diff --git a/404.html b/404.html
index 1e40f8c..e94f62c 100644
--- a/404.html
+++ b/404.html
@@ -31,7 +31,7 @@
     
     <a class="navbar-brand me-2" href="https://sigven.github.io/phenOncoX/index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index e825001..9b303e0 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index fa3362c..2ef0f2f 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index 03fa34c..b522496 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/phenOncoX.html b/articles/phenOncoX.html
index 9ecd7c6..6a03d0a 100644
--- a/articles/phenOncoX.html
+++ b/articles/phenOncoX.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -110,12 +110,12 @@ <h2 id="get-oncotree-terms">Get OncoTree terms<a class="anchor" aria-label="anch
 <span></span>
 <span><span class="va">oncotree</span> <span class="op">&lt;-</span> <span class="fu">phenOncoX</span><span class="fu">::</span><span class="fu"><a href="../reference/get_tree.html">get_tree</a></span><span class="op">(</span></span>
 <span>  cache_dir <span class="op">=</span> <span class="va">download_dir</span>, max_tree_depth <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:01:59] Downloading remote dataset from Google Drive to cache_dir</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:00] Reading from cache_dir = '/tmp/RtmpsNiYs6', argument force_download = FALSE</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:00] Object 'oncotree_core' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:00] md5 checksum is valid: dd4a2050f681a5a06aa9d2f384b6bac1</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:00] Retrieved 799 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:00] Limiting OncoTree terms to those with a maximum tree depth of = '2'</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:00] Downloading remote dataset from Google Drive to cache_dir</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:01] Reading from cache_dir = '/tmp/RtmpoqR28m', argument force_download = FALSE</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:01] Object 'oncotree_core' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:01] md5 checksum is valid: dd4a2050f681a5a06aa9d2f384b6bac1</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:01] Retrieved 799 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:01] Limiting OncoTree terms to those with a maximum tree depth of = '2'</span></span>
 <span></span>
 <span><span class="co">## Number of records</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">oncotree</span><span class="op">$</span><span class="va">records</span><span class="op">)</span></span>
@@ -143,11 +143,11 @@ <h3 id="get-all-oncotree-expanded-cancer-phenotype-terms">Get all (OncoTree-expa
 <span></span>
 <span><span class="va">oncoterms</span> <span class="op">&lt;-</span> <span class="fu">phenOncoX</span><span class="fu">::</span><span class="fu"><a href="../reference/get_terms.html">get_terms</a></span><span class="op">(</span></span>
 <span>  cache_dir <span class="op">=</span> <span class="va">download_dir</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:00] Downloading remote dataset from Google Drive to cache_dir</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:03] Reading from cache_dir = '/tmp/RtmpsNiYs6', argument force_download = FALSE</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:03] Object 'oncotree_expanded' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:03] md5 checksum is valid: 8612461c9bcc75e7d943fc8b206a5406</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:03] Retrieved 25294 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:01] Downloading remote dataset from Google Drive to cache_dir</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:03] Reading from cache_dir = '/tmp/RtmpoqR28m', argument force_download = FALSE</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:03] Object 'oncotree_expanded' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:03] md5 checksum is valid: 8612461c9bcc75e7d943fc8b206a5406</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:03] Retrieved 25294 records</span></span>
 <span></span>
 <span><span class="co">## Number of records</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">oncoterms</span><span class="op">$</span><span class="va">records</span><span class="op">)</span></span>
@@ -164,9 +164,9 @@ <h3 id="number-of-oncotree-expanded-cancer-phenotype-terms-per-primary-tumor-typ
 <span></span>
 <span><span class="va">oncoterms</span> <span class="op">&lt;-</span> <span class="fu">phenOncoX</span><span class="fu">::</span><span class="fu"><a href="../reference/get_terms.html">get_terms</a></span><span class="op">(</span></span>
 <span>  cache_dir <span class="op">=</span> <span class="va">download_dir</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:04] Reading from cache_dir = '/tmp/RtmpsNiYs6', argument force_download = FALSE</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:04] Object 'oncotree_expanded' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-02-08 22:02:04] Retrieved n = 25294 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:03] Reading from cache_dir = '/tmp/RtmpoqR28m', argument force_download = FALSE</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:03] Object 'oncotree_expanded' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-02-08 22:04:03] Retrieved n = 25294 records</span></span>
 <span></span>
 <span><span class="co">## Number of records</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/as.data.frame.html" class="external-link">as.data.frame</a></span><span class="op">(</span><span class="va">oncoterms</span><span class="op">$</span><span class="va">records</span> <span class="op">|&gt;</span></span>
