feat(datasource): decode ingestion steps (#1208)

This PR include the deCODE proteomics ingestion steps along with
new Dataset for MolecularComplex based on ComplexPortal reference files.

Author: project-defiant

.vscode/settings.json

@@ -39,6 +39,7 @@
     "colocalisation",
     "contig",
     "diffpval",
+    "Ensembl",
     "eqtl",
     "finngen",
     "GCST",

docs/python_api/datasets/molecular_complex.md

@@ -0,0 +1,5 @@
+---
+title: Molecular Complex
+---
+
+::: gentropy.dataset.molecular_complex.MolecularComplex

docs/python_api/datasources/_datasources.md

@@ -14,6 +14,11 @@ This section contains information about the data source harmonisation tools avai
 
 1. [GTEx (eQTL catalogue)](eqtl_catalogue/_eqtl_catalogue.md)
 2. [UKB PPP (EUR)](ukb_ppp_eur/_ukb_ppp_eur.md)
+3. [deCODE proteomics](deCODE/_decode.md)
+
+## Protein complexes
+
+1. [Complex Portal](complex_portal/_complex_portal.md)
 
 ## Interaction / Interval-based Experiments
 
@@ -39,5 +44,4 @@ This section contains information about the data source harmonisation tools avai
 
 ## Biological samples
 
-1. [Uberon](biosample_ontologies/_uberon.md)
-2. [Cell Ontology](biosample_ontologies/_cell_ontology.md)
+1. [Uberon and Cell Ontology](biosample_ontologies/_biosample_ontologies.md)

docs/python_api/datasources/complex_portal/_complex_portal.md

@@ -0,0 +1,14 @@
+---
+title: Complex Portal
+---
+
+[Complex Portal](https://www.ebi.ac.uk/complexportal/) is a manually curated resource of macromolecular complexes maintained by EMBL-EBI. It provides two complementary datasets:
+
+- **Experimental** – complexes with direct experimental evidence.
+- **Predicted** – computationally predicted complexes.
+
+Both files are distributed in the **ComplexTAB** flat-file format and are filtered to human complexes (NCBI taxonomy ID 9606) during ingestion.
+
+The resulting `MolecularComplex` dataset is used downstream in the deCODE proteomics pipeline to annotate multi-protein SomaScan aptamers with a `molecularComplexId`.
+
+::: gentropy.datasource.complex_portal.ComplexTab

docs/python_api/datasources/deCODE/.pages

@@ -0,0 +1,6 @@
+nav:
+  - _decode.md
+  - manifest.md
+  - aptamer_metadata.md
+  - study_index.md
+  - summary_stats.md

docs/python_api/datasources/deCODE/_decode.md

@@ -0,0 +1,15 @@
+---
+title: deCODE proteomics
+---
+
+[deCODE proteomics](https://www.nature.com/articles/s41586-023-06563-x) 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](https://www.nature.com/articles/s41586-023-06563-x).
+
+::: gentropy.datasource.decode.deCODEDataSource
+::: gentropy.datasource.decode.deCODEPublicationMetadata

docs/python_api/datasources/deCODE/aptamer_metadata.md

@@ -0,0 +1,5 @@
+---
+title: deCODE Aptamer Metadata
+---
+
+::: gentropy.datasource.decode.aptamer_metadata.AptamerMetadata

docs/python_api/datasources/deCODE/manifest.md

@@ -0,0 +1,5 @@
+---
+title: deCODE manifest
+---
+
+::: gentropy.datasource.decode.manifest.deCODEManifest

docs/python_api/datasources/deCODE/study_index.md

@@ -0,0 +1,6 @@
+---
+title: deCODE Study Index
+---
+
+::: gentropy.datasource.decode.study_index.deCODEStudyIdParts
+::: gentropy.datasource.decode.study_index.deCODEStudyIndex

docs/python_api/datasources/deCODE/summary_stats.md

@@ -0,0 +1,6 @@
+---
+title: deCODE Summary Statistics
+---
+
+::: gentropy.datasource.decode.summary_statistics.deCODEHarmonisationConfig
+::: gentropy.datasource.decode.summary_statistics.deCODESummaryStatistics