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References extraction in papers

Phyks (Lucas Verney) 3 years ago
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+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
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+		<p class="day">19</p>
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+		<p class="month">Janvier</p>
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+	<div class="article">
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+		<header><h1 class="article_title"><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></h1></header>
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+		<!-- 
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+    @author=Phyks
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+    @date=19012016-1445
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+    @title=Comparison of tools to fetch references for scientific papers
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+    @tags=Science,OpenAccess
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+-->
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+
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+<p>Recently, I tried to aggregate in <a href="https://github.com/Phyks/libbmc/">a single place</a> various codes I had written to handle scientific papers. Some feature I was missing, and I would like to add, was the ability to fetch automatically references from a given paper. For arXiv papers, I had a <a href="http://known.phyks.me/2015/lets-some-metadata-on-arxiv">simple solution</a> using the LaTeX sources, but I wanted to have something more universal, taking a simple PDF file in input (thanks <a href="https://www.linkedin.com/in/john-dove-a8825">John</a> for the suggestion, and <a href="http://www.alstevens.org/">Al</a> for the tips on existing software solutions).</p>
61
+<p>I tried a comparison of three existing software to extract references from a PDF file:</p>
62
+<ul>
63
+<li><a href="https://github.com/CrossRef/pdfextract">pdfextract</a> from Crossref, very easy to use, written in Ruby.</li>
64
+<li><a href="https://github.com/kermitt2/grobid">Grobid</a>, more advanced (using machine learning models), written in Java, but quite easy to use too.</li>
65
+<li><a href="https://github.com/CeON/CERMINE">Cermine</a>, using the same approach as Grobid, but I could not get it to build on my computer. I used their <a href="http://cermine.ceon.pl/index.html">REST service</a> instead.</li>
66
+</ul>
67
+<p>To compare them, I asked <a href="http://antonin.delpeuch.eu/">Antonin</a> to build a list of most important journals and take five papers for every such journal, from <a href="http://dissem.in/">Dissemin</a>. This gives us a <a href="http://pub.phyks.me/paper_references_extractor/papers.json">JSON file</a> containing around 500 papers.</p>
68
+<p>I downloaded some articles, to get a (hopefully) representative set, composed of 147 different papers from various journals (I did not had access to some of them, so I could not fetch the full dataset). I ran <code>pdfextract</code>, <code>Grobid</code> and <code>Cermine</code> on each of them and compared the results.</p>
69
+<p>The raw results are available <a href="http://pub.phyks.me/paper_references_extractor/">here</a> for each paper, and I generated a single page comparison to ease the visual diff between the three results, available <a href="http://pub.phyks.me/paper_references_extractor/diff.html">here</a> (note that this webpage is <strong>very</strong> heavy, around 16MB).</p>
70
+<p>Briefly comparing the results, the machine learning based models (Cermine and Grobid) seems to give far better results than the simple approach taken by pdfextract, at the expense of being more difficult to build and run. Cermine gives a bunch of infos, too much in my opinion, and I think Grobid is given the most reusable and complete results. Feel free to compare them yourself. </p>
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+		<footer><p class="date">Le 19/01/2016 à 14:45</p>
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+		<p class="tags">Tags : <a href="//phyks.me/tags/Science.html">Science</a>, <a href="//phyks.me/tags/OpenAccess.html">OpenAccess</a></p></footer>
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+		<p class="day">19</p>
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+		<p class="month">Janvier</p>
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+	<div class="article">
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+		<header><h1 class="article_title"><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></h1></header>
53
+		<!-- 
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+    @author=Phyks
55
+    @date=19012016-1445
56
+    @title=Comparison of tools to fetch references for scientific papers
57
+    @tags=Science,OpenAccess
58
+-->
59
+
60
+<p>Recently, I tried to aggregate in <a href="https://github.com/Phyks/libbmc/">a single place</a> various codes I had written to handle scientific papers. Some feature I was missing, and I would like to add, was the ability to fetch automatically references from a given paper. For arXiv papers, I had a <a href="http://known.phyks.me/2015/lets-some-metadata-on-arxiv">simple solution</a> using the LaTeX sources, but I wanted to have something more universal, taking a simple PDF file in input (thanks <a href="https://www.linkedin.com/in/john-dove-a8825">John</a> for the suggestion, and <a href="http://www.alstevens.org/">Al</a> for the tips on existing software solutions).</p>
61
+<p>I tried a comparison of three existing software to extract references from a PDF file:</p>
62
+<ul>
