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✨ Add Hubmap to atlas docs (#220)
* ✨ Add hubmap * 🎨 Add hubmap * 🎨 Polish * 🎨 Polish
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‎docs/atlases.md

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@@ -9,5 +9,6 @@ The following use cases demonstrate how to use LaminDB to query popular atlases.
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cellxgene
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arc-virtual-cell-atlas
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hubmap
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```

‎docs/hubmap.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Hubmap: scRNA-seq"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"The [HubMAP (Human BioMolecular Atlas Program) consortium](https://hubmapconsortium.org/) is an initiative mapping human cells to create a comprehensive atlas, with its [Data Portal](https://portal.hubmapconsortium.org/) serving as the platform where researchers can access, visualize, and download (single-cell) tissue data.\n",
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"\n",
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"Lamin mirrors most of the datasets for simplified access here: [laminlabs/hubmap](https://lamin.ai/laminlabs/hubmap).\n",
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"\n",
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"If you use the data academically, please cite the original publication [Jain et al. 2023](https://www.nature.com/articles/s41556-023-01194-w).\n",
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"\n",
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"Here, we show how the HubMAP instance is structured and how datasets and be queried and accessed."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Connect to the source instance:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"hide-output"
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]
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},
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"outputs": [],
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"source": [
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"# pip install 'lamindb[jupyter,bionty,wetlab]'\n",
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"!lamin connect laminlabs/hubmap"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"```{note}\n",
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"\n",
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"If you want to transfer artifacts or metadata into your own instance, use `.using(\"laminlabs/hubmap\")` when accessing registries and then `.save()` ({doc}`/transfer`).\n",
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"\n",
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"```"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"hide-output"
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]
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},
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"outputs": [],
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"source": [
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"import lamindb as ln"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Getting HubMAP datasets and data products"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"HubMAP associates several data products, which are the single raw datasets, into higher level datasets.\n",
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"For example, the dataset [HBM983.LKMP.544](https://portal.hubmapconsortium.org/browse/dataset/20ee458e5ee361717b68ca72caf6044e) has three data products:\n",
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"\n",
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"1. [raw_expr.h5ad](https://assets.hubmapconsortium.org/f6eb890063d13698feb11d39fa61e45a/raw_expr.h5ad)\n",
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"1. [expr.h5ad](https://assets.hubmapconsortium.org/f6eb890063d13698feb11d39fa61e45a/expr.h5ad)\n",
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"2. [secondary_analysis.h5ad](https://assets.hubmapconsortium.org/f6eb890063d13698feb11d39fa61e45a/secondary_analysis.h5ad)\n",
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"3. [scvelo_annotated.h5ad](https://assets.hubmapconsortium.org/f6eb890063d13698feb11d39fa61e45a/scvelo_annotated.h5ad)\n",
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"\n",
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"The [laminlabs/hubmap](https://lamin.ai/laminlabs/hubmap) instance registers these data products as {class}`~lamindb.Artifact` that jointly form a {class}`~lamindb.Collection`."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"The `key` attribute of `ln.Artifact` and `ln.Collection` corresponds to the IDs of the URLs.\n",
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"For example, the id in the URL [https://portal.hubmapconsortium.org/browse/dataset/20ee458e5ee361717b68ca72caf6044e](https://portal.hubmapconsortium.org/browse/dataset/20ee458e5ee361717b68ca72caf6044e) is the `key` of the corresponding collection:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"hide-output"
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]
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},
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"outputs": [],
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"source": [
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"small_intenstine_collection = ln.Collection.get(key=\"20ee458e5ee361717b68ca72caf6044e\")\n",
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"small_intenstine_collection"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"We can get all associated data products like:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"hide-output"
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]
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},
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"outputs": [],
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"source": [
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"small_intenstine_collection.artifacts.all().df()"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Note the key of these three `Artifacts` which corresponds to the assets URL.\n",
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"For example, [https://assets.hubmapconsortium.org/f6eb890063d13698feb11d39fa61e45a/expr.h5ad](https://assets.hubmapconsortium.org/f6eb890063d13698feb11d39fa61e45a/expr.h5ad) is the direct URL to the `expr.h5ad` data product.\n",
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"\n",
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"Artifacts can be directly loaded:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"hide-output"
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]
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},
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"outputs": [],
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"source": [
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"small_intenstine_af = (\n",
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" small_intenstine_collection.artifacts.filter(key__icontains=\"raw_expr.h5ad\")\n",
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" .distinct()\n",
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" .one()\n",
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")\n",
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"adata = small_intenstine_af.load()\n",
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"adata"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Querying single-cell datasets"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Currently, only the `Artifacts` of the `raw_expr.h5ad` data products are labeled with metadata.\n",
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"The available metadata includes `ln.Reference`, `bt.Tissue`, `bt.Disease`, `bt.ExperimentalFactor`, and many more.\n",
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"Please have a look at [the instance](https://lamin.ai/laminlabs/hubmap) for more details."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"hide-output"
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]
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},
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"outputs": [],
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"source": [
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"# Get one dataset with a specific type of heart failure\n",
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"heart_failure_adata = (\n",
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" ln.Artifact.filter(diseases__name=\"heart failure with reduced ejection fraction\")\n",
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" .first()\n",
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" .load()\n",
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")\n",
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"heart_failure_adata"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "lamindb",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.8"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎noxfile.py

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run_notebooks("docs/tutorial.ipynb")
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run_notebooks("docs/tutorial2.ipynb")
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run_notebooks("docs/arc-virtual-cell-atlas.ipynb")
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run_notebooks("docs/hubmap.ipynb")
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@nox.session

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