added 'bican_core' to 'from_schema' for 'content_url' slot in library_generation model and regenerated yaml. also renamed 'local_names' tab to slots and the old 'slots' tab to 'attributes

Author: puja-trivedi

linkml-schema/library_generation.yaml

@@ -1822,9 +1822,6 @@ enums:
       years:
         description: years
         meaning: NIMP:PD-AVAVEV39
-slots:
-  content_url:
-    from_schema: https://identifiers.org/brain-bican/library-generation-schema
 classes:
   Donor:
     description: A person or organism that is the source of a biological sample for
@@ -2962,7 +2959,8 @@ classes:
         range: LibraryPool
       digest:
         from_schema: bican_core
-      content_url: {}
+      content_url:
+        from_schema: bican_core
     attributes:
       data_type:
         description: The type of data in the file.

linkml-schema/source_library_generation/gsheet.yaml

@@ -4,15 +4,15 @@ sheets:
     gid: "1511023596"
   - name: "Relations"
     gid: "503493337"
-  - name: "LocalNames"
-    gid: "1773206664"
   - name: "Slots"
+    gid: "1773206664"
+  - name: "Attributes"
     gid: "990672642"
+  - name: "ValueSets"
+    gid: "475538568"
   - name: "Subsets"
     gid: "1299830797"
   - name: "Prefixes"
     gid: "621222810"
   - name: "Schema"
     gid: "1383357145"
-  - name: "ValueSets"
-    gid: "475538568"

