projects and data collections linkml schema

linkml-schema/source_projects_and_data_collection/gsheet.yaml

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+gsheet_id: "1bIovTpHRn1Pkhdmzx7oCWyv7l8puAZ5MSK0i4rtjR9Y"
+sheets:
+  - name: "Classes"
+    gid: "2119320484"
+  - name: "Relations"
+    gid: "0"
+  - name: "Slots"
+    gid: "1826607494"
+  - name: "ValueSets"
+    gid: "1374482547"
+  - name: "Subsets"
+    gid: "960235346"
+  - name: "Prefixes"
+    gid: "632689967"
+  - name: "Schema"
+    gid: "918690188"

linkml-schema/source_projects_and_data_collection/gsheet_output/Classes.tsv

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+class	Inheritance: is_a	Inheritance: mixin	Subsets	Definition	Class URI
+> class	is_a	mixins	in_subset	description	class_uri
+>		internal_separator: "|"	internal_separator: "|"		
+DataCollection					
+Grant					
+License					
+Organization				Respresents an organization. This is primarily used in reference to a project creator or funding source/awardee.	
+Person				Represents a person. This is primarily used in reference to a project creator or contributor.	
+Project					
+WebResource					

linkml-schema/source_projects_and_data_collection/gsheet_output/Prefixes.tsv

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+prefix	URI
+> prefix	prefix_reference
+bican	https://identifiers.org/brain-bican/vocab/
+sdo	http://schema.org/

linkml-schema/source_projects_and_data_collection/gsheet_output/Relations.tsv

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+Subject (Class Name)	Predicate (Slot Name)	Object (Data Type)	Mulltivalued	Definition	Subsets	Proposed BICAN Field Name	BICAN UUID	Nullable	Permissible Values	Data Example	Min Value	Max Value	Unit	Statistical Variable Type 	Version Number	Version Date
+> class	slot	range	multivalued	description	in_subset	ignore	slot_uri: {curie_prefix: bican}	ignore	ignore	ignore	ignore	ignore	ignore	ignore	ignore	ignore
+>		internal_separator: "|"			internal_separator: "|"											
+DataCollection	data_archive	Organization	TRUE	The location (archive) at which the data in a data collection is to be deposited. 	projects_and_data_collections|bican	data collection archive	39498a35-3cb5-46ce-9e23-dc5e499b85c4	FALSE							1	10/9/24
+DataCollection	web_resource	WebResource	TRUE	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.	projects_and_data_collections|bican	data collection web resource	ebdc27a1-37ca-46ec-8914-6d3fae85a3d9	TRUE							1	10/9/24
+DataCollection	license	License	FALSE	A license that is applied to the data in a data collection. 	projects_and_data_collections|bican	data collection license	b184e037-1b45-4ca6-8651-7044b1a74199	FALSE							1	10/9/24
+Grant	funding_agency	Organization	FALSE	Organization that is funding the grant	projects_and_data_collections|bican	grant funding agency		FALSE		National Institute of Mental Health					1	10/9/24
+Grant	awardee	Organization	FALSE	Organization that is receiving funding from the grant	projects_and_data_collections|bican	grant awardee		FALSE		Allen Institute for Brain Science					1	10/9/24
+License	information_web_resource	WebResource	FALSE	A URL or weblink that contains the text for a license.	projects_and_data_collections|bican	license information web resource	387b892c-884d-4fbd-a0d2-eeeb3fed5881	FALSE		https://creativecommons.org/licenses/by/4.0/					1	10/9/24
+Project	contributor	Person	TRUE	A contributor to a project. This is often given as a list.	projects_and_data_collections|bican	project contributor	8a1a747c-c24d-451a-9168-ed14d274a97c	FALSE							1	10/9/24
+Project	funding_source	Grant	TRUE	The funding source for a project.	projects_and_data_collections|bican	project funding source	3f85bc4b-2e03-426e-b376-4607fc9515e3	FALSE							1	10/9/24
+Project	highlighted_web_resource	WebResource	TRUE	A link to relevant tools/pages of a project.	projects_and_data_collections|bican	project highlighted web resource	2bb2472b-73b7-426b-adb2-739924a0751b	TRUE							1	10/9/24
+Project	protocol	WebResource	TRUE	A protocol for a project. 	projects_and_data_collections|bican	project protocol	3e80809a-de1a-4333-98a9-f19549fda246	TRUE							1	10/9/24
+Project	publication	WebResource	FALSE	A publication associated with a project.	projects_and_data_collections|bican	project publication	52d1b518-37e0-4b69-b1d8-36d1ff437376	TRUE							1	10/9/24
+Project	collections	DataCollection	TRUE	The data collections that are part of a project.	projects_and_data_collections|bican	project collections	66093eb6-fdaf-4782-8dba-23f6575254d8	TRUE	[Data Collection CV]						1	10/9/24

