistry is one of the intangibles in a relationship and yet it can make or break it. There are a number of things you can do to &#8220;up the intensity&#8221; of a relationship, some depend on the state of the relationship at the moment and others depend on how committed you are to it.</p>
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		<title>By: Anibal M. Astobiza</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8803</link>
		<dc:creator>Anibal M. Astobiza</dc:creator>
		<pubDate>Fri, 14 Aug 2009 10:17:45 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8803</guid>
		<description>&lt;span class=&quot;topsy_trackback_comment&quot;&gt;&lt;span class=&quot;topsy_twitter_username&quot;&gt;&lt;span class=&quot;topsy_trackback_content&quot;&gt;Next Generation Scientific Articles: Reflections on a changing landscape  http://bit.ly/45wA7i&lt;/span&gt;&lt;/span&gt;</description>
		<content:encoded><![CDATA[<p><span class="topsy_trackback_comment"><span class="topsy_twitter_username"><span class="topsy_trackback_content">Next Generation Scientific Articles: Reflections on a changing landscape  <a href="http://bit.ly/45wA7i" rel="nofollow">http://bit.ly/45wA7i</a></span></span></span></p>
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		<title>By: abhishektiwari</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8802</link>
		<dc:creator>abhishektiwari</dc:creator>
		<pubDate>Thu, 13 Aug 2009 18:38:09 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8802</guid>
		<description>No worries Stuart, Its quite natural-you guys are working hard to come out with best you can, may be our (the vocal guys) expectation are very high from Nature Chemistry. The whole idea to write this article was to put a commentary on how different publishers are working in different direction to deliver article of future. NO one knows what they will look like. Otherwise I strongly agree different points you detailed here. Most of authors are not so much tech savvy as we think, and that&#039;s may be the reason there is a large silent in the community. In past many ideas and implementations have been dropped due to cold response from the community which was really disappointing. Now we all agree that we need to encourage the authors to submit raw data in standardized formats. How you will do that, get a rewarding systems in place first . For example many OA publishers offer concession in OA charges if the manuscript is formatted with EndNote or any other reference manager. So All we need is a rewarding system for the authors those are putting extra effort to submit raw data in standardized format. Reference styles and other issues between publishers can be resolved in same way as DOI or CrossRef was worked out in past.</description>
		<content:encoded><![CDATA[<p>No worries Stuart, Its quite natural-you guys are working hard to come out with best you can, may be our (the vocal guys) expectation are very high from Nature Chemistry. The whole idea to write this article was to put a commentary on how different publishers are working in different direction to deliver article of future. NO one knows what they will look like. Otherwise I strongly agree different points you detailed here. Most of authors are not so much tech savvy as we think, and that&#8217;s may be the reason there is a large silent in the community. In past many ideas and implementations have been dropped due to cold response from the community which was really disappointing. Now we all agree that we need to encourage the authors to submit raw data in standardized formats. How you will do that, get a rewarding systems in place first . For example many OA publishers offer concession in OA charges if the manuscript is formatted with EndNote or any other reference manager. So All we need is a rewarding system for the authors those are putting extra effort to submit raw data in standardized format. Reference styles and other issues between publishers can be resolved in same way as DOI or CrossRef was worked out in past.</p>
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		<title>By: Stuart</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8801</link>
		<dc:creator>Stuart</dc:creator>
		<pubDate>Thu, 13 Aug 2009 15:44:44 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8801</guid>
		<description>Abhishek - apologies for the tone of my comment earlier today, I realise reading it back that it was a little sharper than it needed to be. But, I do maintain that it is easy to criticise publishers and journals - and some of it we deserve, but some of it we don&#039;t. Or at least that&#039;s what I believe - but I am obviously somewhat biased! However, we are willing to have a dialogue with the community - we do want input. We may not want (or be able) to act on all of it, but at least we&#039;re asking! Other publishers are asking too - but there are some notable exceptions...