@@ -233,8 +233,8 @@ <h3 id="get-all-oncotree-expanded-cancer-phenotype-terms-relevant-for-prostate-c
 <span>    buttons <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"csv"</span>, <span class="st">"excel"</span><span class="op">)</span>, </span>
 <span>    dom <span class="op">=</span> <span class="st">"Bfrtip"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p><br></p>
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Prostate Cancer","Treatment-Related Prostate Neuroendocrine Carcinoma","Tumor invasion of perineural tissue absent (prostate)","Tumor of Specialized Prostatic Stroma","Unresectable Castration-Resistant Prostate Carcinoma","Unresectable Prostate Carcinoma","Unresectable Prostate Small Cell Neuroendocrine Carcinoma","Usual Prostate Adenocarcinoma with Neuroendocrine Differentiation","Well Differentiated Prostate 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Pattern","Prostate Granular Cell Tumor","Prostate Hemangioma","Prostate Inflammatory Myofibroblastic Tumor","Prostate Intraductal Carcinoma","Prostate Kaposi Sarcoma","Prostate Large Cell Neuroendocrine Carcinoma","Prostate Malignant Solitary Fibrous Tumor","Prostate Melanoma","Prostate Myeloid Sarcoma","Prostate Neuroendocrine Carcinoma","Prostate Neuroendocrine Tumor","Prostate Osteosarcoma","Prostate Paraganglioma","Prostate Small Cell Neuroendocrine Carcinoma","Prostate Soft Tissue Neoplasm","Prostate Solitary Fibrous Tumor","Prostate Stromal Tumor of Uncertain Malignant Potential","Prostate Synovial Sarcoma","Prostate Undifferentiated Carcinoma","Prostate Undifferentiated Pleomorphic Sarcoma","Prostate Wilms Tumor","Prostate adenocarcinoma","Prostate adenoid cystic carcinoma","Prostate angiosarcoma","Prostate cancer aggressiveness quantitative trait locus on chromosome 19","Prostate cancer care review done","Prostate cancer metastatic to eye","Prostate cancer, somatic","Prostate carcinoma","Prostate embryonal rhabdomyosarcoma","Prostate intraepithelial neoplasia","Prostate leiomyoma","Prostate leiomyosarcoma","Prostate neoplasm","Prostate neuroendocrine neoplasm","Prostate phyllodes tumor","Prostate rhabdomyosarcoma","Prostate sarcoma","Prostate small cell carcinoma","Prostate squamous cell carcinoma","Prostate stromal sarcoma","Prostatic Duct Urothelial Carcinoma","Prostatic Neoplasms, Castration-Resistant","Prostatic acinar adenocarcinoma","Prostatic adenoma","Prostatic urethra urothelial carcinoma","Recurrent Prostate Acinar Adenocarcinoma","Recurrent Prostate Adenocarcinoma","Recurrent Prostate Carcinoma","Recurrent Prostate Small Cell Neuroendocrine Carcinoma","Recurrent malignant neoplasm of prostate","Refractory Prostate Adenocarcinoma","Refractory Prostate Carcinoma","Refractory Prostate Small Cell Neuroendocrine Carcinoma","Secondary Prostate Urothelial Carcinoma","Stage A Prostate Cancer","Stage B Prostate Cancer","Stage C Prostate Cancer","Stage D Prostate Cancer","Stage I Prostate Adenocarcinoma AJCC v7","Stage I Prostate Cancer AJCC v6","Stage I Prostate Cancer AJCC v7","Stage I Prostate Cancer AJCC v8","Stage II Prostate Adenocarcinoma AJCC v7","Stage II Prostate Cancer AJCC v6","Stage II Prostate Cancer AJCC v7","Stage II Prostate Cancer AJCC v8","Stage IIA Prostate Cancer AJCC v7","Stage IIA Prostate Cancer AJCC v8","Stage IIB Prostate Cancer AJCC v7","Stage IIB Prostate Cancer AJCC v8","Stage IIC Prostate Cancer AJCC v8","Stage III Prostate Adenocarcinoma AJCC v7","Stage III Prostate Cancer AJCC v6","Stage III Prostate Cancer AJCC v7","Stage III Prostate Cancer AJCC v8","Stage IIIA Prostate Cancer AJCC v8","Stage IIIB Prostate Cancer AJCC v8","Stage IIIC Prostate Cancer AJCC v8","Stage IV Prostate Adenocarcinoma AJCC v7","Stage IV Prostate Cancer AJCC v6","Stage IV Prostate Cancer AJCC v7","Stage IV Prostate Cancer AJCC v8","Stage IVA Prostate Cancer AJCC v8","Stage IVB Prostate Cancer AJCC v8","Total Gleason Score for Prostate Cancer","Treatment-Related Prostate Neuroendocrine Carcinoma","Tumor invasion of perineural tissue absent (prostate)","Tumor of Specialized Prostatic Stroma","Unresectable Castration-Resistant Prostate Carcinoma","Unresectable Prostate Carcinoma","Unresectable Prostate Small Cell Neuroendocrine Carcinoma","Usual Prostate Adenocarcinoma with Neuroendocrine Differentiation","Well Differentiated Prostate Adenocarcinoma"],["Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS","Prostate_Cancer_NOS"],["Prostate","Basal Cell Carcinoma of Prostate","Prostate Adenocarcinoma","Prostate Neuroendocrine Carcinoma","Prostate Squamous Cell Carcinoma","Prostate Small Cell Carcinoma",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],["1","2","2","2","2","2",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],["PROSTATE","BCCP","PRAD","PRNE","PRSC","PRSCC",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],["PROSTATE","PROSTATE-BCCP","PROSTATE-PRAD","PROSTATE-PRNE","PROSTATE-PRSC","PROSTATE-PRSCC",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],["MONDO:0008315",null,"EFO:0000673","MONDO:0002477",null,"EFO:1000499",null,"EFO:1000064",null,"EFO:1000065",null,null,null,null,null,null,null,null,null,"MONDO:0021510",null,null,"EFO:1000283",null,null,null,null,null,null,null,null,null,"EFO:1000283",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"MONDO:0008315",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"EFO:0000673",null,null,null,null,null,null,"EFO:0001663",null,"EFO:0002621",null,null,"MONDO:0021259","MONDO:0002477",null,"EFO:1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cancer",null,"prostate adenocarcinoma","prostate neuroendocrine neoplasm",null,"Prostate Small Cell Carcinoma",null,"Acinar Prostate Adenocarcinoma, Foamy Gland Variant",null,"Acinar Prostate Mucinous Adenocarcinoma",null,null,null,null,null,null,null,null,null,"benign neoplasm of prostate",null,null,"Grade III Prostatic Intraepithelial Neoplasia",null,null,null,null,null,null,null,null,null,"Grade III Prostatic Intraepithelial Neoplasia",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"prostate cancer",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"prostate 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 </div>
