Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add project, data collection metadata and associated CV tables #22

Open
wants to merge 21 commits into
base: dev
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
21 commits
Select commit Hold shift + click to select a range
903bb6b
Add project, data collection metadata and associated CV tables
pbishwakarma Jul 19, 2023
ba470f6
updating data collection metadata table and README
patrick-lloyd-ray Sep 27, 2023
779d5cc
updating organization metadata and README
patrick-lloyd-ray Sep 27, 2023
36f40ff
updating person metadata and README
patrick-lloyd-ray Sep 27, 2023
208f9aa
updating project metadata and README
patrick-lloyd-ray Sep 27, 2023
e6dd428
updating CV csvs and readme links
patrick-lloyd-ray Sep 27, 2023
2ddc4d7
Fix subdomain and version date for entities
pbishwakarma Aug 7, 2024
677f1a4
Add explicit modeling of web resources
pbishwakarma Aug 7, 2024
83eed30
Point to web resource types in other sub domains
pbishwakarma Aug 7, 2024
28668ed
Remove accessControl code/description and clarify some descritions of…
pbishwakarma Aug 7, 2024
3f63b09
Explicitly model grants
pbishwakarma Aug 7, 2024
6703466
Update protocol data type to be WebResource
pbishwakarma Aug 7, 2024
47fc626
Update naming scheme for grant fields and add license
pbishwakarma Sep 10, 2024
946607f
Correct license reference in data collection from cv to entity
pbishwakarma Sep 10, 2024
ac89a9d
Fix reference to grant in project to be entity
pbishwakarma Sep 10, 2024
d550e0d
Fix typo in grant metadata
pbishwakarma Sep 10, 2024
5e3241d
Naming convention for grant field
pbishwakarma Sep 10, 2024
993af0f
Standardize domain for entities
pbishwakarma Sep 10, 2024
83db9d8
Standardize columns to template
pbishwakarma Sep 10, 2024
93bf71d
Fix subset and class columns
pbishwakarma Sep 10, 2024
7f7f93b
adding UUIDs for license-metadata and webresource-metadata
patrick-lloyd-ray Sep 11, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
Proposed BICAN Field Name,BICAN UUID,Aliases,LinkML Class,Definition,Nullable,Permissible Values,Data Type,Data Example,Min Value,Max Value,Unit,"Statistical Variable Type ",Subsets,Version Number,Version Date
data collection name,f7b04e21-c12d-4b3d-ba0e-b1de6ac92dca,name,DataCollection,"A human-readable, locally unique label that identifies a data collection.",FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
data collection long form title,62208817-6a7f-4e70-9c4a-d262f43d82cc,title,DataCollection,"A long form title of a data collection. ",FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
data collection short form title,f5169355-52cf-4720-904f-946c92489faa,short_title,DataCollection,A short form title of a data collection (fewer than 30 characters).,FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
data collection description,c5188587-2b4f-4889-ae93-224efdb803d2,description,DataCollection,"A description of a data collection that includes a specification of the license of the data collection. ",FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
data collection archive,39498a35-3cb5-46ce-9e23-dc5e499b85c4,data_archive,DataCollection,"The location (archive) at which the data in a data collection is to be deposited. ",FALSE,,[Organization],,,,,,Projects and Data Collections,1,10/9/24
data collection species,7135fb76-5423-44da-ba52-4c33e8626033,species,DataCollection,The common name of the species of the donor from which data were collected for this data collection.,FALSE,[Species CV],[exclusive_categorical],Arctic ground squirrel,,,,,Projects and Data Collections,1,10/9/24
data collection access control,3880e926-d2fb-4960-bf61-4b5789e6c027,access_control,DataCollection,"The level of access specified for a data collection. ",FALSE,open/controlled,exclusive_categorical,,,,,,Projects and Data Collections,1,10/9/24
data collection completion state,456513f2-0af8-45e1-b8f0-338636ed3f61,completion_state,DataCollection,"A value that specifies whether or not additional data is being generated for a data collection. ",FALSE,in progress/complete,exclusive_categorical,,,,,,Projects and Data Collections,1,10/9/24
