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EMBRCprovmodel_example.xml
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<eml:eml xsi:schemaLocation="eml://ecoinformatics.org/eml-2.2.0 https://rs.gbif.org/schema/eml-gbif-profile/1.1/eml.xsd" packageId="eml2.2.0" system="https://www.vliz.be/imis" xml:lang="en">
<dataset>
<title xml:lang="en">Data collected during the maniacal quest of Ahab, captain of the whailing ship Pequod, for vengeance against Moby Dick.</title>
<creator id="https://orcid.org/0000-0000-0000-0000">
<individualName>Ishmael</individualName>
<address>
<country>USA</country>
</address>
<electronicMailAddress>ishmael@sailor.org</electronicMailAddress>
<onlineUrl></onlineUrl>
<userId directory="https://orcid.org">https://orcid.org/0000-0000-0000-0000</userId>
</creator>
<metadataProvider id="https://ror.org/0000000">
<organizationName>Harper&Brothers-DBMS</organizationName>
<address>
<country>USA</country>
</address>
<electronicMailAddress>harperbrothers@info.org</electronicMailAddress>
<userId directory="https://ror.org">https://ror.org/0496vr396</userId>
</metadataProvider>
<associatedParty id="https://orcid.org/0000-0000-0000-0001">
<organizationName>Ahab</organizationName>
<address>
<country>USA</country>
</address>
<electronicMailAddress>old.thunder@captain.org</electronicMailAddress>
<role>Captain of Pequod</role>
<userId directory="https://orcid.org">https://orcid.org/0000-0000-0000-0000</userId>
</associatedParty>
<pubDate>1851</pubDate>
<language>en</language>
<abstract>
This dataset contains data that was collected during the maniacal quest of Ahab, captain of the whailing ship Pequod, for vengeance against Moby Dick.
Unfortunately, both Moby Dick and Captain Ahab died during this quest. However, sailor Ishmael, participating in the quest, managed to retrieve some sample tissues.
Along side this, he also collected both observational and evironmental data. The sample tissues were send off to the institute for Giant Whales for further analyses.
(disclaimer: this dataset is loosely based on the novel 'Moby Dick' by Herman Melville and clearly not real. No whales were harmed in the process.)
</abstract>
<keywordSet>
<keyword>Whaling</keyword>
<keyword>Illegal fishing</keyword>
<keyword>Marine environment</keyword>
<keyword>Illegal fishing</keyword>
<keyword>Genetics</keyword>
<keyword>Sample storage</keyword>
<keywordThesaurus>https://vocabularyserver.com/asfa</keywordThesaurus>
</keywordSet>
<intellectualRights>Unrestricted for academic use</intellectualRights>
<coverage>
<geographicCoverage id="https://marineregions.org/mrgid/1902">
<geographicDescription>Atlantic ocean</geographicDescription>
<boundingCoordinates>
<westBoundingCoordinate>-36,969361</westBoundingCoordinate>
<eastBoundingCoordinate>-36,969361</eastBoundingCoordinate>
<northBoundingCoordinate>3,860181</northBoundingCoordinate>
<southBoundingCoordinate>3,860181</southBoundingCoordinate>
</boundingCoordinates>
</geographicCoverage>
<temporalCoverage>
<rangeOfDates>
<beginDate>
<calendarDate>1841-05-19</calendarDate>
</beginDate>
<endDate>
<calendarDate>1841-05-25</calendarDate>
</endDate>
</rangeOfDates>
</temporalCoverage>
<taxonomicCoverage id="urn:lsid:marinespecies.org:taxname:137119">
<generalTaxonomicCoverage>1821</generalTaxonomicCoverage>
<taxonomicClassification>
<taxonRankName>species</taxonRankName>
<taxonRankValue>Physeter macrocephalus</taxonRankValue>
<taxonId provider="https://www.marinespecies.org/">137119</taxonId>
</taxonomicClassification>
<annotation>
<propertyURI label=”same as”>http://www.w3.org/2002/07/owl#sameAs</propertyURI>
<valueURI>https://www.marinespecies.org/aphia.php?p=taxdetails&id=137119</valueURI>
</annotation>
</taxonomicCoverage>
</coverage>
<maintenance>
<description>
</para>
</description>
<maintenanceUpdateFrequency>unknown</maintenanceUpdateFrequency>
</maintenance>
<contact>
<organizationName>Harper&Brothers-DBMS</organizationName>
<electronicMailAddress>harperbrothers@info.org</electronicMailAddress>
</contact>
<methods>
/// Physical activities: Acquisition - Sampling
<sampling>
<samplingDescription>Giant whale tissue samples collected during the Ahab's maniacal quest. Samples were brutally collected by way of harpooning and retrieved by Ishmael</samplingDescription>
<instrumentation id="http://example.org/device/harpoon23_01">
