commonmeta-py 0.106__py3-none-any.whl → 0.108__py3-none-any.whl

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Files changed (48) hide show
  1. commonmeta/__init__.py +12 -3
  2. commonmeta/api_utils.py +3 -2
  3. commonmeta/base_utils.py +186 -3
  4. commonmeta/cli.py +114 -34
  5. commonmeta/constants.py +20 -0
  6. commonmeta/file_utils.py +112 -0
  7. commonmeta/metadata.py +102 -42
  8. commonmeta/readers/codemeta_reader.py +1 -1
  9. commonmeta/readers/crossref_reader.py +23 -10
  10. commonmeta/readers/crossref_xml_reader.py +1 -1
  11. commonmeta/readers/datacite_reader.py +6 -4
  12. commonmeta/readers/{json_feed_reader.py → jsonfeed_reader.py} +12 -12
  13. commonmeta/resources/crossref/common5.4.0.xsd +1264 -0
  14. commonmeta/resources/crossref/{crossref5.3.1.xsd → crossref5.4.0.xsd} +286 -88
  15. commonmeta/resources/crossref/doi_resources5.4.0.xsd +117 -0
  16. commonmeta/resources/crossref/fundingdata5.4.0.xsd +59 -0
  17. commonmeta/resources/crossref/fundref.xsd +29 -19
  18. commonmeta/resources/crossref/languages5.4.0.xsd +8119 -0
  19. commonmeta/resources/crossref/mediatypes5.4.0.xsd +2207 -0
  20. commonmeta/resources/crossref/module-ali.xsd +14 -6
  21. commonmeta/resources/crossref/standard-modules/mathml3/mathml3-common.xsd +101 -0
  22. commonmeta/resources/crossref/standard-modules/mathml3/mathml3-content.xsd +683 -0
  23. commonmeta/resources/crossref/standard-modules/mathml3/mathml3-presentation.xsd +2092 -0
  24. commonmeta/resources/crossref/standard-modules/mathml3/mathml3-strict-content.xsd +186 -0
  25. commonmeta/resources/crossref/standard-modules/mathml3/mathml3.xsd +9 -0
  26. commonmeta/resources/crossref/standard-modules/mathml3/module-ali.xsd +47 -0
  27. commonmeta/resources/crossref/standard-modules/module-ali.xsd +47 -0
  28. commonmeta/resources/crossref/standard-modules/xlink.xsd +100 -0
  29. commonmeta/resources/crossref/standard-modules/xml.xsd +287 -0
  30. commonmeta/resources/crossref/xml.xsd +287 -0
  31. commonmeta/schema_utils.py +25 -0
  32. commonmeta/utils.py +90 -15
  33. commonmeta/writers/bibtex_writer.py +5 -5
  34. commonmeta/writers/citation_writer.py +10 -5
  35. commonmeta/writers/commonmeta_writer.py +5 -17
  36. commonmeta/writers/crossref_xml_writer.py +1032 -4
  37. commonmeta/writers/csl_writer.py +6 -6
  38. commonmeta/writers/datacite_writer.py +11 -6
  39. commonmeta/writers/inveniordm_writer.py +286 -10
  40. commonmeta/writers/ris_writer.py +3 -3
  41. commonmeta/writers/schema_org_writer.py +10 -5
  42. {commonmeta_py-0.106.dist-info → commonmeta_py-0.108.dist-info}/METADATA +5 -2
  43. {commonmeta_py-0.106.dist-info → commonmeta_py-0.108.dist-info}/RECORD +46 -32
  44. commonmeta/crossref_utils.py +0 -583
  45. commonmeta/resources/crossref/common5.3.1.xsd +0 -1538
  46. {commonmeta_py-0.106.dist-info → commonmeta_py-0.108.dist-info}/WHEEL +0 -0
  47. {commonmeta_py-0.106.dist-info → commonmeta_py-0.108.dist-info}/entry_points.txt +0 -0
  48. {commonmeta_py-0.106.dist-info → commonmeta_py-0.108.dist-info}/licenses/LICENSE +0 -0
commonmeta/resources/crossref/doi_resources5.4.0.xsd ADDED
@@ -0,0 +1,117 @@
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
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+ xmlns="http://www.crossref.org/doi_resources_schema/5.4.0"
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+ targetNamespace="http://www.crossref.org/doi_resources_schema/5.4.0"
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+ xmlns:fr5.4.0="http://www.crossref.org/fundingdata5.4.0.xsd"
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+ xmlns:fr="http://www.crossref.org/fundref.xsd"
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+ xmlns:ai="http://www.crossref.org/AccessIndicators.xsd"
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+ xmlns:rel="http://www.crossref.org/relations.xsd"
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+ xmlns:ct="http://www.crossref.org/clinicaltrials.xsd">
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+
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+ <!-- =============================================================
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+ This is version 5.4.0 of the Crossref resource schema. It supports appending or updating select pieces of metadata to an existing DOI metadata record. Supported metadata includes:
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+
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+ - reference lists
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+ - Crossmark metadata
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+ - clinical trial data
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+ - funding data
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+ - multiple resolution URLs
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+ - relationships
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+ - license metadata
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+
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+ All changes are noted in the release notes for the schema repository in GitLab: https://gitlab.com/crossref/schema/-/releases
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+
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+ ============================================================= -->
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+ <xsd:include schemaLocation="common5.4.0.xsd"/>
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+ <xsd:import namespace="http://www.crossref.org/fundingdata5.4.0.xsd" schemaLocation="fundingdata5.4.0.xsd"/>
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+ <xsd:import namespace="http://www.crossref.org/fundref.xsd" schemaLocation="fundref.xsd"/>
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+ <xsd:import namespace="http://www.crossref.org/AccessIndicators.xsd" schemaLocation="AccessIndicators.xsd"/>
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+ <xsd:import namespace="http://www.crossref.org/relations.xsd" schemaLocation="relations.xsd"/>
