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deCODE

deCODE proteomics is a large-scale proteomics dataset generated by deCODE genetics, a biopharmaceutical company based in Iceland. The dataset includes measurements of protein levels in blood samples from thousands of individuals (up to ~36,000 Icelandic participants), using the SomaScan aptamer-based platform.

Two sub-datasets are provided:

  • RAW (deCODE-proteomics-raw): non-SMP-normalised SomaScan measurements.
  • SMP (deCODE-proteomics-smp): SMP-normalised SomaScan measurements.

For a full description of the dataset and methods, refer to Eldjarn et al., 2023.

gentropy.datasource.decode.deCODEDataSource

Bases: str, Enum

Enumeration of deCODE proteomics data source identifiers.

These project IDs are embedded in study IDs and used throughout the pipeline to distinguish the two SomaScan assay normalisations.

Source code in src/gentropy/datasource/decode/__init__.py 
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class deCODEDataSource(str, Enum):
    """Enumeration of deCODE proteomics data source identifiers.

    These project IDs are embedded in study IDs and used throughout the pipeline
    to distinguish the two SomaScan assay normalisations.
    """

    DECODE_PROTEOMICS_RAW = "deCODE-proteomics-raw"
    """Non-normalised SomaScan measurements."""
    DECODE_PROTEOMICS_SMP = "deCODE-proteomics-smp"
    """SMP-normalised SomaScan measurements."""

DECODE_PROTEOMICS_RAW = 'deCODE-proteomics-raw' class-attribute instance-attribute

Non-normalised SomaScan measurements.

DECODE_PROTEOMICS_SMP = 'deCODE-proteomics-smp' class-attribute instance-attribute

SMP-normalised SomaScan measurements.

gentropy.datasource.decode.deCODEPublicationMetadata

Bases: BaseModel

Bibliographic and cohort metadata for the deCODE proteomics publication.

All fields carry defaults matching the published study and are used to populate the study index with consistent provenance information.

Source code in src/gentropy/datasource/decode/__init__.py 
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class deCODEPublicationMetadata(BaseModel):
    """Bibliographic and cohort metadata for the deCODE proteomics publication.

    All fields carry defaults matching the published study and are used to populate
    the study index with consistent provenance information.
    """

    PUBMED_ID: str = "37794188"
    """PubMed ID for the deCODE proteomics study."""
    PUB_TITLE: str = "Large-scale plasma proteomics comparisons through genetics and disease associations"
    """Title of the deCODE proteomics publication."""
    PUB_FIRST_AUTHOR: str = "Eldjarn GH, Ferkingstad E"
    """First author(s) of the deCODE proteomics publication."""
    PUB_DATE: str = "2023"
    """Publication date of the deCODE proteomics study."""
    PUB_JOURNAL: str = "Nature"
    """Journal where the deCODE proteomics study was published."""
    SMP_SAMPLE_SIZE: int = 35_892
    """Sample size for SMP-normalized proteomics data."""
    SAMPLE_SIZE: int = 36_136
    """Sample size for non-normalized proteomics data."""
    ANCESTRY: str = "Icelandic"
    """Ancestry of the study population."""
    COHORTS: str = "deCODE"
    """Cohorts involved in the deCODE proteomics study."""
    BIOSAMPLE_ID: str = "UBERON_0001969"
    """Biosample ID for deCODE proteomics study - blood plasma."""

ANCESTRY: str = 'Icelandic' class-attribute instance-attribute

Ancestry of the study population.

BIOSAMPLE_ID: str = 'UBERON_0001969' class-attribute instance-attribute

Biosample ID for deCODE proteomics study - blood plasma.

COHORTS: str = 'deCODE' class-attribute instance-attribute

Cohorts involved in the deCODE proteomics study.

PUBMED_ID: str = '37794188' class-attribute instance-attribute

PubMed ID for the deCODE proteomics study.

PUB_DATE: str = '2023' class-attribute instance-attribute

Publication date of the deCODE proteomics study.

PUB_FIRST_AUTHOR: str = 'Eldjarn GH, Ferkingstad E' class-attribute instance-attribute

First author(s) of the deCODE proteomics publication.

PUB_JOURNAL: str = 'Nature' class-attribute instance-attribute

Journal where the deCODE proteomics study was published.

PUB_TITLE: str = 'Large-scale plasma proteomics comparisons through genetics and disease associations' class-attribute instance-attribute

Title of the deCODE proteomics publication.

SAMPLE_SIZE: int = 36136 class-attribute instance-attribute

Sample size for non-normalized proteomics data.

SMP_SAMPLE_SIZE: int = 35892 class-attribute instance-attribute

Sample size for SMP-normalized proteomics data.

  • 2026-02-10
  • 2026-02-10
  • Contributors
    • project-defiant