valuesets 0.3.1__py3-none-any.whl

valuesets/schema/bio/sequencing_platforms.yaml

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+name: sequencing_platforms
+title: Sequencing Platform Value Sets
+description: Value sets for DNA/RNA sequencing platforms, technologies, and methodologies
+id: https://w3id.org/linkml/valuesets/bio/sequencing_platforms
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  OBI: http://purl.obolibrary.org/obo/OBI_
+  SO: http://purl.obolibrary.org/obo/SO_
+  EDAM: http://edamontology.org/
+default_prefix: valuesets
+slots:
+  sequencing_platform:
+    description: Major DNA/RNA sequencing platforms and instruments used in genomics research
+    range: SequencingPlatform
+  sequencing_chemistry:
+    description: Fundamental chemical methods used for DNA/RNA sequencing
+    range: SequencingChemistry
+  library_preparation:
+    description: Methods for preparing sequencing libraries from nucleic acid samples
+    range: LibraryPreparation
+  sequencing_application:
+    description: Primary applications or assays using DNA/RNA sequencing
+    range: SequencingApplication
+  read:
+    description: Configuration of sequencing reads generated by different platforms
+    range: ReadType
+  sequence_file_format:
+    description: Standard file formats used for storing sequence data
+    range: SequenceFileFormat
+  data_processing_level:
+    description: Levels of processing applied to raw sequencing data
+    range: DataProcessingLevel
+enums:
+  SequencingPlatform:
+    title: Sequencing Platforms and Instruments
+    description: Major DNA/RNA sequencing platforms and instruments used in genomics research
+    permissible_values:
+      ILLUMINA_HISEQ_2000:
+        description: Illumina HiSeq 2000
+        meaning: OBI:0002001
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_HISEQ_2500:
+        description: Illumina HiSeq 2500
+        meaning: OBI:0002002
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_HISEQ_3000:
+        description: Illumina HiSeq 3000
+        meaning: OBI:0002048
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_HISEQ_4000:
+        description: Illumina HiSeq 4000
+        meaning: OBI:0002049
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_HISEQ_X:
+        description: Illumina HiSeq X
+        meaning: OBI:0002129
+        aliases:
+        - Illumina HiSeq X Ten
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_NOVASEQ_6000:
+        description: Illumina NovaSeq 6000
+        meaning: OBI:0002630
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_NEXTSEQ_500:
+        description: Illumina NextSeq 500
+        meaning: OBI:0002021
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_NEXTSEQ_550:
+        description: Illumina NextSeq 550
+        meaning: OBI:0003387
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_NEXTSEQ_1000:
+        description: Illumina NextSeq 1000
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_NEXTSEQ_2000:
+        description: Illumina NextSeq 2000
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_MISEQ:
+        description: Illumina MiSeq
+        meaning: OBI:0002003
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      ILLUMINA_ISEQ_100:
+        description: Illumina iSeq 100
+        annotations:
+          manufacturer: Illumina
+          read_type: short
+          chemistry: sequencing by synthesis
+      PACBIO_RS:
+        description: PacBio RS
+        annotations:
+          manufacturer: Pacific Biosciences
+          read_type: long
+          chemistry: single molecule real time
+      PACBIO_RS_II:
+        description: PacBio RS II
+        meaning: OBI:0002012
+        annotations:
+          manufacturer: Pacific Biosciences
+          read_type: long
+          chemistry: single molecule real time
+      PACBIO_SEQUEL:
+        description: PacBio Sequel
+        meaning: OBI:0002632
+        annotations:
+          manufacturer: Pacific Biosciences
+          read_type: long
+          chemistry: single molecule real time
+      PACBIO_SEQUEL_II:
+        description: PacBio Sequel II
+        meaning: OBI:0002633
+        annotations:
+          manufacturer: Pacific Biosciences
+          read_type: long
+          chemistry: single molecule real time