<type>Harpoon</type>
</instrumentation>
<permit id="https://example.org/permit/whalingquest/34545">
<temporalCoverage>
<rangeOfDates>
<beginDate>
<calendarDate>1841-05-19</calendarDate>
</beginDate>
<endDate>
<calendarDate>1841-05-25</calendarDate>
</endDate>
</rangeOfDates>
</temporalCoverage>
</permit>
<coverage>
<geographicCoverage id="https://marineregions.org/mrgid/1902">
<geographicDescription>Atlantic ocean</geographicDescription>
<boundingCoordinates>
<westBoundingCoordinate>-36,969361</westBoundingCoordinate>
<eastBoundingCoordinate>-36,969361</eastBoundingCoordinate>
<northBoundingCoordinate>3,860181</northBoundingCoordinate>
<southBoundingCoordinate>3,860181</southBoundingCoordinate>
</boundingCoordinates>
</geographicCoverage>
<temporalCoverage>
<singleDateTime>
<calendarDate>1842-05-25</calendarDate>
<time>11:45</time>
</singleDateTime>
</temporalCoverage>
</coverage>
<party id="http://example.org/sailor/Ishmael">
<individualName>Ishmael</individualName>
<role>sailor</role>
<electronicMailAddress>ishmael@sailor.org</electronicMailAddress>
</party>
<protocol id="https://example.org/protocol/harpooning/">
<title>Harpooning with type 23B</title>
<description>A manual on how to collect samples using Harpoon 23B. Manufactured by worst-company-every.Inc.</description>
<distribution>
<online>
<url>https://worst-company-ever.org/manuals/harpoon23B</url>
</online>
</distribution>
</protocol>
</sampling>
/// Physical activities: Transport
<methodstep>
<description>TRANSPORT from sampling site to lab/storage. </description>
<permit id="https://example.org/permit/transport/68734"></permit>
<coverage>
<temporalCoverage>
<rangeOfDates>
<beginDate>
<calendarDate>1842-05-25</calendarDate>
</beginDate>
<endDate>
<calendarDate>1842-05-27</calendarDate>
</endDate>
</rangeOfDates>
</temporalCoverage>
</coverage>
/// from sampling site to lab
<party id="example.org/person/1345">
<individualName>Gardiner from Nantucket</individualName>
<role>Transporter</role>
<electronicMailAddress>gardiner@captain.org</electronicMailAddress>
</party>
<party id="example.org/person/1345">
<individualName>Scientist person</individualName>
<role>Receiver</role>
<electronicMailAddress>gardiner@captain.org</electronicMailAddress>
<address>Seabrook Island Road 123, South Carolina 29455, United States</address>
</party>
<protocol id="http://example.org/protocol/sampletransport">
<title>Sample transport by ship</title>
<description>Samples where transported to the Institute forGiant whales by ship. During transport samples were contained in air tight specimen bags, after being transfixed using the right fixative.</description>
</protocol>
</methodstep>
/// Physical activities: Processing
<methodstep>
<description>PROCESSING</description>
<substep>
<description>Storing the collected sample in ethanol.</description>
<instrumentation>20ml of 4% ethanol</instrumentation>
<coverage>
<temporalCoverage>
<singleDateTime>
<calendarDate>1841-06-04</calendarDate>
<time>16:00</time>
</singleDateTime>
</temporalCoverage>
</coverage>
<party id="www.chestofgreatewhales.org/person/1345">
<individualName>Gardiner from Nantucket</individualName>
<role>lab technician</role>
<electronicMailAddress>gardiner@captain.org</electronicMailAddress>
</party>
</substep>
<substep>
<description>A part of the collected tissue samples are processed further into samples for analysis. We followed the Standardized Preomics Workflow for this, making use of the Cell-Tissue- HomogenizerTM, to avoid possibility of cross-contamination.</description>
<instrumentation>Cell-Tissue-HomogenizerTM</instrumentation>
<coverage>
<temporalCoverage>
<singleDateTime>
<calendarDate>1841-06-07</calendarDate>
<time>14:00</time>
</singleDateTime>
</temporalCoverage>
</coverage>
<party id="www.chestofgreatewhales.org/person/2342355">
<individualName>Father Mapple</individualName>
<role>lab technician</role>
<electronicMailAddress>father.mapple@chestofgreatwhales.org</electronicMailAddress>
<address>Seabrook Island Road 123, South Carolina 29455, United States</address>
</party>
<protocol id="www.chestofgreatewhales.org/protocol/456A">
<title>Standardized preomics workflow</title>
<description>A simple yet effective workflow for the cell homogenization of biosamples with minimal possibility of cross-contamination.</description>
