sensasp-mcp 1.0.0__tar.gz

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  1. sensasp_mcp-1.0.0/PKG-INFO +109 -0
  2. sensasp_mcp-1.0.0/README.md +86 -0
  3. sensasp_mcp-1.0.0/pyproject.toml +44 -0
  4. sensasp_mcp-1.0.0/senescence_db_pipeline/README.md +68 -0
  5. sensasp_mcp-1.0.0/sensasp_mcp/__init__.py +2 -0
  6. sensasp_mcp-1.0.0/sensasp_mcp/data/genes.json +1 -0
  7. sensasp_mcp-1.0.0/sensasp_mcp/data/genes_full.json +1 -0
  8. sensasp_mcp-1.0.0/sensasp_mcp/data/metrics.json +47 -0
  9. sensasp_mcp-1.0.0/sensasp_mcp/data/sources.json +26 -0
  10. sensasp_mcp-1.0.0/sensasp_mcp/server.py +227 -0
sensasp_mcp-1.0.0/PKG-INFO ADDED
@@ -0,0 +1,109 @@
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+ Metadata-Version: 2.5
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+ Name: sensasp-mcp
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+ Version: 1.0.0
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+ Summary: SenSASP MCP Server — unified senescence / SASP gene database for Claude and MCP clients
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+ Project-URL: Homepage, https://xuan13hao.github.io/sensasp
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+ Project-URL: Repository, https://github.com/xuan13hao/sensasp
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+ Project-URL: Paper, https://doi.org/10.64898/2026.08.26.747427
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+ Author: Yu Huang, Jiang Bian
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+ Author-email: Xuan Hao <xuanhao@iu.edu>
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+ License: CC-BY-4.0
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+ Keywords: Claude,MCP,SASP,bioinformatics,gene-database,senescence
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+ Classifier: Development Status :: 4 - Beta
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: Free for non-commercial use
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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+ Requires-Python: >=3.10
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+ Requires-Dist: mcp<2,>=1.0
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+ Description-Content-Type: text/markdown
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+
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+ # SenSASP: A Unified, Multi-Layer Database of Senescence and SASP Genes
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+
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+ A fully scripted, one-command-reproducible pipeline that unifies four senescence /
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+ SASP gene resources onto a single canonical identifier and enriches every gene
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+ with cross-species conservation, tissue/cell-type expression, and protein–protein
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+ interaction annotation.
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+
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+ ## Quick start
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+
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+ ```bash
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+ ./main.sh # install deps, run the data pipeline, regenerate all figures
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+ ./main.sh --no-figs # data pipeline only (skip the notebook)
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+ ```
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+
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+ Everything is fetched from public APIs at run time — no manual downloads, no
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+ credentials. Total runtime is a few minutes (the Human Protein Atlas step makes
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+ one request per gene and dominates the wall time).
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+
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+ ## What it does
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+
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+ | Step | Module | Output |
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+ |---|---|---|
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+ | 1 | `step1_acquire.py` | Download CellAge, GenAge, SenMayo, Reactome → `data/raw/seed_lists_raw.json` |
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+ | 2 | `step2_harmonize.py` | Map symbols→Ensembl/UniProt/Entrez via MyGene.info → `data/processed/id_map.{json,csv}` |
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+ | 3 | `step3_unify.py` | Collapse to unique genes on Ensembl ID, record provenance (RQ1) → `data/processed/unified_core.json`, `results/source_overlap.csv` |
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+ | 4 | `step4_conservation.py` | Mouse + zebrafish orthologs via Ensembl BioMart → `data/processed/conservation.json` |
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+ | 5 | `step5_expression.py` | GTEx v8 (54 tissues) + Human Protein Atlas → `data/processed/expression.json` |
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+ | 6 | `step6_interactions.py` | STRING v12 high-confidence network (score≥700) → `data/processed/interaction.json`, `string_network.json` |
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+ | 7 | `step7_assemble.py` | Merge all layers → `results/senescence_sasp_database.{json,csv}` |
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+ | 8 | `step8_metrics.py` | Outcome metrics (RQ1/RQ2) → `results/build_metrics.json`, `summary_report.md` |
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+
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+ Figures are generated separately from the pipeline outputs by
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+ `notebooks/figures.ipynb`.
