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Introduce Contributor record #741

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merged 4 commits into from
Feb 26, 2024
Merged

Introduce Contributor record #741

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67547b8
Add Contributor record, adapt Study object accordingly
bussec Jan 15, 2024
2c85adb
Update v3 Schema, sync to v2 Schema and its copies
bussec Feb 21, 2024
63eaadc
Update R and Python Schema files
bussec Feb 21, 2024
563b22d
Update example and test files for R and Python
bussec Feb 21, 2024
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2 changes: 1 addition & 1 deletion lang/R/R/Schema.R
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Original file line number Diff line number Diff line change
Expand Up @@ -312,7 +312,7 @@ AIRRSchema <- list("Info"=load_schema("InfoObject"),
"SequencingData"=load_schema("SequencingData"),
"DataProcessing"=load_schema("DataProcessing"),
"GermlineSet"=load_schema("GermlineSet"),
"Acknowledgement"=load_schema("Acknowledgement"),
"Contributor"=load_schema("Contributor"),
"RearrangedSequence"=load_schema("RearrangedSequence"),
"UnrearrangedSequence"=load_schema("UnrearrangedSequence"),
"SequenceDelineationV"=load_schema("SequenceDelineationV"),
Expand Down
244 changes: 158 additions & 86 deletions lang/R/inst/extdata/airr-schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -493,30 +493,115 @@ TimePoint:
# TODO: link to global schema with JSON-LD?
#

# An individual
Acknowledgement:
# Contributor record to describe invididuals and their contribution to a data set
#
Contributor:
description: Individual whose contribution to this work should be acknowledged
type: object
required:
- acknowledgement_id
- contributor_id
- name
- institution_name
properties:
acknowledgement_id:
contributor_id:
type: string
description: unique identifier of this Acknowledgement within the file
description: Unique identifier of this contributor within the file
x-airr:
nullable: true
identifier: true
miairr: important
name:
type: string
description: Full name of individual
institution_name:
type: string
description: Individual's department and institution name
description: Full name of contributor
x-airr:
nullable: false
orcid_id:
$ref: '#/Ontology'
description: >
ORCID identifier of the contributor. Note that if present, the label of the ORCID record should take
precedence over the name reported in the `name` property.
title: ORCID iD
example:
id: ORCID:0000-0002-1825-0097
label: Josiah Carberry
x-airr:
nullable: true
adc-query-support: true
format: ontology
ontology:
draft: false
top_node:
id: null
label: null
affiliation:
$ref: '#/Ontology'
description: >
ROR of the contributor's primary affiliation. Note that ROR are only minted for institutions, not
from individuals institutes, divisions or departments.
title: ROR
example:
id: ROR:05h7xva58
label: Wesleyan University
x-airr:
nullable: true
adc-query-support: true
format: ontology
ontology:
draft: false
top_node:
id: null
label: null
affiliation_department:
type: string
description: Individual's ORCID identifier
description: >
Additional information regarding the contributor's primary affiliation. Can be used to specify
individual institutes, divisions or departments.
example: Department for Psychoceramics
x-airr:
nullable: true
contributions:
type: array
description: List of all roles the contributor had in a project
items:
$ref: '#/ContributorContribution'
x-airr:
nullable: true

ContributorContribution:
type: object
required:
- role
properties:
role:
type: string
description: Role according to CRediT taxonomy
enum:
- conceptualization
- data curation
- formal analysis
- funding acquisition
- investigation
- methodology
- project administration
- resources
- software
- supervision
- validation
- visualization
- writing - original draft
- writing - review & editing
x-airr:
nullable: false
degree:
type: string
description: >
Optional specification of the degree of contribution, should be used if multiple individuals serve
the same role.
enum:
- lead
- equal
- supporting
x-airr:
nullable: true

