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Merge branch 'main' into library_source
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‎linkml-schema/library_generation.yaml‎

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description: An activity is something that occurs over a period of time and acts
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upon or with entities; it may include consuming, processing, transforming,
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modifying, relocating, using, or generating entities.
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in_subset:
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- bican
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slots:
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- used
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class_uri: prov:Activity
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ProvEntity:
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mixin: true
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description: An entity is a physical, digital, conceptual, or other kind of thing
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with some fixed aspects; entities may be real or imaginary.
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in_subset:
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- bican
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slots:
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- was_derived_from
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- was_generated_by

‎linkml-schema/source_library_generation/gsheet_output/Classes.tsv‎

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Name Inheritance: is_a Inheritance: mixin Inheritance: slot usage Subsets Definition NIMP API Category AIBS LIMS Primary Table AIBS LIMS Secondary Table
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> class is_a mixins ignore in_subset description exact_mappings: {curie_prefix: NIMP} ignore ignore
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> internal_separator: "|" internal_separator: "|"
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Donor physical entity thing with taxon|ProvEntity A person or organism that is the source of a biological sample for scientific study. Many biological samples are generated from a single donor. Donor aibs:lims:donors
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BrainSlab material sample ProvEntity bican|tissue_specimen A thick flat piece of brain tissue obtained by slicing 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. Slab aibs:lims:specimens
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TissueSample material sample ProvEntity bican|library_generation 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 (ROI) associated with it. Tissue aibs:lims:specimens aibs:lims:cell_prep_roi_plans
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DissociatedCellSample material sample ProvEntity bican|library_generation A collection of dissociated cells or nuclei derived from dissociation of a tissue sample. Dissociated Cell Sample aibs:lims:cell_prep_samples
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EnrichedCellSample material sample ProvEntity bican|library_generation A collection of enriched cells or nuclei after enrichment process, usually via fluorescence-activated cell sorting (FACS) using the enrichment plan, is applied to dissociated cell sample. Enriched Cell Sample aibs:lims:facs_well_templates
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BarcodedCellSample material sample ProvEntity bican|library_generation A collection of molecularly barcoded cells. Input will be either dissociated cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated cell sample or enriched cell sample can lead to multiple barcoded cell samples. The sequences of the molecular barcodes are revealed during alignment of the resulting fastq files for the barcoded cell sample. The barcoded cell sample name and the cell level molecular barcode together uniquely identify a single cell. Barcoded Cell Sample aibs:lims:rna_amplifications
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AmplifiedCdna material sample ProvEntity bican|library_generation A collection of cDNA molecules derived and amplified from an input barcoded cell sample. These cDNA molecules represent the gene expression of each cell, with all cDNA molecules from a given cell retaining that cell's unique barcode from the cell barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods. Amplified cDNA aibs:lims:rna_amplifications
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Library material sample ProvEntity bican|library_generation A collection of fragmented and barcode-indexed DNA molecules for sequencing. An index or barcode is typically introduced to enable identification of library origin to allow libraries to be pooled together for sequencing. Library aibs:lims:rseq_library_preps
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LibraryAliquot material sample ProvEntity bican|library_generation One library in the library pool. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing. The resulting demultiplexed fastq files will include the library aliquot name. A given library may produce multiple library aliquots, which is done in the case of resequencing. Each library aliquot will produce a set of fastq files. Library Aliquot aibs:lims:rseq_experiment_components
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LibraryPool material sample ProvEntity bican|library_generation 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 for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing. Library Pool aibs:lims:rseq_tubes
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DissectionRoiDelineation procedure ProvActivity bican|library_generation The process of outlining a region of interest on a brain slab image to guide the dissection and generation of a tissue sample.
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TissueDissection procedure ProvActivity bican|library_generation The process of dissecting a tissue sample from a brain slab guided by a dissection region of interest (ROI) delineation.
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CellDissociation procedure ProvActivity bican|library_generation The process of generating dissociated cells from an input tissue sample. This process could also introduce a tissue-source barcode (eg cell hashing), allowing mixing of cell dissociation samples at the cell barcoding step.
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CellEnrichment procedure ProvActivity bican|library_generation The process of enriching a dissociated cell sample by including or excluding cells of different types based on an enrichment plan using techniques such as fluorescence-activated cell sorting (FACS). This process could also introduce a tissue-source barcode (eg cell hashing), allowing mixing of cell enriched samples at the cell barcoding step.
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EnrichedCellSampleSplitting procedure ProvActivity bican|library_generation The process of splitting an enriched cell sample into several portions. Each portion may be used by the same or different groups for different scientific studies.
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CellBarcoding procedure ProvActivity bican|library_generation The process of adding a molecular barcode to individual cells in a sample. The input will be either dissociated cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated cell sample or enriched cell sample can lead to multiple barcoded cell samples.
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CdnaAmplification procedure ProvActivity bican|library_generation The process of creating a collection of cDNA molecules derived and amplified from an input barcoded cell sample. A large amount of cDNA is needed to have accurate and reliable sequencing detection of gene expression. This process generates multiple copies of each mRNA transcript (expressed gene) within each cell while retaining the cell's unique barcode from the barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods.
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LibraryConstruction procedure ProvActivity bican|library_generation The process of constructing a library from input material (such as amplified cDNA or barcoded cell sample) derived from one or more cell samples. cDNA is fragmented into smaller pieces appropriate for sequencing and at the same time a library index barcode is incorporated to enable identification of library origin, allowing libraries to be pooled together for sequencing.
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LibraryPooling procedure ProvActivity bican|library_generation The process of constructing of a libray pool by combining library aliquots from a set of input libraries. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing.
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DissectionRoiPolygon entity ProvEntity bican|tissue_specimen A polygon annotated on a brain slab image delineating a region of interest (ROI) for a tissue sample dissectioning. Specimen Dissected ROI