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+
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+ ## Running individual steps
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+
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+ ```bash
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+ PYTHONPATH=. python run_pipeline.py # all steps
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+ PYTHONPATH=. python run_pipeline.py 4 5 6 # only these (reuse earlier outputs)
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+ ```
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+
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+ ## Layout
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+
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+ ```
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+ senescence_db_pipeline/
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+ ├── main.sh # one-click reproduction
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+ ├── run_pipeline.py # step runner
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+ ├── requirements.txt
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+ ├── pipeline/ # step1..step8 modules + config.py
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+ ├── notebooks/figures.ipynb # all figure-generation code
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+ ├── data/raw, data/processed
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+ ├── results/ # database + metrics + report
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+ ├── figures/ # generated PNGs
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+ └── paper/paper.md # manuscript (Intro/Methods/Data/Results/Discussion)
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+ ```
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+
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+ ## Data sources
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+
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+ CellAge & GenAge (HAGR), SenMayo (MSigDB `SAUL_SEN_MAYO` / M45803, Saul et al.
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+ 2022), Reactome Cellular Senescence (R-HSA-2559583); annotation via MyGene.info,
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+ Ensembl BioMart, GTEx v8, Human Protein Atlas, and STRING v12.
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+
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+ ## Web database (GitHub Pages)
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+
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+ The interactive database is served from `docs/` via GitHub Pages:
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+
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+ ```
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+ https://xuan13hao.github.io/sensasp
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+ ```
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+
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+ To enable: **Settings → Pages → Source: Deploy from branch → Branch: `main` → Folder: `/docs`**
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+
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+ To regenerate site data after re-running the pipeline:
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+
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+ ```bash
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+ python3 generate_site_data.py
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+ ```
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+
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+ This rebuilds `docs/data/genes.json`, `genes_full.json`, `metrics.json`, and `sources.json`.
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+
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+ ## Key results
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+
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+ 1,460 summed source entries → **1,250 unique genes** (210 redundant collapsed,
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+ 14.4%); 173 genes confirmed by ≥2 sources, 2 (IL6, JUN) by all four. Net-new
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+ annotation reaches 95.8% (conservation), 97.8% (expression), 92.9%
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+ (interactions), with 89.3% complete across all three layers.
sensasp_mcp-1.0.0/README.md ADDED
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+ # SenSASP: A Unified, Multi-Layer Database of Senescence and SASP Genes
2
+
3
+ A fully scripted, one-command-reproducible pipeline that unifies four senescence /
4
+ SASP gene resources onto a single canonical identifier and enriches every gene
5
+ with cross-species conservation, tissue/cell-type expression, and protein–protein
6
+ interaction annotation.
7
+
8
+ ## Quick start
9
+
10
+ ```bash
11
+ ./main.sh # install deps, run the data pipeline, regenerate all figures
12
+ ./main.sh --no-figs # data pipeline only (skip the notebook)
13
+ ```
14
+
15
+ Everything is fetched from public APIs at run time — no manual downloads, no
16
+ credentials. Total runtime is a few minutes (the Human Protein Atlas step makes
17
+ one request per gene and dominates the wall time).
18
+
19
+ ## What it does
20
+
21
+ | Step | Module | Output |
22
+ |---|---|---|
23
+ | 1 | `step1_acquire.py` | Download CellAge, GenAge, SenMayo, Reactome → `data/raw/seed_lists_raw.json` |
24
+ | 2 | `step2_harmonize.py` | Map symbols→Ensembl/UniProt/Entrez via MyGene.info → `data/processed/id_map.{json,csv}` |
25
+ | 3 | `step3_unify.py` | Collapse to unique genes on Ensembl ID, record provenance (RQ1) → `data/processed/unified_core.json`, `results/source_overlap.csv` |
26
+ | 4 | `step4_conservation.py` | Mouse + zebrafish orthologs via Ensembl BioMart → `data/processed/conservation.json` |
27
+ | 5 | `step5_expression.py` | GTEx v8 (54 tissues) + Human Protein Atlas → `data/processed/expression.json` |
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+ | 6 | `step6_interactions.py` | STRING v12 high-confidence network (score≥700) → `data/processed/interaction.json`, `string_network.json` |
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+ | 7 | `step7_assemble.py` | Merge all layers → `results/senescence_sasp_database.{json,csv}` |
30
+ | 8 | `step8_metrics.py` | Outcome metrics (RQ1/RQ2) → `results/build_metrics.json`, `summary_report.md` |
31
+
32
+ Figures are generated separately from the pipeline outputs by
33
+ `notebooks/figures.ipynb`.
