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	<h1>About Search Workbench</h1>
	<a id="about" class="label label-default" href="index.html">Home</a>
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		<h2>Why Search Workbench?</h2>
    <p>An extension of the work in <a href="https://esperr.github.io/visualizingpubmed/">
      Visualizing PubMed</a>, Search Workbench allows you to examine, edit and visualize your <a href="https://www.ncbi.nlm.nih.gov/pubmed/">PubMed</a> searches. Perhaps most importantly, it also allow you to directly <em>compare</em> searches to one another &mdash;
      facilitating the process of fine-tuning a search strategy.</p>

    <h2>How it works</h2>
    <p>When you enter a search, it is run against PubMed using the <a href="https://www.ncbi.nlm.nih.gov/books/NBK25501/">programmatic interface</a> maintainted by the <a href="https://www.ncbi.nlm.nih.gov/">National Center for Biotechnology Information</a>. You first see how your search
      is tranlated by <a href="https://www.nlm.nih.gov/bsd/disted/pubmedtutorial/020_040.html">Automated Term Mapping</a>. Then you see how the parts of your search relate to one another (using the logic that drives <a href="https://pubvenn.appspot.com/">PubVenn</a>) and how that search performs over time
      (via <a href="https://esperr.github.io/pubmed-by-year/">PubMed-by-year</a>).</p>

    <h3>Search nicknames</h3>
    <p>If you directly edit a PubMed <a href="https://www.nlm.nih.gov/bsd/disted/pubmedtutorial/020_040.html">translation</a>, you'll notice that even simple searches, such as "diabetes and heart disease", quickly turn into something a bit more ungainly:
      <blockquote style="font-size: 90%;">("diabetes mellitus"[MeSH Terms] OR ("diabetes"[All Fields] AND "mellitus"[All Fields]) OR "diabetes mellitus"[All Fields] OR "diabetes"[All Fields] OR "diabetes insipidus"[MeSH Terms] OR ("diabetes"[All Fields] AND "insipidus"[All Fields]) OR "diabetes insipidus"[All Fields]) AND ("heart diseases"[MeSH Terms] OR ("heart"[All Fields] AND "diseases"[All Fields]) OR "heart diseases"[All Fields] OR ("heart"[All Fields] AND "disease"[All Fields]) OR "heart disease"[All Fields])
      </blockquote>
      <img src="nickname.PNG" />
      Using such long strings as search labels makes it difficult to see slight variations in a search. It also makes comparing them on a chart cumbersome.</p>
      <p>In these cases, please take advantage of the ability to <em>nickname</em> a search. Choose a name, click "add", and you'll use that nickname for that search going forward
      </p>

    <h3>Managing and comparing searches</h3>
    <img src="comp1.PNG" />
    <p>Once you have two or more searches, you can easily compare them using the tools found underneath "Searches".</p>
    <p>Select the searches you want to compare from a list of ones already performed &mdash; you will then see that comparison diagrammed using the same chart-by-year and venn diagrams seen at the outset.</p>
    <p>Review (or nickname, or delete) any past search by choosing it from the list.</p>

    <h3>Saving or retrieving a session</h3>
    <p>If you want to save a session for later, you have the option of saving it locally or to a text file. Local sessions are more convenient to work with, but they are <em>only</em> accessible on the browser/machine where you created them. Text files can be used on any machine (and by any user) that can read them.</p>
    <p>You will note the "Load previous session" buttons when you start a session. Just choose the locally saved session (or text file) you want, and you can resume where you left off.</p>

	<h3>Seeing unique records</h3>
	<p>When you are comparing two or more searches, you can choose "Show unique records" to show those citations that show up in one search, but not in any of the others you are comparing at that moment.</p>	
	</div>
	</div>
</div>

<div class="col-sm-5 col-md-5 col-lg-5">
 <div class="panel panel-default">
<div class="panel-body">
<h3>Contact</h3>
<p>PubMed by Year is a project of <a href="https://esperr.github.io/about/"><NAME>, M.L.I.S.</a></p>
<p>Ed can be reached at <a href="mailto:<EMAIL>"><EMAIL></a> or <a href="mailto:<EMAIL>"><EMAIL></a>. Please feel free to reach out with any comments or enhancement requests!</p>
      </div>
   </div>