+      PACBIO_REVIO:
+        description: PacBio Revio
+        annotations:
+          manufacturer: Pacific Biosciences
+          read_type: long
+          chemistry: single molecule real time
+      NANOPORE_MINION:
+        description: Oxford Nanopore MinION
+        meaning: OBI:0002750
+        aliases:
+        - Oxford Nanopore MinION
+        annotations:
+          manufacturer: Oxford Nanopore Technologies
+          read_type: long
+          chemistry: nanopore sequencing
+      NANOPORE_GRIDION:
+        description: Oxford Nanopore GridION
+        meaning: OBI:0002751
+        aliases:
+        - Oxford Nanopore GridION Mk1
+        annotations:
+          manufacturer: Oxford Nanopore Technologies
+          read_type: long
+          chemistry: nanopore sequencing
+      NANOPORE_PROMETHION:
+        description: Oxford Nanopore PromethION
+        meaning: OBI:0002752
+        aliases:
+        - Oxford Nanopore PromethION
+        annotations:
+          manufacturer: Oxford Nanopore Technologies
+          read_type: long
+          chemistry: nanopore sequencing
+      NANOPORE_FLONGLE:
+        description: Oxford Nanopore Flongle
+        annotations:
+          manufacturer: Oxford Nanopore Technologies
+          read_type: long
+          chemistry: nanopore sequencing
+      ELEMENT_AVITI:
+        description: Element Biosciences AVITI
+        annotations:
+          manufacturer: Element Biosciences
+          read_type: short
+          chemistry: sequencing by avidity
+      MGI_DNBSEQ_T7:
+        description: MGI DNBSEQ-T7
+        annotations:
+          manufacturer: MGI/BGI
+          read_type: short
+          chemistry: DNA nanoball sequencing
+      MGI_DNBSEQ_G400:
+        description: MGI DNBSEQ-G400
+        annotations:
+          manufacturer: MGI/BGI
+          read_type: short
+          chemistry: DNA nanoball sequencing
+      MGI_DNBSEQ_G50:
+        description: MGI DNBSEQ-G50
+        annotations:
+          manufacturer: MGI/BGI
+          read_type: short
+          chemistry: DNA nanoball sequencing
+      SANGER_SEQUENCING:
+        description: Sanger chain termination sequencing
+        meaning: OBI:0000695
+        aliases:
+        - chain termination sequencing assay
+        annotations:
+          manufacturer: Various
+          read_type: short
+          chemistry: chain termination
+      ROCHE_454_GS:
+        description: Roche 454 Genome Sequencer
+        meaning: OBI:0000702
+        aliases:
+        - 454 Genome Sequencer FLX
+        annotations:
+          manufacturer: Roche/454
+          read_type: short
+          chemistry: pyrosequencing
+          status: discontinued
+      LIFE_TECHNOLOGIES_ION_TORRENT:
+        description: Life Technologies Ion Torrent
+        annotations:
+          manufacturer: Life Technologies/Thermo Fisher
+          read_type: short
+          chemistry: semiconductor sequencing
+      ABI_SOLID:
+        description: ABI SOLiD
+        annotations:
+          manufacturer: Life Technologies/Applied Biosystems
+          read_type: short
+          chemistry: sequencing by ligation
+          status: discontinued
+  SequencingChemistry:
+    title: Sequencing Chemistry Methods
+    description: Fundamental chemical methods used for DNA/RNA sequencing
+    permissible_values:
+      SEQUENCING_BY_SYNTHESIS:
+        title: SEQUENCING_BY_SYNTHESIS
+        description: Sequencing by synthesis (Illumina)
+        meaning: OBI:0000734
+        aliases:
+        - DNA sequencing by synthesis assay
+      SINGLE_MOLECULE_REAL_TIME:
+        title: SINGLE_MOLECULE_REAL_TIME
+        description: Single molecule real-time sequencing (PacBio)
+      NANOPORE_SEQUENCING:
+        title: NANOPORE_SEQUENCING
+        description: Nanopore sequencing (Oxford Nanopore)
+      PYROSEQUENCING:
+        title: PYROSEQUENCING
+        description: Pyrosequencing (454)
+      SEQUENCING_BY_LIGATION:
+        title: SEQUENCING_BY_LIGATION
+        description: Sequencing by ligation (SOLiD)
+        meaning: OBI:0000723
+        aliases:
+        - DNA sequencing by ligation assay
+      CHAIN_TERMINATION:
+        title: CHAIN_TERMINATION
+        description: Chain termination method (Sanger)