data collection modality,480af9eb-0128-4602-9c8f-01416820cee3,modality,DataCollection,"The modality of the data in a data collection. ",FALSE,[Modality CV],[exclusive_categorical],protein quantification,,,,,Projects and Data Collections,1,10/9/24
data collection technique,bee3bda8-c103-448f-8557-effcaca176bf,technique,DataCollection,"The technique that was used to acquire the data in a collection. ",FALSE,[Techniques CV],[exclusive_categorical],10x Chromium 3' v2 sequencing,,,,,Projects and Data Collections,1,10/9/24
data collection license,b184e037-1b45-4ca6-8651-7044b1a74199,license,DataCollection,"A license that is applied to the data in a data collection. ",FALSE,,License,,,,,,Projects and Data Collections,1,10/9/24
data collection web resource,ebdc27a1-37ca-46ec-8914-6d3fae85a3d9,web_resource,DataCollection,A URL or weblink that provides the location of relevant tools or pages to a data collection. Commonly used to link to landing page that allows for downloading data contained in collection.,TRUE,,[WebResource],,,,,,Projects and Data Collections,1,10/9/24
data collection citation,ea4729c6-df21-40db-8141-5af1d44ba75c,citation,DataCollection,"A data citation for a data collection. ",TRUE,,text,,,,,,Projects and Data Collections,1,10/9/24
7 changes: 7 additions & 0 deletions docs/schemas/project-registration-bican/Grant-metadata.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
Proposed BICAN Field Name,BICAN UUID,Aliases,LinkML Class,Definition,Nullable,Permissible Values,Data Type,Data Example,Min Value,Max Value,Unit,Statistical Variable Type,Subsets,Version Number,Version Date
grant funding agency,,funding_agency,Grant,Organization that is funding the grant,FALSE,,Organization,National Institute of Mental Health,,,,,Projects and Data Collections,1,10/9/24
grant awardee,,awardee,Grant,Organization that is receiving funding from the grant,FALSE,,Organization,Allen Institute for Brain Science,,,,,Projects and Data Collections,1,10/9/24
grant name,,name,Grant,Human readable locally unique identifier for a grant. Typically this a concatenation of the activity code and contact PI for NIH grants. Example: U24 Hawrylycz grant,FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
grant title,,title,Grant,Long form title for a grant. Typically this is the project title from NIH grants.,FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
grant identifier,,grant_identifier,Grant,Unique identifier for a grant resolvable by external authority. Typically this is the project number from NIH grants.,FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
grant report symbol,,report_symbol,Grant,Resource location component in NIH RePorter URL. Symbol in RePorter URL that redirects to project details page in RePorter.,TRUE,,text,10521124,,,,,Projects and Data Collections,1,10/9/24
5 changes: 5 additions & 0 deletions docs/schemas/project-registration-bican/License-metadata.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
Proposed BICAN Field Name,BICAN UUID,Aliases,LinkML Class,Definition,Nullable,Permissible Values,Data Type,Data Example,Min Value,Max Value,Unit,Statistical Variable Type,Subsets,Version Number,Version Date
license name,ddd0c288-b565-4b2d-a3a9-2b46b1a4a2c3,name,License,"A human-readable, locally unique label that identifies a license.",FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
license title,d0183b7b-fb54-455c-92a2-5b126d87d9f1,title,License,Long title for a license.,FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
license short title,3707b072-3846-4113-8f0d-ab8127035f52,short_title,License,Short title for a license.,FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
license information web resource,387b892c-884d-4fbd-a0d2-eeeb3fed5881,information_web_resource,License,A URL or weblink that contains the text for a license.,FALSE,,WebResource,https://creativecommons.org/licenses/by/4.0/,,,,,Projects and Data Collections,1,10/9/24
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
Proposed BICAN Field Name,BICAN UUID,Aliases,LinkML Class,Definition,Nullable,Permissible Values,Data Type,Data Example,Min Value,Max Value,Unit,Statistical Variable Type,Subsets,Version Number,Version Date
organization name,3788d44f-8383-4707-845d-bb8289815b32,name,Organization,"A human-readable, locally unique label that identifies a organization. ",FALSE,,text,,,,,,Projects and Data Collections,1,27-09-2023
