diff --git a/404.html b/404.html
index 9392af1..9121c3b 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://bhklab.github.io/AnnotationGx/index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</small>
 
     
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diff --git a/LICENSE-text.html b/LICENSE-text.html
index c72d646..7c6e142 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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.html b/LICENSE.html
index af3a61f..af88d37 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/Cellosaurus.html b/articles/Cellosaurus.html
index bbdc820..a2338ad 100644
--- a/articles/Cellosaurus.html
+++ b/articles/Cellosaurus.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/PubChemAPI.html b/articles/PubChemAPI.html
index 3ba4c9b..3aa133d 100644
--- a/articles/PubChemAPI.html
+++ b/articles/PubChemAPI.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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 d5a9e11..68f92a4 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/authors.html b/authors.html
index 4a72a19..db04632 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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">
@@ -65,14 +65,14 @@ <h2 id="citation">Citation</h2>
       <p>Joseph J, Eeles C, Haibe-Kains B (2024).
 <em>AnnotationGx: AnnotationGx: A package for building, updating and querying an
 annotation database for pharmaco-genomic data</em>.
-R package version 0.0.0.9061, <a href="https://bhklab.github.io/AnnotationGx/">https://bhklab.github.io/AnnotationGx/</a>. 
+R package version 0.0.0.9062, <a href="https://bhklab.github.io/AnnotationGx/">https://bhklab.github.io/AnnotationGx/</a>. 
 </p>
       <pre>@Manual{,
   title = {AnnotationGx: AnnotationGx: A package for building, updating and querying an
 annotation database for pharmaco-genomic data},
   author = {Jermiah Joseph and Christopher Eeles and Benjamin Haibe-Kains},
   year = {2024},
-  note = {R package version 0.0.0.9061},
+  note = {R package version 0.0.0.9062},
   url = {https://bhklab.github.io/AnnotationGx/},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index f4221ab..a7d5d36 100644
--- a/index.html
+++ b/index.html
@@ -36,7 +36,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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 82ba697..a1a8f77 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   Cellosaurus: Cellosaurus.html
   PubChemAPI: PubChemAPI.html
-last_built: 2024-02-21T19:32Z
+last_built: 2024-02-21T19:41Z
 urls:
   reference: https://bhklab.github.io/AnnotationGx/reference
   article: https://bhklab.github.io/AnnotationGx/articles
diff --git a/reference/AnnotationGx-package.html b/reference/AnnotationGx-package.html
index 414edac..60cef2f 100644
--- a/reference/AnnotationGx-package.html
+++ b/reference/AnnotationGx-package.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/annotatePubchemCompound.html b/reference/annotatePubchemCompound.html
index c09ba69..57cadd2 100644
--- a/reference/annotatePubchemCompound.html
+++ b/reference/annotatePubchemCompound.html
@@ -10,7 +10,7 @@
     
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/cell_model_passports_models.html b/reference/cell_model_passports_models.html
index 2ebbb0b..6348817 100644
--- a/reference/cell_model_passports_models.html
+++ b/reference/cell_model_passports_models.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/dot-build_chembl_request.html b/reference/dot-build_chembl_request.html
index 3ebfee7..b6fd7d1 100644
--- a/reference/dot-build_chembl_request.html
+++ b/reference/dot-build_chembl_request.html
@@ -116,7 +116,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/dot-build_pubchem_rest_query.html b/reference/dot-build_pubchem_rest_query.html
index 37a5d66..f9989f0 100644
--- a/reference/dot-build_pubchem_rest_query.html
+++ b/reference/dot-build_pubchem_rest_query.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/dot-checkThrottlingStatus2.html b/reference/dot-checkThrottlingStatus2.html
index c63b2ae..c5ffc64 100644
--- a/reference/dot-checkThrottlingStatus2.html
+++ b/reference/dot-checkThrottlingStatus2.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/dot-parse_resp_json.html b/reference/dot-parse_resp_json.html
index 67d072c..bec029a 100644
--- a/reference/dot-parse_resp_json.html
+++ b/reference/dot-parse_resp_json.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/dot-perform_request.html b/reference/dot-perform_request.html
index 341049a..87f8095 100644
--- a/reference/dot-perform_request.html
+++ b/reference/dot-perform_request.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/gdsc_sampleMetadata.html b/reference/gdsc_sampleMetadata.html
index 8283d7b..dcf355e 100644
--- a/reference/gdsc_sampleMetadata.html
+++ b/reference/gdsc_sampleMetadata.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/getChemblMechanism.html b/reference/getChemblMechanism.html
index c698ffc..c28f075 100644
--- a/reference/getChemblMechanism.html
+++ b/reference/getChemblMechanism.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/getChemblResourceFields.html b/reference/getChemblResourceFields.html
index 91d3a26..3f0c5f1 100644
--- a/reference/getChemblResourceFields.html
+++ b/reference/getChemblResourceFields.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/getPubchemAnnotationHeadings.html b/reference/getPubchemAnnotationHeadings.html
index 314ed9c..a5e229f 100644
--- a/reference/getPubchemAnnotationHeadings.html
+++ b/reference/getPubchemAnnotationHeadings.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/getPubchemCompound.html b/reference/getPubchemCompound.html
index fb63b42..731bf78 100644
--- a/reference/getPubchemCompound.html
+++ b/reference/getPubchemCompound.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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 9af7bfd..2d7d43d 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/mapCell2Accession.html b/reference/mapCell2Accession.html
index eeee5b9..249cd17 100644
--- a/reference/mapCell2Accession.html
+++ b/reference/mapCell2Accession.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/options.html b/reference/options.html
index 6618dd5..866f34e 100644
--- a/reference/options.html
+++ b/reference/options.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9061</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9062</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/standardize_names.html b/reference/standardize_names.html
index a955b57..725c5da 100644
--- a/reference/standardize_names.html
+++ b/reference/standardize_names.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AnnotationGx</a>
 
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     <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 d3d326a..2885de1 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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Mere interaction user computer network, transfer copy, conveying. interactive user interface displays “Appropriate Legal Notices” extent includes convenient prominently visible feature (1) displays appropriate copyright notice, (2) tells user warranty work (except extent warranties provided), licensees may convey work License, view copy License. interface presents list user commands options, menu, prominent item list meets criterion.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_1-source-code","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"1. Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. 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Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://bhklab.github.io/AnnotationGx/articles/PubChemAPI.html","id":"introduction-to-pubchem-apis","dir":"Articles","previous_headings":"","what":"Introduction to PubChem APIs","title":"Querying PubChem with AnnotationGx","text":"PubChem database chemical molecules biological activities. part National Center Biotechnology Information (NCBI), part National Institutes Health (NIH). PubChem provides set APIs query database. AnnotationGx package provides set functions query PubChem using APIs. first APIs PubChem PUG REST API designed - make specific queries based input identifier return data PubChem labelled computed internally [1]. - API useful querying information specific chemical compound getting standardized PubChem identifier (CID) given chemical name smiles string, getting chemical structure given CID. - provides access wide range data including chemical properties, bioassay data, chemical classification data, given specific identifier. second API PubChem PUG VIEW API designed : - give accesse aggregated annotations given chemical compound [3] mapped data, curated PubChem . - .e provides access annotations external sources UniProt, ChEBI, ChEMBL, given specific identifier.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/articles/PubChemAPI.html","id":"setup","dir":"Articles","previous_headings":"","what":"Setup","title":"Querying PubChem with AnnotationGx","text":"","code":"library(AnnotationGx)"},{"path":[]},{"path":"https://bhklab.github.io/AnnotationGx/articles/PubChemAPI.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"Querying PubChem with AnnotationGx","text":"PUG REST. PubChem Docs [website]. Retrieved https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest. Kim S, Thiessen PA, Cheng T, Yu B, Bolton EE. update PUG-REST: RESTful interface programmatic access PubChem. Nucleic Acids Res. 2018 July 2; 46(W1):W563-570. doi:10.1093/nar/gky294. PUG VIEW. PubChem Docs [webiste]. Retrieved https://pubchemdocs.ncbi.nlm.nih.gov/pug-view. Kim S, Thiessen PA, Cheng T, Zhang J, Gindulyte , Bolton EE. PUG-View: programmatic access chemical annotations integrated PubChem. J Cheminform. 2019 Aug 9; 11:56. doi:10.1186/s13321-019-0375-2.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Jermiah Joseph. Author, maintainer. Christopher Eeles. Author. Benjamin Haibe-Kains. Author.