awarkow · Oct 15, 2026 · Oct 26, 2026 · Oct 29, 2026 · Oct 29, 2026 · Nov 3, 2026
diff --git a/fairgenomes_mapping_comparison.md b/fairgenomes_mapping_comparison.md
@@ -0,0 +1,172 @@
+# Sequencing enums vs. FAIR Genomes lookups
+
+Compares the ontology mappings in the `sequencing-assays` branch (`src/common_access_model/schema/enums/`) with the **`main` branch** of the FAIR Genomes semantic schema ([repo](https://github.com/fairgenomes/fairgenomes-semantic-model/tree/main), [lookups](https://github.com/fairgenomes/fairgenomes-semantic-model/tree/main/lookups); paper: [PMC9008059](https://pmc.ncbi.nlm.nih.gov/articles/PMC9008059/)). The repo has no releases or version tags beyond the paper's v1.1, so `main` is the latest state.
+
+FAIR Genomes lookup files used: `SequencingMethods`, `SequencingPlatform`, `SequencingInstrumentModels`, `GenomeAccessions`, `BiospecimenTypes`, `AnalysesPerformed`. `FG:` terms are IDs minted by FAIR Genomes (`https://w3id.org/fair-genomes/resource/FG_xxxxxxx`). FAIR Genomes has no dedicated lookups for analyte type, library prep, library selection, or library strand.
+
+Status key: **Match** = same ID in both; **Differs** = same concept, different ID or ontology; **Ours only** / **FG only** = no counterpart.
+
+## What changed between v1.1 and `main`
+
+Only `SequencingInstrumentModels` changed among the lookups used here: it grew from 39 to 45 rows. The six new rows are `OBI:0002750` MinION, `OBI:0002751` GridION Mk1, `OBI:0002752` PromethION, `OBI:0002632` PacBio Sequel, `OBI:0002633` PacBio Sequel II, and `OBI:0000710` Li-Cor 4300. `SequencingMethods` (35 rows), `SequencingPlatform` (7), `GenomeAccessions` (29) and the sequencing-related terms in `BiospecimenTypes` are unchanged from v1.1 in the rows I checked.
+
+## Sequencing platform
+
+FAIR Genomes uses GENEPIO platform terms; this model uses NCIT sequencing terms. FAIR Genomes also lists the NCIT terms in its `SequencingMethods` lookup (marked below).
+
+| Concept | This model (`EnumSequencingPlatform`) | FAIR Genomes (`SequencingPlatform`) | Status |
+|---|---|---|---|
+| Illumina | NCIT:C146817 | GENEPIO:0001923 (NCIT:C146817 in `SequencingMethods`) | Differs |
+| Complete Genomics | NCIT:C146815 | GENEPIO:0001924 (NCIT:C146815 in `SequencingMethods`) | Differs |
+| Roche 454 | NCIT:C146809 | GENEPIO:0001926 (NCIT:C146809 in `SequencingMethods`) | Differs |
+| ABI SOLiD | NCIT:C146811 | GENEPIO:0002684 (NCIT:C146811 in `SequencingMethods`) | Differs |
+| PacBio / SMRT | NCIT:C146819 | GENEPIO:0001927 (NCIT:C146819 in `SequencingMethods`) | Differs |
+| Ion Torrent / Ion Semiconductor | NCIT:C125894 | GENEPIO:0002683 (NCIT:C125894 in `SequencingMethods`) | Differs |
+| Oxford Nanopore | NCIT:C146818 (in `SequencingMethods` too) | – | Ours only in `SequencingPlatform` |
+| Helicos | – | GENEPIO:0002682 (NCIT:C146816 in `SequencingMethods`) | FG only |
+
+## Sequencing strategy / method
+
+This model: `EnumSequencingStrategy`. FAIR Genomes: `SequencingMethods`.
