updating branch with ino's changes

addtnl_info/governance.md

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+---
+order: 998
+---
+
+# Governance and Policy
+
+Responsible data sharing requires transparent governance approaches to ensure data contributors, data curators, and data consumers are empowered to share and use data effectively. To this end, members of the DCC work closely with members of the HTAN consortium to develop and implement data sharing agreements and operational policies following the principles of the NCI Cancer Moonshot Public Access and Data Sharing Policy. A Data and Materials Sharing Agreement (DMSA) establishes the responsibilities and boundaries associated with data sharing with the DCC and within the HTAN consortium, while an External Data Sharing Policy ensures a commitment to share all generated data publicly. An Associate Membership Policy provides a mechanism for experts from outside of HTAN to contribute their expertise and knowledge. In addition, specific policies related to publications and the sharing of research protocols and computational tools were developed. A key infrastructure component for the implementation of these data-sharing policies is the Synapse platform, which provides fine-grained access controls at individual and team levels to ensure that data contributors and DCC staff have appropriate access to their data. Synapse teams were used to enable project-level access and tracked against a table of HTAN membership. 
+
+Ensuring the privacy of HTAN research participants is critical and a joint responsibility of the HTAN Centers generating data and the DCC. HTAN Centers are required to fully de-identify data before submission to the DCC via the Synapse platform, and must describe their data and metadata de-identification process in a de-identification plan. Following data submission, the DCC is responsible for implementing additional checks, to ensure patient privacy. Verifying that HTAN imaging data is de-identified is a particular focus of the DCC. For example, the extensive metadata collected alongside HTAN data was noted to theoretically enable the reconstruction of HIPAA-protected dates (such as participant date of birth) from the date of imaging data acquisition through longitudinal metadata attributes. The HTAN DCC therefore developed policies and procedures to confirm that all date attributes, including those in TIFF tags, OME-XML, and other locations, were detected and reported back to data contributors for removal before data release.
+
+## Policy Documents
+
+- [Publication Policy](https://docs.google.com/document/d/1cXqfeHXIU8mPr4rMFFrq8DAj2nDwCULUYuypC5ksPjw/)
+- [Protocol and Computational Tool Sharing Policy](https://docs.google.com/document/d/1APkwsWi8A-PbBYZtWQ58LO0GLRLNHSezYkn9l-4nK6k/edit?usp=sharing)
+- [External Data Sharing Policy](https://docs.google.com/document/d/1zEbYvxQs54585X7VHYoMt6jTmBtXQLQ1cVk2WCm2sfA/edit?usp=sharing)
+- [DUA/MTA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit?usp=sharing)
+- [Cancer Moonshot Public Access Policy](https://www.cancer.gov/research/key-initiatives/moonshot-cancer-initiative/funding/public-access-policy)
+- [Associate Membership Policy](https://docs.google.com/document/d/1n_ldYw7RaGQRQzWcn59Rykr7B6-cHvzw-6Z9BjeZ3t0/edit?usp=sharing)

addtnl_info/usage_analytics.md

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+---
+order: 997
+---
+
+# HTAN Data Usage Analytics
+
+The HTAN portal is used by thousands of people each month all over the world:
+
+![Google Analytics of HTAN Portal](../img/ga_usage_202108_202408.png)
+
+## Data Submission Trajectory
+
+The HTAN Data Coordination Center (DCC) has been working with the HTAN Centers to collect and process data. The following figure shows the number of data submissions to the DCC over time:
+
+![Data Submission Trajectory](../img/data_submission_trajectory.png)
+
+

