stash-merritt 0.0.1

data/lib/stash/merritt/submission_package.rb

@@ -0,0 +1,125 @@
+require 'fileutils'
+require 'tmpdir'
+require 'stash_engine'
+require 'stash_datacite'
+require 'zip'
+require 'datacite/mapping/datacite_xml_factory'
+require 'stash/merritt/submission_package/data_one_manifest_builder'
+require 'stash/merritt/submission_package/merritt_datacite_builder'
+require 'stash/merritt/submission_package/merritt_delete_builder'
+require 'stash/merritt/submission_package/merritt_oaidc_builder'
+require 'stash/merritt/submission_package/stash_wrapper_builder'
+
+module Stash
+  module Merritt
+    class SubmissionPackage
+      attr_reader :resource
+      attr_reader :zipfile
+
+      def initialize(resource:)
+        raise ArgumentError, "Resource (#{resource.id}) must have an identifier before submission" unless resource.identifier_str
+        @resource = resource
+        @zipfile = create_zipfile
+      end
+
+      def resource_id
+        resource.id
+      end
+
+      def dc3_xml
+        @dc3_xml ||= datacite_xml_factory.build_datacite_xml(datacite_3: true)
+      end
+
+      def resource_title
+        primary_title = resource.titles.where(title_type: nil).first
+        primary_title.title.to_s if primary_title
+      end
+
+      def create_zipfile
+        StashDatacite::PublicationYear.ensure_pub_year(resource)
+        zipfile_path = File.join(workdir, "#{resource_id}_archive.zip")
+        Zip::File.open(zipfile_path, Zip::File::CREATE) do |zipfile|
+          builders.each { |builder| write_to_zipfile(zipfile, builder) }
+          uploads.each { |upload| add_to_zipfile(zipfile, upload) }
+        end
+        zipfile_path
+      end
+
+      def cleanup!
+        FileUtils.remove_dir(workdir)
+        @zipfile = nil
+      end
+
+      def to_s
+        "#{self.class}: submission package for resource #{resource_id} (#{resource_title}"
+      end
+
+      private
+
+      def write_to_zipfile(zipfile, builder)
+        return unless (file = builder.write_file(workdir))
+        zipfile.add(builder.file_name, file)
+      end
+
+      def add_to_zipfile(zipfile, upload)
+        path = File.join(resource.upload_dir, upload.upload_file_name)
+        raise ArgumentError("Upload file '#{upload.upload_file_name}' not found in directory #{resource.upload_dir}") unless File.exist?(path)
+        zipfile.add(upload.upload_file_name, path)
+      end
+
+      def builders
+        [stash_wrapper_builder, mrt_datacite_builder, mrt_oaidc_builder, mrt_dataone_manifest_builder, mrt_delete_builder]
+      end
+
+      def stash_wrapper_builder
+        @stash_wrapper_builder ||= StashWrapperBuilder.new(dcs_resource: dc4_resource, version_number: version_number, uploads: uploads)
+      end
+
+      def mrt_datacite_builder
+        @mrt_datacite_builder ||= MerrittDataciteBuilder.new(datacite_xml_factory)
+      end
+
+      def mrt_oaidc_builder
+        @mrt_oaidc_builder ||= MerrittOAIDCBuilder.new(resource_id: resource_id)
+      end
+
+      def mrt_dataone_manifest_builder
+        @mrt_dataone_manifest_builder ||= DataONEManifestBuilder.new(uploads)
+      end
+
+      def mrt_delete_builder
+        @mrt_delete_builder ||= MerrittDeleteBuilder.new(resource_id: resource_id)
+      end
+
+      def total_size_bytes
+        @total_size_bytes ||= uploads.inject(0) { |sum, u| sum + u.upload_file_size }
+      end
+
+      def version_number
+        @version_number ||= resource.version_number
+      end
+
+      def uploads
+        resource.current_file_uploads
+      end
+
+      def datacite_xml_factory
+        @datacite_xml_factory ||= Datacite::Mapping::DataciteXMLFactory.new(doi_value: resource.identifier_value, se_resource_id: resource_id, total_size_bytes: total_size_bytes, version: version_number)
+      end
+
+      def dc4_resource
+        @dc4_resource ||= datacite_xml_factory.build_resource
+      end
+
+      def workdir
+        @workdir ||= begin
+          path = resource.upload_dir
+          FileUtils.mkdir_p(path)
+          tmpdir = Dir.mktmpdir('uploads', path)
+          File.absolute_path(tmpdir)
+        end
+      end
+
+    end
+  end
+end

