Schema Directory

Type

Access Key ID

Lab specific identifiers to reference an object.

A lab specific identifier to reference an object.

Lab Alias

Aliases

Creation Timestamp

Description

Notes

The version of the JSON schema that the server uses to validate the object.

Schema Version

Secret Access Key Hash

Status

Submitted By

Additional information specified by the submitter to be displayed as a comment on the portal.

Submitter Comment

Summary

The user that is assigned to this access key.

User

The unique identifier associated with every object.

UUID

Access Key

A file containing alignment data in bam or cram format.

A unique identifier to be used to reference the object prefixed with IGVF.

Accession

Accessions previously assigned to objects that have been merged with this object.

An accession previously assigned to an object that has been merged with this object.

Alternate Accession

Alternate Accessions

Analysis Step Version

URL linking to the controlled access file that has been deposited at AnVIL workspace.

AnVIL URL

Title(s) of assay from the file set this file belongs to.

Title of assay from the file set this file belongs to.

Assay Title

Assay Titles

Genome assembly applicable for the annotation data.

Genome Assembly

Award

The chemical modifications to bases in a DNA sequence that are detected in this file.

The chemical modification to bases in a DNA sequence that is detected in this file.

Base Modification

Base Modifications

The Checkfiles GitHub version release the file was validated with.

Checkfiles Version

Some samples are part of particular data collections.

Collections

Content MD5sum

A summary of the data in the alignment file.

Content Summary

The mapping locations of input reads with respect to a transcriptome.

Content Type

Boolean value, indicating the file being controlled access, if true.

Controlled Access

Identifiers from external resources that may have 1-to-1 or 1-to-many relationships with IGVF file objects.

Identifier from an external resource that may have 1-to-1 or 1-to-many relationships with IGVF file objects.

External Identifier

External Resources

The files participating as inputs into software to produce this output file.

File Derived From

Derived From

A boolean indicating whether the file has been dervided manually without automated computational methods.

Derived Manually

Documents that provide additional information (not data file).

A document that provides additional information (not data file).

Document

Documents

The file format or extension of the file.

File Format

Documents that describe the file format and fields of this file.

File Format Specifications Document

File Format Specifications Documents

File Set

File Size

Indicates whether the file has gone through some filtering step, for example, removal of PCR duplicates or filtering based on significance calling.

Filtered

File Set(s) that this file is a gene list for.

Gene List For

Download URL

The files which are derived from this file.

Input File For

Construct library set(s) that this file was used for in insert design.

Integrated In

File Set(s) that this file is a loci list for.

Loci List For

The md5sum of the file being transferred.

MD5sum

Preview Timestamp

The quality metrics that are associated with this file.

Quality Metric

Quality Metrics

Number of reads in a bam file. Including both mapped, unmapped, and multi-mapped read counts.

Read Count

Indicates whether the alignments data have been sanitized (redacted) to prevent leakage of private and potentially identifying genomic information.

Redacted

Link to the reference files used to generate this file.

Link to a reference file used to generate this file.

Reference File

Reference Files

Release Timestamp

Explanation of why an object was transitioned to the revoked status.

Revoke Detail

S3 URI

Submitted File Name

The annotation and version of the reference resource.

Transcriptome Annotation

The upload credentials for S3 to submit the file content.

Upload Credentials

The upload/validation status of the file.

Upload Status

Explanation of why the file failed the automated content checks.

Validation Error Detail

Workflow

Alignment File

A file set for analyses. Analysis sets represent the results of a computational analysis of raw genomic data or other analyses.

Title(s) of assays that produced data analyzed in the analysis set.

Title of assay that produced data analyzed in the analysis set.

The construct library sets associated with the samples of this file set.

A construct library set associated with a sample of this file set.

Construct Library Set

Construct Library Sets

The file sets for which this file set is a control.

File Set Controlled By This File Set

File Sets Controlled By This File Set

The type of control this file set represents.

Control Type

The controlled access of the institutional certificates covering the sample associated with this file set which are signed by the same lab (or their partner lab) as the lab that submitted this file set.

The data use limitation summaries of institutional certificates covering the sample associated with this file set which are signed by the same lab (or their partner lab) as the lab that submitted this file set.

A combination of the data use limitation and its modifiers.

Data Use Limitation Summary

Data Use Limitation Summaries

Identifiers from external resources that may have 1-to-1 or 1-to-many relationships with IGVF file sets.

Identifier from an external resource that may have 1-to-1 or 1-to-many relationships with IGVF file sets.

External identifier

The sample(s) associated with this analysis set inferred through demultiplexing.

Demultiplexed Sample

Demultiplexed Samples

The donors of the samples associated with this analysis set.

Donor of a sample associated with this analysis set.

Donor

Donors

Links to the external site where images and related data produced by this analysis are stored.

External Image Data URL

File Set Type

File

Files

The biological processes measured by the functional assays.

Phenotype Term

Functional Assay Mechanisms

The file set(s) required for this analysis.

A file set that serves as input for this file set.

Input File Set

Input File Sets

The file sets that use this file set as an input.

Input For

Links to the protocol(s) for conducting the assay on Protocols.io.

Protocol

Protocols

A summary of the samples associated with input file sets of this analysis set.

Simplified Sample Summary

Samples associated with this analysis set.

Sample associated with this analysis set.

Sample

Samples

The timestamp the first file object in the file_set or associated auxiliary sets was created.

Submitted Files Timestamp

A workflow for computational analysis of genomic data. A workflow is made up of analysis steps.

Workflows

Analysis Set

A matrix where rows represent transcripts and columns represent samples or cells, containing counts of sequencing reads that map to each transcript.

Detailed information about the transcripts detected in a genomic assay, including their genomic coordinates, gene names, and other relevant annotations.

A reference file consisting of nascent transcriptome index which contains both nascent transcripts and cDNAs and therefore can be used for applications where quantifying intron-spanning reads is important, such as single-nucleus RNA-seq or biophysical models that jointly consider spliced and unspliced transcripts.

A reference file consisting of standard transcriptome index which does not contain introns and is therefore only suitable for quantifying bulk and single-cell RNA-seq.

A reference file consisting of all known transcripts or coding regions of the genome.

The quantified changes in expression levels of transcripts between conditions or groups.

A GTF file containing annotations of targeted transcripts by the TAP-seq primer panel.

A step in a computational analysis workflow. For example, a sequence alignment step that represents the phase of the computational analysis in which sequenced reads are being aligned to the reference genome.

The process of generating transcriptome index file.

Analysis Step Types

The analysis step versions associated with this analysis step.

Analysis Step Versions

The content types used as input for the analysis step.

A content type used as input for the analysis step.

Input Content Type

Input Content Types

Name

The content types produced as output by the analysis step.

A content type produced as output by the analysis step.

Output Content Type

Output Content Types

Parent

Parents

Unique lowercased label of the analysis step that includes the relevant assays, the software used, and the purpose of the step, e.g. rampage-grit-peak-calling-step

Step Label

The preferred viewable name of the analysis step, likely the same as the step label.

Title

The computational workflow in which this analysis step belongs.

Analysis Step

A step version in a computational analysis workflow.

The analysis step which this version belongs to.