Repository: ESIPFed/esipDMP
Pull request #9: Adding first draft of content.
Author: login: jibarozzo
Labels: name: documentation
description: Improvements or additions to documentation
name: enhancement
description: New feature or request
Created: 2025-05-22T21:20:55Z | Merged: 2025-05-28T18:54:54Z

This PR brings all the content discussed in our last meeting on 2025-05-13


Diff:
diff --git a/sections/access.qmd b/sections/access.qmd
index 4985efd..9d95042 100644
--- a/sections/access.qmd
+++ b/sections/access.qmd
@@ -5,13 +5,40 @@ title: "Access to Research Outputs"
 ## What Does Access Look Like?
 
 ### Access
-- **Sharing**
-  - Mechanisms for sharing outputs (e.g., repositories, cloud storage).
-- **Provisions/Protection**
-  - Measures to protect sensitive or confidential data (e.g., encryption, access controls).
-- **Timeline for Availability/Access**
-  - When will products be shared or published (e.g., immediately, after embargo period).
-- **License**
-  - Licensing terms (e.g., Creative Commons, MIT License).
-- **Restrictions / Confidentiality / Proprietary Business Info**
-  - Any limitations on access due to confidentiality or proprietary concerns.
\ No newline at end of file
+
+-   BCO-DMO: [Church](https://drive.google.com/file/d/1lFfmFJ0FRqvj4HQU6FX-QFne-2XYPQ6y/view?usp=share_link)
+    -   To increase accessibility to project data and the dissemination of our research findings—particularly among scientists from developing countries—we will make every effort to publish our results as open-access articles or within open-access journals.
+-   **Sharing**
+    -   Mechanisms for sharing outputs (e.g., repositories, cloud storage).
+
+**Archive(s)**
+
+-   Where the data will be stored (e.g., institutional repository, public archive).
+    -   e.g.:
+        -   BCO-DMO: [Saito](https://drive.google.com/file/d/1xJ8EiH436Fr95XrIEsvyYHoQv0mErSwB/view?usp=share_link)
+            -   R2R will ensure that the original underway measurements are archived permanently at NCEI and/or NGDC as appropriate. BCO-DMO will also ensure that project data are submitted to the appropriate national data archive. The PI will work with R2R and BCO-DMO to ensure data are archived appropriately and that proper and complete documentation are archived along with the data. All processed data will be submitted to BCO-DMO. Sequence data will be submitted to NCBI and raw mass spectrometry data will be submitted to ProteomeXchange.\
+        -   BCO-DMO: [Reitzel](https://drive.google.com/file/d/19I3y-pgxbPr-T7yITp5LMhfS7gT4TqOm/view?usp=share_link)
+            -   Sequence data will be archived at NCBI GenBank or SRA, code will be archived on GitHub and processed data files (e.g., vcf files) will be deposited in Dryad. BCO-DMO ensures that the data are archived properly at the appropriate National Data Archive for long-term archive preservation.
+-   **Provisions/Protection**
+    -   Measures to protect sensitive or confidential data (e.g., encryption, access controls).
+-   **Timeline for Availability/Access**
+    -   When will products be shared or published (e.g., immediately, after embargo period).
+    -   e.g.:
+        -   BCO-DMO: [Church](https://drive.google.com/file/d/1lFfmFJ0FRqvj4HQU6FX-QFne-2XYPQ6y/view?usp=share_link)
+            -   All of the data generated in this study will be made publicly available upon publication in a peer-reviewed journal, or within two years of the completion of the project. … Shipboard underway data will be made available within one year via the Rolling Deck to Repository.
+        -   BCO-DMO: [Greer](https://drive.google.com/file/d/1OTn2YkAbrXQBt3CN2hL4ras1sewSg5Vi/view?usp=share_link)
+            -   Once the data have been collected and quality controlled, we will ensure all data are publicly available within two years. In general, we do not intend to impose any data embargos, with the exception of student generated data that will be used for the completion of student theses and publications.
+-   **License**
+    -   Licensing terms (e.g., Creative Commons, MIT License).
+    -   e.g.:
+        -   BCO–DMO: [Church](https://drive.google.com/file/d/1lFfmFJ0FRqvj4HQU6FX-QFne-2XYPQ6y/view?usp=share_link) (right language but not declare license)
+            -   All data from this project are considered within the public domain for all not-for-profit uses and there will be no permission restrictions placed on use of the data.
+        -   [MCR-LTER](https://drive.google.com/file/d/1rNYVmb7wMWjaDMhHGMEFG5hsnr8yhz56/view?usp=share_link)
+            -   \* Our data access/data use policy is the Creative Commons license CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). The user is free to use and adapt the data while giving appropriate credit without any other restrictions. In our data use policy, we make a few additional recommendations for collaboration and suggest that users contact the appropriate MCR personnel if they have any questions or concerns about the data, but these recommendations do not change the general license text.
+-   **Restrictions / Confidentiality / Proprietary Business Info**
+    -   Any limitations on access due to confidentiality or proprietary concerns.
+    -   e.g.:
+        -   BCO-DMO: [Greer](https://drive.google.com/file/d/1OTn2YkAbrXQBt3CN2hL4ras1sewSg5Vi/view?usp=share_link)
+            -   We do not expect that the data we will generate will require any exceptional arrangements due to questions of ethical restrictions or release of indigenous knowledge.
+        -   BCO-DMO: Church
+            -   There are no ethical and privacy issues with these data. There are no human research subjects in our study. The dataset from this project will not be copyrighted.
diff --git a/sections/outputs.qmd b/sections/outputs.qmd
index 77944c3..fd00b34 100644
--- a/sections/outputs.qmd
+++ b/sections/outputs.qmd
@@ -6,35 +6,65 @@ title: "Research Outputs"
 