 </div>
 <div class="section level2">
@@ -266,7 +266,7 @@ <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
 <span><span class="co">#&gt;  [1] jsonlite_1.8.8    dplyr_1.1.4       compiler_4.3.2    crayon_1.5.2     </span></span>
-<span><span class="co">#&gt;  [5] tidyselect_1.2.0  stringr_1.5.1     phenOncoX_0.8.0   jquerylib_0.1.4  </span></span>
+<span><span class="co">#&gt;  [5] tidyselect_1.2.0  stringr_1.5.1     phenOncoX_0.7.1   jquerylib_0.1.4  </span></span>
 <span><span class="co">#&gt;  [9] systemfonts_1.0.5 textshaping_0.3.7 yaml_2.3.8        fastmap_1.1.1    </span></span>
 <span><span class="co">#&gt; [13] R6_2.5.1          generics_0.1.3    curl_5.2.0        knitr_1.45       </span></span>
 <span><span class="co">#&gt; [17] htmlwidgets_1.6.4 tibble_3.2.1      desc_1.4.3        bslib_0.6.1      </span></span>
diff --git a/authors.html b/authors.html
index 78283f9..dbe8158 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -58,13 +58,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Nakken S (2024).
 <em>phenOncoX: A phenotype ontology map for cancer</em>.
-R package version 0.8.0, <a href="https://github.com/sigven/phenOncoX" class="external-link">https://github.com/sigven/phenOncoX</a>. 
+R package version 0.7.1, <a href="https://github.com/sigven/phenOncoX" class="external-link">https://github.com/sigven/phenOncoX</a>. 
 </p>
       <pre>@Manual{,
   title = {phenOncoX: A phenotype ontology map for cancer},
   author = {Sigve Nakken},
   year = {2024},
-  note = {R package version 0.8.0},
+  note = {R package version 0.7.1},
   url = {https://github.com/sigven/phenOncoX},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index a0d4594..9075c84 100644
--- a/index.html
+++ b/index.html
@@ -43,7 +43,7 @@
     
     <a class="navbar-brand me-2" href="index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index c2c936f..8cce848 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   phenOncoX: phenOncoX.html
-last_built: 2024-02-08T22:01Z
+last_built: 2024-02-08T22:03Z
 urls:
   reference: https://sigven.github.io/phenOncoX/reference
   article: https://sigven.github.io/phenOncoX/articles
diff --git a/reference/get_aux_maps.html b/reference/get_aux_maps.html
index 0e1fa40..979babf 100644
--- a/reference/get_aux_maps.html
+++ b/reference/get_aux_maps.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_pox_data.html b/reference/get_pox_data.html
index ed27461..6bf90b0 100644
--- a/reference/get_pox_data.html
+++ b/reference/get_pox_data.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_terms.html b/reference/get_terms.html
index 2c991ad..006b274 100644
--- a/reference/get_terms.html
+++ b/reference/get_terms.html
@@ -30,7 +30,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_tree.html b/reference/get_tree.html
index 12ab804..09be338 100644
--- a/reference/get_tree.html
+++ b/reference/get_tree.html
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 969ba86..5934d67 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/tidyeval.html b/reference/tidyeval.html
index e4de4bb..2c609da 100644
--- a/reference/tidyeval.html
+++ b/reference/tidyeval.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index b6782c9..4913f06 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Getting started","text":"","code":"if (!(\"remotes\" %in% installed.packages()) {   install.packages(\"remotes\") } remotes::install_github('sigven/phenOncoX')"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-oncotree-terms","dir":"Articles","previous_headings":"","what":"Get OncoTree terms","title":"Getting started","text":"shows retrieve cancer phenotype terms , defined OncoTree (max tree depth = 2)","code":"## load the data download_dir <- tempdir()  oncotree <- phenOncoX::get_tree(   cache_dir = download_dir, max_tree_depth = 2) #> INFO  [2024-02-08 22:01:59] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-02-08 22:02:00] Reading from cache_dir = '/tmp/RtmpsNiYs6', argument force_download = FALSE #> INFO  [2024-02-08 22:02:00] Object 'oncotree_core' sucessfully loaded #> INFO  [2024-02-08 22:02:00] md5 checksum is valid: dd4a2050f681a5a06aa9d2f384b6bac1 #> INFO  [2024-02-08 22:02:00] Retrieved 799 records #> INFO  [2024-02-08 22:02:00] Limiting OncoTree terms to those with a maximum tree depth of = '2'  ## Number of records nrow(oncotree$records) #> [1] 252  ## Show metadata for underlying resources oncotree$metadata #>     source                                    source_description #> 1 OncoTree A cancer classification system for precision oncology #>                         source_url #> 1 http://oncotree.mskcc.org/#/home #>                                         source_citation source_version #> 1 Kundra et al., JCO Clin Cancer Inform, 2021; 33625877     2021_11_02 #>   source_abbreviation source_license #> 1            oncotree      CC BY 4.0 #>                             source_license_url #> 1 https://creativecommons.org/licenses/by/4.0/"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-all-oncotree-expanded-cancer-phenotype-terms","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Get all (OncoTree-expanded) cancer phenotype terms","title":"Getting started","text":"","code":"## get all cancer phenotype terms  oncoterms <- phenOncoX::get_terms(   cache_dir = download_dir) #> INFO  [2024-02-08 22:02:00] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-02-08 22:02:03] Reading from cache_dir = '/tmp/RtmpsNiYs6', argument