Enum: FileTypeEnum
URI: FileTypeEnum
Permissible Values
| Value | Meaning | Description |
|---|---|---|
| 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:
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