 Research outputs include a variety of materials and data generated during the research process. These may include:
 
-- **Samples**
-  - Physical samples (e.g., biological, chemical, geological)
-  - Digital samples (e.g., scanned images, 3D models)
-- **Data**
-  - Raw data
-  - Processed data
-  - Metadata
-- **Collections**
-  - Curated sets of samples or data
-- **Software**
-  - Code, scripts, or applications developed for analysis
-- **Materials**
-  - Lab protocols, reagents, or experimental setups
-- **Models**
-  - Statistical, mathematical, or computational models
-- **Documents/Posters/Pre-prints/Publications/Videos**
-  - Research papers, conference posters, pre-prints, and multimedia content
+-   **Samples**
+    -   Physical samples (e.g., biological, chemical, geological)
+        -   e.g.:
+            -   [Mullineaux #2453](https://drive.google.com/file/d/1-N-bHKeJbC1QTouZVT5Ae2MMSAG9CEYA/view?usp=share_link) - Physical samples will include animals, rocks, and water column samples. Rocks and animal specimens for which we extract gut contents will be assigned unique sample identifiers, important for provenance for subsamples to be analyzed for microbes.
+    -   Digital samples (e.g., scanned images, 3D models)
+-   **Data**
+    -   Raw data
+    -   Processed data
+    -   Metadata
+-   **Collections**
+    -   Curated sets of samples or data
+-   **Software**
+    -   Code, scripts, or applications developed for analysis
+-   **Materials**
+    -   Lab protocols, reagents, or experimental setups
+-   **Models**
+    -   Statistical, mathematical, or computational models
+        -   e.g:
+            -   BCO-DMO: [Bianchi](https://drive.google.com/file/d/1pR_HCs9ayvXZXwkAENdRYJ9utfwax6-B/view?usp=share_link)
+                -   Output from model simulations, which will include both physical (T, S, velocities) and biogeochemical (tracer, rates, fluxes) variables. The raw output will be post-processed and analyzed for presentation at meetings and for publication in scientific journals. For model output from the main set of simulations (Table 1 in the proposal), standard model fields (e.g. physical and biogeochemical tracers, current velocities, and the main biogeochemical rates) at monthly resolution will be provided to, and made available through, BCO-DMO and NOAA NCEI in standard NetCDF format.
+-   **Documents/Posters/Pre-prints/Publications/Videos**
+    -   Research papers, conference posters, pre-prints, and multimedia content
+        -   e.g.:
+            -   [Mullineaux #2453](https://drive.google.com/file/d/1-N-bHKeJbC1QTouZVT5Ae2MMSAG9CEYA/view?usp=share_link)
+                -   Imagery at the seafloor will include NDSF vehicle imagery (e.g., 4K video) and PI-provided imagery (e.g., time-lapse still).
+
+::: callout-tip
+## General example
+
+***Note their description of data types, number of experiments performed, file types generated, and repositories for submission.***
+
+-   BCO-DMO: [Alexander](https://drive.google.com/file/d/1xdAynJgxfdbvASA60xuP4oKib8gxm5Nv/view?usp=share_link)
+    -   Description of data types, number of experiments performed, file types generated, and repositories for submission
