incorporate minor fixes (#37)

closes #32 closes #36 - splits cite into two individually linkable sections - adds PMID and PMCID to citations - fixes "biologic class" to "biological process" - renames some rephetio titles to be consistent - adds some other small text
hetio · Jun 24, 2020 · 48752f0 · 48752f0
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diff --git a/Gemfile.lock b/Gemfile.lock
@@ -9,7 +9,9 @@ GEM
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
     eventmachine (1.2.7)
+    eventmachine (1.2.7-x64-mingw32)
     ffi (1.11.1)
+    ffi (1.11.1-x64-mingw32)
     forwardable-extended (2.6.0)
     http_parser.rb (0.6.0)
     i18n (0.9.5)
@@ -60,15 +62,22 @@ GEM
     sass-listen (4.0.0)
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
+    tzinfo (2.0.2)
+      concurrent-ruby (~> 1.0)
+    tzinfo-data (1.2020.1)
+      tzinfo (>= 1.0.0)
+    wdm (0.1.1)
 
 PLATFORMS
   ruby
+  x64-mingw32
 
 DEPENDENCIES
   jekyll (~> 3.8.5)
   jekyll-feed (~> 0.6)
   minima (~> 2.0)
   tzinfo-data
+  wdm (~> 0.1.0)
 
 BUNDLED WITH
-   2.0.2
+   2.1.4
diff --git a/about/index.html b/about/index.html
@@ -99,7 +99,7 @@ <h3>What's in Hetionet?</h3>
       <table>
         <thead>
           <tr>
-            <th width='120'>Metanode</th>
+            <th width="120">Metanode</th>
             <th>Description</th>
           </tr>
         </thead>
@@ -205,7 +205,7 @@ <h3>What's in Hetionet?</h3>
       different types of nodes and edges in the network.
     </p>
     <figure>
-      <a href="metagraph-large.png" target="_blank">
+      <a href="metagraph.png" target="_blank">
         <img src="metagraph.png" width="400px" />
       </a>
     </figure>
@@ -305,29 +305,21 @@ <h3>Acknowledgements</h3>
   </div>
 </section>
 <hr />
-<style>
-  /* override bad altmetric popup css */
-  .altmetric-embed {
-    border-radius: 0 !important;
-  }
-  .altmetric-popover-inner,
-  .altmetric-popover-content {
-    background: #fafafa !important;
-  }
-  .altmetric_arrow {
-    border-top-color: #fafafa !important;
-  }
-  .altmetric-popover-content > div > a {
-    top: 15px !important;
-    right: 15px !important;
-  }
-  .altmetric-popover-content > div > div:last-of-type {
-    display: none !important;
-  }
-</style>
-<section id="cite">
+<section id="cite-repurpose">
   <div class="section">
-    <h3>Cite</h3>
+    <h3>Cite <i>Drug Repurposing (Project Rephetio)</i></h3>
+    <div class="row">
+      <p>
+        For the topics <span class="topic small">eLife: Project Rephetio</span>,
+        <span class="topic small">drug repurposing</span>,
+        <span class="topic small">Hetionet v1.0</span>,
+        <span class="topic small">data licensing</span>,
+        <span class="topic small">realtime open science</span>,
+        <span class="topic small">consensus LINCS L1000 signatures</span>,
+        <span class="topic small">hetnets</span>,
+        <span class="topic small">HNEP</span>, cite the following:
+      </p>
+    </div>
     <div class="row">
       <div class="col_text">
         <span class="semibold"
@@ -338,9 +330,14 @@ <h3>Cite</h3>
         Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D,
         Green A, Khankhanian P, Baranzini SE
         <br />
-        <i>eLife</i> (2017)
-        DOI: <a href="https://doi.org/10.7554/eLife.26726"
-          >10.7554/eLife.26726</a
