OutputType
search: boost: 2.0 ---# Enum: OutputType
Vocabulary from the ENCODE model describing the purpose or content of a file (see "Properties->output_type" in https://www.encodeproject.org/profiles/file).
URI: https://w3id.org/fga-wg/schema/bundle/OutputType
Permissible Values¶
| Value | Meaning | Description |
|---|---|---|
| 3D structure | None | |
| alignments | None | |
| alignments with modifications | None | |
| allele-specific contact matrix | None | |
| allele-specific variants | None | |
| archr project | None | |
| bias models | None | |
| bias-corrected predicted signal profile | None | |
| bidirectional peaks | None | |
| candidate Cis-Regulatory Elements | None | |
| candidate enhancers | None | |
| candidate promoters | None | |
| capture targets | None | |
| cell coordinates | None | |
| cell topic participation | None | |
| cell type data | None | |
| cell type annotations | None | |
| chromatin stripes | None | |
| chromosomes reference | None | |
| chromosome sizes | None | |
| contact domains | None | |
| contact matrix | None | |
| consensus DNase hypersensitivity sites | None | |
| curated binding sites | None | |
| curated SNVs | None | |
| mapping quality thresholded contact matrix | None | |
| conservative IDR thresholded peaks | None | |
| control normalized signal | None | |
| counts sequence contribution scores | None | |
| CpG sites coverage | None | |
| depth normalized signals matrix | None | |
| fold over change matrix | None | |
| DHS peaks | None | |
| DHS regions reference | None | |
| nuclease cleavage frequency | None | |
| differential expression quantifications | None | |
| differential splicing quantifications | None | |
| diploid personal genome alignments | None | |
| divergent peaks | None | |
| DNN-MPRA contribution scores | None | |
| DNN-MPRA predicted signal | None | |
| dsQTLs | None | |
| element barcode mapping | None | |
| elements reference | None | |
| element gene interactions p-value | None | |
| element gene interactions signal | None | |
| element gene links | None | |
| enhancer-gene links | None | |
| thresholded links | None | |
| element quantifications | None | |
| enhancer prediction model | None | |
| enhancer validation | None | |
| enrichment | None | |
| enhancers reference | None | |
| eQTLs | None | |
| exon quantifications | None | |
| exclusion list regions | None | |
| FDR cut rate | None | |
| female genome index | None | |
| female genome reference | None | |
| filtered indels | None | |
| filtered peaks | None | |
| filtered reads | None | |
| filtered regions | None | |
| filtered SNPs | None | |
| fine-mapped variants | None | |
| fold change over control | None | |
| footprints | None | |
| functional conservation mapping | None | |
| functional conservation quantifications | None | |
| fragments | None | |
| gene alignments | None | |
| gene quantifications | None | |
| gene stabilities | None | |
| genic features quantifications | None | |
| genic regions quantifications | None | |
| genome compartments | None | |
| genome index | None | |
| genome reference | None | |
| genome subcompartments | None | |
| gRNAs | None | |
| guide locations | None | |
| guide quantifications | None | |
| haplotype-specific alignments | None | |
| haplotype-specific contact matrix | None | |
| haplotype-specific nuclease cleavage frequency | None | |
| haplotype-specific nuclease cleavage corrected frequency | None | |
| hotspots | None | |
| hotspots1 reference | None | |
| hotspots2 reference | None | |
| idat green channel | None | |
| idat red channel | None | |
| inclusion list | None | |
| index reads | None | |
| intensity values | None | |
| IDR ranked peaks | None | |
| IDR thresholded peaks | None | |
| kmer weights | None | |
| library fraction | None | |
| loops | None | |
| male genome index | None | |
| male genome reference | None | |
| maternal haplotype mapping | None | |
| maternal variant calls | None | |
| merged transcription segment quantifications | None | |
| methylated reads | None | |
| methylation state at CHG | None | |
| methylation state at CHH | None | |
| methylation state at CpG | None | |
| microRNA quantifications | None | |
| miRNA annotations | None | |
| minus strand end position signal | None | |
| minus strand inosine methylation state | None | |
| minus strand m5C methylation state | None | |
| minus strand m6A methylation state | None | |
| minus strand methylation state at CpG | None | |
| minus strand Nm methylation state | None | |
| minus strand normalized end position signal | None | |
