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Merge pull request #90 from cthoyt/more-forms
Add form to matches page
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,93 +1,6 @@ | ||
| {% extends "base.html" %} | ||
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| {% block head %} | ||
| {{ super() }} | ||
| <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/choices.js/public/assets/styles/choices.min.css"> | ||
| <style> | ||
| div.choices { | ||
| margin-bottom: 0; | ||
| } | ||
| </style> | ||
| {% endblock %} | ||
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|
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| {% block gcontent %} | ||
| <script src="https://code.jquery.com/jquery-3.3.1.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> | ||
| <script src="https://cdn.jsdelivr.net/npm/choices.js/public/assets/scripts/choices.min.js"></script> | ||
|
|
||
| <script> | ||
| $(document).ready(function() { | ||
| // see https://github.com/jshjohnson/Choices | ||
| const organismSelect = new Choices('#organism-select'); | ||
| }) | ||
| </script> | ||
|
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| <div class="panel-heading"> | ||
| <h3 class="panel-title">Gilda grounding input</h3> | ||
| </div> | ||
| <div class="panel-body"> | ||
| <form class="form" method="POST" role="form"> | ||
| {{ wtf.form_field(form.text) }} | ||
| {{ wtf.form_field(form.context) }} | ||
| {{ wtf.form_field(form.organisms, class_="form-control") }} | ||
| {{ wtf.form_field(form.submit, class="btn btn-primary")}} | ||
| </form> | ||
| </div> | ||
|
|
||
| <div class="modal fade" id="text-modal" tabindex="-1" role="dialog" aria-labelledby="textModalLabel" aria-hidden="true"> | ||
| <div class="modal-dialog" role="document"> | ||
| <div class="modal-content"> | ||
| <div class="modal-header"> | ||
| <h5 class="modal-title" id="textModalLabel">Text Modal Header</h5> | ||
| <button type="button" class="close" data-dismiss="modal" aria-label="Close"> | ||
| <span aria-hidden="true">×</span> | ||
| </button> | ||
| </div> | ||
| <div class="modal-body"> | ||
| <p> | ||
| Text modal main text | ||
| </p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
|
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| <div class="modal fade" id="context-modal" tabindex="-1" role="dialog" aria-labelledby="contextModalLabel" aria-hidden="true"> | ||
| <div class="modal-dialog" role="document"> | ||
| <div class="modal-content"> | ||
| <div class="modal-header"> | ||
| <h5 class="modal-title" id="contextModalLabel">Context text</h5> | ||
| <button type="button" class="close" data-dismiss="modal" aria-label="Close"> | ||
| <span aria-hidden="true">×</span> | ||
| </button> | ||
| </div> | ||
| <div class="modal-body"> | ||
| <p> | ||
| There is no hard requirement for how much context should be (optionally) provided for disambiguation. In practice, the context provided could be a sentence, a paragraph, or even an entire article. While it is not required that the context contain the entity text being grounded, in practice, context usually consists of text surrounding and including the entity. Overall, given that disambiguation models integrated from Adeft as well as the models made available independently by Gilda rely on word frequency-derived features, it is generally helpful if context text contains terms characteristic to the given sense of the ambiguous string. Additionally, since Adeft models have the ability to recognize defining patterns (i.e., an explicit spelled out definition of an ambiguous acronym), any context text containing such patterns is useful. | ||
| </p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
|
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||
| <div class="modal fade" id="species-modal" tabindex="-1" role="dialog" aria-labelledby="speciesModalLabel" aria-hidden="true"> | ||
| <div class="modal-dialog" role="document"> | ||
| <div class="modal-content"> | ||
| <div class="modal-header"> | ||
| <h5 class="modal-title" id="speciesModalLabel">Species prioritization</h5> | ||
| <button type="button" class="close" data-dismiss="modal" aria-label="Close"> | ||
| <span aria-hidden="true">×</span> | ||
| </button> | ||
