From a0a8e9befcac944f10f99254a43783b5ead0b02b Mon Sep 17 00:00:00 2001 From: Chris-Csonka <108365397+Chris-Csonka@users.noreply.github.com> Date: Tue, 24 Sep 2024 17:21:49 -0400 Subject: [PATCH] Update doc-sitemap-external.md Adding content from draft file --- docs/doc-sitemap-external.md | 66 ++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) diff --git a/docs/doc-sitemap-external.md b/docs/doc-sitemap-external.md index 8b13789..0606349 100644 --- a/docs/doc-sitemap-external.md +++ b/docs/doc-sitemap-external.md @@ -1 +1,67 @@ +# HuBMAP Documentation +## HuBMAP Data +### Developers +Programmatic access to data / metadata via APIs or Tools +#### Search APIs +APIs to find metadata / data: +- Search API: The HuBMAP Search API is a thin wrapper of the Elasticsearch API. + - It handles data indexing and reindexing into the backend Elasticsearch. + - It accepts the search query and passes through to the Elasticsearch with data access security check. + - HuBMAP Parameterized Search - An option for a simpler programatic search mechanism. + - Link to a Parameterized Search tutorial on GitHub. + + - Entity API: The Entity API returns information about HuBMAP data entities. + - Generally, a donor and organ are _required_ in the provenance hierarchy where tissue samples (such as blocks and samples) can be organized based on several different tissue sample types. +#### Getting Data +Tools to get data without going to the Portal: +- Metadata Attributes by Dataset Type - A list of available dataset types with links to the valid metadata attributes. +- Link to a Parameterized Search tutorial on GitHub. +### Other Stakeholders + - View / Access / Download data (via the Portal) + - HuBMAP FAQ: Frequently Asked Questions about HuBMAP Data, Tools, and related topics. + - About HuBMAP: Policies & Procedures, DUA, Protected Data & Access, Citing HuBMAP Data, Funding & Contact info. + - **Training Materials:** Biomedical technologies such as single-cell and spatial approaches are not common at all institutions of higher education. Significant barriers towards making effective use of such data include the lack of available training. + - HuBMAP has created several self-paced training modules to fill this gap. These modules... + - Focus on introducing HuBMAP, including technologies & assays used by HuBMAP, HuBMAP metadata, and example use cases. + - Demonstrate how to include HuBMAP data in research projects, graduate student theses, and classroom teaching. +
+ See Self-paced Training Modules + +
+ + - HuBMAP Publications: See more than 330 featured publications to learn how HuBMAP tools and data are advancing discovery. + +## HuBMAP Tools +- HRA Tools: + - Human Reference Atlas (HRA): a comprehensive, high-resolution, three-dimensional atlas of all the cells in a healthy human body. + - Watch a short video introduction or check out the latest release notes for the HRA. +
+ See additional Tools available from the HRA... +
+- Azimuth: A web application that automates the processing, analysis, and interpretation of new single-cell sequencing experiments. + - This page provides Query references, a general workflow, FAQ, and tips for Preprocessing, Mapping, and other topics. +- FUSION: Functional Unit State Identification and Navigation with WSI - An interactive interface to view spatial transcriptomics data integrated with histopathology, driven by AI. This site contains multiple tutorials and other helpful features. +- STELLAR: A geometric deep learning method for cell type discovery and identification in single-cell datasets. +- Vitessce: Visual integration tool for exploration of spatial single cell experiments. + - Vitessce Documentation + - Vitessce Tutorials +- HuBMAP pipelines and related documentation. Includes pipelines for CODEX, SPRM, Single-cell ATAC-seq, and Single-cell RNA-seq +- Reproducing HuBMAP workflows (Y3 effort)- Note, still in development, more details to follow. +- Using APIs to get information about workflows +- HuBMAP (Data Portal) Workspaces: Explore public HuBMAP data and user-provided data using Python and R in a Jupyter Lab environment. + - Workspaces Tutorials: Learn how to interactively analyze HuBMAP datasets by uploading them in a JupyterLab environment.