+        <i>eLife</i> (2017)<br />
+        DOI:
+        <a href="https://doi.org/10.7554/elife.26726">10.7554/elife.26726</a> ·
+        PMID:
+        <a href="https://www.ncbi.nlm.nih.gov/pubmed/28936969">28936969</a> ·
+        PMCID:
+        <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640425"
+          >PMC5640425</a
         >
       </div>
       <div class="col_image">
@@ -356,31 +353,38 @@ <h3>Cite</h3>
         ></div>
       </div>
     </div>
+  </div>
+</section>
+<hr />
+<section id="cite-disease-genes">
+  <div class="section">
+    <h3>Cite <i>Prioritizing Disease-Associated Genes</i></h3>
     <div class="row">
-      <p>
-        Cite for topics:<br />
-        <span class="topic small">eLife: Project Rephetio</span
-        ><span class="topic small">drug repurposing</span
-        ><span class="topic small">Hetionet v1.0</span
-        ><span class="topic small">data licensing</span
-        ><span class="topic small">realtime open science</span
-        ><span class="topic small">consensus LINCS L1000 signatures</span
-        ><span class="topic small">hetnets</span>
-        <span class="topic small">HNEP</span>
-      </p>
-    </div>
-    <div class="row">
+      <div class="row">
+        <p>
+          For the topics <span class="topic small">PLOS: DWPC</span>,
+          <span class="topic small">predicting disease-gene associations</span>,
+          <span class="topic small">hetnet permutation</span>,
+          <span class="topic small">HNEP</span>, cite the following:
+        </p>
+      </div>
       <div class="col_text">
         <span class="semibold"
           >Heterogeneous Network Edge Prediction: A Data Integration Approach to
           Prioritize Disease-Associated Genes</span
         ><br />
         Himmelstein DS, Baranzini SE<br />
-        <i>PLOS Computational Biology</i> (2015)
-        DOI: <a
-          href="https://doi.org/10.1371/journal.pcbi.1004259"
+        <i>PLOS Computational Biology</i> (2015)<br />
+        DOI:
+        <a href="https://doi.org/10.1371/journal.pcbi.1004259"
           >10.1371/journal.pcbi.1004259</a
         >
+        · PMID:
+        <a href="https://www.ncbi.nlm.nih.gov/pubmed/26158728">26158728</a> ·
+        PMCID:
+        <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497619"
+          >PMC4497619</a
+        >
       </div>
       <div class="col_image">
         <script
@@ -395,15 +399,6 @@ <h3>Cite</h3>
         ></div>
       </div>
     </div>
-    <div class="row">
-      <p>
-        Cite for topics:<br />
-        <span class="topic small">PLOS: DWPC</span
-        ><span class="topic small">predicting disease-gene associations</span
-        ><span class="topic small">hetnet permutation</span
-        ><span class="topic small">HNEP</span>
-      </p>
-    </div>
   </div>
 </section>
 <hr />
@@ -414,8 +409,7 @@ <h3>Contact</h3>
       For questions or feedback regarding existing projects, please open an
       issue on the relevant GitHub repository (under
       <a href="https://github.com/hetio">@hetio</a> or
-      <a href="https://git.io/v5zvX">@dhimmel</a>).
-      For other inquiries, send an
+      <a href="https://git.io/v5zvX">@dhimmel</a>). For other inquiries, send an
       email to
       <a
         href="mailto:Daniel%20Himmelstein%20%[email protected]%3E"