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Joseph J, Eeles C, Haibe-Kains B (2024). AnnotationGx: AnnotationGx: package building, updating querying annotation database pharmaco-genomic data. R package version 0.0.0.9061, https://bhklab.github.io/AnnotationGx/.","code":"@Manual{,   title = {AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data},   author = {Jermiah Joseph and Christopher Eeles and Benjamin Haibe-Kains},   year = {2024},   note = {R package version 0.0.0.9061},   url = {https://bhklab.github.io/AnnotationGx/}, }"},{"path":[]},{"path":"https://bhklab.github.io/AnnotationGx/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"AnnotationGx: A package for building, updating and querying an\n    annotation database for pharmaco-genomic data","text":"can install github using:","code":"remotes::install_github(\"bhklab/AnnotationGx\", build_manual=TRUE, build_vignettes=TRUE)"},{"path":"https://bhklab.github.io/AnnotationGx/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"AnnotationGx: A package for building, updating and querying an\n    annotation database for pharmaco-genomic data","text":"basic example shows solve common problem:","code":"library(AnnotationGx) ## basic example code"},{"path":"https://bhklab.github.io/AnnotationGx/reference/AnnotationGx-package.html","id":null,"dir":"Reference","previous_headings":"","what":"AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data — AnnotationGx-package","title":"AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data — AnnotationGx-package","text":"package building, updating querying annotation database pharmaco-genomic data. Provides API interfaces various bioinformatic chemoinformatic databases, well set functions curating data using annotations retrieved APIs.","code":""},{"path":[]},{"path":"https://bhklab.github.io/AnnotationGx/reference/AnnotationGx-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data — AnnotationGx-package","text":"Maintainer: Jermiah Joseph jermiah.joseph@gmail.com Authors: Christopher Eeles christopher.eeles@uhnresearch.ca Benjamin Haibe-Kains benjamin.haibe.kains@utoronto.ca","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate PubChem Compound — annotatePubchemCompound","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"function retrieves information PubChem compound based provided compound ID (CID).","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"","code":"annotatePubchemCompound(   cid,   heading = \"ChEMBL ID\",   source = NULL,   parse_function = identity )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"cid compound ID (CID) PubChem compound. heading type information retrieve. Default \"ChEMBL ID\". source data source use. Default NULL. parse_function custom parsing function process response. Default identity function.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"annotated information PubChem compound.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"","code":"annotatePubchemCompound(cid = 12345) #> character(0) annotatePubchemCompound(cid = 67890, heading = \"CAS\") #> [1] \"407-59-0\""},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":null,"dir":"Reference","previous_headings":"","what":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"preprocessed version cell model passports dataset. dataset contains following columns: CMP.model_id, CMP.sampleid, CMP.model_name, CMP.cancer_type_ncit_id, CMP.COSMIC_ID, CMP.BROAD_ID, CMP.CCLE_ID, CMP.RRID. dataset used AnnotationGx package map cell line names various sources Cellosaurus database.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"","code":"data(cell_model_passports_models)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"data table 8 columns 1001 rows. CMP.model_id char model id cell line cell model passports dataset. CMP.sample_id char sample id cell line cell model passports dataset. CMP.model_name char name cell line cell model passports dataset. CMP.cancer_type_ncit_id char cancer type ncit id cell line cell model passports dataset. CMP.COSMIC_ID int COSMIC ID cell line cell model passports dataset. CMP.BROAD_ID int BROAD ID cell line cell model passports dataset. CMP.CCLE_ID int CCLE ID cell line cell model passports dataset. CMP.RRID char RRID cell line cell model passports dataset.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"https://cog.sanger.ac.uk/cmp/download/model_list_20240103.csv","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"","code":"data(cell_model_passports_models) head(cell_model_passports_models) #>    CMP.model_id CMP.sample_id CMP.model_name CMP.cancer_type_ncit_id #>          <char>        <char>         <char>                  <char> #> 1:    SIDM01774     SIDS01659          PK-59                   C3850 #> 2:    SIDM00192     SIDS00612       SNU-1033                   C9383 #> 3:    SIDM01447     SIDS01466        SNU-466                   C3058 #> 4:    SIDM01554     SIDS01363      IST-MES-2                  C45662 #> 5:    SIDM01689     SIDS01631         MUTZ-5                   C8644 #> 6:    SIDM01460     SIDS01493          TM-31                  C60781 #>    CMP.COSMIC_ID CMP.BROAD_ID                              CMP.CCLE_ID #>           <char>       <char>                                   <char> #> 1:                 ACH-000205                            PK59_PANCREAS #> 2:                 ACH-000286                  SNU1033_LARGE_INTESTINE #> 3:                 ACH-000289            SNU466_CENTRAL_NERVOUS_SYSTEM #> 4:                 ACH-000331                           ISTMES2_PLEURA #> 5:                 ACH-000492 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE #> 6:                 ACH-000592              TM31_CENTRAL_NERVOUS_SYSTEM #>     CMP.RRID #>       <char> #> 1: CVCL_4897 #> 2: CVCL_5002 #> 3: CVCL_5064 #> 4: CVCL_1312 #> 5: CVCL_1873 #> 6: CVCL_6735"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_chembl_request.html","id":null,"dir":"Reference","previous_headings":"","what":"A general function for creating Queries to the ChEMBL API — .build_chembl_request","title":"A general function for creating Queries to the ChEMBL API — .build_chembl_request","text":"general function creating Queries ChEMBL API www DOT ebi DOT ac DOT uk/chembl/api/data/ ?__<filter_type>=","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_chembl_request.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A general function for creating Queries to the ChEMBL API — .build_chembl_request","text":"","code":".build_chembl_request(   resource,   field = NULL,   filter_type = NULL,   value = NULL,   format = \"json\" )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_chembl_request.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A general function for creating Queries to the ChEMBL API — .build_chembl_request","text":"resource character(1) Resource query field character(1) Field query filter_type character(1) Filter type value character(1) Value query format character(1) Format response","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_pubchem_rest_query.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a query for the PubChem REST API — .build_pubchem_rest_query","title":"Build a query for the PubChem REST API — .build_pubchem_rest_query","text":"function builds query PubChem REST API based provided parameters.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_pubchem_rest_query.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a query for the PubChem REST API — .build_pubchem_rest_query","text":"","code":".build_pubchem_rest_query(   id,   domain = \"compound\",   namespace = \"name\",   operation = \"cids\",   output = \"JSON\",   url = \"https://pubchem.ncbi.nlm.nih.gov/rest/pug\",   raw = FALSE,   query_only = FALSE,   ... )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_pubchem_rest_query.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a query for the PubChem REST API — .build_pubchem_rest_query","text":"id identifier(s) query. namespace 'name', id must single value. domain domain query. Options 'compound', 'substance', 'assay', 'cell', 'gene', 'protein'. namespace namespace query. Options depend chosen domain. operation operation perform. Options depend chosen domain namespace. output desired output format. Options 'JSON', 'XML', 'SDF', 'TXT', 'CSV'. url base URL PubChem REST API. raw Logical indicating whether return raw response parse . query_only Logical indicating whether return query URL . ... Additional arguments passed query.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_pubchem_rest_query.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a query for the PubChem REST API — .build_pubchem_rest_query","text":"query URL parsed response, depending arguments.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-checkThrottlingStatus2.html","id":null,"dir":"Reference","previous_headings":"","what":"names are: request_count, request_time and service\neach has status and percent\nmain throttlers for user are request_count and request_time\nmain statuses are:\nGreen - less than 50% of the permitted request limit has been used\nYellow - between 50% and 75% of the request limit has been used\nRed - more than 75% of the request limit has been reached\nBlack - the limit has been exceeded and requests are being blocked — .checkThrottlingStatus2","title":"names are: request_count, request_time and service\neach has status and percent\nmain throttlers for user are request_count and request_time\nmain statuses are:\nGreen - less than 50% of the permitted request limit has been used\nYellow - between 50% and 75% of the request limit has been used\nRed - more than 75% of the request limit has been reached\nBlack - the limit has been exceeded and requests are being blocked — .checkThrottlingStatus2","text":"names : request_count, request_time service status percent main throttlers user request_count request_time main statuses : Green - less 50% permitted request limit used Yellow - 50% 75% request limit used Red - 75% request limit reached Black - limit exceeded requests blocked","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-checkThrottlingStatus2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"names are: request_count, request_time and service\neach has status and percent\nmain throttlers for user are request_count and request_time\nmain statuses are:\nGreen - less than 50% of the permitted request limit has been used\nYellow - between 50% and 75% of the request limit has been used\nRed - more than 75% of the request limit has been reached\nBlack - the limit has been exceeded and requests are being blocked — .checkThrottlingStatus2","text":"","code":".checkThrottlingStatus2(response, printMessage)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-parse_resp_json.html","id":null,"dir":"Reference","previous_headings":"","what":"Parses the JSON response from an HTTP request. — .parse_resp_json","title":"Parses the JSON response from an HTTP request. — .parse_resp_json","text":"Parses JSON response HTTP request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-parse_resp_json.