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+ <xsd:import namespace="http://www.crossref.org/clinicaltrials.xsd" schemaLocation="clinicaltrials.xsd"/>
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+ <xsd:element name="doi_batch">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="head"/>
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+ <xsd:element ref="body"/>
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+ </xsd:sequence>
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+ <xsd:attribute name="version" type="xsd:string" fixed="5.4.0"/>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="head">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="doi_batch_id"/>
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+ <xsd:element ref="depositor"/>
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+ </xsd:sequence>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="body">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="doi_citations" minOccurs="0" maxOccurs="unbounded"/>
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+ <xsd:element ref="doi_resources" minOccurs="0" maxOccurs="unbounded"/>
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+ <xsd:element ref="crossmark_data" minOccurs="0" maxOccurs="unbounded"/>
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+ <xsd:element ref="fundref_data" minOccurs="0" maxOccurs="unbounded"/>
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+ <xsd:element ref="lic_ref_data" minOccurs="0" maxOccurs="unbounded"/>
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+ <xsd:element ref="doi_relations" minOccurs="0" maxOccurs="unbounded"/>
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+ <xsd:element ref="clinicaltrial_data" minOccurs="0" maxOccurs="unbounded"/>
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+ </xsd:sequence>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="doi_citations">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="doi"/>
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+ <xsd:element ref="citation_list"/>
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+ </xsd:sequence>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="doi_resources">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="doi"/>
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+ <xsd:element ref="collection"/>
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+ </xsd:sequence>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="crossmark_data">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="doi"/>
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+ <xsd:element ref="crossmark"/>
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+ </xsd:sequence>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="fundref_data">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="doi"/>
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+ <xsd:element ref="fr:program"/>
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+ </xsd:sequence>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="lic_ref_data">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="doi"/>
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+ <xsd:element ref="ai:program"/>
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+ </xsd:sequence>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="doi_relations">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="doi"/>
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+ <xsd:element ref="rel:program"/>
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+ </xsd:sequence>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="clinicaltrial_data">
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="doi"/>
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+ <xsd:element ref="ct:program"/>
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+ </xsd:sequence>
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+ </xsd:complexType>
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+ </xsd:element>
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+ </xsd:schema>
commonmeta/resources/crossref/fundingdata5.4.0.xsd ADDED
@@ -0,0 +1,59 @@
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
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+ targetNamespace="http://www.crossref.org/fundingdata5.4.0.xsd"
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+ xmlns="http://www.crossref.org/fundingdata5.4.0.xsd">
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+
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+ <!--=========Change History===========
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+ 10/9/24 (PDF) added ror identifier
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+ 5/2/13 (PDF) changed funding_identifier to award_number
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+ 04/10/24 (PDF) added ror and grant_doi
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+ -->
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+
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+ <xsd:element name="program">
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+ <xsd:annotation>
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+ <xsd:documentation>Information about registering funding data is available in our documentation: https://www.crossref.org/documentation/funder-registry/funding-data-deposits/</xsd:documentation>
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+ </xsd:annotation>
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+ <xsd:complexType>
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+ <xsd:sequence>
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+ <xsd:element ref="assertion" minOccurs="0" maxOccurs="unbounded"/>
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+ </xsd:sequence>
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+ <xsd:attribute name="name" type="xsd:string" fixed="fundref"/>
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+ </xsd:complexType>
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+ </xsd:element>
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+ <xsd:element name="assertion">
