Merge pull request #2 from Wang-Cankun/main

[ci skip] This build is based on 985ed1f. This commit was created by the following CI build and job: https://github.com/biocypher/biochatter-paper/commit/985ed1f8a14d402b9120a0c91e4acd8d901b672a/checks https://github.com/biocypher/biochatter-paper/actions/runs/7357240178
biocypher · Dec 29, 2023 · 67f23b4 · 67f23b4
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diff --git a/manuscript.docx b/manuscript.docx
diff --git a/manuscript.html b/manuscript.html
@@ -6,6 +6,9 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
   <meta name="author" content="Sebastian Lobentanzer" />
   <meta name="author" content="Andreas Maier" />
+  <meta name="author" content="Cankun Wang" />
+  <meta name="author" content="Qin Ma" />
+  <meta name="author" content="Shaohong Feng" />
   <meta name="author" content="Julio Saez-Rodriguez" />
   <meta name="dcterms.date" content="2023-12-29" />
   <meta name="keywords" content="biomedicine, bioinformatics, large language models, framework" />
@@ -55,8 +58,8 @@
   <meta name="dc.date" content="2023-12-29" />
   <meta name="citation_publication_date" content="2023-12-29" />
   <meta property="article:published_time" content="2023-12-29" />
-  <meta name="dc.modified" content="2023-12-29T13:56:02+00:00" />
-  <meta property="article:modified_time" content="2023-12-29T13:56:02+00:00" />
+  <meta name="dc.modified" content="2023-12-29T14:00:02+00:00" />
+  <meta property="article:modified_time" content="2023-12-29T14:00:02+00:00" />
   <meta name="dc.language" content="en-UK" />
   <meta name="citation_language" content="en-UK" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -70,6 +73,17 @@
   <meta name="citation_author" content="Andreas Maier" />
   <meta name="citation_author_institution" content="Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany" />
   <meta name="citation_author_orcid" content="0000-0003-4408-0068" />
+  <meta name="citation_author" content="Cankun Wang" />
+  <meta name="citation_author_institution" content="Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA" />
+  <meta name="citation_author_orcid" content="0000-0002-0225-9855" />
+  <meta name="twitter:creator" content="@Wang-Cankun" />
+  <meta name="citation_author" content="Qin Ma" />
+  <meta name="citation_author_institution" content="Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA" />
+  <meta name="citation_author_orcid" content="0000-0002-3264-8392" />
+  <meta name="twitter:creator" content="@QinMaBMBL" />
+  <meta name="citation_author" content="Shaohong Feng" />
+  <meta name="citation_author_institution" content="Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA" />
+  <meta name="citation_author_orcid" content="0009-0000-8124-3626" />
   <meta name="citation_author" content="Julio Saez-Rodriguez" />
   <meta name="citation_author_institution" content="Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany" />
   <meta name="citation_author_orcid" content="0000-0002-8552-8976" />
@@ -80,9 +94,9 @@
   <meta name="citation_fulltext_html_url" content="https://biocypher.github.io/biochatter-paper/" />
   <meta name="citation_pdf_url" content="https://biocypher.github.io/biochatter-paper/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://biocypher.github.io/biochatter-paper/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://biocypher.github.io/biochatter-paper/v/f083f323b3d0e1cb6b418fc3fdd066ce494d8df4/" />
-  <meta name="manubot_html_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/f083f323b3d0e1cb6b418fc3fdd066ce494d8df4/" />
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+  <link rel="alternate" type="text/html" href="https://biocypher.github.io/biochatter-paper/v/985ed1f8a14d402b9120a0c91e4acd8d901b672a/" />
+  <meta name="manubot_html_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/985ed1f8a14d402b9120a0c91e4acd8d901b672a/" />
+  <meta name="manubot_pdf_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/985ed1f8a14d402b9120a0c91e4acd8d901b672a/manuscript.pdf" />
   <meta property="og:type" content="article" />
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@@ -99,9 +113,9 @@ <h1 class="title">A Platform for the Biomedical Application of Large Language Mo