diff --git a/about/metagraph-large.png b/about/metagraph-large.png
diff --git a/about/metagraph-src.png b/about/metagraph-src.png
diff --git a/about/metagraph.drawio b/about/metagraph.drawio
@@ -0,0 +1 @@
+<mxfile modified="2020-06-23T03:15:13.089Z" host="app.diagrams.net" agent="5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/83.0.4103.106 Safari/537.36" etag="HeKBAv_65v5gAL9jmVvw" version="13.3.0" type="device"><diagram id="7j_7Ax2Yb4UZenCjmv76" name="Page-1">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</diagram></mxfile>
diff --git a/about/metagraph.png b/about/metagraph.png
diff --git a/about/metagraph.svg b/about/metagraph.svg
diff --git a/about/page.css b/about/page.css
@@ -15,7 +15,27 @@ td {
 }
 .topic {
   display: inline-block;
-  margin: 8px 12px 0 0;
-  white-space: nowrap;
-  font-style: italic;
-}
+  background-color: var(--light-gray);
+  margin-bottom: 2px;
+  padding: 0 4px;
+  border-radius: 2px;
+}
+
+/* override bad altmetric popup css */
+.altmetric-embed {
+  border-radius: 0 !important;
+}
+.altmetric-popover-inner,
+.altmetric-popover-content {
+  background: #fafafa !important;
+}
+.altmetric_arrow {
+  border-top-color: #fafafa !important;
+}
+.altmetric-popover-content > div > a {
+  top: 15px !important;
+  right: 15px !important;
+}
+.altmetric-popover-content > div > div:last-of-type {
+  display: none !important;
+}
diff --git a/disease-genes/index.html b/disease-genes/index.html
@@ -1,6 +1,6 @@
 ---
 layout: default
-title: Disease-Associated Genes
+title: Prioritizing Disease-Associated Genes
 icon: fas fa-dna
 category: studies
 ---
@@ -18,9 +18,10 @@
       <a
         href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004259"
         class="button"
+        title="Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes (PLOS Computational Biology, 2015)"
         >Read the paper<i class="fas fa-scroll" data-right></i
       ></a>
-      <a href="/about/#cite" class="button"
+      <a href="/about/#cite-disease-genes" class="button"
         >Cite these results<i class="fas fa-info-circle" data-right></i
       ></a>
       <a

diff --git a/repurpose/index.html b/repurpose/index.html
@@ -1,25 +1,28 @@
 ---
 layout: default
-title: Project Rephetio (Drug Repurposing)
+title: Drug Repurposing (Project Rephetio)
 icon: fas fa-prescription-bottle-alt
 category: studies
 ---
 
 <section>
   <div class="section">
     <p>
-      Project Rephetio was an study to predict new uses for existing drugs.
+      "Project Rephetio" was an study to predict new uses for existing drugs.
       Predictions are based on predicting treatment edges in
       <a href="http://localhost:4000/about/#what-is-hetionet">Hetionet v1.0</a>.
       Our approach learns network patterns of drug efficacy, translating the
       paths between a compound and disease into a predicted probability of
       treatment.
     </p>
     <div class="center">
-      <a href="https://elifesciences.org/articles/26726" class="button"
+      <a
+        href="https://elifesciences.org/articles/26726"
+        class="button"
+        title="Systematic integration of biomedical knowledge prioritizes drugs for repurposing (eLife, 2017)"
         >Read the paper<i class="fas fa-scroll" data-right></i
       ></a>
-      <a href="/about/#cite" class="button"
+      <a href="/about/#cite-repurpose" class="button"
         >Cite these results<i class="fas fa-info-circle" data-right></i
       ></a>
     </div>
@@ -40,7 +43,6 @@
   </div>
 </section>
 
-
 <hr />
 
 <section>

diff --git a/studies/index.html b/studies/index.html
@@ -16,6 +16,9 @@ <h3>Drug Repurposing (Project Rephetio)</h3>
           study's 209,168 predictions and the evidence behind them to explore
           new uses for existing drugs.
         </p>
+        <p>
+          <i>From Himmelstein et al (2017) eLife</i>
+        </p>
         <a href="/repurpose" class="button"
           >Go to the project page<i class="fas fa-arrow-right" data-right></i
         ></a>
@@ -38,6 +41,9 @@ <h3>Prioritizing Disease-Associated Genes</h3>
           55,4364 results to prioritize genome-wide association studies by
           narrowing down the search.
         </p>
+        <p>
+          <i>From Himmelstein et al (2015) PLOS Computational Biology</i>
+        </p>
         <a href="/disease-genes" class="button"
           >Go to the project page<i class="fas fa-arrow-right" data-right></i
         ></a>
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