README.md

Overview

This API pulls reaction data from https://www.rhea-db.org/. The rhea.rdf file with this information is structured in a flat format chunked into <rdf:description> tags. The parser takes these chunks one by one to walk through the rdf file.

An example of output RHEA objects:

{
    "rhea_id": "RHEA:10192",
    "equation": "ATP + H2O + sulfate(out) = ADP + H(+) + phosphate + sulfate(in)",
    "is_transport": true,
    "ec_link": "http://purl.uniprot.org/enzyme/7.3.2.3",
    "ec_id": "7.3.2.3",
    "status": "Approved",
    "citations": [
        "PMID:7608089"
    ],
    "children_rheas": [
        "RHEA:10193",
        "RHEA:10194",
        "RHEA:10195"
    ],
    "side_l": [
        {
            "comp_num": "6372",
            "chebi_id": "CHEBI:30616",
            "name": "ATP",
            "formula": "C10H12N5O13P3",
            "charge": "-4",
            "stoich": "1"
        },
        {
            "comp_num": "1283",
            "chebi_id": "CHEBI:15377",
            "name": "H2O",
            "formula": "H2O",
            "charge": "0",
            "stoich": "1"
        },
        {
            "comp_num": "5441",
            "chebi_id": "CHEBI:16189",
            "name": "sulfate",
            "formula": "O4S",
            "charge": "-2",
            "stoich": "1",
            "location": "out"
        }
    ],
    "side_r": [
        {
            "comp_num": "2710",
            "chebi_id": "CHEBI:456216",
            "name": "ADP",
            "formula": "C10H12N5O10P2",
            "charge": "-3",
            "stoich": "1"
        },
        {
            "comp_num": "3249",
            "chebi_id": "CHEBI:15378",
            "name": "H(+)",
            "formula": "H",
            "charge": "1",
            "stoich": "1"
        },
        {
            "comp_num": "5518",
            "chebi_id": "CHEBI:43474",
            "name": "phosphate",
            "formula": "HO4P",
            "charge": "-2",
            "stoich": "1"
        },
        {
            "comp_num": "5441",
            "chebi_id": "CHEBI:16189",
            "name": "sulfate",
            "formula": "O4S",
            "charge": "-2",
            "stoich": "1",
            "location": "in"
        }
    ]
}

Important notes:

• Rhea id's have the CURIE "RHEA:##" with variable number of numbers as the unique ID. .
• Every reaction has 4 rhea id's associated with it (e.g. RHEA:10000, RHEA:10001, RHEA:10002, RHEA:10003). Each are the same except have different directionality of the reaction associated. Each rhea_entry yielded by parser.py groups all 4 rhea's into one dictionary object. The primary id (first of the set of 4) is associated with the key "rhea_id". The other 3 rhea id's can be accessed with the key "children_rheas".
• Some rhea IDs are obsolete but still included in the output however these have a value of "Obsolete" associated with the "status" key for the rhea entry.
• Reaction participant information can be accessed with the two keys "side_l" and "side_r".
• Not all participant compounds have a chebi_id but most do. Some instead have a poly_id (for polymer entries) or a generic_id for generic compounds (example of a generic compound: [protein]-dithiol). ChEBI id's have the CURIE "CHEBI:##"
• Citation information can be accessed for all rhea's that have it with the key "citations". Citations are all pubmed citations with the the CURIE "PMID:"

RHEA Object Construction

Although rhea.rdf is a flat file, the entity relationships of our interest can be described as in the 4 tables below.

erDiagram
    reaction {
        str rhea_id PK 
        str equation
        bool is_transport
        str ec_link
        str ec_id
        str status
        list citations "list of PMID strings"
        list children_rheas "list of RHEA ID strings"
        list side_l "list of left side components"
        list side_r "list of right side components"
    }

    side_component {
        str rhea_id PK
        str side_key PK "a string of 'side_l' or 'side_r'"
        str comp_num FK
        str stoich "stoichiometry of the referred compound"
        str location "a string of 'in' or 'out'; only when the referred compound appears in both sides of a transport reaction"
    }

    compound {
        str comp_num PK
        str chebi_id "only when the compound is 'rh:SmallMolecule'"
        str generic_id "only when the compound is 'rh:GenericCompound' (a macromolecule)"
        str poly_id "only when the compound is 'rh:Polymer'"
        str name
        str formula
        str charge
        List reactive_parts "a list of reactive parts; only when the compound is 'rh:GenericCompound' (a macromolecule)"
    }

    reactive_part {
        str comp_num FK
        str name
        str formula
        str charge
        str chebi_id
    }

    reaction ||--|{ side_component : "contains"
    side_component ||--|| compound : "refers to"
    compound ||--o{ reactive_part : "may have as a part"

Loading

Each table corresponds to a DataFactory class in our parser.py.

To learn all the entity relationships in the rhea.rdf, please read Rhea RDF documentation (version: November 2020).