| </div> | ||
| <div class="modal-body"> | ||
| <p> | ||
| Species prioritization is applied in case matches are found to proteins from multiple species (human, | ||
| mouse, yeast, etc). In case of matches to multiple species for a given input, | ||
| this (optional) input list is used to prioritize matches. The priority list can be determined | ||
| based on the user case or knowledge about the context in which the given entity text | ||
| appeared. The species list is adopted from UniProt's "popular organisms" list (https://www.uniprot.org/help/filter_options). | ||
| </p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| {{ render_form(form) }} | ||
| {% endblock %} | ||
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|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,54 +1,60 @@ | ||
| {% extends "base.html" %} | ||
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| {% block gcontent %} | ||
| <div class="panel-heading"> | ||
| <h3 class="panel-title">Gilda grounding results</h3> | ||
| </div> | ||
| <div class="panel-body"> | ||
| <p> | ||
| Results for <code>{{ text }}</code> | ||
| {% if context %} with context | ||
| <i>{{ context }}</i>{% endif %}. | ||
| </p> | ||
| <p> | ||
| The table below contains the retrieved Groundings ordered by descreasing | ||
| score. The standard name for the entry is given in the Name column. | ||
| Additional groundings are provided for some entries where a match was | ||
| found to an equivalent term in a namespace different from the primary | ||
| grounding's. | ||
| </p> | ||
| </div> | ||
| <table class="table table-striped table-hover"> | ||
| <thead> | ||
| <tr> | ||
| <th>Grounding</th> | ||
| <th>Name</th> | ||
| <th>Score</th> | ||
| <th>Additional Groundings</th> | ||
| </tr> | ||
| </thead> | ||
| <tbody> | ||
| {% for match in matches %} | ||
| <tr> | ||
| {% set match_curie = match.term.get_curie() %} | ||
| <td> | ||
| <a class="label label-primary" href="{{ match['url'] }}"> | ||
| {{ match_curie }} | ||
| </a> | ||
| </td> | ||
| <td>{{ match['term']['entry_name'] }}</td> | ||
| <td class="text-right">{{ match['score'] | round(4)}}</td> | ||
| <td> | ||
| {% for xref_curie, xref_url in match.get_grounding_dict().items() %} | ||
| {% if xref_curie != match_curie %} | ||
| <a class="label label-info" href="{{ xref_url }}"> | ||
| {{ xref_curie }} | ||
| </a> | ||
| {% if form is defined %} | ||
| {{ render_form(form) }} | ||
| {% endif %} | ||
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| <div class="panel panel-default"> | ||
| <div class="panel-heading"> | ||
| <h3 class="panel-title">Grounding Results for <code>{{ text }}</code></h3> | ||
| </div> | ||
| <div class="panel-body"> | ||
| {% if context %} | ||
| <p> | ||
| Using context: <i>{{ context }}</i> | ||
| </p> | ||
| {% endif %} | ||
| <p> | ||
| The table below contains the retrieved Groundings ordered by decreasing | ||
| score. The standard name for the entry is given in the Name column. | ||
| Additional groundings are provided for some entries where a match was | ||
| found to an equivalent term in a namespace different from the primary | ||
| grounding's. | ||
| </p> | ||
| </div> | ||
| <table class="table table-striped table-hover"> | ||
| <thead> | ||
| <tr> | ||
| <th>Grounding</th> | ||
| <th>Name</th> | ||
| <th>Score</th> | ||
| <th>Additional Groundings</th> | ||
| </tr> | ||
| </thead> | ||
| <tbody> | ||
| {% for match in matches %} | ||
| <tr> | ||
| {% set match_curie = match.term.get_curie() %} | ||
| <td> | ||
| <a class="label label-primary" href="{{ match['url'] }}"> | ||
| {{ match_curie }} | ||
| </a> | ||
| </td> | ||
| <td>{{ match['term']['entry_name'] }}</td> | ||
| <td class="text-right">{{ match['score'] | round(4) }}</td> | ||
| <td> | ||
| {% for xref_curie, xref_url in match.get_grounding_dict().items() %} | ||
| {% if xref_curie != match_curie %} | ||
| <a class="label label-info" href="{{ xref_url }}"> | ||
| {{ xref_curie }} | ||
| </a> | ||
| {% endif %} | ||
| {% endfor %} | ||
| </td> | ||
| </tr> | ||
| {% endfor %} | ||
| </td> | ||
| </tr> | ||
| {% endfor %} | ||
| </tbody> | ||
| </table> | ||
| </tbody> | ||
| </table> | ||
| </div> | ||
| {% endblock %} |