| lang | title |
|---|---|
en |
Data Management Plan |
Contact person
: - [Clara Qin]{.contact-name}
([[email protected]]{.contact-email}, [[]{.mini-orcid-icon-16}
0000-0002-9561-4704]{.contact-orcid})
University of California, Santa
Cruz
Based on : Common DSW Knowledge Model, 2.3.0 ([[dsw]{.organization-id}:[root]{.km-id}:[2.3.0]{.version}]{.package-id})
Created by : [Amy Schuler]{.contact-name} ([[email protected]]{.contact-email})
Generated on : 22 Mar 2021
Data Management Plan created in Data Stewardship Wizard «ds-wizard.org»
We will be working on the following projects and for those are the data and work described in this DMP.
::: {.project}
Acronym : Cary test
Start date : 03/01/2021
End date : 05/01/2021
Funding
: - National Science Foundation: n/a (planned)
::: {.section .abstract} Basically this is a test drive of DSW for the Cary Institute. Right now we have a "home grown" data management plan template that many researchers use for (mainly) US federal grants. Most researchers create their own based on that template, and perhaps a couple have used DMPTool. I like the idea that DSWizard creates a machine readable data management plan. ::: :::
::: {.project}
Acronym : Clara thesis
Start date : 04/01/2014
End date : 09/13/2019
Funding
: - Stanford Undergraduate Advising and Research (UAR) Major Grant: grant number not yet given (granted) - A.W. Mellon Foundation / Stanford University Grant for Student Research at Jasper Ridge Biological Preserve: grant number not yet given (granted)
::: {.section .abstract} Soil microbial communities regulate and respond to key biogeochemical cycles and influence plant community patterns. However, microbial communities also respond to disturbance events, motivating an assessment of the relative roles of decadal multi�factor global change, disturbance and plant community structure on microbial community responses.
We used high�throughput amplicon sequencing to characterize the diversity and composition of bacterial and fungal communities in bulk soil (0--7 cm) collected in 2014 from the Jasper Ridge Global Change Experiment, a full�factorial field experiment in which ambient and elevated levels of nitrogen deposition (+7 g N m−2 yr−1 calcium nitrate), CO2 concentration (+275 ppm), temperature (+1--2°C) and precipitation (+50% volume with +3 weeks duration) were applied to a California annual grassland from 1998 to 2014. We used linear mixed�effects modelling to test for the effects of global change on microbial diversity (observed richness, Shannon index). We also used generalized dissimilarity modelling (GDM) to study controls on compositional dissimilarity in fungal and bacterial communities.
Bacterial community composition was best explained by exposure to fires in 2003 and 2011, whereas fungal community composition was best explained by plant community composition. The richness of fungi increased under elevated nitrogen deposition; bacterial diversity metrics decreased under warmer temperatures. Interactions between global change factors were statistically insignificant or weak.
Synthesis. Our results indicate that even on decadal time�scales, the effects of fire history and plant community composition on bacterial and fungal community composition, respectively, outweigh the effects of multi�factor global change. Furthermore, global change factors have mostly additive effects on microbial diversity patterns. Our results show that highly variable mediators such as fire history and plant community composition limit the generalizability of soil microbial responses to long�term global change. ::: ::: :::
::: {#dmp-content} ::: {#sec-data-summary .section .dmp-section}
- Data Summary
::: {#q-data-summary .question} ::: {.answer}
The non-equipment datasets are:
- Plant biomass [--]{.separator} Plant biomass (g m-2 y-1) by species in each quadrant of each plot in the Jasper Ridge Global Change experiment in 2014.
We will use the following reference datasets:
-
Cary Institute data repository. Supplementary File 5 - Fischhoff et al. 2021. (https://doi.org/10.25390/caryinstitute.13721254.v1)
We will use version "v1" of this dataset. If a new version becomes available during the project, new analyses will be done with the new version.
-
Data from: Fire history and plant community composition outweigh decadal multi�factor global change as drivers of microbial composition in an annual grassland (https://doi.org/10.5061/dryad.nf481q8)
We will be using the following data formats and types:
-
It is a standardized format. This is a suitable format for long-term archiving. We will have only a small amount of data stored in this format.
-
It is a standardized format. This is a suitable format for long-term archiving. We will have only a small amount of data stored in this format.
-
Biological Observation Matrix Ontology
It is a standardized format. This is a suitable format for long-term archiving. We expect to have 0.0088 GB of data in this format.