Tony makes a great point in that to encourage authors to submit data, we need to offer them tools to make it easy - we (and by &#039;we&#039; I mean journals in general, not just Nature ones) make authors jump through a lot of hoops to submit a paper - probably too many hoops; but these things don&#039;t change overnight - however much some of us on the &#039;inside&#039; might wish them to. As long as journals are receptive to authors wanting to submit data - which I know Nature Chemistry and those at the RSC are, then at least there is a possibility for change; but it must be driven by the academic community. Whether it&#039;s a top-notch journal or otherwise, it is not a practical model to force authors to submit data. The &#039;make it easy&#039; argument is supported by the fact that the only type of data file we actually host as Supplementary Information are cif files - and these are standard when you get a crystal structure. The problem is that for other types of experimental data, there is no widely recognised universal standard (ask a bunch of practising chemists what JCAMP files are and I bet not many will know).

Perhaps it is because chemistry is an older discipline that it is harder for change to be embraced. Because systems biology is a newer field, it is not weighed down by &#039;old-fashioned&#039; ways of doing things - or not so much anyway.

The other thing to consider is that while there are a number of people very vocal about publishing chemistry in new ways - this is still very much a small number. There is a large silent majority - what do they want? I do not say this to justify not changing anything, but I really do believe that this needs to be a community driven effort. If more people submit data to journals that are capable and willing to host it, then this practice will likely gain traction. As new generations of graduate students become academics and in turn their students know nothing other than the digital age, things will get easier. But, a journal cannot mandate this.

And as for references, I agree. But if you put the major chemistry publishers in a room and try and get them to agree on a format for references, it would get very messy...</description>
		<content:encoded><![CDATA[<p>Abhishek &#8211; apologies for the tone of my comment earlier today, I realise reading it back that it was a little sharper than it needed to be. But, I do maintain that it is easy to criticise publishers and journals &#8211; and some of it we deserve, but some of it we don&#8217;t. Or at least that&#8217;s what I believe &#8211; but I am obviously somewhat biased! However, we are willing to have a dialogue with the community &#8211; we do want input. We may not want (or be able) to act on all of it, but at least we&#8217;re asking! Other publishers are asking too &#8211; but there are some notable exceptions&#8230;</p>
<p>Tony makes a great point in that to encourage authors to submit data, we need to offer them tools to make it easy &#8211; we (and by &#8216;we&#8217; I mean journals in general, not just Nature ones) make authors jump through a lot of hoops to submit a paper &#8211; probably too many hoops; but these things don&#8217;t change overnight &#8211; however much some of us on the &#8216;inside&#8217; might wish them to. As long as journals are receptive to authors wanting to submit data &#8211; which I know Nature Chemistry and those at the RSC are, then at least there is a possibility for change; but it must be driven by the academic community. Whether it&#8217;s a top-notch journal or otherwise, it is not a practical model to force authors to submit data. The &#8216;make it easy&#8217; argument is supported by the fact that the only type of data file we actually host as Supplementary Information are cif files &#8211; and these are standard when you get a crystal structure. The problem is that for other types of experimental data, there is no widely recognised universal standard (ask a bunch of practising chemists what JCAMP files are and I bet not many will know).</p>
<p>Perhaps it is because chemistry is an older discipline that it is harder for change to be embraced. Because systems biology is a newer field, it is not weighed down by &#8216;old-fashioned&#8217; ways of doing things &#8211; or not so much anyway.</p>
<p>The other thing to consider is that while there are a number of people very vocal about publishing chemistry in new ways &#8211; this is still very much a small number. There is a large silent majority &#8211; what do they want? I do not say this to justify not changing anything, but I really do believe that this needs to be a community driven effort. If more people submit data to journals that are capable and willing to host it, then this practice will likely gain traction. As new generations of graduate students become academics and in turn their students know nothing other than the digital age, things will get easier. But, a journal cannot mandate this.</p>