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parses the JSON response from an HTTP request. — .parse_resp_json","text":"","code":".parse_resp_json(resp)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-parse_resp_json.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parses the JSON response from an HTTP request. — .parse_resp_json","text":"resp response object HTTP request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-parse_resp_json.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parses the JSON response from an HTTP request. — .parse_resp_json","text":"parsed JSON response.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-perform_request.html","id":null,"dir":"Reference","previous_headings":"","what":"Performs an HTTP request. — .perform_request","title":"Performs an HTTP request. — .perform_request","text":"Performs HTTP request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-perform_request.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Performs an HTTP request. — .perform_request","text":"","code":".perform_request(request)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-perform_request.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Performs an HTTP request. — .perform_request","text":"request HTTP request perform.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-perform_request.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Performs an HTTP request. — .perform_request","text":"response HTTP request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"preprocessed version sample metadata GDSC dataset. dataset contains following columns: GDSC.Sample_Name, GDSC.BROAD_ID, GDSC.RRID, GDSC.COSMIC_ID, CCLE.sampleid. dataset used AnnotationGx package map cell line names various sources Cellosaurus database.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"","code":"data(gdsc_sampleMetadata)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"data table 5 columns 1001 rows. GDSC.Sample_Name char name cell line GDSC dataset. GDSC.COSMIC_ID int COSMIC ID cell line GDSC dataset.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"https://www.cancerrxgene.org/","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"","code":"data(gdsc_sampleMetadata) head(gdsc_sampleMetadata) #>    GDSC.Sample_Name GDSC.COSMIC_ID #>              <char>          <num> #> 1:             A253         906794 #> 2:         BB30-HNC         753531 #> 3:         BB49-HNC         753532 #> 4:              BHY         753535 #> 5:           BICR10        1290724 #> 6:           BICR22        1240121"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":null,"dir":"Reference","previous_headings":"","what":"Get ChEMBL Mechanism — getChemblMechanism","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"function retrieves information mechanism action given ChEMBL ID.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"","code":"getChemblMechanism(   chembl.ID,   resources = \"mechanism\",   field = \"molecule_chembl_id\",   filter_type = \"in\",   returnURL = FALSE,   raw = FALSE )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"chembl.ID ChEMBL ID molecule. resources ChEMBL resource query (default: \"mechanism\"). field field filter (default: \"molecule_chembl_id\"). filter_type filter type use (default: \"\"). returnURL Logical indicating whether return constructed URL (default: FALSE). raw Logical indicating whether return raw response JSON (default: FALSE).","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"data.table containing retrieved mechanism information.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"","code":"getChemblMechanism(\"CHEMBL1413\") #>        action_type binding_site_comment direct_interaction disease_efficacy #>             <char>               <lgcl>              <int>            <int> #> 1: CHELATING AGENT                   NA                  1                1 #> 2: CHELATING AGENT                   NA                  1                1 #>    max_phase mec_id #>        <int>  <int> #> 1:         4   2200 #> 2:         4   2224 #>                                                                                                                                                  mechanism_comment #>                                                                                                                                                             <char> #> 1: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #> 2: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #>          mechanism_of_action    mechanism_refs molecular_mechanism #>                       <char>            <list>               <int> #> 1:      Iron chelating agent <data.frame[3x3]>                   1 #> 2: Aluminium chelating agent <data.frame[3x3]>                   1 #>    molecule_chembl_id parent_molecule_chembl_id record_id selectivity_comment #>                <char>                    <char>     <int>              <lgcl> #> 1:         CHEMBL1413                CHEMBL1413   1343970                  NA #> 2:         CHEMBL1413                CHEMBL1413   1343970                  NA #>    site_id target_chembl_id variant_sequence #>     <lgcl>           <char>           <lgcl> #> 1:      NA    CHEMBL2363058               NA #> 2:      NA    CHEMBL2366381               NA getChemblMechanism(\"CHEMBL1413\", resources = \"mechanism\", field = \"molecule_chembl_id\",                    filter_type = \"in\", returnURL = FALSE, raw = FALSE) #>        action_type binding_site_comment direct_interaction disease_efficacy #>             <char>               <lgcl>              <int>            <int> #> 1: CHELATING AGENT                   NA                  1                1 #> 2: CHELATING AGENT                   NA                  1                1 #>    max_phase mec_id #>        <int>  <int> #> 1:         4   2200 #> 2:         4   2224 #>                                                                                                                                                  mechanism_comment #>                                                                                                                                                             <char> #> 1: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #> 2: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #>          mechanism_of_action    mechanism_refs molecular_mechanism #>                       <char>            <list>               <int> #> 1:      Iron chelating agent <data.frame[3x3]>                   1 #> 2: Aluminium chelating agent <data.frame[3x3]>                   1 #>    molecule_chembl_id parent_molecule_chembl_id record_id selectivity_comment #>                <char>                    <char>     <int>              <lgcl> #> 1:         CHEMBL1413                CHEMBL1413   1343970                  NA #> 2:         CHEMBL1413                CHEMBL1413   1343970                  NA #>    site_id target_chembl_id variant_sequence #>     <lgcl>           <char>           <lgcl> #> 1:      NA    CHEMBL2363058               NA #> 2:      NA    CHEMBL2366381               NA"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the fields of a Chembl resource — getChemblResourceFields","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"function retrieves fields Chembl resource.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"","code":"getChemblResourceFields(resource)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"resource Chembl resource.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"character vector containing names fields.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"","code":"getChemblResourceFields(\"molecule\") #>  [1] \"atc_classifications\"  \"availability_type\"    \"biotherapeutic\"       #>  [4] \"black_box_warning\"    \"chebi_par_id\"         \"chemical_probe\"       #>  [7] \"chirality\"            \"cross_references\"     \"dosed_ingredient\"     #> [10] \"first_approval\"       \"first_in_class\"       \"helm_notation\"        #> [13] \"indication_class\"     \"inorganic_flag\"       \"max_phase\"            #> [16] \"molecule_chembl_id\"   \"molecule_hierarchy\"   \"molecule_properties\"  #> [19] \"molecule_structures\"  \"molecule_synonyms\"    \"molecule_type\"        #> [22] \"natural_product\"      \"oral\"                 \"parenteral\"           #> [25] \"polymer_flag\"         \"pref_name\"            \"prodrug\"              #> [28] \"score\"                \"structure_type\"       \"therapeutic_flag\"     #> [31] \"topical\"              \"usan_stem\"            \"usan_stem_definition\" #> [34] \"usan_substem\"         \"usan_year\"            \"withdrawn_flag\""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":null,"dir":"Reference","previous_headings":"","what":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"Get annotation headings (name ) based type heading criteria.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"","code":"getPubchemAnnotationHeadings(type = \"all\", heading = NULL)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"type type annotation headings retrieve. Options include \"Compound\", \"Gene\", \"Taxonomy\", \"Element\", \"Assay\", \"Protein\", \"Cell\", \"Pathway\", \"\" (default). heading specific heading filter results . Defaults NULL, retrieves headings.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"data.table containing annotation headings types.