+
+| Term | This model | FAIR Genomes | Status |
+|---|---|---|---|
+| Whole Genome Sequencing | NCIT:C101294 | NCIT:C101294 | Match |
+| Whole Exome Sequencing | NCIT:C101295 | NCIT:C101295 | Match |
+| mRNA Sequencing | NCIT:C129432 | NCIT:C129432 | Match |
+| MicroRNA Sequencing | NCIT:C156057 | NCIT:C156057 | Match |
+| Targeted Transcriptome Sequencing | NCIT:C158252 | NCIT:C158252 | Match |
+| Targeted Genome Sequencing | NCIT:C158253 | NCIT:C158253 | Match |
+| Oxford Nanopore Sequencing | NCIT:C146818 | NCIT:C146818 | Match |
+| RNA Sequence Analysis | NCIT:C192768 | – | Ours only |
+| Single Cell RNA Sequencing | NCIT:C171152 | – | Ours only |
+| Tumor Panel Sequencing | NCIT:C165600 | – | Ours only |
+| Disease Panel Gene Sequencing | NCIT:C173599 | – | Ours only |
+| Multi-gene Panel Sequencing | NCIT:C198412 | – | Ours only |
+| Targeted Capture Sequencing | NCIT:C204828 | – | Ours only |
+| Methyl-binding Domain Sequencing | NCIT:C204820 | – | Ours only |
+| Methylated DNA Immunoprecipitation Sequencing | NCIT:C204821 | – | Ours only |
+| Methylation-Sensitive Restriction Enzyme Sequencing | NCIT:C204822 | – | Ours only |
+| Proteomics | NCIT:C20085 | EDAM:topic_0121 (in `AnalysesPerformed`, a different field) | Differs |
+| Long Read Sequencing | NCIT:C223895 | – | Ours only |
+| Whole Transcriptome Sequencing | (in `EnumLibraryPrep`: NCIT:C124261) | NCIT:C124261 | Match (different field) |
+| Next Generation Sequencing | – | NCIT:C101293 | FG only |
+| Next Generation Targeted Sequencing | – | NCIT:C130177 | FG only |
+| DNA Sequencing | – | NCIT:C153598 | FG only |
+| Nucleic Acid Sequencing | – | NCIT:C18881 | FG only |
+| DNA Resequencing | – | NCIT:C41254 | FG only |
+| Large-Scale Sequencing | – | NCIT:C19645 | FG only |
+| Population Sequencing | – | NCIT:C135457 | FG only |
+| Shotgun Sequencing | – | NCIT:C19646 | FG only |
+| Whole-Genome Shotgun Sequencing | – | NCIT:C19653 | FG only |
+| Paired-End Sequencing | – | NCIT:C150423 | FG only (library layout) |
+| Sequence-based Typing | – | NCIT:C130180 | FG only |
+| Immune Repertoire Deep Sequencing | – | NCIT:C158249 | FG only |
+| Dideoxy Chain Termination DNA Sequencing | – | NCIT:C19641 | FG only |
+| Capillary Sequencing | – | NCIT:C146814 | FG only |
+| Radioactive Sequencing | – | NCIT:C19658 | FG only |
+| Pyrosequencing | – | NCIT:C99481 | FG only |
+| BGISEQ-500 Sequencing | – | NCIT:C146812 | FG only (platform) |
+
+## Library strand
+
+This model: `EnumLibraryStrand`. FAIR Genomes carries these terms inside `SequencingMethods`.
+
+| Term | This model | FAIR Genomes | Status |
+|---|---|---|---|
+| Unstranded Library Sequencing | NCIT:C150427 | NCIT:C150427 | Match |
+| First-strand Library Sequencing | NCIT:C150428 | NCIT:C150428 | Match |
+| Second-strand Library Sequencing | NCIT:C150426 | NCIT:C150426 | Match |
+
+## Library prep and library selection
+
+FAIR Genomes has no dedicated lookups for these fields, but its `BiospecimenTypes` lookup (a sample-type list) includes the NCIT genomic-library terms that this model uses for library selection. They match by ID.