<p>And as for references, I agree. But if you put the major chemistry publishers in a room and try and get them to agree on a format for references, it would get very messy&#8230;</p>
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		<title>By: abhishektiwari</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8800</link>
		<dc:creator>abhishektiwari</dc:creator>
		<pubDate>Thu, 13 Aug 2009 13:54:49 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8800</guid>
		<description>Thanks Antony for your comment. I also agree with Stuart comments that authors are generally not willing to submit data, but we are talking about top notch journals, at least the data which was used to create  plots in figure section should be available for download. Time to time I use digitizer to get  numerical values hidden in those plots, can&#039;t we make it little simple by just asking author to provide the Excel file used to draw the plots. Community wide efforts in  systems biology have made easier for authors to publish their model in SBML formats. Surprisingly Chemistry is a very old discipline  compared to systems biology but best practices are still not well established . Hope this will not continue for longer.</description>
		<content:encoded><![CDATA[<p>Thanks Antony for your comment. I also agree with Stuart comments that authors are generally not willing to submit data, but we are talking about top notch journals, at least the data which was used to create  plots in figure section should be available for download. Time to time I use digitizer to get  numerical values hidden in those plots, can&#8217;t we make it little simple by just asking author to provide the Excel file used to draw the plots. Community wide efforts in  systems biology have made easier for authors to publish their model in SBML formats. Surprisingly Chemistry is a very old discipline  compared to systems biology but best practices are still not well established . Hope this will not continue for longer.</p>
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		<title>By: ChemSpiderman</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8799</link>
		<dc:creator>ChemSpiderman</dc:creator>
		<pubDate>Thu, 13 Aug 2009 13:24:01 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8799</guid>
		<description>Thanks for the &quot;FishEye Perspective&quot;. The article of the future is morphing quickly. In many cases the technologies already exist to enhance the articles and both you and Stuart are correct in your comments. You are correct to challenge in regards to &quot;one format&quot; for references. I&#039;ve written over 100 peer-reviewed publications and that specific issue of reformatting citations is a depressing trial every time..and if resolved &quot;someone&quot; will win with their format and I judge that is part of the challenge.
I can agree with Stuart however that until you have &quot;been&quot; a publisher it&#039;s easy to criticize from the outside. Having now moved from outside to inside publishing I am more aware of the challenges. And..I am only slightly immersed in the processes at present so I can only imagine what I am going to learn while at the RSC!

Stuart comments that authors are generally not willing to submit data. I think this is generally true. It is work to prepare data and binary file formats are not supported for even general spectral data and have to be converted to JCAMP for example. It&#039;s possible, but it&#039;s work. Some people will do it but they are few and far between. In my judgment many of the enhancements of the future will come from greater support from the authors and we have to provide tools to make it easy for them. We&#039;re all busy and MORE work is unlikely to create a following. We&#039;re building tools to make it easy for authors...</description>
		<content:encoded><![CDATA[<p>Thanks for the &#8220;FishEye Perspective&#8221;. The article of the future is morphing quickly. In many cases the technologies already exist to enhance the articles and both you and Stuart are correct in your comments. You are correct to challenge in regards to &#8220;one format&#8221; for references. I&#8217;ve written over 100 peer-reviewed publications and that specific issue of reformatting citations is a depressing trial every time..and if resolved &#8220;someone&#8221; will win with their format and I judge that is part of the challenge.<br />
