From 4677b3cd98a67fccbcda2fed5b1fb9c6751ff359 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 4 Dec 2024 01:28:34 +0000 Subject: [PATCH] generate new version of the linkml model --- linkml-schema/library_generation.yaml | 46 +------------ .../gsheet_output/Prefixes.tsv | 4 +- .../gsheet_output/Relations.tsv | 66 +++++++++---------- .../gsheet_output/Slots.tsv | 2 +- 4 files changed, 40 insertions(+), 78 deletions(-) diff --git a/linkml-schema/library_generation.yaml b/linkml-schema/library_generation.yaml index e521502f6..7a3589a72 100644 --- a/linkml-schema/library_generation.yaml +++ b/linkml-schema/library_generation.yaml @@ -16,6 +16,7 @@ prefixes: schema: http://schema.org/ ncbi: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi NIMP: http://example.org/NIMP/ + bican_prov: https://github.com/brain-bican/models/blob/main/linkml-schema/bican_prov.yaml default_prefix: bican default_range: string subsets: @@ -1846,8 +1847,6 @@ classes: description: Name of person or organism that is the source of a biological sample for scientific study. Many biological samples are generated from a single donor. - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: biological_sex: local_names: @@ -1942,8 +1941,6 @@ classes: a whole brain, brain hemisphere or subdivision with a blade at regular interval. When multiple brain slabs are obtained from the slicing process, an ordinal is assigned to provide information about the relative positioning of the slabs. - category: - pattern: ^bican:[A-Z][A-Za-z]+$ TissueSample: description: The final intact piece of tissue before cell or nuclei prep. This piece of tissue will be used in dissociation and has an region of interest polygon @@ -1982,8 +1979,6 @@ classes: exact_mappings: - NIMP:PD-LJCRCC35 slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269 - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: dissection_was_guided_by: description: The dissection ROI polygon that was used to guide the dissection. @@ -2036,8 +2031,6 @@ classes: exact_mappings: - NIMP:PD-RQRWHS40 slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2 - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: cell_prep_type: local_names: @@ -2112,8 +2105,6 @@ classes: exact_mappings: - NIMP:PD-BERWTM41 slot_uri: bican:bb3fc701-23a7-45c1-890d-7471730e0ec1 - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: enrichment_population: local_names: @@ -2202,8 +2193,6 @@ classes: exact_mappings: - NIMP:PD-XEMDJF38 slot_uri: bican:4c0e6380-e53f-4173-a474-d41e836fefe3 - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: number_of_expected_cells: local_names: @@ -2264,8 +2253,6 @@ classes: exact_mappings: - NIMP:PD-YAAGGG39 slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089 - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: quantity_ng: local_names: @@ -2352,8 +2339,6 @@ classes: exact_mappings: - NIMP:PD-AJJUCC35 slot_uri: bican:f717e254-3630-4342-be7b-4d56376e7afe - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: average_size_bp: local_names: @@ -2437,7 +2422,7 @@ classes: exact_mappings: - NIMP:PD-VLLMWZ60 slot_uri: bican:c94b5d8a-e92d-47af-8c0e-ea3b58be4d06 - alias: R1/R2 index name + alias: R1_R2 index name range: library_r1_r2_index LibraryAliquot: description: One library in the library pool. Each library aliquot in a library @@ -2478,8 +2463,6 @@ classes: exact_mappings: - NIMP:PD-XCXCCC35 slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e - category: - pattern: ^bican:[A-Z][A-Za-z]+$ LibraryPool: description: A library pool is made up of library aliquots from multiple libraries. Each library aliquot in a library pool will have a unique R1/R2 index to allow @@ -2522,8 +2505,6 @@ classes: exact_mappings: - NIMP:PD-KKIAPA48 slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: local_tube_id: local_names: @@ -2557,9 +2538,8 @@ classes: slot_usage: used: description: The brain slab that was annotated by the delineation process. + from_schema: bican_prov range: BrainSlab - category: - pattern: ^bican:[A-Z][A-Za-z]+$ TissueDissection: description: The process of dissecting a tissue sample from a brain slab guided by a dissection region of interest (ROI) delineation. @@ -2576,8 +2556,6 @@ classes: used: description: The brain slab from which the tissue sample was dissected from. range: BrainSlab - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: was_guided_by: description: The dissection ROI polygon which was used to guide the tissue @@ -2603,8 +2581,6 @@ classes: was derived from. range: TissueSample multivalued: true - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: process_date: local_names: @@ -2635,8 +2611,6 @@ classes: cell sample was derived from. range: DissociatedCellSample multivalued: true - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: process_date: local_names: @@ -2664,8 +2638,6 @@ classes: description: The enrichment cell sample splitting process from which the enriched cell sample was generated by. range: EnrichedCellSample - category: - pattern: ^bican:[A-Z][A-Za-z]+$ CellBarcoding: description: The process of adding a molecular barcode to individual cells in a sample. The input will be either dissociated cell sample or enriched cell @@ -2689,8 +2661,6 @@ classes: exactly_one_of: - range: DissociatedCellSample - range: EnrichedCellSample - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: port_well: local_names: @@ -2760,8 +2730,6 @@ classes: description: The input barcoded cell sample from which amplified cDNA was derived from. range: BarcodedCellSample - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: pcr_cycles: local_names: @@ -2824,8 +2792,6 @@ classes: any_of: - range: BarcodedCellSample - range: AmplifiedCdna - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: method: local_names: @@ -2904,8 +2870,6 @@ classes: from. range: LibraryAliquot multivalued: true - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: process_date: local_names: @@ -2941,8 +2905,6 @@ classes: local_name_source: NIMP description: Name of a polygon annotated on a brain slab image delineating a region of interest (ROI) for a tissue sample dissectioning. - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: annotates: description: The brain slab that was annotated by the delineation process. @@ -2964,8 +2926,6 @@ classes: range: LibraryPool digest: {} content_url: {} - category: - pattern: ^bican:[A-Z][A-Za-z]+$ attributes: data_type: description: The type of data in the file diff --git a/linkml-schema/source_library_generation/gsheet_output/Prefixes.tsv b/linkml-schema/source_library_generation/gsheet_output/Prefixes.tsv index 9040acfc8..52bc6bf85 100644 --- a/linkml-schema/source_library_generation/gsheet_output/Prefixes.tsv +++ b/linkml-schema/source_library_generation/gsheet_output/Prefixes.tsv @@ -4,4 +4,6 @@ linkml https://w3id.org/linkml/ bican https://identifiers.org/brain-bican/vocab/ spdx http://spdx.org/rdf/terms# schema http://schema.org/ -ncbi https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi \ No newline at end of file +ncbi https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi +NIMP http://example.org/NIMP/ +bican_prov https://github.com/brain-bican/models/blob/main/linkml-schema/bican_prov.yaml \ No newline at end of file diff --git a/linkml-schema/source_library_generation/gsheet_output/Relations.tsv b/linkml-schema/source_library_generation/gsheet_output/Relations.tsv index 936091b29..4f0427062 100644 --- a/linkml-schema/source_library_generation/gsheet_output/Relations.tsv +++ b/linkml-schema/source_library_generation/gsheet_output/Relations.tsv @@ -1,33 +1,33 @@ -Object Predicate (more general) Predicate (more specific) Subject Multivalued ExactlyOneOf (True/False, default=False) Slot Definition LIMS Object Class NIMP Relationship NIMP Subject Category -> class slot attribute range multivalued ignore description ignore exact_mappings: {curie_prefix: NIMP} ignore -> -BrainSlab was_derived_from Donor|BrainSlab FALSE The donor from which the brain slab was derived from. aibs:lims:specimens has_parent Donor -TissueSample was_derived_from Donor FALSE The donor or brain slab from which the tissue sample was derived from. aibs:lims:specimens has_parent Donor -DissectionRoiDelineation used BrainSlab FALSE The brain slab that was annotated by the delineation process. -DissectionRoiPolygon was_generated_by DissectionRoiDelineation FALSE The delineation process from which the dissection ROI polygon was generated by. -DissectionRoiPolygon annotates BrainSlab FALSE The brain slab that was annotated by the delineation process. has_parent Slab -TissueDissection was_guided_by DissectionRoiPolygon FALSE The dissection ROI polygon which was used to guide the tissue dissection. -TissueDissection used BrainSlab FALSE The brain slab from which the tissue sample was dissected from. -TissueSample was_generated_by TissueDissection FALSE The dissection process from which the tissue sample was generated by. -TissueSample dissection_was_guided_by DissectionRoiPolygon FALSE The dissection ROI polygon that was used to guide the dissection. aibs:lims:specimens has_parent -CellDissociation used TissueSample TRUE The input tissue sample(s) from which the dissociated cell sample was derived