+    -   *Genetic sequencing*: mRNA and DNA sequencing from E. huxleyi cultures grown in the lab will be collected. Sequencing will be performed at the Columbia Genome Center (New York, NY). All raw sequence data will be deposited in the short-read archive (SRA) through the NCBI. Assembled genomes will be deposited under the same project number through the NCBI's Assembly database. Assembled transcriptomes will be deposited on the NCBI's Transcriptome Shotgun Assembly (TSA) database. Associated annotation files will be uploaded with the genome and transcriptome files to the appropriate database. File types: Short-read archive (.sra), raw sequencing files (.fastq), assembled fasta files (.fasta), annotation files (.gff). Repository: NCBI; accession numbers will be provided to BCO-DMO.
+    -   *Physiological experiment data*: Physiological experiments carried out on 10 different *E. huxleyi* strains will be conducted in the lab. Physiological and chemical parameters of the cultures will be collected over time including: growth rate, cell size, Fv/Fm, chlorophyll, particulate organic carbon, particulate inorganic carbon, dissolved nitrogen and phosphorus, and particulate nitrogen and phosphorus. File types: csv files. Repository: BCO-DMO.
+    -   *Bioinformatic pipelines*: Analysis of all genetic sequencing data will be done through the construction of reproducible pipelines designed in Snakemake. These pipelines will be made public on GitHub and archived and provided a doi through Zenodo. Repository: Zenodo; doi will be provided to BCO-DMO.
+:::
 
 ## Number and Size of Research Outputs
 
-- **Number of files, samples, collections, etc.**
-  - Estimated count of each type of output.
-- **Size of each file, sample, etc.**
-  - File sizes (e.g., MB, GB, TB) for digital outputs.
-  - Physical dimensions or quantities for physical samples.
+-   **Number of files, samples, collections, etc.**
+    -   Estimated count of each type of output.
+-   **Size of each file, sample, etc.**
+    -   File sizes (e.g., MB, GB, TB) for digital outputs.
+    -   Physical dimensions or quantities for physical samples.
+        -   e.g.:
+            -   [Sosik](https://drive.google.com/file/d/1-kTwz8I46snB0tfNk4U8bk8suVjF8xjG/view?usp=drive_link) LTER
+                -   By mid-year 6 of our project, our IM team stores \~60 TB of data (\~55 on premises and \~5 cloud). For WHOI’s institutional research data storage (RDS) on premises, we have \>40 TB to share within WHOI a subset of our towed plankton imaging data, 12 TB for a subset of our coupled physical-biological model output, and 1 TB for (low-volume) data products including those served by our web-based REST API. However, additional storage is required for plankton imagery (e.g., PI Sosik’s network attached storage serving \~10 TB publicly available IFCB data), acoustic data collected by vessels and Stingray towed vehicle, and physical and coupled biological-physical model output; these and some other high-volume data types (e.g., high throughput sequencing data) are necessarily managed by PIs.
 
