Sync organagechronologicalolink1500esophagus

README.md

@@ -0,0 +1,42 @@
+---
+license: other
+license_name: original-author-license
+license_link: https://huggingface.co/pyaging/organagechronologicalolink1500esophagus/blob/main/organagechronologicalolink1500esophagus.LICENSE.txt
+library_name: pyaging
+tags:
+- pyaging
+- aging-clock
+- biology
+- proteomics
+---
+
+# organagechronologicalolink1500esophagus
+
+Esophagus OrganAge chronological model for Olink Explore 1536, using author-recommended fold 1. Input columns are the original case-sensitive protein symbols and values are Olink NPX, already normalized. No additional centering or cohort scaling is applied. Absent proteins contribute zero; NaNs in supplied proteins propagate, matching the original Example_Script.R scoring expressions. For other assays, prepare and rescale protein values according to the author guidance before prediction. Output is predicted age in years. Models labelled Female and Male contain protein features; neither requires a sex covariate. Academic/non-commercial research use only; commercial use requires a separate license from the authors.
+
+Model weights retain the original authors' terms; the pyaging software license does not relicense them. See the [original author license](organagechronologicalolink1500esophagus.LICENSE.txt). These weights are restricted to research use under the authors' terms.
+
+| | |
+|---|---|
+| **Predicts** | biological age |
+| **Species** | Homo sapiens |
+| **Tissue** | blood |
+| **Data type** | proteomics |
+| **Model type** | elastic net regression |
+| **Year** | 2025 |
+
+## Use with pyaging
+
+```python
+import pyaging as pya
+
+pya.pred.predict_age(adata, ["organagechronologicalolink1500esophagus"])
+```
+
+Browse every clock in the [pyaging Clock Catalogue](https://pyaging.readthedocs.io).
+
+## Citation
+
+Goeminne, L. J. E., et al. "Plasma protein-based organ-specific aging and mortality models unveil diseases as accelerated aging of organismal systems." Cell Metabolism 37, 205–222.e6 (2025).
+
+https://doi.org/10.1016/j.cmet.2024.10.005

config.json

@@ -0,0 +1,35 @@
+{
+ "approved_by_author": "\u231b",
+ "citation": "Goeminne, L. J. E., et al. \"Plasma protein-based organ-specific aging and mortality models unveil diseases as accelerated aging of organismal systems.\" Cell Metabolism 37, 205\u2013222.e6 (2025).",
+ "citations": 128,
+ "citations_date": "2026-10-02",
+ "clock_name": "organagechronologicalolink1500esophagus",
+ "data_type": "proteomics",
+ "doi": "https://doi.org/10.1016/j.cmet.2024.10.005",
+ "journal": "Cell Metabolism",
+ "last_author": "Vadim N. Gladyshev",
+ "model_type": "elastic net regression",
+ "n_features": 1,
+ "notes": "Esophagus OrganAge chronological model for Olink Explore 1536, using author-recommended fold 1. Input columns are the original case-sensitive protein symbols and values are Olink NPX, already normalized. No additional centering or cohort scaling is applied. Absent proteins contribute zero; NaNs in supplied proteins propagate, matching the original Example_Script.R scoring expressions. For other assays, prepare and rescale protein values according to the author guidance before prediction. Output is predicted age in years. Models labelled Female and Male contain protein features; neither requires a sex covariate. Academic/non-commercial research use only; commercial use requires a separate license from the authors.",
+ "platform": [
+  "Olink Explore 1536"
+ ],
+ "population": "adults",
+ "predicts": [
+  "biological age"
+ ],
+ "reference_values": true,
+ "research_only": true,
+ "species": "Homo sapiens",
+ "tissue": [
+  "blood"
+ ],
+ "training_target": [
+  "chronological age"
+ ],
+ "unit": [
+  "years"
+ ],
+ "version": "0.5.4",
+ "year": 2025
+}

organagechronologicalolink1500esophagus.LICENSE.txt

@@ -0,0 +1,36 @@
+(Academic / Non-Commercial License)
+
+Copyright (c) 2025
+Ludger J.E. Goeminne and Vadim N. Gladyshev
+
+This software and its associated files (the “Software”) are licensed under a dual-license model:
+
+Academic / Non-Commercial License (this license)
+Commercial License (available separately)
+Permission is hereby granted, free of charge, to any individual or institution, to use, copy, modify, and distribute the Software solely for non-commercial academic or research purposes, subject to the following conditions:
+
+1. Non-Commercial Use Only
+The Software may not be used, in whole or in part, for any commercial purpose. Commercial purposes include, but are not limited to:
+
+Use in a commercial product or service
+Use by a for-profit entity for internal research or development
+Use to generate revenue, directly or indirectly
+Use in regulatory submissions or clinical decision support systems
+
+2. Attribution
+Any academic or research use of the Software must include appropriate citation of the following publication:
+
+Ludger J.E. Goeminne, Anastasiya Vladimirova, Alec Eames, Alexander Tyshkovskiy,
+M. Austin Argentieri, Kejun Ying, Mahdi Moqri, Vadim N. Gladyshev (2025).
+Plasma protein-based organ-specific aging and mortality models unveil diseases as accelerated aging of organismal systems,
+Cell Metabolism, Volume 37, Issue 1, p205–222.e6.
+DOI: https://doi.org/10.1016/j.cmet.2024.10.005
+
+3. No Warranty
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES, OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT, OR OTHERWISE, ARISING FROM, OUT OF, OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+4. Third-Party Software
+The Software depends on third-party packages that are licensed under their own respective licenses. This license applies only to the original portions of the Software and does not override or modify the terms of any third-party licenses, including but not limited to GPL-licensed components.
+
+5. Commercial Licensing
+Any commercial use of the Software requires a separate commercial license. Interested parties should contact the copyright holders or their institutional technology transfer office to negotiate commercial licensing terms.

organagechronologicalolink1500esophagus.provenance.json

@@ -0,0 +1,9 @@
+{
+  "repository": "https://github.com/ludgergoeminne/organAging",
+  "commit": "5147b0301ec7f4abdb10ef650d04f47454ddc8fd",
+  "coefficient_path": "data/output_Python/feature_reduced/chronological_models/Esophagus_coefs_GTEx_4x_FC_longitudinal.csv",
+  "coefficient_sha256": "454e4cea77d66fb74ec90902b204089467b023e9a722a3486d08294dfcbb5ff8",
+  "prediction_code_path": "scripts/R/Example_Script.R",
+  "prediction_code_sha256": "02fc291721d6018bafa5a49adf4aff3841c7e9d085d682088b9ac0feeee31e63",
+  "fold": 1
+}

organagechronologicalolink1500esophagus.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:64fbad57fb003b6e86d69c13e540ff6e83aa570d7897334cfd4a2d313a6b1866
+size 8613