# WELCOME

> The HTAN Manual provides an overview of Human Tumor Atlas Network (HTAN) data, including details regarding data access and data contribution. If you have any questions regarding the manual or HTAN data, please contact us: HTAN Help Desk.

- [WELCOME](https://docs.humantumoratlas.org/readme.md): WELCOME
- [Frequently Asked Questions (FAQ)](https://docs.humantumoratlas.org/faq.md): What is the Human Tumor Atlas Network (HTAN)?

## Overview

- [Introduction to HTAN](https://docs.humantumoratlas.org/overview/introduction.md): The Human Tumor Atlas Network (HTAN) is a National Cancer Institute-funded Cancer Moonshot initiative focused on studying the transitions of human cancers as they evolve from precancerous lesions to advanced disease.
- [HTAN Centers](https://docs.humantumoratlas.org/overview/centers.md): HTAN is currently in Phase 2, which includes five pre-cancer atlases and five tumor atlases.
- [HTAN Data Access and Data Releases](https://docs.humantumoratlas.org/overview/data_access.md): HTAN data is categorized into two data access levels:
- [HTAN Tool Catalog](https://docs.humantumoratlas.org/overview/tool_catalog.md): The HTAN Network has built an array of computational tools, including bioinformatic methods, bioinformatic pipelines, and visualization tools.

## Data Model

- [Data Model Introduction](https://docs.humantumoratlas.org/data_model/overview.md): All HTAN Centers are required to encode their data and metadata in a common HTAN Data Model. The HTAN Data Model is created via a community Request for
- [Metadata Standards](https://docs.humantumoratlas.org/data_model/metadata_standards.md): Metadata means data about data. Metadata enables both data searchability and interpretability.
- [File Standards](https://docs.humantumoratlas.org/data_model/file_standards.md): The HTAN Data Model includes requirements for Assay Files. These include:
- [Identifiers](https://docs.humantumoratlas.org/data_model/identifiers.md): All research participants, biospecimens and derived data within HTAN are associated with unique HTAN identifiers. The relationship between the identifiers is visually represented in Figure 1.
- [Relationship Model](https://docs.humantumoratlas.org/data_model/relationships.md): HTAN Centers have multiple research participants, who have donated biospecimens (see Figure below). Metadata submitted by HTAN Centers allows one to trace back any data file to the donated biospecimen.

## Data Access

- [Introduction](https://docs.humantumoratlas.org/data_access/introduction.md): HTAN Data includes both assay files and metadata. All HTAN metadata are open access data whereas assay files may be either access-controlled or open access.
- [Citing HTAN](https://docs.humantumoratlas.org/data_access/citing_htan.md): If you use HTAN data, please cite the following HTAN publications:
- [Using the HTAN Data Portal](https://docs.humantumoratlas.org/data_access/portal.md): The HTAN Data Portal provides an interactive interface with which to explore HTAN data. It provides mechanisms to:
- [Requesting dbGaP Access](https://docs.humantumoratlas.org/data_access/db_gap.md): For access-controlled HTAN data, you must first complete a dbGaP request.
- [Google BigQuery](https://docs.humantumoratlas.org/data_access/biq_query.md): Google BigQuery is a massively-parallel analytics engine ideal for working with tabular data. Through our collaboration with the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC), open-access HTAN BigQuery tables are now available, and updated with each major HTAN release.
- [Gen3-Client](https://docs.humantumoratlas.org/data_access/cds_gen3.md): HTAN files available through the NCI CRDC Cancer Data Service can be downloaded in the terminal using the gen3-client. The gen3-client provides an
- [Accessing CRDC Data in SB-CGC](https://docs.humantumoratlas.org/data_access/cds_cgc.md): Seven Bridges Cancer Genomics Cloud (SB-CGC) is a cloud platform for the analysis and storage of large cancer datasets. There are two mechanisms for
- [Accessing Synapse Open Access Data in SB-CGC](https://docs.humantumoratlas.org/data_access/synapse_to_cds.md): Seven Bridges Cancer Genomics Cloud (SB-CGC) is a cloud platform for the analysis and storage of large cancer datasets.

## Data Visualization

- [Visualizing Single Cell Data via CellxGene](https://docs.humantumoratlas.org/data_visualization/cell_by_gene.md): Through our collaboration with the Chan Zuckerberg Initiative (CZI), we make HTAN single cell RNA seq data available via CellxGene. CellxGene enables you to visualize and explore large-scale single cell data sets.
- [Visualizing Data via Xena](https://docs.humantumoratlas.org/data_visualization/xena.md): Xena is a platform developed by the University of California Santa Cruz Genomics Institute to support visualization and analysis of multiomics data. Please see their tutorial pages for more information regarding the type of analyses possible in Xena.
- [Visualizing Multiplex Imaging Data via Minerva](https://docs.humantumoratlas.org/data_visualization/minerva.md): Through our collaboration with the Laboratory of Systems Pharmacology (LSP) at Harvard Medical School, many HTAN images can be visualized via Minerva, a web-based tool that enables interactive viewing and fast sharing of large image data.

