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<h2>About PubChem
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<h3>Data Types</h3>
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<br>
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<div class="row">
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<p>PubChem has many different categories for data that you can search for and access. This section will briefly introduce each data type to prepare you to search PubChem.</p>
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<li class="text-bg-success p-2 col"><a href="#bioassays">BioAssays</a></li>
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<li class="text-bg-success p-2 col"><a href="#targets">Targets: Genes and Proteins</a></li>
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<li class="text-bg-primary p-2 col"><a href="#pathways">Pathways</a></li>
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<div id="substances"></div>
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<h4>Substances</h4>
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<p>Data sources submit data about a chemical; that data becomes a Substance record in PubChem. These can include chemical structures, synonyms, registration IDs, descriptions, related URLs, patent identifiers, database cross-references to PubMed, protein 3D structures, and biological screening results.</p>
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<p>Every time a data source submits new information about a chemical, a new Substance record is generated. Substance summaries help you see who provided what.</p>
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<p>This is an example of a Substance record for the chemical <a href="https://pubchem.ncbi.nlm.nih.gov/substance/472677687" title="https://pubchem.ncbi.nlm.nih.gov/substance/472677687" target="_blank">Semaglutide</a>. The source of this Substance in PubChem is the chemical vendor ChemShuttle.</p>
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<div class="col-lg-6 mx-auto text-center">
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<div class="graphic">
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<a href="img/PubChem_Substance.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_Substance.png" alt="PubChem Substance Record showing Semaglutide and ChemShuttle as the source."></a>
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<br>
|
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<div id="compounds"></div>
|
||
<h4>Compounds</h4>
|
||
<p>The Compound summary is an aggregated view of all available information in PubChem about a chemical.</p>
|
||
|
||
<p>This is an example of a Compound summary for <a href="https://pubchem.ncbi.nlm.nih.gov/compound/56843331" title="https://pubchem.ncbi.nlm.nih.gov/compound/56843331" target="_blank">Semaglutide</a>. The summary includes information about Semaglutide from multiple different sources; for example, it has Chemical Classes information from Drugs@FDA and the European Medicines Agency (EMA).</p>
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<div class="col-lg-6 mx-auto text-center">
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||
<div class="graphic">
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||
<a href="img/PubChem_Compound.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_Compound.png" alt="PubChem Compound record for Semaglutide."></a>
|
||
</div>
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||
</div>
|
||
|
||
<div class="col-lg-6 mx-auto text-center">
|
||
<div class="graphic">
|
||
<a href="img/PubChem_Compound2.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_Compound2.png" alt="PubChem Compound record for Semaglutide showing Drugs@FDA and the European Medicines Agency circled under 3.3.1."></a>
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||
</div>
|
||
</div>
|
||
|
||
<br>
|
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|
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<p>Read more about the difference between a Substance and a Compound record in the <a href="https://pubchem.ncbi.nlm.nih.gov/docs/compound-vs-substance" title="PubChem Docs" target="_blank">PubChem Documentation</a>.</p>
|
||
|
||
<div id="bioassays"></div>
|
||
<h4>BioAssays</h4>
|
||
<p>When a data source submits to PubChem the description of biological assay experiments and bioactivity test results on substances, each experiment becomes a BioAssay record.</p>
|
||
<p>Here is an example of a BioAssay record in PubChem titled <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/1247343" title="https://pubchem.ncbi.nlm.nih.gov/bioassay/1247343" target="_blank">"Displacement of [125I]-GLP1 from human GLP1 receptor expressed in BHK cells after 2 hrs in absence of human serum albumin."</a> The source of this BioAssay record is ChEMBL database from the European Bioinformatics Institute.</p>
