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Enum: FileTypeEnum

URI: FileTypeEnum

Permissible Values

Value Meaning Description
Metagenome Raw Reads None Interleaved paired-end raw sequencing data
Metagenome Raw Read 1 None Read 1 raw sequencing data, aka forward reads
Metagenome Raw Read 2 None Read 2 raw sequencing data, aka reverse reads
FT ICR-MS Analysis Results None FT ICR-MS-based molecular formula assignment results table
GC-MS Metabolomics Results None GC-MS-based metabolite assignment results table
Metaproteomics Workflow Statistics None Aggregate workflow statistics file
Protein Report None Filtered protein report file
Peptide Report None Filtered peptide report file
Unfiltered Metaproteomics Results None MSGFjobs and MASIC output file
Read Count and RPKM None Annotation read count and RPKM per feature JSON
QC non-rRNA R2 None QC removed rRNA reads (R2) fastq
QC non-rRNA R1 None QC removed rRNA reads (R1) fastq
Metagenome Bins None Metagenome bin contigs fasta
Metagenome HQMQ Bins Compression File None Compressed file containing high qulaity and medium quality metagenome bins an...
Metagenome LQ Bins Compression File None Compressed file containing low quality metagenome bins and associated files
Metagenome Bins Info File None File containing version information on the binning workflow
CheckM Statistics None CheckM statistics report
Metagenome Bins Heatmap None The Heatmap presents the pdf file containing the KO analysis results for meta...
Metagenome Bins Barplot None The Bar chart presents the pdf file containing the KO analysis results for me...
Metagenome Bins Krona Plot None The Krona plot presents the HTML file containing the KO analysis results for ...
Read Based Analysis Info File None File containing reads based analysis information
GTDBTK Bacterial Summary None GTDBTK bacterial summary
GTDBTK Archaeal Summary None GTDBTK archaeal summary
GOTTCHA2 Krona Plot None GOTTCHA2 krona plot HTML file
GOTTCHA2 Classification Report None GOTTCHA2 classification report file
GOTTCHA2 Report Full None GOTTCHA2 report file
Kraken2 Krona Plot None Kraken2 krona plot HTML file
Centrifuge Krona Plot None Centrifuge krona plot HTML file
Centrifuge output report file None Centrifuge output report file
Kraken2 Classification Report None Kraken2 output report file
Kraken2 Taxonomic Classification None Kraken2 output read classification file
Centrifuge Classification Report None Centrifuge output report file
Centrifuge Taxonomic Classification None Centrifuge output read classification file
Structural Annotation GFF None GFF3 format file with structural annotations
Structural Annotation Stats Json None Structural annotations stats json
Functional Annotation GFF None GFF3 format file with functional annotations
Annotation Info File None File containing annotation info
Annotation Amino Acid FASTA None FASTA amino acid file for annotated proteins
Annotation Enzyme Commission None Tab delimited file for EC annotation
Annotation KEGG Orthology None Tab delimited file for KO annotation
Assembly Info File None File containing assembly info
Assembly Coverage BAM None Sorted bam file of reads mapping back to the final assembly
Assembly AGP None An AGP format file that describes the assembly
Assembly Scaffolds None Final assembly scaffolds fasta
Assembly Contigs None Final assembly contigs fasta
Assembly Coverage Stats None Assembled contigs coverage information
Contig Mapping File None Contig mappings between contigs and scaffolds
Error Corrected Reads None Error corrected reads fastq
Filtered Sequencing Reads None Reads QC result fastq (clean data)
Read Filtering Info File None File containing read filtering information
QC Statistics Extended None Extended report including methods and results for read filtering
QC Statistics None Reads QC summary statistics
TIGRFam Annotation GFF None GFF3 format file with TIGRfam
CRT Annotation GFF None GFF3 format file with CRT
Genemark Annotation GFF None GFF3 format file with Genemark
Prodigal Annotation GFF None GFF3 format file with Prodigal
TRNA Annotation GFF None GFF3 format file with TRNA
Misc Annotation GFF None GFF3 format file with Misc
RFAM Annotation GFF None GFF3 format file with RFAM
TMRNA Annotation GFF None GFF3 format file with TMRNA
Crispr Terms None Crispr Terms
Product Names None Product names file
Gene Phylogeny tsv None Gene Phylogeny tsv
Scaffold Lineage tsv None phylogeny at the scaffold level
Clusters of Orthologous Groups (COG) Annotation GFF None GFF3 format file with COGs
KO_EC Annotation GFF None GFF3 format file with KO_EC
CATH FunFams (Functional Families) Annotation GFF None GFF3 format file with CATH FunFams
SUPERFam Annotation GFF None GFF3 format file with SUPERFam
SMART Annotation GFF None GFF3 format file with SMART
Pfam Annotation GFF None GFF3 format file with Pfam
Annotation Statistics None Annotation statistics report
Direct Infusion FT ICR-MS Raw Data None Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance mass spect...
LC-DDA-MS/MS Raw Data None Liquid chromatographically separated MS1 and Data-Dependent MS2 binary instru...