data/lib/stash/merritt/sword_helper.rb

@@ -0,0 +1,58 @@
+require 'stash/sword'
+
+module Stash
+  module Merritt
+    class SwordHelper
+      attr_reader :logger
+      attr_reader :package
+
+      def initialize(package:, logger: nil)
+        @logger = logger
+        @package = package
+      end
+
+      def submit!
+        if (update_uri = resource.update_uri)
+          do_update(update_uri)
+        else
+          do_create
+        end
+        resource.version_zipfile = zipfile
+        resource.save!
+      end
+
+      private
+
+      def resource
+        package.resource
+      end
+
+      def tenant
+        resource.tenant
+      end
+
+      def identifier_str
+        resource.identifier_str
+      end
+
+      def zipfile
+        package.zipfile
+      end
+
+      def sword_client
+        @sword_client ||= Stash::Sword::Client.new(logger: logger, **tenant.sword_params)
+      end
+
+      def do_create
+        receipt = sword_client.create(doi: identifier_str, zipfile: zipfile)
+        resource.download_uri = receipt.em_iri
+        resource.update_uri = receipt.edit_iri
+      end
+
+      def do_update(update_uri)
+        sword_client.update(edit_iri: update_uri, zipfile: zipfile)
+      end
+
+    end
+  end
+end

data/lib/stash/merritt.rb

@@ -0,0 +1,5 @@
+module Stash
+  module Merritt
+    Dir.glob(File.expand_path('../merritt/*.rb', __FILE__)).sort.each(&method(:require))
+  end
+end

data/lib/stash.rb

@@ -0,0 +1,5 @@
+require 'logger'
+
+module Stash
+  Dir.glob(File.expand_path('../stash/*.rb', __FILE__)).sort.each(&method(:require))
+end

data/spec/.rubocop.yml

@@ -0,0 +1,10 @@
+inherit_from: ../.rubocop.yml
+
+Metrics/MethodLength:
+  Enabled: false
+
+Metrics/ModuleLength:
+  Enabled: false
+
+Metrics/BlockLength:
+  Enabled: false

data/spec/config/app_config.yml

@@ -0,0 +1,3 @@
+test:
+  feedback_email_from: stash-noreply@example.edu
+  feedback_email_to: [stash-dev@example.edu, stash-ops@example.edu]

data/spec/config/database.yml

@@ -0,0 +1,7 @@
+# TODO: separate database
+test:
+  host: localhost
+  adapter: mysql2
+  database: stash_merritt
+  username: travis
+  encoding: utf8mb4

data/spec/config/licenses.yml

@@ -0,0 +1,18 @@
+# this file has license information starting with an identifier for the license
+# and then uri and name
+
+cc0:
+  uri: https://creativecommons.org/publicdomain/zero/1.0/
+  name: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
+  explanation: >
+    This releases your work to the public domain for any use.
+  badge: icon_cc-zero.svg
+
+
+cc_by:
+  uri: https://creativecommons.org/licenses/by/4.0/
+  name: Creative Commons Attribution 4.0 International (CC BY 4.0)
+  explanation: >
+    This license lets others distribute, modify, and build upon your work, even commercially, as
+    long as they credit you for the original creation.
+  badge: icon_cc-by.svg