+        meaning: OBI:0000695
+        aliases:
+        - chain termination sequencing assay
+      SEMICONDUCTOR_SEQUENCING:
+        description: Semiconductor/Ion semiconductor sequencing
+      DNA_NANOBALL_SEQUENCING:
+        description: DNA nanoball sequencing (MGI/BGI)
+      SEQUENCING_BY_AVIDITY:
+        description: Sequencing by avidity (Element Biosciences)
+  LibraryPreparation:
+    title: Library Preparation Methods
+    description: Methods for preparing sequencing libraries from nucleic acid samples
+    permissible_values:
+      GENOMIC_DNA:
+        description: Genomic DNA library preparation
+      WHOLE_GENOME_AMPLIFICATION:
+        description: Whole genome amplification (WGA)
+      PCR_AMPLICON:
+        description: PCR amplicon sequencing
+      RNA_SEQ:
+        description: RNA sequencing library prep
+      SMALL_RNA_SEQ:
+        description: Small RNA sequencing
+      SINGLE_CELL_RNA_SEQ:
+        description: Single-cell RNA sequencing
+      ATAC_SEQ:
+        description: ATAC-seq (chromatin accessibility)
+      CHIP_SEQ:
+        description: ChIP-seq (chromatin immunoprecipitation)
+      BISULFITE_SEQ:
+        description: Bisulfite sequencing (methylation)
+      HI_C:
+        description: Hi-C (chromosome conformation capture)
+      CUT_AND_RUN:
+        description: CUT&RUN (chromatin profiling)
+      CUT_AND_TAG:
+        description: CUT&Tag (chromatin profiling)
+      CAPTURE_SEQUENCING:
+        description: Target capture/enrichment sequencing
+      EXOME_SEQUENCING:
+        description: Whole exome sequencing
+      METAGENOMICS:
+        description: Metagenomic sequencing
+      AMPLICON_SEQUENCING:
+        description: 16S/ITS amplicon sequencing
+      DIRECT_RNA:
+        description: Direct RNA sequencing (nanopore)
+      CDNA_SEQUENCING:
+        description: cDNA sequencing
+      RIBOSOME_PROFILING:
+        description: Ribosome profiling (Ribo-seq)
+  SequencingApplication:
+    title: Sequencing Applications
+    description: Primary applications or assays using DNA/RNA sequencing
+    permissible_values:
+      WHOLE_GENOME_SEQUENCING:
+        title: WHOLE_GENOME_SEQUENCING
+        description: Whole genome sequencing (WGS)
+        meaning: EDAM:topic_3673
+      WHOLE_EXOME_SEQUENCING:
+        title: WHOLE_EXOME_SEQUENCING
+        description: Whole exome sequencing (WES)
+        meaning: EDAM:topic_3676
+        aliases:
+        - Exome sequencing
+      TRANSCRIPTOME_SEQUENCING:
+        title: TRANSCRIPTOME_SEQUENCING
+        description: RNA sequencing (RNA-seq)
+        meaning: EDAM:topic_3170
+        aliases:
+        - RNA-Seq
+      TARGETED_SEQUENCING:
+        description: Targeted gene panel sequencing
+      EPIGENOMICS:
+        description: Epigenomic profiling
+      METAGENOMICS:
+        title: METAGENOMICS
+        description: Metagenomic sequencing
+        meaning: EDAM:topic_3837
+        aliases:
+        - Metagenomic sequencing
+      SINGLE_CELL_GENOMICS:
+        description: Single-cell genomics
+      SINGLE_CELL_TRANSCRIPTOMICS:
+        title: SINGLE_CELL_TRANSCRIPTOMICS
+        description: Single-cell transcriptomics
+        meaning: EDAM:topic_4028
+        aliases:
+        - Single-cell sequencing
+      CHROMATIN_IMMUNOPRECIPITATION:
+        title: CHROMATIN_IMMUNOPRECIPITATION
+        description: ChIP-seq
+        meaning: EDAM:topic_3656
+        aliases:
+        - Immunoprecipitation experiment
+      CHROMATIN_ACCESSIBILITY:
+        description: ATAC-seq/FAIRE-seq
+      DNA_METHYLATION:
+        description: Bisulfite/methylation sequencing
+      CHROMOSOME_CONFORMATION:
+        description: Hi-C/3C-seq
+      VARIANT_CALLING:
+        description: Genetic variant discovery
+      PHARMACOGENOMICS:
+        description: Pharmacogenomic sequencing
+      CLINICAL_DIAGNOSTICS:
+        description: Clinical diagnostic sequencing
+      POPULATION_GENOMICS:
+        description: Population-scale genomics
+  ReadType:
+    title: Sequencing Read Types
+    description: Configuration of sequencing reads generated by different platforms
+    permissible_values:
+      SINGLE_END:
+        title: SINGLE_END
+        description: Single-end reads