63
+<li><a href="https://github.com/CrossRef/pdfextract">pdfextract</a> from Crossref, very easy to use, written in Ruby.</li>
64
+<li><a href="https://github.com/kermitt2/grobid">Grobid</a>, more advanced (using machine learning models), written in Java, but quite easy to use too.</li>
65
+<li><a href="https://github.com/CeON/CERMINE">Cermine</a>, using the same approach as Grobid, but I could not get it to build on my computer. I used their <a href="http://cermine.ceon.pl/index.html">REST service</a> instead.</li>
66
+</ul>
67
+<p>To compare them, I asked <a href="http://antonin.delpeuch.eu/">Antonin</a> to build a list of most important journals and take five papers for every such journal, from <a href="http://dissem.in/">Dissemin</a>. This gives us a <a href="http://pub.phyks.me/paper_references_extractor/papers.json">JSON file</a> containing around 500 papers.</p>
68
+<p>I downloaded some articles, to get a (hopefully) representative set, composed of 147 different papers from various journals (I did not had access to some of them, so I could not fetch the full dataset). I ran <code>pdfextract</code>, <code>Grobid</code> and <code>Cermine</code> on each of them and compared the results.</p>
69
+<p>The raw results are available <a href="http://pub.phyks.me/paper_references_extractor/">here</a> for each paper, and I generated a single page comparison to ease the visual diff between the three results, available <a href="http://pub.phyks.me/paper_references_extractor/diff.html">here</a> (note that this webpage is <strong>very</strong> heavy, around 16MB).</p>
70
+<p>Briefly comparing the results, the machine learning based models (Cermine and Grobid) seems to give far better results than the simple approach taken by pdfextract, at the expense of being more difficult to build and run. Cermine gives a bunch of infos, too much in my opinion, and I think Grobid is given the most reusable and complete results. Feel free to compare them yourself. </p>
71
+		<footer><p class="date">Le 19/01/2016 à 14:45</p>
72
+		<p class="tags">Tags : <a href="//phyks.me/tags/Science.html">Science</a>, <a href="//phyks.me/tags/OpenAccess.html">OpenAccess</a></p></footer>
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+		<p class="day">19</p>
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+		<p class="month">Janvier</p>
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+		<header><h1 class="article_title"><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></h1></header>
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+		<!-- 
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+    @author=Phyks
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+    @date=19012016-1445
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+    @title=Comparison of tools to fetch references for scientific papers
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+    @tags=Science,OpenAccess
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+-->
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+
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+<p>Recently, I tried to aggregate in <a href="https://github.com/Phyks/libbmc/">a single place</a> various codes I had written to handle scientific papers. Some feature I was missing, and I would like to add, was the ability to fetch automatically references from a given paper. For arXiv papers, I had a <a href="http://known.phyks.me/2015/lets-some-metadata-on-arxiv">simple solution</a> using the LaTeX sources, but I wanted to have something more universal, taking a simple PDF file in input (thanks <a href="https://www.linkedin.com/in/john-dove-a8825">John</a> for the suggestion, and <a href="http://www.alstevens.org/">Al</a> for the tips on existing software solutions).</p>
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+<p>I tried a comparison of three existing software to extract references from a PDF file:</p>
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+<ul>
63
+<li><a href="https://github.com/CrossRef/pdfextract">pdfextract</a> from Crossref, very easy to use, written in Ruby.</li>
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+<li><a href="https://github.com/kermitt2/grobid">Grobid</a>, more advanced (using machine learning models), written in Java, but quite easy to use too.</li>
65
+<li><a href="https://github.com/CeON/CERMINE">Cermine</a>, using the same approach as Grobid, but I could not get it to build on my computer. I used their <a href="http://cermine.ceon.pl/index.html">REST service</a> instead.</li>
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+</ul>
67
+<p>To compare them, I asked <a href="http://antonin.delpeuch.eu/">Antonin</a> to build a list of most important journals and take five papers for every such journal, from <a href="http://dissem.in/">Dissemin</a>. This gives us a <a href="http://pub.phyks.me/paper_references_extractor/papers.json">JSON file</a> containing around 500 papers.</p>
68
+<p>I downloaded some articles, to get a (hopefully) representative set, composed of 147 different papers from various journals (I did not had access to some of them, so I could not fetch the full dataset). I ran <code>pdfextract</code>, <code>Grobid</code> and <code>Cermine</code> on each of them and compared the results.</p>
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+<p>The raw results are available <a href="http://pub.phyks.me/paper_references_extractor/">here</a> for each paper, and I generated a single page comparison to ease the visual diff between the three results, available <a href="http://pub.phyks.me/paper_references_extractor/diff.html">here</a> (note that this webpage is <strong>very</strong> heavy, around 16MB).</p>