from. -DissociatedCellSample was_generated_by CellDissociation FALSE The cell dissociation process from which the dissociated cell sample was generated by. -DissociatedCellSample was_derived_from TissueSample TRUE The input tissue sample(s) from which dissociated cell sample was derived from. aibs:lims:cell_prep_samples has_parent Tissue -CellEnrichment used DissociatedCellSample TRUE The input dissociated cell sample(s) from which the enriched cell sample was derived from. -EnrichedCellSample was_generated_by CellEnrichment|EnrichedCellSampleSplitting FALSE The cell enrichment or sample splitting process from which the enriched cell sample was generated by. -EnrichedCellSample was_derived_from DissociatedCellSample|EnrichedCellSample TRUE TRUE The dissociated or enriched cell sample(s) from which the enriched cell sample was derived from. aibs:lims:facs_well_templates has_parent Dissociated Cell Sample -EnrichedCellSampleSplitting used EnrichedCellSample FALSE The enrichment cell sample splitting process from which the enriched cell sample was generated by. -CellBarcoding used DissociatedCellSample|EnrichedCellSample TRUE TRUE The input dissociated or enriched cell sample(s) from which the barcoded cell sample was derived from. -BarcodedCellSample was_generated_by CellBarcoding FALSE The barcoding process from which the barcoded cell sample is generated from. -BarcodedCellSample was_derived_from DissociatedCellSample|EnrichedCellSample TRUE TRUE The input dissociated or enriched cell sample(s) from which the barcoded cell sample was derived from. aibs:lims:rna_amplifications has_parent Specimen Dissected ROI -CdnaAmplification used BarcodedCellSample FALSE The input barcoded cell sample from which amplified cDNA was derived from. -AmplifiedCdna was_generated_by CdnaAmplification FALSE The cDNA amplification process from which the amplified cDNA was generated by. -AmplifiedCdna was_derived_from BarcodedCellSample FALSE The input barcoded cell sample from which amplified cDNA was derived from. aibs:lims:rna_amplifications has_parent aibs:lims:rna_amplifications -LibraryConstruction used BarcodedCellSample|AmplifiedCdna FALSE The input barcoded cell sample or amplified cDNA from which the library was derived from. -Library was_generated_by LibraryConstruction FALSE The library construction process from which the library was generated by. -Library was_derived_from BarcodedCellSample|AmplifiedCdna FALSE The input barcoded cell sample or amplified cDNA from which the library was derived from. aibs:lims:rseq_library_preps has_parent #N/A -LibraryAliquot was_derived_from Library FALSE The input library from which the library aliquot was derived from. aibs:lims:rseq_experiment_components has_parent Library -LibraryPooling used LibraryAliquot TRUE The input aliquot(s) from which the library pool was derived from. -LibraryPool was_generated_by LibraryPooling FALSE The pooling process from which the library pool was generated by. -LibraryPool was_derived_from LibraryAliquot TRUE The input aliquot(s) from which the library pool was derived from. aibs:lims:rseq_tubes has_parent Library Aliquot -DigitalAsset was_derived_from LibraryPool FALSE \ No newline at end of file +Object Predicate (more general) Predicate (more specific) Subject Multivalued ExactlyOneOf (True/False, default=False) Slot Definition LIMS Object Class NIMP Relationship NIMP Subject Category +> class slot attribute range from_schema multivalued ignore description ignore exact_mappings: {curie_prefix: NIMP} ignore +> +BrainSlab was_derived_from Donor|BrainSlab FALSE The donor from which the brain slab was derived from. aibs:lims:specimens has_parent Donor +TissueSample was_derived_from Donor FALSE The donor or brain slab from which the tissue sample was derived from. aibs:lims:specimens has_parent Donor +DissectionRoiDelineation used BrainSlab bican_prov FALSE The brain slab that was annotated by the delineation process. +DissectionRoiPolygon was_generated_by DissectionRoiDelineation FALSE The delineation process from which the dissection ROI polygon was generated by. +DissectionRoiPolygon annotates BrainSlab FALSE The brain slab that was annotated by the delineation process. has_parent Slab +TissueDissection was_guided_by DissectionRoiPolygon FALSE The dissection ROI polygon which was used to guide the tissue dissection. +TissueDissection used BrainSlab FALSE The brain slab from which the tissue sample was dissected from. +TissueSample was_generated_by TissueDissection FALSE The dissection process from which the tissue sample was generated by. +TissueSample dissection_was_guided_by DissectionRoiPolygon