diff --git a/fairgenomes_mapping_comparison.md b/fairgenomes_mapping_comparison.md new file mode 100644 index 00000000..1ac0262b --- /dev/null +++ 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 index 61919d10..a1a98d6a 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 +66,17 @@ 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 \ No newline at end of file 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..4ff266fd --- /dev/null +++ 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 \ 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..414579a5 --- /dev/null +++ b/src/common_access_model/schema/enums/EnumLibraryPrep.yaml @@ -0,0 +1,25 @@ +--- +id: https://includedcc.org/common-access-model/EnumLibraryPrep +name: EnumLibraryPrep +enums: + EnumLibraryPrep: + description: + 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 + NCIT:C163988: + title: Poly-A Enriched Genomic Library + 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: NCIT:C163988 + NCIT:C124261: + title: Whole Transcriptome Sequencing + description: A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an individual. + meaning: NCIT:C124261 \ 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..40cd6199 --- /dev/null +++ b/src/common_access_model/schema/enums/EnumLibrarySelection.yaml @@ -0,0 +1,58 @@ +--- +id: https://includedcc.org/common-access-model/EnumLibrarySelection +name: EnumLibrarySelection +enums: + EnumLibrarySelection: + description: null + reachable_from: + source_ontology: bioregistry:ncit + source_nodes: + - NCIT:C15241 + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + NCIT:C163986: + title: Hybrid Selected Genomic Library + description: + A genomic library where the sample has been subjected to enrichment + via nucleic acid hybridization. + meaning: NCIT:C163986 + NCIT:C163987: + title: Affinity Enriched Genomic Library + 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: NCIT:C163987 + NCIT:C163988: + title: Poly-A Enriched Genomic Library + 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: NCIT:C163988 + NCIT:C163989: + title: Randomly Selected Genomic Library + 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. The + fragments can then be cloned or sequenced directly. + meaning: NCIT:C163989 + NCIT:C163990: + title: rRNA Depleted Genomic Library + description: + A genomic library where the sample has been subjected to a ribosomal + RNA depletion step before it is amplified. + meaning: NCIT:C163990 + NCIT:C163991: + title: miRNA Size Fractionated Genomic Library + description: + A RNA library that has been fractionated by size exclusion methods + to enrich for microRNAs. + meaning: NCIT:C163991 + NCIT:C17003: + title: Polymerase Chain Reaction + 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. This results in duplication of the targeted DNA region. Newly synthesized DNA strands can subsequently serve as additional templates for the same primer sequences, so that successive rounds of primer annealing, strand elongation, and dissociation produce rapid and highly specific amplification of the desired sequence. PCR also can be used to detect the existence of the defined sequence in a DNA sample. + meaning: NCIT:C17003 diff --git a/src/common_access_model/schema/enums/EnumLibraryStrand.yaml b/src/common_access_model/schema/enums/EnumLibraryStrand.yaml new file mode 100644 index 00000000..d89d86c3 --- /dev/null +++ b/src/common_access_model/schema/enums/EnumLibraryStrand.yaml @@ -0,0 +1,19 @@ +id: https://includedcc.org/common-access-model/EnumLibraryStrand +name: EnumLibraryStrand +enums: + EnumLibraryStrand: + title: Library Strand + description: Sequencing library strandedness, indicating whether the library is single-stranded, double-stranded, or unstranded. + permissible_values: + NCIT:C150427: + title: Unstranded Library Sequencing + description: Non-directional sequencing, where the reads can map from either the transcript strand or its complement. + meaning: NCIT:C150427 + NCIT:C150428: + title: First-strand Library Sequencing + description: Directional sequencing, where the first read (or the only read in case of single end reads) is from the complement strand. + meaning: NCIT:C150428 + NCIT:C150426: + title: Second-strand Library Sequencing + description: Directional sequencing, where the first read of the read pair (or in case of single end reads, the only read) is from the transcript strand. + meaning: NCIT:C150426 \ No newline at end of file diff --git a/src/common_access_model/schema/enums/EnumReadGroupQualityScale.yaml