From a8e6247609d0b78785d6253fed3343678fa3dd14 Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Sun, 10 Mar 2024 20:54:42 +0100 Subject: [PATCH 1/3] Enable `qualified_attribution` for `Distribution`s This made it necessary to move the inline definition of agents. This is now down at the `DatasetVersionObject` level via `was_attributed_to`. This is essentially a list of all relevant agents without any further qualification re the nature of the attribution. This is then done via `qualified_attribution` of whatever object via its `meta_code` identifier. --- .../DatasetVersionObject-affiliation.json | 27 +++--- .../DatasetVersionObject-affiliation.yaml | 22 ++--- .../DatasetVersionObject-penguins.json | 83 +++++++++++-------- .../DatasetVersionObject-penguins.yaml | 64 +++++++------- ...setVersionObject-rocrate-attributions.json | 43 ++++++++++ ...setVersionObject-rocrate-attributions.yaml | 29 +++++++ .../DatasetVersionObject-rocrate-minimal.json | 25 ++++++ .../DatasetVersionObject-rocrate-minimal.yaml | 23 +++++ .../DatasetVersionObject-roleattribution.json | 25 +++--- .../DatasetVersionObject-roleattribution.yaml | 22 ++--- src/linkml/ontology/datasets.yaml | 2 + src/linkml/schemas/dataset-version.yaml | 14 +++- 12 files changed, 269 insertions(+), 110 deletions(-) create mode 100644 src/examples/dataset-version/DatasetVersionObject-rocrate-attributions.json create mode 100644 src/examples/dataset-version/DatasetVersionObject-rocrate-attributions.yaml create mode 100644 src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.json create mode 100644 src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.yaml diff --git a/src/examples/dataset-version/DatasetVersionObject-affiliation.json b/src/examples/dataset-version/DatasetVersionObject-affiliation.json index fbe6795..8106485 100644 --- a/src/examples/dataset-version/DatasetVersionObject-affiliation.json +++ b/src/examples/dataset-version/DatasetVersionObject-affiliation.json @@ -1,22 +1,27 @@ { + "was_attributed_to": [ + { + "meta_code": "doe", + "meta_type": "dlco:ResearchContributorObject", + "name": "Jane Doe", + "email": "doe@example.com", + "affiliation": "DFG" + }, + { + "meta_code": "DFG", + "meta_type": "dlco:OrganizationObject", + "name": "Deutsche Forschungsgemeinschaft" + } + ], "qualified_attribution": [ { - "agent": { - "meta_type": "dlco:ResearchContributorObject", - "name": "Jane Doe", - "email": "doe@example.com", - "affiliation": "DFG" - }, + "agent": "doe", "had_role": [ "marcrel:aut" ] }, { - "agent": { - "meta_type": "dlco:OrganizationObject", - "name": "Deutsche Forschungsgemeinschaft", - "meta_code": "DFG" - }, + "agent": "DFG", "had_role": [ "marcrel:sht" ] diff --git a/src/examples/dataset-version/DatasetVersionObject-affiliation.yaml b/src/examples/dataset-version/DatasetVersionObject-affiliation.yaml index 503b911..533d76d 100644 --- a/src/examples/dataset-version/DatasetVersionObject-affiliation.yaml +++ b/src/examples/dataset-version/DatasetVersionObject-affiliation.yaml @@ -1,18 +1,20 @@ description: >- Some key facts about the data +was_attributed_to: + - meta_type: dlco:ResearchContributorObject + meta_code: doe + name: Jane Doe + email: doe@example.com + # reference organization by meta_code + affiliation: DFG + - meta_type: dlco:OrganizationObject + meta_code: DFG + name: Deutsche Forschungsgemeinschaft qualified_attribution: - - agent: - meta_type: dlco:ResearchContributorObject - name: Jane Doe - email: doe@example.com - # reference organization by meta_code - affiliation: DFG + - agent: doe had_role: - marcrel:aut - - agent: - meta_type: dlco:OrganizationObject - meta_code: DFG - name: Deutsche Forschungsgemeinschaft + - agent: DFG had_role: # Supporting host - marcrel:sht diff --git a/src/examples/dataset-version/DatasetVersionObject-penguins.json b/src/examples/dataset-version/DatasetVersionObject-penguins.json index d91e240..850c3a7 100644 --- a/src/examples/dataset-version/DatasetVersionObject-penguins.json +++ b/src/examples/dataset-version/DatasetVersionObject-penguins.json @@ -63,71 +63,82 @@ "identifier": [ "https://doi.org/10.5281/zenodo.3960218" ], + "was_attributed_to": [ + { + "meta_code": "ahorst", + "meta_type": "dlco:ResearchContributorObject", + "name": "Allison Horst", + "email": "ahorst@example.com", + "affiliation": "UCSB", + "orcid": "0000-0002-6047-5564" + }, + { + "meta_code": "ahill", + "meta_type": "dlco:ResearchContributorObject", + "name": "Allison Hill", + "email": "ahill@example.com", + "affiliation": "Rstudio", + "orcid": "0000-0002-8082-1890" + }, + { + "meta_code": "kgorman", + "meta_type": "dlco:ResearchContributorObject", + "name": "Kirsten Gorman", + "email": "kgorman@example.com", + "affiliation": "UAF", + "orcid": "0000-0002-0258-9264" + }, + { + "meta_code": "UCSB", + "meta_type": "dlco:OrganizationObject", + "name": "UC Santa Barbara: Santa Barbara, CA, US" + }, + { + "meta_code": "RStudio", + "meta_type": "dlco:OrganizationObject", + "name": "RStudio: Boston, MA, US" + }, + { + "meta_code": "UAF", + "meta_type": "dlco:OrganizationObject", + "name": "University of Alaska Fairbanks: Fairbanks, AK, US" + } + ], "qualified_attribution": [ { - "agent": { - "meta_type": "dlco:ResearchContributorObject", - "name": "Allison Horst", - "email": "ahorst@example.com", - "affiliation": "UCSB", - "orcid": "0000-0002-6047-5564" - }, + "agent": "ahorst", "had_role": [ "marcrel:aut", "dpv:DataController" ] }, { - "agent": { - "meta_type": "dlco:ResearchContributorObject", - "name": "Allison Hill", - "email": "ahill@example.com", - "affiliation": "Rstudio", - "orcid": "0000-0002-8082-1890" - }, + "agent": "ahill", "had_role": [ "marcrel:aut" ] }, { - "agent": { - "meta_type": "dlco:ResearchContributorObject", - "name": "Kirsten Gorman", - "email": "kgorman@example.com", - "affiliation": "UAF", - "orcid": "0000-0002-0258-9264" - }, + "agent": "kgorman", "had_role": [ "marcrel:aut", "marcrel:cre" ] }, { - "agent": { - "meta_type": "dlco:OrganizationObject", - "name": "UC Santa Barbara: Santa Barbara, CA, US", - "meta_code": "UCSB" - }, + "agent": "UCSB", "had_role": [ "marcrel:sht" ] }, { - "agent": { - "meta_type": "dlco:OrganizationObject", - "name": "RStudio: Boston, MA, US", - "meta_code": "RStudio" - }, + "agent": "RStudio", "had_role": [ "marcrel:sht" ] }, { - "agent": { - "meta_type": "dlco:OrganizationObject", - "name": "University of Alaska Fairbanks: Fairbanks, AK, US", - "meta_code": "UAF" - }, + "agent": "UAF", "had_role": [ "marcrel:sht" ] diff --git a/src/examples/dataset-version/DatasetVersionObject-penguins.yaml b/src/examples/dataset-version/DatasetVersionObject-penguins.yaml index cda3f23..b5c94b0 100644 --- a/src/examples/dataset-version/DatasetVersionObject-penguins.yaml +++ b/src/examples/dataset-version/DatasetVersionObject-penguins.yaml @@ -20,50 +20,54 @@ keyword: - isotopes identifier: - https://doi.org/10.5281/zenodo.3960218 +was_attributed_to: + - meta_type: dlco:ResearchContributorObject + meta_code: ahorst + name: Allison Horst + email: ahorst@example.com + orcid: 0000-0002-6047-5564 + affiliation: UCSB + - meta_type: dlco:ResearchContributorObject + meta_code: ahill + name: Allison Hill + email: ahill@example.com + orcid: 0000-0002-8082-1890 + affiliation: Rstudio + - meta_type: dlco:ResearchContributorObject + meta_code: kgorman + name: Kirsten Gorman + email: kgorman@example.com + orcid: 0000-0002-0258-9264 + affiliation: UAF + - meta_type: dlco:OrganizationObject + meta_code: UCSB + name: 'UC Santa Barbara: Santa Barbara, CA, US' + - meta_type: dlco:OrganizationObject + meta_code: RStudio + name: 'RStudio: Boston, MA, US' + - meta_type: dlco:OrganizationObject + meta_code: UAF + name: 'University of Alaska Fairbanks: Fairbanks, AK, US' qualified_attribution: - - agent: - meta_type: dlco:ResearchContributorObject - name: Allison Horst - email: ahorst@example.com - orcid: 0000-0002-6047-5564 - affiliation: UCSB + - agent: ahorst had_role: - marcrel:aut - dpv:DataController - - agent: - meta_type: dlco:ResearchContributorObject - name: Allison Hill - email: ahill@example.com - orcid: 0000-0002-8082-1890 - affiliation: Rstudio + - agent: ahill had_role: - marcrel:aut - - agent: - meta_type: dlco:ResearchContributorObject - name: Kirsten Gorman - email: kgorman@example.com - orcid: 0000-0002-0258-9264 - affiliation: UAF + - agent: kgorman had_role: - marcrel:aut - marcrel:cre - - agent: - meta_type: dlco:OrganizationObject - meta_code: UCSB - name: 'UC Santa Barbara: Santa Barbara, CA, US' + - agent: UCSB had_role: # Supporting host - marcrel:sht - - agent: - meta_type: dlco:OrganizationObject - meta_code: RStudio - name: 'RStudio: Boston, MA, US' + - agent: RStudio had_role: - marcrel:sht - - agent: - meta_type: dlco:OrganizationObject - meta_code: UAF - name: 'University of Alaska Fairbanks: Fairbanks, AK, US' + - agent: UAF had_role: - marcrel:sht qualified_relation: diff --git a/src/examples/dataset-version/DatasetVersionObject-rocrate-attributions.json b/src/examples/dataset-version/DatasetVersionObject-rocrate-attributions.json new file mode 100644 index 0000000..90a97cd --- /dev/null +++ b/src/examples/dataset-version/DatasetVersionObject-rocrate-attributions.json @@ -0,0 +1,43 @@ +{ + "distribution": { + "meta_type": "dlco:FileContainerObject", + "meta_code": "./", + "has_part": [ + { + "meta_type": "dlco:DigitalDocumentObject", + "meta_code": "data1.txt", + "qualified_attribution": [ + { + "agent": "alice", + "had_role": [ + "marcrel:aut" + ] + } + ] + }, + { + "meta_type": "dlco:DigitalDocumentObject", + "meta_code": "data2.txt" + } + ], + "qualified_part": [ + { + "relation": "data1.txt", + "name": "data1.txt" + }, + { + "relation": "data2.txt", + "name": "data2.txt" + } + ] + }, + "was_attributed_to": [ + { + "meta_code": "alice", + "meta_type": "dlco:PersonObject", + "name": "Alice" + } + ], + "title": "Example RO-Crate", + "@type": "DatasetVersionObject" +} diff --git a/src/examples/dataset-version/DatasetVersionObject-rocrate-attributions.yaml b/src/examples/dataset-version/DatasetVersionObject-rocrate-attributions.yaml new file mode 100644 index 0000000..2992629 --- /dev/null +++ b/src/examples/dataset-version/DatasetVersionObject-rocrate-attributions.yaml @@ -0,0 +1,29 @@ +# +# This example is the RO-Crate example from +# https://stain.github.io/ro-crate/1.1/appendix/jsonld.html +# +title: Example RO-Crate +was_attributed_to: + - meta_type: dlco:PersonObject + meta_code: alice + name: Alice + # "description": "One of hopefully many Contextual Entities" +distribution: + meta_type: dlco:FileContainerObject + meta_code: ./ + #description: >- + #The RO-Crate Root Data Entity + has_part: + - meta_type: dlco:DigitalDocumentObject + meta_code: data1.txt + qualified_attribution: + - agent: alice + had_role: + - marcrel:aut + - meta_type: dlco:DigitalDocumentObject + meta_code: data2.txt + qualified_part: + - name: data1.txt + relation: data1.txt + - name: data2.txt + relation: data2.txt diff --git a/src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.json b/src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.json new file mode 100644 index 0000000..4e52d3a --- /dev/null +++ b/src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.json @@ -0,0 +1,25 @@ +{ + "distribution": { + "meta_type": "dlco:FileContainerObject", + "meta_code": "./", + "has_part": [ + { + "meta_type": "dlco:DigitalDocumentObject", + "meta_code": "ro-crate-metadata.json" + } + ], + "license": "https://creativecommons.org/licenses/by-nc-sa/3.0/au/", + "qualified_part": [ + { + "relation": "ro-crate-metadata.json", + "name": "ro-crate-metadata.json" + } + ] + }, + "identifier": [ + "https://doi.org/10.4225/59/59672c09f4a4b" + ], + "description": "Palliative care planning for nursing home residents with advanced dementia ...", + "title": "\"Data files associated with the manuscript:Effects of facilitated family case conferencing for ...\"", + "@type": "DatasetVersionObject" +} diff --git a/src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.yaml b/src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.yaml new file mode 100644 index 0000000..84a4f03 --- /dev/null +++ b/src/examples/dataset-version/DatasetVersionObject-rocrate-minimal.yaml @@ -0,0 +1,23 @@ +# +# This example is the RO-Crate minimal example from +# https://stain.github.io/ro-crate/1.1/root-data-entity.html#minimal-example-of-ro-crate +# +title: >- + "Data files associated with the manuscript:Effects of facilitated family case conferencing for ..." +description: >- + Palliative care planning for nursing home residents with advanced dementia ... +identifier: + - https://doi.org/10.4225/59/59672c09f4a4b +# "datePublished": "2017", +distribution: + meta_type: dlco:FileContainerObject + meta_code: ./ + license: https://creativecommons.org/licenses/by-nc-sa/3.0/au/ + has_part: + - meta_type: dlco:DigitalDocumentObject + meta_code: ro-crate-metadata.json + # "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"}, + # "about": {"@id": "./"} + qualified_part: + - name: ro-crate-metadata.json + relation: ro-crate-metadata.json diff --git a/src/examples/dataset-version/DatasetVersionObject-roleattribution.json b/src/examples/dataset-version/DatasetVersionObject-roleattribution.json index c02c0b4..eeaf4da 100644 --- a/src/examples/dataset-version/DatasetVersionObject-roleattribution.json +++ b/src/examples/dataset-version/DatasetVersionObject-roleattribution.json @@ -1,22 +1,27 @@ { + "was_attributed_to": [ + { + "meta_code": "doe", + "meta_type": "dlco:PersonObject", + "name": "Jane Doe", + "email": "doe@example.com" + }, + { + "meta_code": "DFG", + "meta_type": "dlco:OrganizationObject", + "name": "Deutsche Forschungsgemeinschaft" + } + ], "qualified_attribution": [ { - "agent": { - "meta_type": "dlco:PersonObject", - "name": "Jane Doe", - "email": "doe@example.com" - }, + "agent": "doe", "had_role": [ "marcrel:aut", "marcrel:cur" ] }, { - "agent": { - "meta_type": "dlco:OrganizationObject", - "name": "Deutsche Forschungsgemeinschaft", - "meta_code": "DFG" - }, + "agent": "DFG", "had_role": [ "marcrel:fnd" ] diff --git a/src/examples/dataset-version/DatasetVersionObject-roleattribution.yaml