## Submitting Data

- [Introduction](https://docs.humantumoratlas.org/data_submission/overview.md): Only HTAN Centers and Associate Members can submit data to HTAN repositories. The Data Submission Section of this Manual is intended as a guide for HTAN Centers and Associate Members.
- [Data Submission Overview](https://docs.humantumoratlas.org/data_submission/clin_biospec_assay.md): Data Submission Introduction provides a general overview for submitting data and metadata to HTAN. This page provides details regarding those steps.
- [Data Release](https://docs.humantumoratlas.org/data_submission/data_release.md): A calendar with specific dates and release timelines for HTAN Phase2 is available for HTAN Centers in the HTAN2 Synapse Wiki. The HTAN DCC will update the calendar with new dates as they are established.
- [Information for New HTAN Centers](https://docs.humantumoratlas.org/data_submission/information_new_centers.md): Welcome to the Human Tumor Atlas Network! Please see the Onboarding Checklist on this page for Step by Step instructions to complete onboarding for your Center.
- [HTAN Checklist for Acceptance of Data](https://docs.humantumoratlas.org/data_submission/checklist.md): When an HTAN Data Contributor is considering contribution of data to the HTAN DCC, this checklist should be used by the Data Contributor to determine if the data meets basic HTAN contribution requirements.
- [Creating HTAN Identifiers](https://docs.humantumoratlas.org/data_submission/creating_ids.md): This page contains step by step instructions for HTAN Centers and Trans Network Projects (TNPs) to create and manage HTAN identifiers. HTAN identifiers should be created for all entities (participants, biospecimens and data-files) within individual research projects.
- [Data Liaisons](https://docs.humantumoratlas.org/data_submission/data_liaisons.md): Upon joining HTAN, Centers are assigned a data liaison from the DCC. Trans-Network Projects (TNPs) are also assigned liaisons. The DCC liaisons assist each of the research centers in successfully uploading data and metadata files.
- [Data De-identification](https://docs.humantumoratlas.org/data_submission/data_deidentification.md): As outlined in the HTAN Internal Data and Materials Sharing Agreement (HTAN DMSA) , data submitted to the Data Coordinating Center (DCC) must be fully de-identified.
- [Metadata Requirements](https://docs.humantumoratlas.org/data_submission/metadata.md): Metadata Requirements are explicitly outlined in the HTAN Phase 2 Data Model (Metadata) Documentation. This documentation is directly linked to the underlying github repository code and will be updated as additional assays are added to the Phase 2 Data Model.
- [AGE_IN_DAYS vs Index Dates](https://docs.humantumoratlas.org/data_submission/dates.md): HTAN cannot accept dates because they are considered Protect Health Information (PHI). In order to obfuscate dates, they should be converted to days from birth.
- [Phase 2 Clinical Data](https://docs.humantumoratlas.org/data_submission/clin_data_submission.md): In HTAN Phase 2, there are two clinical metadata tiers.
- [Phase 2 Digital Pathology](https://docs.humantumoratlas.org/data_submission/digital_pathology.md): Digital pathology includes patch, tile, region of interest (ROI) or whole-slide imaging (WSI) derived from hematoxylin and eosin (H&E) or other tissue-based assays.
- [Phase 2 Multiplex Microscopy](https://docs.humantumoratlas.org/data_submission/multiplex_microscopy.md): Multiplex Microscopy defines standards for 2-dimensional (2D) multiplexed and/or cyclic immunofluorescence imaging assays. It focuses exclusively on multiplexed tissue imaging assays that rely on fluorescence, metal-based, or iterative immunostaining approaches.
- [Phase 2 sc/snRNA-seq](https://docs.humantumoratlas.org/data_submission/scrnaseq_data_submission.md): In HTAN Phase 2, the following files are submitted for single cell/single nuclei RNA-sequencing (sc/snRNA-seq) data:
- [Phase 2 SpatialOmics](https://docs.humantumoratlas.org/data_submission/spatialomics_submission.md): SpatialOmics is defined as spatially resolved sequencing and sequence-hybridization based omics technologies which molecular profiling of tissues while preserving spatial context.
- [Phase 2 Whole Exome Sequencing](https://docs.humantumoratlas.org/data_submission/wes.md): Phase 2 HTAN data standards for Whole Exome Sequencing (WES) are similar to those implemented in Phase 1 under the assay type "Bulk DNA-seq".

## Additional Information

- [Submitting Tools and Protocols](https://docs.humantumoratlas.org/addtnl_info/tool_protocol.md): The HTAN Portal Analysis Tools page lists computational tools developed or used to support HTAN research projects. The Data Coordinating Center (DCC) regularly checks HTAN pre-prints and publications for new HTAN Tools to add to the page.
- [Submitting Publications](https://docs.humantumoratlas.org/addtnl_info/publications.md): The HTAN Data Coordinating Center (DCC) supports HTAN Center publications in the following ways:
- [Governance and Policy](https://docs.humantumoratlas.org/addtnl_info/governance.md): Responsible data sharing requires transparent governance approaches to ensure data contributors, data curators, and data consumers are empowered to share and use data effectively.
- [HTAN Data Usage Analytics](https://docs.humantumoratlas.org/addtnl_info/usage_analytics.md): The HTAN portal is used by thousands of people each month all over the world:
- [Working Groups and Internal Communications](https://docs.humantumoratlas.org/addtnl_info/wg_internal.md): Information regarding Network Working Groups and Internal Communications can be found on the HTAN Phase 2 Synapse Wiki page.
- [The RFC Process and Data Model Changes](https://docs.humantumoratlas.org/addtnl_info/rfc.md): The HTAN Data Model is expected to evolve with advances in science. This evolution is a community-driven, peer-reviewed process, where members of a working group will first assess established community data standards and create a request for comment (RFC) document soliciting community feedback.
- [Trans-Network Projects (TNPs)](https://docs.humantumoratlas.org/addtnl_info/tnps.md): Trans-Network Projects are multi-center projects created to facilitate collaborative research. Examples include cross-testing experimental and analytical protocols, exchange of personnel to disseminate SOPs or pursuit of additional HTAN critical methods or technologies.