PRIDE v1.0

The pride profile models a proteomics dataset for submission to PRIDE / ProteomeXchange. Its root entity is Dataset, which carries the submission-level metadata and nests the samples, data files, instruments, modifications, contacts, publications and species that describe a proteomics experiment.

Entities

Entity	Role
Dataset	Root — submission metadata (identifier, title, protocols, keywords)
Sample	A biological sample, with species/tissue/disease annotations
Species	An organism the dataset covers (name + NCBI taxonomy id)
Instrument	A mass spectrometer, referenced by a PSI-MS CV accession
Modification	A protein/peptide modification (PSI-MOD/UNIMOD accession)
Publication	An associated publication (DOI / PubMed id)
Contact	A submitter, lab head or principal investigator
DataFile	A raw/peak/result file, optionally linked to samples
CustomAttribute	A free name/value annotation on a sample

Entity-Relationship Diagram

erDiagram
    Dataset {
        string identifier
        string accession
        string title
        string submission_type
        list keywords
    }
    Species {
        string name
        string ncbi_taxonomy_id
    }
    Instrument {
        string name
        string cv_accession
    }
    Modification {
        string name
        string cv_accession
        float mass_delta
    }
    Contact {
        string name
        string email
        string role
    }
    Publication {
        string title
        string doi
        string pubmed_id
    }
    Sample {
        string name
        string species
        string ncbi_taxonomy_id
        string tissue
    }
    DataFile {
        string filename
        string file_type
        string checksum
    }
    CustomAttribute {
        string name
        string value
    }

    Dataset ||--o{ Species : species
    Dataset ||--o{ Instrument : instruments
    Dataset ||--o{ Modification : modifications
    Dataset ||--o{ Contact : contacts
    Dataset ||--o{ Publication : publications
    Dataset ||--o{ Sample : samples
    Dataset ||--o{ DataFile : files
    Sample ||--o{ CustomAttribute : custom_attributes

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Usage

from metaseed import pride

p = pride()

dataset = p.Dataset(
    identifier="PXD000001",
    accession="PXD000001",
    title="Example proteomics dataset",
    description=(
        "A demonstration ProteomeXchange proteomics dataset submission record."
    ),
    sample_processing_protocol=(
        "Proteins were reduced, alkylated and digested with trypsin overnight."
    ),
    data_processing_protocol=(
        "Raw files were searched with MaxQuant against the reference proteome."
    ),
    submission_type="COMPLETE",
    keywords=["proteomics", "mass spectrometry"],
    species=[{"name": "Homo sapiens", "ncbi_taxonomy_id": "9606"}],
    instruments=[{"name": "LTQ Orbitrap", "cv_accession": "MS:1000449"}],
    contacts=[
        {
            "name": "Jane Doe",
            "email": "jane@example.org",
            "affiliation": "Example University",
            "role": "submitter",
        }
    ],
    samples=[{"name": "S1", "species": "Homo sapiens", "ncbi_taxonomy_id": "9606"}],
    files=[{"filename": "run1.raw", "file_type": "RAW"}],
)

References

Resource	URL
PRIDE Archive	https://www.ebi.ac.uk/pride/
ProteomeXchange	https://www.proteomexchange.org/
PSI-MS controlled vocabulary	https://www.ebi.ac.uk/ols4/ontologies/ms