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+ <xsd:annotation>
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+ <xsd:documentation>Funding data attributes included in assertion are:
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+ * fundgroup: used to group funding info for items with multiple funding sources. Required for items with multiple award_number assertions, optional for items with a single award_number
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+ * funder_identifier: funding agency identifier, must be nested within the funder_name assertion
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+ * ror: ROR ID of a funder
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+ * funder_name: name of the funding agency (required)
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+ * award_number: grant number or other fund identifier
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+ </xsd:documentation>
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+ </xsd:annotation>
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+ <xsd:complexType mixed="true">
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+ <xsd:sequence>
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+ <xsd:element ref="assertion" minOccurs="0" maxOccurs="unbounded"/>
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+ </xsd:sequence>
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+ <xsd:attribute name="provider" default="publisher">
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+ <xsd:simpleType>
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+ <xsd:restriction base="xsd:NMTOKEN">
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+ <xsd:enumeration value="publisher"/>
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+ <xsd:enumeration value="crossref"/>
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+ </xsd:restriction>
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+ </xsd:simpleType>
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+ </xsd:attribute>
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+ <xsd:attribute name="name" use="required">
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+ <xsd:simpleType>
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+ <xsd:restriction base="xsd:NMTOKEN">
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+ <xsd:enumeration value="fundgroup"/>
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+ <xsd:enumeration value="funder_identifier"/>
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+ <xsd:enumeration value="ror"/>
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+ <xsd:enumeration value="funder_name"/>
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+ <xsd:enumeration value="award_number"/>
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+ <!--<xsd:enumeration value="grant_doi"/> -->
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+ </xsd:restriction>
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+ </xsd:simpleType>
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+ </xsd:attribute>
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+ </xsd:complexType>
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+ </xsd:element>
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+ </xsd:schema>
commonmeta/resources/crossref/fundref.xsd CHANGED
@@ -1,14 +1,17 @@
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- <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="http://www.crossref.org/fundref.xsd" targetNamespace="http://www.crossref.org/fundref.xsd"><!-- =========Change History===========
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
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+ targetNamespace="http://www.crossref.org/fundref.xsd"
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+ xmlns="http://www.crossref.org/fundref.xsd">
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+
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+ <!--=========Change History===========
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+ 10/9/24 (PDF) added ror identifier
2
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  5/2/13 (PDF) changed funding_identifier to award_number
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- -->
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+ 04/10/24 (PDF) added ror and grant_doi
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+ -->
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+
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  <xsd:element name="program">
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  <xsd:annotation>
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- <xsd:documentation> FundRef documentation and examples: http://help.crossref.org/#fundref As part of CrossMark metadata, a deposit may contain what is called FundRef info. This details the funding behind a published article. The schema is a sequence of nested <assertion> tags. If a DOI is not participating in CrossMark, FundRef data may be deposited as part of the <journal_article> metadata. Note: Some rules will be enforced by the deposit logic (e.g. not the schema). FundRef data includes one or more award numbers (award_number), each of which may have one or more funders (funder_name). Each funder may have one or more optional identifiers (funder_identifier). A FundRef deposit begins with a <fr:program> tag within the <crossmark> structure (where fr is the namespace for the FundRef program). The <program> element is an implicit funder_group and will typically contain: A) one or more funder_name assertions and an award_number assertion. or B) one or more funder_group assertions where each funder_group should contain one or more funder_name assertions and at least one award_number assertion. Multiple &apos;award_number&apos;s may be included in a single program or fundgroup. Deposits without an award_number will be accepted, but award_number should be provided whenever possible. Items with several award numbers associated with a single funding organization should be grouped together by enclosing the &quot;funder_name&quot;, &quot;funder_identifier&quot;, and award_number(s) within a &quot;fundgroup&quot; assertion. </program>