 ## Metadata Critical for Data Interpretation and Reuse
 
-- **Sensor metadata**
-  - Information about instruments or sensors used to collect data.
-- **Sampling effort metadata**
-  - Details about sampling methods, locations, and conditions.
\ No newline at end of file
+-   **Sensor metadata**
+    -   Information about instruments or sensors used to collect data.
+        -   e.g.:
+            -   BCO–DMO: [Church](https://drive.google.com/file/d/1lFfmFJ0FRqvj4HQU6FX-QFne-2XYPQ6y/view?usp=share_link)
+                -   All underway optical data including imaging flow cytometry will be time-synchronized with the ship’s GPS and thermosalinograph. At sea all data will be visualized in real time to evaluate data quality and instrument stability; data will be stored on a customized raspberry-PI based data logger and backed up onto a separate hard drive. Post-cruise, all continuous optical data will be merged to 1-min averages and submitted to BCO-DMO; Imaging flow cytometry data are sampled at \~20 min intervals; a composite cruise file of all imaged particles and their individual morphometrics and optical properties will be generated and submitted to BCO-DMO.
+-   **Sampling effort metadata**
+    -   Details about sampling methods, locations, and conditions
+
+        -   e.g.:
+
+            -   BCO-DMO: [Reitzel](https://drive.google.com/file/d/19I3y-pgxbPr-T7yITp5LMhfS7gT4TqOm/view?usp=share_link) - Sequence data will be annotated with essential information for each sample, which will include description of the sample (e.g., location of origin for population, date), method for library generation, and the sequencing method. These data tags for description will be included with data submitted to SRA and BCO-DMO. Nucleic acids extracted from collected animals will be labeled with precise site of origin (latitude, longitude), date of collection, and species and archived in the Reitzel and Burt laboratories. Field temperature data will be stored in flat ASCII files, which can be read easily by different software packages. Field data will include date, time, latitude, longitude, and temperature, as appropriate.
diff --git a/sections/pids.qmd b/sections/pids.qmd
index b3ad9e3..9141acc 100644
--- a/sections/pids.qmd
+++ b/sections/pids.qmd
@@ -3,13 +3,41 @@ title: "Persistent Identifiers (PIDs)"
 ---
 
 ## Research Outputs
-- Use of PIDs (e.g., DOI, Handle, ARK) to uniquely identify outputs.
+
+-   Use of PIDs (e.g., DOI, Handle, ARK) to uniquely identify outputs.
 
 ## Formats and Standards
-- PIDs for metadata schemas and standards.
+
+-   PIDs for metadata schemas and standards.
 
 ## Access
-- PIDs for access protocols and repositories.
+
+-   PIDs for access protocols and repositories.
 
 ## Data Management
-- PIDs for datasets and related documentation.
\ No newline at end of file
+
+-   PIDs for datasets and related documentation.
+
+Example PIDs:
+
+-   [ORCID](https://orcid.org) - person PIDs
+
+-   [ROR](https://ror.org) - research organization PIDs
+
+-   [Re3data](https://www.re3data.org) - specifically PIDs for data repositories
+
+-   Funding Award Numbers
+
+-   [RAID](https://raid.org) - project meta-PID
+
+-   [RRID](https://www.rrids.org)
+
+-   [DataCite (DOIs)](https://datacite.org)
+
+::: callout-tip
+## Additional reading
+
+**[Ten simple rules for getting and giving credit for data](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010476)**
+
+-   Wood-Charlson EM, Crockett Z, Erdmann C, Arkin AP, Robinson CB (2022) Ten simple rules for getting and giving credit for data. PLOS Computational Biology 18(9): e1010476. <https://doi.org/10.1371/journal.pcbi.1010476>
+:::
diff --git a/sections/roles_responsibilities.qmd b/sections/roles_responsibilities.qmd
index d3b11db..789ba6e 100644
--- a/sections/roles_responsibilities.qmd
+++ b/sections/roles_responsibilities.qmd
@@ -3,16 +3,48 @@ title: "Roles and Responsibilities"
 ---
 
