[awarkow]

Summary

This PR adresses #89 by adding sequencing-specific assay classes to the Common Access Model. They extend the existing generic Assay class so we can capture experiment metadata for whole genome, whole exome and RNA sequencing data.

New Assay Classes

The new classes form a hierarchy under the existing Assay class:
Assay
└── SequencingAssay
├── GenomicsAssay (WGS/WXS)
└── TranscriptomicsAssay (RNA-Seq)

Each subclass inherits all slots from its parent. Every sequencing assay therefore keeps the core Assay fields (assay_id, subject_id, sample_id, file_id, assay_type, etc.) and adds its own experiment metadata.

SequencingAssay

Sequencing Experiment Assay: a sequencing experiment performed on a Biospecimen. This is the shared base for all sequencing assays.

Slot	Range	Description
sequencing_center_id		The sequencing center that performed the experiment
library_name	string	Name of the sequencing library
experiment_date	date	Date the sequencing experiment was performed
experiment_strategy	EnumSequencingStrategy	Sequencing strategy used
is_paired_end	boolean	Whether reads are paired-end
platform	EnumSequencingPlatform	Sequencing platform used
instrument_model	EnumSequencingInstrument	Sequencing instrument model used
total_reads	integer	Total number of reads generated
is_adapter_trimmed	boolean	Whether adapter sequences were trimmed
adapter_sequencing	string	Adapter sequence used, if known (expected when is_adapter_trimmed is false)
quality_scale	EnumReadGroupQualityScale	Quality score scale used for the read group
reference_genome	EnumReferenceGenome	Reference genome build the data was aligned to or generated against
workflow_type	string	Type of workflow that produced the file (Kids First Dataservice: workflow_type)
workflow_tool	string	Tool used by the workflow (Kids First Dataservice: workflow_tool)
workflow_version	string	Version of the workflow tool
workflow_endpoint		Workflow endpoint
flow_cell	string	Flow cell identifier for the read group
lane_number	integer	Lane number for the read group

GenomicsAssay

WGS/WXS Assay: a whole genome or whole exome sequencing experiment performed on a Biospecimen. It extends SequencingAssay with alignment and coverage metrics.

Slot	Range	Description
max_insert_size	integer	Maximum insert size (bp)
mean_insert_size	float	Mean insert size (bp)
mean_depth	float	Mean sequencing depth of coverage
mean_read_length	integer	Mean read length (bp)
target_capture_kit	string	Target capture kit used, if any (relevant for WXS)

TranscriptomicsAssay

RNA Sequencing Assay: an RNA sequencing experiment performed on a Biospecimen. It extends SequencingAssay with library construction details.

Slot	Range	Description
library_strand	EnumLibraryStrand	Strandedness of the sequencing library
library_prep	EnumLibraryPrep	Library preparation method
library_selection	EnumLibrarySelection	Library selection method

New Enums

Caution

Work in progress. The new slots reference several enums. Only the 3 below are defined so far. Need to pair others with correct ontologies

EnumLibraryPrep

Library preparation methods for RNA sequencing. Values are drawn from OBI and constrained to subclasses of an OBI source node.

Value	Title	Description
OBI:0000848	polyA RNA extraction	An RNA extraction process, typically using poly dT oligomers, whose desired output material is polyA RNA.
OBI:0000855	total RNA depletion	An RNA extraction process in which total cellular and organelle RNA are extracted.

EnumAnalyteType

The type of analyte extracted from the biospecimen. Values are drawn from NCIt and constrained to subclasses of NCIt C706 (including the source node itself).

Value	Title	Description
C449	DNA	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.
C812	RNA	Single-stranded long chain of nucleotides containing ribose.

EnumLibrarySelection

Library selection methods used to enrich or select nucleic acid for sequencing. Values are drawn from NCIt and constrained to subclasses of NCIt C15241 (including the source node itself).

Value	Title	Description
C163986	Hybrid Selection	A genomic library where the sample has been subjected to enrichment via nucleic acid hybridization.
C17003	PCR	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.
C163987	Affinity Enrichment	A genomic library where the sample has been subjected to enrichment via binding to a target protein or oligonucleotide prior to molecular analysis.
C163988	Poly-T Enrichment	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.
C163989	Random	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.
C163990	rRNA Depletion	A genomic library where the sample has been subjected to a ribosomal RNA depletion step before it is amplified.
C163991	miRNA Size Fractionation	A RNA library that has been fractionated by size exclusion methods to enrich for microRNAs.

Open Questions

• Is library_prep the same thing as library_construction? If so, should we rename or alias it?
• Should adapter_sequencing be conditionally required when is_adapter_trimmed is false? Can we enforce this with a LinkML rule?