data/spec/data/archive/mrt-datacite.xml

@@ -0,0 +1,121 @@
+<?xml version='1.0'?>
+<resource xsi:schemaLocation='http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xmlns='http://datacite.org/schema/kernel-3'>
+  <identifier identifierType='DOI'>10.15146/R3RG6G</identifier>
+  <creators>
+    <creator>
+      <creatorName>Chen, Hao</creatorName>
+      <nameIdentifier nameIdentifierScheme='ORCID' schemeURI='http://orcid.org/'>0123-4567-8910-1112</nameIdentifier>
+      <affiliation>North Carolina Central University</affiliation>
+    </creator>
+  </creators>
+  <titles>
+    <title>A Zebrafish Model for Studies on Esophageal Epithelial Biology</title>
+    <title titleType='Subtitle'>
+      Characterizing a region of stratified squamous epithelium in the zebrafish
+      upper digestive tract
+    </title>
+  </titles>
+  <publisher>DataONE</publisher>
+  <publicationYear>2016</publicationYear>
+  <subjects>
+    <subject>Zebrafish</subject>
+    <subject>Epithelium</subject>
+    <subject>Barrett&apos;s esophagus</subject>
+  </subjects>
+  <contributors>
+    <contributor contributorType='ProjectMember'>
+      <contributorName>Chen, Xiaoxin</contributorName>
+      <nameIdentifier nameIdentifierScheme='ORCID' schemeURI='http://orcid.org/'>1234-5678-9101-1121</nameIdentifier>
+      <affiliation>University of North Carolina at Chapel Hill</affiliation>
+    </contributor>
+    <contributor contributorType='DataManager'>
+      <contributorName>Wilson, James</contributorName>
+    </contributor>
+    <contributor contributorType="Funder">
+      <contributorName>U.S. Environmental Protection Agency</contributorName>
+    </contributor>
+    <contributor contributorType="Funder">
+      <contributorName>
+        CYBER-ShARE Center of Excellence National Science Foundation (NSF) CREST grants
+      </contributorName>
+    </contributor>
+    <contributor contributorType="Funder">
+      <contributorName>CI-Team Grant</contributorName>
+    </contributor>
+  </contributors>
+  <dates>
+    <date dateType='Available'>2015-12-02</date>
+    <date dateType='Collected'>2009/2011</date>
+  </dates>
+  <language>en</language>
+  <resourceType resourceTypeGeneral='Dataset'>application/octet-stream</resourceType>
+  <alternateIdentifiers>
+    <alternateIdentifier alternateIdentifierType='URL'>
+      https://oneshare.cdlib.org/xtf/view?docId=dataone/ark%2B%3Dc5146%3Dr3rg6g/mrt-datacite.xml
+    </alternateIdentifier>
+  </alternateIdentifiers>
+  <relatedIdentifiers>
+    <relatedIdentifier relationType='IsCitedBy' relatedIdentifierType='DOI'>10.1371/journal.pone.0143878</relatedIdentifier>
+    <relatedIdentifier relationType='IsDocumentedBy' relatedIdentifierType='URL'>http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143878</relatedIdentifier>
+  </relatedIdentifiers>
+  <sizes>
+    <size>3286679 bytes</size>
+  </sizes>
+  <formats>
+    <format>text/plain</format>
+    <format>text/application/vnd.openxmlformats-officedocument.wordprocessingml.document</format>
+    <format>application/xml</format>
+    <format>application/pdf</format>
+  </formats>
+  <version>1</version>
+  <rightsList>
+    <rights rightsURI='https://creativecommons.org/publicdomain/zero/1.0/'>CC0 1.0 Universal (CC0 1.0) Public Domain Dedication</rights>
+  </rightsList>
+  <descriptions>
+    <description descriptionType='Abstract'>
+      Mammalian esophagus exhibits a remarkable change in epithelial structure
+      during the transition from embryo to adult. However, the molecular
+      mechanisms of esophageal epithelial development are not well understood.
+      Zebrafish (Danio rerio), a common model organism for vertebrate
+      development and gene function, has not previously been characterized as a
+      model system for esophageal epithelial development. In this study, we
+      characterized a piece of non-keratinized stratified squamous epithelium
+      similar to human esophageal epithelium in the upper digestive tract of
+      developing zebrafish. Under the microscope, this piece was detectable at
+      5dpf and became stratified at 7dpf. Expression of esophageal epithelial
+      marker genes (Krt5, P63, Sox2 and Pax9) was detected by
+      immunohistochemistry and in situ hybridization. Knockdown of P63, a gene
+      known to be critical for esophageal epithelium, disrupted the development
+      of this epithelium. With this model system, we found that Pax9 knockdown
+      resulted in loss or disorganization of the squamous epithelium, as well as
+      down-regulation of the differentiation markers Krt4 and Krt5. In summary,
+      we characterized a region of stratified squamous epithelium in the
+      zebrafish upper digestive tract which can be used for functional studies
+      of candidate genes involved in esophageal epithelial biology.
+    </description>
+    <description descriptionType='Other'>
+      Data were created with funding from U.S. Environmental Protection Agency
+      under grant(s) EPA STAR Fellowship 2011.
+    </description>
+    <description descriptionType='Other'>
+      Data were created with funding from CYBER-ShARE Center of Excellence
+      National Science Foundation (NSF) CREST grants under grant(s) HRD-0734825
+      and HRD-1242122.
+    </description>
+    <description descriptionType='Other'>
+      Data were created with funding from CI-Team Grant under grant(s)
+      OCI-1135525.
+    </description>
+  </descriptions>
+  <geoLocations>
+    <geoLocation>
+      <geoLocationBox>37.046 -119.211 37.075 -119.182</geoLocationBox>
+      <geoLocationPlace>Providence Creek (Lower, Upper and P301)</geoLocationPlace>
+    </geoLocation>
+    <geoLocation>
+      <geoLocationPoint>31.233 -67.302</geoLocationPoint>
+      <geoLocationBox>41.09 -71.032 42.893 -68.211</geoLocationBox>
+      <geoLocationPlace>Atlantic Ocean</geoLocationPlace>
+    </geoLocation>
+  </geoLocations>
+</resource>