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||
|
||
<div class="col-lg-6 mx-auto text-center">
|
||
<div class="graphic">
|
||
<a href="img/PubChem_BioAssay.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_BioAssay.png" alt="PubChem BioAssay record for Displacement of [125I]-GLP1 from human GLP1 receptor expressed in BHK cells after 2 hrs in absence of human serum albumin."></a>
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||
</div>
|
||
</div>
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|
||
<br>
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||
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<p>Read more about BioAssays in the <a href="https://pubchem.ncbi.nlm.nih.gov/docs/bioassays" title="PubChem Docs" target="_blank">PubChem Documentation</a>.</p>
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||
|
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<div id="targets"></div>
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<h4>Targets: Genes and Proteins</h4>
|
||
<p>PubChem Protein and Gene records include chemical information available for a given protein or gene, including bioactivity data of chemicals that are tested against the corresponding protein or gene. PubChem has genes and proteins for different taxons. Gene and Protein records can include information from different sources.</p>
|
||
|
||
<p>This is an example of a Protein record for <a href="https://pubchem.ncbi.nlm.nih.gov/protein/P01911" title="https://pubchem.ncbi.nlm.nih.gov/protein/P01911" target="_blank">HLA class II histocompatibility antigen, DRB1 beta chain (human)</a>.</p>
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<div class="col-lg-6 mx-auto text-center">
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||
<div class="graphic">
|
||
<a href="img/PubChem_Protein.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_Protein.png" alt="PubChem Protein record for HLA class II histocompatibility antigen, DRB1 beta chain (human)."></a>
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</div>
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</div>
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<br>
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<p>Here is an example of a Gene record for <a href="https://pubchem.ncbi.nlm.nih.gov/gene/3123" title="https://pubchem.ncbi.nlm.nih.gov/gene/3123" target="_blank">HLA-DRB1 – major histocompatibility complex, class II, DR beta 1 (human)</a>.</p>
|
||
|
||
<div class="col-lg-6 mx-auto text-center">
|
||
<div class="graphic">
|
||
<a href="img/PubChem_Gene.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_Gene.png" alt="PubChem Gene record for HLA-DRB1 – major histocompatibility complex, class II, DR beta 1 (human)."></a>
|
||
</div>
|
||
</div>
|
||
|
||
<br>
|
||
|
||
<p>Learn more about <a href="https://pubchem.ncbi.nlm.nih.gov/docs/genes" title="genes" target="_blank">genes</a> and <a href="https://pubchem.ncbi.nlm.nih.gov/docs/proteins" title="proteins" target="new">proteins</a> in the PubChem Documentation.</p>
|
||
|
||
<div id="pathways"></div>
|
||
<h4>Pathways</h4>
|
||
<p>PubChem Pathway summaries include information about chemicals, genes, or diseases involved in or associated with a biological pathway. The <a href="https://www.genome.gov/about-genomics/fact-sheets/Biological-Pathways-Fact-Sheet#:~:text=A%20biological%20pathway%20is%20a,spur%20a%20cell%20to%20move." title="NIH National Human Genome Research Institute" target="_blank">NIH National Human Genome Research Institute</a> defines a biological pathway as "a series of actions among molecules in a cell that leads to a certain product or a change in the cell. It can trigger the assembly of new molecules, such as a fat or protein, turn genes on and off, or spur a cell to move."</p>
|
||
|
||
<p>This is an example of an <a href="https://pubchem.ncbi.nlm.nih.gov/pathway/PathBank:SMP0000590" title="https://pubchem.ncbi.nlm.nih.gov/pathway/PathBank:SMP0000590" target="_blank">Ibuprofen Metabolism Pathway</a> summary from the academic source PathBank.</p>
|
||
|
||
<div class="col-lg-6 mx-auto text-center">
|
||
<div class="graphic">
|
||
<a href="img/PubChem_Pathway.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_Pathway.png" alt="PubChem Ibuprofen Metabolism Pathway summary from the academic source PathBank."></a>
|
||
</div>
|
||
</div>
|
||
|
||
<br>
|
||
|
||
<p>Learn more about Pathways in the <a href="https://pubchemdocs.ncbi.nlm.nih.gov/pathways" title="PubChem Docs" target="_blank">PubChem Documentation</a>.</p>
|
||
|
||
<div id="cellline"></div>
|
||
<h4>Cell Line</h4>
|
||