‎linkml-schema/source_library_generation/gsheet_output/LocalNames.tsv‎

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Proposed BICAN Field BICAN UUID SubGroup/LinkML Class Name LinkML Slot or Attribute Name Aliases Definition Nullable Permissible Values Data Type Data Examples Min Value Max Value Unit Statistical Type Subsets Notes NIMP Category NIMP Terminology NHash NIMP Variable Name
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> ignore slot_uri: {curie_prefix: bican} class slot ignore description ignore ignore ignore ignore ignore ignore ignore ignore ignore ignore ignore exact_mappings: {curie_prefix: NIMP} ignore
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tissue sample label 2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269 TissueSample name tissue name|tissue sample label Identifier name for final intact piece of tissue before cell or nuclei prep. This piece of tissue will be used in dissociation and has an ROI associated with it. FALSE text analysis, tracking Tissue PD-LJCRCC35 tissue_sample_local_name
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amplified cDNA label e2606a11-114e-472f-9e05-33f9b6fc3089 AmplifiedCdna name amplified cdna name Name of a collection of cDNA molecules derived and amplified from an input barcoded_cell_sample. These cDNA molecules represent the gene expression of each cell, with all cDNA molecules from a given cell retaining that cell's unique barcode from the cell barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods. TRUE Text analysis Amplified cDNA PD-YAAGGG39 amplified_cdna_local_name
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barcoded cell sample label 4c0e6380-e53f-4173-a474-d41e836fefe3 BarcodedCellSample name barcoded cell sample name Name of a collection of barcoded cells. Input will be either dissociated_cell_sample or enriched_cell_sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated_cell_sample or enriched_cell_sample can lead to multiple barcoded_cell_samples. FALSE Text analysis, tracking, alignment Barcoded Cell Sample PD-XEMDJF38 barcoded_cell_sample_local_name
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dissociated cell sample label 65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2 DissociatedCellSample name dissociated cell sample name Name of a collection of dissociated cells or nuclei derived from dissociation of a tissue sample. TRUE Text analysis Dissociated Cell Sample PD-RQRWHS40 dissociated_cell_sample_local_name
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enriched cell sample name bb3fc701-23a7-45c1-890d-7471730e0ec1 EnrichedCellSample name Name of collection of enriched cells or nuclei after enrichment process (usually via FACS using the Enrichment Plan) applied to dissociated_cell_sample. TRUE Text analysis Enriched Cell Sample PD-BERWTM41 enriched_cell_sample_local_name
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library label f717e254-3630-4342-be7b-4d56376e7afe Library name library name Name of a library, which is a collection of fragmented and barcode-indexed DNA molecules for sequencing. An index or barcode is typically introduced to enable identification of library origin to allow libraries to be pooled together for sequencing. TRUE Text analysis, tracking Library PD-AJJUCC35 library_local_name
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library aliquot label 34191bad-d167-4335-8224-ade897d3728e LibraryAliquot name library aliquot name One library in the library pool. Each Library_aliquot_name in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing. The resulting demultiplexed fastq files will include the library_aliquot_name. FALSE Text analysis, tracking, alignment Library Aliquot PD-XCXCCC35 library_aliquot_local_name
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library pool label 29e0578b-6427-4c93-b29b-bde27fbadeec LibraryPool name local pool name Library lab's library pool name. For some labs this may be the same as "Libray pool tube local name". Other labs distinguish between the local tube label of the library pool and the library pool name provided to SeqCore for tracking. Local Pool Name is used to communicate sequencing status between SeqCore and Library Labs. FALSE Text analysis, tracking Library Pool PD-KKIAPA48 library_pool_local_name
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Donor name 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. Donor donor_local_id
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BrainSlab name Name of a thick flat piece of brain tissue obtained by slicing 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. Slab local_name
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DissectionRoiPolygon name Name of a polygon annotated on a brain slab image delineating a region of interest (ROI) for a tissue sample dissectioning. Specimen Dissected ROI local_name