Slots

Name Description
data_object_type The type of file represented by the data object

Identifier and Mapping Information

Schema Source

LinkML Source

name: FileTypeEnum
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
permissible_values:
  Metagenome Raw Reads:
    text: Metagenome Raw Reads
    description: Interleaved paired-end raw sequencing data
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: ^\.fastq(\.gz)?$
  Metagenome Raw Read 1:
    text: Metagenome Raw Read 1
    description: Read 1 raw sequencing data, aka forward reads
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: ^.+_R1\.fastq(\.gz)?$
    examples:
    - value: BMI_H25VYBGXH_19S_31WellG1_R1.fastq.gz
  Metagenome Raw Read 2:
    text: Metagenome Raw Read 2
    description: Read 2 raw sequencing data, aka reverse reads
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: ^.+_R2\.fastq(\.gz)?$
    examples:
    - value: BMI_H25VYBGXH_19S_31WellG1_R2.fastq.gz
  FT ICR-MS Analysis Results:
    text: FT ICR-MS Analysis Results
    description: FT ICR-MS-based molecular formula assignment results table
  GC-MS Metabolomics Results:
    text: GC-MS Metabolomics Results
    description: GC-MS-based metabolite assignment results table
  Metaproteomics Workflow Statistics:
    text: Metaproteomics Workflow Statistics
    description: Aggregate workflow statistics file
  Protein Report:
    text: Protein Report
    description: Filtered protein report file
  Peptide Report:
    text: Peptide Report
    description: Filtered peptide report file
  Unfiltered Metaproteomics Results:
    text: Unfiltered Metaproteomics Results
    description: MSGFjobs and MASIC output file
  Read Count and RPKM:
    text: Read Count and RPKM
    description: Annotation read count and RPKM per feature JSON
  QC non-rRNA R2:
    text: QC non-rRNA R2
    description: QC removed rRNA reads (R2) fastq
  QC non-rRNA R1:
    text: QC non-rRNA R1
    description: QC removed rRNA reads (R1) fastq
  Metagenome Bins:
    text: Metagenome Bins
    description: Metagenome bin contigs fasta
  Metagenome HQMQ Bins Compression File:
    text: Metagenome HQMQ Bins Compression File
    description: Compressed file containing high qulaity and medium quality metagenome
      bins and associated files
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[mag_wf_activity_id]_hqmq_bin.zip'
  Metagenome LQ Bins Compression File:
    text: Metagenome LQ Bins Compression File
    description: Compressed file containing low quality metagenome bins and associated
      files
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[mag_wf_activity_id]_lq_bin.zip'
  Metagenome Bins Info File:
    text: Metagenome Bins Info File
    description: File containing version information on the binning workflow
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[mag_wf_activity_id]_bin.info'
  CheckM Statistics:
    text: CheckM Statistics
    description: CheckM statistics report
  Metagenome Bins Heatmap:
    text: Metagenome Bins Heatmap
    description: The Heatmap presents the pdf file containing the KO analysis results
      for metagenome bins
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[mag_wf_activity_id]_heatmap.pdf'
  Metagenome Bins Barplot:
    text: Metagenome Bins Barplot
    description: The Bar chart presents the pdf file containing the KO analysis results
      for metagenome bins
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[mag_wf_activity_id]_barplot.pdf'
  Metagenome Bins Krona Plot:
    text: Metagenome Bins Krona Plot
    description: The Krona plot presents the HTML file containing the KO analysis
      results for metagenome bins
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[mag_wf_activity_id]_kronaplot.html'
  Read Based Analysis Info File:
    text: Read Based Analysis Info File
    description: File containing reads based analysis information
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: profiler.info
  GTDBTK Bacterial Summary:
    text: GTDBTK Bacterial Summary
    description: GTDBTK bacterial summary
  GTDBTK Archaeal Summary:
    text: GTDBTK Archaeal Summary
    description: GTDBTK archaeal summary
