{% extends "base.html" %}

{% import "bootstrap/wtf.html" as wtf %}
{% import "bootstrap/fixes.html" as fixes %}
{% import "bootstrap/utils.html" as util %}

{% block title %}About{% endblock %}

{% block scripts %}
    {{ super() }}
    <script type="text/javascript">
        var maxHeight = 0;
        $(".panel-body").find(".row").find(".col-sm-6").find(".thumbnail").each(function (idx, item) {
            var height = $(item).height();
            maxHeight = maxHeight > height ? maxHeight : height;
        });
        $(".panel-body").find(".row").find(".col-sm-6").find(".thumbnail").height(maxHeight);
    </script>
{% endblock %}

{% block content %}
    <div class="container">
        {{ util.flashed_messages(dismissible=True, container=False) }}

        <div class="panel panel-default">
            <div class="panel-heading">
                <h3 class="panel-title">Curation Protocol</h3>
            </div>
            <div class="panel-body">
                <p>As an application scenario, ComPath was used to generate the pathway mappings between three of the
                    major public pathway databases (<a href="http://www.kegg.jp/">KEGG</a>, <a
                            href="https://reactome.org/">Reactome</a>,
                    and <a href="https://www.wikipathways.org/index.php/WikiPathways">WikiPathways</a>). The protocol
                    established for the mapping is described below.
                </p>

                <h4>Mapping Files</h4>

                <p>A total of 3 mapping files were curated, one for each pairwise comparison:
                </p>

                <ul>
                    <li>KEGG vs Reactome</li>
                    <li>KEGG vs WikiPathways</li>
                    <li>Reactome vs WikiPathways</li>
                </ul>

                <h4>Description</h4>

                <p>
                    For each pairwise pathway database comparison (resource 1 vs resource 2), we generated all possible
                    mappings between pathways in each database (KEGG-WikiPathways, KEGG-Reactome, and
                    WikiPathways-Reactome) and prioritized them based on the follow two independent metrics that have
                    been proposed to calculate pathway similarity (Belinky et al., 2015):

                </p>

                <ol>
                    <li>Lexical similarity between each pair of pathways' names was calculated using the Levenshtein
                        distance (Levenshtein, 1966).
                    </li>

                    <li>Content similarity between each pair of pathways' genes was calculated using the previously
                        described Szymkiewicz-Simpson coefficient.
                    </li>

                </ol>

                <p>
                    With the help of this prioritization exercise, three curators from different areas of expertise
                    (neuroscience, medicine, and biology) independently assigned the mapping types and mark false
                    positives after evaluating the equivalent scope in both pathway descriptions. Links to the pathway
                    descriptions were attached so that the curator can confirm that the focus and context of the
                    pathways remain the same, even if the both have high similarity or name.
                    Furthermore, we investigated possible intra-database mappings within KEGG and WikiPathways since
                    these resources do not yet contain hierarchical relationships.
                </p>

                <h4>Inter-curator agreement</h4>

                <p>
                    The final step of the curation exercise was to agree on the proposed mappings. Therefore, all three
                    curators examined together one by one the combination of all mappings independently generated to
                    reach a consensus on a final set of mappings that are available at
                    <a href="https://github.com/ComPath/resources">ComPath Resources</a> under the MIT License.
                </p>
            </div>
        </div>

        <div class="panel panel-default">
            <div class="panel-heading">
                <h3 class="panel-title">Types of Mappings</h3>
            </div>
            <div class="panel-body">

                <p>ComPath curation interface allows for two types of mappings: equivalentTo and isPartOf.</p>

                <ul>

                    <li><b>equivalentTo</b>. An undirected relationship denoting both pathways refer to the same
                        biological process. The requirements for this relationship are:

                        <ul>
                            <li>
                                <b>Scope:</b> both pathways represent the same biological pathway information.
                            </li>
                            <li>
                                <b>Similarity:</b> both pathways must share at minimum of one overlapping gene.
                            </li>
                            <li>
                                <b>Context:</b> both pathways should take place in the same context (e.g., cell line,
                                physiology).
                            </li>

                        </ul>
                    </li>

                    <li><b>isPartOf</b>. A directed relationship denoting the hierarchical relationship between the
                        pathway 1 (child) and 2 (parent). The requirements are:

                        <ul>
                            <li>
                                <b>Subset:</b> The subject (pathway 1) is a subset of pathway 2 (e.g., Reactome pathway
                                hierarchy).
                            </li>
                            <li>
                                <b>Similarity:</b> same as above.
                            </li>
                            <li>
                                <b>Context:</b> same as above.
                            </li>

                        </ul>
                    </li>
                </ul>


            </div>
        </div>

        <div class="panel panel-default">
            <div class="panel-heading">
                <h3 class="panel-title">References</h3>
            </div>
            <div class="panel-body">
                <ul>
                    <li>
                        Belinky, F., et al. PathCards: multi-source consolidation of human biological pathways.
                        Database, 2015 (2015).
                    </li>

                    <li>
                        Levenshtein, V. I. Binary codes capable of correcting deletions, insertions, and reversals.
                        Soviet Physics Doklady. 10 (8): 707–710 (1966).
                    </li>
                </ul>
            </div>
        </div>


    </div>
    {% include "meta/footer.html" %}
{% endblock %}