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index.html

@@ -320,7 +320,7 @@ <h1>
             <section class="normal" id="section-">
 <div id="header">
 <h1 class="title">The OBIS manual</h1>
-<p class="date"><em>11 September, 2024</em></p>
+<p class="date"><em>13 September, 2024</em></p>
 </div>
 <div style="page-break-after: always;"></div>
 <p><img src="images/obis_logo.png" style="width:50.0%" /></p>

linklist.html

@@ -321,25 +321,35 @@ <h1>
 <div id="quick-links-to-resources" class="section level2 hasAnchor" number="1.6">
 <h2><span class="header-section-number">1.6</span> Quick links to resources<a href="linklist.html#quick-links-to-resources" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>Below you will find a convenient list of important or relevant websites and resources that are mentioned in this Manual. Links are organized by category.</p>
-<div id="general-links-and-guides" class="section level4 hasAnchor" number="1.6.0.1">
-<h4><span class="header-section-number">1.6.0.1</span> General links and guides<a href="linklist.html#general-links-and-guides" class="anchor-section" aria-label="Anchor link to header"></a></h4>
+<div id="general-links-and-guides" class="section level4 unnumbered hasAnchor">
+<h4>General links and guides<a href="linklist.html#general-links-and-guides" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <ul>
 <li><a href="https://obis.org/">OBIS home page</a></li>
 <li><a href="checklist.html#darwin-core-term-checklist-for-obis">Darwin Core term OBIS Checklist</a></li>
 <li><a href="FAQ.html">OBIS FAQ</a></li>
 <li><a href="https://join.slack.com/t/obishq/shared_invite/zt-1yiucrrrq-RZRPU7c4rm7OungiBseWVA">OBIS Slack</a></li>
 <li><a href="https://github.com/iobis/helpdesk">OBIS GitHub helpdesk</a></li>
 <li><a href="https://obis.org/contact/">List of OBIS nodes</a></li>
+<li><svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"/></svg> <a href="https://www.youtube.com/playlist?list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF">OBIS How-To Use &amp; Publish Data YouTube series</a>: this series covers topics including but not limited to:
+<ul>
+<li>How to construct <a href="https://www.youtube.com/watch?v=Upt6LPJ0Bn8&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=2&amp;t=6s">eventIDs</a>,</li>
+<li>How to create and format the <a href="https://www.youtube.com/watch?v=jyy6QO_p7v8&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=4">Event</a>, <a href="https://www.youtube.com/watch?v=G_AmAmS7ILc&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=5">Occurrence</a>, and <a href="https://www.youtube.com/watch?v=EjM0HRrF1B4&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=6">eMoF</a> tables,</li>
+<li>How to access data from OBIS using the <a href="https://www.youtube.com/watch?v=9PSPEtqgjUI&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=11&amp;t=1s">Mapper</a> or <a href="https://www.youtube.com/watch?v=8Ep4fGICQWU&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=12">R</a>,</li>
+<li>How to <a href="https://www.youtube.com/watch?v=jJ8nlMlg-cY&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=16">conduct taxon matching</a>,</li>
+<li>How to <a href="https://www.youtube.com/watch?v=sNzipC6-r90&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=7">quality control check a dataset</a>,</li>
+<li>How to <a href="https://www.youtube.com/watch?v=i2P8mjo128o&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=8">publish data to OBIS using the IPT</a></li>
+<li>How to <a href="https://www.youtube.com/watch?v=HciufRG9hiI&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=10">publish an OBIS dataset to GBIF</a></li>
+<li>How to use the <a href="https://www.youtube.com/watch?v=XM23WEvE364&amp;list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF&amp;index=14">OBIS MapTool</a></li>
+</ul></li>
 <li><a href="https://dwc.tdwg.org/terms/">Darwin Core term Quick Reference Guide</a></li>
 <li><a href="https://dwc.tdwg.org/text/">Darwin Core text guide</a></li>
 <li><a href="https://docs.gbif.org/publishing-dna-derived-data/en/">Publishing DNA-derived data guide</a></li>