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"","code":"getPubchemAnnotationHeadings() #>               Heading     Type #>                <char>   <char> #>   1:  11B NMR Spectra Compound #>   2:  13C NMR Spectra Compound #>   3:  15N NMR Spectra Compound #>   4:  17O NMR Spectra Compound #>   5:  19F NMR Spectra Compound #>  ---                           #> 630: Wiley References Compound #> 631:      WormBase ID     Gene #> 632:      WormBase ID  Protein #> 633:  Xenbase Gene ID     Gene #> 634:          ZFIN ID     Gene getPubchemAnnotationHeadings(type = \"Compound\") #>                                        Heading     Type #>                                         <char>   <char> #>   1:                           11B NMR Spectra Compound #>   2:                           13C NMR Spectra Compound #>   3:                           15N NMR Spectra Compound #>   4:                           17O NMR Spectra Compound #>   5:                           19F NMR Spectra Compound #>  ---                                                    #> 472: Volatilization from Water/Soil (Complete) Compound #> 473:                   WHO Essential Medicines Compound #> 474:                                  Wikidata Compound #> 475:                                 Wikipedia Compound #> 476:                          Wiley References Compound getPubchemAnnotationHeadings(heading = \"ChEMBL*\") #>                Heading     Type #>                 <char>   <char> #> 1: ChEMBL Cell Line ID     Cell #> 2:           ChEMBL ID Compound #> 3:    ChEMBL Target ID  Protein getPubchemAnnotationHeadings(type = \"Compound\", heading = \"ChEMBL*\") #>      Heading     Type #>       <char>   <char> #> 1: ChEMBL ID Compound"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve PubChem compound information — getPubchemCompound","title":"Retrieve PubChem compound information — getPubchemCompound","text":"function retrieves compound information PubChem using PubChem REST API.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve PubChem compound information — getPubchemCompound","text":"","code":"getPubchemCompound(   ids,   from = \"cid\",   to = \"property\",   properties = c(\"Title\", \"InChIKey\"),   raw = FALSE,   query_only = FALSE,   output = \"JSON\",   ... )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve PubChem compound information — getPubchemCompound","text":"ids vector compound identifiers. source namespace compound identifiers. Default 'cid'. target namespace compound information. Default 'property'. properties character vector specifying properties retrieve. raw Logical indicating whether return raw query results. Default FALSE. query_only Logical indicating whether perform query without retrieving results. Default FALSE. output format query results. Default 'JSON'. ... Additional arguments passed query_pubchem_rest function.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve PubChem compound information — getPubchemCompound","text":"data.table containing retrieved compound information.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve PubChem compound information — getPubchemCompound","text":"","code":"properties=c('Title', 'MolecularFormula', 'InChIKey', 'CanonicalSMILES') getPubchemCompound(c(3672, 176870), from = 'cid', to = 'property', properties = properties) #>       CID MolecularFormula                                      CanonicalSMILES #>     <int>           <char>                                               <char> #> 1:   3672         C13H18O2                        CC(C)CC1=CC=C(C=C1)C(C)C(=O)O #> 2: 176870       C22H23N3O4 COCCOC1=C(C=C2C(=C1)C(=NC=N2)NC3=CC=CC(=C3)C#C)OCCOC #>                       InChIKey     Title #>                         <char>    <char> #> 1: HEFNNWSXXWATRW-UHFFFAOYSA-N Ibuprofen #> 2: AAKJLRGGTJKAMG-UHFFFAOYSA-N Erlotinib"},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":null,"dir":"Reference","previous_headings":"","what":"Maps cell line names to accession numbers — mapCell2Accession","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"function takes vector cell line names maps accession numbers using Cellosaurus database. performs parallel request retrieve mapping information returns data table results.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"","code":"mapCell2Accession(   ids,   numResults = 1,   from = \"id\",   to = c(\"id\", \"ac\"),   query_only = FALSE,   raw = FALSE,   BPPARAM = BiocParallel::SerialParam(),   ... )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"ids character vector cell line names. numResults number results return query. Default 1. field query . Default \"id\". field query . Default \"id\" \"ac\". query_only TRUE, returns query URL instead results. Default FALSE. raw TRUE, returns raw response instead data table. Default FALSE. BPPARAM BiocParallel parameter object controlling parallelization. ... Additional arguments pass request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"data table mapping information, including cell line name, accession number, Cellosaurus ID.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"","code":"mapCell2Accession(c(\"A549\", \"HeLa\")) #>           id        ac   query query:id #>       <char>    <char>  <char>   <char> #> 1: A549 Cas9 CVCL_DX70 id:A549     A549 #> 2:      HeLa CVCL_0030 id:HeLa     HeLa"},{"path":"https://bhklab.github.io/AnnotationGx/reference/options.html","id":null,"dir":"Reference","previous_headings":"","what":"AnnotationGx Options — options","title":"AnnotationGx Options — options","text":"Internally used, package-specific options. options prioritize R options() values, fall back environment variables undefined. neither option environment variable set, default value used.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/options.html","id":"checking-option-values","dir":"Reference","previous_headings":"","what":"Checking Option Values","title":"AnnotationGx Options — options","text":"Option values specific AnnotationGx can accessed passing package name env.","code":"options::opts(env = \"AnnotationGx\")  options::opt(x, default, env = \"AnnotationGx\")"},{"path":"https://bhklab.github.io/AnnotationGx/reference/options.html","id":"options","dir":"Reference","previous_headings":"","what":"Options","title":"AnnotationGx Options — options","text":"log_level default: \"WARNING\" option: annotationgx_log_level envvar: ANNOTATIONGX_LOGLEVEL (evaluated possible, raw string otherwise) verbose default: FALSE option: annotationgx_verbose envvar: ANNOTATIONGX_VERBOSE (evaluated possible, raw string otherwise)","code":"\"WARNING\" FALSE"},{"path":[]},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardize Names — standardize_names","title":"Standardize Names — standardize_names","text":"function takes character vector standardizes names converting lowercase, removing trailing information comma, removing information within square brackets parentheses, removing non-alphanumeric characters, replacing empty names \"invalid\", converting names uppercase.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardize Names — standardize_names","text":"","code":"standardize_names(object)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standardize Names — standardize_names","text":"object character vector containing names standardized.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardize Names — standardize_names","text":"character vector standardized names.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Standardize Names — standardize_names","text":"","code":"standardize_names(c(\"John Doe\", \"Jane Smith (Manager)\", \"Alice, PhD\")) #> [1] \"JOHNDOE\"   \"JANESMITH\" \"ALICE\"     # Output: [1] \"JOHNDOE\" \"JANESMITH\" \"ALICE\""}]
+[{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. Developers use GNU GPL protect rights two steps: (1) assert copyright software, (2) offer License giving legal permission copy, distribute /modify . developers’ authors’ protection, GPL clearly explains warranty free software. users’ authors’ sake, GPL requires modified versions marked changed, problems attributed erroneously authors previous versions. devices designed deny users access install run modified versions software inside , although manufacturer can . fundamentally incompatible aim protecting users’ freedom change software. systematic pattern abuse occurs area products individuals use, precisely unacceptable. Therefore, designed version GPL prohibit practice products. problems arise substantially domains, stand ready extend provision domains future versions GPL, needed protect freedom users. Finally, every program threatened constantly software patents. States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. However, include work’s System Libraries, general-purpose tools generally available free programs used unmodified performing activities part work. example, Corresponding Source includes interface definition files associated source files work, source code shared libraries dynamically linked subprograms work specifically designed require, intimate data communication control flow subprograms parts work. Corresponding Source need include anything users can regenerate automatically parts Corresponding Source. Corresponding Source work source code form work.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_2-basic-permissions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"2. Basic Permissions","title":"GNU General Public License","text":"rights granted License granted term copyright Program, irrevocable provided stated conditions met. License explicitly affirms unlimited permission run unmodified Program. output running covered work covered License output, given content, constitutes covered work. License acknowledges rights fair use equivalent, provided copyright law. may make, run propagate covered works convey, without conditions long license otherwise remains force. may convey covered works others sole purpose make modifications exclusively , provide facilities running works, provided comply terms License conveying material control copyright. thus making running covered works must exclusively behalf, direction control, terms prohibit making copies copyrighted material outside relationship . Conveying circumstances permitted solely conditions stated . Sublicensing allowed; section 10 makes unnecessary.