Metadata schema

These are subdivided into three categories (File, Sample, and General). The recommended practice is to enter as much metadata as possible when you first upload files to the Platform. For instance, for raw sequencing files, you should enter Platform (sequencing platform) and Sample ID. Of these fields, there are seven metadata fields that we highly suggest you set for your data. While your tasks may run correctly without them, these metadata fields will help optimize your analyses. These fields are labeled in the table below with a suggested tag in the Name column.

Please keep in mind the fields have to be specified exactly as listed in the tables below under the Name column. This means that if the field is not listed exactly as in the table, the Platform will interpret it is a custom metadata field (see below).

File

In the following table, you will find the name, description, and values of metadata fields for File. The second column, API key, allows you to access the specified metadata field through the API. Learn more about accessing metadata via the API.

There are six metadata fields that we highly suggest you set for your data. While your tasks may run correctly without them, these metadata fields will help optimize your analyses. These fields are labeled in the table below with a red suggested tag in the Name column.

Name

API key

Description

Values

Reference genome

reference_genome

The reference assembly (such as HG19 or GRCh37) to which the nucleotide sequence of a case can be aligned.

string

Suggested values:

human_g1k_v37
human_g1k_v37_decoy
ucsc.hg19
Homo_sapiens.Ensembl.GRCh37
Homo_sapiens.GRCh38.dna.primary_assembly
ion_torrent.hg19
mouse_mm9_ucsc
ens_mouse_mm9_genome
mouse_mm10_ucsc

Quality scale
suggested

quality_scale

For raw reads, this value denotes the sequencing technology and quality format. For BAM and SAM files, this value should always be ‘Sanger’.

Enter this value for all FASTQ files, unless they are used in a workflow with a FASTQ quality scale detector wrapper.

Choose from one of the following options:

sanger
llumina13
illumina15
illumina18
solexa
Or, enter no value.

Platform
suggested

platform

Only some tools and workflows may require a value for the Platform field. However, it is recommended that you set it whenever possible, unless you are certain that your workflow will work without it.

string

Suggested values:

Illumina HiSeq
Illumina GA
ABI capillary sequencer
Illumina MiSeq
ABI SOLiD
Ion Torrent PGM
LS 454
Illumina HiSeq X Ten
Illumina
Helicos
PacBio
Not available

Platform unit ID
suggested

platform_unit_id

This is an identifier for lanes (Illumina), or for slides (SOLiD) in the case that a library was split and ran over multiple lanes on the flow cell or slides. The platform unit ID refers to the lane ID or the slide ID.

The value supplied in the Platform unit ID field will be written to the read group tag (@RG:PU) in SAM or BAM files. All aligner apps add read group fields to the aligned BAM file on the basis of Platform unit ID metadata.

string

Paired end
suggested

paired_end

For paired-end sequencing, this value determines the end of the fragment sequenced.

For paired-end read files, this field indicates whether the read file is left end or right end. Set ‘1’ for left end and ‘2’ for right end reads. This is used to group pairs. If the FASTQ file is a single-end read this field should be left as ‘-’.

Note: It is important for two members of paired-end reads to have identical Sample ID, Library ID, Platform unit ID, and File segment number.

This takes a value of 1 or 2.

Note: For single-end sequencing no value is needed.

Library ID
suggested

library_id

This is an identifier for the sequencing library preparation.

The value set in this field does not affect whether or not the workflow runs successfully. However, all files that come from the same sequencing library must have the same value.

The Library ID will be written to the read group tag (@RG:LB) in SAM or BAM files. All aligner apps are programmed to add RG fields to the aligned BAM according to the Library ID.

string

File segment number
suggested

file_segment_number

If the sequencing reads for a single library, sample and lane are divided into multiple (smaller) files, the File segment number is used to enumerate these. Otherwise, this field can be left blank.

This information can be used for batching when processing files with a workflow.

Integer.

Experimental strategy

experimental_strategy

This is the method or protocol used to perform the laboratory analysis.

string

Suggested values:

DNA-Seq
WXS
WGS
Amplicon
Bisulfite-Seq
RNA-Seq
miRNA-Seq
Total RNA-Seq
Not available

Sample

In the table below, you will find the name, description, and values of metadata fields for Sample. The second column, API key, allows you to access the specified metadata field through the API. Learn more about accessing metadata via the API.

There is one metadata field below that we highly suggest you set for your data. While your tasks may run correctly without this field, it will help optimize your analyses. This field is labeled in the table below with a suggested tag in the Name column.

Name

API key

Description

Value

Sample ID
suggested

sample_id

A human readable identifier for a sample or specimen, which could contain some metadata information. A sample or specimen is material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes, including but not limited to tissues, body fluids, cells, organs, embryos, body excretory products, etc.

Tools use Sample ID to separate files that come from different samples.

For SAM and BAM files, the value supplied in the Sample ID field is written to the read group tag (@RG:SM). All aligners add read group fields to the aligned BAM file using the file’s Sample ID metadata.

string

Sample type

sample_type

The type of material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes. This includes tissues, body fluids, cells, organs, embryos, body excretory products, etc.

string

Suggested values:

Blood normal
Tumor tissue
Normal tissue
Primary cells
Stem cells
Embryo
Cell Line
Saliva
Control
Not available

General

In the following table, you will find the name, description, and values of metadata fields for General. The second column, API key, allows you to access the specified metadata field through the API. Learn more about accessing metadata via the API.

Name

API key

Description

Value

Species

species

A group of organisms having some common characteristic or qualities, that differ from all other groups of organisms and that are capable of breeding and producing fertile offspring.

String

Suggested values:

Homo sapiens
Mus musculus

Investigation

investigation

A value denoting the project or study that generated the data.

String

Case ID

case_id

This is a human-readable identifier, such as a number or a string for a subject who has taken part in the investigation or study.

String

Batch number

batch_number

This is an assigned distinctive alpha-numeric identification code that signifies grouping.

Integer

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Apart from the standard set of metadata fields that can be seen through the visual interface, custom metadata fields can be added via the command line uploader or via the API.