I can agree with Stuart however that until you have &#8220;been&#8221; a publisher it&#8217;s easy to criticize from the outside. Having now moved from outside to inside publishing I am more aware of the challenges. And..I am only slightly immersed in the processes at present so I can only imagine what I am going to learn while at the RSC!</p>
<p>Stuart comments that authors are generally not willing to submit data. I think this is generally true. It is work to prepare data and binary file formats are not supported for even general spectral data and have to be converted to JCAMP for example. It&#8217;s possible, but it&#8217;s work. Some people will do it but they are few and far between. In my judgment many of the enhancements of the future will come from greater support from the authors and we have to provide tools to make it easy for them. We&#8217;re all busy and MORE work is unlikely to create a following. We&#8217;re building tools to make it easy for authors&#8230;</p>
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		<title>By: Andrew Spong</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8804</link>
		<dc:creator>Andrew Spong</dc:creator>
		<pubDate>Thu, 13 Aug 2009 10:40:10 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8804</guid>
		<description>&lt;span class=&quot;topsy_trackback_comment&quot;&gt;&lt;span class=&quot;topsy_twitter_username&quot;&gt;&lt;span class=&quot;topsy_trackback_content&quot;&gt;Analysis of several recent high-profile blog posts: Next-gen scientific articles http://ow.ly/jUyf &#124; (fisheye perspective)&lt;/span&gt;&lt;/span&gt;</description>
		<content:encoded><![CDATA[<p><span class="topsy_trackback_comment"><span class="topsy_twitter_username"><span class="topsy_trackback_content">Analysis of several recent high-profile blog posts: Next-gen scientific articles <a href="http://ow.ly/jUyf" rel="nofollow">http://ow.ly/jUyf</a> | (fisheye perspective)</span></span></span></p>
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		<title>By: Andrew Spong</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8805</link>
		<dc:creator>Andrew Spong</dc:creator>
		<pubDate>Thu, 13 Aug 2009 10:40:10 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8805</guid>
		<description>&lt;span class=&quot;topsy_trackback_comment&quot;&gt;&lt;span class=&quot;topsy_twitter_username&quot;&gt;&lt;span class=&quot;topsy_trackback_content&quot;&gt;Analysis of several recent high-profile blog posts: Next-gen scientific articles http://ow.ly/jUyf &#124; (fisheye perspective)&lt;/span&gt;&lt;/span&gt;</description>
		<content:encoded><![CDATA[<p><span class="topsy_trackback_comment"><span class="topsy_twitter_username"><span class="topsy_trackback_content">Analysis of several recent high-profile blog posts: Next-gen scientific articles <a href="http://ow.ly/jUyf" rel="nofollow">http://ow.ly/jUyf</a> | (fisheye perspective)</span></span></span></p>
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		<title>By: abhishektiwari</title>
		<link>http://abhishek-tiwari.com/2009/08/next-generation-scientific-articles.html/comment-page-1#comment-8798</link>
		<dc:creator>abhishektiwari</dc:creator>
		<pubDate>Thu, 13 Aug 2009 05:09:23 +0000</pubDate>
		<guid isPermaLink="false">http://abhishek-tiwari.com/2009/next-generation-scientific-articles-reflections-on-a-changing-landscape/#comment-8798</guid>
		<description>First of all there is no mere criticism (every one appreciated what publishers are doing with the articles), secondly and  certainly I have no idea how scientific publishing actually works on a day-to-day basis, but I do have some common sense. Why there are more than 200 citation styles, what exactly is stopping the publishers to agree on a single citation style. NO they will not otherwise it will become easy for the authors. If Nature or Nature Chemistry think that they have enough experience to deal with these kind of issues then why they asked for feedback and inputs  from the readers or why Elsevier will organize Article 2.0 contest?</description>
		<content:encoded><![CDATA[<p>First of all there is no mere criticism (every one appreciated what publishers are doing with the articles), secondly and  certainly I have no idea how scientific publishing actually works on a day-to-day basis, but I do have some common sense. Why there are more than 200 citation styles, what exactly is stopping the publishers to agree on a single citation style. NO they will not otherwise it will become easy for the authors. If Nature or Nature Chemistry think that they have enough experience to deal with these kind of issues then why they asked for feedback and inputs  from the readers or why Elsevier will organize Article 2.0 contest?</p>
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