+
+| Term | This model | FAIR Genomes | Status |
+|---|---|---|---|
+| Hybrid Selected Genomic Library | `EnumLibrarySelection`: NCIT:C163986 | `BiospecimenTypes`: NCIT:C163986 | Match (different field) |
+| Affinity Enriched Genomic Library | `EnumLibrarySelection`: NCIT:C163987 | `BiospecimenTypes`: NCIT:C163987 | Match (different field) |
+| Poly-A Enriched Genomic Library | `EnumLibraryPrep` and `EnumLibrarySelection`: NCIT:C163988 | `BiospecimenTypes`: NCIT:C163988, labelled "Poly-T Enriched Genomic Library" | Match (ID); label differs |
+| Randomly Selected Genomic Library | `EnumLibrarySelection`: NCIT:C163989 | `BiospecimenTypes`: NCIT:C163989 | Match (different field) |
+| rRNA Depleted Genomic Library | `EnumLibrarySelection`: NCIT:C163990 | `BiospecimenTypes`: NCIT:C163990 | Match (different field) |
+| miRNA Size Fractionated Genomic Library | `EnumLibrarySelection`: NCIT:C163991 | `BiospecimenTypes`: NCIT:C163991 | Match (different field) |
+| Whole Transcriptome Sequencing | `EnumLibraryPrep`: NCIT:C124261 | `SequencingMethods`: NCIT:C124261 | Match (different field) |
+| Polymerase Chain Reaction | `EnumLibrarySelection`: NCIT:C17003 | – | Ours only |
+| polyA RNA extraction | `EnumLibraryPrep`: OBI:0000848 | – | Ours only |
+| total RNA depletion | `EnumLibraryPrep`: OBI:0000855 | – | Ours only |
+| Genomic Library (root of your `reachable_from`) | NCIT:C15241 | `BiospecimenTypes`: NCIT:C15241 | Match (different field) |
+| DNA Library / cDNA Library / Sequencing Library | – | `BiospecimenTypes`: NCIT:C16223 / C15727 / C148073 | FG only |
+
+## Sequencing instrument
+
+This model: `EnumSequencingInstrument` (OBI only). FAIR Genomes: `SequencingInstrumentModels` (45 rows; OBI, GENEPIO and FG terms). Rows marked **new** were added after v1.1.
+
+| Instrument | This model | FAIR Genomes | Status |
+|---|---|---|---|
+| Illumina HiSeq 1000 | OBI:0002022 | OBI:0002022 | Match |
+| Illumina HiSeq 2000 | OBI:0002001 | OBI:0002001 | Match |
+| Illumina HiSeq 2500 | OBI:0002002 | OBI:0002002 | Match |
+| Illumina HiSeq 3000 | OBI:0002048 | OBI:0002048 | Match |
+| Illumina HiSeq 4000 | OBI:0002049 | OBI:0002049 | Match |
+| Illumina HiSeq X Ten | OBI:0002129 | FG:0000005 | Differs (OBI term exists) |
+| Illumina HiSeq 1500 | OBI:0003386 | – | Ours only |
+| Illumina HiSeq Sequencer | – | GENEPIO:0001939 | FG only |
+| Illumina HiSeq X Five | – | FG:0000004 | FG only |
+| MiSeq | – | OBI:0002003 | FG only |
+| NextSeq 500 | – | OBI:0002021 | FG only |
+| Genome Analyzer IIx | – | OBI:0002000 | FG only |
+| Illumina Genome Analyzer II | – | OBI:0000703 | FG only |
+| Genome Analyzer IIe | – | OBI:0002027 | FG only |
+| PacBio RS II | – | OBI:0002012 | FG only |
+| PacBio Sequel (**new**) | – | OBI:0002632 | FG only |
+| PacBio Sequel II (**new**) | – | OBI:0002633 | FG only |
+| Oxford Nanopore MinION (**new**) | – | OBI:0002750 | FG only |
+| Oxford Nanopore GridION Mk1 (**new**) | – | OBI:0002751 | FG only |
+| Oxford Nanopore PromethION (**new**) | – | OBI:0002752 | FG only |
+| Li-Cor 4300 DNA Analysis System (**new**) | – | OBI:0000710 | FG only |
+| HeliScope Single Molecule Sequencer | – | OBI:0000717 | FG only |
+| 454 Genome Sequence 20 | – | OBI:0000689 | FG only |
+| 454 Genome Sequencer FLX | – | OBI:0000702 | FG only |
+| 454 Genome Sequencer FLX Titanium | – | GENEPIO:0001936 | FG only |
+| 454 Genome Sequencer | – | GENEPIO:0001937 | FG only |
+| 454 Genome Sequencer Junior | – | GENEPIO:0001938 | FG only |
+| AB SOLiD System | – | OBI:0000696 | FG only |
+| SOLiD 3 Plus System | – | OBI:0002007 | FG only |
+| SOLiD 4 System | – | OBI:0002024 | FG only |
+| SOLiD 4hq System | – | GENEPIO:0001928 | FG only |
+| SOLiD 5500 | – | GENEPIO:0001929 | FG only |
+| SOLiD 5500xl | – | GENEPIO:0001930 | FG only |
+| SOLiD PI System | – | GENEPIO:0001931 | FG only |
+| SOLiD System 2.0 | – | GENEPIO:0001932 | FG only |
+| SOLiD System 3.0 | – | GENEPIO:0001933 | FG only |
+| Ion Torrent PGM | – | GENEPIO:0001935 | FG only |
+| Illumina MiniSeq | – | FG:0000006 | FG only |
+| Illumina iSeq 100 | – | FG:0000007 | FG only |
+| Illumina NextSeq 550 | – | FG:0000008 | FG only |
+| Illumina NextSeq 2000 | – | FG:0000009 | FG only |
+| Illumina NovaSeq 6000 | – | FG:0000010 | FG only |
+| Illumina NextSeq 1000 | – | FG:0000011 | FG only |
+| Illumina NextSeq 550Dx | – | FG:0000012 | FG only |
+| Illumina MiSeqDx | – | FG:0000013 | FG only |
+| Illumina MiSeq FGx | – | FG:0000014 | FG only |
+
+## Reference genome
+
+This model: `EnumReferenceGenome` (LOINC answer codes, no patch levels). FAIR Genomes: `GenomeAccessions` (NCBI assembly accessions, one term per patch release; only the unpatched builds are shown).