data/spec/data/archive/mrt-dataone-manifest.txt

@@ -0,0 +1,32 @@
+#%dataonem_0.1
+#%profile | http://uc3.cdlib.org/registry/ingest/manifest/mrt-dataone-manifest
+#%prefix | dom: | http://uc3.cdlib.org/ontology/dataonem
+#%prefix | mrt: | http://uc3.cdlib.org/ontology/mom
+#%fields | dom:scienceMetadataFile | dom:scienceMetadataFormat | dom:scienceDataFile | mrt:mimeType
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | Laney_300394_Exempt_Determination_Letter.pdf | application/pdf
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | Laney_300394_Exempt_Determination_Letter.pdf | application/pdf
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | Laney_IRBProposal.docx | application/vnd.openxmlformats-officedocument.wordprocessingml.document
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | Laney_IRBProposal.docx | application/vnd.openxmlformats-officedocument.wordprocessingml.document
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | SensorSurvey_Printout.pdf | application/pdf
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | SensorSurvey_Printout.pdf | application/pdf
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | clean_survey_data_no_ids.csv | text/csv
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | clean_survey_data_no_ids.csv | text/csv
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | research_coords.csv | text/csv
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | research_coords.csv | text/csv
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q10/research_sites.R | text/plain
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q10/research_sites.R | text/plain
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q11-23/sensors_platforms.R | text/plain
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q11-23/sensors_platforms.R | text/plain
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q24/limitsToExpansion.R | text/plain
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q24/limitsToExpansion.R | text/plain
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q25-32/data_metadata_management.R | text/plain
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q25-32/data_metadata_management.R | text/plain
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q3-9/respondent_info.R | text/plain
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q3-9/respondent_info.R | text/plain
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q33-37/networking.R | text/plain
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q33-37/networking.R | text/plain
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey/Q38-42/publications.R | text/plain
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey/Q38-42/publications.R | text/plain
+mrt-datacite.xml | http://datacite.org/schema/kernel-3.1 | survey_data_prep.R | text/plain
+mrt-oaidc.xml | http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd | survey_data_prep.R | text/plain
+#%eof