organization Research Organization Registry ID,3fd3913c-0e36-4fe0-ac99-073f496c0919,ror,Organization,"A Research Organization Registry ID that identifies an organization. ",TRUE,,text,,,,,,Projects and Data Collections,1,27-09-2023
5 changes: 5 additions & 0 deletions docs/schemas/project-registration-bican/Person-metadata.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
Proposed BICAN Field Name,BICAN UUID,Aliases,LinkML Class,Definition,Nullable,Permissible Values,Data Type,Data Example,Min Value,Max Value,Unit,Statistical Variable Type,Subsets,Version Number,Version Date
person name,da5203bf-0202-4cd0-b0c2-5cc05806e2e4,name,Person,"A full name of a person in [given name],[family name] format.",FALSE,,text,,,,,,Projects and Data Collections,1,27-09-2023
person given name,2354176f-40f2-4110-98d9-0c203314bfde,given_name,Person,"A given name of a person. ",FALSE,,text,,,,,,Projects and Data Collections,1,27-09-2023
person family name,f5d8f1a3-ce30-45eb-ac26-13a8998c2f5a,family_name,Person,"A family name of a person. ",FALSE,,text,,,,,,Projects and Data Collections,1,27-09-2023
person ORCID,e834467e-a05e-4b9f-8348-5c0079bdaac8,orcid,Person,"An ORCID that identifies a person. ",TRUE,,text,0000-0002-9802-0493,,,,,Projects and Data Collections,1,27-09-2023
14 changes: 14 additions & 0 deletions docs/schemas/project-registration-bican/Project-metadata.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
Proposed BICAN Field Name,BICAN UUID,Aliases,LinkML Class,Definition,Nullable,Permissible Values,Data Type,Data Example,Min Value,Max Value,Unit,Statistical Variable Type,Subsets,Version Number,Version Date
project name,a0d7797f-aaf1-4d3e-8289-51a94237b9c8,name,Project,"A human readable, locally unique identifier that denotes a project.",FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
project title,34e55bb4-17db-4b7f-bd7d-7272ffe1c9f2,title,Project,A long form project title.,FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
project short title,216cc403-423a-4b43-b935-b9b61dbb8a26,short_title,Project,A short form project title.,FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
project description,c51e8c8d-d62b-4b79-843b-a3a6810fe709,description,Project,A long form project description.,FALSE,,text,,,,,,Projects and Data Collections,1,10/9/24
project subprogram,cfd9d928-673a-428a-b5f0-c04e2fdd8ec9,subprogram,Project,A subprogram to which a project belongs. See subprogram controlled vocabulary.,FALSE,[Subprogram CV],exclusive_categorical,,,,,,Projects and Data Collections,1,10/9/24
project contact,62381d66-c414-4fe9-8b07-0a00ee855e71,contact,Project,A primary contact for a project. This is typically a person but can also be an institution.,TRUE,,Person | Organization,,,,,,Projects and Data Collections,1,10/9/24
project creator,34c891d4-d721-4023-bbf9-06b84f6a93cc,creator,Project,A creator of a project. This is either a person or institution.,FALSE,,[Person | Organization],,,,,,Projects and Data Collections,1,10/9/24
project contributor,8a1a747c-c24d-451a-9168-ed14d274a97c,contributor,Project,A contributor to a project. This is often given as a list.,FALSE,,[Person],,,,,,Projects and Data Collections,1,10/9/24
project funding source,3f85bc4b-2e03-426e-b376-4607fc9515e3,funding_source,Project,The funding source for a project.,FALSE,,[Grant],,,,,,Projects and Data Collections,1,10/9/24
project collections,66093eb6-fdaf-4782-8dba-23f6575254d8,collections,Project,The data collections that are part of a project.,TRUE,[Data Collection CV],[Collection],,,,,,Projects and Data Collections,1,10/9/24
project highlighted web resource,2bb2472b-73b7-426b-adb2-739924a0751b,highlighted_web_resource,Project,A link to relevant tools/pages of a project.,TRUE,,[WebResource],,,,,,Projects and Data Collections,1,10/9/24
project protocol,3e80809a-de1a-4333-98a9-f19549fda246,protocol,Project,"A protocol for a project. ",TRUE,,[WebResource],,,,,,Projects and Data Collections,1,10/9/24
project publication,52d1b518-37e0-4b69-b1d8-36d1ff437376,publication,Project,A publication associated with a project.,TRUE,,WebResource,,,,,,Projects and Data Collections,1,10/9/24
Loading