mirror of
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213 lines
6.8 KiB
HTML
213 lines
6.8 KiB
HTML
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<!DOCTYPE html>
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<html lang="en" >
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta property="og:title" content="October, 2024" />
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<meta property="og:description" content="2024-10-03
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I had an idea to get abstracts from OpenAlex
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For copyright reasons they don’t include plain abstracts, but the pyalex library can convert them on the fly
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2024-10/" />
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<meta property="article:published_time" content="2024-10-03T11:01:00+03:00" />
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<meta property="article:modified_time" content="2024-10-03T11:01:00+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="October, 2024"/>
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<meta name="twitter:description" content="2024-10-03
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I had an idea to get abstracts from OpenAlex
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For copyright reasons they don’t include plain abstracts, but the pyalex library can convert them on the fly
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"/>
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<meta name="generator" content="Hugo 0.133.1">
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<script type="application/ld+json">
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{
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"headline": "October, 2024",
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"url": "https://alanorth.github.io/cgspace-notes/2024-10/",
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"wordCount": "125",
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"datePublished": "2024-10-03T11:01:00+03:00",
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"dateModified": "2024-10-03T11:01:00+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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},
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"keywords": "Notes"
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}
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</script>
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2024-10/">
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<title>October, 2024 | CGSpace Notes</title>
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<!-- combined, minified CSS -->
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<link href="https://alanorth.github.io/cgspace-notes/css/style.c6ba80bc50669557645abe05f86b73cc5af84408ed20f1551a267bc19ece8228.css" rel="stylesheet" integrity="sha256-xrqAvFBmlVdkWr4F+GtzzFr4RAjtIPFVGiZ7wZ7Ogig=" crossorigin="anonymous">
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<!-- minified Font Awesome for SVG icons -->
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<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz+lcnA=" crossorigin="anonymous"></script>
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</head>
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<body>
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<div class="blog-masthead">
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<div class="container">
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<nav class="nav blog-nav">
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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</nav>
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</div>
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</div>
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<header class="blog-header">
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<div class="container">
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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</div>
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</header>
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<div class="container">
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<div class="row">
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<div class="col-sm-8 blog-main">
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2024-10/">October, 2024</a></h2>
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<p class="blog-post-meta">
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<time datetime="2024-10-03T11:01:00+03:00">Thu Oct 03, 2024</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2024-10-03">2024-10-03</h2>
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<ul>
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<li>I had an idea to get abstracts from OpenAlex
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<ul>
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<li>For <a href="https://docs.openalex.org/api-entities/works/work-object#abstract_inverted_index">copyright reasons they don’t include plain abstracts</a>, but the <a href="https://github.com/J535D165/pyalex">pyalex</a> library can convert them on the fly</li>
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</ul>
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</li>
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</ul>
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<ul>
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<li>I filtered for journal articles that were Creative Commons and missing abstracts:</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ csvcut -c <span style="color:#e6db74">'id,dc.title[en_US],dcterms.abstract[en_US],cg.identifier.doi[en_US],dcterms.type[en_US],dcterms.language[en_US],dcterms.license[en_US]'</span> ~/Downloads/2024-09-30-cgspace.csv | csvgrep -c <span style="color:#e6db74">'dcterms.type[en_US]'</span> -r <span style="color:#e6db74">'^Journal Article$'</span> | csvgrep -c <span style="color:#e6db74">'cg.identifier.doi[en_US]'</span> -r <span style="color:#e6db74">'^.+$'</span> | csvgrep -c <span style="color:#e6db74">'dcterms.license[en_US]'</span> -r <span style="color:#e6db74">'^CC-'</span> | csvgrep -c <span style="color:#e6db74">'dcterms.abstract[en_US]'</span> -r <span style="color:#e6db74">'^$'</span> | csvgrep -c <span style="color:#e6db74">'dcterms.language[en_US]'</span> -r <span style="color:#e6db74">'^en$'</span> | grep -v <span style="color:#e6db74">"||"</span> | grep -v -- <span style="color:#e6db74">'-ND'</span> | grep -v -E <span style="color:#e6db74">'https://doi.org/10.(2499|4160|17528)/'</span> > /tmp/missing-abstracts.csv
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</span></span></code></pre></div><ul>
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<li>Then wrote a script to get them from OpenAlex
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<ul>
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<li>After inspecting and cleaning a few dozen up in OpenRefine (removing “Keywords:” and copyright, and HTML entities, etc) I managed to get about 440</li>
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</ul>
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</li>
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</ul>
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<!-- raw HTML omitted -->
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2024-10/">October, 2024</a></li>
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<li><a href="/cgspace-notes/2024-09/">September, 2024</a></li>
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<li><a href="/cgspace-notes/2024-08/">August, 2024</a></li>
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<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
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<li><a href="/cgspace-notes/2024-06/">June, 2024</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p dir="auto">
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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</p>
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<p>
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<a href="#">Back to top</a>
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</p>
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</footer>
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</body>
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</html>
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