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8 changes: 4 additions & 4 deletions _sources/usecases/uvvis_metadata.ipynb
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" <td><b>Format</b></td>\n",
" </tr>\n",
" <tr>\n",
" <td style=\"word-wrap: break-word; max-width: 400px;valign: top;\">Data matrix (with or without column headings)</td>\n",
" <td style=\"word-wrap: break-word; max-width: 400px;valign: top;\">Spectrophotometer output as tabular data (absorbance and wavelength)</td>\n",
" <td style=\"word-wrap: break-word; max-width: 400px;\"valign: top;>Essential</td>\n",
" <td style=\"word-wrap: break-word; max-width: 400px;\"valign: top;>CSV (.csv)<br/>JCAMP–DX (.jdx)</td>\n",
" <td style=\"word-wrap: break-word; max-width: 400px;vertical-align: top;\">Data matrix (with or without column headings)</td>\n",
" <td style=\"word-wrap: break-word; max-width: 400px;vertical-align: top;\">Spectrophotometer output as tabular data (absorbance and wavelength)</td>\n",
" <td style=\"word-wrap: break-word; max-width: 400px;vertical-align: top;\">Essential</td>\n",
" <td style=\"word-wrap: break-word; max-width: 400px;vertical-align: top;\">CSV (.csv)<br/>JCAMP–DX (.jdx)</td>\n",
" </tr>\n",
" <tr style=\"background-color:gray;\">\n",
" <td colspan='4'><strong> Sample level metadata </strong></td>\n",
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2 changes: 1 addition & 1 deletion datasources/goldbook_api.html
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Expand Up @@ -574,7 +574,7 @@ <h2>Step 5: Use the term code to retrieve its definition<a class="headerlink" hr
</div>
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<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;2024-01-29T17:43:54+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;2024-01-29T17:53:49+00:00&#39;}}
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4 changes: 3 additions & 1 deletion datasources/pubchem_pugrest1.html
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Expand Up @@ -523,7 +523,9 @@ <h3>2. Construct a PUG-REST API and retrieve data<a class="headerlink" href="#co
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>REQEST URL: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/property/MolecularFormula/txt
OUTPUT : C9H8O4
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>OUTPUT : C9H8O4
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6 changes: 3 additions & 3 deletions manipulations/computing_inchis.html
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Expand Up @@ -526,7 +526,7 @@ <h3>1.2 Create a Molecular Object from SMILES<a class="headerlink" href="#create
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;rdkit.Chem.rdchem.Mol object at 0x7f9c073a0eb0&gt;
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;rdkit.Chem.rdchem.Mol object at 0x7f32539dcf20&gt;
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;rdkit.Chem.rdchem.Mol object at 0x7f9c073a1460&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f9c073a14d0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f9c073a1850&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f9c073a18c0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f9c073a1930&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f9c073a19a0&gt;]
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;rdkit.Chem.rdchem.Mol object at 0x7f32539dd3f0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f32539dd4d0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f32539dd8c0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f32539dd930&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f32539dd9a0&gt;, &lt;rdkit.Chem.rdchem.Mol object at 0x7f32539dda10&gt;]
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</div>