linkml-schema/source_projects_and_data_collection/gsheet_output/Schema.tsv

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+Schema	uri	Description	Schema Prefix	Imports	Title
+> schema	id	description	default_prefix	imports	title
+>				internal_separator: "|"	
+ProjectsAndDataCollectionTaxonomy	https:/w3id.org/brain-bican/projects-and-data-collection	The BICAN Projects and Data Collections Metadata schema specifies the minimum metadata required to register a project and data collection with BCDC. 	bican	bican_biolink	

linkml-schema/source_projects_and_data_collection/gsheet_output/Slots.tsv

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+LinkML Class	LinkML Slot Name	Data Type	Multivalued	Definition	Data Example	BICAN UUID	Subsets	Proposed BICAN Field Name	Nullable	Permissible Values	Min Value	Max Value	Unit	Statistical Variable Type 	Version Number	Version Date
+> class	slot	range	multivalued	description	examples	slot_uri: {curie_prefix: bican}	in_subset	ignore	ignore	ignore	ignore	ignore	ignore	ignore	ignore	ignore
+>							internal_separator: "|"									
+DataCollection	name	string	FALSE	A human-readable, locally unique label that identifies a data collection.		f7b04e21-c12d-4b3d-ba0e-b1de6ac92dca	projects_and_data_collections|bican	data collection name	FALSE						1	10/9/24
+DataCollection	title	string	FALSE	A long form title of a data collection. 		62208817-6a7f-4e70-9c4a-d262f43d82cc	projects_and_data_collections|bican	data collection long form title	FALSE						1	10/9/24
+DataCollection	short_title	string	FALSE	A short form title of a data collection (fewer than 30 characters).		f5169355-52cf-4720-904f-946c92489faa	projects_and_data_collections|bican	data collection short form title	FALSE						1	10/9/24
+DataCollection	description	string	FALSE	A description of a data collection that includes a specification of the license of the data collection. 		c5188587-2b4f-4889-ae93-224efdb803d2	projects_and_data_collections|bican	data collection description	FALSE						1	10/9/24
+DataCollection	species	Species	TRUE	The common name of the species of the donor from which data were collected for this data collection.	Arctic ground squirrel	7135fb76-5423-44da-ba52-4c33e8626033	projects_and_data_collections|bican	data collection species	FALSE	[Species CV]					1	10/9/24
+DataCollection	access_control	AccessControl	FALSE	The level of access specified for a data collection. 		3880e926-d2fb-4960-bf61-4b5789e6c027	projects_and_data_collections|bican	data collection access control	FALSE	open/controlled					1	10/9/24
+DataCollection	completion_state	CompletionState	FALSE	A value that specifies whether or not additional data is being generated for a data collection. 		456513f2-0af8-45e1-b8f0-338636ed3f61	projects_and_data_collections|bican	data collection completion state	FALSE	in progress/complete					1	10/9/24
+DataCollection	modality	Modality	TRUE	The modality of the data in a data collection. 	protein quantification	480af9eb-0128-4602-9c8f-01416820cee3	projects_and_data_collections|bican	data collection modality	FALSE	[Modality CV]					1	10/9/24
+DataCollection	technique	Technique	TRUE	The technique that was used to acquire the data in a collection. 	10x Chromium 3' v2 sequencing	bee3bda8-c103-448f-8557-effcaca176bf	projects_and_data_collections|bican	data collection technique	FALSE	[Techniques CV]					1	10/9/24
+DataCollection	citation	string	FALSE	A data citation for a data collection. 		ea4729c6-df21-40db-8141-5af1d44ba75c	projects_and_data_collections|bican	data collection citation	TRUE						1	10/9/24
+Grant	name	string	FALSE	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			projects_and_data_collections|bican	grant name	FALSE						1	10/9/24
+Grant	title	string	FALSE	Long form title for a grant. Typically this is the project title from NIH grants.			projects_and_data_collections|bican	grant title	FALSE						1	10/9/24
