deploy: 78d5481

_sources/datasources/pubchem.md

@@ -2,7 +2,22 @@
 
 ## What is PubChem?
 
-PubChem [(https://pubchem.ncbi.nlm.nih.gov)](https://pubchem.ncbi.nlm.nih.gov) {cite:p}`Kim2023` is a very popular chemistry information resource for biomedical research communities in many areas, including cheminformatics, chemical biology, medicinal chemistry, and drug discovery. PubChem's information content, collected from hundreds of data sources, is organized into multiple data collections, including Substance, Compound, BioAssay, Gene, Protein, Pathway, Cell Line, Taxonomy, and Patent {cite:p}`Kim2022`. Substance archives the chemical data submitted by individual data sources and Compound stores the unique chemical structures extracted from Substance through chemical structure standardization. BioAssay contains biological assay descriptions and test results deposited by assay data providers. The record identifiers (IDs) used in Substance, Compound, and BioAssay are called Substance ID (SID), Compound ID (CID), and Assay ID (AID), respectively. The other data collections (i.e., Gene, Protein, Pathway, Cell Line, Taxonomy, and Patent) provide alternative views of PubChem data, related to a specific gene, protein, pathway, cell line, taxon, and patent document, respectively. Each record in the data collections has a dedicated web page (called a Summary page), which presents information available in PubChem for that record. This page also presents relevant annotations collected by PubChem from authoritative data sources.  Here are some example Summary pages for PubChem records.
+PubChem [(https://pubchem.ncbi.nlm.nih.gov)](https://pubchem.ncbi.nlm.nih.gov) {cite:p}`Kim2023` is a very popular 
+chemistry information resource for biomedical research communities in many areas, including cheminformatics, 
+chemical biology, medicinal chemistry, and drug discovery. PubChem's information content, collected from 
+hundreds of data sources, is organized into multiple data collections, including Substance, Compound, BioAssay, 
+Gene, Protein, Pathway, Cell Line, Taxonomy, and Patent {cite:p}`Kim2022`.
+
+Substance archives the chemical data submitted by individual data sources and Compound stores the unique 
+chemical structures extracted from Substance through chemical structure standardization. BioAssay contains 
+biological assay descriptions and test results deposited by assay data providers. The record identifiers (IDs)
+used in Substance, Compound, and BioAssay are called Substance ID (SID), Compound ID (CID), and Assay ID (AID),
+respectively. The other data collections (i.e., Gene, Protein, Pathway, Cell Line, Taxonomy, and Patent) 
+provide alternative views of PubChem data, related to a specific gene, protein, pathway, cell line, taxon, 
+and patent document, respectively. Each record in the data collections has a dedicated web page (called 
+a Summary page), which presents information available in PubChem for that record. This page also presents 
+relevant annotations collected by PubChem from authoritative data sources.  Here are some example Summary 
+pages for PubChem records.
 
 - Compound (CID 60823, aspirin):<br>
 https://pubchem.ncbi.nlm.nih.gov/compound/2244
@@ -43,7 +58,6 @@ In addition, the following paper {cite:p}`Kim2021` provides step-by-step instruc
 >Kim S. **Exploring Chemical Information in PubChem.** Curr. Protoc.; 2021 Aug 9; 1(8):e217. doi: https://doi.org/10.1002/cpz1.217.  
 >[\[PubMed PMID: 34370395\]](https://pubmed.ncbi.nlm.nih.gov/34370395/) [\[PubMed Central PMCID: PMC8363119\]](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8363119/) [\[Free Full Text\]](https://doi.org/10.1002/cpz1.217)
 
-
 This paper includes several protocols designed to help users to get familiar with PubChem's data and tools.
 