b/src/common_access_model/schema/enums/EnumReadGroupQualityScale.yaml new file mode 100644 index 00000000..db6de563 --- /dev/null +++ b/src/common_access_model/schema/enums/EnumReadGroupQualityScale.yaml @@ -0,0 +1,37 @@ +--- +id: https://includedcc.org/common-access-model/EnumReadGroupQualityScale +name: EnumReadGroupQualityScale +enums: + EnumReadGroupQualityScale: + title: Read Group Quality Scale + description: Quality score encoding used in FASTQ files, from the LinkML valuesets + SequenceQualityEncoding. + reachable_from: + source_ontology: linkml:valuesets + source_nodes: + - SequenceQualityEncoding + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + ILLUMINA_1:3: + title: ILLUMINA_1_3 + description: Illumina 1.3+ (PHRED+64, ASCII offset 64) + meaning: ILLUMINA_1:3 + ILLUMINA_1:5: + title: ILLUMINA_1_5 + description: Illumina 1.5+ (PHRED+64, special handling for 0-2) + meaning: ILLUMINA_1:5 + ILLUMINA_1:8: + title: ILLUMINA_1_8 + description: Illumina 1.8+ (PHRED+33, modern standard) + meaning: ILLUMINA_1:8 + SANGER: + title: SANGER + description: Sanger/Phred+33 (PHRED scores, ASCII offset 33) + meaning: SANGER + SOLEXA: + title: SOLEXA + description: Solexa+64 (Solexa scores, ASCII offset 64) + meaning: SOLEXA diff --git a/src/common_access_model/schema/enums/EnumReferenceGenome.yaml b/src/common_access_model/schema/enums/EnumReferenceGenome.yaml new file mode 100644 index 00000000..383d272e --- /dev/null +++ b/src/common_access_model/schema/enums/EnumReferenceGenome.yaml @@ -0,0 +1,17 @@ +id: https://includedcc.org/common-access-model/EnumReferenceGenome +name: EnumReferenceGenome +enums: + EnumReferenceGenome: + title: Reference Genome + permissible_values: + loinc:LA14029-5: + title: GRCh37 + meaning: loinc:LA14029-5 + loinc:LA26806-2: + title: GRCh38 + meaning: loinc:LA26806-2 + # hs37d5: + # title: hs37d5 + loinc:LA14025-3: + title: hg19 + meaning: loinc:LA14025-3 \ No newline at end of file diff --git a/src/common_access_model/schema/enums/EnumSequencingCenter.yaml b/src/common_access_model/schema/enums/EnumSequencingCenter.yaml new file mode 100644 index 00000000..d41bcd3e --- /dev/null +++ b/src/common_access_model/schema/enums/EnumSequencingCenter.yaml @@ -0,0 +1,80 @@ +--- +id: https://w3id.org/carrollaboratory/kf-access-model/EnumSequencingCenter +name: EnumSequencingCenter +enums: + EnumSequencingCenter: + title: Sequencing Center + description: >- + Sequencing centers with an ID in Kids First, from + kf_lib_data_ingest.common.constants.SEQUENCING.CENTER. + permissible_values: + SC_0CNMF82N: + title: Ashion + SC_A1JNZAZH: + title: Baylor College of Medicine + SC_FN7NH453: + title: British Columbia Cancer Agency Genome Sciences Centre + SC_WWEQ9HFY: + title: BGI@CHOP Genome Center + SC_FAD4KCQG: + title: BGI + SC_DGDDQVYR: + title: Broad Institute + SC_31369RXZ: + title: CBTN Unsequenced + SC_9NSC532X: + title: CHOP + SC_ZZPPF973: + title: CHOP DGD + SC_D30SEWS4: + title: Complete Genomics + SC_MDY0AZMZ: + title: CSIR - Institute of Genomics and Integrative Biology, Delhi, India + SC_CATTVETT: + title: Feline Diagnostics LLC + SC_XXXXXXX2: + title: fg + SC_5EDC0A25: + title: GeneDx + SC_75KENA7A: + title: Humangenetik Tübingen + SC_X1N69WJM: + title: HudsonAlpha Institute for Biotechnology + SC_N1EVHSME: + title: NantOmics + SC_2ZBAMKK0: + title: Novogene + SC_BJW95TMY: + title: New York Genome Center + SC_F6RZ51K9: + title: National Cancer Institute, Khan Lab + SC_HEXD2E5R: + title: National Institutes of Health + SC_V4CCQ3WE: + title: Princess Maxima Center + SC_9WMJKQ1X: + title: SickKids + SC_KE2ASNJM: + title: Genomic Clinical Core at Sidra Medical and Research Center + SC_1K3QGW4V: + title: St Jude + SC_SJJ0B9GN: + title: TEMP + SC_TQ8HJWGE: + title: Tempus + SC_KQ9JZG3P: + title: The Translational Genomics Research Institute + SC_5A2B1T4K: + title: 'UNKNOWN:CHRIS_JONES' + SC_MSQP04K7: + title: UCSF CAT + SC_T2A19FHX: + title: Variantyx + SC_BATJDPHB: + title: Virtual + SC_K52V7463: + title: Washington University + SC_31W52VNX: + title: Yale + SC_8JXH42X1: + title: Fred Hutchinson Cancer Research Center diff --git a/src/common_access_model/schema/enums/EnumSequencingInstrument.yaml b/src/common_access_model/schema/enums/EnumSequencingInstrument.yaml new file mode 100644 index 00000000..716cdfd4 --- /dev/null +++ b/src/common_access_model/schema/enums/EnumSequencingInstrument.yaml @@ -0,0 +1,58 @@ +--- +id: https://includedcc.org/common-access-model/EnumSequencingInstrument +name: EnumSequencingInstrument +enums: + EnumSequencingInstrument: + title: Sequencing Instrument + reachable_from: + source_ontology: bioregistry:obi + source_nodes: + - OBI:0003683 + include_self: false + is_direct: false + relationship_types: + - rdfs:subClassOf + permissible_values: + OBI:0002001: + title: Illumina HiSeq 2000 + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 55 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for multiple samples in a single run. + meaning: OBI:0002001 + OBI:0002002: + title: Illumina HiSeq 2500 + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 160 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for batching multiple samples or rapid results on a few samples. + meaning: OBI:0002002 + OBI:0002022: + title: Illumina HiSeq 1000 + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35 Gb per day. It supports + sequencing of single, long or short insert paired end clone libraries relying + on sequencing by synthesis technology. + meaning: OBI:0002022 + OBI:0002048: + title: Illumina HiSeq 3000 + description: A DNA sequencer manufactured by Illumina corporation, with a + single flow cell and a throughput of more than 200 Gb per day. + meaning: OBI:0002048 + OBI:0002049: + title: Illumina HiSeq 4000 + description: A DNA sequencer manufactured by Illumina corporation, with two + flow cell and a throughput of more than 400 Gb per day. + meaning: OBI:0002049 + OBI:0002129: + title: Illumina HiSeq X Ten + description: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing + Systems. + meaning: OBI:0002129 + OBI:0003386: + title: Illumina HiSeq 1500 + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell. Built upon sequencing by synthesis technology, + the machine employs dual surface imaging and offers two high-output options + and one rapid-run option. + meaning: OBI:0003386 diff --git a/src/common_access_model/schema/enums/EnumSequencingPlatform.yaml b/src/common_access_model/schema/enums/EnumSequencingPlatform.yaml new file mode 100644 index 00000000..10769b79 --- /dev/null +++ b/src/common_access_model/schema/enums/EnumSequencingPlatform.yaml @@ -0,0 +1,47 @@ +--- +id: https://includedcc.org/common-access-model/EnumSequencingPlatform +name: EnumSequencingPlatform +enums: + EnumSequencingPlatform: + title: Sequencing Platform + reachable_from: + source_ontology: bioregistry:ncit + source_nodes: + - NCIT:C146815 + - NCIT:C146811 + - NCIT:C146817 + - NCIT:C146809 + - NCIT:C146818 + - NCIT:C146819 + - NCIT:C125894 + include_self: true + is_direct: false + permissible_values: + NCIT:C146815: + title: Complete Genomics Sequencing + description: Complete Genomics Sequencing + meaning: NCIT:C146815 + NCIT:C146811: + title: ABI SOLiD Sequencing + description: ABI SOLiD Sequencing + meaning: NCIT:C146811 + NCIT:C146817: + title: Illumina Sequencing + description: Illumina Sequencing + meaning: NCIT:C146817 + NCIT:C146809: + title: 454 Sequencing + description: 454 Sequencing + meaning: NCIT:C146809 + NCIT:C146818: + title: Nanopore Sequencing + description: Nanopore Sequencing + meaning: NCIT:C146818 + NCIT:C146819: + title: SMRT Sequencing + description: SMRT Sequencing + meaning: NCIT:C146819 + NCIT:C125894: + title: Ion Semiconductor Sequencing + description: Ion Semiconductor Sequencing + meaning: NCIT:C125894 diff --git a/src/common_access_model/schema/enums/EnumSequencingStrategy.yaml b/src/common_access_model/schema/enums/EnumSequencingStrategy.yaml new file mode 100644 index 00000000..7f6cde53 --- /dev/null +++ b/src/common_access_model/schema/enums/EnumSequencingStrategy.yaml @@ -0,0 +1,139 @@ +--- +id: https://includedcc.org/common-access-model/EnumSequencingStrategy +name: EnumSequencingStrategy +enums: + EnumSequencingStrategy: + description: + permissible_values: + + # WGS + NCIT:C101294: + title: Whole Genome Sequencing + description: A procedure that can determine the DNA sequence for nearly the + entire genome of an individual. + meaning: NCIT:C101294 + # WES + NCIT:C101295: + title: Whole Exome Sequencing + description: A procedure that can determine the DNA sequence for all of the + exons in an individual. + meaning: NCIT:C101295 + + # Linked-read WGS (10x) + + # RNA + NCIT:C192768: + title: RNA Sequence Analysis + description: The determination of the sequence of purines and pyrimidines in a sample containing ribonucleic acid (RNA). + meaning: NCIT:C192768 + + # MRNA + NCIT:C129432: + title: mRNA Sequencing + description: A procedure that can determine the RNA sequences for all or part + of the poly-A