34
+
35
+ ## Running individual steps
36
+
37
+ ```bash
38
+ PYTHONPATH=. python run_pipeline.py # all steps
39
+ PYTHONPATH=. python run_pipeline.py 4 5 6 # only these (reuse earlier outputs)
40
+ ```
41
+
42
+ ## Layout
43
+
44
+ ```
45
+ senescence_db_pipeline/
46
+ ├── main.sh # one-click reproduction
47
+ ├── run_pipeline.py # step runner
48
+ ├── requirements.txt
49
+ ├── pipeline/ # step1..step8 modules + config.py
50
+ ├── notebooks/figures.ipynb # all figure-generation code
51
+ ├── data/raw, data/processed
52
+ ├── results/ # database + metrics + report
53
+ ├── figures/ # generated PNGs
54
+ └── paper/paper.md # manuscript (Intro/Methods/Data/Results/Discussion)
55
+ ```
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+
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+ ## Data sources
58
+
59
+ CellAge & GenAge (HAGR), SenMayo (MSigDB `SAUL_SEN_MAYO` / M45803, Saul et al.
60
+ 2022), Reactome Cellular Senescence (R-HSA-2559583); annotation via MyGene.info,
61
+ Ensembl BioMart, GTEx v8, Human Protein Atlas, and STRING v12.
62
+
63
+ ## Web database (GitHub Pages)
64
+
65
+ The interactive database is served from `docs/` via GitHub Pages:
66
+
67
+ ```
68
+ https://xuan13hao.github.io/sensasp
69
+ ```
70
+
71
+ To enable: **Settings → Pages → Source: Deploy from branch → Branch: `main` → Folder: `/docs`**
72
+
73
+ To regenerate site data after re-running the pipeline:
74
+
75
+ ```bash
76
+ python3 generate_site_data.py
77
+ ```
78
+
79
+ This rebuilds `docs/data/genes.json`, `genes_full.json`, `metrics.json`, and `sources.json`.
80
+
81
+ ## Key results
82
+
83
+ 1,460 summed source entries → **1,250 unique genes** (210 redundant collapsed,
84
+ 14.4%); 173 genes confirmed by ≥2 sources, 2 (IL6, JUN) by all four. Net-new
85
+ annotation reaches 95.8% (conservation), 97.8% (expression), 92.9%
86
+ (interactions), with 89.3% complete across all three layers.
sensasp_mcp-1.0.0/pyproject.toml ADDED
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+ [build-system]
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+ requires = ["hatchling"]
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+ build-backend = "hatchling.build"
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+
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+ [project]
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+ name = "sensasp-mcp"
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+ version = "1.0.0"
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+ description = "SenSASP MCP Server — unified senescence / SASP gene database for Claude and MCP clients"
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+ readme = "README.md"
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+ license = { text = "CC-BY-4.0" }
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+ authors = [
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+ { name = "Xuan Hao", email = "xuanhao@iu.edu" },
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+ { name = "Yu Huang" },
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+ { name = "Jiang Bian" },
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+ ]
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+ keywords = ["senescence", "SASP", "bioinformatics", "MCP", "Claude", "gene-database"]
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+ classifiers = [
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+ "Development Status :: 4 - Beta",
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+ "Intended Audience :: Science/Research",
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+ "Topic :: Scientific/Engineering :: Bio-Informatics",
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+ "License :: Free for non-commercial use",
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+ "Programming Language :: Python :: 3",
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+ "Programming Language :: Python :: 3.10",
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+ "Programming Language :: Python :: 3.11",
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+ "Programming Language :: Python :: 3.12",
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+ ]
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+ requires-python = ">=3.10"
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+ dependencies = [
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+ "mcp>=1.0,<2",
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+ ]
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+
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+ [project.urls]
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+ Homepage = "https://xuan13hao.github.io/sensasp"
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+ Repository = "https://github.com/xuan13hao/sensasp"
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+ Paper = "https://doi.org/10.64898/2026.08.26.747427"
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+
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+ [project.scripts]
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+ sensasp-mcp = "sensasp_mcp.server:main"
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+
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+ [tool.hatch.build.targets.wheel]
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+ packages = ["sensasp_mcp"]
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+
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+ [tool.hatch.build.targets.sdist]
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+ include = ["sensasp_mcp/", "README.md", "pyproject.toml"]
sensasp_mcp-1.0.0/senescence_db_pipeline/README.md ADDED
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1
+ # Unified Cellular Senescence / SASP Gene Database — Pipeline
2
+
3
+ A fully scripted, one-command-reproducible pipeline that unifies four senescence /
4
+ SASP gene resources onto a single canonical identifier and enriches every gene
5
+ with cross-species conservation, tissue/cell-type expression, and protein–protein
6
+ interaction annotation.
