01-intro.Rmd

```{r, include = FALSE}
ottrpal::set_knitr_image_path()
```

# (PART\*) Introduction {-}

# Video Introduction

Check out the video below. It provides a summary of the introduction to this course.

<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/XQkmYWhpQ2s" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

# Why This New DMS Policy

First, we will discuss the motivations behind the new data management and sharing policy. This policy is applicable for (most) grant proposals submitted to the NIH as of January 25, 2023.

```{r, echo=FALSE, fig.alt='We are on the first step of the pathway- understanding the motivations of the policy.', out.width = '80%', fig.align = 'center'}
ottrpal::include_slide("https://docs.google.com/presentation/d/1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak/edit#slide=id.g16b04bd80e5_1_103")
```

Why is the NIH doing this? There are several reasons why sharing data can be beneficial to the scientific community.

- **Transparency** - Sharing data provides more clarity about how studies are performed. Many scientists also believe in an ethical responsibility to study participants [@bauchner_citation_2016].
- **Reproducibility and rigor** - Having the data accessible allows others to try to reproduce study findings. This can further enable studies that may replicate or validate the initial findings with different data. 
- **Multi-modal work** - Scientists can perform studies using multiple types of data when this data is easily accessible [@thessen_citation_2021]. 
- **Efficiency and cost effectiveness** - Some data are especially difficult or expensive to produce. Resources that might have been used to regenerate the data can be used elsewhere.
- **Researcher Inclusion** - Data generation can be especially difficult for those at institutes with fewer resources. Publicly available data can therefore be used by these researchers to better enable their participation. 
- **Impact** - Papers that share their data in repositories appear to be cited more often based on the study by @colavizza_citation_2020 .
- **Collaboration opportunities** - Available data can inspire other researchers to explore new directions or extend upon previous work. These researchers might reach out to collaborate.
- **Data citations** - Due to the importance of data generation and sharing to the NIH, data will now be seen as research product that demonstrates a contribution to the scientific community.

```{r, echo=FALSE, fig.alt='Scientist examines the result of a plate assay, which is a test that allows scientists to count how many flu virus particles (virions) are in a mixture', out.width = '80%', fig.align = 'center'}
ottrpal::include_slide("https://docs.google.com/presentation/d/1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak/edit#slide=id.g29f8bf18fa1_80_0")
```

## Key terms 

<div class = "dictionary_long">

**Data Management**

The work involved with validating, organizing, protecting, maintaining, and processing scientific data to ensure the accessibility, reliability, and quality of the scientific data for use in research. All research data should be actively managed.

**Data Sharing**

The act of making scientific data available for use by others (e.g., the larger research community, institutions, the broader public), for example, via an established repository. Some data carry limitations on how data sharing can be done and some meet criteria that make them exempt from data sharing.   

**Metadata**

Data that provide additional information intended to make scientific data interpretable and reusable.  Metadata can include features like dates, independent sample and variable construction and description, methodology, data provenance, data transformations, any intermediate or descriptive observational variables.

**Data Management and Sharing Plan**

A plan describing an approach to data management, preservation, and sharing of scientific data and accompanying metadata.

</div>

# Discussion on Benefits of Data Sharing

## Discussion

Please see below for a self-directed reflection.

<div class = "reflection">

Writing grants takes time and can be a lot of work. You might be thinking that adding an additional plan to your proposal is just more paperwork. If applicable, consider some ways that sharing your data and managing it effectively might benefit you in the long term.

</div>

# Video Your Considerations

Check out the video below. It provides a summary of the personal considerations to keep in mind as you are developing your proposal and a DMS Plan.

<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/TZbA_IloRdQ" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

# How Will This Policy Affect Me

> You can refer to the [NIH overview](https://sharing.nih.gov/data-management-and-sharing-policy/about-data-management-and-sharing-policy/research-covered-under-the-data-management-sharing-policy#after){target="_blank"} of which research will be covered by this new policy.  

```{r, echo=FALSE, fig.alt='We are on the second step of the pathway - personal considerations of the policy.', out.width = '80%', fig.align = 'center'}
ottrpal::include_slide("https://docs.google.com/presentation/d/1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak/edit#slide=id.g16b04bd80e5_4_12")
```

The major requirement of the policy is that all grant proposals (submitted after January 25th, 2023) for mechanisms that require compliance, **must include a plan** for how they will manage and share their data. 

For certain grant mechanisms for projects that do not generate data, you will not need to submit a DMS plan. For certain types of data, sharing is not possible, and a justification will be required instead. 