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://biocypher.github.io/biochatter-paper/v/f083f323b3d0e1cb6b418fc3fdd066ce494d8df4/">permalink</a>)
+(<a href="https://biocypher.github.io/biochatter-paper/v/985ed1f8a14d402b9120a0c91e4acd8d901b672a/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/biocypher/biochatter-paper/tree/f083f323b3d0e1cb6b418fc3fdd066ce494d8df4">biocypher/biochatter-paper@f083f32</a>
+from <a href="https://github.com/biocypher/biochatter-paper/tree/985ed1f8a14d402b9120a0c91e4acd8d901b672a">biocypher/biochatter-paper@985ed1f</a>
 on December 29, 2023.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -128,6 +142,40 @@ <h2 id="authors">Authors</h2>
 <small>
 Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
 </small></p></li>
+<li><p><strong>Cankun Wang</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0000-0002-0225-9855">0000-0002-0225-9855</a>
+· <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
+<a href="https://github.com/Wang-Cankun">Wang-Cankun</a>
+· <img src="images/twitter.svg" class="inline_icon" width="16" height="16" alt="Twitter icon" />
+<a href="https://twitter.com/Wang-Cankun">Wang-Cankun</a>
+<br>
+<small>
+Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
+</small></p></li>
+<li><p><strong>Qin Ma</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0000-0002-3264-8392">0000-0002-3264-8392</a>
+· <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
+<a href="https://github.com/maqin2001">maqin2001</a>
+· <img src="images/twitter.svg" class="inline_icon" width="16" height="16" alt="Twitter icon" />
+<a href="https://twitter.com/QinMaBMBL">QinMaBMBL</a>
+<br>
+<small>
+Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
+</small></p></li>
+<li><p><strong>Shaohong Feng</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0009-0000-8124-3626">0009-0000-8124-3626</a>
+· <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
+<a href="https://github.com/fengsh27">fengsh27</a>
+<br>
+<small>
+Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
+</small></p></li>
 <li><p><strong>Julio Saez-Rodriguez</strong>
 <sup><a href="#correspondence">✉</a></sup><br>
 <img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />

diff --git a/manuscript.md b/manuscript.md
@@ -10,6 +10,9 @@ date-meta: '2023-12-29'
 author-meta:
 - Sebastian Lobentanzer
 - Andreas Maier
+- Cankun Wang
+- Qin Ma
+- Shaohong Feng
 - Julio Saez-Rodriguez
 header-includes: |
   <!--
@@ -25,8 +28,8 @@ header-includes: |
   <meta name="dc.date" content="2023-12-29" />
   <meta name="citation_publication_date" content="2023-12-29" />
   <meta property="article:published_time" content="2023-12-29" />
-  <meta name="dc.modified" content="2023-12-29T13:56:02+00:00" />
-  <meta property="article:modified_time" content="2023-12-29T13:56:02+00:00" />
+  <meta name="dc.modified" content="2023-12-29T14:00:02+00:00" />
+  <meta property="article:modified_time" content="2023-12-29T14:00:02+00:00" />
   <meta name="dc.language" content="en-UK" />
   <meta name="citation_language" content="en-UK" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -40,6 +43,17 @@ header-includes: |
   <meta name="citation_author" content="Andreas Maier" />
   <meta name="citation_author_institution" content="Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany" />
   <meta name="citation_author_orcid" content="0000-0003-4408-0068" />
+  <meta name="citation_author" content="Cankun Wang" />
+  <meta name="citation_author_institution" content="Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA" />
+  <meta name="citation_author_orcid" content="0000-0002-0225-9855" />
+  <meta name="twitter:creator" content="@Wang-Cankun" />
+  <meta name="citation_author" content="Qin Ma" />
+  <meta name="citation_author_institution" content="Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA" />
+  <meta name="citation_author_orcid" content="0000-0002-3264-8392" />
+  <meta name="twitter:creator" content="@QinMaBMBL" />
+  <meta name="citation_author" content="Shaohong Feng" />
+  <meta name="citation_author_institution" content="Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA" />