7
+
8
+ ## Quick start
9
+
10
+ ```bash
11
+ ./main.sh # install deps, run the data pipeline, regenerate all figures
12
+ ./main.sh --no-figs # data pipeline only (skip the notebook)
13
+ ```
14
+
15
+ Everything is fetched from public APIs at run time — no manual downloads, no
16
+ credentials. Total runtime is a few minutes (the Human Protein Atlas step makes
17
+ one request per gene and dominates the wall time).
18
+
19
+ ## What it does
20
+
21
+ | Step | Module | Output |
22
+ |---|---|---|
23
+ | 1 | `step1_acquire.py` | Download CellAge, GenAge, SenMayo, Reactome → `data/raw/seed_lists_raw.json` |
24
+ | 2 | `step2_harmonize.py` | Map symbols→Ensembl/UniProt/Entrez via MyGene.info → `data/processed/id_map.{json,csv}` |
25
+ | 3 | `step3_unify.py` | Collapse to unique genes on Ensembl ID, record provenance (RQ1) → `data/processed/unified_core.json`, `results/source_overlap.csv` |
26
+ | 4 | `step4_conservation.py` | Mouse + zebrafish orthologs via Ensembl BioMart → `data/processed/conservation.json` |
27
+ | 5 | `step5_expression.py` | GTEx v8 (54 tissues) + Human Protein Atlas → `data/processed/expression.json` |
28
+ | 6 | `step6_interactions.py` | STRING v12 high-confidence network (score≥700) → `data/processed/interaction.json`, `string_network.json` |
29
+ | 7 | `step7_assemble.py` | Merge all layers → `results/senescence_sasp_database.{json,csv}` |
30
+ | 8 | `step8_metrics.py` | Outcome metrics (RQ1/RQ2) → `results/build_metrics.json`, `summary_report.md` |
31
+
32
+ Figures are generated separately from the pipeline outputs by
33
+ `notebooks/figures.ipynb`.
34
+
35
+ ## Running individual steps
36
+
37
+ ```bash
38
+ PYTHONPATH=. python run_pipeline.py # all steps
39
+ PYTHONPATH=. python run_pipeline.py 4 5 6 # only these (reuse earlier outputs)
40
+ ```
41
+
42
+ ## Layout
43
+
44
+ ```
45
+ senescence_db_pipeline/
46
+ ├── main.sh # one-click reproduction
47
+ ├── run_pipeline.py # step runner
48
+ ├── requirements.txt
49
+ ├── pipeline/ # step1..step8 modules + config.py
50
+ ├── notebooks/figures.ipynb # all figure-generation code
51
+ ├── data/raw, data/processed
52
+ ├── results/ # database + metrics + report
53
+ ├── figures/ # generated PNGs
54
+ └── paper/paper.md # manuscript (Intro/Methods/Data/Results/Discussion)
55
+ ```
56
+
57
+ ## Data sources
58
+
59
+ CellAge & GenAge (HAGR), SenMayo (MSigDB `SAUL_SEN_MAYO` / M45803, Saul et al.
60
+ 2022), Reactome Cellular Senescence (R-HSA-2559583); annotation via MyGene.info,
61
+ Ensembl BioMart, GTEx v8, Human Protein Atlas, and STRING v12.
62
+
63
+ ## Key results
64
+
65
+ 1,460 summed source entries → **1,250 unique genes** (210 redundant collapsed,
66
+ 14.4%); 173 genes confirmed by ≥2 sources, 2 (IL6, JUN) by all four. Net-new
67
+ annotation reaches 95.8% (conservation), 97.8% (expression), 92.9%
68
+ (interactions), with 89.3% complete across all three layers.
sensasp_mcp-1.0.0/sensasp_mcp/__init__.py ADDED
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+ """SenSASP MCP Server — unified senescence / SASP gene database."""
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+ __version__ = "1.0.0"