-<li><svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"/></svg> <a href="https://www.youtube.com/playlist?list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF">OBIS Data formatting tutorial YouTube series</a>: this series covers topics including creating identifiers (eventID, occurrenceID), creating data tables (event, Occurrence, eMoF), accessing OBIS data, taxon matching, running QC checks, etc.</li>
 <li>De Pooter et al. 2017. Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences. Biodiversity Data Journal 5: e10989. hdl.handle.net/10.3897/BDJ.5.e10989</li>
 <li>Duncan et al. (2021). A standard approach to structuring classified habitat data using the Darwin Core Extended Measurement or Fact Extension. EMODnet report. <a href="https://www.emodnet-seabedhabitats.eu/resources/documents-and-outreach/#h3298bcd0a15741a8a0ac1c8b4576f7c5" class="uri">https://www.emodnet-seabedhabitats.eu/resources/documents-and-outreach/#h3298bcd0a15741a8a0ac1c8b4576f7c5</a> (note you must refine search to Technical Reports from 2021 to identify this report as it does not have an individual link)</li>
 </ul>
 </div>
-<div id="data-access-mappinggeoreferencing-tools" class="section level4 hasAnchor" number="1.6.0.2">
-<h4><span class="header-section-number">1.6.0.2</span> Data Access &amp; Mapping/Georeferencing Tools<a href="linklist.html#data-access-mappinggeoreferencing-tools" class="anchor-section" aria-label="Anchor link to header"></a></h4>
+<div id="data-access-mappinggeoreferencing-tools" class="section level4 unnumbered hasAnchor">
+<h4>Data Access &amp; Mapping/Georeferencing Tools<a href="linklist.html#data-access-mappinggeoreferencing-tools" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <ul>
 <li><a href="https://mapper.obis.org/">OBIS Mapper</a>: map-based tool for obtaining OBIS data, allowing various filters to be applied</li>
 <li><a href="https://github.com/iobis/robis">R package robis</a></li>
@@ -352,8 +362,8 @@ <h4><span class="header-section-number">1.6.0.2</span> Data Access &amp; Mapping
 <li><a href="https://www.getty.edu/research/tools/vocabularies/tgn/">Getty Thesaurus of Geographic Names</a>: search interface for place names</li>
 </ul>
 </div>
-<div id="controlled-vocabulary" class="section level4 hasAnchor" number="1.6.0.3">
-<h4><span class="header-section-number">1.6.0.3</span> Controlled vocabulary<a href="linklist.html#controlled-vocabulary" class="anchor-section" aria-label="Anchor link to header"></a></h4>
+<div id="controlled-vocabulary" class="section level4 unnumbered hasAnchor">
+<h4>Controlled vocabulary<a href="linklist.html#controlled-vocabulary" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <ul>
 <li><svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"/></svg> <a href="https://www.youtube.com/playlist?list=PLlgUwSvpCFS4hADB7Slf44V1KJauEU6Ul">OBIS YouTube Vocabulary series</a>: this series demonstrates how to use the <a href="vocabulary#selecting-p01-codes-for-measurementtypeid">vocabulary decision tree</a> in conjunction with the SeaDataNet P01 facet search in order to find/select vocabularies for eMoF measurements</li>
 <li><a href="https://vocab.seadatanet.org/p01-facet-search">SeaDataNet P01 facet search</a>: recommended interface to search for P01 codes used to populate measurementTypeID field. Note that the free text search is best used by supplying one search term at a time (it does not search the same way we use Google)</li>
@@ -364,8 +374,8 @@ <h4><span class="header-section-number">1.6.0.3</span> Controlled vocabulary<a h
 <li><a href="https://vocab.nerc.ac.uk/search_nvs/">NERC Vocabulary Server</a>: interface to search through the entire NERC Vocabulary Server to find vocabulary terms. As with the SeaDataNet facet search, the search does not function the same way Google does and you may have to adjust how you search for terms.</li>
 </ul>
 </div>
-<div id="tools-for-taxonomy-dates" class="section level4 hasAnchor" number="1.6.0.4">
-<h4><span class="header-section-number">1.6.0.4</span> Tools for Taxonomy &amp; Dates<a href="linklist.html#tools-for-taxonomy-dates" class="anchor-section" aria-label="Anchor link to header"></a></h4>
+<div id="tools-for-taxonomy-dates" class="section level4 unnumbered hasAnchor">
+<h4>Tools for Taxonomy &amp; Dates<a href="linklist.html#tools-for-taxonomy-dates" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <ul>
