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UPLOAD ANNOTATIONS

Pathways, gene ontology (GO) terms, ABR genes, and VEP (Variant Effect Predictor) files are classified as annotations and can be uploaded through the ANNOTATIONS (Fig.) tab.

ABR and GO_OBO upload has two fields:

  1. Organism: Name of the organism
  2. Tag: The version number of the annotation file

Gene Model, VEP, and Variations upload have three fields:

  1. Organism: Name of the organism
  2. Reference version: Version of the reference file
  3. Tag: Version of the annotation file

GO and Pathway  upload has four fields:

  1. Organism: Name of the organism
  2. Reference version: Version of the reference file
  3. GTF version: Version of the gene model file
  4. Tag: Version 

Different types of annotations and their allowed formats are explained in Table below.

Tag

Data Type

Format

Details

Gene models

Gene annotations

Gtf, Gff3

Source: Ensembl.

Should correspond to the Ensembl genome versions

Pathway

Pathways

Tab, Gmt

Source: Wiki pathways

Gene Ontology

Gene Ontology associations

Obo, Tab, Txt

GO terms

VEP

Variant annotations

Custom

Source: Ensembl.

Should correspond to the Ensembl genome versions

Variations

GATK variants

VCF

Source: Ensembl
Table. Annotation file formats. Compressed files are allowed as long as each file is compressed separately.

 

Fig. 1. ANNOTATION FILES upload window. One of the radio icons needs to be selected to upload the data.

 

Similar to Sequence and reference file uploads, the following actions are performed on the uploaded annotation files:

  • Uncompression of the files
  • Validation of the format and integrity of the file and its compatibility to genome/gene annotation file.
  • Registration into the ANNOTATIONS
  • Status notification through email

Successfully uploaded files are stored in ANNOTATIONS and can be accessed while executing the pipelines.

 

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