tail-containing messenger RNA transcripts in an individual. + meaning: NCIT:C129432 + NCIT:C156057: + title: MicroRNA Sequencing + description: A next-generation or massively parallel high-throughput DNA sequencing-based + procedure that can identify and quantify the microRNA sequences present + in a biological sample. + meaning: NCIT:C156057 + + # scRNA + NCIT:C171152: + title: Single Cell RNA Sequencing + description: A procedure that can determine the nucleotide sequence for all + of the RNA transcripts in an amplified nucleotide sample that was derived + from a single cell. + meaning: NCIT:C171152 + + # snRNA? + + # Panel + NCIT:C165600: + title: Tumor Panel Sequencing + description: An application of next-generation targeted sequencing where tumor-specific + genes are selected for sequencing. Using next-generation techniques, chosen + sequences can be sequenced to high depths that facilitate the identification + of variants that are present at low allele frequencies. + meaning: NCIT:C165600 + NCIT:C173599: + title: Disease Panel Gene Sequencing + description: An application of next-generation targeted sequencing where a + disease-specific group of genes or loci are assayed for sequence alterations + as a screening procedure for the disease. + meaning: NCIT:C173599 + NCIT:C198412: + title: Multi-gene Panel Sequencing + description: An application of next-generation targeted sequencing where the + sequencing primers are designed to specifically target a panel of multiple + genes or loci of interest. + meaning: NCIT:C198412 + + # Targeted + NCIT:C204828: + title: Targeted Capture Sequencing + description: A method to enrich and sequence genomic regions of interest. + Sequences are selected by oligonucleotides that are used to pull-down complementary + DNA through hybridization. + meaning: NCIT:C204828 + NCIT:C158253: + title: Targeted Genome Sequencing + description: A DNA sequencing technique in which selected regions of an individual's + genome are sequenced. + meaning: NCIT:C158253 + NCIT:C158252: + title: Targeted Transcriptome Sequencing + description: A type of whole transcriptome shotgun sequencing technique in + which select portions of the transcriptome are selected for sequencing. + meaning: NCIT:C158252 + + + # Methyl + NCIT:C204820: + title: Methyl-binding Domain Sequencing + description: A strategy to obtain DNA sequences from (all) methylated sites. + Genomic DNA is randomly fragmented with ultrasonication and then methylated + fragments are captured by a protein with high affinity for double-stranded + DNA harboring methylated CpGs; non-methylated DNA fragments are washed away. + The methylation-enriched fraction is then barcode tagged and sequenced. + meaning: NCIT:C204820 + NCIT:C204821: + title: Methylated DNA Immunoprecipitation Sequencing + description: A strategy to obtain DNA sequences from methylated sites. Genomic + DNA is randomly sheared by sonication and immunoprecipitated with a monoclonal + antibody that specifically recognizes 5-methylcytidine. The DNA fragments + are then isolated and sequenced. + meaning: NCIT:C204821 + NCIT:C204822: + title: Methylation-Sensitive Restriction Enzyme Sequencing + description: A method to study DNA methylation. Genomic DNA is separately + digested with different methylation sensitive restriction enzymes and the + fragments are used to generate a library. Deep sequencing of the library + allows for accurate detection of methylation sites in the genome. + meaning: NCIT:C204822 + + + # Proteomics + NCIT:C20085: + title: Proteomics + description: The global analysis of cellular proteins. Proteomics uses a combination of sophisticated techniques including two-dimensional (2D) gel electrophoresis, image analysis, mass spectrometry, amino acid sequencing, and bio-informatics to resolve comprehensively, to quantify, and to characterize proteins. The application of proteomics provides major opportunities to elucidate disease mechanisms and to identify new diagnostic markers and therapeutic targets. + meaning: NCIT:C20085 + + # ONT WGS + NCIT:C146818: + title: Oxford Nanopore Sequencing + description: A proprietary next-generation DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence a DNA molecule as it passes through a nanopore, driven by electrophoresis. + meaning: NCIT:C146818 + + + # CCS_WGS, CLR_WGS + NCIT:C223895: + title: Long Read Sequencing + description: The sequencing of long, continuous DNA fragments. + meaning: NCIT:C223895 + + # CCS RNA + + # CLR RNA \ No newline at end of file