<distribution>
<online>
<url>http://www.chestofgreatewhales.org/protocol/456A</url>
</online>
</distribution>
</protocol>
</substep>
</methodstep>
/// Physical activities: Storage
<methodstep>
<description>STORAGE</description>
<substep>
<description>Sample stored in ship's fridge, at 30°F. </description>
<instrumentation>ship's fridge</instrumentation>
<coverage>
<temporalCoverage>
<rangeOfDates>
<beginDate><calendarDate>1841-06-07</calendarDate></beginDate>
<endDate><calendarDate>1841-06-09</calendarDate></endDate>
</rangeOfDates>
</temporalCoverage>
</coverage>
<party>
<references>www.chestofgreatewhales.org/person/1345</references>
</party>
</substep>
<substep>
<description>Samples are labelled with individual barcodes and stored at -80°C temperature maintained by liquid nitrogen circulating in a closed evaporator system.</description>
<instrumentation>automation compatible racks on independent storage towers</instrumentation>
<coverage>
<temporalCoverage>
<rangeOfDates>
<beginDate><calendarDate>1841-06-12</calendarDate></beginDate>
<endDate><calendarDate>1841-06-17</calendarDate></endDate>
</rangeOfDates>
</temporalCoverage>
</coverage>
<party>
<organizationName>Chest of Great Whales Facility</organizationName>
<role>Biobanking facility</role>
<electronicMailAddress>greatwhalechest@info.org</electronicMailAddress>
<address>Seabrook Island Road 123, South Carolina 29455, United States</address>
</party>
</substep>
<substep>
/// specifically for case of Bio-banking!
<description>biobanked in the greatwhaleschest-facility with ID: gwcf28</description>
<coverage>
<temporalCoverage>
<singleDateTime><calendarDate>1841-06-17</calendarDate></singleDateTime>
</temporalCoverage>
</coverage>
<party id="http://greatwhalechest-biobank.org/">
<organizationName>Chest of Great Whales Facility</organizationName>
<address>Seabrook Island Road 123, South Carolina 29455, United States</address>
<role>biobank</role>
</party>
<protocol id="www.greatwhalechest.org/protocol/234235">
<title>Whale sample biobanking protocol</title>
<description>Protocol on the biobanking.</description>
<distribution>
<online>
<url>"http://www.greatwhalechest.org/protocol/234235"</url>
</online>
</distribution>
</protocol>
</substep>
</methodstep>
/// Physical activities: Acquisition - Ordering
<methodstep>
<description>Ordering material from a biobank</description>
<dataSource id="gwcf28"> ///id can also hold non-url in case if no online url is available
<associatedParty>
<organizationName>Chest of Great Whales Facility</organizationName>
<address>Seabrook Island Road 123, South Carolina 29455, United States</address>
<role>biobank</role>
<onlineUrl>http://greatwhalechest-biobank.org/</onlineUrl>
</associatedParty>
<distribution>
<online>
<url>http://greatwhalechest-biobank.org/gwcf28</url>
</online>
</distribution>
</dataSource>
<permit></permit>
<coverage>
<temporalCoverage>
<singleDateTime>
<calendarDate></calendarDate>
<time></time>
</singleDateTime>
</temporalCoverage>
</coverage>
</methodstep>
/// Digital activities: Data retrieval
<methodStep>
<description>DATA RETRIEVAL</description>
<dataSource id="">
<purpose></purpose>
<distribution>
<online>
<url></url>
</online>
</distribution>
<literatureCited>
<citation>
<distribution>
<online>
<url></url>
</online>
</distribution>
</citation>
</literatureCited>
...
</dataSource>
</methodStep>
/// Digital activities: Software Processing
<methodStep>
<software id="">
<title></title>
<version></version>
<distribution></distribution>
<implementation></implementation> /// list elements that we think are important to put in here
<dependencies></dependencies>
...
</software>
<party>
<individualName></individualName>
<organizationName></organizationName>
<role></role>
<electronicMailAddress></electronicMailAddress>
</party>
<protocol id="">
<title></title>
<description></description>
<distribution></distribution>
</protocol>
</methodStep>
/// Digital activities: Quality Control
<qualityControl>
<description></description>
<software id=""></software>
<party>
<individualName></individualName>
<organizationName></organizationName>
<role></role>
<electronicMailAddress></electronicMailAddress>
</party>
<protocol id="">
<title></title>
<description></description>
<distribution></distribution>
</protocol>
</qualityControl>
</methods>
</dataset>
</eml:eml>