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_3-protecting-users-legal-rights-from-anti-circumvention-law","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"3. Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. Conveying Verbatim Copies","title":"GNU General Public License","text":"may convey verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice; keep intact notices stating License non-permissive terms added accord section 7 apply code; keep intact notices absence warranty; give recipients copy License along Program. may charge price price copy convey, may offer support warranty protection fee.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_5-conveying-modified-source-versions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"5. Conveying Modified Source Versions","title":"GNU General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: ) work must carry prominent notices stating modified , giving relevant date. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. 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Conveying Non-Source Forms","title":"GNU General Public License","text":"may convey covered work object code form terms sections 4 5, provided also convey machine-readable Corresponding Source terms License, one ways: ) Convey object code , embodied , physical product (including physical distribution medium), accompanied Corresponding Source fixed durable physical medium customarily used software interchange. b) Convey object code , embodied , physical product (including physical distribution medium), accompanied written offer, valid least three years valid long offer spare parts customer support product model, give anyone possesses object code either (1) copy Corresponding Source software product covered License, durable physical medium customarily used software interchange, price reasonable cost physically performing conveying source, (2) access copy Corresponding Source network server charge. c) Convey individual copies object code copy written offer provide Corresponding Source. alternative allowed occasionally noncommercially, received object code offer, accord subsection 6b. d) Convey object code offering access designated place (gratis charge), offer equivalent access Corresponding Source way place charge. need require recipients copy Corresponding Source along object code. place copy object code network server, Corresponding Source may different server (operated third party) supports equivalent copying facilities, provided maintain clear directions next object code saying find Corresponding Source. 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Access network may denied modification materially adversely affects operation network violates rules protocols communication across network. Corresponding Source conveyed, Installation Information provided, accord section must format publicly documented (implementation available public source code form), must require special password key unpacking, reading copying.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_7-additional-terms","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"7. Additional Terms","title":"GNU General Public License","text":"“Additional permissions” terms supplement terms License making exceptions one conditions. Additional permissions applicable entire Program shall treated though included License, extent valid applicable law. additional permissions apply part Program, part may used separately permissions, entire Program remains governed License without regard additional permissions. convey copy covered work, may option remove additional permissions copy, part . (Additional permissions may written require removal certain cases modify work.) may place additional permissions material, added covered work, can give appropriate copyright permission. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. Termination rights section terminate licenses parties received copies rights License. rights terminated permanently reinstated, qualify receive new licenses material section 10.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_9-acceptance-not-required-for-having-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"9. Acceptance Not Required for Having Copies","title":"GNU General Public License","text":"required accept License order receive run copy Program. Ancillary propagation covered work occurring solely consequence using peer--peer transmission receive copy likewise require acceptance. However, nothing License grants permission propagate modify covered work. actions infringe copyright accept License. Therefore, modifying propagating covered work, indicate acceptance License .","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_10-automatic-licensing-of-downstream-recipients","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"10. Automatic Licensing of Downstream Recipients","title":"GNU General Public License","text":"time convey covered work, recipient automatically receives license original licensors, run, modify propagate work, subject License. responsible enforcing compliance third parties License. “entity transaction” transaction transferring control organization, substantially assets one, subdividing organization, merging organizations. propagation covered work results entity transaction, party transaction receives copy work also receives whatever licenses work party’s predecessor interest give previous paragraph, plus right possession Corresponding Source work predecessor interest, predecessor can get reasonable efforts. may impose restrictions exercise rights granted affirmed License. example, may impose license fee, royalty, charge exercise rights granted License, may initiate litigation (including cross-claim counterclaim lawsuit) alleging patent claim infringed making, using, selling, offering sale, importing Program portion .","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_11-patents","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"11. Patents","title":"GNU General Public License","text":"“contributor” copyright holder authorizes use License Program work Program based. work thus licensed called contributor’s “contributor version”. contributor’s “essential patent claims” patent claims owned controlled contributor, whether already acquired hereafter acquired, infringed manner, permitted License, making, using, selling contributor version, include claims infringed consequence modification contributor version. purposes definition, “control” includes right grant patent sublicenses manner consistent requirements License. contributor grants non-exclusive, worldwide, royalty-free patent license contributor’s essential patent claims, make, use, sell, offer sale, import otherwise run, modify propagate contents contributor version. following three paragraphs, “patent license” express agreement commitment, however denominated, enforce patent (express permission practice patent covenant sue patent infringement). “grant” patent license party means make agreement commitment enforce patent party. convey covered work, knowingly relying patent license, Corresponding Source work available anyone copy, free charge terms License, publicly available network server readily accessible means, must either (1) cause Corresponding Source available, (2) arrange deprive benefit patent license particular work, (3) arrange, manner consistent requirements License, extend patent license downstream recipients. “Knowingly relying” means actual knowledge , patent license, conveying covered work country, recipient’s use covered work country, infringe one identifiable patents country reason believe valid. , pursuant connection single transaction arrangement, convey, propagate procuring conveyance , covered work, grant patent license parties receiving covered work authorizing use, propagate, modify convey specific copy covered work, patent license grant automatically extended recipients covered work works based . patent license “discriminatory” include within scope coverage, prohibits exercise , conditioned non-exercise one rights specifically granted License. may convey covered work party arrangement third party business distributing software, make payment third party based extent activity conveying work, third party grants, parties receive covered work , discriminatory patent license () connection copies covered work conveyed (copies made copies), (b) primarily connection specific products compilations contain covered work, unless entered arrangement, patent license granted, prior 28 March 2007. Nothing License shall construed excluding limiting implied license defenses infringement may otherwise available applicable patent law.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_12-no-surrender-of-others-freedom","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"12. No Surrender of Others’ Freedom","title":"GNU General Public License","text":"conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. convey covered work satisfy simultaneously obligations License pertinent obligations, consequence may convey . example, agree terms obligate collect royalty conveying convey Program, way satisfy terms License refrain entirely conveying Program.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_13-use-with-the-gnu-affero-general-public-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"13. Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://bhklab.github.io/AnnotationGx/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://bhklab.github.io/AnnotationGx/articles/PubChemAPI.html","id":"introduction-to-pubchem-apis","dir":"Articles","previous_headings":"","what":"Introduction to PubChem APIs","title":"Querying PubChem with AnnotationGx","text":"PubChem database chemical molecules biological activities. part National Center Biotechnology Information (NCBI), part National Institutes Health (NIH). PubChem provides set APIs query database. AnnotationGx package provides set functions query PubChem using APIs. first APIs PubChem PUG REST API designed - make specific queries based input identifier return data PubChem labelled computed internally [1]. - API useful querying information specific chemical compound getting standardized PubChem identifier (CID) given chemical name smiles string, getting chemical structure given CID. - provides access wide range data including chemical properties, bioassay data, chemical classification data, given specific identifier. second API PubChem PUG VIEW API designed : - give accesse aggregated annotations given chemical compound [3] mapped data, curated PubChem . - .e provides access annotations external sources UniProt, ChEBI, ChEMBL, given specific identifier.