Projects and the resources nested inside them.
The structure below follows the nesting of the endpoint paths, starting at
/new_api/projects/.
1. Project data
Metadata of a project: name, version, owner, disease and organism annotations, license, upload date, processing status and the identifier of its top map.
See full documentation.
2. Owner
The user that owns the project, and the operation that hands the project over to another user.
See full documentation.
3. License
The license assigned to the project, and the operations that assign or remove it.
See full documentation.
4. Top map
The map that opens when the project is browsed, and the operation that points it at another submap.
See full documentation.
5. Organism
The species the project describes, expressed as a taxonomy annotation.
See full documentation.
6. Disease
The disease the project describes, expressed as a MeSH annotation.
See full documentation.
7. Chemicals
Chemicals related to the disease annotated on the project, looked up in the Comparative Toxicogenomics Database and matched against the elements of its maps.
See full documentation.
8. Drugs
Drugs acting on the targets found in the project, looked up in Open Targets and matched against the elements of its maps.
See full documentation.
9. Glyphs
Images uploaded to the project and drawn on its maps as element icons.
See full documentation.
10. Overview images
Optional images giving a graphical overview of the processes described in the project, with clickable areas linking to its maps.
See full documentation.
11. Shapes
The shapes available for drawing elements of the project.
See full documentation.
12. Arrow types
The arrow heads available for drawing reactions of the project.
See full documentation.
13. Line types
The line styles available for drawing on the maps of the project.
See full documentation.
14. Overlays
Data overlays of the project - the colouring layers put on top of its maps - and the operations that create, update and remove them.
See full documentation.
14.1. Overlay entries
The individual rows of an overlay, each saying how one bio entity should be coloured.
See full documentation.
14.2. Overlay groups
The groups the calling user organises their overlays into.
See full documentation.
15. Maps
The maps (submaps) the project consists of, and everything drawn on them.
See full documentation.
15.1. BioEntities
Search across the elements and reactions of a map, when the type of the result does not matter.
See full documentation.
15.1.1. Elements
The nodes of a map - species, complexes, compartments and the other entities reactions connect.
See full documentation.
15.1.2. Elements sub-resources
Everything that belongs to a single element:
-
Glyph - the image drawn instead of the default shape.
-
Annotations - links to external databases.
-
Modifications - modification states such as phosphorylation.
-
Synonyms - alternative names of the element.
-
Former symbols - symbols the element was known by before.
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Children - elements nested inside it, such as complex members.
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Compartment - the compartment the element lies in.
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Complex - the complex the element belongs to.
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Submap - the map the element links to.
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Unit - the unit of the value carried by the element.
15.1.3. Reactions
The edges of a map - the reactions connecting its elements.
See full documentation.
15.1.4. Reactions sub-resources
Everything that belongs to a single reaction:
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Reactants - what the reaction consumes.
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Reactant element - the map element a reactant points at.
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Products - what the reaction produces.
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Product element - the map element a product points at.
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Modifiers - what catalyses or inhibits the reaction.
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Modifier element - the map element a modifier points at.
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Operators - the logical operators (AND, OR, …) on its branches.
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Operator inputs - what enters an operator.
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Operator outputs - what leaves an operator.
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Annotations - links to external databases.
15.2. Layers
The drawing layers of a map, holding the graphics added on top of the pathway itself.
See full documentation.
15.2.1. Images
Images placed on a layer.
See full documentation.
15.2.2. Texts
Text boxes placed on a layer.
See full documentation.
15.2.3. Lines
Lines (polylines) drawn on a layer.
See full documentation.
15.2.4. Ovals
Ovals drawn on a layer.
See full documentation.
15.2.5. Rectangles
Rectangles drawn on a layer.
See full documentation.
15.3. Comments
Comments left by users at given coordinates of a map.
See full documentation.
15.4. Authors
The authors credited on a map.
See full documentation.
15.5. Annotations
Annotations of the map itself, linking it to external databases.
See full documentation.
15.6. SBML Functions
Function definitions taken from the SBML file the map was created from.
See full documentation.
15.7. SBML Parameters
Global parameters taken from the SBML file the map was created from.
See full documentation.
15.8. SBML Units
Units of quantity defined at the map level, taken from the SBML file the map was created from.
See full documentation.