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;openbabel.pybel.Molecule object at 0x7f9c05ba8cd0&gt;, &lt;openbabel.pybel.Molecule object at 0x7f9c05ba8e10&gt;, &lt;openbabel.pybel.Molecule object at 0x7f9c05ba9090&gt;, &lt;openbabel.pybel.Molecule object at 0x7f9c05ba9150&gt;, &lt;openbabel.pybel.Molecule object at 0x7f9c05ba9050&gt;, &lt;openbabel.pybel.Molecule object at 0x7f9c05ba8f10&gt;]
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;openbabel.pybel.Molecule object at 0x7f3251dba9d0&gt;, &lt;openbabel.pybel.Molecule object at 0x7f3251db9190&gt;, &lt;openbabel.pybel.Molecule object at 0x7f3251db8f90&gt;, &lt;openbabel.pybel.Molecule object at 0x7f3251db92d0&gt;, &lt;openbabel.pybel.Molecule object at 0x7f3251db94d0&gt;, &lt;openbabel.pybel.Molecule object at 0x7f3251db95d0&gt;]
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2 changes: 1 addition & 1 deletion manipulations/dataset_search.html
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Expand Up @@ -1015,7 +1015,7 @@ <h3>2.1 - Authentication to the FAIRSharing API<a class="headerlink" href="#auth
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;success&#39;: True, &#39;jwt&#39;: &#39;eyJhbGciOiJIUzI1NiJ9.eyJqdGkiOiI0YjVkNzQyMi1hOTg3LTRlZWYtYjQyYi1hN2U3Yjc2MTM0ZTEiLCJzdWIiOiI4NTA5Iiwic2NwIjoidXNlciIsImF1ZCI6bnVsbCwiaWF0IjoxNzA2NTUwMjc0LCJleHAiOjE3MDY2MzY2NzR9.k5_TrDKXCs6vJHfke57nENICtHD2h_-qHWplpUENDRQ&#39;, &#39;username&#39;: &#39;ChemCookbook&#39;, &#39;id&#39;: 8509, &#39;role&#39;: &#39;user&#39;, &#39;profile_type&#39;: &#39;none&#39;, &#39;watched_records&#39;: [], &#39;is_curator&#39;: False, &#39;is_super_curator&#39;: False, &#39;third_party&#39;: False, &#39;expiry&#39;: 1706636674, &#39;message&#39;: &#39;Authentication successful&#39;}
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;success&#39;: True, &#39;jwt&#39;: &#39;eyJhbGciOiJIUzI1NiJ9.eyJqdGkiOiI0YjVkNzQyMi1hOTg3LTRlZWYtYjQyYi1hN2U3Yjc2MTM0ZTEiLCJzdWIiOiI4NTA5Iiwic2NwIjoidXNlciIsImF1ZCI6bnVsbCwiaWF0IjoxNzA2NTUwODY5LCJleHAiOjE3MDY2MzcyNjl9.AsF6bAJXFAr8Uy_-GhSC7riYuGwjSgHMvWrpRrUkSOY&#39;, &#39;username&#39;: &#39;ChemCookbook&#39;, &#39;id&#39;: 8509, &#39;role&#39;: &#39;user&#39;, &#39;profile_type&#39;: &#39;none&#39;, &#39;watched_records&#39;: [], &#39;is_curator&#39;: False, &#39;is_super_curator&#39;: False, &#39;third_party&#39;: False, &#39;expiry&#39;: 1706637269, &#39;message&#39;: &#39;Authentication successful&#39;}
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2 changes: 1 addition & 1 deletion searchindex.js

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8 changes: 4 additions & 4 deletions usecases/uvvis_metadata.html
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Expand Up @@ -538,10 +538,10 @@ <h3>3.2 File hierarchy<a class="headerlink" href="#file-hierarchy" title="Permal
<td><b>Format</b></td>
</tr>
<tr>
<td style="word-wrap: break-word; max-width: 400px;valign: top;">Data matrix (with or without column headings)</td>
<td style="word-wrap: break-word; max-width: 400px;valign: top;">Spectrophotometer output as tabular data (absorbance and wavelength)</td>
<td style="word-wrap: break-word; max-width: 400px;"valign: top;>Essential</td>
<td style="word-wrap: break-word; max-width: 400px;"valign: top;>CSV (.csv)<br/>JCAMP–DX (.jdx)</td>
<td style="word-wrap: break-word; max-width: 400px;vertical-align: top;">Data matrix (with or without column headings)</td>
<td style="word-wrap: break-word; max-width: 400px;vertical-align: top;">Spectrophotometer output as tabular data (absorbance and wavelength)</td>
<td style="word-wrap: break-word; max-width: 400px;vertical-align: top;">Essential</td>
<td style="word-wrap: break-word; max-width: 400px;vertical-align: top;">CSV (.csv)<br/>JCAMP–DX (.jdx)</td>
</tr>
<tr style="background-color:gray;">
<td colspan='4'><strong> Sample level metadata </strong></td>
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