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+<p>Briefly comparing the results, the machine learning based models (Cermine and Grobid) seems to give far better results than the simple approach taken by pdfextract, at the expense of being more difficult to build and run. Cermine gives a bunch of infos, too much in my opinion, and I think Grobid is given the most reusable and complete results. Feel free to compare them yourself. </p>
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+		<footer><p class="date">Le 19/01/2016 à 14:45</p>
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+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
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+		<p class="day">19</p>
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+		<p class="month">Janvier</p>
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+	<div class="article">
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+		<header><h1 class="article_title"><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></h1></header>
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+		<!-- 
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+    @title=Comparison of tools to fetch references for scientific papers
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+-->
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+
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+<p>Recently, I tried to aggregate in <a href="https://github.com/Phyks/libbmc/">a single place</a> various codes I had written to handle scientific papers. Some feature I was missing, and I would like to add, was the ability to fetch automatically references from a given paper. For arXiv papers, I had a <a href="http://known.phyks.me/2015/lets-some-metadata-on-arxiv">simple solution</a> using the LaTeX sources, but I wanted to have something more universal, taking a simple PDF file in input (thanks <a href="https://www.linkedin.com/in/john-dove-a8825">John</a> for the suggestion, and <a href="http://www.alstevens.org/">Al</a> for the tips on existing software solutions).</p>
61
+<p>I tried a comparison of three existing software to extract references from a PDF file:</p>
62
+<ul>
63
+<li><a href="https://github.com/CrossRef/pdfextract">pdfextract</a> from Crossref, very easy to use, written in Ruby.</li>
64
+<li><a href="https://github.com/kermitt2/grobid">Grobid</a>, more advanced (using machine learning models), written in Java, but quite easy to use too.</li>
65
+<li><a href="https://github.com/CeON/CERMINE">Cermine</a>, using the same approach as Grobid, but I could not get it to build on my computer. I used their <a href="http://cermine.ceon.pl/index.html">REST service</a> instead.</li>
66
+</ul>
67
+<p>To compare them, I asked <a href="http://antonin.delpeuch.eu/">Antonin</a> to build a list of most important journals and take five papers for every such journal, from <a href="http://dissem.in/">Dissemin</a>. This gives us a <a href="http://pub.phyks.me/paper_references_extractor/papers.json">JSON file</a> containing around 500 papers.</p>
68
+<p>I downloaded some articles, to get a (hopefully) representative set, composed of 147 different papers from various journals (I did not had access to some of them, so I could not fetch the full dataset). I ran <code>pdfextract</code>, <code>Grobid</code> and <code>Cermine</code> on each of them and compared the results.</p>
69
+<p>The raw results are available <a href="http://pub.phyks.me/paper_references_extractor/">here</a> for each paper, and I generated a single page comparison to ease the visual diff between the three results, available <a href="http://pub.phyks.me/paper_references_extractor/diff.html">here</a> (note that this webpage is <strong>very</strong> heavy, around 16MB).</p>
70
+<p>Briefly comparing the results, the machine learning based models (Cermine and Grobid) seems to give far better results than the simple approach taken by pdfextract, at the expense of being more difficult to build and run. Cermine gives a bunch of infos, too much in my opinion, and I think Grobid is given the most reusable and complete results. Feel free to compare them yourself. </p>
71
+		<footer><p class="date">Le 19/01/2016 à 14:45</p>
72
+		<p class="tags">Tags : <a href="//phyks.me/tags/Science.html">Science</a>, <a href="//phyks.me/tags/OpenAccess.html">OpenAccess</a></p></footer>
73
+	</div>
74
+</article>
75
+<article>
76
+	<aside>
48 77
 		<p class="day">26</p>
49 78
 		<p class="month">Décembre</p>
50 79
 	</aside>
@@ -932,37 +961,6 @@ grunt server:dist
932 961
 		<p class="tags">Tags : <a href="//phyks.me/tags/Phyks.html">Phyks</a></p></footer>
933 962
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934 963
 </article>
935
-<article>
936
-	<aside>
937
-		<p class="day">09</p>
938
-		<p class="month">Novembre</p>
939
-	</aside>
940
-	<div class="article">
941
-		<header><h1 class="article_title"><a href="//phyks.me/2014/11/ipv6_kimsufi.html">Getting ipv6 to work with a Kimsufi server</a></h1></header>
942
-		<!-- 
943
-    @author=Phyks
944
-    @date=09112014-1945
945
-    @title=Getting ipv6 to work with a Kimsufi server
946
-    @tags=Phyks
947
--->
948
-
949
-<p>Starting from yesterday, my server (<a href="http://phyks.me">phyks.me</a>) should be available using ipv6. This was not the case before due to laziness and a lack of configuration. However, as setting ipv6 on a Kimsufi seems to not be really straight-forward (out of date documentation, information disseminated over the web and difficult to find between basic mistakes and real errors…), I think it may be useful to keep some notes here. Hope it can help anyone.</p>
950