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- </crossmark>
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- </fr:program>
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- </journal_article>
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- </assertion>
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- </xsd:documentation>
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+ <xsd:documentation>Information about registering funding data is available in our documentation: https://www.crossref.org/documentation/funder-registry/funding-data-deposits/</xsd:documentation>
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  </xsd:annotation>
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  <xsd:complexType>
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  <xsd:sequence>
@@ -19,7 +22,13 @@
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  </xsd:element>
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  <xsd:element name="assertion">
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  <xsd:annotation>
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- <xsd:documentation>FundRef attributes included in assertion are: fundgroup: used to group funding info for items with multiple funding sources. Required for items with multiple award_number assertions, optional for items with a single award_number funder_identifier: funding agency identifier, must be nested within the funder_name assertion funder_name: name of the funding agency (required) award_number: grant number or other fund identifier</xsd:documentation>
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+ <xsd:documentation>Funding data attributes included in assertion are:
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+ * fundgroup: used to group funding info for items with multiple funding sources. Required for items with multiple award_number assertions, optional for items with a single award_number
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+ * funder_identifier: funding agency identifier, must be nested within the funder_name assertion
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+ * ror: ROR ID of a funder
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+ * funder_name: name of the funding agency (required)
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+ * award_number: grant number or other fund identifier
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+ </xsd:documentation>
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  </xsd:annotation>
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  <xsd:complexType mixed="true">
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  <xsd:sequence>
@@ -27,23 +36,24 @@
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  </xsd:sequence>
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  <xsd:attribute name="provider" default="publisher">
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  <xsd:simpleType>
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- <xsd:restriction base="xsd:NMTOKEN">
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- <xsd:enumeration value="publisher"/>
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- <xsd:enumeration value="crossref"/>
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- </xsd:restriction>
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+ <xsd:restriction base="xsd:NMTOKEN">
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+ <xsd:enumeration value="publisher"/>
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+ <xsd:enumeration value="crossref"/>
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+ </xsd:restriction>
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  </xsd:simpleType>
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  </xsd:attribute>
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  <xsd:attribute name="name" use="required">
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  <xsd:simpleType>
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  <xsd:restriction base="xsd:NMTOKEN">
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- <xsd:enumeration value="fundgroup"/><!-- fundgroup: used to group funding info for items with multiple funding sources.
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- Required for items with multiple award_number assertions, optional for items with a single award_number -->
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- <xsd:enumeration value="funder_identifier"/><!-- funder_identifier: funding agency identifier, must be nested within the funder_name assertion -->
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- <xsd:enumeration value="funder_name"/><!-- funder_name: name of the funding agency -->
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- <xsd:enumeration value="award_number"/><!-- -award_number: grant number or other fund identifier -->
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+ <xsd:enumeration value="fundgroup"/>
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+ <xsd:enumeration value="funder_identifier"/>
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+ <xsd:enumeration value="ror"/>
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+ <xsd:enumeration value="funder_name"/>
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+ <xsd:enumeration value="award_number"/>
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+ <!--<xsd:enumeration value="grant_doi"/> -->
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  </xsd:restriction>
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  </xsd:simpleType>
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  </xsd:attribute>
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  </xsd:complexType>
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  </xsd:element>
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- </xsd:schema>
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+ </xsd:schema>