	<div class="panel panel-default">
	<div class="panel-body">
  	<h3>Technologies</h3>
		<p>PubMed by Year is put together with <a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript">JavaScript</a> and <a href="http://jquery.com/">jQuery</a>. Search translations and counts are fetched with NCBI's <a href="https://www.ncbi.nlm.nih.gov/books/NBK25501/">
      Entrez Programming Utilities</a>. NCBI does not yet have an easy way to grab by-year counts for a search (short of launching 50+ calls to the API), so a <a href="https://github.com/esperr/med-by-year">custom webservice</a>
      is used.</p>
      <p><a href="https://developers.google.com/chart/interactive/docs/gallery/linechart">Google Charts</a> is used to draw the line charts, and <NAME>'s <a href="https://github.com/benfred/venn.js/tree/master">venn.js</a> overlay of Mike Bostock's <a href="https://d3js.org/">d3.js</a>
      performs the set visualization. Responsive layout is made easier with <a href="http://getbootstrap.com/">Bootstrap</a>.</p>
    <p>You can find the source code for this application at <a href="https://github.com/esperr/search-workbench">GitHub</a>.</p>

    <h3>License</h3>
		<p>Please note that the information provided here comes ultimately from the <a href="http://www.ncbi.nlm.nih.gov/">National Center for Biotechnology Information</a> and is subject to the terms listed under their
		<a href="http://www.ncbi.nlm.nih.gov/About/disclaimer.html">Disclaimer and Copyright notice</a>.</p>
    <p>Feel free to use this tool as you wish, but if you use Search Workbench for publication, I'd appreciate a citation:
      <blockquote>
        Sperr E. Search Workbench [Internet]. 2017 [cited <em>your_date_here</em>]. Available from https://esperr.github.io/search-workbench/
      </blockquote>
    </p>

  </div>
	</div>



  <div class="panel panel-default">
  <div class="panel-body">
    <h2>See also...</h2>
    <p>Want to have even more fun with MEDLINE visualizations? Check out the full versions of PubVenn and
      PubMed by Year as well as other cool tools at <a href="https://esperr.github.io/visualizingpubmed/">
        Visualizing PubMed</a>.</p>
  </div>
  </div>

      </div>

</div>
</div>
</body><commit_msg>content edit<commit_after><!DOCTYPE html>
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<style>
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	<h1>About Search Workbench</h1>
	<a id="about" class="label label-default" href="index.html">Home</a>
</div>
   <div class="row">

<div class="col-sm-7 col-md-7 col-lg-7 aboutleft">
	<div class="panel panel-default">
	<div class="panel-body">
		<h2>Why Search Workbench?</h2>
    <p>An extension of the work in <a href="https://esperr.github.io/visualizingpubmed/">
      Visualizing PubMed</a>, Search Workbench allows you to examine, edit and visualize your <a href="https://www.ncbi.nlm.nih.gov/pubmed/">PubMed</a> searches. Perhaps most importantly, it also allow you to directly <em>compare</em> searches to one another &mdash;
      facilitating the process of fine-tuning a search strategy.</p>

    <h2>How it works</h2>
    <p>When you enter a search, it is run against PubMed using the <a href="https://www.ncbi.nlm.nih.gov/books/NBK25501/">programmatic interface</a> maintainted by the <a href="https://www.ncbi.nlm.nih.gov/">National Center for Biotechnology Information</a>. You first see how your search
      is tranlated by <a href="https://www.nlm.nih.gov/bsd/disted/pubmedtutorial/020_040.html">Automated Term Mapping</a>. Then you see how the parts of your search relate to one another (using the logic that drives <a href="https://pubvenn.appspot.com/">PubVenn</a>) and how that search performs over time
      (via <a href="https://esperr.github.io/pubmed-by-year/">PubMed-by-year</a>).</p>

    <h3>Search nicknames</h3>
    <p>If you directly edit a PubMed <a href="https://www.nlm.nih.gov/bsd/disted/pubmedtutorial/020_040.html">translation</a>, you'll notice that even simple searches, such as "diabetes and heart disease", quickly turn into something a bit more ungainly:</p>
      <blockquote style="font-size: 90%;">
        ("diabetes mellitus"[MeSH Terms] OR ("diabetes"[All Fields] AND "mellitus"[All Fields]) OR "diabetes mellitus"[All Fields] OR "diabetes"[All Fields] OR "diabetes insipidus"[MeSH Terms] OR ("diabetes"[All Fields] AND "insipidus"[All Fields]) OR "diabetes insipidus"[All Fields]) AND ("heart diseases"[MeSH Terms] OR ("heart"[All Fields] AND "diseases"[All Fields]) OR "heart diseases"[All Fields] OR ("heart"[All Fields] AND "disease"[All Fields]) OR "heart disease"[All Fields])
      </blockquote>
      <img src="nickname.PNG" alt="screenshot snippet" />
      <p>Using such long strings as search labels makes it difficult to see slight variations in a search. It also makes comparing them on a chart cumbersome.</p>
      <p>In these cases, please take advantage of the ability to <em>nickname</em> a search. Choose a name, click "add", and you'll use that nickname for that search going forward
      </p>

