Crate pombase_gocam 

A library for parsing and processing GO-CAM JSON format model files

GoCamRawModel is a low level representation which closely matches the JSON data, containing Fact, Individual and Annotation structs.

GoCamModel is a higher level representation, implemented as a graph of nodes (activities, chemical, complexes etc.) and edges (mostly causal relations).

This high level representation is somewhat similar to the GO CAM Data Model - gocam-py.

Example

use std::fs::File;
use pombase_gocam::raw::gocam_parse_raw;

let mut source = File::open("tests/data/gomodel_66187e4700001744.json").unwrap();

// Low level representation:
let raw_model = gocam_parse_raw(&mut source).unwrap();
assert_eq!(raw_model.id(), "gomodel:66187e4700001744");

for fact in raw_model.facts() {
    let subject_id = &fact.subject;
    println!("subject_id: {}", subject_id);
    let subject_individual = raw_model.get_individual(subject_id);
    let first_type = &subject_individual.types[0];
    if let Some(ref label) = first_type.label {
        println!("type label: {}", label);
    }
}

// Higher level representation:
use pombase_gocam::{GoCamModel, GoCamNodeType, GoCamActivity};
let model = GoCamModel::new(raw_model);

for (_, node) in model.node_iterator() {
    println!("node: {}", node);
    if let GoCamNodeType::Activity(GoCamActivity { ref enabler, inputs: _, outputs: _ }) = node.node_type {
        println!("enabler ID: {}", enabler.id());
    }
}

Modules

gocam_py

Code for parsing gocam-py YAML models See: https://github.com/geneontology/gocam-py

graph

Graph algorithms

raw

The module contains code for reading the low-level JSON representation of GO-CAM models.

Structs

GoCamActivity

GoCamChemical

A chemical which will be the input, output or enabler of an activity

GoCamComplex

A complex can have a GO complex ID (from the CC GO aspect) or a Complex Portal ID

GoCamComplexComponent

The component for the ComplexComponent variant of GoCamComponent

GoCamEdge

An edge in the model - a causal relation between two activities.

GoCamGene

A gene in a GoCamNode, possibly enabling an activity

GoCamInput

The has_input of an activity

GoCamMRNA

An mRNA - either an input/output or the enabler of an activity

GoCamModel

A high level representation of the model with nodes for activities, chemicals, complexes etc. and edges for causal dependencies between nodes/activities.

GoCamModifiedProtein

A PRO modified protein in a node, possibly enabling an activity

GoCamNode

A gene, chemical, complex or modified protein OR an activity (enabled by gene, chemical, complex or modified protein). These fields more or less match Figure 1 in the GO-CAM paper except for:

GoCamNodeOverlap

An overlap returned by GoCamModel::find_overlaps()

GoCamOtherComponent

The component for the OtherComponent variant of GoCamComponent

GoCamOutput

The has_output of an activity

GoCamProcess

A GO biological process

NodeIterator

An iterator over GoCamNode, returned by GoCamModel::node_iterator()

Enums

GoCamComponent

A complex or a GO cellular component

GoCamDirection

GoCamEnabledBy

An enabler of an activity

GoCamNodeType

The type of a node in a GoCamModel

RemoveType

Statics

REL_NAMES

A map of edge relation term IDs to term names. Example: “RO:0002211” => “regulates”,

Functions

parse_gocam_model

Read from a JSON source and return a GoCamModel.

Type Aliases

GoCamGeneIdentifier

A gene ID with DB prefix, like “PomBase:SPAC9E9.05”

GoCamGeneName

A gene name like “cdc2”

GoCamGraph

The Graph representation of a GO-CAM model. See: GoCamModel::graph()

GoCamModelId

GoCamModelIdTitle

GoCamModelTitle