incorporate minor fixes

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

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="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/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"

about/metagraph.drawio

@@ -0,0 +1 @@
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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;
+}

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

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:https://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>

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>