From 8cadb9f206d4361394fe6ef1c15c343e2a6acc53 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Thu, 15 Oct 2026 14:18:20 -0400 Subject: [PATCH 1/2] setup base class --- .../schema/common_access_model.yaml | 157 ++++++++++++++++++ 1 file changed, 157 insertions(+) diff --git a/src/common_access_model/schema/common_access_model.yaml b/src/common_access_model/schema/common_access_model.yaml index 61919d10..99219db3 100644 --- a/src/common_access_model/schema/common_access_model.yaml +++ b/src/common_access_model/schema/common_access_model.yaml @@ -662,6 +662,52 @@ classes: assay_type: required: true + + SequencingAssay: + title: Sequencing Experiment Assay + description: A sequencing experiment performed on a Biospecimen. + is_a: Assay + slots: + - sequencing_center_id + - library_name + - experiment_date + - experiment_strategy + - is_paired_end + - platform + - instrument_model + - total_reads + - is_adapter_trimmed + - adapter_sequencing # required if is_adapter_trimmed is false + - quality_scale + - reference_genome + - workflow_type + - workflow_tool + - workflow_version + - workflow_endpoint + - flow_cell + - lane_number + + GenomicsAssay: + title: WGS/WXS Assay + description: A whole genome or whole exome sequencing experiment performed on a Biospecimen. + is_a: SequencingAssay + slots: + - max_insert_size + - mean_insert_size + - mean_depth + - mean_read_length + - target_capture_kit + + TranscriptomicsAssay: + title: RNA Sequencing Assay + description: An RNA sequencing experiment performed on a Biospecimen. + is_a: SequencingAssay + slots: + - library_strand + - library_prep # is this equivalent to library_construction? + - library_selection + + Dataset: title: Dataset description: Set of files grouped together for release. @@ -1354,3 +1400,114 @@ slots: description: The date that data collection started. May include only a year. #TODO: We could re-evaluate these as dates, but that may be too implementation specific range: string + + +# Sequencing Assay slots + reference_genome: + title: Reference Genome + description: >- + The reference genome build this file is aligned to or was generated + against. + range: EnumReferenceGenome + workflow_type: + title: Workflow Type + description: >- + The type of workflow that produced this file. (Kids First + Dataservice field: worflow_type) + range: string + workflow_tool: + title: Workflow Tool + description: >- + The tool used by the workflow that produced this file. (Kids First + Dataservice field: worflow_tool) + range: string + workflow_version: + title: Workflow Version + description: The version of the workflow tool used to produce this file. + range: string + flow_cell: + title: Flow Cell + description: The flow cell identifier for this read group. + range: string + lane_number: + title: Lane Number + description: The lane number for this read group. + range: integer + quality_scale: + title: Quality Scale + description: The quality score scale used for this read group. + range: EnumReadGroupQualityScale + library_name: + title: Library Name + description: The name of the sequencing library. + range: string + experiment_date: + title: Experiment Date + description: The date the sequencing experiment was performed. + range: date + experiment_strategy: + title: Experiment Strategy + description: The sequencing strategy used. + range: EnumSequencingStrategy + library_strand: + title: Library Strand + description: The strandedness of the sequencing library. + range: EnumLibraryStrand + library_prep: + title: Library Prep + description: The library preparation method used. + range: EnumLibraryPrep + library_selection: + title: Library Selection + description: The library selection method used. + range: EnumLibrarySelection + is_paired_end: + title: Is Paired End + description: Whether the sequencing reads are paired-end. + range: boolean + platform: + title: Platform + description: The sequencing platform used. + range: EnumSequencingPlatform + instrument_model: + title: Instrument Model + description: The sequencing instrument model used. + range: EnumSequencingInstrument + max_insert_size: + title: Max Insert Size + description: The maximum insert size, in base pairs. + range: integer + mean_insert_size: + title: Mean Insert Size + description: The mean insert size, in base pairs. + range: float + mean_depth: + title: Mean Depth + description: The mean sequencing depth of coverage. + range: float + total_reads: + title: Total Reads + description: The total number of reads generated. + range: integer + mean_read_length: + title: Mean Read Length + description: The mean read length, in base pairs. + range: integer + target_capture_kit: + title: Target Capture Kit + description: The target capture kit used, if any. + range: string + read_pair_number: + title: Read Pair Number + description: >- + The read pair number (1 or 2) for this read group, for paired-end + sequencing. + range: integer + is_adapter_trimmed: + title: Is Adapter Trimmed + description: Whether adapter sequences were trimmed. + range: boolean + adapter_sequencing: + title: Adapter Sequence + description: The adapter sequence used, if known. + range: string \ No newline at end of file From 7808acc13b087edccd45ab5f863c40a26046e003 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 26 Oct 2026 15:11:47 -0400 Subject: [PATCH 