Annotations

OpenGenomeBrowser is designed to be flexible when it comes to annotations. There are default annotation types, but they can be changed and new ones can be added.

Default annotation types

By default, OpenGenomeBrowser supports these types of annotations:

Annotation type	Description	Source
GC	Gene code	GenBank file
GP	Gene product	GenBank file
EP	Eggnog product	Eggnog file
ED	Eggnog description	Eggnog file
EO	Eggnog ortholog	Eggnog file
EC	Enzyme commission	GenBank file and Eggnog file
KG	KEGG gene	Eggnog file
KR	KEGG reaction	Eggnog file
GO	Gene ontology	Eggnog file
SL	Subcellular location	-
OL	Ortholog	OrthoFinder

These are defined in the file annotations.json, located next to the organisms folder.

├── organisms
│    └── ...
└── annotations.json

Custom annotation types

New annotation types can simply be added by adding a new entry to this annotations.json file.

For example, this is what the definition of the EC annotation type looks like:

{
  "EC": {
    "name": "EC Number",
    "color": "rgb(222,203,228)",
    "regex": "^EC:[0-9\\.-]{1,12}$",
    "hyperlinks": [
      {
        "name": "SIB Rhea DB",
        "url": "https://www.rhea-db.org/rhea?query=${annotation}"
      },
      {
        "name": "BRENDA",
        "url": "https://www.brenda-enzymes.org/enzyme.php?ecno=${annotation.substring(3)}"
      }
    ]
  },
  "GO": "etc..."
}

Custom annotation files

Create files that map genes to annotations in this way: A valid custom_annotations file must be in this format: locustag\tannotation1, annotation2, annotation3

I.e., this would be a valid file:

EXAMPLE1234-2-1.1_000001	K000001
EXAMPLE1234-2-1.1_000004
EXAMPLE1234-2-1.1_000008	K000001, K000002

Add them to genome.json as described here.

Annotation descriptions (optional)

OpenGenomeBrowser allows its users to extend annotation identifiers such as e.g. K01695, EC:4.2.1.20 and GO:0005829 with a short description to in order to facilitate interpretation. To use this feature, simply provide a file for each annotation type which maps the annotation identifiers to their description. These files must be located in the folder annotation-descriptions and named {annotation_type}.tsv}.

├── organisms
│    └── ...
├── annotations.json
└── annotation-descriptions
     ├── EC.tsv
     └── ...

This is the expected format: annotation\tdescription

EC:4.2.1.17	beta-hydroxyacyl-CoA dehydrase
EC:4.2.1.18	methylglutaconyl-CoA hydratase
EC:4.2.1.19	imidazoleglycerol-phosphate dehydratase
EC:4.2.1.20	L-tryptophan synthetase

Import annotation descriptions

This step is only required if these files were added after the genomes were imported.

1. [Open a terminal in the container]https://github.com/opengenomebrowser/opengenomebrowser-docker-template#open-a-terminal-in-the-container
2. run python db_setup/manage_ogb.py import-annotation-descriptions