<p>A Cell Line summary presents PubChem data associated with a given cell line. Cells in a cell line are often used in scientific research. Cell line information in PubChem can come from a variety of sources.</p>
|
||
|
||
<p>This is an example of a Cell summary for <a href="https://pubchem.ncbi.nlm.nih.gov/cell/31" title="https://pubchem.ncbi.nlm.nih.gov/cell/31" target="_blank">MCF-7</a>.</p>
|
||
|
||
<div class="col-lg-6 mx-auto text-center">
|
||
<div class="graphic">
|
||
<a href="img/PubChem_Cell.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_Cell.png" alt="PubChem Cell summary page for MCF-7."></a>
|
||
</div>
|
||
</div>
|
||
|
||
<br>
|
||
|
||
<p>Learn more about cell lines in the <a href="https://pubchem.ncbi.nlm.nih.gov/docs/cell-lines" title="PubChem Docs" target="_blank">PubChem Documentation</a>.</p>
|
||
|
||
<div id="taxonomy"></div>
|
||
<h4>Taxonomy</h4>
|
||
<p>Taxonomy summaries in PubChem display data associated with a specific organism, like a human or Norway rat. Taxonomy summaries can include information from multiple sources.</p>
|
||
|
||
<p>This is an example of a Taxonomy record for <a href="https://pubchem.ncbi.nlm.nih.gov/taxonomy/104688" title="https://pubchem.ncbi.nlm.nih.gov/taxonomy/104688" target="_blank">Bactrocera oleae (olive fruit fly)</a>.</p>
|
||
|
||
<div class="col-lg-6 mx-auto text-center">
|
||
<div class="graphic">
|
||
<a href="img/PubChem_Taxonomy.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_Taxonomy.png" alt="PubChem Taxonomy record for Bactrocera oleae (olive fruit fly)."></a>
|
||
</div>
|
||
</div>
|
||
|
||
<br>
|
||
|
||
<p>Learn more about taxonomies in the <a href="https://pubchemdocs.ncbi.nlm.nih.gov/taxonomies" title="PubChem Docs" target="_blank">PubChem Documentation</a>.</p>
|
||
|
||
<div id="patents"></div>
|
||
<h4>Patents</h4>
|
||
<p>The PubChem Patent collection contains information on what chemicals are mentioned in a given patent document.</p>
|
||
|
||
<p>Here is an example of a Patent record titled <a href="https://pubchem.ncbi.nlm.nih.gov/patent/US-2021206800-A1" title="https://pubchem.ncbi.nlm.nih.gov/patent/US-2021206800-A1" target="_blank">"Process for purifying semaglutide and liraglutide."</a></p>
|
||
|
||
<div class="col-lg-6 mx-auto text-center">
|
||
<div class="graphic">
|
||
<a href="img/PubChem_Patent.png" target="_blank"><img class="img-fluid shadow" src="img/PubChem_Patent.png" alt="PubChem Patent record titled Process for purifying semaglutide and liraglutide."></a>
|
||
</div>
|
||
</div>
|
||
|
||
<br>
|
||
|
||
|
||
<p>Learn more about patents in the <a href="https://pubchemdocs.ncbi.nlm.nih.gov/patents" title="PubChem Docs" target="_blank">PubChem Documentation</a>.</p>
|
||
|
||
<br>
|
||
|
||
<h4><i class="fas fa-user-edit"></i> Exercises</h4>
|
||
<div>
|
||
<p>Answer these questions to check your understanding of the data types in PubChem:</p>
|
||
|
||
<div class="card shadow-sm">
|
||
<div class="card-body">
|
||
|
||
<ol class="pubmed-numbers p-l-0">
|
||
<li><strong>When a data source submits new information about a chemical, a _____ record is created.</strong></li>
|
||
</ol>
|
||
<br>
|
||
<div class="form-check mb-2">
|
||
<input class="form-check-input" type="radio" name="flexRadioDefaultQ3" id="flexRadioDefault5">
|
||
<label class="form-check-label" for="flexRadioDefault5">
|
||
a) Compound
|
||
</label>
|
||
</div>
|
||
<div class="form-check mb-2">
|
||
<input class="form-check-input" type="radio" name="flexRadioDefaultQ3" id="flexRadioDefault6">
|
||
<label class="form-check-label" for="flexRadioDefault6">
|
||
b) Gene
|
||
</label>
|
||
</div>
|
||
<div class="form-check mb-2">
|
||
<input class="form-check-input" type="radio" name="flexRadioDefaultQ3" id="flexRadioDefault7">
|
||
<label class="form-check-label" for="flexRadioDefault7">
|
||
c) BioAssay
|
||
</label>
|
||
</div>
|
||
<div class="form-check mb-2">
|
||
<input class="form-check-input" type="radio" name="flexRadioDefaultQ3" id="flexRadioDefault8">
|
||
<label class="form-check-label" for="flexRadioDefault8">
|
||
d) Substance
|
||
</label>
|
||
</div>
|
||
|
||
|
||
<!-- Button trigger modal -->
|
||
<div class="text-center">
|
||
<button type="button" class="btn btn-primary" data-bs-toggle="modal" data-bs-target="#Exercise3Modal">
|
||
Show Answer
|
||
</button>
|
||
</div>
|
||
|
||
<!-- Modal -->
|
||
<div class="modal fade" id="Exercise3Modal" tabindex="-1" role="dialog" aria-labelledby="Exercise3ModalLabel" aria-hidden="true">
|
||
<div class="modal-dialog" role="document">
|
||
<div class="modal-content">
|
||
<div class="modal-header">
|
||
<h5 class="modal-title" id="Exercise3ModalLabel">Answer</h5>
|
||
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close">
|
||
</button>
|
||
</div>
|
||
<div class="modal-body">
|
||
<p><strong>d) Substance.</strong> (Hint: Review the definitions above to find the right answer.)