2/2] add paired enums --- .../schema/common_access_model.yaml | 5 +++ .../schema/enums/EnumAnalyteType.yaml | 22 ++++++++++ .../schema/enums/EnumLibraryPrep.yaml | 23 ++++++++++ .../schema/enums/EnumLibrarySelection.yaml | 43 +++++++++++++++++++ 4 files changed, 93 insertions(+) create mode 100644 src/common_access_model/schema/enums/EnumAnalyteType.yaml create mode 100644 src/common_access_model/schema/enums/EnumLibraryPrep.yaml create mode 100644 src/common_access_model/schema/enums/EnumLibrarySelection.yaml diff --git a/src/common_access_model/schema/common_access_model.yaml b/src/common_access_model/schema/common_access_model.yaml index 99219db3..aea5b0e1 100644 --- a/src/common_access_model/schema/common_access_model.yaml +++ b/src/common_access_model/schema/common_access_model.yaml @@ -29,6 +29,7 @@ prefixes: NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_ CAMO: https://github.com/include-dcc/camo/releases/latest/download/camo.owl# ucum: https://units-of-measurement.org/ + valuesets: https://w3id.org/valuesets/ default_prefix: cam default_range: string @@ -65,6 +66,10 @@ imports: - enums/EnumUnknownOther - enums/EnumVitalStatus + - enums/EnumAnalyteType + - enums/EnumLibraryPrep + - enums/EnumLibrarySelection + types: ptGlobalID: uri: xsd:string diff --git a/src/common_access_model/schema/enums/EnumAnalyteType.yaml b/src/common_access_model/schema/enums/EnumAnalyteType.yaml new file mode 100644 index 00000000..c6322084 --- /dev/null +++ b/src/common_access_model/schema/enums/EnumAnalyteType.yaml @@ -0,0 +1,22 @@ +id: https://includedcc.org/common-access-model/EnumAnalyteType +name: EnumAnalyteType +enums: + EnumAnalyteType: + description: The type of analyte that was extracted from the biospecimen. + reachable_from: + source_ontology: bioregistry:ncit + source_nodes: + - C706 + include_self: true + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + C449: + title: DNA + description: A long linear double-stranded polymer formed from nucleotides attached to a deoxyribose backbone and found in the nucleus of a cell; associated with the transmission of genetic information. + meaning: C449 + C812: + title: RNA + description: Single-stranded long chain of nucleotides containing ribose. + meaning: C812 \ No newline at end of file diff --git a/src/common_access_model/schema/enums/EnumLibraryPrep.yaml b/src/common_access_model/schema/enums/EnumLibraryPrep.yaml new file mode 100644 index 00000000..b7c67102 --- /dev/null +++ b/src/common_access_model/schema/enums/EnumLibraryPrep.yaml @@ -0,0 +1,23 @@ +--- +id: https://includedcc.org/common-access-model/EnumLibraryPrep +name: EnumLibraryPrep +enums: + EnumLibraryPrep: + description: + reachable_from: + source_ontology: bioregistry:obi + source_nodes: + - OBI:0666666 + include_self: true + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + OBI:0000848: + title: polyA RNA extraction + description: A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. + meaning: OBI:0000848 + OBI:0000855: + title: total RNA depletion + description: A RNA extraction process in which total cellular and organelle RNA are extracted. + meaning: OBI:0000855 \ No newline at end of file diff --git a/src/common_access_model/schema/enums/EnumLibrarySelection.yaml b/src/common_access_model/schema/enums/EnumLibrarySelection.yaml new file mode 100644 index 00000000..39b1f72e --- /dev/null +++ b/src/common_access_model/schema/enums/EnumLibrarySelection.yaml @@ -0,0 +1,43 @@ +--- +id: https://includedcc.org/common-access-model/EnumLibrarySelection +name: EnumLibrarySelection +enums: + EnumLibrarySelection: + description: + reachable_from: + source_ontology: bioregistry:ncit + source_nodes: + - C15241 + include_self: true + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + C163986: + title: Hybrid Selection + description: A genomic library where the sample has been subjected to enrichment via nucleic acid hybridization. + meaning: C163986 + C17003: + title: PCR + description: A method for amplifying a DNA base sequence using multiple rounds of heat denaturation of the DNA and annealing of oligonucleotide primers complementary to flanking regions in the presence of a heat-stable polymerase + meaning: C17003 + C163987: + title: Affinity Enrichment + description: A genomic library where the sample has been subjected to enrichment via binding to a target protein or oligonucleotide prior to molecular analysis. + meaning: C163987 + C163988: + title: Poly-T Enrichment + description: A genomic library where the sample has been subjected to enrichment via binding to immobilized poly-T oligonucleotides, which will preferentially isolate polyadenylated (poly-A) RNAs. + meaning: C163988 + C163989: + title: Random + description: A genomic library constructed to generate random DNA fragments by subjecting a genomic sample to either amplification using random primers or fragmentation via exposure to restriction enzymes or shear stress. + meaning: C163989 + C163990: + title: rRNA Depletion + description: A genomic library where the sample has been subjected to a ribosomal RNA depletion step before it is amplified. + meaning: C163990 + C163991: + title: miRNA Size Fractionation + description: A RNA library that has been fractionated by size exclusion methods to enrich for microRNAs. + meaning: C163991 \ No newline at end of file