| --- |
| pretty_name: SampleExplorer databases (ARCHS4 v2.7, release 1) |
| language: |
| - en |
| tags: |
| - RNA-seq |
| - GEO |
| - ARCHS4 |
| - gene-set-search |
| - transcriptomics |
| - SampleExplorer |
| size_categories: |
| - 1M<n<10M |
| --- |
| |
| # SampleExplorer databases (ARCHS4 v2.7, release 1) |
|
|
| Databases for [SampleExplorer](https://github.com/wlchin/SampleExplorer): one SQLite file per species. |
| Each is a single file with nothing to unzip. This repository is the home of the files: every release is a tag |
| here, and the desktop app's catalogue points at these tags. Check a download against the sha256 below. |
|
|
| | File | Species | Studies | Samples | Size | sha256 | |
| |---|---|---|---|---|---| |
| | `sampleexplorer-human-v2.7-r1.sqlite` | human | 38,761 | 1,098,771 | 1,556,414,464 bytes (1.6 GB) | `ba3c7446968d719c965241dd3dcc16a040257976c5037e7026d345e7fd3f488c` | |
| | `sampleexplorer-mouse-v2.7-r1.sqlite` | mouse | 40,620 | 1,225,044 | 1,717,370,880 bytes (1.7 GB) | `852056fff702f0cad8e39ccd8d81814a81d6529d30ab12647886a3e35b14f530` | |
|
|
| ## Download |
|
|
| With the Hugging Face CLI (resumable, checks the hash for you): |
|
|
| ``` |
| uvx --from huggingface_hub hf download Wlchin/sampleexplorer-databases sampleexplorer-human-v2.7-r1.sqlite --repo-type dataset --local-dir . |
| uvx --from huggingface_hub hf download Wlchin/sampleexplorer-databases sampleexplorer-mouse-v2.7-r1.sqlite --repo-type dataset --local-dir . |
| ``` |
|
|
| From Python: |
|
|
| ```python |
| from huggingface_hub import hf_hub_download |
| path = hf_hub_download("Wlchin/sampleexplorer-databases", "sampleexplorer-human-v2.7-r1.sqlite", |
| repo_type="dataset", revision="r1") |
| ``` |
|
|
| With curl (resumes with `-C -`): |
|
|
| ``` |
| curl -L -C - -o sampleexplorer-human-v2.7-r1.sqlite https://huggingface.co/datasets/Wlchin/sampleexplorer-databases/resolve/r1/sampleexplorer-human-v2.7-r1.sqlite |
| ``` |
|
|
| Check a download with `shasum -a 256 <file>` on macOS and Linux, or `certutil -hashfile <file> SHA256` on Windows. |
|
|
| ## Use |
|
|
| Open a file in the SampleExplorer desktop app with **Locate database file…**, or read it with any `sqlite3`. |
| Open both files to search across species. |
|
|
| ## What each file holds |
|
|
| - GEO study and sample text |
| - the per-sample gene index for gene-set search |
| - MiniLM text vectors and the MiniLM model |
| - the response bases for the Same response search |
| - the BM25 keyword index |
| - MedCPT article vectors and the MedCPT query encoder |
| - the 50 MSigDB Hallmark pathway sets and the pathway bank behind Compare pathways |
|
|
| The file's `meta` table records the ARCHS4 version, the build rules, content hashes and the sha256 of every bundled model |
| and of the pathway sources. |
|
|
| ## Source data |
|
|
| Expression and sample metadata come from [ARCHS4](https://maayanlab.cloud/archs4/) v2.7 (Lachmann et al., 2018, |
| *Nature Communications* 9:1366), which reprocesses public RNA-seq from GEO and SRA. Study and sample text come from |
| [GEO](https://www.ncbi.nlm.nih.gov/geo/). Please cite ARCHS4 and GEO alongside SampleExplorer when you use these files. |
|
|
| ## Pathway gene sets: sources and attribution |
|
|
| The pathway data (the `pathway_sets` table, the `pathway_bank` array and meta `pathways`) come from two sources: |
|
|
| - **MSigDB Hallmark v2023.2.Hs** (`h.all.v2023.2.Hs.symbols.gmt`, 50 sets) from the |
| [Molecular Signatures Database](https://www.gsea-msigdb.org/gsea/msigdb), UC San Diego and Broad Institute, under |
| [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/). Each set is kept as its genes in the file's gene universe, |
| and the file stores directions computed from them; the set names are unchanged. Cite Liberzon et al., 2015, |
| *Cell Systems* 1:417–425 ([doi:10.1016/j.cels.2015.12.004](https://doi.org/10.1016/j.cels.2015.12.004)) and MSigDB |
| (Subramanian et al., 2005, *PNAS* 102:15545–15550). |
| - **MGI's mouse–human homology report** (`HOM_MouseHumanSequence.rpt`, dated 2026-10-28), mouse file only: it maps the |
| human sets to one-to-one mouse orthologues. From [Mouse Genome Informatics](https://www.informatics.jax.org), The Jackson |
| Laboratory; cite Baldarelli et al., 2024, *Genetics* 227:iyae031 |
| ([doi:10.1093/genetics/iyae031](https://doi.org/10.1093/genetics/iyae031)). |
|
|
| The full notice, with the changes made, the sha256 of both source files and the MGI data citation, is in |
| `LICENSES/CC-BY-4.0-MSigDB-Hallmark.txt`. |
|
|
| ## Bundled models and their licences |
|
|
| Two text encoders are stored inside each file as ONNX exports, so the app needs no PyTorch and no separate download. |
| Converting them to ONNX and bundling them is the only change made to them. |
|
|
| | Model | Used for | Source | Licence | |
| |---|---|---|---| |
| | paraphrase-MiniLM-L6-v2 | search by meaning | [sentence-transformers/paraphrase-MiniLM-L6-v2](https://huggingface.co/sentence-transformers/paraphrase-MiniLM-L6-v2), revision `c9a2bfebc254878aee8c3aca9e6844d5bbb102d1` (Reimers & Gurevych, UKP Lab) | Apache-2.0 | |
| | MiniLM base weights | base of the above | Microsoft MiniLM | MIT | |
| | MedCPT query encoder | keyword + semantic search | [ncbi/MedCPT-Query-Encoder](https://huggingface.co/ncbi/MedCPT-Query-Encoder) (Jin et al., 2023) | public domain (US Government work) | |
| | MedCPT article encoder | article vectors (vectors stored, encoder not bundled) | [ncbi/MedCPT-Article-Encoder](https://huggingface.co/ncbi/MedCPT-Article-Encoder) | public domain (US Government work) | |
|
|
| The Apache-2.0 licence text is in `LICENSES/Apache-2.0.txt` and the MIT text in `LICENSES/MIT-MiniLM.txt` in this |
| repository, as the Apache licence requires for redistribution. |
|
|
| ## Versions |
|
|
| Each release is a tag (`r1`, `r2`, …) on this repository. A released file is never changed: a new build gets a new file |
| name (`-r2`), a new commit and a new tag, and the old tag keeps serving the old bytes. Download by tag or by commit |
| hash, not from `main`, so a link always returns the same file. Every push is a commit, so the full history of the |
| repository is the release history. |
|
|
| ## Citation |
|
|
| Until the paper is out, cite this repository by its DOI (generated from the repository settings; added here once minted) |
| and the release tag: |
|
|
| > SampleExplorer databases (ARCHS4 v2.7, release 1), tag `r1`. Hugging Face. DOI: to be added. |
|
|
| How to cite the paper: added when the paper is published. |
|
|