 * **Basic Protocol 1**: [Finding genes and proteins that interact with a given compound](https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.217#cpz1217-prot-0001)

_sources/intro.md

@@ -1,23 +1,6 @@
-# Using the Cookbook
-
-The IUPAC FAIR Chemistry Cookbook is intended to be an open, collaborative, community focused resource on working with 
-FAIR data in chemistry. FAIR data are findable, accessible, interoperable, and reusable for machine processing 
-{cite:p}`Wilkinson2016`, the new paradigm for reporting research data. This cookbook aims to support best practices 
-using chemical data standards through practical, interactive tutorials, provided by the International Union of Pure 
-and Applied Chemistry (IUPAC) through the EU funded WorldFAIR project 
-(see [About this project](https://iupac.github.io/WFChemCookbook/about.html)). 
-
-## Recipes 
-- Many of the recipes on this site will take advantage of Juypter Notebooks to run Python code 
- in the browser for an interactive (and educational) feel for the user.
-- We have tried to provide useful information about each recipe in the collapsable 'header'
- that is below the title of the recipe.  We are hoping this provides users with some sense
- of the how, what and when a recipe might be useful.
-- As part of the header we have included bullets for skills and learning objectives but have also
- thought to add use cases.  If you have any ideas about how we should characterize recipes we would love to 
- hear them!
-
-## Contributing to the Cookbook
-
-We welcome feedback & suggestions for additional content.  For ways to do this go to our [feedback page](feedback.md)!
+# Welcome to the IUPAC FAIR Chemistry Cookbook
 
+Welcome to the IUPAC FAIR Chemistry Cookbook, a self-serve web-based toolbox of interactive demonstrations of 
+community best practices in machine-readable chemical data management. The Cookbook is an openly accessible 
+collaborative resource supported by IUPAC to exemplify the FAIR principles and standards in cheminformatics 
+and provide hands-on executable content for experiential learning. 

about_cookbook.html

@@ -65,7 +65,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="How to use the Cookbook" href="use_cookbook.html" />
-    <link rel="prev" title="Using the Cookbook" href="intro.html" />
+    <link rel="prev" title="Welcome to the IUPAC FAIR Chemistry Cookbook" href="intro.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="None"/>
   </head>
@@ -442,7 +442,7 @@ <h1>About the IUPAC FAIR Chemistry Cookbook<a class="headerlink" href="#about-th
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Using the Cookbook</p>
+        <p class="prev-next-title">Welcome to the IUPAC FAIR Chemistry Cookbook</p>
       </div>
     </a>
     <a class="right-next"

bibliography.html

@@ -404,9 +404,6 @@ <h1>Bibliography<a class="headerlink" href="#bibliography" title="Permalink to t
 <dt class="label" id="id6"><span class="brackets">KCH+22</span></dt>
 <dd><p>Sunghwan Kim, Tiejun Cheng, Siqian He, Paul A. Thiessen, Qingliang Li, Asta Gindulyte, and Evan E. Bolton. Pubchem protein, gene, pathway, and taxonomy data collections: bridging biology and chemistry through target-centric views of pubchem data. <em>Journal of Molecular Biology</em>, 434(11):167514, 2022. URL: <a class="reference external" href="https://doi.org/10.1016/j.jmb.2022.167514">https://doi.org/10.1016/j.jmb.2022.167514</a>.</p>
 </dd>
-<dt class="label" id="id2"><span class="brackets">Wil16</span></dt>
-<dd><p>Mark D. et al. Wilkinson. The fair guiding principles for scientific data management and stewardship. <em>Scientific Data</em>, 3:160018, 2016. <a class="reference external" href="https://doi.org/10.1038/sdata.2016.18">doi:10.1038/sdata.2016.18</a>.</p>
-</dd>
 </dl>
 </div>
 </section>