-
It is a standardized format. This is a suitable format for long-term archiving. We will have only a small amount of data stored in this format.
::: {#q-findable .question} ::: {.answer}
- https://datadryad.org/stash/dataset/doi:10.5061/dryad.nf481q8
(published)
There won't be different versions of this data over time.
We will be adding a reference to the published data to at least one data catalogue.
There are no 'Minimal Metadata About ...' (MIA...) standards for our experiments. However, we have a good idea of what metadata is needed to make it possible for others to read and interpret your data in the future.
We will use lab notebooks to make sure that there is good provenance of the data analysis. ::: :::
::: {#q-accessible .question} ::: {.answer} We will be working with the philosophy as open as possible for our data.
All of our data can become completely open immediately.
All data will be owned by the Principal Investigator.
For the reference and non-reference data sets that we reuse, conditions are as follows:
- Cary Institute data repository. Supplementary File 5 - Fischhoff et al. 2021. [--]{.separator} freely available with obligation to quote the source (e.g. CC-BY).
- Data from: Fire history and plant community composition outweigh decadal multi�factor global change as drivers of microbial composition in an annual grassland [--]{.separator} freely available with obligation to quote the source (e.g. CC-BY).
For our produced data, conditions are as follows:
- https://datadryad.org/stash/dataset/doi:10.5061/dryad.nf481q8
(published)
A user of this data can use it without any specific software. ::: :::
::: {#q-interoperable .question}
We will be using the following data formats and types:
-
It is a standardized format.
-
It is a standardized format.
-
Biological Observation Matrix Ontology
It is a standardized format.
-
It is a standardized format.
We will be using the following standards (encodings, terminologies, vocabularies, ontologies):
::: {#q-reusable .question} ::: {.answer} The metadata for our produced data will be kept as follows:
- https://datadryad.org/stash/dataset/doi:10.5061/dryad.nf481q8 (published) [--]{.separator} This data set will be kept available as long as technically possible.
As stated already in Section 2.2, all of our data can become completely open immediately.
We do not plan to be archiving data (using so-called cold storage) for long term preservation already during your project.
To validate the integrity of the results, the following will be done:
- We will run a subset of our jobs several times across the different compute infrastructures.
- We will be instrumenting the tools into pipelines and workflows using automated tools.
- We will use independently developed duplicate tools or workflows for critical steps to reduce or eliminate human errors.
- We will run part of the data set repeatedly to catch unexpected changes in results. ::: ::: :::
::: {#q-resource-allocation .question} ::: {.answer} FAIR is a central part of our data management; it is considered at every decision in our data management plan. We use the FAIR data process ourselves to make our use of the data as efficient as possible. Making our data FAIR is therefore not a cost that can be separated from the rest of the project.
None of the used repositories charge for their services.
We have a reserved budget for the time and effort it will take to prepare the data for publication.
Amy Schuler is responsible for implementing the DMP, and ensuring it is reviewed and revised.
Amy Schuler is responsible for reviewing, enhancing, cleaning, or standardizing metadata and the associated data submitted for storage, use and maintenance within a data centre or repository.
To execute the DMP, no additional specialist expertise is required.
We do not require any hardware or software in addition to what is usually available in the institute. ::: ::: :::
::: {#q-data-security .question} ::: {.answer} Project members can carry data with them on password-protected laptops. All data centers where project data is stored carry sufficient certifications. All project web services addressed via secure http (https://...). Project members have been instructed about both generic and specific risks to the project.
The possible impact to the project or organization if information is lost is small. The possible impact to the project or organization if information is leaked is small. The possible impact to the project or organization if information is vandalised is small.
We are not using any personal information. ::: ::: :::
::: {#q-ethical-aspects .question} ::: {.answer} For the data we produce, the ethical aspects are as followsS:
- https://datadryad.org/stash/dataset/doi:10.5061/dryad.nf481q8
- It does not contain personal data.
- It does not contain sensitive data.
We don't need any consent for collected data because those are not personal. ::: ::: :::
::: {#q-other-issues .question} ::: {.answer} We use the Data Stewardship Wizard with its Common DSW Knowledge Model (ID: [[dsw]{.organization-id}:[root]{.km-id}:[2.3.0]{.version}]{.package-id}) knowledge model to make our DMP. More specifically, we use the https://demo.ds-wizard.org DSW instance where the project has direct URL: https://demo.ds-wizard.org/projects/65bcd8d4-f7d0-4bbd-be2e-8cf4a2030c51. ::: ::: ::: :::