b/src/examples/dataset-version/DatasetVersionObject-roleattribution.yaml index ed4f25d..fbf6982 100644 --- a/src/examples/dataset-version/DatasetVersionObject-roleattribution.yaml +++ b/src/examples/dataset-version/DatasetVersionObject-roleattribution.yaml @@ -1,20 +1,22 @@ description: >- Some key facts about the data +was_attributed_to: + - # to distinguish people from organizations and maybe even + # software agents + meta_type: dlco:PersonObject + meta_code: doe + name: Jane Doe + email: doe@example.com + - meta_type: dlco:OrganizationObject + meta_code: DFG + name: Deutsche Forschungsgemeinschaft qualified_attribution: - - agent: - # to distinguish people from organizations and maybe even - # software agents - meta_type: dlco:PersonObject - name: Jane Doe - email: doe@example.com + - agent: doe had_role: # for simplicity of edits/composition, we allow for multiple # roles - marcrel:aut - marcrel:cur - - agent: - meta_type: dlco:OrganizationObject - meta_code: DFG - name: Deutsche Forschungsgemeinschaft + - agent: DFG had_role: - marcrel:fnd diff --git a/src/linkml/ontology/datasets.yaml b/src/linkml/ontology/datasets.yaml index b2a051e..8024018 100644 --- a/src/linkml/ontology/datasets.yaml +++ b/src/linkml/ontology/datasets.yaml @@ -187,6 +187,7 @@ classes: - title - type - version + - was_attributed_to slot_usage: has_part: range: Resource @@ -324,6 +325,7 @@ classes: - has_part - license - qualified_access + - qualified_attribution comments: - >- Compared to `DCAT:Distribution` this class has a `qualified_access` diff --git a/src/linkml/schemas/dataset-version.yaml b/src/linkml/schemas/dataset-version.yaml index a9799bc..c1ebf2f 100644 --- a/src/linkml/schemas/dataset-version.yaml +++ b/src/linkml/schemas/dataset-version.yaml @@ -68,6 +68,11 @@ classes: license: inlined: false range: LicenseDocumentObject + qualified_attribution: + inlined: true + inlined_as_list: true + multivalued: true + range: AgentInfluenceObject FileContainerObject: class_uri: dlco:FileContainerObject @@ -146,6 +151,11 @@ classes: # range: GitShaIDedPartObject license: range: LicenseDocumentObject + was_attributed_to: + inlined: true + inlined_as_list: true + multivalued: true + range: AgentObject qualified_attribution: inlined: true inlined_as_list: true @@ -165,6 +175,7 @@ classes: description: >- Schema-specific implementation of [AgentObject](https://concepts.datalad.org/ontology/AgentObject). slots: + - meta_code - meta_type PersonObject: @@ -193,8 +204,6 @@ classes: - Organization description: >- Schema-specific implementation of [OrganizationObject](https://concepts.datalad.org/ontology/OrganizationObject). - slots: - - meta_code EntityObject: class_uri: dlco:EntityObject @@ -236,7 +245,6 @@ classes: Schema-specific implementation of [AgentInfluenceObject](https://concepts.datalad.org/ontology/AgentInfluenceObject). slot_usage: agent: - inlined: true range: AgentObject had_role: multivalued: true From e42026ab8de7cc3391390ba3b367ab9faa0fcac3 Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Sun, 10 Mar 2024 21:10:34 +0100 Subject: [PATCH 2/3] Align entity relation and qualification with agent setup --- .../DatasetVersionObject-funding.json | 20 +++-- .../DatasetVersionObject-funding.yaml | 14 ++-- .../DatasetVersionObject-penguins.json | 74 +++++++++++-------- .../DatasetVersionObject-penguins.yaml | 63 ++++++++-------- src/linkml/ontology/datasets.yaml | 3 + src/linkml/schemas/dataset-version.yaml | 7 +- 6 files changed, 105 insertions(+), 76 deletions(-) diff --git a/src/examples/dataset-version/DatasetVersionObject-funding.json b/src/examples/dataset-version/DatasetVersionObject-funding.json index c7ecd22..830e11e 100644 --- a/src/examples/dataset-version/DatasetVersionObject-funding.json +++ b/src/examples/dataset-version/DatasetVersionObject-funding.json @@ -1,19 +1,23 @@ { "qualified_relation": [ { - "entity": { - "meta_type": "dlco:GrantObject", - "identifier": "https://gepris.dfg.de/gepris/projekt/431549029", - "sponsor": { - "name": "Deutsche Forschungsgemeinschaft" - }, - "name": "SFB1451" - }, + "entity": "sfb1451", "had_role": [ "schema:funding" ] } ], + "relation": [ + { + "meta_code": "sfb1451", + "meta_type": "dlco:GrantObject", + "identifier": "https://gepris.dfg.de/gepris/projekt/431549029", + "sponsor": { + "name": "Deutsche Forschungsgemeinschaft" + }, + "name": "SFB1451" + } + ], "description": "Some key facts about the data", "@type": "DatasetVersionObject" } diff --git a/src/examples/dataset-version/DatasetVersionObject-funding.yaml b/src/examples/dataset-version/DatasetVersionObject-funding.yaml index 04b1032..a9b8524 100644 --- a/src/examples/dataset-version/DatasetVersionObject-funding.yaml +++ b/src/examples/dataset-version/DatasetVersionObject-funding.yaml @@ -1,11 +1,13 @@ description: >- Some key facts about the data +relation: + - meta_type: dlco:GrantObject + meta_code: sfb1451 + name: SFB1451 + identifier: https://gepris.dfg.de/gepris/projekt/431549029 + sponsor: + name: Deutsche Forschungsgemeinschaft qualified_relation: - - entity: - meta_type: dlco:GrantObject - name: SFB1451 - identifier: https://gepris.dfg.de/gepris/projekt/431549029 - sponsor: - name: Deutsche Forschungsgemeinschaft + - entity: sfb1451 had_role: - schema:funding diff --git a/src/examples/dataset-version/DatasetVersionObject-penguins.json b/src/examples/dataset-version/DatasetVersionObject-penguins.json index 850c3a7..22bcfa7 100644 --- a/src/examples/dataset-version/DatasetVersionObject-penguins.json +++ b/src/examples/dataset-version/DatasetVersionObject-penguins.json @@ -146,59 +146,69 @@ ], "qualified_relation": [ { - "entity": { - "meta_type": "dlco:GrantObject", - "identifier": "0217282", - "sponsor": { - "name": "NSF Office of Polar Programs" - }, - "name": "LTER: PALMER, ANTARCTICA LTER: Climate Change, Ecosystem Migration and Teleconnections in an Ice-Dominated Environment", - "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282&HistoricalAwards=false" - }, + "entity": "nsf0217282", "had_role": [ "schema:funding" ] }, { - "entity": { - "meta_type": "dlco:GrantObject", - "identifier": "0823101", - "sponsor": { - "name": "NSF Office of Polar Programs" - }, - "name": "Palmer, Antarctica Long Term Ecological Research Project", - "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0823101" - }, + "entity": "nsf0823101", "had_role": [ "schema:funding" ] }, { - "entity": { - "meta_type": "dlco:GrantObject", - "identifier": "0741351", - "sponsor": { - "name": "NSF Office of Polar Programs" - }, - "name": "Collaborative Research: Possible Climate-induced Change in the Distribution of Pleuragramma Antarcticum on the Western Antarctic Peninsula Shelf", - "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0741351" - }, + "entity": "nsf0741351", "had_role": [ "schema:funding" ] }, { - "entity": { - "meta_type": "dlco:PublicationObject", - "citation": "'Gorman KB, Williams TD, Fraser WR (2014) Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis). PLoS ONE 