data/spec/data/archive/mrt-oaidc.xml

@@ -0,0 +1,38 @@
+<qualifieddc xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xsi:noNamespaceSchemaLocation="http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd">
+    <dc:creator>Chen, Hao</dc:creator>
+    <dc:contributor>Chen, Xiaoxin</dc:contributor>
+    <dc:contributor>Wilson, James</dc:contributor>
+    <dc:title>A Zebrafish Model for Studies on Esophageal Epithelial Biology</dc:title>
+    <dc:publisher>DataONE</dc:publisher>
+    <dc:date>2016</dc:date>
+    <dc:subject>Zebrafish</dc:subject>
+    <dc:subject>Epithelium</dc:subject>
+    <dc:subject>Barrett's esophagus</dc:subject>
+    <dc:type>dataset</dc:type>
+    <dc:rights>CC0 1.0 Universal (CC0 1.0) Public Domain Dedication</dc:rights>
+    <dcterms:license xsi:type="dcterms:URI">https://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
+    <dc:description>Mammalian esophagus exhibits a remarkable change in epithelial structure
+        during the transition from embryo to adult. However, the molecular
+        mechanisms of esophageal epithelial development are not well understood.
+        Zebrafish (Danio rerio), a common model organism for vertebrate
+        development and gene function, has not previously been characterized as a
+        model system for esophageal epithelial development. In this study, we
+        characterized a piece of non-keratinized stratified squamous epithelium
+        similar to human esophageal epithelium in the upper digestive tract of
+        developing zebrafish. Under the microscope, this piece was detectable at
+        5dpf and became stratified at 7dpf. Expression of esophageal epithelial
+        marker genes (Krt5, P63, Sox2 and Pax9) was detected by
+        immunohistochemistry and in situ hybridization. Knockdown of P63, a gene
+        known to be critical for esophageal epithelium, disrupted the development
+        of this epithelium. With this model system, we found that Pax9 knockdown
+        resulted in loss or disorganization of the squamous epithelium, as well as
+        down-regulation of the differentiation markers Krt4 and Krt5. In summary,
+        we characterized a region of stratified squamous epithelium in the
+        zebrafish upper digestive tract which can be used for functional studies
+        of candidate genes involved in esophageal epithelial biology.</dc:description>
+    <dc:description>Data were created with funding from U.S. Environmental Protection Agency under grant(s) EPA STAR Fellowship 2011</dc:description>
+    <dc:description>Data were created with funding from CYBER-ShARE Center of Excellence National Science Foundation (NSF) CREST grants under grant(s) HRD-0734825 and HRD-1242122</dc:description>
+    <dc:description>Data were created with funding from CI-Team Grant under grant(s) OCI-1135525</dc:description>
+    <dcterms:isReferencedBy>DOI: 10.1371/journal.pone.0143878</dcterms:isReferencedBy>
+    <dcterms:relation>URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143878</dcterms:relation>
+</qualifieddc>