datasources/goldbook_api.html

@@ -574,7 +574,7 @@ <h2>Step 5: Use the term code to retrieve its definition<a class="headerlink" hr
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;term&#39;: {&#39;id&#39;: &#39;01093&#39;, &#39;doi&#39;: &#39;10.1351/goldbook.C01093&#39;, &#39;code&#39;: &#39;C01093&#39;, &#39;status&#39;: &#39;current&#39;, &#39;longtitle&#39;: &#39;IUPAC Gold Book - cis-trans isomers&#39;, &#39;title&#39;: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39;, &#39;termversion&#39;: &#39;2.3.3&#39;, &#39;lastupdated&#39;: &#39;2014-02-24&#39;, &#39;definitions&#39;: [{&#39;id&#39;: &#39;1&#39;, &#39;text&#39;: &#39;Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]&#39;, &#39;chemicals&#39;: [{&#39;type&#39;: &#39;chemimage&#39;, &#39;title&#39;: &#39;molecular structures showing cis/trans isomerism&#39;, &#39;file&#39;: &#39;https://goldbook.iupac.org/img/inline/C01093.png&#39;}], &#39;links&#39;: [{&#39;title&#39;: &#39;Stereoisomeric&#39;, &#39;type&#39;: &#39;internal&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/S05983&#39;}, {&#39;title&#39;: &#39;olefins&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/O04281&#39;}, {&#39;title&#39;: &#39;cycloalkanes&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01497&#39;}, {&#39;title&#39;: &#39;isomer&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/I03289&#39;}, {&#39;title&#39;: &#39;trans&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01092&#39;}], &#39;sources&#39;: [&quot;PAC, 1996, 68, 2193. &#39;Basic terminology of stereochemistry (IUPAC Recommendations 1996)&#39; on page 2204 (https://doi.org/10.1351/pac199668122193)&quot;]}], &#39;referencedin&#39;: [{&#39;title&#39;: &#39;Wikipedia - Cis-trans izomerie (cs)&#39;, &#39;url&#39;: &#39;https://cs.wikipedia.org/wiki/Cis-trans_izomerie&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis-trans izoméria (sk)&#39;, &#39;url&#39;: &#39;https://sk.wikipedia.org/wiki/Cis-trans_izoméria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis–trans isomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Cis–trans_isomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria cis-trans (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria geométrica (pt)&#39;, &#39;url&#39;: &#39;https://pt.wikipedia.org/wiki/Isomeria_geométrica&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomería cis-trans (es)&#39;, &#39;url&#39;: &#39;https://es.wikipedia.org/wiki/Isomería_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Isomer (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Isomer&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Stereoisomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Stereoisomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис-транс изомеризъм (bg)&#39;, &#39;url&#39;: &#39;https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис–транс ізомерія (uk)&#39;, &#39;url&#39;: &#39;https://uk.wikipedia.org/wiki/Цис–транс_ізомерія&#39;}, {&#39;title&#39;: &#39;Wikipedia - ایزومری سیس–ترانس (fa)&#39;, &#39;url&#39;: &#39;https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس&#39;}, {&#39;title&#39;: &#39;Wikipedia - 顺反异构 (zh)&#39;, &#39;url&#39;: &#39;https://zh.wikipedia.org/wiki/顺反异构&#39;}], &#39;links&#39;: {&#39;html&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/html&#39;, &#39;json&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/json&#39;, &#39;xml&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/xml&#39;, &#39;plain&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/plain&#39;, &#39;pdf&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/pdf&#39;}, &#39;citation&#39;: &quot;Citation: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39; in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093&quot;, &#39;license&#39;: &#39;The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.&#39;, &#39;collection&#39;: &#39;If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .&#39;, &#39;disclaimer&#39;: &#39;The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.&#39;, &#39;accessed&#39;: &#39;2024-01-29T20:29:00+00:00&#39;}}