#
# Germline gene schema
Expand Down Expand Up @@ -783,8 +868,7 @@ AlleleDescription:
type: object
required:
- allele_description_id
- maintainer
- lab_address
- acknowledgements
- release_version
- release_date
- release_description
Expand All @@ -810,21 +894,15 @@ AlleleDescription:
example: OGRDB:Human_IGH:IGHV1-69*01.001
x-airr:
miairr: important
maintainer:
type: string
description: Maintainer of this sequence record
x-airr:
miairr: defined
acknowledgements:
type: array
description: List of individuals whose contribution to the gene description should be acknowledged
description: >
List of individuals whose contribution to the gene description should be acknowledged. Note that these
are not necessarily identical with the authors on an associated manuscript or other scholarly
communication. Further note that typically at least the three CRediT contributor roles "supervision",
"investigation" and "data curation" should be assigned. The current maintainer should be listed first.
items:
$ref: '#/Acknowledgement'
lab_address:
type: string
description: Institution and full address of corresponding author
x-airr:
miairr: defined
$ref: '#/Contributor'
release_version:
type: integer
description: Version number of this record, updated whenever a revised version is published or released
Expand Down Expand Up @@ -1084,9 +1162,7 @@ GermlineSet:
All genes in a GermlineSet should be from a single locus.
required:
- germline_set_id
- author
- lab_name
- lab_address
- acknowledgements
- release_version
- release_description
- release_date
Expand All @@ -1104,26 +1180,15 @@ GermlineSet:
x-airr:
identifier: true
miairr: important
author:
type: string
description: Corresponding author
x-airr:
miairr: important
lab_name:
type: string
description: Department of corresponding author
x-airr:
miairr: important
lab_address:
type: string
description: Institutional address of corresponding author
x-airr:
miairr: important
acknowledgements:
type: array
description: List of individuals whose contribution to the germline set should be acknowledged
description: >
List of individuals whose contribution to the germline set should be acknowledged. Note that these are
not necessarily identical with the authors on an associated manuscript or other scholarly communication.
Further note that typically at least the three CRediT contributor roles "supervision", "investigation"
and "data curation" should be assigned. The coresponding author should be listed last.
items:
$ref: '#/Acknowledgement'
$ref: '#/Contributor'
release_version:
type: number
description: Version number of this record, allocated automatically
Expand Down Expand Up @@ -1506,10 +1571,7 @@ Study:
- study_type
- inclusion_exclusion_criteria
- grants
- collected_by
- lab_name
- lab_address
- submitted_by
- contributors
- pub_ids
- keywords_study
properties:
Expand Down Expand Up @@ -1593,71 +1655,81 @@ Study:
set: 1
subset: study
name: Grant funding agency
contributors:
type: array
description: >
List of individuals who contributed to the study. Note that these are not necessarily identical with
the authors on an associated manuscript or other scholarly communication. Further note that typically
at least the three CRediT contributor roles "supervision", "investigation" and "data curation" should
be assigned. The coresponding author should be listed last.
title: Contributors
items:
$ref: '#/Contributor'
x-airr:
nullable: false
miairr: essential
adc-query-support: true
set: 1
subset: study
name: Contributors
study_contact:
type: string
description: >
Full contact information of the contact persons for this study This should include an e-mail address
and a persistent identifier such as an ORCID ID.
title: Contact information (study)
example: Dr. P. Stibbons, [email protected], https://orcid.org/0000-0002-1825-0097
x-airr:
nullable: true
adc-query-support: true
name: Contact information (study)
deprecated: true
deprecated-description: >
Acknowledgements and contact information was re-organized into the contributors property, which
is an array of Contributor objects.
deprecated-replaced-by:
- contributors
collected_by:
type: string
description: >
Full contact information of the data collector, i.e. the person who is legally responsible for data
collection and release. This should include an e-mail address and a persistent identifier such as an
ORCID ID.
title: Contact information (data collection)
example: Dr. P. Stibbons, [email protected], https://orcid.org/0000-0002-1825-0097
x-airr:
miairr: important
nullable: true
adc-query-support: true
set: 1
subset: study
name: Contact information (data collection)
deprecated: true
deprecated-description: >
Acknowledgements and contact information was re-organized into the contributors property, which
is an array of Contributor objects.
deprecated-replaced-by:
- contributors
lab_name:
type: string
description: Department of data collector
title: Lab name
example: Department for Planar Immunology
x-airr:
miairr: important
nullable: true
adc-query-support: true
set: 1
subset: study
name: Lab name
deprecated: true
deprecated-description: >
Acknowledgements and contact information was re-organized into the contributors property, which
is an array of Contributor objects.
deprecated-replaced-by:
- contributors
lab_address:
type: string
description: Institution and institutional address of data collector
title: Lab address
example: School of Medicine, Unseen University, Ankh-Morpork, Disk World
x-airr:
miairr: important
nullable: true
adc-query-support: true
set: 1
subset: study
name: Lab address
deprecated: true
deprecated-description: >
Acknowledgements and contact information was re-organized into the contributors property, which
is an array of Contributor objects.
deprecated-replaced-by:
- contributors
submitted_by:
type: string
description: >
Full contact information of the data depositor, i.e., the person submitting the data to a repository.
This should include an e-mail address and a persistent identifier such as an ORCID ID. This is
supposed to be a short-lived and technical role until the submission is relased.
title: Contact information (data deposition)
example: Adrian Turnipseed, [email protected], https://orcid.org/0000-0002-1825-0097
x-airr:
miairr: important
nullable: true
adc-query-support: true
set: 1
subset: study
name: Contact information (data deposition)
deprecated: true
deprecated-description: >
Acknowledgements and contact information was re-organized into the contributors property, which
is an array of Contributor objects.
deprecated-replaced-by:
- contributors
pub_ids:
type: array
items:
Expand Down
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