faq.md

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+# Frequently Asked Questions (FAQ)
+
+- [What is the Human Tumor Atlas Network (HTAN)?](#what-is-the-human-tumor-atlas-network-htan)
+- [What is the HTAN Portal?](#what-is-the-htan-portal)
+- [Who can use the HTAN Portal?](#who-can-use-the-htan-portal)
+- [What types of data are available on the HTAN Portal?](#what-types-of-data-are-available-on-the-htan-portal)
+- [How can I access the data on the HTAN Portal?](#how-can-i-access-the-data-on-the-htan-portal)
+- [Do I need an account to access the HTAN data?](#do-i-need-an-account-to-access-the-htan-data)
+- [How is the data on the HTAN Portal generated?](#how-is-the-data-on-the-htan-portal-generated)
+- [Can I upload my own data to the HTAN Portal?](#can-i-upload-my-own-data-to-the-htan-portal)
+- [Is there any support or documentation available for using the HTAN Portal?](#is-there-any-support-or-documentation-available-for-using-the-htan-portal)
+- [How is privacy and data security handled on the HTAN Portal?](#how-is-privacy-and-data-security-handled-on-the-htan-portal)
+- [Can I use HTAN data for my own research?](#can-i-use-htan-data-for-my-own-research)
+- [Where can I find updates on new data or features added to the HTAN Portal?](#where-can-i-find-updates-on-new-data-or-features-added-to-the-htan-portal)
+- [Is there healthy data?](#is-there-healthy-data)
+- [Is there 3D data?](#is-there-3d-data)
+- [Is there temporal data?](#is-there-temporal-data)
+- [How can I contact the HTAN team for additional questions?](#how-can-i-contact-the-htan-team-for-additional-questions)
+
+---
+
+### What is the Human Tumor Atlas Network (HTAN)?
+
+The **Human Tumor Atlas Network (HTAN)** is a collaborative research initiative funded by the National Cancer Institute (NCI). It aims to create comprehensive, dynamic 3D atlases of tumors across multiple cancer types and stages. These atlases provide insights into how tumors evolve, from early formation to metastasis and treatment resistance.
+
+### What is the HTAN Portal?
+
+The [HTAN Portal](https://humantumoratlas.org) is an interactive platform where researchers, clinicians, and the public can access, explore, and analyze data generated by HTAN. The portal contains data such as genomic, transcriptomic, proteomic, and imaging data related to tumor development.
+
+### Who can use the HTAN Portal?
+
+The HTAN Portal is open to anyone interested in cancer research, including scientists, clinicians, and students. It is especially useful for cancer researchers seeking to explore tumor evolution and heterogeneity through a rich collection of multi-omics and imaging datasets.
+
+### What types of data are available on the HTAN Portal?
+
+The portal provides access to various types of data, including:
+
+- Genomic data
+- Transcriptomic data
+- Proteomic data
+- Single-cell sequencing data
+- Imaging and other spatial data 
+
+These datasets are gathered from different stages of cancer progression, including healthy, precancerous, primary tumors, metastases, and treatment-resistant cancers.
+
+### How can I access the data on the HTAN Portal?
+
+Users can access the data through the [Explore Page](https://humantumoratlas.org/explore) on the HTAN Portal
+
+### Do I need an account to access the HTAN data?
+
+No, an account is not required to explore the public data available on the HTAN Portal. However for accessing the lower level data, dbGap access needs to be obtained. See the [Acccess-Controlled Data](.//access_controlled/introduction/) section for more information.
+
+### How is the data on the HTAN Portal generated?
+
+The data is collected from participating HTAN centers across the United States. These centers generate multi-omics data, imaging datasets, and other relevant tumor information using advanced technologies, such as single-cell sequencing, proteomics, and spatial imaging techniques.
+
+### Can I upload my own data to the HTAN Portal?
+
+At this time, the HTAN Portal does not support user-uploaded data
+
+### Is there any support or documentation available for using the HTAN Portal?