+Grant	grant_identifier	string	FALSE	Unique identifier for a grant resolvable by external authority. Typically this is the project number from NIH grants.			projects_and_data_collections|bican	grant identifier	FALSE						1	10/9/24
+Grant	report_symbol	string	FALSE	Resource location component in NIH RePorter URL. Symbol in RePorter URL that redirects to project details page in RePorter.	10521124		projects_and_data_collections|bican	grant report symbol	TRUE						1	10/9/24
+License	name	string	FALSE	A human-readable, locally unique label that identifies a license.		ddd0c288-b565-4b2d-a3a9-2b46b1a4a2c3	projects_and_data_collections|bican	license name	FALSE						1	10/9/24
+License	title	string	FALSE	Long title for a license.		d0183b7b-fb54-455c-92a2-5b126d87d9f1	projects_and_data_collections|bican	license title	FALSE						1	10/9/24
+License	short_title	string	FALSE	Short title for a license.		3707b072-3846-4113-8f0d-ab8127035f52	projects_and_data_collections|bican	license short title	FALSE						1	10/9/24
+Organization	name	string	FALSE	A human-readable, locally unique label that identifies a organization. 		3788d44f-8383-4707-845d-bb8289815b32	projects_and_data_collections|bican	organization name	FALSE						1	27-09-2023
+Organization	ror	string	FALSE	A Research Organization Registry ID that identifies an organization. 		3fd3913c-0e36-4fe0-ac99-073f496c0919	projects_and_data_collections|bican	organization Research Organization Registry ID	TRUE						1	27-09-2023
+Person	name	string	FALSE	A full name of a person in [given name],[family name] format.		da5203bf-0202-4cd0-b0c2-5cc05806e2e4	projects_and_data_collections|bican	person name	FALSE						1	27-09-2023
+Person	given_name	string	FALSE	A given name of a person. 		2354176f-40f2-4110-98d9-0c203314bfde	projects_and_data_collections|bican	person given name	FALSE						1	27-09-2023
+Person	family_name	string	FALSE	A family name of a person. 		f5d8f1a3-ce30-45eb-ac26-13a8998c2f5a	projects_and_data_collections|bican	person family name	FALSE						1	27-09-2023
+Person	orcid	string	FALSE	An ORCID that identifies a person. 	0000-0002-9802-0493	e834467e-a05e-4b9f-8348-5c0079bdaac8	projects_and_data_collections|bican	person ORCID	TRUE						1	27-09-2023
+Project	name	string	FALSE	A human readable, locally unique identifier that denotes a project.		a0d7797f-aaf1-4d3e-8289-51a94237b9c8	projects_and_data_collections|bican	project name	FALSE						1	10/9/24
+Project	title	string	FALSE	A long form project title.		34e55bb4-17db-4b7f-bd7d-7272ffe1c9f2	projects_and_data_collections|bican	project title	FALSE						1	10/9/24
+Project	short_title	string	FALSE	A short form project title.		216cc403-423a-4b43-b935-b9b61dbb8a26	projects_and_data_collections|bican	project short title	FALSE						1	10/9/24
+Project	description	string	FALSE	A long form project description.		c51e8c8d-d62b-4b79-843b-a3a6810fe709	projects_and_data_collections|bican	project description	FALSE						1	10/9/24
+Project	subprogram	Subprogram	TRUE	A subprogram to which a project belongs. See subprogram controlled vocabulary.		cfd9d928-673a-428a-b5f0-c04e2fdd8ec9	projects_and_data_collections|bican	project subprogram	FALSE	[Subprogram CV]					1	10/9/24
+WebResource	web_resource_type	WebResourceType	FALSE	Denotes the type of web resource - whether the resource routes to a download link, an informational resource or an interactive tool. 		a0f60904-2e0e-4864-9921-b6eb340aef74	projects_and_data_collections|bican	web resource type	FALSE	information | view | explore | download					1	10/9/24
+WebResource	title	string	FALSE	A long form title for a web resource.		5638df22-4eec-48d6-9e71-c644b8429c5c	projects_and_data_collections|bican	web resource title	FALSE						1	10/9/24
+WebResource	short_title	string	FALSE	A short title for a web resource.		364ff486-8038-4e10-90a0-dda63b804eb7	projects_and_data_collections|bican	web resource short title	FALSE						1	10/9/24
+WebResource	url	string	FALSE	Path to a resource.		7bc3c2c7-a15c-4f47-bb6e-4423953c0ad2	projects_and_data_collections|bican	web resource universal resource locator	FALSE						1	10/9/24