 ## Data Manager
-- Oversees data management practices.
-- Ensures compliance with the Data Management Plan (DMP).
+
+-   Oversees data management practices.
+
+-   Ensures compliance with the Data Management Plan (DMP).
+
+    -   e.g.:
+
+        -   [Mullineaux #2453](https://drive.google.com/file/d/1-N-bHKeJbC1QTouZVT5Ae2MMSAG9CEYA/view?usp=share_link)
+
+            -   Observations at seafloor: All PIs
+
+            -   Imagery at seafloor - PI3 and PI4
+
+            -   Physical sample cataloging:
+
+                -   PI1 will obtain IGSNs for rock samples; PI2 will provide unique
+
+            -   Animal specimen identifiers:
+
+                -   Each PI will catalog his/her respective subsamples associated to identifier, when applicable.
+
+            -   Data for animals - PI-3 and PI-4
+
+            -   Data for microbes - PI-1 and PI-2
+
+            -   Data for minerals - PI-3
+
+            -   Derived data from integrating: All PIs
 
 ## Point of Contact for the DMP
-- Primary individual responsible for DMP updates and communication.
-- Ensures the DMP is followed by the research team.
 
-## Contractor/Consultant/Third Party Contact Information
-- Details of external parties involved in data management.
+-   Primary individual responsible for DMP updates and communication.
+
+-   Ensures the DMP is followed by the research team.
+
+    -   e.g: [Mullineaux #2453](https://drive.google.com/file/d/1-N-bHKeJbC1QTouZVT5Ae2MMSAG9CEYA/view?usp=share_link):
+
+        -   Lead PI will ensure compliance to this data management plan.
+
+-   Details of external parties involved in data management.
 
 ## Plan for Personnel Turnover/Transfer
-- Procedures for transferring responsibilities in case of personnel changes.
-- Documentation of roles and access permissions.
\ No newline at end of file
+
+-   Procedures for transferring responsibilities in case of personnel changes.
+-   Documentation of roles and access permissions.
diff --git a/sections/standardization.qmd b/sections/standardization.qmd
index 7b7b403..6763186 100644
--- a/sections/standardization.qmd
+++ b/sections/standardization.qmd
@@ -5,13 +5,34 @@ title: "Standardization of Data and Metadata"
 ## How Will It Be Standardized?
 
 ### Data / Metadata Formats
-- Use of widely accepted formats (e.g., CSV, JSON, HDF5 for data; XML, JSON-LD for metadata).
-- Consistent naming conventions and file structures.
+
+-   Use of widely accepted formats (e.g., CSV, JSON, HDF5 for data; XML, JSON-LD for metadata).
+
+    -   e.g.:
+
+        -   BCO-DMO [Mullineaux #2453](https://drive.google.com/file/d/1-N-bHKeJbC1QTouZVT5Ae2MMSAG9CEYA/view?usp=share_link)
+
+            -   Field observation data will be stored in flat ASCII files, which can be read easily by different software packages. Observational and experimental data from processed samples will be stored mainly as spreadsheets. Imagery from the seafloor will be stored in original resolution (this will be the biggest data volume in this project). Metadata will be prepared in accordance with BCO-DMO conventions (i.e. using the BCO-DMO metadata forms) and will include detailed descriptions of collection and analysis procedures.
+
+-   Consistent naming conventions and file structures.
 