9(3): e90081.'", - "doi": "https://doi.org/10.1371/journal.pone.0090081" - }, + "entity": "gormanetal", "had_role": [ "CiTO:citesAsAuthority", "CiTO:isCitedAsDataSourceBy" ] } ], + "relation": [ + { + "meta_code": "nsf0217282", + "meta_type": "dlco:GrantObject", + "identifier": "0217282", + "sponsor": { + "name": "NSF Office of Polar Programs" + }, + "name": "LTER: PALMER, ANTARCTICA LTER: Climate Change, Ecosystem Migration and Teleconnections in an Ice-Dominated Environment", + "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282&HistoricalAwards=false" + }, + { + "meta_code": "nsf0823101", + "meta_type": "dlco:GrantObject", + "identifier": "0823101", + "sponsor": { + "name": "NSF Office of Polar Programs" + }, + "name": "Palmer, Antarctica Long Term Ecological Research Project", + "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0823101" + }, + { + "meta_code": "nsf0741351", + "meta_type": "dlco:GrantObject", + "identifier": "0741351", + "sponsor": { + "name": "NSF Office of Polar Programs" + }, + "name": "Collaborative Research: Possible Climate-induced Change in the Distribution of Pleuragramma Antarcticum on the Western Antarctic Peninsula Shelf", + "cites_as_authority": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=0741351" + }, + { + "meta_code": "gormanetal", + "meta_type": "dlco:PublicationObject", + "citation": "'Gorman KB, Williams TD, Fraser WR (2014) Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis). PLoS ONE 9(3): e90081.'", + "doi": "https://doi.org/10.1371/journal.pone.0090081" + } + ], "description": "The goal of palmerpenguins is to provide a great dataset for data exploration and visualization, as an alternative to iris. Data were collected and made available by Dr. Kristen Gorman and the Palmer Station, Antarctica LTER, a member of the Long Term Ecological Research Network.", "keyword": [ "penguins", diff --git a/src/examples/dataset-version/DatasetVersionObject-penguins.yaml b/src/examples/dataset-version/DatasetVersionObject-penguins.yaml index b5c94b0..e777efc 100644 --- a/src/examples/dataset-version/DatasetVersionObject-penguins.yaml +++ b/src/examples/dataset-version/DatasetVersionObject-penguins.yaml @@ -70,45 +70,50 @@ qualified_attribution: - agent: UAF had_role: - marcrel:sht +relation: + - meta_type: dlco:GrantObject + meta_code: nsf0217282 + name: "LTER: PALMER, ANTARCTICA LTER: Climate Change, Ecosystem Migration and Teleconnections in an Ice-Dominated Environment" + identifier: 0217282 + sponsor: + name: NSF Office of Polar Programs + cites_as_authority: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282&HistoricalAwards=false + - meta_type: dlco:GrantObject + meta_code: nsf0823101 + name: Palmer, Antarctica Long Term Ecological Research Project + identifier: "0823101" + sponsor: + name: NSF Office of Polar Programs + cites_as_authority: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0823101 + - meta_type: dlco:GrantObject + meta_code: nsf0741351 + name: "Collaborative Research: Possible Climate-induced Change in the Distribution of Pleuragramma Antarcticum on the Western Antarctic Peninsula Shelf" + identifier: "0741351" + sponsor: + name: NSF Office of Polar Programs + cites_as_authority: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0741351 + - meta_type: dlco:PublicationObject + meta_code: gormanetal + citation: >- + 'Gorman KB, Williams TD, Fraser WR (2014) Ecological Sexual Dimorphism + and Environmental Variability within a Community of Antarctic Penguins (Genus + Pygoscelis). PLoS ONE 9(3): e90081.' + #date_published: '2014-03-05' + doi: https://doi.org/10.1371/journal.pone.0090081 qualified_relation: - had_role: - schema:funding - entity: - meta_type: dlco:GrantObject - name: "LTER: PALMER, ANTARCTICA LTER: Climate Change, Ecosystem Migration and Teleconnections in an Ice-Dominated Environment" - identifier: 0217282 - sponsor: - name: NSF Office of Polar Programs - cites_as_authority: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0217282&HistoricalAwards=false + entity: nsf0217282 - had_role: - schema:funding - entity: - meta_type: dlco:GrantObject - name: Palmer, Antarctica Long Term Ecological Research Project - identifier: "0823101" - sponsor: - name: NSF Office of Polar Programs - cites_as_authority: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0823101 + entity: nsf0823101 - had_role: - schema:funding - entity: - meta_type: dlco:GrantObject - name: "Collaborative Research: Possible Climate-induced Change in the Distribution of Pleuragramma Antarcticum on the Western Antarctic Peninsula Shelf" - identifier: "0741351" - sponsor: - name: NSF Office of Polar Programs - cites_as_authority: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0741351 + entity: nsf0741351 - had_role: - CiTO:citesAsAuthority - CiTO:isCitedAsDataSourceBy - entity: - meta_type: dlco:PublicationObject - citation: >- - 'Gorman KB, Williams TD, Fraser WR (2014) Ecological Sexual Dimorphism - and Environmental Variability within a Community of Antarctic Penguins (Genus - Pygoscelis). PLoS ONE 9(3): e90081.' - #date_published: '2014-03-05' - doi: https://doi.org/10.1371/journal.pone.0090081 + entity: gormanetal distribution: meta_type: dlco:FileContainerObject meta_code: ./ diff --git a/src/linkml/ontology/datasets.yaml b/src/linkml/ontology/datasets.yaml index 8024018..dd44f86 100644 --- a/src/linkml/ontology/datasets.yaml +++ b/src/linkml/ontology/datasets.yaml @@ -184,6 +184,7 @@ classes: - qualified_attribution - qualified_relation - qualified_part + - relation - title - type - version @@ -216,6 +217,8 @@ classes: # concept classes inlined: true inlined_as_list: true + relation: + multivalued: true type: description: >- Type of resource, e.g. `Dataset`. diff --git a/src/linkml/schemas/dataset-version.yaml b/src/linkml/schemas/dataset-version.yaml index c1ebf2f..deb1e49 100644 --- a/src/linkml/schemas/dataset-version.yaml +++ b/src/linkml/schemas/dataset-version.yaml @@ -166,6 +166,11 @@ classes: inlined_as_list: true multivalued: true range: EntityInfluenceObject + relation: + inlined: true + inlined_as_list: true + multivalued: true + range: EntityObject AgentObject: class_uri: dlco:AgentObject @@ -211,6 +216,7 @@ classes: mixins: - Entity slots: + - meta_code - meta_type description: >- Schema-specific implementation of [EntityObject](https://concepts.datalad.org/ontology/EntityObject). @@ -259,7 +265,6 @@ classes: Schema-specific implementation of [EntityInfluenceObject](https://concepts.datalad.org/ontology/EntityInfluenceObject). slot_usage: entity: - inlined: true range: EntityObject had_role: multivalued: true From e8429dca75db2112e9ea2cfef039330bcb0f259a Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Sun, 10 Mar 2024 21:18:05 +0100 Subject: [PATCH 3/3] Passify codespell --- .github/workflows/codespell.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml index 7c9eafb..baaa56a 100644 --- a/.github/workflows/codespell.yml +++ b/.github/workflows/codespell.yml @@ -21,3 +21,5 @@ jobs: uses: actions/checkout@v4 - name: Codespell uses: codespell-project/actions-codespell@v2 + with: + ignore_words_list: crate