linkml-schema/source_projects_and_data_collection/gsheet_output/Subsets.tsv

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+Name	Description
+> subset	description
+projects_and_data_collections	A subset of classes that are associated with the projects and data collection schema.
+bican	A subset of classes that are associated with BICAN.

linkml-schema/source_projects_and_data_collection/gsheet_output/ValueSets.tsv

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+variable_name	value	description	given value from spreadsheet (pre-formatting)
+> enum	permissible_value	description	ignore
+AccessControl	OPEN		open
+AccessControl	CONTROLLED		controlled
+CompletionState	COMPLETE		complete
+CompletionState	IN_PROGRESS		in progress
+Modality	ANATOMY		anatomy
+Modality	CELL_MORPHOLOGY		cell morphology
+Modality	CONNECTIVITY		connectivity
+Modality	ELECTROPHYSIOLOGY		electrophysiology
+Modality	EPIGENOMICS		epigenomics
+Modality	GENOMICS		genomics
+Modality	HISTOLOGY_IMAGING		histology imaging
+Modality	MULTIMODAL		multimodal
+Modality	OPTICAL_PHYSIOLOGY		optical physiology
+Modality	POPULATION_IMAGING		population imaging
+Modality	PROTEIN_QUANTIFICATION		protein quantification
+Modality	SPATIAL_TRANSCRIPTOMICS		spatial transcriptomics
+Modality	TRANSCRIPTOMICS		transcriptomics
+Species	ARCTIC_GROUND_SQUIRREL		Arctic ground squirrel
+Species	BABOON		baboon
+Species	CHIMPANZEE		chimpanzee
+Species	COMMON_TREE_SHREW		common tree shrew
+Species	COYOTE		coyote
+Species	CRAB-EATING_MACAQUE		crab-eating macaque
+Species	DOMESTIC_CAT		domestic cat
+Species	DOMESTIC_FERRET		domestic ferret
+Species	GRAY_SHORT-TAILED_OPOSSUM		gray short-tailed opossum
+Species	GREEN_MONKEY		green monkey
+Species	HUMAN		human
+Species	MA'S_NIGHT_MONKEY		Ma's night monkey
+Species	MARMOSET		marmoset
+Species	MOUSE		mouse
+Species	NINE-BANDED_ARMADILLO		nine-banded armadillo
+Species	NORWAY_RAT		Norway rat
+Species	PIG		pig
+Species	PIG-TAILED_MACAQUE		pig-tailed macaque
+Species	RABBIT		rabbit
+Species	RHESUS_MACAQUE		rhesus macaque
+Species	SMALL-EARED_GALAGO		small-eared galago
+Species	SQUIRREL_MONKEY		squirrel monkey
+Species	WESTERN_GORILLA		western gorilla
+Subprogram	ACTD		ACTD
+Subprogram	ADMBA		ADMBA
+Subprogram	AHBA		AHBA
+Subprogram	AMBA		AMBA
+Subprogram	AMBCA		AMBCA
+Subprogram	ASCA		ASCA
+Subprogram	BRAINSPAN		BrainSpan
+Subprogram	IVYGBM		IvyGBM
+Subprogram	MICRONSEM		MICrONSEM
+Subprogram	NHP		NHP
+Subprogram	R24_GHOSH		R24 Ghosh
+Subprogram	R24_HERTZANO		R24 Hertzano