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/articles/PubChemAPI.html","id":"setup","dir":"Articles","previous_headings":"","what":"Setup","title":"Querying PubChem with AnnotationGx","text":"","code":"library(AnnotationGx)"},{"path":[]},{"path":"https://bhklab.github.io/AnnotationGx/articles/PubChemAPI.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"Querying PubChem with AnnotationGx","text":"PUG REST. PubChem Docs [website]. Retrieved https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest. Kim S, Thiessen PA, Cheng T, Yu B, Bolton EE. update PUG-REST: RESTful interface programmatic access PubChem. Nucleic Acids Res. 2018 July 2; 46(W1):W563-570. doi:10.1093/nar/gky294. PUG VIEW. PubChem Docs [webiste]. Retrieved https://pubchemdocs.ncbi.nlm.nih.gov/pug-view. Kim S, Thiessen PA, Cheng T, Zhang J, Gindulyte , Bolton EE. PUG-View: programmatic access chemical annotations integrated PubChem. J Cheminform. 2019 Aug 9; 11:56. doi:10.1186/s13321-019-0375-2.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Jermiah Joseph. Author, maintainer. Christopher Eeles. Author. Benjamin Haibe-Kains. Author.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Joseph J, Eeles C, Haibe-Kains B (2024). AnnotationGx: AnnotationGx: package building, updating querying annotation database pharmaco-genomic data. R package version 0.0.0.9062, https://bhklab.github.io/AnnotationGx/.","code":"@Manual{,   title = {AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data},   author = {Jermiah Joseph and Christopher Eeles and Benjamin Haibe-Kains},   year = {2024},   note = {R package version 0.0.0.9062},   url = {https://bhklab.github.io/AnnotationGx/}, }"},{"path":[]},{"path":"https://bhklab.github.io/AnnotationGx/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"AnnotationGx: A package for building, updating and querying an\n    annotation database for pharmaco-genomic data","text":"can install github using:","code":"remotes::install_github(\"bhklab/AnnotationGx\", build_manual=TRUE, build_vignettes=TRUE)"},{"path":"https://bhklab.github.io/AnnotationGx/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"AnnotationGx: A package for building, updating and querying an\n    annotation database for pharmaco-genomic data","text":"basic example shows solve common problem:","code":"library(AnnotationGx) ## basic example code"},{"path":"https://bhklab.github.io/AnnotationGx/reference/AnnotationGx-package.html","id":null,"dir":"Reference","previous_headings":"","what":"AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data — AnnotationGx-package","title":"AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data — AnnotationGx-package","text":"package building, updating querying annotation database pharmaco-genomic data. Provides API interfaces various bioinformatic chemoinformatic databases, well set functions curating data using annotations retrieved APIs.","code":""},{"path":[]},{"path":"https://bhklab.github.io/AnnotationGx/reference/AnnotationGx-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"AnnotationGx: AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data — AnnotationGx-package","text":"Maintainer: Jermiah Joseph jermiah.joseph@gmail.com Authors: Christopher Eeles christopher.eeles@uhnresearch.ca Benjamin Haibe-Kains benjamin.haibe.kains@utoronto.ca","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate PubChem Compound — annotatePubchemCompound","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"function retrieves information PubChem compound based provided compound ID (CID).","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"","code":"annotatePubchemCompound(   cid,   heading = \"ChEMBL ID\",   source = NULL,   parse_function = identity )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"cid compound ID (CID) PubChem compound. heading type information retrieve. Default \"ChEMBL ID\". source data source use. Default NULL. parse_function custom parsing function process response. Default identity function.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"annotated information PubChem compound.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Annotate PubChem Compound — annotatePubchemCompound","text":"","code":"annotatePubchemCompound(cid = 12345) #> character(0) annotatePubchemCompound(cid = 67890, heading = \"CAS\") #> [1] \"407-59-0\""},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":null,"dir":"Reference","previous_headings":"","what":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"preprocessed version cell model passports dataset. dataset contains following columns: CMP.model_id, CMP.sampleid, CMP.model_name, CMP.cancer_type_ncit_id, CMP.COSMIC_ID, CMP.BROAD_ID, CMP.CCLE_ID, CMP.RRID. dataset used AnnotationGx package map cell line names various sources Cellosaurus database.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"","code":"data(cell_model_passports_models)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"data table 8 columns 1001 rows. CMP.model_id char model id cell line cell model passports dataset. CMP.sample_id char sample id cell line cell model passports dataset. CMP.model_name char name cell line cell model passports dataset. CMP.cancer_type_ncit_id char cancer type ncit id cell line cell model passports dataset. CMP.COSMIC_ID int COSMIC ID cell line cell model passports dataset. CMP.BROAD_ID int BROAD ID cell line cell model passports dataset. CMP.CCLE_ID int CCLE ID cell line cell model passports dataset. CMP.RRID char RRID cell line cell model passports dataset.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"https://cog.sanger.ac.uk/cmp/download/model_list_20240103.csv","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/cell_model_passports_models.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"cell_model_passports_models is a preprocessed version of the cell model passports dataset — cell_model_passports_models","text":"","code":"data(cell_model_passports_models) head(cell_model_passports_models) #>    CMP.model_id CMP.sample_id CMP.model_name CMP.cancer_type_ncit_id #>          <char>        <char>         <char>                  <char> #> 1:    SIDM01774     SIDS01659          PK-59                   C3850 #> 2:    SIDM00192     SIDS00612       SNU-1033                   C9383 #> 3:    SIDM01447     SIDS01466        SNU-466                   C3058 #> 4:    SIDM01554     SIDS01363      IST-MES-2                  C45662 #> 5:    SIDM01689     SIDS01631         MUTZ-5                   C8644 #> 6:    SIDM01460     SIDS01493          TM-31                  C60781 #>    CMP.COSMIC_ID CMP.BROAD_ID                              CMP.CCLE_ID #>           <char>       <char>                                   <char> #> 1:                 ACH-000205                            PK59_PANCREAS #> 2:                 ACH-000286                  SNU1033_LARGE_INTESTINE #> 3:                 ACH-000289            SNU466_CENTRAL_NERVOUS_SYSTEM #> 4:                 ACH-000331                           ISTMES2_PLEURA #> 5:                 ACH-000492 MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE #> 6:                 ACH-000592              TM31_CENTRAL_NERVOUS_SYSTEM #>     CMP.RRID #>       <char> #> 1: CVCL_4897 #> 2: CVCL_5002 #> 3: CVCL_5064 #> 4: CVCL_1312 #> 5: CVCL_1873 #> 6: CVCL_6735"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_chembl_request.html","id":null,"dir":"Reference","previous_headings":"","what":"A general function for creating Queries to the ChEMBL API — .build_chembl_request","title":"A general function for creating Queries to the ChEMBL API — .build_chembl_request","text":"general function creating Queries ChEMBL API www DOT ebi DOT ac DOT uk/chembl/api/data/ ?__<filter_type>=","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_chembl_request.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A general function for creating Queries to the ChEMBL API — .build_chembl_request","text":"","code":".build_chembl_request(   resource,   field = NULL,   filter_type = NULL,   value = NULL,   format = \"json\" )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_chembl_request.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A general function for creating Queries to the ChEMBL API — .build_chembl_request","text":"resource character(1) Resource query field character(1) Field query filter_type character(1) Filter type value character(1) Value query format character(1) Format response","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_pubchem_rest_query.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a query for the PubChem REST API — .build_pubchem_rest_query","title":"Build a query for the PubChem REST API — .build_pubchem_rest_query","text":"function builds query PubChem REST API based provided parameters.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_pubchem_rest_query.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a query for the PubChem REST API — .build_pubchem_rest_query","text":"","code":".build_pubchem_rest_query(   id,   domain = \"compound\",   namespace = \"name\",   operation = \"cids\",   output = \"JSON\",   url = \"https://pubchem.ncbi.nlm.nih.gov/rest/pug\",   raw = FALSE,   query_only = FALSE,   ... )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_pubchem_rest_query.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a query for the PubChem REST API — .build_pubchem_rest_query","text":"id identifier(s) query. namespace 'name', id must single value. domain domain query. Options 'compound', 'substance', 'assay', 'cell', 'gene', 'protein'. namespace namespace query. Options depend chosen domain. operation operation perform. Options depend chosen domain namespace. output desired output format. Options 'JSON', 'XML', 'SDF', 'TXT', 'CSV'. url base URL PubChem REST API. raw Logical indicating whether return raw response parse . query_only Logical indicating whether return query URL . ... Additional arguments passed query.