| minus strand pseudouridine methylation state | None | |
| minus strand signal of all reads | None | |
| minus strand signal of unique reads | None | |
| mitochondrial exclusion list regions | None | |
| mitochondrial genome index | None | |
| mitochondrial genome reference | None | |
| model performance metrics | None | |
| models | None | |
| motif clusters reference | None | |
| motif model | None | |
| mRNA stabilities | None | |
| nanopore signal | None | |
| negative control regions | None | |
| nested contact domains | None | |
| non-targeting gRNAs | None | |
| normalized bias-corrected predicted signal profile | None | |
| normalized signal of all reads | None | |
| normalized observed signal profile | None | |
| normalized observed signal profile (minus strand) | None | |
| normalized observed signal profile (plus strand) | None | |
| normalized predicted bias profile | None | |
| normalized predicted signal profile | None | |
| normalized predicted signal profile (minus strand) | None | |
| normalized predicted signal profile (plus strand) | None | |
| novel peptides | None | |
| observed bias profile | None | |
| observed control profile (minus strand) | None | |
| observed control profile (plus strand) | None | |
| observed signal profile | None | |
| observed signal profile (minus strand) | None | |
| observed signal profile (plus strand) | None | |
| open chromatin regions | None | |
| optimal IDR thresholded peaks | None | |
| pairs | None | |
| paternal haplotype mapping | None | |
| paternal variant calls | None | |
| peaks | None | |
| peaks and background as input for IDR | None | |
| peptide quantifications | None | |
| personalized genome assembly | None | |
| perturbation signal | None | |
| phastcons score reference | None | |
| phased mapping | None | |
| phased variant calls | None | |
| plus strand end position signal | None | |
| plus strand inosine methylation state | None | |
| plus strand m5C methylation state | None | |
| plus strand m6A methylation state | None | |
| plus strand methylation state at CpG | None | |
| plus strand Nm methylation state | None | |
| plus strand normalized end position signal | None | |
| plus strand pseudouridine methylation state | None | |
| plus strand signal of all reads | None | |
| plus strand signal of unique reads | None | |
| polyA sites | None | |
| positive control regions | None | |
| predicted bias profile | None | |
| predicted enhancers | None | |
| predicted signal profile | None | |
| predicted signal profile (minus strand) | None | |
| predicted signal profile (plus strand) | None | |
| predicted 3D structural ensembles | None | |
| preprocessed alignments | None | |
| profile sequence contribution scores | None | |
| promoter prediction model | None | |
| promoters reference | None | |
| protein expression quantifications | None | |
| pseudoreplicated peaks | None | |
| pseudoreplicated IDR thresholded peaks | None | |
| PWMs | None | |
| R2C2 subreads | None | |
| raw imaging signal | None | |
| raw minus strand signal | None | |
| raw normalized signal | None | |
| raw plus strand signal | None | |
| raw signal | None | |
| ranked gRNAs | None | |
| read-depth normalized signal | None | |
| read annotations | None | |
| reads | None | |
| repeat elements annotation | None | |
| repeats reference | None | |
| reference variants | None | |
| regulatory elements | None | |
| relative replication signal | None | |
| replicated peaks | None | |
| replication timing profile | None | |
| reporter code counts | None | |
| representative DNase hypersensitivity sites | None | |
| representative IDR thresholded peaks | None | |
| restriction enzyme site locations | None | |
| RNA-binding protein associated mRNAs | None | |
| rRNA reference | None | |
| safe-targeting gRNAs | None | |
| scaled RNA stability | None | |
| selected regions for bias-corrected predicted signal profile | None | |
| selected regions for count sequence contribution scores | None | |
| selected regions for predicted bias profile | None | |
| selected regions for predicted signal and sequence contribution scores | None | |
| selected regions for predicted signal profile | None | |
| selected regions for predicted signal profile (minus strand) | None | |
| selected regions for predicted signal profile (plus strand) | None | |
| selected regions for profile sequence contribution scores | None | |
| semi-automated genome annotation | None | |
| sequence adapters | None | |
| sequence barcodes | None | |
| sequence motifs report | None | |
| sequence motifs | None | |