-<p>The <a href="http://help.ovh.co.uk/Ipv4Ipv6">doc</a> explains that OVH has not set ipv6 autoconfig on their servers, and that you should configure the default route and IP address yourself.</p>
951
-<p>To find your ip address, it is pretty easy: just go to your manager and look for the ipv6 address in the IP section.</p>
952
-<p><code>ip -6 addr add YOUR_IPV6_ADDRESS/64 dev eth0</code></p>
953
-<p>This will add the ipv6 address to your network device. Then, you have to manually add the default gateway. To get its address, you should remove the last two digits of your ipv6 address and put <code>FF:FF:FF:FF:FF</code> instead. This means that <code>2001:41d0:1:4462::1/64</code> will give you a default gateway <code>2001:41d0:1:44FF:FF:FF:FF:FF</code>.</p>
954
-<p>Then, you should add a default route <em>via</em> this gateway</p>
955
-<p><code>ip -6 r a default via 2001:41d0:1:44FF:FF:FF:FF:FF</code></p>
956
-<p>This is the standard procedure explained in OVH guide and many posts around the web such as <a href="https://www.skyminds.net/serveur-dedie-mise-en-place-de-lipv6/">this one</a> (in French). It may work in some cases, however, in my case, I could not reach the default gateway and then, I could not add this route.</p>
957
-<p>I found <a href="http://forum.ovh.co.uk/showthread.php?6435-Getting-IPv6-working-on-kimsufi&amp;p=44965&amp;viewfull=1#post44965">a comment</a> on the OVH forum giving a solution.</p>
958
-<p>You should first add a route to reach the gateway</p>
959
-<p><code>ip -6 r a 2001:41d0:1:44FF:FF:FF:FF:FF dev eth0</code></p>
960
-<p>and then, you can add the default route <em>via</em> this gateway</p>
961
-<p><code>ip -6 r a default via 2001:41d0:1:44FF:FF:FF:FF:FF</code></p>
962
-		<footer><p class="date">Le 09/11/2014 à 19:45</p>
963
-		<p class="tags">Tags : <a href="//phyks.me/tags/Phyks.html">Phyks</a></p></footer>
964
-	</div>
965
-</article>
966 964
 <p class="archives"><a href="//phyks.me/archives.html">Archives</a></p>            </div>
967 965
             <footer id="rss">
968 966
                 <p><a href="//phyks.me/rss.xml"><img src="//phyks.me/img/rss.png" alt="RSS"/></a></p>

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8 8
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9 9
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10
-		<lastBuildDate>Sat, 26 Dec 2015 21:18:05 -0000</lastBuildDate>
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+		<lastBuildDate>Tue, 19 Jan 2016 12:45:31 -0000</lastBuildDate>
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+		<item>
12
+			<title>Comparison of tools to fetch references for scientific papers</title>
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+			<guid isPermaLink="true">http://phyks.me/2016/01/fetching_references_papers.html</guid>
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+Recently, I tried to aggregate in a single place various codes I had written to handle scientific paper…</description>
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21
+<header></header>
22
+<!-- 
23
+    @author=Phyks
24
+    @date=19012016-1445
25
+    @title=Comparison of tools to fetch references for scientific papers
26
+    @tags=Science,OpenAccess
27
+-->
28
+<p>Recently, I tried to aggregate in <a href="https://github.com/Phyks/libbmc/">a single place</a> various codes I had written to handle scientific papers. Some feature I was missing, and I would like to add, was the ability to fetch automatically references from a given paper. For arXiv papers, I had a <a href="http://known.phyks.me/2015/lets-some-metadata-on-arxiv">simple solution</a> using the LaTeX sources, but I wanted to have something more universal, taking a simple PDF file in input (thanks <a href="https://www.linkedin.com/in/john-dove-a8825">John</a> for the suggestion, and <a href="http://www.alstevens.org/">Al</a> for the tips on existing software solutions).</p>
29
+<p>I tried a comparison of three existing software to extract references from a PDF file:</p>
30
+<ul>
31
+<li><a href="https://github.com/CrossRef/pdfextract">pdfextract</a> from Crossref, very easy to use, written in Ruby.</li>
32
+<li><a href="https://github.com/kermitt2/grobid">Grobid</a>, more advanced (using machine learning models), written in Java, but quite easy to use too.</li>
33
+<li><a href="https://github.com/CeON/CERMINE">Cermine</a>, using the same approach as Grobid, but I could not get it to build on my computer. I used their <a href="http://cermine.ceon.pl/index.html">REST service</a> instead.</li>
34
+</ul>
35
+<p>To compare them, I asked <a href="http://antonin.delpeuch.eu/">Antonin</a> to build a list of most important journals and take five papers for every such journal, from <a href="http://dissem.in/">Dissemin</a>. This gives us a <a href="http://pub.phyks.me/paper_references_extractor/papers.json">JSON file</a> containing around 500 papers.</p>
36
+<p>I downloaded some articles, to get a (hopefully) representative set, composed of 147 different papers from various journals (I did not had access to some of them, so I could not fetch the full dataset). I ran <code>pdfextract</code>, <code>Grobid</code> and <code>Cermine</code> on each of them and compared the results.</p>
37
+<p>The raw results are available <a href="http://pub.phyks.me/paper_references_extractor/">here</a> for each paper, and I generated a single page comparison to ease the visual diff between the three results, available <a href="http://pub.phyks.me/paper_references_extractor/diff.html">here</a> (note that this webpage is <strong>very</strong> heavy, around 16MB).</p>
38