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-build_pubchem_rest_query.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a query for the PubChem REST API — .build_pubchem_rest_query","text":"query URL parsed response, depending arguments.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-checkThrottlingStatus2.html","id":null,"dir":"Reference","previous_headings":"","what":"names are: request_count, request_time and service\neach has status and percent\nmain throttlers for user are request_count and request_time\nmain statuses are:\nGreen - less than 50% of the permitted request limit has been used\nYellow - between 50% and 75% of the request limit has been used\nRed - more than 75% of the request limit has been reached\nBlack - the limit has been exceeded and requests are being blocked — .checkThrottlingStatus2","title":"names are: request_count, request_time and service\neach has status and percent\nmain throttlers for user are request_count and request_time\nmain statuses are:\nGreen - less than 50% of the permitted request limit has been used\nYellow - between 50% and 75% of the request limit has been used\nRed - more than 75% of the request limit has been reached\nBlack - the limit has been exceeded and requests are being blocked — .checkThrottlingStatus2","text":"names : request_count, request_time service status percent main throttlers user request_count request_time main statuses : Green - less 50% permitted request limit used Yellow - 50% 75% request limit used Red - 75% request limit reached Black - limit exceeded requests blocked","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-checkThrottlingStatus2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"names are: request_count, request_time and service\neach has status and percent\nmain throttlers for user are request_count and request_time\nmain statuses are:\nGreen - less than 50% of the permitted request limit has been used\nYellow - between 50% and 75% of the request limit has been used\nRed - more than 75% of the request limit has been reached\nBlack - the limit has been exceeded and requests are being blocked — .checkThrottlingStatus2","text":"","code":".checkThrottlingStatus2(response, printMessage)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-parse_resp_json.html","id":null,"dir":"Reference","previous_headings":"","what":"Parses the JSON response from an HTTP request. — .parse_resp_json","title":"Parses the JSON response from an HTTP request. — .parse_resp_json","text":"Parses JSON response HTTP request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-parse_resp_json.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parses the JSON response from an HTTP request. — .parse_resp_json","text":"","code":".parse_resp_json(resp)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-parse_resp_json.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parses the JSON response from an HTTP request. — .parse_resp_json","text":"resp response object HTTP request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-parse_resp_json.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parses the JSON response from an HTTP request. — .parse_resp_json","text":"parsed JSON response.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-perform_request.html","id":null,"dir":"Reference","previous_headings":"","what":"Performs an HTTP request. — .perform_request","title":"Performs an HTTP request. — .perform_request","text":"Performs HTTP request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-perform_request.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Performs an HTTP request. — .perform_request","text":"","code":".perform_request(request)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-perform_request.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Performs an HTTP request. — .perform_request","text":"request HTTP request perform.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/dot-perform_request.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Performs an HTTP request. — .perform_request","text":"response HTTP request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"preprocessed version sample metadata GDSC dataset. dataset contains following columns: GDSC.Sample_Name, GDSC.BROAD_ID, GDSC.RRID, GDSC.COSMIC_ID, CCLE.sampleid. dataset used AnnotationGx package map cell line names various sources Cellosaurus database.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"","code":"data(gdsc_sampleMetadata)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"data table 5 columns 1001 rows. GDSC.Sample_Name char name cell line GDSC dataset. GDSC.COSMIC_ID int COSMIC ID cell line GDSC dataset.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"https://www.cancerrxgene.org/","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/gdsc_sampleMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset — gdsc_sampleMetadata","text":"","code":"data(gdsc_sampleMetadata) head(gdsc_sampleMetadata) #>    GDSC.Sample_Name GDSC.COSMIC_ID #>              <char>          <num> #> 1:             A253         906794 #> 2:         BB30-HNC         753531 #> 3:         BB49-HNC         753532 #> 4:              BHY         753535 #> 5:           BICR10        1290724 #> 6:           BICR22        1240121"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":null,"dir":"Reference","previous_headings":"","what":"Get ChEMBL Mechanism — getChemblMechanism","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"function retrieves information mechanism action given ChEMBL ID.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"","code":"getChemblMechanism(   chembl.ID,   resources = \"mechanism\",   field = \"molecule_chembl_id\",   filter_type = \"in\",   returnURL = FALSE,   raw = FALSE )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"chembl.ID ChEMBL ID molecule. resources ChEMBL resource query (default: \"mechanism\"). field field filter (default: \"molecule_chembl_id\"). filter_type filter type use (default: \"\"). returnURL Logical indicating whether return constructed URL (default: FALSE). raw Logical indicating whether return raw response JSON (default: FALSE).","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"data.table containing retrieved mechanism information.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get ChEMBL Mechanism — getChemblMechanism","text":"","code":"getChemblMechanism(\"CHEMBL1413\") #>        action_type binding_site_comment direct_interaction disease_efficacy #>             <char>               <lgcl>              <int>            <int> #> 1: CHELATING AGENT                   NA                  1                1 #> 2: CHELATING AGENT                   NA                  1                1 #>    max_phase mec_id #>        <int>  <int> #> 1:         4   2200 #> 2:         4   2224 #>                                                                                                                                                  mechanism_comment #>                                                                                                                                                             <char> #> 1: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #> 2: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #>          mechanism_of_action    mechanism_refs molecular_mechanism #>                       <char>            <list>               <int> #> 1:      Iron chelating agent <data.frame[3x3]>                   1 #> 2: Aluminium chelating agent <data.frame[3x3]>                   1 #>    molecule_chembl_id parent_molecule_chembl_id record_id selectivity_comment #>                <char>                    <char>     <int>              <lgcl> #> 1:         CHEMBL1413                CHEMBL1413   1343970                  NA #> 2:         CHEMBL1413                CHEMBL1413   1343970                  NA #>    site_id target_chembl_id variant_sequence #>     <lgcl>           <char>           <lgcl> #> 1:      NA    CHEMBL2363058               NA #> 2:      NA    CHEMBL2366381               NA getChemblMechanism(\"CHEMBL1413\", resources = \"mechanism\", field = \"molecule_chembl_id\",                    filter_type = \"in\", returnURL = FALSE, raw = FALSE) #>        action_type binding_site_comment direct_interaction disease_efficacy #>             <char>               <lgcl>              <int>            <int> #> 1: CHELATING AGENT                   NA                  1                1 #> 2: CHELATING AGENT                   NA                  1                1 #>    max_phase mec_id #>        <int>  <int> #> 1:         4   2200 #> 2:         4   2224 #>                                                                                                                                                  mechanism_comment #>                                                                                                                                                             <char> #> 1: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #> 2: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #>          mechanism_of_action    mechanism_refs molecular_mechanism #>                       <char>            <list>               <int> #> 1:      Iron chelating agent <data.frame[3x3]>                   1 #> 2: Aluminium chelating agent <data.frame[3x3]>                   1 #>    molecule_chembl_id parent_molecule_chembl_id record_id selectivity_comment #>                <char>                    <char>     <int>              <lgcl> #> 1:         CHEMBL1413                CHEMBL1413   1343970                  NA #> 2:         CHEMBL1413                CHEMBL1413   1343970                  NA #>    site_id target_chembl_id variant_sequence #>     <lgcl>           <char>           <lgcl> #> 1:      NA    CHEMBL2363058               NA #> 2:      NA    CHEMBL2366381               NA"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the fields of a Chembl resource — getChemblResourceFields","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"function retrieves fields Chembl resource.