FALSE The dissection ROI polygon that was used to guide the dissection. aibs:lims:specimens has_parent +CellDissociation used TissueSample TRUE The input tissue sample(s) from which the dissociated cell sample was derived from. +DissociatedCellSample was_generated_by CellDissociation FALSE The cell dissociation process from which the dissociated cell sample was generated by. +DissociatedCellSample was_derived_from TissueSample TRUE The input tissue sample(s) from which dissociated cell sample was derived from. aibs:lims:cell_prep_samples has_parent Tissue +CellEnrichment used DissociatedCellSample TRUE The input dissociated cell sample(s) from which the enriched cell sample was derived from. +EnrichedCellSample was_generated_by CellEnrichment|EnrichedCellSampleSplitting FALSE The cell enrichment or sample splitting process from which the enriched cell sample was generated by. +EnrichedCellSample was_derived_from DissociatedCellSample|EnrichedCellSample TRUE TRUE The dissociated or enriched cell sample(s) from which the enriched cell sample was derived from. aibs:lims:facs_well_templates has_parent Dissociated Cell Sample +EnrichedCellSampleSplitting used EnrichedCellSample FALSE The enrichment cell sample splitting process from which the enriched cell sample was generated by. +CellBarcoding used DissociatedCellSample|EnrichedCellSample TRUE TRUE The input dissociated or enriched cell sample(s) from which the barcoded cell sample was derived from. +BarcodedCellSample was_generated_by CellBarcoding FALSE The barcoding process from which the barcoded cell sample is generated from. +BarcodedCellSample was_derived_from DissociatedCellSample|EnrichedCellSample TRUE TRUE The input dissociated or enriched cell sample(s) from which the barcoded cell sample was derived from. aibs:lims:rna_amplifications has_parent Specimen Dissected ROI +CdnaAmplification used BarcodedCellSample FALSE The input barcoded cell sample from which amplified cDNA was derived from. +AmplifiedCdna was_generated_by CdnaAmplification FALSE The cDNA amplification process from which the amplified cDNA was generated by. +AmplifiedCdna was_derived_from BarcodedCellSample FALSE The input barcoded cell sample from which amplified cDNA was derived from. aibs:lims:rna_amplifications has_parent aibs:lims:rna_amplifications +LibraryConstruction used BarcodedCellSample|AmplifiedCdna FALSE The input barcoded cell sample or amplified cDNA from which the library was derived from. +Library was_generated_by LibraryConstruction FALSE The library construction process from which the library was generated by. +Library was_derived_from BarcodedCellSample|AmplifiedCdna FALSE The input barcoded cell sample or amplified cDNA from which the library was derived from. aibs:lims:rseq_library_preps has_parent #N/A +LibraryAliquot was_derived_from Library FALSE The input library from which the library aliquot was derived from. aibs:lims:rseq_experiment_components has_parent Library +LibraryPooling used LibraryAliquot TRUE The input aliquot(s) from which the library pool was derived from. +LibraryPool was_generated_by LibraryPooling FALSE The pooling process from which the library pool was generated by. +LibraryPool was_derived_from LibraryAliquot TRUE The input aliquot(s) from which the library pool was derived from. aibs:lims:rseq_tubes has_parent Library Aliquot +DigitalAsset was_derived_from LibraryPool FALSE \ No newline at end of file diff --git a/linkml-schema/source_library_generation/gsheet_output/Slots.tsv b/linkml-schema/source_library_generation/gsheet_output/Slots.tsv index ed3a81b31..edf8eb2f0 100644 --- a/linkml-schema/source_library_generation/gsheet_output/Slots.tsv +++ b/linkml-schema/source_library_generation/gsheet_output/Slots.tsv @@ -28,7 +28,7 @@ Library library prep pass-fail pass_fail_result 6817ede2-7ead-402d-9dbc-131aca62 LibraryConstruction library prep set set b124ffa9-9134-4a61-a30d-bb191b2fc7fa Library set, containing multiple library_names that were processed at the same time. TRUE FALSE string 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 TRUE FALSE float 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 TRUE FALSE float 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. FALSE FALSE library_r1_r2_index library_r1_r2_index analysis|tracking Library PD-VLLMWZ60 library_r1_r2_index 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. FALSE FALSE library_r1_r2_index library_r1_r2_index 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'. FALSE FALSE string 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 FALSE sex sex Donor PD-LXUBTM45 sex NIMP