 ### Standards
-- Adherence to domain-specific standards (e.g., Darwin Core for biodiversity data, DICOM for medical imaging).
-- Compliance with FAIR principles (Findable, Accessible, Interoperable, Reusable).
+
+-   Adherence to domain-specific standards (e.g., Darwin Core for biodiversity data, DICOM for medical imaging).
+    -   e.g.:
+        -   BCO-DMO: [Mullineaux #2453](https://drive.google.com/file/d/1-N-bHKeJbC1QTouZVT5Ae2MMSAG9CEYA/view?usp=share_link)
+            -   Specifically for animals: We will utilize the World Register of Marine Species (WoRMS) taxonomic classification. We will standardize to Darwin Core format to provide occurrence data to OBIS and GBIF. Specifically for microbes: Genetic sequence data will be prepared in accordance with the minimum information about a marker gene sequence (MIMARKS) and about a metagenome sequence (MIMS) developed by the Genomic Standards Consortium, with quality control screening of raw reads from 16S/18S rRNA sequencing and raw metagenomic sequences. Specifically for minerals: Rock samples will be assigned International Geo Sample Numbers (IGSN) through SESAR (System for Earth Sample Registration)
+-   Compliance with FAIR principles (Findable, Accessible, Interoperable, Reusable).
+    -   e.g.:
+        -   LTER [Sosik](https://drive.google.com/file/d/1-kTwz8I46snB0tfNk4U8bk8suVjF8xjG/view?usp=drive_link)
+            -   To contribute FAIR (Findable, Accessible, Interoperable, Reusable) data products to DataONE and other community repositories, our IM team uses non-proprietary data formats, standardizes metadata, and promotes the use of controlled vocabularies.
 
 ### QA/QC Methods
-- Implementation of quality assurance and quality control processes.
-- Regular audits and validation checks to ensure data integrity.
\ No newline at end of file
+
+-   Implementation of quality assurance and quality control processes.
+-   Regular audits and validation checks to ensure data integrity.
+    -   e.g.:
+        -   BCO-DMO: [Saito](https://drive.google.com/file/d/1xJ8EiH436Fr95XrIEsvyYHoQv0mErSwB/view?usp=share_link)
+            -   Quality flags will be assigned according to the ODS IODE Quality Flag scheme (IOC Manuals and Guides, 54, volume 3; \[http://www.iode.org/mg54\\\_3\](http://www.iode.org/mg54_3) ).
+        -   IOOS: [SCCOOS](https://sccoos.org/)
+            -   For sources that do not provide quality flags, the SCCOOS DMAC Sub-System runs QARTOD tests after ingesting observation data. Tests are run using the open-source [ioos\\\_qc library](https://github.com/ioos/ioos\_qc), which implements a suite of QARTOD tests as well as other quality control algorithms. The quality test code and test thresholds are documented and publicly available through the CalOOS Data Portal. Links to the ioos\\\_qc methods used are available both within data charts and on sensor pages within the CalOOS Data Portal. Thresholds used for each test are also viewable on sensor pages and users are linked to the test code in GitHub.


Reviews:
user: login: copilot-pull-request-reviewer[bot]
body: ## Pull Request Overview

This PR introduces a first draft of detailed examples and guidance across multiple documentation sections, enhancing clarity around data standardization, roles, PIDs, outputs, and access.

- Expanded each section with concrete “e.g.” case studies and repository links  
- Added callout tips and supplementary reading pointers  
- Populated roles and responsibilities, persistent identifiers, and access timelines with actionable details

### Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 5 comments.

<details>
<summary>Show a summary per file</summary>

| File                                 | Description                                                              |
| ------------------------------------ | ------------------------------------------------------------------------ |
| sections/standardization.qmd         | Added example implementations for formats, domain standards, and QA/QC   |
| sections/roles_responsibilities.qmd  | Expanded Data Manager duties with PI assignments and contact info        |
| sections/pids.qmd                    | Listed common PIDs and included an additional reading callout            |
| sections/outputs.qmd                 | Provided sample, model, and document output examples with details        |
| sections/access.qmd                  | Clarified archival repositories, licensing, and access restrictions      |
</details>