 <li><a href="https://www.marinespecies.org/aphia.php?p=match">WoRMS Taxon match tool</a>: used to match a list of species names to taxonomic authority and obtain LSIDs for species</li>
 <li><a href="https://www.gbif.org/tools/name-parser">GBIF Name parser</a>: tool to divide scientific names into their components and to check them against the taxonomic backbone used by GBIF</li>
@@ -376,8 +386,8 @@ <h4><span class="header-section-number">1.6.0.4</span> Tools for Taxonomy &amp;
 <li><a href="https://data.canadensys.net/tools/dates#:~:text=Use%20this%20tool%20to%20parse,a%20tab%20or%20a%20pipe.">Canadensys Date parser</a>: tool to parse dates into component parts</li>
 </ul>
 </div>
-<div id="data-qc-tools-links" class="section level4 hasAnchor" number="1.6.0.5">
-<h4><span class="header-section-number">1.6.0.5</span> Data QC Tools &amp; Links<a href="linklist.html#data-qc-tools-links" class="anchor-section" aria-label="Anchor link to header"></a></h4>
+<div id="data-qc-tools-links" class="section level4 unnumbered hasAnchor">
+<h4>Data QC Tools &amp; Links<a href="linklist.html#data-qc-tools-links" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <ul>
 <li><a href="https://github.com/iobis/obis-qc">List of Quality Checks conducted by OBIS</a> on published data</li>
 <li><a href="https://github.com/iobis/obis-qc/blob/master/obisqc/util/flags.py">List of QC Flags</a> implemented by OBIS</li>
@@ -386,16 +396,16 @@ <h4><span class="header-section-number">1.6.0.5</span> Data QC Tools &amp; Links
 <li><a href="https://hbiostat.org/r/hmisc/">Hmisc R package</a> for summarizing data, useful for checking data quality and outliers</li>
 </ul>
 </div>
-<div id="template-tools" class="section level4 hasAnchor" number="1.6.0.6">
-<h4><span class="header-section-number">1.6.0.6</span> Template Tools<a href="linklist.html#template-tools" class="anchor-section" aria-label="Anchor link to header"></a></h4>
+<div id="template-tools" class="section level4 unnumbered hasAnchor">
+<h4>Template Tools<a href="linklist.html#template-tools" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <ul>
 <li>GBIF Excel templates: <a href="https://ipt.gbif.org/manual/en/ipt/latest/sampling-event-data#templates">Event table</a> and <a href="https://ipt.gbif.org/manual/en/ipt/latest/occurrence-data#templates">Occurrence table</a></li>
 <li><a href="https://zenodo.org/record/6453921#.Y9KsQkHMKmU">Excel to Darwin Core Standard (DwC) Tool</a>: a macro Excel spreadsheet for setup, data entry, data validation and file export to DwC (Darwin Core Standard) files. Creates templates for Event, Occurrence, MeasurementsOrFacts, Extended MeasurementsOrFacts (EMoF), and Simple Multimedia tables.</li>
 <li><a href="https://sios-svalbard.org/aen/template-generator/">Darwin Core Template Generator for Event and Occurrence tables</a>: allows selection of DwC terms to generate template for Event and Occurrence tables, developed by Luke Marsden, &amp; Olaf Schneider</li>
 </ul>
 </div>
-<div id="publishing-tools-links" class="section level4 hasAnchor" number="1.6.0.7">
-<h4><span class="header-section-number">1.6.0.7</span> Publishing Tools &amp; Links<a href="linklist.html#publishing-tools-links" class="anchor-section" aria-label="Anchor link to header"></a></h4>
+<div id="publishing-tools-links" class="section level4 unnumbered hasAnchor">
+<h4>Publishing Tools &amp; Links<a href="linklist.html#publishing-tools-links" class="anchor-section" aria-label="Anchor link to header"></a></h4>
 <ul>
 <li><a href="https://ipt.gbif.org/manual/en/ipt/latest/">Integrated Publishing Toolkit (IPT) User Manual</a>: manual with more details on how to use the IPT for publishing datasets</li>
 <li><a href="https://eml.ecoinformatics.org/">Ecological Metadata Language (EML) guide</a>

reference-keys.txt

@@ -16,13 +16,6 @@ disclaimer
 getting-help-in-obis
 frequently-asked-questions
 quick-links-to-resources
-general-links-and-guides
-data-access-mappinggeoreferencing-tools
-controlled-vocabulary
-tools-for-taxonomy-dates
-data-qc-tools-links
-template-tools
-publishing-tools-links
 what-can-you-contribute-and-how
 why-publish-data-to-obis
 how-to-handle-sensitive-data