+
+Yes, the HTAN Portal offers extensive documentation to help users navigate and utilize the platform effectively. Additionally, the portal provides a [Help Desk](https://sagebionetworks.jira.com/servicedesk/customer/portal/1) for support.
+
+### How is privacy and data security handled on the HTAN Portal?
+
+The HTAN Portal adheres to strict data security and privacy protocols to ensure that sensitive information, including patient-related data, is protected. Any identifiable information is removed or de-identified before being made available to the public, in compliance with ethical standards and legal regulations. More information can be found in the [Governance and Policy](.//addtnl_info/governance) section.
+
+### Can I use HTAN data for my own research?
+
+Yes, researchers are encouraged to use HTAN data for their own studies. The data is publicly available, but users must acknowledge HTAN and the publication of the source data in any resulting publications
+
+### Where can I find updates on new data or features added to the HTAN Portal?
+
+The portal is regularly updated with new data and features. You can find updates in the [News](https://humantumoratlas.org/data-updates) section of the HTAN Portal.
+
+### Is there healthy data?
+
+There is "healthy" and precancerous data on the HTAN Portal. No specific “healthy” filter exists at the moment, but one can find all samples without an unknown or reported disease with [this HTAN portal filter](https://humantumoratlas.org/explore?selectedFilters=%5B%7B%22value%22%3A%22Not+Reported%22%2C%22group%22%3A%22PrimaryDiagnosis%22%2C%22count%22%3A11996%2C%22isSelected%22%3Afalse%7D%2C%7B%22value%22%3A%22unknown%22%2C%22group%22%3A%22PrimaryDiagnosis%22%2C%22count%22%3A3388%2C%22isSelected%22%3Afalse%7D%5D). Note however that some of these may be tumors of unknown primary, or the information is missing for another reason. There is an [open ticket](https://github.com/ncihtan/htan-portal/issues/678) to improve the selection of healthy/normal and precancerous tissue.
+
+### Is there 3D data?
+
+A number of three-dimensional datasets have been released on the HTAN data portal, including 3D microscopy data and serial sections for H&E and multiplexed tissue imaging. Examples include [multiple serial section of CRC analyzed by CyCIF for the SARDANA trans-network partnership](https://data.humantumoratlas.org/explore?selectedFilters=%5B%7B%22value%22%3A%22CyCIF%22%2C%22group%22%3A%22assayName%22%2C%22count%22%3A3789%2C%22isSelected%22%3Afalse%7D%2C%7B%22value%22%3A%22HTAN+TNP+SARDANA%22%2C%22group%22%3A%22AtlasName%22%2C%22count%22%3A190%2C%22isSelected%22%3Afalse%7D%5D), and [electron microscopy data from OHSU](https://data.humantumoratlas.org/explore?selectedFilters=%5B%7B%22value%22%3A%22Electron+Microscopy%22%2C%22group%22%3A%22assayName%22%2C%22count%22%3A93000%2C%22isSelected%22%3Afalse%7D%5D). The DCC expects to receive and share 3D datasets including confocal and light-sheet microscopy in the future.
+
+### Is there temporal data?
+
+There are a few different types of temporal data, e.g., precancerous vs cancerous tumors, primary vs metastatic tumor samples, as well as a patient's longitudinal treatment and diagnosis information. The former can be found by search for specific biospecimens. The latter can now be explored per atlas in the longitudinal data section of the [HTAN Data Submission Dashboard](https://htan_dashboard.surge.sh/), as well as on [cBioPortal for the OHSU breast cancer dataset](https://www.cbioportal.org/patient?studyId=brca_hta9_htan_2022&caseId=HTA9_1#navCaseIds=brca_hta9_htan_2022:HTA9_1). We are working on improving the search and filter capabilities for temporal data on the HTAN Portal.
+
+
+### How can I contact the HTAN team for additional questions?
+
+You can contact the HTAN team through the [Help Desk](https://sagebionetworks.jira.com/servicedesk/customer/portal/1)

retype.yml

@@ -1,6 +1,6 @@
 input: .
 output: .retype
-url: jen-dfci.github.io/htan_missing_manual/
+url: docs.humantumoratlas.org
 branding:
     title: HTAN
     label: Manual