+<p>Briefly comparing the results, the machine learning based models (Cermine and Grobid) seems to give far better results than the simple approach taken by pdfextract, at the expense of being more difficult to build and run. Cermine gives a bunch of infos, too much in my opinion, and I think Grobid is given the most reusable and complete results. Feel free to compare them yourself. </p>
39
+<footer>
40
+<p class="tags">Tags : <a href="http://phyks.me/tags/Science.html">Science</a>, <a href="http://phyks.me/tags/OpenAccess.html">OpenAccess</a></p></footer>
41
+</div>]]></content:encoded>
42
+			<pubDate>Tue, 19 Jan 2016 12:45:00 -0000</pubDate>
43
+			<category>Science</category>
44
+			<category>OpenAccess</category>
45
+			<author>webmaster@phyks.me (Phyks)</author>
46
+		</item>
11 47
 		<item>
12 48
 			<title>Localizing a webapp with webL10n.js</title>
13 49
 			<link>http://phyks.me/2015/12/localizing_webapp.html</link>
@@ -1008,42 +1044,5 @@ Lorsqu'on fait de la recherche scientifique (ou de la veille), on est très vite
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1009 1045
 			<author>webmaster@phyks.me (Phyks)</author>
1010 1046
 		</item>
1011
-		<item>
1012
-			<title>Getting ipv6 to work with a Kimsufi server</title>
1013
-			<link>http://phyks.me/2014/11/ipv6_kimsufi.html</link>
1014
-			<guid isPermaLink="true">http://phyks.me/2014/11/ipv6_kimsufi.html</guid>
1015
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1016
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1017
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1018
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1019
-Starting from yesterday, my server (phyks.me) should be available using ipv6. This was not the case before due to laziness and a lack of configuratio…</description>
1020
-			<content:encoded><![CDATA[<div class="article">
1021
-<header></header>
1022
-<!-- 
1023
-    @author=Phyks
1024
-    @date=09112014-1945
1025
-    @title=Getting ipv6 to work with a Kimsufi server
1026
-    @tags=Phyks
1027
--->
1028
-<p>Starting from yesterday, my server (<a href="http://phyks.me">phyks.me</a>) should be available using ipv6. This was not the case before due to laziness and a lack of configuration. However, as setting ipv6 on a Kimsufi seems to not be really straight-forward (out of date documentation, information disseminated over the web and difficult to find between basic mistakes and real errors…), I think it may be useful to keep some notes here. Hope it can help anyone.</p>
1029
-<p>The <a href="http://help.ovh.co.uk/Ipv4Ipv6">doc</a> explains that OVH has not set ipv6 autoconfig on their servers, and that you should configure the default route and IP address yourself.</p>
1030
-<p>To find your ip address, it is pretty easy: just go to your manager and look for the ipv6 address in the IP section.</p>
1031
-<p><code>ip -6 addr add YOUR_IPV6_ADDRESS/64 dev eth0</code></p>
1032
-<p>This will add the ipv6 address to your network device. Then, you have to manually add the default gateway. To get its address, you should remove the last two digits of your ipv6 address and put <code>FF:FF:FF:FF:FF</code> instead. This means that <code>2001:41d0:1:4462::1/64</code> will give you a default gateway <code>2001:41d0:1:44FF:FF:FF:FF:FF</code>.</p>
1033
-<p>Then, you should add a default route <em>via</em> this gateway</p>
1034
-<p><code>ip -6 r a default via 2001:41d0:1:44FF:FF:FF:FF:FF</code></p>
1035
-<p>This is the standard procedure explained in OVH guide and many posts around the web such as <a href="https://www.skyminds.net/serveur-dedie-mise-en-place-de-lipv6/">this one</a> (in French). It may work in some cases, however, in my case, I could not reach the default gateway and then, I could not add this route.</p>
1036
-<p>I found <a href="http://forum.ovh.co.uk/showthread.php?6435-Getting-IPv6-working-on-kimsufi&amp;p=44965&amp;viewfull=1#post44965">a comment</a> on the OVH forum giving a solution.</p>
1037
-<p>You should first add a route to reach the gateway</p>
1038
-<p><code>ip -6 r a 2001:41d0:1:44FF:FF:FF:FF:FF dev eth0</code></p>
1039
-<p>and then, you can add the default route <em>via</em> this gateway</p>
1040
-<p><code>ip -6 r a default via 2001:41d0:1:44FF:FF:FF:FF:FF</code></p>
1041
-<footer>
1042
-<p class="tags">Tags : <a href="http://phyks.me/tags/Phyks.html">Phyks</a></p></footer>
1043
-</div>]]></content:encoded>
1044
-			<pubDate>Sun, 09 Nov 2014 17:45:00 -0000</pubDate>
1045
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1046
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1049 1048
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19
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20 20
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21 21
 
22 22
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23 23
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24
-                            <li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/2015/05/servos_rpi.html">Controlling servomotors on a Raspberry Pi</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
24
+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
25 25
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26 26
 
27 27
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+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
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24
+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
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 <article>
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+		<p class="day">19</p>
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+		<p class="month">Janvier</p>
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+	</aside>
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+	<div class="article">
52
+		<header><h1 class="article_title"><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></h1></header>
