mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-10-23 01:13:01 +02:00
213 lines
6.8 KiB
HTML
213 lines
6.8 KiB
HTML
<!DOCTYPE html>
|
|
<html lang="en" >
|
|
|
|
<head>
|
|
<meta charset="utf-8">
|
|
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
|
|
|
|
|
<meta property="og:title" content="October, 2024" />
|
|
<meta property="og:description" content="2024-10-03
|
|
|
|
I had an idea to get abstracts from OpenAlex
|
|
|
|
For copyright reasons they don’t include plain abstracts, but the pyalex library can convert them on the fly
|
|
|
|
|
|
" />
|
|
<meta property="og:type" content="article" />
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2024-10/" />
|
|
<meta property="article:published_time" content="2024-10-03T11:01:00+03:00" />
|
|
<meta property="article:modified_time" content="2024-10-03T11:01:00+03:00" />
|
|
|
|
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="October, 2024"/>
|
|
<meta name="twitter:description" content="2024-10-03
|
|
|
|
I had an idea to get abstracts from OpenAlex
|
|
|
|
For copyright reasons they don’t include plain abstracts, but the pyalex library can convert them on the fly
|
|
|
|
|
|
"/>
|
|
<meta name="generator" content="Hugo 0.133.1">
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "BlogPosting",
|
|
"headline": "October, 2024",
|
|
"url": "https://alanorth.github.io/cgspace-notes/2024-10/",
|
|
"wordCount": "125",
|
|
"datePublished": "2024-10-03T11:01:00+03:00",
|
|
"dateModified": "2024-10-03T11:01:00+03:00",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"keywords": "Notes"
|
|
}
|
|
</script>
|
|
|
|
|
|
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2024-10/">
|
|
|
|
<title>October, 2024 | CGSpace Notes</title>
|
|
|
|
|
|
<!-- combined, minified CSS -->
|
|
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.c6ba80bc50669557645abe05f86b73cc5af84408ed20f1551a267bc19ece8228.css" rel="stylesheet" integrity="sha256-xrqAvFBmlVdkWr4F+GtzzFr4RAjtIPFVGiZ7wZ7Ogig=" crossorigin="anonymous">
|
|
|
|
|
|
<!-- minified Font Awesome for SVG icons -->
|
|
|
|
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz+lcnA=" crossorigin="anonymous"></script>
|
|
|
|
<!-- RSS 2.0 feed -->
|
|
|
|
|
|
|
|
|
|
</head>
|
|
|
|
<body>
|
|
|
|
|
|
<div class="blog-masthead">
|
|
<div class="container">
|
|
<nav class="nav blog-nav">
|
|
<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
|
|
</nav>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
|
|
|
|
<header class="blog-header">
|
|
<div class="container">
|
|
<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
|
|
<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
|
|
</div>
|
|
</header>
|
|
|
|
|
|
|
|
|
|
<div class="container">
|
|
<div class="row">
|
|
<div class="col-sm-8 blog-main">
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2024-10/">October, 2024</a></h2>
|
|
<p class="blog-post-meta">
|
|
<time datetime="2024-10-03T11:01:00+03:00">Thu Oct 03, 2024</time>
|
|
in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2024-10-03">2024-10-03</h2>
|
|
<ul>
|
|
<li>I had an idea to get abstracts from OpenAlex
|
|
<ul>
|
|
<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>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<ul>
|
|
<li>I filtered for journal articles that were Creative Commons and missing abstracts:</li>
|
|
</ul>
|
|
<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
|
|
</span></span></code></pre></div><ul>
|
|
<li>Then wrote a script to get them from OpenAlex
|
|
<ul>
|
|
<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>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<!-- raw HTML omitted -->
|
|
|
|
|
|
|
|
|
|
|
|
</article>
|
|
|
|
|
|
|
|
</div> <!-- /.blog-main -->
|
|
|
|
<aside class="col-sm-3 ml-auto blog-sidebar">
|
|
|
|
|
|
|
|
<section class="sidebar-module">
|
|
<h4>Recent Posts</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
|
|
<li><a href="/cgspace-notes/2024-10/">October, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-09/">September, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-08/">August, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-06/">June, 2024</a></li>
|
|
|
|
</ol>
|
|
</section>
|
|
|
|
|
|
|
|
|
|
<section class="sidebar-module">
|
|
<h4>Links</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
|
|
|
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
|
|
|
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
|
|
|
</ol>
|
|
</section>
|
|
|
|
</aside>
|
|
|
|
|
|
</div> <!-- /.row -->
|
|
</div> <!-- /.container -->
|
|
|
|
|
|
|
|
<footer class="blog-footer">
|
|
<p dir="auto">
|
|
|
|
Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
|
|
|
|
</p>
|
|
<p>
|
|
<a href="#">Back to top</a>
|
|
</p>
|
|
</footer>
|
|
|
|
|
|
</body>
|
|
|
|
</html>
|