‎linkml-schema/source_library_generation/gsheet_output/Prefixes.tsv‎

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prefix uri default schema imports title description id
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bican library-generation-schema bican_biolink Library Generation Schema The Library Generation schema is designed to represent types and relationships of samples and digital data assets generated during processes that generate multimodal genomic data. https://identifiers.org/brain-bican/library-generation-schema
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> prefix prefix_reference default_prefix schema imports title description id
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linkml https://w3id.org/linkml/
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bican https://identifiers.org/brain-bican/vocab/
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spdx http://spdx.org/rdf/terms#
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schema http://schema.org/
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ncbi https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi

‎linkml-schema/source_library_generation/gsheet_output/Relations.tsv‎

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Object Predicate (more general) Predicate (more specific) Subject Multivalued ExactlyOneOf Slot Definition LIMS Object Class NIMP Relationship NIMP Subject Category
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> class slot attribute range multivalued exactly_one_of description ignore exact_mappings: {curie_prefix: NIMP} ignore
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> inner_key: range
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BrainSlab was_derived_from Donor FALSE Donor|BrainSlab The donor from which the brain slab was derived from. aibs:lims:specimens has_parent Donor
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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
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DissectionRoiDelineation used BrainSlab FALSE The brain slab that was annotated by the delineation process.
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DissectionRoiPolygon was_generated_by DissectionRoiDelineation FALSE The delineation process from which the dissection ROI polygon was generated by.
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DissectionRoiPolygon annotates BrainSlab FALSE The brain slab that was annotated by the delineation process. has_parent Slab
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TissueDissection was_guided_by DissectionRoiPolygon FALSE The dissection ROI polygon which was used to guide the tissue dissection.
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TissueDissection used BrainSlab FALSE The brain slab from which the tissue sample was dissected from.
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TissueSample was_generated_by TissueDissection FALSE The dissection process from which the tissue sample was generated by.
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TissueSample dissection_was_guided_by DissectionRoiPolygon FALSE The dissection ROI polygon that was used to guide the dissection. aibs:lims:specimens has_parent
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CellDissociation used TissueSample TRUE The input tissue sample(s) from which the dissociated cell sample was derived from.
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DissociatedCellSample was_generated_by CellDissociation FALSE The cell dissociation process from which the dissociated cell sample was generated by.
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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
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CellEnrichment used DissociatedCellSample TRUE The input dissociated cell sample(s) from which the enriched cell sample was derived from.
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EnrichedCellSample was_generated_by FALSE CellEnrichment|EnrichedCellSampleSplitting The cell enrichment or sample splitting process from which the enriched cell sample was generated by.
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EnrichedCellSample was_derived_from TRUE DissociatedCellSample|EnrichedCellSample 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
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EnrichedCellSampleSplitting used EnrichedCellSample FALSE The enrichment cell sample splitting process from which the enriched cell sample was generated by.
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CellBarcoding used TRUE DissociatedCellSample|EnrichedCellSample The input dissociated or enriched cell sample(s) from which the barcoded cell sample was derived from.
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BarcodedCellSample was_generated_by CellBarcoding FALSE The barcoding process from which the barcoded cell sample is generated from.
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BarcodedCellSample was_derived_from TRUE DissociatedCellSample|EnrichedCellSample 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
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CdnaAmplification used BarcodedCellSample FALSE The input barcoded cell sample from which amplified cDNA was derived from.
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AmplifiedCdna was_generated_by CdnaAmplification FALSE The cDNA amplification process from which the amplified cDNA was generated by.
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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
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LibraryConstruction used FALSE BarcodedCellSample|AmplifiedCdna The input barcoded cell sample or amplified cDNA from which the library was derived from.
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Library was_generated_by LibraryConstruction FALSE The library construction process from which the library was generated by.
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Library was_derived_from FALSE BarcodedCellSample|AmplifiedCdna The input barcoded cell sample or amplified cDNA from which the library was derived from. aibs:lims:rseq_library_preps has_parent #N/A
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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
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LibraryPooling used LibraryAliquot TRUE The input aliquot(s) from which the library pool was derived from.
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LibraryPool was_generated_by LibraryPooling FALSE The pooling process from which the library pool was generated by.
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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

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