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I had an idea to get abstracts from OpenAlex
For copyright reasons they don&rsquo;t include plain abstracts, but the pyalex library can convert them on the fly
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I had an idea to get abstracts from OpenAlex
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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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<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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<time datetime="2024-10-03T11:01:00+03:00">Thu Oct 03, 2024</time>
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<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&rsquo;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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<li>I filtered for journal articles that were Creative Commons and missing abstracts:</li>
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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">&#39;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]&#39;</span> ~/Downloads/2024-09-30-cgspace.csv | csvgrep -c <span style="color:#e6db74">&#39;dcterms.type[en_US]&#39;</span> -r <span style="color:#e6db74">&#39;^Journal Article$&#39;</span> | csvgrep -c <span style="color:#e6db74">&#39;cg.identifier.doi[en_US]&#39;</span> -r <span style="color:#e6db74">&#39;^.+$&#39;</span> | csvgrep -c <span style="color:#e6db74">&#39;dcterms.license[en_US]&#39;</span> -r <span style="color:#e6db74">&#39;^CC-&#39;</span> | csvgrep -c <span style="color:#e6db74">&#39;dcterms.abstract[en_US]&#39;</span> -r <span style="color:#e6db74">&#39;^$&#39;</span> | csvgrep -c <span style="color:#e6db74">&#39;dcterms.language[en_US]&#39;</span> -r <span style="color:#e6db74">&#39;^en$&#39;</span> | grep -v <span style="color:#e6db74">&#34;||&#34;</span> | grep -v -- <span style="color:#e6db74">&#39;-ND&#39;</span> | grep -v -E <span style="color:#e6db74">&#39;https://doi.org/10.(2499|4160|17528)/&#39;</span> &gt; /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 &ldquo;Keywords:&rdquo; and copyright, and HTML entities, etc) I managed to get about 440</li>
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</li>
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<h4>Recent Posts</h4>
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<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>
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<h4>Links</h4>
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<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>
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