    <h3>Managing and comparing searches</h3>
    <img src="comp1.PNG" alt="screenshot snippet" />
    <p>Once you have two or more searches, you can easily compare them using the tools found underneath "Searches".</p>
    <p>Select the searches you want to compare from a list of ones already performed &mdash; you will then see that comparison diagrammed using the same chart-by-year and venn diagrams seen at the outset.</p>
    <p>Review (or nickname, or delete) any past search by choosing it from the list.</p>

    <h3>Saving or retrieving a session</h3>
    <p>If you want to save a session for later, you have the option of saving it locally or to a text file. Local sessions are more convenient to work with, but they are <em>only</em> accessible on the browser/machine where you created them. Text files can be used on any machine (and by any user) that can read them.</p>
    <p>You will note the "Load previous session" buttons when you start a session. Just choose the locally saved session (or text file) you want, and you can resume where you left off.</p>

    <h3>Seeing unique records</h3>
    <p>When you are comparing two or more searches, you can choose "Show unique records" to show those citations that show up in one search, but not in any of the others you are comparing at that moment.</p>

	</div>
	</div>
</div>

<div class="col-sm-5 col-md-5 col-lg-5">
 <div class="panel panel-default">
<div class="panel-body">
<h3>Contact</h3>
<p>PubMed by Year is a project of <a href="https://esperr.github.io/about/"><NAME>, M.L.I.S.</a></p>
<p>Ed can be reached at <a href="mailto:<EMAIL>"><EMAIL></a> or <a href="mailto:<EMAIL>"><EMAIL></a>. Please feel free to reach out with any comments or enhancement requests!</p>
      </div>
   </div>

	<div class="panel panel-default">
	<div class="panel-body">
  	<h3>Technologies</h3>
		<p>PubMed by Year is put together with <a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript">JavaScript</a> and <a href="http://jquery.com/">jQuery</a>. Search translations and counts are fetched with NCBI's <a href="https://www.ncbi.nlm.nih.gov/books/NBK25501/">
      Entrez Programming Utilities</a>. NCBI does not yet have an easy way to grab by-year counts for a search (short of launching 50+ calls to the API), so a <a href="https://github.com/esperr/med-by-year">custom webservice</a>
      is used.</p>
      <p><a href="https://developers.google.com/chart/interactive/docs/gallery/linechart">Google Charts</a> is used to draw the line charts, and <NAME>'s <a href="https://github.com/benfred/venn.js/tree/master">venn.js</a> overlay of <NAME>'s <a href="https://d3js.org/">d3.js</a>
      performs the set visualization. Responsive layout is made easier with <a href="http://getbootstrap.com/">Bootstrap</a>.</p>
    <p>You can find the source code for this application at <a href="https://github.com/esperr/search-workbench">GitHub</a>.</p>

    <h3>License</h3>
		<p>Please note that the information provided here comes ultimately from the <a href="http://www.ncbi.nlm.nih.gov/">National Center for Biotechnology Information</a> and is subject to the terms listed under their
		<a href="http://www.ncbi.nlm.nih.gov/About/disclaimer.html">Disclaimer and Copyright notice</a>.</p>
    <p>Feel free to use this tool as you wish, but if you use Search Workbench for publication, I'd appreciate a citation:
    </p><blockquote>
        Sperr E. Search Workbench [Internet]. 2017 [cited <em>your_date_here</em>]. Available from https://esperr.github.io/search-workbench/
      </blockquote>


  </div>
	</div>



  <div class="panel panel-default">
  <div class="panel-body">
    <h2>See also...</h2>
    <p>Want to have even more fun with MEDLINE visualizations? Check out the full versions of PubVenn and
      PubMed by Year as well as other cool tools at <a href="https://esperr.github.io/visualizingpubmed/">
        Visualizing PubMed</a>.</p>
  </div>
  </div>

      </div>

</div>
</div>
</body>
{'fraction_non_alphanumeric': 0.14518597378401757, 'fraction_numerical': 0.01171069266085568, 'mean_word_length': 4.11572498298162, 'pattern_counts': {'":': 0, '<': 352, '<?xml version=': 0, '>': 352, 'https://': 42, 'lorem ipsum': 0, 'www.': 18, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7000529', 'n_tokens_mistral': 5103, 'n_tokens_neox': 4705, 'n_words': 1630}