53
+		<!-- 
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+    @author=Phyks
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+    @date=19012016-1445
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+    @title=Comparison of tools to fetch references for scientific papers
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+    @tags=Science,OpenAccess
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+-->
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+
60
+<p>Recently, I tried to aggregate in <a href="https://github.com/Phyks/libbmc/">a single place</a> various codes I had written to handle scientific papers. Some feature I was missing, and I would like to add, was the ability to fetch automatically references from a given paper. For arXiv papers, I had a <a href="http://known.phyks.me/2015/lets-some-metadata-on-arxiv">simple solution</a> using the LaTeX sources, but I wanted to have something more universal, taking a simple PDF file in input (thanks <a href="https://www.linkedin.com/in/john-dove-a8825">John</a> for the suggestion, and <a href="http://www.alstevens.org/">Al</a> for the tips on existing software solutions).</p>
61
+<p>I tried a comparison of three existing software to extract references from a PDF file:</p>
62
+<ul>
63
+<li><a href="https://github.com/CrossRef/pdfextract">pdfextract</a> from Crossref, very easy to use, written in Ruby.</li>
64
+<li><a href="https://github.com/kermitt2/grobid">Grobid</a>, more advanced (using machine learning models), written in Java, but quite easy to use too.</li>
65
+<li><a href="https://github.com/CeON/CERMINE">Cermine</a>, using the same approach as Grobid, but I could not get it to build on my computer. I used their <a href="http://cermine.ceon.pl/index.html">REST service</a> instead.</li>
66
+</ul>
67
+<p>To compare them, I asked <a href="http://antonin.delpeuch.eu/">Antonin</a> to build a list of most important journals and take five papers for every such journal, from <a href="http://dissem.in/">Dissemin</a>. This gives us a <a href="http://pub.phyks.me/paper_references_extractor/papers.json">JSON file</a> containing around 500 papers.</p>
68
+<p>I downloaded some articles, to get a (hopefully) representative set, composed of 147 different papers from various journals (I did not had access to some of them, so I could not fetch the full dataset). I ran <code>pdfextract</code>, <code>Grobid</code> and <code>Cermine</code> on each of them and compared the results.</p>
69
+<p>The raw results are available <a href="http://pub.phyks.me/paper_references_extractor/">here</a> for each paper, and I generated a single page comparison to ease the visual diff between the three results, available <a href="http://pub.phyks.me/paper_references_extractor/diff.html">here</a> (note that this webpage is <strong>very</strong> heavy, around 16MB).</p>
70
+<p>Briefly comparing the results, the machine learning based models (Cermine and Grobid) seems to give far better results than the simple approach taken by pdfextract, at the expense of being more difficult to build and run. Cermine gives a bunch of infos, too much in my opinion, and I think Grobid is given the most reusable and complete results. Feel free to compare them yourself. </p>
71
+		<footer><p class="date">Le 19/01/2016 à 14:45</p>
72
+		<p class="tags">Tags : <a href="//phyks.me/tags/Science.html">Science</a>, <a href="//phyks.me/tags/OpenAccess.html">OpenAccess</a></p></footer>
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+	</div>
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+</article>
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+<article>
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+	<aside>
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49 78
 		<p class="month">Décembre</p>
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+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
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24
+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
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24
+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
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46 46
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+		<p class="day">19</p>
49
+		<p class="month">Janvier</p>
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+	</aside>
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+	<div class="article">
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+		<header><h1 class="article_title"><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></h1></header>
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+		<!-- 
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+    @author=Phyks
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+    @date=19012016-1445
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+    @title=Comparison of tools to fetch references for scientific papers
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+    @tags=Science,OpenAccess
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+-->
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+
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+<p>Recently, I tried to aggregate in <a href="https://github.com/Phyks/libbmc/">a single place</a> various codes I had written to handle scientific papers. Some feature I was missing, and I would like to add, was the ability to fetch automatically references from a given paper. For arXiv papers, I had a <a href="http://known.phyks.me/2015/lets-some-metadata-on-arxiv">simple solution</a> using the LaTeX sources, but I wanted to have something more universal, taking a simple PDF file in input (thanks <a href="https://www.linkedin.com/in/john-dove-a8825">John</a> for the suggestion, and <a href="http://www.alstevens.org/">Al</a> for the tips on existing software solutions).</p>