linkml-schema/source_library_generation/gsheet_output/Attributes.tsv

@@ -0,0 +1,41 @@
+SubGroup/LinkML Class Name	Proposed BICAN Field	LinkML Slot or Attribute Name	BICAN UUID	Aliases	Definition	Data Type	Multivalued	Permissible Values	Nullable	Data Examples	Min Value	Max Value	Unit	Statistical Type	Subsets	Notes	NIMP Category	NIMP Terminology NHash	NIMP Variable Name	NIMP Variable Name: Source
+> class	alias	attribute	slot_uri: {curie_prefix: bican}	ignore	description	range	multivalued	ignore	ignore	ignore	ignore	ignore	ignore	ignore	in_subset	ignore	ignore	exact_mappings: {curie_prefix: NIMP}	local_names	local_names
+>															internal_separator: "|"				inner_key: local_name_value	inner_key: local_name_source
+AmplifiedCdna	amplified cDNA amplified quantity ng	quantity_ng	0db79d05-8612-4896-b9d3-eb1558841449	amplified quantity ng	Amount of cDNA produced after cDNA amplification measured in nanograms.	float	FALSE		TRUE						analysis		Amplified cDNA	PD-TITIIC26	amplified_cdna_amplified_quantity_ng	NIMP
+CdnaAmplification	amplified cDNA PCR cycles	pcr_cycles	3827634c-3f8f-4760-b358-86ce4b030238	cDNA amplification cycles	Number of PCR cycles used during cDNA amplification for this cDNA.	integer	FALSE		TRUE						analysis		Amplified cDNA	PD-OKOKQD38	amplified_cdna_pcr_cycles	NIMP
+CdnaAmplification	cDNA amplification process date	process_date	6cc333e7-9b98-497f-b7b1-eae904db2400	cDNA amplification date	Date of cDNA amplification.	date	FALSE		TRUE								Amplified cDNA	PD-BYBYBY24	amplified_cdna_preparation_date	NIMP
+AmplifiedCdna	amplified cDNA RNA amplification pass-fail	pass_fail_result	bc62bdb2-7dc8-4404-bb84-ce0bbcae59e5	cDNA amplification pass-fail result	Pass or Fail result based on qualitative assessment of cDNA yield and size.	amplified_cdna_rna_amplification_pass_fail	FALSE	amplified_cdna_rna_amplification_pass_fail	TRUE						analysis		Amplified cDNA	PD-XXXXFQ31	amplified_cdna_rna_amplification_pass_fail	NIMP
+AmplifiedCdna	amplified cDNA percent cDNA longer than 400bp	percent_cdna_longer_than_400bp	8d150467-f69e-461c-b54c-bcfd22f581e5	cDNA amplification percent cDNA greater than 400bp	QC metric to measure mRNA degradation of cDNA.  Higher % is higher quality starting material.  Over 400bp is used as a universal cutoff for intact (full length) vs degraded cDNA and is a common output from Bioanalyzer and Fragment Analyzer elecropheragrams.	float	FALSE		TRUE						analysis		Amplified cDNA	PD-JJJJWD35	amplified_cdna_percent_cdna_longer_than_400bp	NIMP
+CdnaAmplification	cDNA amplification set	set	42e98a88-50b3-4ea2-871b-2142f6a0dfdd		cDNA amplification set, containing multiple amplified_cDNA_names that were processed at the same time.	string	FALSE		TRUE						analysis		Amplified cDNA	PD-SCSCTM41	cdna_amplification_set	NIMP
+CellBarcoding	barcoded cell sample port well 	port_well	aca38100-d245-4be4-9be3-ba27192779fe	10x chip port well	Specific position of the loaded port of the 10x chip.  An Enriched or Dissociated Cell Sample is loaded into a port on a chip (creating a Barcoded Cell Sample). Can be left null for non-10x methods.	string	FALSE		TRUE						analysis		Barcoded Cell Sample	PD-KJKJZK32	barcoded_cell_sample_port_well	NIMP
+CellBarcoding	barcoded cell input quantity count	input_quantity	aa534269-7c9b-4b63-b990-eea8cda56d0e		Number of enriched or dissociated cells/nuclei going into the barcoding process.	integer	FALSE		TRUE						analysis		Barcoded Cell Sample	PD-ZZZZWQ40	barcoded_cell_input_quantity_count	NIMP
+BarcodedCellSample	expected cell capture	number_of_expected_cells	f10e928d-5a2b-4943-af18-d8fe5d05528d		Expected number of cells/nuclei of a barcoded_cell_sample that will be barcoded and available for sequencing.  This is a derived number from 'Barcoded cell input quantity count' that is dependent on the "capture rate" of the barcoding method.  It is usually a calculated fraction of the 'Barcoded cell input quantity count' going into the barcoding method.	integer	FALSE		TRUE						analysis		Barcoded Cell Sample	PD-ONONEV39	barcoded_cell_sample_number_of_expected_cells	NIMP
+CellBarcoding		process_date			Date of cell barcoding process.		FALSE										Barcoded Cell Sample	PD-SHSHZS25	barcoded_cell_sample_preparation_date	NIMP
