Enum: FileTypeEnum

URI: FileTypeEnum

Permissible Values

Value	Meaning	Description
Virus Summary	None	Tab separated file listing the viruses found by geNomad
Plasmid Summary	None	Tab separated file listing the plasmids found be geNomad
GeNomad Aggregated Classification	None	Tab separated file which combines the results from neural network-based class...
Reference Calibration File	None	A file that contains data used to calibrate a natural organic matter or metab...
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...
Configuration toml	None	A configuration toml file used by various programs to store settings that are...
LC-MS Lipidomics Results	None	LC-MS-based lipid assignment results table
Contaminants Amino Acid FASTA	None	FASTA amino acid file for contaminant proteins commonly observed in proteomic...
Analysis Tool Parameter File	None	A configuration file used by a single computational software tool that stores...
Workflow Operation Summary	None	A human readable record of analysis steps applied during an instance of a wor...
Metatranscriptome Expression	None	Metatranscriptome expression values and read counts for gene features predict...
Metatranscriptome Expression Intergenic	None	Metatranscriptome expression values and read counts for intergenic regions
Metatranscriptome Expression Info File	None	File containing version information on the expression workflow
rRNA Filtered Sequencing Reads	None	File containing ribosomal reads from the read qc filtering step
BAI File	None	An index file found in the same directory as the binary alignment map (BAM) f...

Slots

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

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/nmdc/nmdc

LinkML Source

name: FileTypeEnum
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
permissible_values:
  Virus Summary:
    text: Virus Summary
    description: Tab separated file listing the viruses found by geNomad.
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: ^_virus_summary\.tsv?$
    see_also:
    - https://portal.nersc.gov/genomad/
  Plasmid Summary:
    text: Plasmid Summary
    description: Tab separated file listing the plasmids found be geNomad.
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: ^_plasmid_summary\.tsv?$
    see_also:
    - https://portal.nersc.gov/genomad/
  GeNomad Aggregated Classification:
    text: GeNomad Aggregated Classification
    description: Tab separated file which combines the results from neural network-based
      classification and marker-based classification for virus and plasmid detection
      with geNomad.
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: ^_aggregated_classification\.tsv?$
    see_also:
    - https://portal.nersc.gov/genomad/
  Reference Calibration File:
    text: Reference Calibration File
    description: A file that contains data used to calibrate a natural organic matter
      or metabalomics analysis.
  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
  Configuration toml:
    text: Configuration toml
    description: A configuration toml file used by various programs to store settings
      that are specific to their respective software.
    broad_mappings:
    - edam.format:4005
  LC-MS Lipidomics Results:
    text: LC-MS Lipidomics Results
    description: LC-MS-based lipid assignment results table.
  Contaminants Amino Acid FASTA:
    text: Contaminants Amino Acid FASTA
    description: FASTA amino acid file for contaminant proteins commonly observed
      in proteomics data.
  Analysis Tool Parameter File:
    text: Analysis Tool Parameter File
    description: A configuration file used by a single computational software tool
      that stores settings that are specific to that tool.
  Workflow Operation Summary:
    text: Workflow Operation Summary
    description: A human readable record of analysis steps applied during an instance
      of a workflow operation.
  Metatranscriptome Expression:
    text: Metatranscriptome Expression
    description: Metatranscriptome expression values and read counts for gene features
      predicted on contigs
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '*.rnaseq_gea.txt'
  Metatranscriptome Expression Intergenic:
    text: Metatranscriptome Expression Intergenic
    description: Metatranscriptome expression values and read counts for intergenic
      regions.
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '*.rnaseq_gea.intergenic.txt'
  Metatranscriptome Expression Info File:
    text: Metatranscriptome Expression Info File
    description: File containing version information on the expression workflow
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '*_readcount.info'
  rRNA Filtered Sequencing Reads:
    text: rRNA Filtered Sequencing Reads
    description: File containing ribosomal reads from the read qc filtering step.
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '*.rRNA.fastq.gz'
  BAI File:
    text: BAI File
    description: An index file found in the same directory as the binary alignment
      map (BAM) file, a compressed binary version of a sequence alignment/map (SAM)
      file.
    annotations:
      file_name_pattern:
        tag: file_name_pattern
        value: '*.pairedMapped_sorted.bam.bai'
    exact_mappings:
    - NCIT:C190163