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+<p>I tried a comparison of three existing software to extract references from a PDF file:</p>
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+<ul>
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+<li><a href="https://github.com/CrossRef/pdfextract">pdfextract</a> from Crossref, very easy to use, written in Ruby.</li>
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+<li><a href="https://github.com/kermitt2/grobid">Grobid</a>, more advanced (using machine learning models), written in Java, but quite easy to use too.</li>
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+<li><a href="https://github.com/CeON/CERMINE">Cermine</a>, using the same approach as Grobid, but I could not get it to build on my computer. I used their <a href="http://cermine.ceon.pl/index.html">REST service</a> instead.</li>
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+</ul>
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+<p>To compare them, I asked <a href="http://antonin.delpeuch.eu/">Antonin</a> to build a list of most important journals and take five papers for every such journal, from <a href="http://dissem.in/">Dissemin</a>. This gives us a <a href="http://pub.phyks.me/paper_references_extractor/papers.json">JSON file</a> containing around 500 papers.</p>
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+<p>I downloaded some articles, to get a (hopefully) representative set, composed of 147 different papers from various journals (I did not had access to some of them, so I could not fetch the full dataset). I ran <code>pdfextract</code>, <code>Grobid</code> and <code>Cermine</code> on each of them and compared the results.</p>
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+<p>The raw results are available <a href="http://pub.phyks.me/paper_references_extractor/">here</a> for each paper, and I generated a single page comparison to ease the visual diff between the three results, available <a href="http://pub.phyks.me/paper_references_extractor/diff.html">here</a> (note that this webpage is <strong>very</strong> heavy, around 16MB).</p>
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+<p>Briefly comparing the results, the machine learning based models (Cermine and Grobid) seems to give far better results than the simple approach taken by pdfextract, at the expense of being more difficult to build and run. Cermine gives a bunch of infos, too much in my opinion, and I think Grobid is given the most reusable and complete results. Feel free to compare them yourself. </p>
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+		<footer><p class="date">Le 19/01/2016 à 14:45</p>
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+		<p class="tags">Tags : <a href="//phyks.me/tags/Science.html">Science</a>, <a href="//phyks.me/tags/OpenAccess.html">OpenAccess</a></p></footer>
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+	</div>
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+</article>
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+<article>
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+	<aside>
48 77
 		<p class="day">26</p>
49 78
 		<p class="month">Décembre</p>
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+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
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+<article>
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+	<aside>
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+		<p class="day">19</p>
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+		<p class="month">Janvier</p>
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+	</aside>
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+	<div class="article">
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+		<header><h1 class="article_title"><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></h1></header>
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+		<!-- 
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+    @author=Phyks
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+    @date=19012016-1445
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+    @title=Comparison of tools to fetch references for scientific papers
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+    @tags=Science,OpenAccess
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+-->
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+
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+<p>Recently, I tried to aggregate in <a href="https://github.com/Phyks/libbmc/">a single place</a> various codes I had written to handle scientific papers. Some feature I was missing, and I would like to add, was the ability to fetch automatically references from a given paper. For arXiv papers, I had a <a href="http://known.phyks.me/2015/lets-some-metadata-on-arxiv">simple solution</a> using the LaTeX sources, but I wanted to have something more universal, taking a simple PDF file in input (thanks <a href="https://www.linkedin.com/in/john-dove-a8825">John</a> for the suggestion, and <a href="http://www.alstevens.org/">Al</a> for the tips on existing software solutions).</p>
16
+<p>I tried a comparison of three existing software to extract references from a PDF file:</p>
17
+<ul>
18
+<li><a href="https://github.com/CrossRef/pdfextract">pdfextract</a> from Crossref, very easy to use, written in Ruby.</li>
19
+<li><a href="https://github.com/kermitt2/grobid">Grobid</a>, more advanced (using machine learning models), written in Java, but quite easy to use too.</li>