The following text will discuss several key questions:

- [**Is my research exempt from the policy?**](#no-sharing)
- [**Does my research generate scientific data?**](#scientific-data)
- [**Do grant renewals require compliance with the policy?**](#grant-renewals)
- [**How will the policy impact the review process?**](#review-process)
- [**When do I need to share my data?**](#sharing-timeline) 
- [**When should I not share data?**](#when-to-not-share) 

To determine if your research requires compliance with other policies that may influence how you share your data, take this [quiz](https://sharing.nih.gov/other-sharing-policies/which-policies-apply-to-my-research).

<div class = "ethics"> 
In addition to these questions, there are ethical considerations that you may want to think about. See the [ethics section](#ethics) of the appendix for more information. 
</div>

## Grant Mechanisms {#no-sharing}

<div class = "question">
What grant mechanisms require compliance with the DMS policy? 
</div>

The DMS Policy applies to all research that generates [scientific data](#scientific-data) (regardless of the funding level), including:

- Research Projects
- Some Career Development Awards (K)
- Small Business SBIR/STTR 
- Research Centers

The DMS Policy does not apply to research and other activities that do not generate scientific data, including:

- Training (T)
- Fellowships (F)
- Construction (C06)
- Conference Grants (R13)
- Resource (G)
- Research-Related Infrastructure Programs (e.g., S06)

You can look up your NIH Activity Code [here](https://sharing.nih.gov/node/112){target="_blank"} to see if you are required to submit a DMS Plan.

For example, I am interested in applying to a **R03** award.

```{r, echo=FALSE, fig.alt='I can find the R03 activity code in the request for applications.', out.width = '100%', fig.align = 'center'}
ottrpal::include_slide("https://docs.google.com/presentation/d/1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak/edit#slide=id.g1740f401082_0_56")
```

According to the table, a **DMS Plan is required** for this particular award.

```{r, echo=FALSE, fig.alt='I can determine if a DMS plan is required using the table here: https://sharing.nih.gov/sites/default/files/List-of-Activity-Codes-Applicable-to-DMS-Policy.pdf', out.width = '100%', fig.align = 'center'}
ottrpal::include_slide("https://docs.google.com/presentation/d/1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak/edit#slide=id.g1740f401082_0_64")
```

### Data-generating Research {#scientific-data}

<div class = "question"> 
Does my research generate scientific data?
</div>

The NIH Data Management and Sharing (DMS) Policy applies to **all NIH-supported research generating scientific data**. But what is "scientific data"?

```{r, echo=FALSE, fig.alt='Scientific data should be shared under the new DMS policy, but there are many scientific products that are not considered scientific data.', out.width = '70%', fig.align = 'center'}
ottrpal::include_slide("https://docs.google.com/presentation/d/1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak/edit#slide=id.g1740f401082_0_0")
```

#### Scientific data

Scientific data are the “recorded factual material of sufficient quality to validate and replicate research findings, regardless of whether the data are used to support scholarly publications”. This can include any of the following if they are applicable to your study:

- unpublished results
- null results
- results used to publish papers

#### Not Scientific Data

You are not expected to share:

- lab notebooks
- preliminary analyses
- case report forms
- drafts of scientific papers
- plans for future research
- peer reviews
- communications with colleagues
- physical objects (such as biospecimens)

<!-- <div class = "warning"> -->

<!-- You might be wondering if it is required to share raw data.  -->

<!-- The DMS Policy applies to **final research data**. This is data that is recorded factual material commonly accepted in the scientific community as necessary to **validate and replicate** research findings. For many scientific areas, final research data includes both raw data and analyses conducted on the data.  -->

<!-- For example, final research data for a clinical study would include a dataset that was used in the published study, but not the clinical documents (for example, medical records) that the dataset was derived from.  -->

<!-- For genomic data, raw sequence reads are generally not expected unless a de novo sequencing experiment was performed. Sequence alignments however are expected to be shared. For more information about genomic data sharing, see the details of the policy [here](https://sharing.nih.gov/genomic-data-sharing-policy/submitting-genomic-data/data-submission-and-release-expectations){target="_blank"}. -->

<!-- </div> -->

## Grant Renewals {#grant-renewals}

<div class = "question">
Do grant renewals need to comply with the policy?
</div>

If you submit a grant renewal application for any of the grants mechanisms that require compliance after January 25th, 2023, then your renewal will need to include a DMS Plan even if the grant was originally funded before January 25th, 2023. 

## Impact on Reviews {#review-process}

<div class = "question">
How will this influence the grant review process?
</div>

For most proposals -- those where data sharing is not part of the Funding Opportunity Announcement -- the following will happen during the review process:

- Reviewers will not have access to your DMS plan.
- Reviewers will however see your budget which will include some descriptions of how money will be spent to manage and share data.
- Thus, the DMS plan should not influence your grant score. 
- After a grant receives a fundable score, a Program Officer will review the DMS plan and will work with the PI to address any concerns. Changes based on this process can be made during the [Just-in-Time](https://grants.nih.gov/grants/policy/nihgps/HTML5/section_2/2.5.1_just-in-time_procedures.htm) procedures.

