Merge pull request #50 from ncihtan/main

update with Ethan's most recent changes

data_submission/Information_New_Centers.md

@@ -8,10 +8,10 @@ Welcome to the Human Tumor Atlas Network!
 
 The [Goverance and Policy page](../addtnl_info/governance.md) of this manual provides documentation and applicable policies detailing the requirements for publications, data sharing, and data use.  
 
-All HTAN members must have an executed Human Tumor Atlas Network DMSA  (Internal Data and Materials Sharing Agreement) [(HTAN DMSA)](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) with Sage Bionetworks prior to contributing data to the HTAN Data Coordinating Center [(DCC)](https://humantumoratlas.org/htan-dcc). To initiate execution of the HTAN DMSA, contact Sage HTAN Governance ([email protected]). Please include the name and contact information of your HTAN PI and Institution Signatory to enable routing the HTAN DMSA for execution.
+All HTAN centers must have an executed Human Tumor Atlas Network DMSA  (Internal Data and Materials Sharing Agreement) [(HTAN DMSA)](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) with Sage Bionetworks prior to contributing data to the HTAN Data Coordinating Center [(DCC)](https://humantumoratlas.org/htan-dcc).  See also [HTAN Checklist for Acceptance of Data](../data_submission/checklist.html).  Sean Hanlon from the NCI will be reaching out to new Centers to coordinate collection of DMSA signatures.
 
-HTAN Centers are assigned a [data liaison](../data_submission/Data_Liaisons.md) from the [(DCC)](https://humantumoratlas.org/htan-dcc). Trans-Network Projects (TNPs) are also assigned liaisons. Your liaison will help guide you through setting up a new atlas or project, creating HTAN identifiers, and submitting metadata and data files.  Please keep your liaison informed of publications timelines and new data submissions.  
+HTAN centers are assigned a [data liaison](../data_submission/Data_Liaisons.md) from the [(DCC)](https://humantumoratlas.org/htan-dcc). Trans-Network Projects (TNPs) are also assigned liaisons. Your liaison will help guide you through setting up a new atlas or project, [creating HTAN identifiers](../data_submission/creating_ids.md), and [submitting metadata and data files](../data_submission/clin_biospec_assay/).  Please keep your liaison informed of publications timelines and new data submissions.  
 
-Please see the appropriate page of this manual for additional details about HTAN center responsibilities for data de-identification, including submitting a data de-identification plan, and specific instructions regarding how to submit data.  Clinical, biospecimen, and assay data submitted to the DCC are distributed to repositories based on access levels.  Information regarding how data are accessed by external users is described more in [other parts of this manual](../overview/data_levels.md).
+Please see the appropriate page of this manual for additional details about HTAN center responsibilities for [data de-identification](../data_submission/data_deidentification/), including submitting a data de-identification plan, and specific instructions regarding how to submit data.  Clinical, biospecimen, and assay data submitted to the DCC are distributed to repositories based on access levels.  Information regarding how data are accessed by external users is described more in [other parts of this manual](../overview/data_levels.md).
 
-In order to support the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for scientific data production, the DCC has developed a [data model](../data_model/) based on established standards in the scientific research community. 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. The RFC process is described in more detail in later pages of this manual.  We look forward to working with you and learning from your expertise as we improve upon our current model.
+In order to support the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for scientific data production, the DCC has developed a [data model](../data_model/overview.md) based on established standards in the scientific research community. 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)](../addtnl_info/rfc/) document soliciting community feedback.  We look forward to working with you and learning from your expertise as we improve upon our current model.

data_submission/checklist.md

@@ -4,22 +4,25 @@ order: 999
 
 # HTAN Checklist for Acceptance of Data
 
-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. 
+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.
+
+!!! All HTAN centers must have an executed Human Tumor Atlas Network DMSA  (Internal Data and Materials Sharing Agreement) [(HTAN DMSA)](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) with Sage Bionetworks prior to contributing data to the HTAN Data Coordinating Center [(DCC)](https://humantumoratlas.org/htan-dcc).  Sean Hanlon from the NCI will be reaching out to new Centers to coordinate collection of DMSA signatures.
+!!!
 
