Merge pull request #61 from ncihtan/phase2_chgs

Remove 'member'; update docs to pdfs

addtnl_info/governance.md

@@ -10,9 +10,9 @@ Ensuring the privacy of HTAN research participants is critical and a joint respo
 
 ## 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)
+- [Publication Policy](https://drive.google.com/file/d/1DVys8U1s92Mv5fRUxk97q2sSJFJ5kOjA/view)
+- [Protocol and Computational Tool Sharing Policy](https://drive.google.com/file/d/1L3Azfs4R4RWqVf5uCzDE3Ln97r-k0Jm3/view)
+- [External Data Sharing Policy](https://drive.google.com/file/d/17vN_8zcWsPNBtnLe1mOr35wqhUbuMaWI/view)
+- [HTAN Internal Data and Materials Sharing Agreement](https://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view)
 - [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)
+- [Associate Membership Policy](https://drive.google.com/file/d/1MPE8ecIF9nRQsI--Sfo8CZfCyamyJZnV/view)

data_submission/Data_Deidentification.md

@@ -7,7 +7,7 @@ order: 997
 !!! **HTAN Centers are responsible for data deidentification.**
 !!!
 
-As outlined in the HTAN [DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit#heading=h.gjdgxs), data submitted to the Data Coordinating Center (DCC) must be fully de-identified.
+As outlined in the HTAN Internal Data and Materials Sharing Agreement [(DMSA)](https://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view), data submitted to the Data Coordinating Center (DCC) must be fully de-identified.
 
 By signing the HTAN DMSA, HTAN members’ institutional signing officials and PIs accept responsibility for the de-identification of data prior to transfer to the DCC and confirm that: 
 
@@ -19,8 +19,6 @@ By signing the HTAN DMSA, HTAN members’ institutional signing officials and PI
 
 - an IRB/Privacy Board or equivalent body has assured that submission and subsequent sharing of data are consistent with the Informed Consent of the Data Subject(s) from whom the data were obtained. In addition, the data are protected by an NIH Certificate of Confidentiality.
 
-New HTAN Centers should develop and submit a De-identification Plan using the [HTAN Atlas De-Identification Plan Template](https://docs.google.com/document/d/1jFXYVMhLEGVcMNBh3L-U1rr4B-KLG7gK-ETc1SzMHhs/edit?usp=sharing).
-
 Prior to transferring data to the HTAN DCC, members are responsible for fully de-identifying the data being transferred. Full de-identification of data includes confirmation that data file names do not contain any information that could be used to re-identify that data subject. 
 
 

data_submission/Information_New_Centers.md

@@ -9,7 +9,7 @@ Welcome to the Human Tumor Atlas Network! Please see the [Onboarding Checklist](
 ## General Information
 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 Institutions 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 Institutions to coordinate collection of DMSA signatures.
+All HTAN Institutions must have an executed Human Tumor Atlas Network DMSA  (Internal Data and Materials Sharing Agreement) [(HTAN DMSA)](https://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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.md).  Sean Hanlon from the NCI will be reaching out to new Institutions 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 onboarding to work with the DCC, [creating HTAN identifiers](../data_submission/creating_ids.md), and [submitting metadata and data files](../data_submission/clin_biospec_assay/).  Please keep your DCC Data Liaison informed of publications timelines and new data submissions.  
 
@@ -27,10 +27,10 @@ Step 1
 Step 2
 : Identify a Center Data Wrangler for your center.  
 
-> The Center Data Wrangler will be the primary point of contact for all data submissions from your Center. Note that while multiple Center members may be performing data submission, the Data Wrangler should be the main point of contact with the DCC.  Please email contact information for your Data Wrangler to Alex Lash at:  alexl@ds.dfci.harvard.edu.
+> The Center Data Wrangler will be the primary point of contact for all data submissions from your Center. Note that while multiple individuals may be performing data submission for your Center, the Data Wrangler should be the main point of contact with the DCC.  Please email contact information for your Data Wrangler to Alex Lash at:  alexl@ds.dfci.harvard.edu.
 
 Step 3
-: Sign the Internal Data and Materials Sharing Agreement ([HTAN DMSA](https://docs.google.com/document/d/1RPFm9MBJv8DjZmYZyIv0jbjtNJ8fnwGjYDjlK4lL4nc/edit)).
+: Sign the Internal Data and Materials Sharing Agreement ([HTAN DMSA](https://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view)).
 
 > Sean Hanlon from the NCI will be reaching out to new Institutions to coordinate collection of DMSA signatures. Your DCC Data Liason will be able to direct you to Lisa Pasquale, Privacy and Data Protection Analyst at Sage Bionetworks who will be avaliable to assist you amd your institutions' representatives with DMSA-related questions.
 
@@ -56,7 +56,6 @@ Step 8
 
 > Once all Centers have been on-boarded, the DCC will organize a series of information sessions. All Center Data Wranglers and data submitters will be required to attend information sessions. For those unable to attend, the event will be recorded and posted to the Synapse wiki.
 
-
 ## Coming Soon!: DCC Information Sessions
 
 The following DCC Information Sessions are being planned.

data_submission/checklist.md

@@ -6,21 +6,21 @@ order: 999
 
 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.
+!!! All HTAN centers must have an executed Human Tumor Atlas Network DMSA  (Internal Data and Materials Sharing Agreement) [(HTAN DMSA)](https://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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. 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 meets my data quality control standards and those established by the HTAN DCC. | [HTAN DMSA](https://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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. See [Data De-identification](../data_submission/Data_Deidentification.md).| [HTAN DMSA](https://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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 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.” |
+| 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://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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](hhttps://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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://drive.google.com/file/d/1gJvxOM1mdFAw6kioNLNOD8NPWmxLlM4H/view) 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](../data_submission/Data_Liaisons.md) to begin the data contribution process.