force_download = FALSE #> INFO  [2024-02-08 22:02:03] Object 'oncotree_expanded' sucessfully loaded #> INFO  [2024-02-08 22:02:03] md5 checksum is valid: 8612461c9bcc75e7d943fc8b206a5406 #> INFO  [2024-02-08 22:02:03] Retrieved 25294 records  ## Number of records nrow(oncoterms$records) #> [1] 25294"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"number-of-oncotree-expanded-cancer-phenotype-terms-per-primary-tumor-typetissue","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Number of (OncoTree-expanded) cancer phenotype terms per primary tumor type/tissue","title":"Getting started","text":"","code":"## get all cancer phenotype terms  oncoterms <- phenOncoX::get_terms(   cache_dir = download_dir) #> INFO  [2024-02-08 22:02:04] Reading from cache_dir = '/tmp/RtmpsNiYs6', argument force_download = FALSE #> INFO  [2024-02-08 22:02:04] Object 'oncotree_expanded' sucessfully loaded #> INFO  [2024-02-08 22:02:04] Retrieved n = 25294 records  ## Number of records as.data.frame(oncoterms$records |>   dplyr::filter(!is.na(primary_site)) |>   dplyr::group_by(primary_site) |>    dplyr::summarise(num_terms = dplyr::n(),                    .groups = \"drop\") |>   dplyr::arrange(dplyr::desc(num_terms))) #>                 primary_site num_terms #> 1                   Lymphoid      4047 #> 2                Soft Tissue      2808 #> 3                  CNS/Brain      2270 #> 4              Head and Neck      2176 #> 5                       Skin      1992 #> 6                    Myeloid      1743 #> 7                       Lung      1067 #> 8               Colon/Rectum       953 #> 9       Ovary/Fallopian Tube       826 #> 10                    Breast       747 #> 11         Esophagus/Stomach       723 #> 12                      Bone       559 #> 13     Bladder/Urinary Tract       481 #> 14                    Uterus       461 #> 15             Biliary Tract       421 #> 16                     Liver       413 #> 17                    Kidney       385 #> 18                  Pancreas       328 #> 19 Peripheral Nervous System       293 #> 20                    Cervix       289 #> 21                       Eye       273 #> 22              Vulva/Vagina       265 #> 23                   Thyroid       249 #> 24                    Testis       234 #> 25                  Prostate       203 #> 26             Other/Unknown       176 #> 27                    Pleura       125 #> 28                Peritoneum       101 #> 29                    Thymus        87 #> 30             Adrenal Gland        68 #> 31                     Penis        62 #> 32          Ampulla of Vater        46"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-all-oncotree-expanded-cancer-phenotype-terms-relevant-for-prostate-cancer","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Get all (OncoTree-expanded) cancer phenotype terms relevant for prostate cancer","title":"Getting started","text":"","code":"## get all oncoterms for prostate cancer oncoterms_prostate <- phenOncoX::get_terms(   cache_dir = download_dir,    site = \"Prostate\")  ## Make as datatable prostate_terms_table <- DT::datatable(   dplyr::select(     oncoterms_prostate$records,      primary_site, cui, cui_name,     dplyr::everything()),   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\"))"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Getting started","text":"","code":"# set eval = FALSE if you don't want this info (useful for reproducibility)  # to appear sessionInfo() #> R version 4.3.2 (2023-10-31) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> loaded via a namespace (and not attached): #>  [1] jsonlite_1.8.8    dplyr_1.1.4       compiler_4.3.2    crayon_1.5.2      #>  [5] tidyselect_1.2.0  stringr_1.5.1     phenOncoX_0.8.0   jquerylib_0.1.4   #>  [9] systemfonts_1.0.5 textshaping_0.3.7 yaml_2.3.8        fastmap_1.1.1     #> [13] R6_2.5.1          generics_0.1.3    curl_5.2.0        knitr_1.45        #> [17] htmlwidgets_1.6.4 tibble_3.2.1      desc_1.4.3        bslib_0.6.1       #> [21] pillar_1.9.0      rlang_1.1.3       DT_0.31           utf8_1.2.4        #> [25] cachem_1.0.8      stringi_1.8.3     lgr_0.4.4         xfun_0.41         #> [29] fs_1.6.3          sass_0.4.8        memoise_2.0.1     cli_3.6.2         #> [33] withr_3.0.0       pkgdown_2.0.7     magrittr_2.0.3    crosstalk_1.2.1   #> [37] digest_0.6.34     lifecycle_1.0.4   vctrs_0.6.5       evaluate_0.23     #> [41] gargle_1.5.2      glue_1.7.0        ragg_1.2.7        googledrive_2.1.1 #> [45] fansi_1.0.6       httr_1.4.7        rmarkdown_2.25    purrr_1.0.2       #> [49] ellipsis_0.3.2    tools_4.3.2       pkgconfig_2.0.3   htmltools_0.5.7"},{"path":[]},{"path":"https://sigven.github.io/phenOncoX/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sigve Nakken. Author, maintainer.","code":""},{"path":"https://sigven.github.io/phenOncoX/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Nakken S (2024). phenOncoX: phenotype ontology map cancer. R package version 0.8.0, https://github.com/sigven/phenOncoX.","code":"@Manual{,   title = {phenOncoX: A phenotype ontology map for cancer},   author = {Sigve Nakken},   year = {2024},   note = {R package version 0.8.0},   url = {https://github.com/sigven/phenOncoX}, }"},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"phenoncox-","dir":"","previous_headings":"","what":"A phenotype ontology map for cancer","title":"A phenotype ontology map for cancer","text":"ontological definition disease enables type disease singularly classified formalized structure. intention, use disease ontology terms facilitate cross-link information separate disease-related knowledge resources given domain. However, multiple disease ontology frameworks developed human disease (.e. OncoTree, Experimental Factor Ontology (EFO), Disease Ontology (), UMLS, ICD-10), used different extents across knowledge resources oncology domain, following: gene-disease associations drug-disease indications variant-disease associations order integrate knowledge resources, henceforth need cross-link map entries across disease ontologies extent possible. phenOncoX R data package attempts address challenge. short, phenOncoX provides global cross-mapped set phenotype ontology terms attributed cancer phenotypes. mapping established within phenOncoX semi-manually curated, using OncoTree starting point list UMLS phenotype terms per cancer subtype/primary site. Next, phenOncoX appends number phenotypes attributed heritable cancer conditions. Furthermore, cancer subtype entry OncoTree expanded additional subtypes found UMLS child-parent hierarchy disease terms. entry final list phenotype terms, make cross-mappings phenotype terms EFO, , ICD10 classification. early February 2024, following ontology versions used create mapping: OncoTree (2021_11_02) Experimental Factor Ontology v3.62.0 (2024-01-15) Disease Ontology (v2024-01-31) package offers pre-processed datasets, along metadata, user can retrieve use projects set-ups. package utilizes googledrive R package download pre-processed documented datasets local cache directory provided user. IMPORTANT NOTE: mapping established phenOncoX attempts comprehensive, acknowledge presence missing erroneous cross-references might still occur.","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"A phenotype ontology map for cancer","text":"Installation instructions Usage examples","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"A phenotype ontology map for cancer","text":"sigven ifi.uio.","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"A phenotype ontology map for cancer","text":"Please note project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":null,"dir":"Reference","previous_headings":"","what":"Get auxiliary phenotype ontology maps — get_aux_maps","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"Downloads returns multiple phenotype dictionaries used cross-referencing terms, including UMLS, EFO, , ICD10. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - list object multiple lists/data.frames","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"","code":"get_aux_maps(cache_dir = NA, force_download = FALSE)"},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache)","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"metadata - data frame 4 rows 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - list following elements: umls - List UMLS data dictionaries - Data frame identifiers/names efo - List EFO data dictionaries icd10 - Data frame CUI ICD10 cross-reference","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"","code":"if (FALSE) { library(phenOncoX) oncology_terms <- get_aux_maps(cache_dir = tempdir()) }"},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"Function retrieves phenOncoX data Google Drive/local cache","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"","code":"get_pox_data(cache_dir = NA, force_download = FALSE, db = \"oncotree_core\")"},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) db type dataset retrieved","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"pre-processed ontology terms records/metadata auxiliary maps","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":null,"dir":"Reference","previous_headings":"","what":"Get oncology-relevant phenotype terms — get_terms","title":"Get oncology-relevant phenotype terms — get_terms","text":"Downloads returns dataset expanded set oncology-relevant phenotype terms (UMLS), using OncoTree starting point. expansion conducted tracking MeSH/UMLS tree structure phenotype terms. record comes cross-references Disease Ontology (), Experimental Factor Ontology (EFO), ICD10 wherever available. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - data frame phenotype terms","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get oncology-relevant phenotype terms — get_terms","text":"","code":"get_terms(   cache_dir = NA,   force_download = FALSE,   site = NA,   ignore_minor_type = FALSE )"},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get oncology-relevant phenotype terms — get_terms","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) site limit phenotype terms relevant given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', '/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina' ignore_minor_type logical indicating minor tumor types excluded ","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get oncology-relevant phenotype terms — get_terms","text":"metadata - data frame 5 rows 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - data frame following columns: primary_site - Primary tumor type/site ot_main_type - Main tumor type (OncoTree) ot_name - Phenotype name (OncoTree) ot_level - Tree level (OncoTree) ot_code - Phenotype code (OncoTree) ot_code_path - Tree code path (OncoTree) cui - Concept unique identifier (UMLS) cui_name - Phenotype name (UMLS) efo_id - EFO identifier efo_name - EFO name do_id - identifier do_name - name do_cancer_slim - identifier part cancer slim dictionary (TRUE/FALSE) minor_type - logical indicating whether term part minor tumor type/site icd10_code - ICD10 identifier source - term indicating dataset source","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get oncology-relevant phenotype terms — get_terms","text":"","code":"if (FALSE) { library(phenOncoX) oncology_terms <- get_terms(cache_dir = tempdir()) }"},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Get core phenotype terms from OncoTree — get_tree","title":"Get core phenotype terms from OncoTree — get_tree","text":"Downloads returns dataset curated phenotype terms (UMLS) OncoTree. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - data frame phenotype terms","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get core phenotype terms from OncoTree — get_tree","text":"","code":"get_tree(   cache_dir = NA,   force_download = FALSE,   site = NA,   max_tree_depth = 6,   ignore_minor_type = FALSE )"},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get core phenotype terms from OncoTree — get_tree","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) site limit OncoTree terms relevant given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', '/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina' max_tree_depth consider terms given depth OncoTree (integer 1-6, default: 6) ignore_minor_type logical indicating minor tumor types excluded ","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get core phenotype terms from OncoTree — get_tree","text":"metadata - data frame 1 row 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - data frame following columns: primary_site - Primary tumor type/site ot_main_type - Main tumor type (OncoTree) ot_name - Phenotype name (OncoTree) ot_level - Tree level (OncoTree) ot_code - Phenotype code (OncoTree) ot_code_path - Tree code path (OncoTree) cui - Concept unique identifier (UMLS) cui_name - Phenotype name (UMLS) minor_type - logical indicating whether term part minor tumor type/site source - term indicating dataset source","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get core phenotype terms from OncoTree — get_tree","text":"","code":"if (FALSE) { library(phenOncoX) oncology_terms <- get_tree(cache_dir = tempdir()) }"},{"path":"https://sigven.github.io/phenOncoX/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html","code":""}]
+[{"path":[]},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Getting started","text":"","code":"if (!(\"remotes\" %in% installed.packages()) {   install.packages(\"remotes\") } remotes::install_github('sigven/phenOncoX')"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-oncotree-terms","dir":"Articles","previous_headings":"","what":"Get OncoTree terms","title":"Getting started","text":"shows retrieve cancer phenotype terms , defined OncoTree (max tree depth = 2)","code":"## load the data download_dir <- tempdir()  oncotree <- phenOncoX::get_tree(   cache_dir = download_dir, max_tree_depth = 2) #> INFO  [2024-02-08 22:04:00] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-02-08 22:04:01] Reading from cache_dir = '/tmp/RtmpoqR28m', argument force_download = FALSE #> INFO  [2024-02-08 22:04:01] Object 'oncotree_core' sucessfully loaded #> INFO  [2024-02-08 22:04:01] md5 checksum is valid: dd4a2050f681a5a06aa9d2f384b6bac1 #> INFO  [2024-02-08 22:04:01] Retrieved 799 records #> INFO  [2024-02-08 22:04:01] Limiting OncoTree terms to those with a maximum tree depth of = '2'  ## Number of records nrow(oncotree$records) #> [1] 252  ## Show metadata for underlying resources oncotree$metadata #>     source                                    source_description #> 1 OncoTree A cancer classification system for precision oncology #>                         source_url #> 1 http://oncotree.mskcc.org/#/home #>                                         source_citation source_version #> 1 Kundra et al., JCO Clin Cancer Inform, 2021; 33625877     2021_11_02 #>   source_abbreviation source_license #> 1            oncotree      CC BY 4.0 #>                             source_license_url #> 1 https://creativecommons.org/licenses/by/4.0/"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-all-oncotree-expanded-cancer-phenotype-terms","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Get all (OncoTree-expanded) cancer phenotype terms","title":"Getting started","text":"","code":"## get all cancer phenotype terms  oncoterms <- phenOncoX::get_terms(   cache_dir = download_dir) #> INFO  [2024-02-08 22:04:01] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-02-08 22:04:03] Reading from cache_dir = '/tmp/RtmpoqR28m', argument force_download = FALSE #> INFO  [2024-02-08 22:04:03] Object 'oncotree_expanded' sucessfully loaded #> INFO  [2024-02-08 22:04:03] md5 checksum is valid: 8612461c9bcc75e7d943fc8b206a5406 #> INFO  [2024-02-08 22:04:03] Retrieved 25294 records  ## Number of records nrow(oncoterms$records) #> [1] 25294"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"number-of-oncotree-expanded-cancer-phenotype-terms-per-primary-tumor-typetissue","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Number of (OncoTree-expanded) cancer phenotype terms per primary tumor type/tissue","title":"Getting started","text":"","code":"## get all cancer phenotype terms  oncoterms <- phenOncoX::get_terms(   cache_dir = download_dir) #> INFO  [2024-02-08 22:04:03] Reading from cache_dir = '/tmp/RtmpoqR28m', argument force_download = FALSE #> INFO  [2024-02-08 22:04:03] Object 'oncotree_expanded' sucessfully loaded #> INFO  [2024-02-08 22:04:03] Retrieved n = 25294 records  ## Number of records as.data.frame(oncoterms$records |>   dplyr::filter(!is.na(primary_site)) |>   dplyr::group_by(primary_site) |>    dplyr::summarise(num_terms = dplyr::n(),                    .groups = \"drop\") |>   dplyr::arrange(dplyr::desc(num_terms))) #>                 primary_site num_terms #> 1                   Lymphoid      4047 #> 2                Soft Tissue      2808 #> 3                  CNS/Brain      2270 #> 4              Head and Neck      2176 #> 5                       Skin      1992 #> 6                    Myeloid      1743 #> 7                       Lung      1067 #> 8               Colon/Rectum       953 #> 9       Ovary/Fallopian Tube       826 #> 10                    Breast       747 #> 11         Esophagus/Stomach       723 #> 12                      Bone       