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@AlexanderPico
AlexanderPico committed Sep 21, 2024
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2 changes: 1 addition & 1 deletion feed.xml
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<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.9.3">Jekyll</generator><link href="https://pfocr.wikipathways.org/feed.xml" rel="self" type="application/atom+xml" /><link href="https://pfocr.wikipathways.org/" rel="alternate" type="text/html" /><updated>2024-09-20T17:03:11-07:00</updated><id>https://pfocr.wikipathways.org/feed.xml</id><title type="html">Pathway Figure OCR</title><subtitle>Mining the published literature for pathway figures and making their contents accessible for science.</subtitle></feed>
<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.9.3">Jekyll</generator><link href="https://pfocr.wikipathways.org/feed.xml" rel="self" type="application/atom+xml" /><link href="https://pfocr.wikipathways.org/" rel="alternate" type="text/html" /><updated>2024-09-20T18:28:29-07:00</updated><id>https://pfocr.wikipathways.org/feed.xml</id><title type="html">Pathway Figure OCR</title><subtitle>Mining the published literature for pathway figures and making their contents accessible for science.</subtitle></feed>
26 changes: 13 additions & 13 deletions rmd/stats.html
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Expand Up @@ -109,10 +109,10 @@ <h2 id="read-pfocr-rds-files">Read PFOCR .rds files</h2>

<p>Read in files</p>

<div class="language-r highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">figs</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_figures.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">genes</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_genes.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">chems</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_chemicals.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">dis</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_diseases.rds"</span><span class="p">))</span><span class="w">
<div class="language-r highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">figs</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_figures_draft.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">genes</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_genes_draft.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">chems</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_chemicals_draft.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">dis</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_diseases_draft.rds"</span><span class="p">))</span><span class="w">
</span></code></pre></div></div>

<h2 id="contents-and-counts">Contents and counts</h2>
Expand Down Expand Up @@ -156,8 +156,8 @@ <h2 id="contents-and-counts">Contents and counts</h2>
</span><span class="n">row.names</span><span class="p">(</span><span class="n">data</span><span class="p">)</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="s2">"Genes"</span><span class="p">,</span><span class="w"> </span><span class="s2">"Chemicals"</span><span class="p">,</span><span class="w"> </span><span class="s2">"Diseases"</span><span class="p">)</span><span class="w">
</span></code></pre></div></div>

<p>The Pathway Figure OCR project has identified 105451 pathway figures
from 89737 published papers.</p>
<p>The Pathway Figure OCR project has identified 110408 pathway figures
from 93057 published papers.</p>

<table>
<thead>
Expand All @@ -171,21 +171,21 @@ <h2 id="contents-and-counts">Contents and counts</h2>
<tbody>
<tr>
<td style="text-align: left">Genes</td>
<td style="text-align: right">4,534,575</td>
<td style="text-align: left">147613 (ncbigene)</td>
<td style="text-align: left">18441 (human)</td>
<td style="text-align: right">4,687,583</td>
<td style="text-align: left">147974 (ncbigene)</td>
<td style="text-align: left">18586 (human)</td>
</tr>
<tr>
<td style="text-align: left">Chemicals</td>
<td style="text-align: right">319,846</td>
<td style="text-align: right">346,094</td>
<td style="text-align: left">14212 (mesh)</td>
<td style="text-align: left">4120 (chebi)</td>
<td style="text-align: left">6785 (chebi)</td>
</tr>
<tr>
<td style="text-align: left">Diseases</td>
<td style="text-align: right">43,218</td>
<td style="text-align: right">44,598</td>
<td style="text-align: left">1632 (mesh)</td>
<td style="text-align: left">204 (doid)</td>
<td style="text-align: left">673 (doid)</td>
</tr>
</tbody>
</table>
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30 changes: 15 additions & 15 deletions stats.html
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Expand Up @@ -109,10 +109,10 @@ <h2 id="read-pfocr-rds-files">Read PFOCR .rds files</h2>

<p>Read in files</p>

<div class="language-r highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">figs</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_figures.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">genes</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_genes.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">chems</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_chemicals.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">dis</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_diseases.rds"</span><span class="p">))</span><span class="w">
<div class="language-r highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">figs</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_figures_draft.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">genes</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_genes_draft.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">chems</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_chemicals_draft.rds"</span><span class="p">))</span><span class="w">
</span><span class="n">dis</span><span class="w"> </span><span class="o">&lt;-</span><span class="w"> </span><span class="n">readRDS</span><span class="p">(</span><span class="n">file.path</span><span class="p">(</span><span class="n">local.path</span><span class="p">,</span><span class="s2">"pfocr_diseases_draft.rds"</span><span class="p">))</span><span class="w">
</span></code></pre></div></div>

<h2 id="contents-and-counts">Contents and counts</h2>
Expand Down Expand Up @@ -156,8 +156,8 @@ <h2 id="contents-and-counts">Contents and counts</h2>
</span><span class="n">row.names</span><span class="p">(</span><span class="n">data</span><span class="p">)</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="s2">"Genes"</span><span class="p">,</span><span class="w"> </span><span class="s2">"Chemicals"</span><span class="p">,</span><span class="w"> </span><span class="s2">"Diseases"</span><span class="p">)</span><span class="w">
</span></code></pre></div></div>

<p>The Pathway Figure OCR project has identified 103009 pathway figures
from 87705 published papers.</p>
<p>The Pathway Figure OCR project has identified 110408 pathway figures
from 93057 published papers.</p>

<table>
<thead>
Expand All @@ -171,21 +171,21 @@ <h2 id="contents-and-counts">Contents and counts</h2>
<tbody>
<tr>
<td style="text-align: left">Genes</td>
<td style="text-align: right">4,426,921</td>
<td style="text-align: left">146866 (ncbigene)</td>
<td style="text-align: left">18383 (human)</td>
<td style="text-align: right">4,687,583</td>
<td style="text-align: left">147974 (ncbigene)</td>
<td style="text-align: left">18586 (human)</td>
</tr>
<tr>
<td style="text-align: left">Chemicals</td>
<td style="text-align: right">309,761</td>
<td style="text-align: left">13979 (mesh)</td>
<td style="text-align: left">4085 (chebi)</td>
<td style="text-align: right">346,094</td>
<td style="text-align: left">14212 (mesh)</td>
<td style="text-align: left">6785 (chebi)</td>
</tr>
<tr>
<td style="text-align: left">Diseases</td>
<td style="text-align: right">41,738</td>
<td style="text-align: left">1602 (mesh)</td>
<td style="text-align: left">201 (doid)</td>
<td style="text-align: right">44,598</td>
<td style="text-align: left">1632 (mesh)</td>
<td style="text-align: left">673 (doid)</td>
</tr>
</tbody>
</table>
Expand Down

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