|
||
</p>
|
||
</div>
|
||
<div class="modal-footer">
|
||
<button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
|
||
<br>
|
||
|
||
<div class="card shadow-sm">
|
||
<div class="card-body">
|
||
|
||
<ol class="pubmed-numbers p-l-0" style="counter-reset: my-counter 1">
|
||
<li><strong>The summary page of a __________record provides an aggregated view of all available information in PubChem about a chemical.</strong></li>
|
||
</ol>
|
||
<br>
|
||
<div class="form-check mb-2">
|
||
<input class="form-check-input" type="radio" name="flexRadioDefaultQ4" id="flexRadioDefault9">
|
||
<label class="form-check-label" for="flexRadioDefault9">
|
||
a) Substance
|
||
</label>
|
||
</div>
|
||
<div class="form-check mb-2">
|
||
<input class="form-check-input" type="radio" name="flexRadioDefaultQ4" id="flexRadioDefault10">
|
||
<label class="form-check-label" for="flexRadioDefault10">
|
||
b) Compound
|
||
</label>
|
||
</div>
|
||
<div class="form-check mb-2">
|
||
<input class="form-check-input" type="radio" name="flexRadioDefaultQ4" id="flexRadioDefault11">
|
||
<label class="form-check-label" for="flexRadioDefault11">
|
||
c) Protein
|
||
</label>
|
||
</div>
|
||
<div class="form-check mb-2">
|
||
<input class="form-check-input" type="radio" name="flexRadioDefaultQ4" id="flexRadioDefault12">
|
||
<label class="form-check-label" for="flexRadioDefault12">
|
||
d) BioAssay
|
||
</label>
|
||
</div>
|
||
|
||
|
||
<!-- Button trigger modal -->
|
||
<div class="text-center">
|
||
<button type="button" class="btn btn-primary" data-bs-toggle="modal" data-bs-target="#Exercise4Modal">
|
||
Show Answer
|
||
</button>
|
||
</div>
|
||
|
||
<!-- Modal -->
|
||
<div class="modal fade" id="Exercise4Modal" tabindex="-1" role="dialog" aria-labelledby="Exercise4ModalLabel" aria-hidden="true">
|
||
<div class="modal-dialog" role="document">
|
||
<div class="modal-content">
|
||
<div class="modal-header">
|
||
<h5 class="modal-title" id="Exercise4ModalLabel">Answer</h5>
|
||
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close">
|
||
</button>
|
||
</div>
|
||
<div class="modal-body">
|
||
<p><strong>b) Compound.</strong> (Hint: Review the definitions above to find the right answer.)
|
||
</p>
|
||
</div>
|
||
<div class="modal-footer">
|
||
<button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
|
||
</div>
|
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</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<br>
|
||
|
||
<h4>Summary</h4>
|
||
|
||
<p>The table below summarizes PubChem Data Types:</p>
|
||
|
||
<table class="table">
|
||
<thead>
|
||
<tr>
|
||
<th scope="col">Date Type</th>
|
||
<th scope="col">Description</th>
|
||
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<th scope="row">Substance</th>
|
||
<td>Submitted data about a chemical from a source</td>
|
||
|
||
</tr>
|
||
<tr>
|
||
<th scope="row">Compound</th>
|
||
<td>An aggregated view of all available information in PubChem about a chemical</td>
|
||
|
||
</tr>
|
||
<tr>
|
||
<th scope="row">BioAssays</th>
|
||
<td>Description of biological assay experiments and bioactivity test results on substances</td>
|
||
|
||
</tr>
|
||
<tr>
|
||
<th scope="row">Targets: Proteins and Genes</th>
|
||
<td>Chemical information available for a given protein or gene (or protein encoded by the gene)</td>
|
||
|
||
</tr>
|
||
<tr>
|
||
<th scope="row">Pathways</th>
|
||
<td>Information about chemicals, genes, or diseases involved in or associated with a biological pathway</td>
|
||
|
||
</tr>
|
||
<tr>
|
||
<th scope="row">Cell Lines</th>
|
||
<td>Chemical information associated with a given cell line</td>
|
||
|
||
</tr>
|
||
<tr>
|
||
<th scope="row">Taxonomy</th>
|
||
<td>Chemical information associated with a specific organism</td>
|
||
|
||
</tr>
|
||
<tr>
|
||
<th scope="row">Patents</th>
|
||
<td>Chemical information mentioned in a given patent</td>
|
||
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
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</div>
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