| sequence motifs instances | None | |
| signal of all reads | None | |
| signal of unique reads | None | |
| signal p-value | None | |
| spike-ins | None | |
| smoothed methylation state at CpG | None | |
| sparse gene count matrix | None | |
| sparse gene count matrix of all reads | None | |
| sparse gene count matrix of unique reads | None | |
| sparse gRNA count matrix | None | |
| sparse peak count matrix | None | |
| sparse transcript count matrix | None | |
| splice junctions | None | |
| subreads | None | |
| TF binding prediction model | None | |
| TF peaks matrix | None | |
| thresholded element gene links | None | |
| topic gene weights | None | |
| training and test regions | None | |
| training set | None | |
| transcribed region quantifications | None | |
| transcript quantifications | None | |
| transcription start sites | None | |
| transcription segment quantifications | None | |
| transcriptome alignments | None | |
| transcriptome annotations | None | |
| transcriptome index | None | |
| transcriptome reference | None | |
| transposable element TF ancestral origin percent by motif | None | |
| transposable element TF ancestral origin percent by subfamily | None | |
| TSS reference | None | |
| unfiltered alignments | None | |
| unfiltered sparse gene count matrix of all reads | None | |
| unfiltered sparse gene count matrix of unique reads | None | |
| unfiltered sparse splice junction count matrix of unique reads | None | |
| unidirectional peaks | None | |
| UV enriched segment quantifications | None | |
| variant calls | None | |
| variant effect quantifications | None | |
| variant reference | None | |
| variants contact matrix | None | |
| variant functional prediction | None | |
| z scores matrix | None |
Slots¶
| Name | Description |
|---|---|
| data_content | Classification describing the file's purpose or contents. |
Identifier and Mapping Information¶
Schema Source¶
- from schema: https://w3id.org/fga-wg/schema/bundle
LinkML Source¶
name: OutputType
description: Vocabulary from the ENCODE model describing the purpose or content of
a file (see "Properties->output_type" in https://www.encodeproject.org/profiles/file).
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
permissible_values:
3D structure:
text: 3D structure
alignments:
text: alignments
alignments with modifications:
text: alignments with modifications
allele-specific contact matrix:
text: allele-specific contact matrix
allele-specific variants:
text: allele-specific variants
archr project:
text: archr project
bias models:
text: bias models
bias-corrected predicted signal profile:
text: bias-corrected predicted signal profile
bidirectional peaks:
text: bidirectional peaks
candidate Cis-Regulatory Elements:
text: candidate Cis-Regulatory Elements
candidate enhancers:
text: candidate enhancers
candidate promoters:
text: candidate promoters
capture targets:
text: capture targets
cell coordinates:
text: cell coordinates
cell topic participation:
text: cell topic participation
cell type data:
text: cell type data
cell type annotations:
text: cell type annotations
chromatin stripes:
text: chromatin stripes
chromosomes reference:
text: chromosomes reference
chromosome sizes:
text: chromosome sizes
contact domains:
text: contact domains
contact matrix:
text: contact matrix
consensus DNase hypersensitivity sites:
text: consensus DNase hypersensitivity sites
curated binding sites:
text: curated binding sites
curated SNVs:
text: curated SNVs
mapping quality thresholded contact matrix:
text: mapping quality thresholded contact matrix
conservative IDR thresholded peaks:
text: conservative IDR thresholded peaks
control normalized signal:
text: control normalized signal
counts sequence contribution scores:
text: counts sequence contribution scores
CpG sites coverage:
text: CpG sites coverage
depth normalized signals matrix:
text: depth normalized signals matrix
fold over change matrix:
text: fold over change matrix
DHS peaks:
text: DHS peaks
DHS regions reference:
text: DHS regions reference
nuclease cleavage frequency:
text: nuclease cleavage frequency
differential expression quantifications:
text: differential expression quantifications
differential splicing quantifications:
text: differential splicing quantifications
diploid personal genome alignments:
text: diploid personal genome alignments
divergent peaks:
text: divergent peaks
DNN-MPRA contribution scores:
text: DNN-MPRA contribution scores
DNN-MPRA predicted signal:
text: DNN-MPRA predicted signal
dsQTLs:
text: dsQTLs
element barcode mapping:
text: element barcode mapping