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"","code":"getChemblResourceFields(resource)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"resource Chembl resource.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"character vector containing names fields.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the fields of a Chembl resource — getChemblResourceFields","text":"","code":"getChemblResourceFields(\"molecule\") #>  [1] \"atc_classifications\"  \"availability_type\"    \"biotherapeutic\"       #>  [4] \"black_box_warning\"    \"chebi_par_id\"         \"chemical_probe\"       #>  [7] \"chirality\"            \"cross_references\"     \"dosed_ingredient\"     #> [10] \"first_approval\"       \"first_in_class\"       \"helm_notation\"        #> [13] \"indication_class\"     \"inorganic_flag\"       \"max_phase\"            #> [16] \"molecule_chembl_id\"   \"molecule_hierarchy\"   \"molecule_properties\"  #> [19] \"molecule_structures\"  \"molecule_synonyms\"    \"molecule_type\"        #> [22] \"natural_product\"      \"oral\"                 \"parenteral\"           #> [25] \"polymer_flag\"         \"pref_name\"            \"prodrug\"              #> [28] \"score\"                \"structure_type\"       \"therapeutic_flag\"     #> [31] \"topical\"              \"usan_stem\"            \"usan_stem_definition\" #> [34] \"usan_substem\"         \"usan_year\"            \"withdrawn_flag\""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":null,"dir":"Reference","previous_headings":"","what":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"Get annotation headings (name ) based type heading criteria.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"","code":"getPubchemAnnotationHeadings(type = \"all\", heading = NULL)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"type type annotation headings retrieve. Options include \"Compound\", \"Gene\", \"Taxonomy\", \"Element\", \"Assay\", \"Protein\", \"Cell\", \"Pathway\", \"\" (default). heading specific heading filter results . Defaults NULL, retrieves headings.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"data.table containing annotation headings types.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get annotation headings (name only) based on type and heading criteria. — getPubchemAnnotationHeadings","text":"","code":"getPubchemAnnotationHeadings() #>               Heading     Type #>                <char>   <char> #>   1:  11B NMR Spectra Compound #>   2:  13C NMR Spectra Compound #>   3:  15N NMR Spectra Compound #>   4:  17O NMR Spectra Compound #>   5:  19F NMR Spectra Compound #>  ---                           #> 630: Wiley References Compound #> 631:      WormBase ID     Gene #> 632:      WormBase ID  Protein #> 633:  Xenbase Gene ID     Gene #> 634:          ZFIN ID     Gene getPubchemAnnotationHeadings(type = \"Compound\") #>                                        Heading     Type #>                                         <char>   <char> #>   1:                           11B NMR Spectra Compound #>   2:                           13C NMR Spectra Compound #>   3:                           15N NMR Spectra Compound #>   4:                           17O NMR Spectra Compound #>   5:                           19F NMR Spectra Compound #>  ---                                                    #> 472: Volatilization from Water/Soil (Complete) Compound #> 473:                   WHO Essential Medicines Compound #> 474:                                  Wikidata Compound #> 475:                                 Wikipedia Compound #> 476:                          Wiley References Compound getPubchemAnnotationHeadings(heading = \"ChEMBL*\") #>                Heading     Type #>                 <char>   <char> #> 1: ChEMBL Cell Line ID     Cell #> 2:           ChEMBL ID Compound #> 3:    ChEMBL Target ID  Protein getPubchemAnnotationHeadings(type = \"Compound\", heading = \"ChEMBL*\") #>      Heading     Type #>       <char>   <char> #> 1: ChEMBL ID Compound"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve PubChem compound information — getPubchemCompound","title":"Retrieve PubChem compound information — getPubchemCompound","text":"function retrieves compound information PubChem using PubChem REST API.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve PubChem compound information — getPubchemCompound","text":"","code":"getPubchemCompound(   ids,   from = \"cid\",   to = \"property\",   properties = c(\"Title\", \"InChIKey\"),   raw = FALSE,   query_only = FALSE,   output = \"JSON\",   ... )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve PubChem compound information — getPubchemCompound","text":"ids vector compound identifiers. source namespace compound identifiers. Default 'cid'. target namespace compound information. Default 'property'. properties character vector specifying properties retrieve. raw Logical indicating whether return raw query results. Default FALSE. query_only Logical indicating whether perform query without retrieving results. Default FALSE. output format query results. Default 'JSON'. ... Additional arguments passed query_pubchem_rest function.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve PubChem compound information — getPubchemCompound","text":"data.table containing retrieved compound information.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve PubChem compound information — getPubchemCompound","text":"","code":"properties=c('Title', 'MolecularFormula', 'InChIKey', 'CanonicalSMILES') getPubchemCompound(c(3672, 176870), from = 'cid', to = 'property', properties = properties) #>       CID MolecularFormula                                      CanonicalSMILES #>     <int>           <char>                                               <char> #> 1:   3672         C13H18O2                        CC(C)CC1=CC=C(C=C1)C(C)C(=O)O #> 2: 176870       C22H23N3O4 COCCOC1=C(C=C2C(=C1)C(=NC=N2)NC3=CC=CC(=C3)C#C)OCCOC #>                       InChIKey     Title #>                         <char>    <char> #> 1: HEFNNWSXXWATRW-UHFFFAOYSA-N Ibuprofen #> 2: AAKJLRGGTJKAMG-UHFFFAOYSA-N Erlotinib"},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":null,"dir":"Reference","previous_headings":"","what":"Maps cell line names to accession numbers — mapCell2Accession","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"function takes vector cell line names maps accession numbers using Cellosaurus database. performs parallel request retrieve mapping information returns data table results.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"","code":"mapCell2Accession(   ids,   numResults = 1,   from = \"id\",   to = c(\"id\", \"ac\"),   query_only = FALSE,   raw = FALSE,   BPPARAM = BiocParallel::SerialParam(),   ... )"},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"ids character vector cell line names. numResults number results return query. Default 1. field query . Default \"id\". field query . Default \"id\" \"ac\". query_only TRUE, returns query URL instead results. Default FALSE. raw TRUE, returns raw response instead data table. Default FALSE. BPPARAM BiocParallel parameter object controlling parallelization. ... Additional arguments pass request.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"data table mapping information, including cell line name, accession number, Cellosaurus ID.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maps cell line names to accession numbers — mapCell2Accession","text":"","code":"mapCell2Accession(c(\"A549\", \"HeLa\")) #>           id        ac   query query:id #>       <char>    <char>  <char>   <char> #> 1: A549 Cas9 CVCL_DX70 id:A549     A549 #> 2:      HeLa CVCL_0030 id:HeLa     HeLa"},{"path":"https://bhklab.github.io/AnnotationGx/reference/options.html","id":null,"dir":"Reference","previous_headings":"","what":"AnnotationGx Options — options","title":"AnnotationGx Options — options","text":"Internally used, package-specific options. options prioritize R options() values, fall back environment variables undefined. neither option environment variable set, default value used.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/options.html","id":"checking-option-values","dir":"Reference","previous_headings":"","what":"Checking Option Values","title":"AnnotationGx Options — options","text":"Option values specific AnnotationGx can accessed passing package name env.","code":"options::opts(env = \"AnnotationGx\")  options::opt(x, default, env = \"AnnotationGx\")"},{"path":"https://bhklab.github.io/AnnotationGx/reference/options.html","id":"options","dir":"Reference","previous_headings":"","what":"Options","title":"AnnotationGx Options — options","text":"log_level default: \"WARNING\" option: annotationgx_log_level envvar: ANNOTATIONGX_LOGLEVEL (evaluated possible, raw string otherwise) verbose default: FALSE option: annotationgx_verbose envvar: ANNOTATIONGX_VERBOSE (evaluated possible, raw string otherwise)","code":"\"WARNING\" FALSE"},{"path":[]},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardize Names — standardize_names","title":"Standardize Names — standardize_names","text":"function takes character vector standardizes names converting lowercase, removing trailing information comma, removing information within square brackets parentheses, removing non-alphanumeric characters, replacing empty names \"invalid\", converting names uppercase.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardize Names — standardize_names","text":"","code":"standardize_names(object)"},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standardize Names — standardize_names","text":"object character vector containing names standardized.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardize Names — standardize_names","text":"character vector standardized names.","code":""},{"path":"https://bhklab.github.io/AnnotationGx/reference/standardize_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Standardize Names — standardize_names","text":"","code":"standardize_names(c(\"John Doe\", \"Jane Smith (Manager)\", \"Alice, PhD\")) #> [1] \"JOHNDOE\"   \"JANESMITH\" \"ALICE\"     # Output: [1] \"JOHNDOE\" \"JANESMITH\" \"ALICE\""}]