+  <meta name="citation_author_orcid" content="0009-0000-8124-3626" />
   <meta name="citation_author" content="Julio Saez-Rodriguez" />
   <meta name="citation_author_institution" content="Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany" />
   <meta name="citation_author_orcid" content="0000-0002-8552-8976" />
@@ -50,9 +64,9 @@ header-includes: |
   <meta name="citation_fulltext_html_url" content="https://biocypher.github.io/biochatter-paper/" />
   <meta name="citation_pdf_url" content="https://biocypher.github.io/biochatter-paper/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://biocypher.github.io/biochatter-paper/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://biocypher.github.io/biochatter-paper/v/f083f323b3d0e1cb6b418fc3fdd066ce494d8df4/" />
-  <meta name="manubot_html_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/f083f323b3d0e1cb6b418fc3fdd066ce494d8df4/" />
-  <meta name="manubot_pdf_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/f083f323b3d0e1cb6b418fc3fdd066ce494d8df4/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://biocypher.github.io/biochatter-paper/v/985ed1f8a14d402b9120a0c91e4acd8d901b672a/" />
+  <meta name="manubot_html_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/985ed1f8a14d402b9120a0c91e4acd8d901b672a/" />
+  <meta name="manubot_pdf_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/985ed1f8a14d402b9120a0c91e4acd8d901b672a/manuscript.pdf" />
   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -74,9 +88,9 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://biocypher.github.io/biochatter-paper/v/f083f323b3d0e1cb6b418fc3fdd066ce494d8df4/))
+([permalink](https://biocypher.github.io/biochatter-paper/v/985ed1f8a14d402b9120a0c91e4acd8d901b672a/))
 was automatically generated
-from [biocypher/biochatter-paper@f083f32](https://github.com/biocypher/biochatter-paper/tree/f083f323b3d0e1cb6b418fc3fdd066ce494d8df4)
+from [biocypher/biochatter-paper@985ed1f](https://github.com/biocypher/biochatter-paper/tree/985ed1f8a14d402b9120a0c91e4acd8d901b672a)
 on December 29, 2023.
 </em></small>
 
@@ -110,6 +124,43 @@ on December 29, 2023.
      Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
   </small>
 
++ **Cankun Wang**
+  <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    [0000-0002-0225-9855](https://orcid.org/0000-0002-0225-9855)
+    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
+    [Wang-Cankun](https://github.com/Wang-Cankun)
+    · ![Twitter icon](images/twitter.svg){.inline_icon width=16 height=16}
+    [Wang-Cankun](https://twitter.com/Wang-Cankun)
+    <br>
+  <small>
+     Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
+  </small>
+
++ **Qin Ma**
+  <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    [0000-0002-3264-8392](https://orcid.org/0000-0002-3264-8392)
+    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
+    [maqin2001](https://github.com/maqin2001)
+    · ![Twitter icon](images/twitter.svg){.inline_icon width=16 height=16}
+    [QinMaBMBL](https://twitter.com/QinMaBMBL)
+    <br>
+  <small>
+     Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
+  </small>
+
++ **Shaohong Feng**
+  <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    [0009-0000-8124-3626](https://orcid.org/0009-0000-8124-3626)
+    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
+    [fengsh27](https://github.com/fengsh27)
+    <br>
+  <small>
+     Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
+  </small>
+
 + **Julio Saez-Rodriguez**
   ^[✉](#correspondence)^<br>
     ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/spelling-errors.txt b/spelling-errors.txt
@@ -10,6 +10,7 @@ BioChatter’s
 BioCypher
 bioinformatics
 biomedicine
+Cankun
 ChatGPT
 ChatGSE
 complemetary
@@ -19,6 +20,8 @@ Dimitrov
 Dugourd
 embeddings
 ensembling
+Feng
+fengsh
 GPT
 GPUs
 GSK
@@ -37,6 +40,7 @@ LLM’s
 LLMs
 Lobentanzer
 Maier
+maqin
 Milvus
 Mompel
 ontologies
@@ -46,6 +50,8 @@ parameterisation
 Pau
 py
 Pytest
+Qin
+QinMaBMBL
 quantisations
 recency
 reproducibility
@@ -54,6 +60,7 @@ saezlab
 saezrodriguez
 Sanofi
 Schumacher
+Shaohong
 siloed
 SL
 slobentanzer