elements reference:
text: elements reference
element gene interactions p-value:
text: element gene interactions p-value
element gene interactions signal:
text: element gene interactions signal
element gene links:
text: element gene links
enhancer-gene links:
text: enhancer-gene links
thresholded links:
text: thresholded links
element quantifications:
text: element quantifications
enhancer prediction model:
text: enhancer prediction model
enhancer validation:
text: enhancer validation
enrichment:
text: enrichment
enhancers reference:
text: enhancers reference
eQTLs:
text: eQTLs
exon quantifications:
text: exon quantifications
exclusion list regions:
text: exclusion list regions
FDR cut rate:
text: FDR cut rate
female genome index:
text: female genome index
female genome reference:
text: female genome reference
filtered indels:
text: filtered indels
filtered peaks:
text: filtered peaks
filtered reads:
text: filtered reads
filtered regions:
text: filtered regions
filtered SNPs:
text: filtered SNPs
fine-mapped variants:
text: fine-mapped variants
fold change over control:
text: fold change over control
footprints:
text: footprints
functional conservation mapping:
text: functional conservation mapping
functional conservation quantifications:
text: functional conservation quantifications
fragments:
text: fragments
gene alignments:
text: gene alignments
gene quantifications:
text: gene quantifications
gene stabilities:
text: gene stabilities
genic features quantifications:
text: genic features quantifications
genic regions quantifications:
text: genic regions quantifications
genome compartments:
text: genome compartments
genome index:
text: genome index
genome reference:
text: genome reference
genome subcompartments:
text: genome subcompartments
gRNAs:
text: gRNAs
guide locations:
text: guide locations
guide quantifications:
text: guide quantifications
haplotype-specific alignments:
text: haplotype-specific alignments
haplotype-specific contact matrix:
text: haplotype-specific contact matrix
haplotype-specific nuclease cleavage frequency:
text: haplotype-specific nuclease cleavage frequency
haplotype-specific nuclease cleavage corrected frequency:
text: haplotype-specific nuclease cleavage corrected frequency
hotspots:
text: hotspots
hotspots1 reference:
text: hotspots1 reference
hotspots2 reference:
text: hotspots2 reference
idat green channel:
text: idat green channel
idat red channel:
text: idat red channel
inclusion list:
text: inclusion list
index reads:
text: index reads
intensity values:
text: intensity values
IDR ranked peaks:
text: IDR ranked peaks
IDR thresholded peaks:
text: IDR thresholded peaks
kmer weights:
text: kmer weights
library fraction:
text: library fraction
loops:
text: loops
male genome index:
text: male genome index
male genome reference:
text: male genome reference
maternal haplotype mapping:
text: maternal haplotype mapping
maternal variant calls:
text: maternal variant calls
merged transcription segment quantifications:
text: merged transcription segment quantifications
methylated reads:
text: methylated reads
methylation state at CHG:
text: methylation state at CHG
methylation state at CHH:
text: methylation state at CHH
methylation state at CpG:
text: methylation state at CpG
microRNA quantifications:
text: microRNA quantifications
miRNA annotations:
text: miRNA annotations
minus strand end position signal:
text: minus strand end position signal
minus strand inosine methylation state:
text: minus strand inosine methylation state
minus strand m5C methylation state:
text: minus strand m5C methylation state
minus strand m6A methylation state:
text: minus strand m6A methylation state
minus strand methylation state at CpG:
text: minus strand methylation state at CpG
minus strand Nm methylation state:
text: minus strand Nm methylation state
minus strand normalized end position signal:
text: minus strand normalized end position signal
minus strand pseudouridine methylation state:
text: minus strand pseudouridine methylation state
minus strand signal of all reads:
text: minus strand signal of all reads
minus strand signal of unique reads:
text: minus strand signal of unique reads
mitochondrial exclusion list regions:
text: mitochondrial exclusion list regions
mitochondrial genome index:
text: mitochondrial genome index
mitochondrial genome reference:
text: mitochondrial genome reference
model performance metrics:
text: model performance metrics
models:
text: models
motif clusters reference:
text: motif clusters reference
motif model:
text: motif model
mRNA stabilities:
text: mRNA stabilities