+
+| Build | This model | FAIR Genomes | Status |
+|---|---|---|---|
+| GRCh37 | loinc:LA14029-5 | GCF_000001405.13 | Differs |
+| GRCh38 | loinc:LA26806-2 | GCF_000001405.26 | Differs |
+| hg19 | loinc:LA14025-3 | – | Ours only |
+| GRCh37.p1 – p13, GRCh38.p1 – p13, hs38d1 | – | GCA/GCF accessions | FG only |
+
+## Analyte type
+
+This model: `EnumAnalyteType` (SNOMEDCT:24851008 DNA, SNOMEDCT:27888000 RNA). FAIR Genomes has no analyte-type lookup and no generic DNA/RNA terms. Its `BiospecimenTypes` lookup has only more specific nucleic-acid sample types: Blood DNA (NCIT:C158416), Total RNA (NCIT:C163995), Nucleic RNA Sample (NCIT:C174108), Formalin-Fixed Paraffin-Embedded DNA (NCIT:C156435), Formalin-Fixed Paraffin-Embedded RNA (NCIT:C156436), Nucleic Acid Aliquot (NCIT:C171176), Ancient DNA (NCIT:C95946) and Environmental DNA (NCIT:C169106). None of these match your SNOMED CT IDs.
+
+## Not compared
+
+- `EnumSequencingCenter` and `EnumReadGroupQualityScale` have no FAIR Genomes counterpart.
+- FAIR Genomes `NGSKits` (library prep kits, all `FG:` terms) has no counterpart in this model.
+- `main` also has new imaging, treatment and biomarker lookups (e.g. `AssayType`, `ImagingDevice`, `Modality`) that are unrelated to the sequencing enums.
diff --git 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 +66,17 @@ imports:
   - enums/EnumUnknownOther
   - enums/EnumVitalStatus
 
+  - enums/EnumAnalyteType
+  - enums/EnumLibraryStrand
+  - enums/EnumLibraryPrep
+  - enums/EnumLibrarySelection
+  - enums/EnumSequencingInstrument
+  - enums/EnumSequencingCenter
+  - enums/EnumSequencingPlatform
+  - enums/EnumSequencingStrategy
+  - enums/EnumReadGroupQualityScale
+  - enums/EnumReferenceGenome
+
 types:
   ptGlobalID:
     uri: xsd:string
@@ -662,6 +674,52 @@ 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 +1412,122 @@ 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
+  sequencing_center_id:
+    title: Sequencing Center ID
+    description: The unique identifier for the sequencing center that performed the assay.
+    range: EnumSequencingCenter
+  reference_genome:
+    title: Reference Genome
+    description: >-
+      The reference genome build this file is aligned to or was generated
+      against.
+    range: EnumReferenceGenome
+  workflow_endpoint:
+    title: Workflow Endpoint
+    description: The endpoint of the workflow that produced this file. (Kids First Dataservice field - worflow_endpoint)
+    range: string
+  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
diff --git a/src/common_access_model/schema/enums/EnumAnalyteType.yaml b/src/common_access_model/schema/enums/EnumAnalyteType.yaml
@@ -0,0 +1,12 @@
+id: https://includedcc.org/common-access-model/EnumAnalyteType
+name: EnumAnalyteType
+enums:
+  EnumAnalyteType:
+    description: The type of analyte that was extracted from the biospecimen.
+    permissible_values:
+      SNOMEDCT:24851008:
+        title: DNA
+        meaning: SNOMEDCT:24851008
+      SNOMEDCT:27888000:
+        title: RNA
+        meaning: SNOMEDCT:27888000