20
+<li><a href="https://github.com/CeON/CERMINE">Cermine</a>, using the same approach as Grobid, but I could not get it to build on my computer. I used their <a href="http://cermine.ceon.pl/index.html">REST service</a> instead.</li>
21
+</ul>
22
+<p>To compare them, I asked <a href="http://antonin.delpeuch.eu/">Antonin</a> to build a list of most important journals and take five papers for every such journal, from <a href="http://dissem.in/">Dissemin</a>. This gives us a <a href="http://pub.phyks.me/paper_references_extractor/papers.json">JSON file</a> containing around 500 papers.</p>
23
+<p>I downloaded some articles, to get a (hopefully) representative set, composed of 147 different papers from various journals (I did not had access to some of them, so I could not fetch the full dataset). I ran <code>pdfextract</code>, <code>Grobid</code> and <code>Cermine</code> on each of them and compared the results.</p>
24
+<p>The raw results are available <a href="http://pub.phyks.me/paper_references_extractor/">here</a> for each paper, and I generated a single page comparison to ease the visual diff between the three results, available <a href="http://pub.phyks.me/paper_references_extractor/diff.html">here</a> (note that this webpage is <strong>very</strong> heavy, around 16MB).</p>
25
+<p>Briefly comparing the results, the machine learning based models (Cermine and Grobid) seems to give far better results than the simple approach taken by pdfextract, at the expense of being more difficult to build and run. Cermine gives a bunch of infos, too much in my opinion, and I think Grobid is given the most reusable and complete results. Feel free to compare them yourself. </p>
26
+		<footer><p class="date">Le 19/01/2016 à 14:45</p>
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+		<p class="tags">Tags : <a href="//phyks.me/tags/Science.html">Science</a>, <a href="//phyks.me/tags/OpenAccess.html">OpenAccess</a></p></footer>
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+	</div>
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+                            <li><a href="//phyks.me/2016/01/fetching_references_papers.html">Comparison of tools to fetch references for scientific papers</a></li><li><a href="//phyks.me/2015/12/localizing_webapp.html">Localizing a webapp with webL10n.js</a></li><li><a href="//phyks.me/2015/12/putting_metadata_on_arxiv.html">Let's add some metadata on arXiv!</a></li><li><a href="//phyks.me/2015/10/low_cost_telepresence.html">Doing low cost telepresence (for under $200)</a></li><li><a href="//phyks.me/2015/10/working_in_paris.html">Working on the go in Paris</a></li><li><a href="//phyks.me/archives.html">Archives</a></li>
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+<!--
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+	@author=Phyks
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+	@date=19012016-1445
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+	@title=Comparison of tools to fetch references for scientific papers
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+	@tags=Science,OpenAccess
6
+-->
7
+
8
+Recently, I tried to aggregate in [a single place](https://github.com/Phyks/libbmc/) various codes I had written to handle scientific papers. Some feature I was missing, and I would like to add, was the ability to fetch automatically references from a given paper. For arXiv papers, I had a [simple solution](http://known.phyks.me/2015/lets-some-metadata-on-arxiv) using the LaTeX sources, but I wanted to have something more universal, taking a simple PDF file in input (thanks [John](https://www.linkedin.com/in/john-dove-a8825) for the suggestion, and [Al](http://www.alstevens.org/) for the tips on existing software solutions).
9
+
10
+I tried a comparison of three existing software to extract references from a PDF file:
11
+
12
+* [pdfextract](https://github.com/CrossRef/pdfextract) from Crossref, very easy to use, written in Ruby.
13
+* [Grobid](https://github.com/kermitt2/grobid), more advanced (using machine learning models), written in Java, but quite easy to use too.
14
+* [Cermine](https://github.com/CeON/CERMINE), using the same approach as Grobid, but I could not get it to build on my computer. I used their [REST service](http://cermine.ceon.pl/index.html) instead.
15
+
16
+
17
+To compare them, I asked [Antonin](http://antonin.delpeuch.eu/) to build a list of most important journals and take five papers for every such journal, from [Dissemin](http://dissem.in/). This gives us a [JSON file](http://pub.phyks.me/paper_references_extractor/papers.json) containing around 500 papers.
18
+
19
+I downloaded some articles, to get a (hopefully) representative set, composed of 147 different papers from various journals (I did not had access to some of them, so I could not fetch the full dataset). I ran `pdfextract`, `Grobid` and `Cermine` on each of them and compared the results.
20
+
21
+
22
+The raw results are available [here](http://pub.phyks.me/paper_references_extractor/) for each paper, and I generated a single page comparison to ease the visual diff between the three results, available [here](http://pub.phyks.me/paper_references_extractor/diff.html) (note that this webpage is **very** heavy, around 16MB).
23
+
24
+
25
+Briefly comparing the results, the machine learning based models (Cermine and Grobid) seems to give far better results than the simple approach taken by pdfextract, at the expense of being more difficult to build and run. Cermine gives a bunch of infos, too much in my opinion, and I think Grobid is given the most reusable and complete results. Feel free to compare them yourself.