<details>
<summary>Comments suppressed due to low confidence (2)</summary>

**sections/standardization.qmd:36**
* The markdown link contains extra backslashes which may prevent correct rendering. Use a single escape for the underscore (e.g., `mg54_3`) or remove unnecessary backslashes.
```
-   Quality flags will be assigned according to the ODS IODE Quality Flag scheme (IOC Manuals and Guides, 54, volume 3; \[http://www.iode.org/mg54\\_3\](http://www.iode.org/mg54_3) ).
```
**sections/access.qmd:19**
* There’s a trailing backslash at the end of this line which may break the list. Remove the backslash.
```
-        -   BCO-DMO: [Saito](https://drive.google.com/file/d/1xJ8EiH436Fr95XrIEsvyYHoQv0mErSwB/view?usp=share_link)\
```
</details>


state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-05-22T21:23:05Z

Review comments:
diff_hunk: @@ -3,16 +3,48 @@ title: "Roles and Responsibilities"
 ---
 
 ## Data Manager
-- Oversees data management practices.
-- Ensures compliance with the Data Management Plan (DMP).
+
+-   Oversees data management practices.
+
+-   Ensures compliance with the Data Management Plan (DMP).
+
+    -   e.g.:
+
+        -   [Mullineaux #2453](https://drive.google.com/file/d/1-N-bHKeJbC1QTouZVT5Ae2MMSAG9CEYA/view?usp=share_link)
+
+            -   Observations at seafloor: All PIs
+
+            -   Imagery at seafloor - PI3 and PI4
+
+            -   Physical sample cataloging:
+
+                -   PI1will obtain IGSNs for rock samples; PI2 will provide unique
path: sections/roles_responsibilities.qmd
user: login: Copilot
body: There is a missing space between `PI1` and `will`. It should read `PI1 will obtain IGSNs…`.
```suggestion
                -   PI1 will obtain IGSNs for rock samples; PI2 will provide unique
```
created_at: 2025-05-22T21:23:04Z
author_association: CONTRIBUTOR
diff_hunk: @@ -3,16 +3,48 @@ title: "Roles and Responsibilities"
 ---
 
 ## Data Manager
-- Oversees data management practices.
-- Ensures compliance with the Data Management Plan (DMP).
+
+-   Oversees data management practices.
+
+-   Ensures compliance with the Data Management Plan (DMP).
+
+    -   e.g.:
+
+        -   [Mullineaux #2453](https://drive.google.com/file/d/1-N-bHKeJbC1QTouZVT5Ae2MMSAG9CEYA/view?usp=share_link)
+
+            -   Observations at seafloor: All PIs
+
+            -   Imagery at seafloor - PI3 and PI4
+
+            -   Physical sample cataloging:
+
+                -   PI1will obtain IGSNs for rock samples; PI2 will provide unique
+
+            -   Animal specimen identifiers:
+
+                -   Each PI will catalog his/her respective subsamples associated to identifier, when applicable.
+
+            -   Data for animals - PI-3 and PI-4
+
+            -   Data for microbes - PI-1 and PI-2
+
+            -   Data for minerals - PI-3
+
+            -   Derived data from integrating: All PIs
 
 ## Point of Contact for the DMP
-- Primary individual responsible for DMP updates and communication.
-- Ensures the DMP is followed by the research team.
 
-## Contractor/Consultant/Third Party Contact Information
-- Details of external parties involved in data management.
+-   Primary individual responsible for DMP updates and communication.
+
+-   Ensures the DMP is followed by the research team.
+
+    -   e.g: [Mullineaux #2453](https://drive.google.com/file/d/1-N-bHKeJbC1QTouZVT5Ae2MMSAG9CEYA/view?usp=share_link):
+
+        -   Lead PI will ensure compliance to this data management plan. \## Contractor/Consultant/Third Party Contact Information
path: sections/roles_responsibilities.qmd
user: login: Copilot
body: A stray `\## Contractor/Consultant/Third Party Contact Information` appears inside this bullet. Remove or relocate this Markdown header so it doesn’t break the list.
```suggestion
        -   Lead PI will ensure compliance to this data management plan.
```
created_at: 2025-05-22T21:23:05Z
author_association: CONTRIBUTOR
diff_hunk: @@ -3,13 +3,41 @@ title: "Persistent Identifiers (PIDs)"
 ---
 
 ## Research Outputs
-- Use of PIDs (e.g., DOI, Handle, ARK) to uniquely identify outputs.
+
+-   Use of PIDs (e.g., DOI, Handle, ARK) to uniquely identify outputs.
 