559 #> 13     Bladder/Urinary Tract       481 #> 14                    Uterus       461 #> 15             Biliary Tract       421 #> 16                     Liver       413 #> 17                    Kidney       385 #> 18                  Pancreas       328 #> 19 Peripheral Nervous System       293 #> 20                    Cervix       289 #> 21                       Eye       273 #> 22              Vulva/Vagina       265 #> 23                   Thyroid       249 #> 24                    Testis       234 #> 25                  Prostate       203 #> 26             Other/Unknown       176 #> 27                    Pleura       125 #> 28                Peritoneum       101 #> 29                    Thymus        87 #> 30             Adrenal Gland        68 #> 31                     Penis        62 #> 32          Ampulla of Vater        46"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-all-oncotree-expanded-cancer-phenotype-terms-relevant-for-prostate-cancer","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Get all (OncoTree-expanded) cancer phenotype terms relevant for prostate cancer","title":"Getting started","text":"","code":"## get all oncoterms for prostate cancer oncoterms_prostate <- phenOncoX::get_terms(   cache_dir = download_dir,    site = \"Prostate\")  ## Make as datatable prostate_terms_table <- DT::datatable(   dplyr::select(     oncoterms_prostate$records,      primary_site, cui, cui_name,     dplyr::everything()),   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\"))"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Getting started","text":"","code":"# set eval = FALSE if you don't want this info (useful for reproducibility)  # to appear sessionInfo() #> R version 4.3.2 (2023-10-31) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> loaded via a namespace (and not attached): #>  [1] jsonlite_1.8.8    dplyr_1.1.4       compiler_4.3.2    crayon_1.5.2      #>  [5] tidyselect_1.2.0  stringr_1.5.1     phenOncoX_0.7.1   jquerylib_0.1.4   #>  [9] systemfonts_1.0.5 textshaping_0.3.7 yaml_2.3.8        fastmap_1.1.1     #> [13] R6_2.5.1          generics_0.1.3    curl_5.2.0        knitr_1.45        #> [17] htmlwidgets_1.6.4 tibble_3.2.1      desc_1.4.3        bslib_0.6.1       #> [21] pillar_1.9.0      rlang_1.1.3       DT_0.31           utf8_1.2.4        #> [25] cachem_1.0.8      stringi_1.8.3     lgr_0.4.4         xfun_0.41         #> [29] fs_1.6.3          sass_0.4.8        memoise_2.0.1     cli_3.6.2         #> [33] withr_3.0.0       pkgdown_2.0.7     magrittr_2.0.3    crosstalk_1.2.1   #> [37] digest_0.6.34     lifecycle_1.0.4   vctrs_0.6.5       evaluate_0.23     #> [41] gargle_1.5.2      glue_1.7.0        ragg_1.2.7        googledrive_2.1.1 #> [45] fansi_1.0.6       httr_1.4.7        rmarkdown_2.25    purrr_1.0.2       #> [49] ellipsis_0.3.2    tools_4.3.2       pkgconfig_2.0.3   htmltools_0.5.7"},{"path":[]},{"path":"https://sigven.github.io/phenOncoX/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sigve Nakken. Author, maintainer.","code":""},{"path":"https://sigven.github.io/phenOncoX/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Nakken S (2024). phenOncoX: phenotype ontology map cancer. R package version 0.7.1, https://github.com/sigven/phenOncoX.","code":"@Manual{,   title = {phenOncoX: A phenotype ontology map for cancer},   author = {Sigve Nakken},   year = {2024},   note = {R package version 0.7.1},   url = {https://github.com/sigven/phenOncoX}, }"},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"phenoncox-","dir":"","previous_headings":"","what":"A phenotype ontology map for cancer","title":"A phenotype ontology map for cancer","text":"ontological definition disease enables type disease singularly classified formalized structure. intention, use disease ontology terms facilitate cross-link information separate disease-related knowledge resources given domain. However, multiple disease ontology frameworks developed human disease (.e. OncoTree, Experimental Factor Ontology (EFO), Disease Ontology (), UMLS, ICD-10), used different extents across knowledge resources oncology domain, following: gene-disease associations drug-disease indications variant-disease associations order integrate knowledge resources, henceforth need cross-link map entries across disease ontologies extent possible. phenOncoX R data package attempts address challenge. short, phenOncoX provides global cross-mapped set phenotype ontology terms attributed cancer phenotypes. mapping established within phenOncoX semi-manually curated, using OncoTree starting point list UMLS phenotype terms per cancer subtype/primary site. Next, phenOncoX appends number phenotypes attributed heritable cancer conditions. Furthermore, cancer subtype entry OncoTree expanded additional subtypes found UMLS child-parent hierarchy disease terms. entry final list phenotype terms, make cross-mappings phenotype terms EFO, , ICD10 classification. early February 2024, following ontology versions used create mapping: OncoTree (2021_11_02) Experimental Factor Ontology v3.62.0 (2024-01-15) Disease Ontology (v2024-01-31) package offers pre-processed datasets, along metadata, user can retrieve use projects set-ups. package utilizes googledrive R package download pre-processed documented datasets local cache directory provided user. IMPORTANT NOTE: mapping established phenOncoX attempts comprehensive, acknowledge presence missing erroneous cross-references might still occur.","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"A phenotype ontology map for cancer","text":"Installation instructions Usage examples","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"A phenotype ontology map for cancer","text":"sigven ifi.uio.","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"A phenotype ontology map for cancer","text":"Please note project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":null,"dir":"Reference","previous_headings":"","what":"Get auxiliary phenotype ontology maps — get_aux_maps","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"Downloads returns multiple phenotype dictionaries used cross-referencing terms, including UMLS, EFO, , ICD10. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - list object multiple lists/data.frames","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"","code":"get_aux_maps(cache_dir = NA, force_download = FALSE)"},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache)","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"metadata - data frame 4 rows 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - list following elements: umls - List UMLS data dictionaries - Data frame identifiers/names efo - List EFO data dictionaries icd10 - Data frame CUI ICD10 cross-reference","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"","code":"if (FALSE) { library(phenOncoX) oncology_terms <- get_aux_maps(cache_dir = tempdir()) }"},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"Function retrieves phenOncoX data Google Drive/local cache","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"","code":"get_pox_data(cache_dir = NA, force_download = FALSE, db = \"oncotree_core\")"},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) db type dataset retrieved","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"pre-processed ontology terms records/metadata auxiliary maps","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":null,"dir":"Reference","previous_headings":"","what":"Get oncology-relevant phenotype terms — get_terms","title":"Get oncology-relevant phenotype terms — get_terms","text":"Downloads returns dataset expanded set oncology-relevant phenotype terms (UMLS), using OncoTree starting point. expansion conducted tracking MeSH/UMLS tree structure phenotype terms. record comes cross-references Disease Ontology (), Experimental Factor Ontology (EFO), ICD10 wherever available. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - data frame phenotype terms","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get oncology-relevant phenotype terms — get_terms","text":"","code":"get_terms(   cache_dir = NA,   force_download = FALSE,   site = NA,   ignore_minor_type = FALSE )"},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get oncology-relevant phenotype terms — get_terms","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) site limit phenotype terms relevant given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', '/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina' ignore_minor_type logical indicating minor tumor types excluded ","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get oncology-relevant phenotype terms — get_terms","text":"metadata - data frame 5 rows 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - data frame following columns: primary_site - Primary tumor type/site ot_main_type - Main tumor type (OncoTree) ot_name - Phenotype name (OncoTree) ot_level - Tree level (OncoTree) ot_code - Phenotype code (OncoTree) ot_code_path - Tree code path (OncoTree) cui - Concept unique identifier (UMLS) cui_name - Phenotype name (UMLS) efo_id - EFO identifier efo_name - EFO name do_id - identifier do_name - name do_cancer_slim - identifier part cancer slim dictionary (TRUE/FALSE) minor_type - logical indicating whether term part minor tumor type/site icd10_code - ICD10 identifier source - term indicating dataset source","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get oncology-relevant phenotype terms — get_terms","text":"","code":"if (FALSE) { library(phenOncoX) oncology_terms <- get_terms(cache_dir = tempdir()) }"},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Get core phenotype terms from OncoTree — get_tree","title":"Get core phenotype terms from OncoTree — get_tree","text":"Downloads returns dataset curated phenotype terms (UMLS) OncoTree. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - data frame phenotype terms","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get core phenotype terms from OncoTree — get_tree","text":"","code":"get_tree(   cache_dir = NA,   force_download = FALSE,   site = NA,   max_tree_depth = 6,   ignore_minor_type = FALSE )"},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get core phenotype terms from OncoTree — get_tree","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) site limit OncoTree terms relevant given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', '/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina' max_tree_depth consider terms given depth OncoTree (integer 1-6, default: 6) ignore_minor_type logical indicating minor tumor types excluded ","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get core phenotype terms from OncoTree — get_tree","text":"metadata - data frame 1 row 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - data frame following columns: primary_site - Primary tumor type/site ot_main_type - Main tumor type (OncoTree) ot_name - Phenotype name (OncoTree) ot_level - Tree level (OncoTree) ot_code - Phenotype code (OncoTree) ot_code_path - Tree code path (OncoTree) cui - Concept unique identifier (UMLS) cui_name - Phenotype name (UMLS) minor_type - logical indicating whether term part minor tumor type/site source - term indicating dataset source","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get core phenotype terms from OncoTree — get_tree","text":"","code":"if (FALSE) { library(phenOncoX) oncology_terms <- get_tree(cache_dir = tempdir()) }"},{"path":"https://sigven.github.io/phenOncoX/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html","code":""}]