data/spec/data/archive/stash-wrapper.xml

@@ -0,0 +1,213 @@
+<?xml version='1.0'?>
+<st:stash_wrapper xsi:schemaLocation='http://dash.cdlib.org/stash_wrapper/ http://dash.cdlib.org/stash_wrapper/stash_wrapper.xsd' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xmlns:st='http://dash.cdlib.org/stash_wrapper/'>
+  <st:identifier type='DOI'>10.15146/R3RG6G</st:identifier>
+  <st:stash_administrative>
+    <st:version>
+      <st:version_number>1</st:version_number>
+      <st:date>2015-08-17Z</st:date>
+    </st:version>
+    <st:license>
+      <st:name>CC0 1.0 Universal (CC0 1.0) Public Domain Dedication</st:name>
+      <st:uri>https://creativecommons.org/publicdomain/zero/1.0/</st:uri>
+    </st:license>
+    <st:embargo>
+      <st:type>none</st:type>
+      <st:period>none</st:period>
+      <st:start>2015-12-02Z</st:start>
+      <st:end>2015-12-02Z</st:end>
+    </st:embargo>
+    <st:inventory num_files='13'>
+      <st:file>
+        <st:pathname>survey/Q11-23/sensors_platforms.R</st:pathname>
+        <st:size unit='B'>26414</st:size>
+        <st:mime_type>text/plain</st:mime_type>
+      </st:file>
+      <st:file>
+        <st:pathname>survey/Q25-32/data_metadata_management.R</st:pathname>
+        <st:size unit='B'>9794</st:size>
+        <st:mime_type>text/plain</st:mime_type>
+      </st:file>
+      <st:file>
+        <st:pathname>survey/Q10/research_sites.R</st:pathname>
+        <st:size unit='B'>1180</st:size>
+        <st:mime_type>text/plain</st:mime_type>
+      </st:file>
+      <st:file>
+        <st:pathname>clean_survey_data_no_ids.csv</st:pathname>
+        <st:size unit='B'>320890</st:size>
+        <st:mime_type>text/csv</st:mime_type>
+      </st:file>
+      <st:file>
+        <st:pathname>survey/Q3-9/respondent_info.R</st:pathname>
+        <st:size unit='B'>13784</st:size>
+        <st:mime_type>text/plain</st:mime_type>
+      </st:file>
+      <st:file>
+        <st:pathname>Laney_IRBProposal.docx</st:pathname>
+        <st:size unit='B'>1097848</st:size>
+        <st:mime_type>application/vnd.openxmlformats-officedocument.wordprocessingml.document</st:mime_type>
+      </st:file>
+      <st:file>
+        <st:pathname>survey_data_prep.R</st:pathname>
+        <st:size unit='B'>4359</st:size>
+        <st:mime_type>text/plain</st:mime_type>
+      </st:file>
+      <st:file>
+        <st:pathname>research_coords.csv</st:pathname>
+        <st:size unit='B'>5827</st:size>
+        <st:mime_type>text/csv</st:mime_type>
+      </st:file>
+      <st:file>
+        <st:pathname>Laney_300394_Exempt_Determination_Letter.pdf</st:pathname>
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+      <identifier identifierType='DOI'>10.15146/R3RG6G</identifier>
+      <creators>
+        <creator>
+          <creatorName>Chen, Hao</creatorName>
+          <nameIdentifier nameIdentifierScheme='ORCID' schemeURI='http://orcid.org/'>0123-4567-8910-1112</nameIdentifier>
+          <affiliation>North Carolina Central University</affiliation>
+        </creator>
+      </creators>
+      <titles>
+        <title>A Zebrafish Model for Studies on Esophageal Epithelial Biology</title>
+        <title titleType='Subtitle'>
+          Characterizing a region of stratified squamous epithelium in the
+          zebrafish upper digestive tract
+        </title>
+      </titles>
+      <publisher>DataONE</publisher>
+      <publicationYear>2016</publicationYear>
+      <subjects>
+        <subject>Zebrafish</subject>
+        <subject>Epithelium</subject>
+        <subject>Barrett&apos;s esophagus</subject>
+      </subjects>
+      <fundingReferences>
+        <fundingReference>
+          <funderName>U.S. Environmental Protection Agency</funderName>
+          <awardNumber>EPA STAR Fellowship 2011</awardNumber>
+        </fundingReference>
+        <fundingReference>
+          <funderName>CYBER-ShARE Center of Excellence National Science Foundation (NSF) CREST grants</funderName>
+          <awardNumber>HRD-0734825 and HRD-1242122</awardNumber>
+        </fundingReference>
+        <fundingReference>
+          <funderName>CI-Team Grant</funderName>
+          <awardNumber>OCI-1135525</awardNumber>
+        </fundingReference>
+      </fundingReferences>
+      <contributors>
+        <contributor contributorType='ProjectMember'>
+          <contributorName>Chen, Xiaoxin</contributorName>
+          <nameIdentifier nameIdentifierScheme='ORCID' schemeURI='http://orcid.org/'>1234-5678-9101-1121</nameIdentifier>
+          <affiliation>University of North Carolina at Chapel Hill</affiliation>
+        </contributor>
+        <contributor contributorType='DataManager'>
+          <contributorName>Wilson, James</contributorName>
+        </contributor>
+      </contributors>
+      <dates>
+        <date dateType='Available'>2015-12-02</date>
+        <date dateType='Collected'>2009/2011</date>
+      </dates>
+      <language>en</language>
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+        <relatedIdentifier relationType='IsCitedBy' relatedIdentifierType='DOI'>10.1371/journal.pone.0143878 </relatedIdentifier>
+        <relatedIdentifier relationType='IsDocumentedBy' relatedIdentifierType='URL'> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143878 </relatedIdentifier>
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+      <rightsList>
+        <rights rightsURI='https://creativecommons.org/publicdomain/zero/1.0/'>CC0 1.0 Universal (CC0 1.0) Public Domain Dedication</rights>
+      </rightsList>
+      <descriptions>
+        <description descriptionType='Abstract'>
+          Mammalian esophagus exhibits a remarkable change in epithelial
+          structure during the transition from embryo to adult. However, the
+          molecular mechanisms of esophageal epithelial development are not well
+          understood. Zebrafish (Danio rerio), a common model organism for
+          vertebrate development and gene function, has not previously been
+          characterized as a model system for esophageal epithelial development.
+          In this study, we characterized a piece of non-keratinized stratified
+          squamous epithelium similar to human esophageal epithelium in the
+          upper digestive tract of developing zebrafish. Under the microscope,
+          this piece was detectable at 5dpf and became stratified at 7dpf.
+          Expression of esophageal epithelial marker genes (Krt5, P63, Sox2 and
+          Pax9) was detected by immunohistochemistry and in situ hybridization.
+          Knockdown of P63, a gene known to be critical for esophageal
+          epithelium, disrupted the development of this epithelium. With this
+          model system, we found that Pax9 knockdown resulted in loss or
+          disorganization of the squamous epithelium, as well as down-regulation
+          of the differentiation markers Krt4 and Krt5. In summary, we
+          characterized a region of stratified squamous epithelium in the
+          zebrafish upper digestive tract which can be used for functional
+          studies of candidate genes involved in esophageal epithelial biology.
+        </description>
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