Pathway maps (optional)

OpenGenomeBrowser is able to dynamically color pathway maps.

├── organisms
    └── ...
└── pathway_maps
     ├── type_dictionary.json
     └── svg
         ├── map1.svg
         └── ...

Required SVG format

The svg should have a title attribute. Example:

<svg
        title='Phenylalanine, tyrosine and tryptophan biosynthesis'
        version='1.1' baseProfile='full' xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink'
        <!-- other attributes -->
        >

Each enzyme in the SVG needs to belong to the class shape and have the data-annotations-attribute. Example:

<circle cx='978' cy='930' r='4' fill='transparent'  <!-- Must not be circle, can be any other SVG element -->
        title='C00296 (Quinate)'  <!-- will tooltip -->
        class='shape compound'  <!-- only class 'shape' is required -->
        data-annotations='[{"description": "L-Ectoine", "name": "C06231", "type": "KEGG Compound"}]'>  <!-- see below -->
        />

The data-annotations-attribute tells OpenGenomeBrowser which annotations are behind the shape.

Example:

[
  {
    "description": "L-Ectoine",
    "name": "C06231",
    "type": "KEGG Compound"
  }
]

Note: To allow users to click on the shapes, they must be in the foreground or other SVG-elements need the property style='pointer-events: none'.

type_dictionary.json

In order to allow more freedom for SVG-creators, the type of the annotations must not adhere to OpenGenomeBrowser nomenclature.

Instead, another file is required: type_dictionary.json. It consists of a mapping of all shape types that occur in the SVGs to OpenGenomeBrowser types. If a type does not correspond to an OpenGenomeBrowser type, simply map it to ignore.

Example:

{
  "Gene Product": "GP",
  "Gene Code": "GC",
  "Ortholog": "OL",
  "Custom Annotation": "CU",
  "K": "KG",
  "R": "KR",
  "EC": "EC",
  "GO": "GO",
  "C": "ignore",
  "G": "ignore",
  "D": "ignore",
  "DG": "ignore",
  "BR": "ignore",
  "MAP": "ignore",
  "Unknown": "ignore"
}

OpenGenomeBrowser types:

• KG: (KEGG gene, format: K000000)
• KR: (KEGG reaction, format: R00000)
• GO: (Gene ontology, format: GO:0000000)
• EC: (Enzyme commission, format: EC:0.0, EC:0.0.0 or EC:0.0.0.0)
• CU: (Custom)

Import pathway svgs

1. Open a terminal in the container
2. run python db_setup/manage_ogb.py import-pathway-maps