+      PAIRED_END:
+        title: PAIRED_END
+        description: Paired-end reads
+      MATE_PAIR:
+        description: Mate-pair reads (large insert)
+      LONG_READ:
+        description: Long reads (>1kb typical)
+      ULTRA_LONG_READ:
+        description: Ultra-long reads (>10kb)
+      CONTINUOUS_LONG_READ:
+        description: Continuous long reads (nanopore)
+  SequenceFileFormat:
+    title: Sequence File Formats
+    description: Standard file formats used for storing sequence data
+    permissible_values:
+      FASTA:
+        description: FASTA sequence format
+        meaning: EDAM:format_1929
+        annotations:
+          extensions: .fa, .fasta, .fna, .ffn, .faa, .frn
+          content: sequences only
+      FASTQ:
+        description: FASTQ sequence with quality format
+        meaning: EDAM:format_1930
+        annotations:
+          extensions: .fq, .fastq
+          content: sequences and quality scores
+      SAM:
+        description: Sequence Alignment Map format
+        meaning: EDAM:format_2573
+        annotations:
+          extensions: .sam
+          content: aligned sequences (text)
+      BAM:
+        description: Binary Alignment Map format
+        meaning: EDAM:format_2572
+        annotations:
+          extensions: .bam
+          content: aligned sequences (binary)
+      CRAM:
+        description: Compressed Reference-oriented Alignment Map
+        annotations:
+          extensions: .cram
+          content: compressed aligned sequences
+      VCF:
+        description: Variant Call Format
+        meaning: EDAM:format_3016
+        annotations:
+          extensions: .vcf
+          content: genetic variants
+      BCF:
+        description: Binary Variant Call Format
+        meaning: EDAM:format_3020
+        annotations:
+          extensions: .bcf
+          content: genetic variants (binary)
+      GFF3:
+        description: Generic Feature Format version 3
+        annotations:
+          extensions: .gff, .gff3
+          content: genomic annotations
+      GTF:
+        description: Gene Transfer Format
+        annotations:
+          extensions: .gtf
+          content: gene annotations
+      BED:
+        description: Browser Extensible Data format
+        annotations:
+          extensions: .bed
+          content: genomic intervals
+      BIGWIG:
+        description: BigWig format for continuous data
+        annotations:
+          extensions: .bw, .bigwig
+          content: continuous genomic data
+      BIGBED:
+        description: BigBed format for interval data
+        annotations:
+          extensions: .bb, .bigbed
+          content: genomic intervals (indexed)
+      HDF5:
+        description: Hierarchical Data Format 5
+        annotations:
+          extensions: .h5, .hdf5
+          content: multi-dimensional arrays
+      SFF:
+        description: Standard Flowgram Format (454)
+        meaning: EDAM:format_3284
+        annotations:
+          extensions: .sff
+          content: 454 sequencing data
+          status: legacy
+      FAST5:
+        description: Fast5 format (Oxford Nanopore)
+        annotations:
+          extensions: .fast5
+          content: nanopore raw signal data
+      POD5:
+        description: POD5 format (Oxford Nanopore, newer)
+        annotations:
+          extensions: .pod5
+          content: nanopore raw signal data (compressed)
+  DataProcessingLevel:
+    title: Sequence Data Processing Levels
+    description: Levels of processing applied to raw sequencing data
+    permissible_values:
+      RAW:
+        description: Raw unprocessed sequencing reads
+      QUALITY_FILTERED:
+        description: Quality filtered reads
+      TRIMMED:
+        description: Adapter/quality trimmed reads
+      ALIGNED:
+        description: Aligned to reference genome
+      DEDUPLICATED:
+        description: PCR duplicates removed
+      RECALIBRATED:
+        description: Base quality score recalibrated
+      VARIANT_CALLED:
+        description: Variants called from alignments
+      NORMALIZED:
+        description: Expression normalized (RNA-seq)
+      ASSEMBLED:
+        description: De novo assembled sequences
+      ANNOTATED:
+        description: Functionally annotated sequences