  GOTTCHA2 Krona Plot:
    text: GOTTCHA2 Krona Plot
    description: GOTTCHA2 krona plot HTML file
  GOTTCHA2 Classification Report:
    text: GOTTCHA2 Classification Report
    description: GOTTCHA2 classification report file
  GOTTCHA2 Report Full:
    text: GOTTCHA2 Report Full
    description: GOTTCHA2 report file
  Kraken2 Krona Plot:
    text: Kraken2 Krona Plot
    description: Kraken2 krona plot HTML file
  Centrifuge Krona Plot:
    text: Centrifuge Krona Plot
    description: Centrifuge krona plot HTML file
  Centrifuge output report file:
    text: Centrifuge output report file
    description: Centrifuge output report file
  Kraken2 Classification Report:
    text: Kraken2 Classification Report
    description: Kraken2 output report file
  Kraken2 Taxonomic Classification:
    text: Kraken2 Taxonomic Classification
    description: Kraken2 output read classification file
  Centrifuge Classification Report:
    text: Centrifuge Classification Report
    description: Centrifuge output report file
  Centrifuge Taxonomic Classification:
    text: Centrifuge Taxonomic Classification
    description: Centrifuge output read classification file
  Structural Annotation GFF:
    text: Structural Annotation GFF
    description: GFF3 format file with structural annotations
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_structural_annotation.gff'
  Structural Annotation Stats Json:
    text: Structural Annotation Stats Json
    description: Structural annotations stats json
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_structural_annotation_stats.json'
  Functional Annotation GFF:
    text: Functional Annotation GFF
    description: GFF3 format file with functional annotations
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_functional_annotation.gff'
  Annotation Info File:
    text: Annotation Info File
    description: File containing annotation info
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_imgap.info'
  Annotation Amino Acid FASTA:
    text: Annotation Amino Acid FASTA
    description: FASTA amino acid file for annotated proteins
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_proteins.faa'
  Annotation Enzyme Commission:
    text: Annotation Enzyme Commission
    description: Tab delimited file for EC annotation
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_ec.tsv'
  Annotation KEGG Orthology:
    text: Annotation KEGG Orthology
    description: Tab delimited file for KO annotation
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_ko.tsv'
  Assembly Info File:
    text: Assembly Info File
    description: File containing assembly info
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: README.txt
  Assembly Coverage BAM:
    text: Assembly Coverage BAM
    description: Sorted bam file of reads mapping back to the final assembly
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_pairedMapped.sam.gz'
  Assembly AGP:
    text: Assembly AGP
    description: An AGP format file that describes the assembly
  Assembly Scaffolds:
    text: Assembly Scaffolds
    description: Final assembly scaffolds fasta
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_assembly.contigs.fasta'
  Assembly Contigs:
    text: Assembly Contigs
    description: Final assembly contigs fasta
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: assembly.contigs.fasta
  Assembly Coverage Stats:
    text: Assembly Coverage Stats
    description: Assembled contigs coverage information
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_pairedMapped_sorted.bam.cov'
  Contig Mapping File:
    text: Contig Mapping File
    description: Contig mappings between contigs and scaffolds
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_contig_names_mapping.tsv'
  Error Corrected Reads:
    text: Error Corrected Reads
    description: Error corrected reads fastq
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: input.corr.fastq.gz
  Filtered Sequencing Reads:
    text: Filtered Sequencing Reads
    description: Reads QC result fastq (clean data)
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '/.+?(?=filter)/filter-METAGENOME.fastq.gz '
  Read Filtering Info File:
    text: Read Filtering Info File
    description: File containing read filtering information
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[rqc_wf_activity_id]_readsQC.info'
  QC Statistics Extended:
    text: QC Statistics Extended
    description: Extended report including methods and results for read filtering
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: /.+?(?=filter)/filtered-report.txt
  QC Statistics:
    text: QC Statistics
    description: Reads QC summary statistics
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[rqc_wf_activity_id]_filterStats2.txt'
  TIGRFam Annotation GFF:
    text: TIGRFam Annotation GFF
    description: GFF3 format file with TIGRfam
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_tigrfam.gff'
  CRT Annotation GFF:
    text: CRT Annotation GFF
    description: GFF3 format file with CRT
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_crt.gff'
  Genemark Annotation GFF:
    text: Genemark Annotation GFF
    description: GFF3 format file with Genemark
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_genemark.gff'
  Prodigal Annotation GFF:
    text: Prodigal Annotation GFF
    description: GFF3 format file with Prodigal
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_prodigal.gff'
  TRNA Annotation GFF:
    text: TRNA Annotation GFF
    description: GFF3 format file with TRNA
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_trna.gff'
  Misc Annotation GFF:
    text: Misc Annotation GFF
    description: GFF3 format file with Misc
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff'
  RFAM Annotation GFF:
    text: RFAM Annotation GFF
    description: GFF3 format file with RFAM
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_rfam.gff'
  TMRNA Annotation GFF:
    text: TMRNA Annotation GFF
    description: GFF3 format file with TMRNA
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_rfam_ncrna_tmrna.gff'
  Crispr Terms:
    text: Crispr Terms
    description: Crispr Terms
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_crt.crisprs'
  Product Names:
    text: Product Names
    description: Product names file
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_product_names.tsv'
  Gene Phylogeny tsv:
    text: Gene Phylogeny tsv
    description: Gene Phylogeny tsv
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_gene_phylogeny.tsv'
  Scaffold Lineage tsv:
    text: Scaffold Lineage tsv
    description: phylogeny at the scaffold level
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_scaffold_lineage.tsv'
  Clusters of Orthologous Groups (COG) Annotation GFF:
    text: Clusters of Orthologous Groups (COG) Annotation GFF
    description: GFF3 format file with COGs
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_cog.gff'
  KO_EC Annotation GFF:
    text: KO_EC Annotation GFF
    description: GFF3 format file with KO_EC
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_ko_ec.gff'
  CATH FunFams (Functional Families) Annotation GFF:
    text: CATH FunFams (Functional Families) Annotation GFF
    description: GFF3 format file with CATH FunFams
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_cath_funfam.gff'
  SUPERFam Annotation GFF:
    text: SUPERFam Annotation GFF
    description: GFF3 format file with SUPERFam
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_supfam.gff'
  SMART Annotation GFF:
    text: SMART Annotation GFF
    description: GFF3 format file with SMART
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_smart.gff'
  Pfam Annotation GFF:
    text: Pfam Annotation GFF
    description: GFF3 format file with Pfam
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '[GOLD-AP]_pfam.gff'
  Annotation Statistics:
    text: Annotation Statistics
    description: Annotation statistics report
  Direct Infusion FT ICR-MS Raw Data:
    text: Direct Infusion FT ICR-MS Raw Data
    description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance
      mass spectrometry raw data acquired in broadband full scan mode
  LC-DDA-MS/MS Raw Data:
    text: LC-DDA-MS/MS Raw Data
    description: Liquid chromatographically separated MS1 and Data-Dependent MS2 binary
      instrument file