For proposals where data sharing is specified as part of the Funding Opportunity Announcement the following will happen during the review process: 

 - The reviewers will have access to the plan and it may be part of the review criteria.
 - Program staff will also review the DMS plan.
 
## Sharing Timeline {#sharing-timeline} 

<div class = "question">
When does the data need to be shared by?
</div>

Data should be made available **no later than publication or end of the award**. This means that data underlying findings that are not published in peer-reviewed journals should be made available by the end of the award.

### No-cost Extensions

Scientific data should be made accessible as soon as possible, and no later than the time of an associated publication or the end of the performance period of the extramural award that generated the data. If a no cost extension is granted for an extramural award, scientific data should be made accessible no later than the time of an associated publication, or the end of the no cost extension, whichever comes first.

## When to Not Share Data {#when-to-not-share}

<div class = "question">
Is it possible to not share data?
</div>

There are legitimate reasons you might not share your data. Data might not be shareable due to ethical, legal, or technical concerns. **You will still need to submit a DMS Plan even if you plan to withhold data sharing**. You must explain your reasoning in your DMS Plan.

```{r, echo=FALSE, fig.alt='Researchers with scientific data must justify why they will not share data with an appropriate exception.', out.width = '70%', fig.align = 'center'}
ottrpal::include_slide("https://docs.google.com/presentation/d/1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak/edit#slide=id.g1740f401082_0_36")
```

Justifiable ethical, legal, and technical factors for limiting sharing of data include: 

- Informed consent will not permit or will limit the scope or extent of sharing and future research use

- Existing consent (e.g., for previously collected biospecimens) prohibits sharing or limits the scope or extent of sharing and future research use

- Privacy or safety of research participants would be compromised or place them at greater risk of re-identification or suffering harm, and protective measures such as de-identification and [Certificates of Confidentiality](https://grants.nih.gov/policy/humansubjects/coc.htm) would be insufficient. _At Fred Hutch, you should get in contact with the [Institutional Review Office](https://centernet.fredhutch.org/cn/u/iro.html){target="_blank"} if you have questions about compliance of your research._

- Explicit federal, state, local, or Tribal law, regulation, or policy prohibits disclosure 

- Restrictions are imposed by existing or anticipated agreements with other parties 
- Datasets cannot practically be digitized with reasonable efforts

<div class = "ethics"> 
For additional information about potential ethical considerations, including if data is of sufficient quality to be shared, see the [ethics section](#ethics) of the appendix.
</div>

<div class = "click_to_expand_block">

<details> <summary> What if my data are proprietary? (click for more information) </summary>

**Considerations for Proprietary Data (directly from the NIH)**

NIH understands that some scientific data generated with NIH funds may be proprietary. Under the Small Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) Program Policy Directive, effective May 2, 2019, SBIR and STTR awardees may withhold applicable data for 20 years after the award date, as stipulated in the specific SBIR/STTR funding agreement and consistent with achieving program goals. SBIR and STTR awardees are expected to submit a Data Management & Sharing Plan per DMS Policy requirements.

Issues related to proprietary data also can arise when co-funding is provided by the private sector (for example, the pharmaceutical or biotechnology industries). NIH recognizes that the extent of data sharing may be limited by restrictions imposed by licensing limitations attached to materials needed to conduct the research. Applicants should discuss projects with proposed collaborators early to avoid agreements that prohibit or unnecessarily restrict data sharing. NIH staff will evaluate the justifications of investigators who believe that they are unable to share data.

For questions or concerns about data sharing expectations for proprietary data, please contact the [Office of Science Policy](mailto:SciencePolicy@od.nih.gov). Small businesses may wish to contact the [NIH SEED Office](https://public.era.nih.gov/commons/public/servicedesk/initseed.era).

</details>

</div>

Some additional reasons to limit sharing:

- NIH respects Tribal sovereignty and supports responsible management/sharing of American Indian / Alaska Native participant data, which can include limiting sharing
- SBIR/STTR Program Policy Directive permits withholding data for 20 years, as stipulated in agreements and consistent with program goals 

The following are **NOT** good reasons to limit the sharing of your data: 

- Data are considered too small 
- Researchers anticipate data will not be widely used
- Data are not thought to have a suitable repository 
- You don't have the right personnel to manage data or share data
- You don't want to pay for data storage

# Video Introduction Wrap Up

Check out the video below. It concludes the introduction to this course.

<iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/9h6EvNDoKVo" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>