nanopore signal:
text: nanopore signal
negative control regions:
text: negative control regions
nested contact domains:
text: nested contact domains
non-targeting gRNAs:
text: non-targeting gRNAs
normalized bias-corrected predicted signal profile:
text: normalized bias-corrected predicted signal profile
normalized signal of all reads:
text: normalized signal of all reads
normalized observed signal profile:
text: normalized observed signal profile
normalized observed signal profile (minus strand):
text: normalized observed signal profile (minus strand)
normalized observed signal profile (plus strand):
text: normalized observed signal profile (plus strand)
normalized predicted bias profile:
text: normalized predicted bias profile
normalized predicted signal profile:
text: normalized predicted signal profile
normalized predicted signal profile (minus strand):
text: normalized predicted signal profile (minus strand)
normalized predicted signal profile (plus strand):
text: normalized predicted signal profile (plus strand)
novel peptides:
text: novel peptides
observed bias profile:
text: observed bias profile
observed control profile (minus strand):
text: observed control profile (minus strand)
observed control profile (plus strand):
text: observed control profile (plus strand)
observed signal profile:
text: observed signal profile
observed signal profile (minus strand):
text: observed signal profile (minus strand)
observed signal profile (plus strand):
text: observed signal profile (plus strand)
open chromatin regions:
text: open chromatin regions
optimal IDR thresholded peaks:
text: optimal IDR thresholded peaks
pairs:
text: pairs
paternal haplotype mapping:
text: paternal haplotype mapping
paternal variant calls:
text: paternal variant calls
peaks:
text: peaks
peaks and background as input for IDR:
text: peaks and background as input for IDR
peptide quantifications:
text: peptide quantifications
personalized genome assembly:
text: personalized genome assembly
perturbation signal:
text: perturbation signal
phastcons score reference:
text: phastcons score reference
phased mapping:
text: phased mapping
phased variant calls:
text: phased variant calls
plus strand end position signal:
text: plus strand end position signal
plus strand inosine methylation state:
text: plus strand inosine methylation state
plus strand m5C methylation state:
text: plus strand m5C methylation state
plus strand m6A methylation state:
text: plus strand m6A methylation state
plus strand methylation state at CpG:
text: plus strand methylation state at CpG
plus strand Nm methylation state:
text: plus strand Nm methylation state
plus strand normalized end position signal:
text: plus strand normalized end position signal
plus strand pseudouridine methylation state:
text: plus strand pseudouridine methylation state
plus strand signal of all reads:
text: plus strand signal of all reads
plus strand signal of unique reads:
text: plus strand signal of unique reads
polyA sites:
text: polyA sites
positive control regions:
text: positive control regions
predicted bias profile:
text: predicted bias profile
predicted enhancers:
text: predicted enhancers
predicted signal profile:
text: predicted signal profile
predicted signal profile (minus strand):
text: predicted signal profile (minus strand)
predicted signal profile (plus strand):
text: predicted signal profile (plus strand)
predicted 3D structural ensembles:
text: predicted 3D structural ensembles
preprocessed alignments:
text: preprocessed alignments
profile sequence contribution scores:
text: profile sequence contribution scores
promoter prediction model:
text: promoter prediction model
promoters reference:
text: promoters reference
protein expression quantifications:
text: protein expression quantifications
pseudoreplicated peaks:
text: pseudoreplicated peaks
pseudoreplicated IDR thresholded peaks:
text: pseudoreplicated IDR thresholded peaks
PWMs:
text: PWMs
R2C2 subreads:
text: R2C2 subreads
raw imaging signal:
text: raw imaging signal
raw minus strand signal:
text: raw minus strand signal
raw normalized signal:
text: raw normalized signal
raw plus strand signal:
text: raw plus strand signal
raw signal:
text: raw signal
ranked gRNAs:
text: ranked gRNAs
read-depth normalized signal:
text: read-depth normalized signal
read annotations:
text: read annotations
reads:
text: reads
repeat elements annotation:
text: repeat elements annotation
repeats reference:
text: repeats reference
reference variants:
text: reference variants
regulatory elements:
text: regulatory elements
relative replication signal:
text: relative replication signal
replicated peaks:
text: replicated peaks
replication timing profile:
text: replication timing profile
reporter code counts:
text: reporter code counts
representative DNase hypersensitivity sites:
text: representative DNase hypersensitivity sites
representative IDR thresholded peaks:
text: representative IDR thresholded peaks
restriction enzyme site locations:
text: restriction enzyme site locations
RNA-binding protein associated mRNAs:
text: RNA-binding protein associated mRNAs
rRNA reference:
text: rRNA reference
safe-targeting gRNAs:
text: safe-targeting gRNAs
scaled RNA stability:
text: scaled RNA stability
selected regions for bias-corrected predicted signal profile:
text: selected regions for bias-corrected predicted signal profile
selected regions for count sequence contribution scores:
text: selected regions for count sequence contribution scores
selected regions for predicted bias profile:
text: selected regions for predicted bias profile
selected regions for predicted signal and sequence contribution scores:
text: selected regions for predicted signal and sequence contribution scores
selected regions for predicted signal profile:
text: selected regions for predicted signal profile
selected regions for predicted signal profile (minus strand):
text: selected regions for predicted signal profile (minus strand)
selected regions for predicted signal profile (plus strand):
text: selected regions for predicted signal profile (plus strand)
selected regions for profile sequence contribution scores:
text: selected regions for profile sequence contribution scores
semi-automated genome annotation:
text: semi-automated genome annotation
sequence adapters:
text: sequence adapters
sequence barcodes:
text: sequence barcodes
sequence motifs report:
text: sequence motifs report
sequence motifs:
text: sequence motifs
sequence motifs instances:
text: sequence motifs instances
signal of all reads:
text: signal of all reads
signal of unique reads:
text: signal of unique reads
signal p-value:
text: signal p-value
spike-ins:
text: spike-ins
smoothed methylation state at CpG:
text: smoothed methylation state at CpG
sparse gene count matrix:
text: sparse gene count matrix
sparse gene count matrix of all reads:
text: sparse gene count matrix of all reads
sparse gene count matrix of unique reads:
text: sparse gene count matrix of unique reads
sparse gRNA count matrix:
text: sparse gRNA count matrix
sparse peak count matrix:
text: sparse peak count matrix
sparse transcript count matrix:
text: sparse transcript count matrix
splice junctions:
text: splice junctions
subreads:
text: subreads
TF binding prediction model:
text: TF binding prediction model
TF peaks matrix:
text: TF peaks matrix
thresholded element gene links:
text: thresholded element gene links
topic gene weights:
text: topic gene weights
training and test regions:
text: training and test regions
training set:
text: training set
transcribed region quantifications:
text: transcribed region quantifications
transcript quantifications:
text: transcript quantifications
transcription start sites:
text: transcription start sites
transcription segment quantifications:
text: transcription segment quantifications
transcriptome alignments:
text: transcriptome alignments
transcriptome annotations:
text: transcriptome annotations
transcriptome index:
text: transcriptome index
transcriptome reference:
text: transcriptome reference
transposable element TF ancestral origin percent by motif:
text: transposable element TF ancestral origin percent by motif
transposable element TF ancestral origin percent by subfamily:
text: transposable element TF ancestral origin percent by subfamily
TSS reference:
text: TSS reference
unfiltered alignments:
text: unfiltered alignments
unfiltered sparse gene count matrix of all reads:
text: unfiltered sparse gene count matrix of all reads
unfiltered sparse gene count matrix of unique reads:
text: unfiltered sparse gene count matrix of unique reads
unfiltered sparse splice junction count matrix of unique reads:
text: unfiltered sparse splice junction count matrix of unique reads
unidirectional peaks:
text: unidirectional peaks
UV enriched segment quantifications:
text: UV enriched segment quantifications
variant calls:
text: variant calls
variant effect quantifications:
text: variant effect quantifications
variant reference:
text: variant reference
variants contact matrix:
text: variants contact matrix
variant functional prediction:
text: variant functional prediction
z scores matrix:
text: z scores matrix