+Subprogram	R24_ROPELEWSKI		R24 Ropelewski
+Subprogram	R24_WHITE		R24 White
+Subprogram	RF1_ADEY		RF1 Adey
+Subprogram	RF1_BOYDEN		RF1 Boyden
+Subprogram	RF1_CAI		RF1 Cai
+Subprogram	RF1_CHUNG		RF1 Chung
+Subprogram	RF1_FAN		RF1 Fan
+Subprogram	RF1_HAWRYLYCZ		RF1 Hawrylycz
+Subprogram	RF1_HILLMAN		RF1 Hillman
+Subprogram	RF1_HUANG		RF1 Huang
+Subprogram	RF1_IGLESIAS_GONZALEZ		RF1 Iglesias Gonzalez
+Subprogram	RF1_KIM		RF1 Kim
+Subprogram	RF1_LASKIN		RF1 Laskin
+Subprogram	RF1_LEE		RF1 Lee
+Subprogram	RF1_MACOSKO		RF1 Macosko
+Subprogram	RF1_MITRA		RF1 Mitra
+Subprogram	RF1_MITRA_ZHANG		RF1 Mitra Zhang
+Subprogram	RF1_MUELLER		RF1 Mueller
+Subprogram	RF1_MUKAMEL		RF1 Mukamel
+Subprogram	RF1_NOWAKOWSKI		RF1 Nowakowski
+Subprogram	RF1_REGEV		RF1 Regev
+Subprogram	RF1_REID		RF1 Reid
+Subprogram	RF1_REN		RF1 Ren
+Subprogram	RF1_ROUSSOS		RF1 Roussos
+Subprogram	RF1_SHEPHERD		RF1 Shepherd
+Subprogram	RF1_SHI		RF1 Shi
+Subprogram	RF1_TASIC		RF1 Tasic
+Subprogram	RF1_TILGNER		RF1 Tilgner
+Subprogram	RF1_VOGELSTEIN		RF1 Vogelstein
+Subprogram	RF1_WELCH		RF1 Welch
+Subprogram	RF1_YANG		RF1 Yang
+Subprogram	RF1_YIN		RF1 Yin
+Subprogram	SEA-AD		SEA-AD
+Subprogram	SYNPHYS		SynPhys
+Subprogram	TBI		TBI
+Subprogram	TRANSCHAR		TransChar
+Subprogram	U01_CHUNG		U01 Chung
+Subprogram	U01_DONG		U01 Dong
+Subprogram	U01_ECKER		U01 Ecker
+Subprogram	U01_FENG		U01 Feng
+Subprogram	U01_FISCHL		U01 Fischl
+Subprogram	U01_KRIEGSTEIN		U01 Kriegstein
+Subprogram	U01_LEIN		U01 Lein
+Subprogram	U01_MACOSKO		U01 Macosko
+Subprogram	U01_OSTEN		U01 Osten
+Subprogram	U01_SESTAN		U01 Sestan
+Subprogram	U01_SNYDER-MACKLER		U01 Snyder-Mackler
+Subprogram	U01_YANG		U01 Yang
+Subprogram	U01_ZHANGKUN		U01 ZhangKun
+Subprogram	U01_ZHANGLI		U01 ZhangLi
+Subprogram	U19_ECKER		U19 Ecker
+Subprogram	U19_HUANG		U19 Huang
+Subprogram	U19_ZENG		U19 Zeng
+Subprogram	U24_HAWRYLYCZ		U24 Hawrylycz
+Subprogram	UF1_TASIC		UF1 Tasic
+Subprogram	VISUALBEHAVIOR		VisualBehavior
+Subprogram	VISUALCODING		VisualCoding
+Technique	10X_CHROMIUM_3'_V2_SEQUENCING		10x Chromium 3' v2 sequencing
+Technique	10X_CHROMIUM_3'_V3_SEQUENCING		10x Chromium 3' v3 sequencing
+Technique	10X_GENOMICS_MULTIOME		10X Genomics Multiome
+Technique	ANTEROGRADE_TRACING		anterograde tracing
+Technique	ATAC-SEQ		ATAC-seq
+Technique	CALCIUM_IMAGING		calcium imaging
+Technique	CISI		CISI
+Technique	CLINICAL_OBSERVATION		clinical observation
+Technique	CONFOCAL_MICROSCOPY		confocal microscopy
+Technique	CRE-DEPENDENT_ANTEROGRADE_TRACING		cre-dependent anterograde tracing