 | Checklist of Requirements | Agreement / Policy Reference |
 |---------------------------|------------------------------|
 | The data meets my data quality control standards and those established by the HTAN DCC. | [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) Section 2.a: “Contributor will transfer to the HTAN-DCC De-identified Datasets generated as part of the HTAN that either pass the QC standards that are in effect for HTAN at the time, or pass the Contributor’s QC standards in cases where HTAN standards do not exist.” |
 | The data contribution includes all extra information needed to interpret and understand the data. | [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) Section 2.b: “Supporting information including the Data annotation manifest necessary to interpret the submitted Data must be included with the submission and will be reviewed by the HTAN-DCC for completeness.”|
-|The data are de-identified according to the current standards for HTAN. | [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) Section 6.a: “The Parties agree that all Data disclosed to and from the Parties shall be De-identified so that Data Subjects cannot be ascertained directly or through secondary data use in accordance with HIPAA.” |
+|The data are de-identified according to the current standards for HTAN. See [Data De-identification](../data_submission/Data_Deidentification.md).| [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) Section 6.a: “The Parties agree that all Data disclosed to and from the Parties shall be De-identified so that Data Subjects cannot be ascertained directly or through secondary data use in accordance with HIPAA.” |
 | The data were collected according to protocols approved by an IRB or its equivalent. | [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) Section 6.b:  “Contributor represents that all Data and Material derived from HTAN that Contributor provides to Recipient were collected pursuant to and in accordance with protocols approved by an IRB or its equivalent;[...]”|
 | The contribution of the data is consistent with applicable U.S. laws, regulations, and its institutional policies. | [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) Section 6.c: “Contributor represents that the Data and Material submission to the HTAN-DCC and/or Recipient are consistent with applicable U.S. laws, regulations, and its institutional policies;{...]”| 
 | I affirm that an IRB or its equivalent assures that the data and sharing of the data is consistent with the Informed Consent of the Data Subject(s) from whom the Data and Materials were obtained. | [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) Section 6.d: “The Contributor represents that an IRB/Privacy Board or equivalent body, as applicable, has assured that submission and subsequent sharing of Data and Materials are consistent with the Informed Consent of the Data Subject(s) from whom the Data and Materials were obtained.” |
 | The data contribution includes acceptable HTAN data types: clinical data, biospecimen data, genomic sequencing data and/or multiplex imaging, contextual assay metadata and/or assay data files. | [HTAN Data Standards](https://humantumoratlas.org/standards) |
-| I understand the data I contribute will be hosted and shared via the HTAN-DCC Portal or other HTAN-designated repositories and will be subject to and governed by all the terms and conditions of this Agreement, the NIH Data Sharing Policy and NIH Genomic Data Sharing Policy. | [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit)Section 3.a: ”Any Data that Contributor generates as part of the HTAN Project will be hosted and shared using the HTAN-DCC Portal or other HTAN-designated repositories and will be subject to and governed by all the terms and conditions of this Agreement, the NIH Data Sharing Policy and NIH Genomic Data Sharing Policy.”|
+| I understand the data I contribute will be hosted and shared via the HTAN-DCC Portal or other HTAN-designated repositories and will be subject to and governed by all the terms and conditions of this Agreement, the NIH Data Sharing Policy and NIH Genomic Data Sharing Policy. | [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) Section 3.a: ”Any Data that Contributor generates as part of the HTAN Project will be hosted and shared using the HTAN-DCC Portal or other HTAN-designated repositories and will be subject to and governed by all the terms and conditions of this Agreement, the NIH Data Sharing Policy and NIH Genomic Data Sharing Policy.”|
 | I understand that if the data are found to include PHI, then the data will be removed from the HTAN-DCC Portal and that it is my responsibility to remove the PHI and re-submit the data to the HTAN-DCC as soon as possible.|[HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) Section 2.c: “The HTAN-DCC and the Data Contributor will review Data after submission, before it is released, to verify that no PHI has been submitted accidentally. If there is presence of PHI, i. HTAN-DCC will notify the Contributor of the presence of PHI and delete files that contain PHI from the HTAN-DCC Portal, ii. Contributor will resubmit Data without PHI. Data quality corrections will be submitted as soon as possible. [...]”|
 |I understand that if data quality corrections for the data are required, then I am responsible for removing the data from the HTAN-DCC Portal, making corrections, and re-submitting the data as soon as possible. | [HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit) 2.c: “[...] Data quality corrections will be submitted as soon as possible.” |
 
-If the Data Contributor is able to affirm their understanding of this checklist and that the data meet the criteria in this checklist, then the Data Contributor may engage their HTAN Data Liaison to begin the data contribution process. 
+If the Data Contributor is able to affirm their understanding of this checklist and that the data meet the criteria in this checklist, then the Data Contributor may engage their HTAN [Data Liaison](../data_submission/Data_Liaisons.md) to begin the data contribution process. 
 
 If the Data Contributor has concerns about the acceptability of their data contribution, the Data Contributor may contact the HTAN DCC to request Data Contribution Support via the HTAN Help Desk: https://sagebionetworks.jira.com/servicedesk/customer/portal/1