+CellBarcoding		method			Standardized nomenclature to describe the general barcoding method used.  For example: Multiome, ATAC Only, GEX Only or snm3C-seq. 	barcoded_cell_sample_technique	FALSE	barcoded_cell_sample_technique									Barcoded Cell Sample	PD-TDTDDF25	barcoded_cell_sample_technique	NIMP
+DissociatedCellSample	dissociated cell sample cell prep type	cell_prep_type	baae4ac3-f959-4594-b943-3a82ec19bd34	cell prep type	The type of cell preparation. For example: Cells, Nuclei. This is a property of dissociated_cell_sample.	dissociated_cell_sample_cell_prep_type	FALSE	dissociated_cell_sample_cell_prep_type	FALSE						analysis|tracking		Dissociated Cell Sample	PD-RELLGO26	dissociated_cell_sample_cell_prep_type	NIMP
+DissociatedCellSample	dissociated cell oligo tag name	cell_source_oligo_name	184abbaf-baff-4b5f-b51e-dd38de6006af		Name of cell source oligo used in cell plexing.  The oligo molecularly tags all the cells in the dissociated cell sample and allows separate dissociated cell samples to be combined downstream in the barcoded cell sample.  The oligo name is associated with a sequence in a lookup table.  This sequence will be needed during alignment to associate reads with the parent source dissociated cell sample.  	dissociated_cell_sample_cell_label_barcode	FALSE	dissociated_cell_sample_cell_label_barcode	TRUE								Dissociated Cell Sample	PD-CFCFPS27	dissociated_cell_sample_cell_label_barcode	NIMP
+CellDissociation		process_date			Date of cell dissociation process.		FALSE										Dissociated Cell Sample	PD-BUBUFE27	dissociated_cell_sample_preparation_date	NIMP
+EnrichedCellSample	enrichment population	enrichment_population	875f1c70-f5aa-45e3-94b9-5e482f6c4830		Actual percentage of cells as a result of using set of fluorescent marker label(s) to enrich dissociated_cell_sample with desired mix of cell populations.  This plan can also be used to describe 'No FACS' where no enrichment was performed.  This is a property of enriched_cell_prep_container.	string	FALSE		TRUE						analysis		Enriched Cell Sample	PD-TZTZPI37	enrichment_population	NIMP
+EnrichedCellSample		cell_source_oligo_name			Name of cell source oligo used in cell plexing.  The oligo molecularly tags all the cells in the enriched cell sample and allows separate enriched cell samples to be combined downstream in the barcoded cell sample.  The oligo name is associated with a sequence in a lookup table.  This sequence will be needed during alignment to associate reads with the parent source enriched cell sample.		FALSE										Enriched Cell Sample	PD-CFCFPS27	enriched_cell_sample_cell_label_barcode	NIMP
+CellEnrichment		process_date			Date of cell enrichment process.		FALSE										Enriched Cell Sample	PD-PFPFFC28	enriched_cell_sample_preparation_date	NIMP
+EnrichedCellSample		histone_modification_marker			Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used in conjunction with an Enriched Cell Source Barcode in order to combine multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome method. Each of the Histone antibodies captures an essential part of the epigenome.		FALSE										Enriched Cell Sample	PD-ESESLW44	histone_modification_marker	NIMP
+Library	library avg size bp	average_size_bp	f851eba9-56d1-4472-9d0c-d7f8bc33000a		Average size of the library in terms of base pairs.  This is used to calculate the molarity before pooling and sequencing.	integer	FALSE		TRUE						analysis		Library	PD-VJVJLC46	library_avg_size_bp	NIMP
+LibraryConstruction	library method 	method	7b60d59e-fdd7-4b27-a2d4-cae9b69103a6	library chemistry method	Standardized nomenclature to describe the specific library method used.  This specifies the alignment method required for the library.  For example, 10xV3.1 (for RNASeq single assay), 10xMult-GEX (for RNASeq multiome assay), and 10xMult-ATAC (for ATACSeq multiome assay).	library_technique	FALSE	library_technique	FALSE						analysis|tracking|alignment		Library	PD-AJAJCN35	library_technique	NIMP
+Library	library concentration nm 	concentration_nm	90805b3f-f380-4f23-b159-e7eaa0c8f052		Concentration of library in terms of nM (nMol/L).  Number of molecules is needed for accurate pooling of the libraries and for generating the number of target reads/cell in sequencing.	float	FALSE		TRUE								Library	PD-DCDCLD43	library_concentration_nm	NIMP