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;term&#39;: {&#39;id&#39;: &#39;01093&#39;, &#39;doi&#39;: &#39;10.1351/goldbook.C01093&#39;, &#39;code&#39;: &#39;C01093&#39;, &#39;status&#39;: &#39;current&#39;, &#39;longtitle&#39;: &#39;IUPAC Gold Book - cis-trans isomers&#39;, &#39;title&#39;: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39;, &#39;termversion&#39;: &#39;2.3.3&#39;, &#39;lastupdated&#39;: &#39;2014-02-24&#39;, &#39;definitions&#39;: [{&#39;id&#39;: &#39;1&#39;, &#39;text&#39;: &#39;Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]&#39;, &#39;chemicals&#39;: [{&#39;type&#39;: &#39;chemimage&#39;, &#39;title&#39;: &#39;molecular structures showing cis/trans isomerism&#39;, &#39;file&#39;: &#39;https://goldbook.iupac.org/img/inline/C01093.png&#39;}], &#39;links&#39;: [{&#39;title&#39;: &#39;Stereoisomeric&#39;, &#39;type&#39;: &#39;internal&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/S05983&#39;}, {&#39;title&#39;: &#39;olefins&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/O04281&#39;}, {&#39;title&#39;: &#39;cycloalkanes&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01497&#39;}, {&#39;title&#39;: &#39;isomer&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/I03289&#39;}, {&#39;title&#39;: &#39;trans&#39;, &#39;type&#39;: &#39;goldify&#39;, &#39;url&#39;: &#39;https://goldbook.iupac.org/terms/view/C01092&#39;}], &#39;sources&#39;: [&quot;PAC, 1996, 68, 2193. &#39;Basic terminology of stereochemistry (IUPAC Recommendations 1996)&#39; on page 2204 (https://doi.org/10.1351/pac199668122193)&quot;]}], &#39;referencedin&#39;: [{&#39;title&#39;: &#39;Wikipedia - Cis-trans izomerie (cs)&#39;, &#39;url&#39;: &#39;https://cs.wikipedia.org/wiki/Cis-trans_izomerie&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis-trans izoméria (sk)&#39;, &#39;url&#39;: &#39;https://sk.wikipedia.org/wiki/Cis-trans_izoméria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Cis–trans isomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Cis–trans_isomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria cis-trans (it)&#39;, &#39;url&#39;: &#39;https://it.wikipedia.org/wiki/Isomeria_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomeria geométrica (pt)&#39;, &#39;url&#39;: &#39;https://pt.wikipedia.org/wiki/Isomeria_geométrica&#39;}, {&#39;title&#39;: &#39;Wikipedia - Isomería cis-trans (es)&#39;, &#39;url&#39;: &#39;https://es.wikipedia.org/wiki/Isomería_cis-trans&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Isomer (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Isomer&#39;}, {&#39;title&#39;: &#39;Wikipedia - Talk:Stereoisomerism (en)&#39;, &#39;url&#39;: &#39;https://en.wikipedia.org/wiki/Talk:Stereoisomerism&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис-транс изомеризъм (bg)&#39;, &#39;url&#39;: &#39;https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм&#39;}, {&#39;title&#39;: &#39;Wikipedia - Цис–транс ізомерія (uk)&#39;, &#39;url&#39;: &#39;https://uk.wikipedia.org/wiki/Цис–транс_ізомерія&#39;}, {&#39;title&#39;: &#39;Wikipedia - ایزومری سیس–ترانس (fa)&#39;, &#39;url&#39;: &#39;https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس&#39;}, {&#39;title&#39;: &#39;Wikipedia - 顺反异构 (zh)&#39;, &#39;url&#39;: &#39;https://zh.wikipedia.org/wiki/顺反异构&#39;}], &#39;links&#39;: {&#39;html&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/html&#39;, &#39;json&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/json&#39;, &#39;xml&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/xml&#39;, &#39;plain&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/plain&#39;, &#39;pdf&#39;: &#39;https://goldbook.iupac.org/terms/view/C01093/pdf&#39;}, &#39;citation&#39;: &quot;Citation: &#39;&lt;i&gt;cis&lt;/i&gt;-&lt;i&gt;trans&lt;/i&gt; isomers&#39; in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093&quot;, &#39;license&#39;: &#39;The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.&#39;, &#39;collection&#39;: &#39;If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .&#39;, &#39;disclaimer&#39;: &#39;The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.&#39;, &#39;accessed&#39;: &#39;2024-01-30T18:22:22+00:00&#39;}}
 </pre></div>
 </div>
 </div>