+Technique	DNASEQ		DNAseq
+Technique	DROP-SEQ		Drop-seq
+Technique	ELECTRON_MICROSCOPY		electron microscopy
+Technique	ENHANCER_VIRUS_LABELING		enhancer virus labeling
+Technique	FISH		FISH
+Technique	FMOST		fMOST
+Technique	HISTOLOGY		histology
+Technique	IN_SITU_HYBRIDIZATION		in situ hybridization
+Technique	LABORATORY_ASSESSMENT		laboratory assessment
+Technique	LIGHT_SHEET_MICROSCOPY		light sheet microscopy
+Technique	M3C-SEQ		m3C-seq
+Technique	MC-SEQ2		mC-seq2
+Technique	MC-SEQ3		mC-seq3
+Technique	MERFISH		MERFISH
+Technique	MICROARRAY		microarray
+Technique	MORF_GENETIC_SPARSE_LABELING		MORF genetic sparse labeling
+Technique	MOUSELIGHT		mouselight
+Technique	MRI		MRI
+Technique	MULTI_ELECTRODE_EXTRACELLULAR_ELECTROPHYSIOLOGY_TECHNIQUE		multi electrode extracellular electrophysiology technique
+Technique	MULTIPLEX_IMMUNOASSAY		multiplex immunoassay
+Technique	NEURON_MORPHOLOGY_RECONSTRUCTION		neuron morphology reconstruction
+Technique	OCT		OCT
+Technique	OLST		OLST
+Technique	OSMFISH		osmFISH
+Technique	OXFORD_NANOPORE_LONG-READ_SEQUENCING		Oxford Nanopore long-read sequencing
+Technique	PACBIO_LONG-READ_SEQUENCING		PacBio long-read sequencing
+Technique	PAIRED-TAG		Paired-Tag
+Technique	PATCH-SEQ		Patch-seq
+Technique	RETROGRADE_TRACING		retrograde tracing
+Technique	RETROGRADE_TRANSYNAPTIC_TRACING		retrograde transsynaptic tracing
+Technique	RNASEQ		RNAseq
+Technique	SCI-ATAC-SEQ3		sci-ATAC-seq3
+Technique	SCI-RNA-SEQ3		sci-RNA-seq3
+Technique	SEQFISH		seqFISH
+Technique	SHARE-SEQ		SHARE-seq
+Technique	SLIDE-SEQ		Slide-seq
+Technique	SMART-SEQ_V4		SMART-seq v4
+Technique	SMART-SEQ2		Smart-seq2
+Technique	SNARE-SEQ2		SNARE-seq2
+Technique	SNM3C-SEQ		snm3C-seq
+Technique	STPT		STPT
+Technique	TEMPO-SEQ		TempO-seq
+Technique	TRIO_TRACING		TRIO tracing
+Technique	VISOR		VISor
+Technique	WHOLE_CELL_PATCH_CLAMP		whole cell patch clamp
+Technique	WHOLE_GENOME_SEQUENCING		whole genome sequencing
+WebResourceType	INFORMATION	Resource containing additional information about a project or collection, for example an about page on a website.	information
+WebResourceType	VIEW	Resource that typically contains more technical information about the data in a collection, for example a protocol document or a paper.	view
+WebResourceType	EXPLORE	Resource that points to a tool to visualize or explore data in a collection.	explore
+WebResourceType	DOWNLOAD	Resource that points to a location to download data in a collection.	download