+LibraryConstruction	library creation date	process_date	9c2f575d-1b64-451d-894f-656861afe07a	library construction date	Date of library construction.	date	FALSE		TRUE								Library	PD-JCJCNM35	library_preparation_date	NIMP
+LibraryConstruction	library input ng	input_quantity_ng	e4d31d97-722d-4771-a0e4-e6062190f2c1		Amount of cDNA going into library construction in nanograms.	float	FALSE		TRUE						analysis		Library	PD-AFAFXP37	library_input_ng	NIMP
+Library	library prep pass-fail	pass_fail_result	6817ede2-7ead-402d-9dbc-131aca627c6c	library prep pass-fail result	Pass or Fail result based on qualitative assessment of library yield and size.	library_prep_pass_fail	FALSE	library_prep_pass_fail	TRUE						analysis		Library	PD-QHQHQB42	library_prep_pass_fail	NIMP
+LibraryConstruction	library prep set	set	b124ffa9-9134-4a61-a30d-bb191b2fc7fa		Library set, containing multiple library_names that were processed at the same time.	string	FALSE		TRUE						analysis		Library	PD-PCPCVR50	library_prep_set	NIMP
+Library	library quantification fmol	quantity_fmol	4c09ada7-c116-48bc-8fb1-0dcf5c4b939a		Amount of library generated in terms of femtomoles	float	FALSE		TRUE						analysis		Library	PD-JYJYDK42	library_quantification_fmol	NIMP
+Library	library quantification ng	quantity_ng	318b2d3a-dae7-4c63-bfbb-93862b92f63e		Amount of library generated in terms of nanograms	float	FALSE		TRUE								Library	PD-TNTNXP37	library_quantification_ng	NIMP
+Library	R1_R2 index name	r1_r2_index	c94b5d8a-e92d-47af-8c0e-ea3b58be4d06		Name of the pair of library indexes used for sequencing.  Indexes allow libraries to be pooled together for sequencing.  Sequencing output (fastq) are demultiplexed by using the indexes for each library.  The name will be associated with the sequences of i7, i5, and i5as, which are needed by SeqCores for demultiplexing.  The required direction of the sequence (sense or antisense) of the index can differ depending on sequencing instruments.	library_r1_r2_index	FALSE	library_r1_r2_index	FALSE						analysis|tracking		Library	PD-VLLMWZ60	library_r1_r2_index	NIMP
+LibraryPool	library_pool_tube_internal_label	local_tube_id	f1fdea98-7849-4def-a62f-a04cbbf98922	libray pool tube local name	Library Pool Tube local name.  Label of the tube containing the library pool, which is made up of multiple library_aliquots.  This is a Library Lab local tube name, before the pool is aliquoted to the Seq Core provided tube 'Library Pool Tube Name'.	string	FALSE		FALSE						analysis|tracking		Library Pool	PD-WNYWPA48	library_pool_local_tube_id	NIMP
+LibraryPooling		process_date			Date of library pooling process.		FALSE										Library Pool	PD-XUXUNM35	library_pool_preparation_date	NIMP
+Donor		biological_sex	632d3d3f-f85b-4efc-a1ab-010fe417ae81		Biological sex of donor at birth	sex	FALSE	sex									Donor	PD-LXUBTM45	sex	NIMP
+Donor		age_at_death_description	0630a265-4a63-48f4-8853-66b929002306		Text description of the age of death following typical scientific convention for the species or developmental stage. For example: P56, E11.5		FALSE										Donor	PD-ZJZJLE33	age_at_death_description	NIMP
+Donor		age_at_death_reference_point	3bed1f94-9d82-4ed7-afdf-79d896b24dbb		The reference point for an age interval; for example, birth or conception.	age_at_death_reference_point	FALSE	age_at_death_reference_point									Donor	PD-RARAGG39	age_at_death_reference_point	NIMP
+Donor		age_at_death_unit	b5436e99-f0a7-4c30-825d-56b88ee2ac1d		The unit used for representing the donor age from the reference point.	age_at_death_unit	FALSE	age_at_death_unit									Donor	PD-AVAVEV39	age_at_death_unit	NIMP
+Donor		age_at_death_value	57e24d3c-c9c7-4ef3-9809-a35802d563ec		The value representing the donor age from the reference point.	float	FALSE										Donor	PD-FTFTCP24	age_at_death	NIMP
+Donor	donor_species	species	6837cb02-6bd7-4fb8-838c-9062ead96ba4		Species of donor.		FALSE										Donor		donor_species	NIMP
+TissueSample	tissue_sample_structure	structure			Structure of tissue sample.		TRUE												structure	NIMP
+DigitalAsset		data_type			The type of data in the file.