 ## Formats and Standards
-- PIDs for metadata schemas and standards.
+
+-   PIDs for metadata schemas and standards.
 
 ## Access
-- PIDs for access protocols and repositories.
+
+-   PIDs for access protocols and repositories.
 
 ## Data Management
-- PIDs for datasets and related documentation.
\ No newline at end of file
+
+-   PIDs for datasets and related documentation.
+
+Example PIDs:
+
+-   [ORCID](https://orcid.org) - person PIDs
+
+-   [ROR](https://ror.org)- research organization PIDs
path: sections/pids.qmd
user: login: Copilot
body: Add a space after the closing parenthesis so it reads `[ROR](https://ror.org) - research organization PIDs` for consistency.
```suggestion
-   [ROR](https://ror.org) - research organization PIDs
```
created_at: 2025-05-22T21:23:05Z
author_association: CONTRIBUTOR
diff_hunk: @@ -5,13 +5,40 @@ title: "Access to Research Outputs"
 ## What Does Access Look Like?
 
 ### Access
-- **Sharing**
-  - Mechanisms for sharing outputs (e.g., repositories, cloud storage).
-- **Provisions/Protection**
-  - Measures to protect sensitive or confidential data (e.g., encryption, access controls).
-- **Timeline for Availability/Access**
-  - When will products be shared or published (e.g., immediately, after embargo period).
-- **License**
-  - Licensing terms (e.g., Creative Commons, MIT License).
-- **Restrictions / Confidentiality / Proprietary Business Info**
-  - Any limitations on access due to confidentiality or proprietary concerns.
\ No newline at end of file
+
+-   BCO-DMO: Church
path: sections/access.qmd
user: login: Copilot
body: The entry `BCO-DMO: Church` lacks a hyperlink; consider adding the relevant URL to match other examples.
```suggestion
-   BCO-DMO: [Church](https://drive.google.com/file/d/1lFfmFJ0FRqvj4HQU6FX-QFne-2XYPQ6y/view?usp=share_link)
```
created_at: 2025-05-22T21:23:05Z
author_association: CONTRIBUTOR
diff_hunk: @@ -5,13 +5,40 @@ title: "Access to Research Outputs"
 ## What Does Access Look Like?
 
 ### Access
-- **Sharing**
-  - Mechanisms for sharing outputs (e.g., repositories, cloud storage).
-- **Provisions/Protection**
-  - Measures to protect sensitive or confidential data (e.g., encryption, access controls).
-- **Timeline for Availability/Access**
-  - When will products be shared or published (e.g., immediately, after embargo period).
-- **License**
-  - Licensing terms (e.g., Creative Commons, MIT License).
-- **Restrictions / Confidentiality / Proprietary Business Info**
-  - Any limitations on access due to confidentiality or proprietary concerns.
\ No newline at end of file
+
+-   BCO-DMO: Church
+    -   To increase accessibility to project data and the dissemination of our research findings—particularly among scientists from developing countries—we will make every effort to publish our results as open-access articles or within open-access journals.
+-   **Sharing**
+    -   Mechanisms for sharing outputs (e.g., repositories, cloud storage).
+
+**Archive(s)**\`
path: sections/access.qmd
user: login: Copilot
body: There’s a stray backtick after `**Archive(s)**`. Remove the backtick to prevent Markdown rendering issues.
```suggestion
**Archive(s)**
```
created_at: 2025-05-22T21:23:05Z
author_association: CONTRIBUTOR

PR comments:
user: login: jibarozzo
created_at: 2025-05-22T21:49:27Z
body: @elishawc @reblake @cberys Take a look and let me know before merging. The website should be live
author_association: COLLABORATOR
user: login: jibarozzo
created_at: 2025-05-28T19:04:34Z
body: Closes #8 
author_association: COLLABORATOR