Index File

Type

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

Accession

Lab specific identifiers to reference an object.

A lab specific identifier to reference an object.

Lab Alias

Aliases

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

The assembly associated with the index file.

Genome Assembly

Award

The Checkfiles GitHub version release the file was validated with.

Checkfiles Version

Some samples are part of particular data collections.

Collections

Content MD5sum

Content Type

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

Controlled Access

Creation Timestamp

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

Description

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 reads that did not pass a filtering step, such as PCR duplicates, have been removed from the file.

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

Notes

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

Redacted

Release Timestamp

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

Revoke Detail

S3 URI

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

Schema Version

Status

Submitted By

Submitted File Name

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

Submitter Comment

Summary

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

The unique identifier associated with every object.

UUID

Explanation of why the file failed the automated content checks.

Index File

Changelog for `index_file.json`

Minor changes since schema version 1

Index File

Changelog for index_file.json

Minor changes since schema version 1

Changelog for `index_file.json`