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Data Management Plan

DMP Template v2.0.1 (2015-01-01)

Please provide the following information, and submit to the NOAA DM Plan Repository.

Reference to Master DM Plan (if applicable)

As stated in Section IV, Requirement 1.3, DM Plans may be hierarchical. If this DM Plan inherits provisions from a higher-level DM Plan already submitted to the Repository, then this more-specific Plan only needs to provide information that differs from what was provided in the Master DM Plan.

URL of higher-level DM Plan (if any) as submitted to DM Plan Repository:
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1. General Description of Data to be Managed

1.1. Name of the Data, data collection Project, or data-producing Program:
Colony-level annotations using Structure-from-Motion models from sites surveyed across the Main Hawaiian Islands during the 2019 bleaching event
1.2. Summary description of the data:

Coral adult colony demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers. The data were collected by the NOAA Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) and [on Hawaii Island] in partnership with State of Hawaii Department of Land and Natural Resources (DLNR), Division of Aquatic Resources (DAR) during the 2019 bleaching event in the Main Hawaiian Islands.

The SfM surveys were conducted at fixed sites ranging in depth from 18-52'. Sites were photographed using underwater cameras for later processing using one of two SfM approaches: using a spiral swim pattern (where divers take images continuously in a circular pattern covering a circle of 12m diameter), or within a defined box where divers swam back and forth to cover a 10 x 10m area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for adult coral colony demographic metrics. Data was collected for each site within at least 10 randomly generated 0.49m2 quadrats. Additional quadrats were analyzed if necessary until the sample sizes per species of interest were met. If a species had very low density at a given site (< 10 patches recorded within the first 10 quadrats), it was dropped from further observations. However, the data for these patches remains in the raw data in order to provide presence/absence data. Therefore, data should be carefully analyzed to ensure accurate species density calculations are done. For each adult coral colony patch (>= 5cm in diameter), maximum diameter, ID (to lowest taxonomic level), morphology, bleaching extent (% of the patch with reduced pigmentation), and bleaching severity (1-3 from least to most severe) were recorded.

Taken From: Item Identification | Abstract
Notes: Only a maximum of 4000 characters will be included.
1.3. Is this a one-time data collection, or an ongoing series of measurements?
One-time data collection
Taken From: Extents / Time Frames | Time Frame Type
Notes: Data collection is considered ongoing if a time frame of type "Continuous" exists.
1.4. Actual or planned temporal coverage of the data:
2019-10-08 to 2019-11-13
Taken From: Extents | Time Frame - Start, Time Frame - End
Notes: All time frames from all extent groups are included.
1.5. Actual or planned geographic coverage of the data:
W: -158.0667, E: -155.830367, N: 21.47959, S: 19.42335

Main Hawaiian Islands (MHI), including Hawaii, Maui, Oahu, and Lanai.

Taken From: Extents | Geographic Area Bounds, Geographic Area Description
Notes: All geographic areas from all extent groups are included.
1.6. Type(s) of data:
(e.g., digital numeric data, imagery, photographs, video, audio, database, tabular data, etc.)
Table (digital)
1.7. Data collection method(s):
(e.g., satellite, airplane, unmanned aerial system, radar, weather station, moored buoy, research vessel, autonomous underwater vehicle, animal tagging, manual surveys, enforcement activities, numerical model, etc.)
No information found
1.8. If data are from a NOAA Observing System of Record, indicate name of system:
Always left blank due to field exemption
1.8.1. If data are from another observing system, please specify:
Always left blank due to field exemption

2. Point of Contact for this Data Management Plan (author or maintainer)

2.1. Name:
Brooke Olenski
Taken From: Support Roles (Metadata Contact) | Person
Notes: The name of the Person of the most recent Support Role of type "Metadata Contact" is used. The support role must be in effect.
2.2. Title:
Metadata Contact
Always listed as "Metadata Contact"
2.3. Affiliation or facility:
Taken From: Support Roles (Metadata Contact) | Organization
Notes: The name of the Organization of the most recent Support Role of type "Metadata Contact" is used. This field is required if applicable.
2.4. E-mail address:
brooke.olenski@noaa.gov
Notes: The email address is taken from the address listed for the Person assigned as the Metadata Contact in Support Roles.
2.5. Phone number:
No information found
Notes: The phone number is taken from the number listed for the Person assigned as the Metadata Contact in Support Roles. If the phone number is missing or incorrect, please contact your Librarian to update the Person record.

3. Responsible Party for Data Management

Program Managers, or their designee, shall be responsible for assuring the proper management of the data produced by their Program. Please indicate the responsible party below.

3.1. Name:
Morgan S Winston
Taken From: Support Roles (Data Steward) | Person
Notes: The name of the Person of the most recent Support Role of type "Data Steward" is used. The support role must be in effect.
3.2. Position Title:
Data Steward
Always listed as "Data Steward"

4. Resources

Programs must identify resources within their own budget for managing the data they produce.

4.1. Have resources for management of these data been identified?
Yes
4.2. Approximate percentage of the budget for these data devoted to data management (specify percentage or "unknown"):
Unknown

5. Data Lineage and Quality

NOAA has issued Information Quality Guidelines for ensuring and maximizing the quality, objectivity, utility, and integrity of information which it disseminates.

5.1. Processing workflow of the data from collection or acquisition to making it publicly accessible
(describe or provide URL of description):

Lineage Statement:
The benthic SfM survey methodology, employed by the NOAA Ecosystem Sciences Division (ESD), began in 2019. Benthic imagery is collected and generated into orthomosaic images using Agisoft Metashape software. Orthomosaics are scaled using Viscore software and imported into ArcGIS for annotation. Annotation of SfM orthomosaics collected during the 2019 bleaching event included coral species identification, maximum diameter measurement, morphology, bleaching extent and bleaching severity.

Process Steps:

  • SfM benthic surveys were collected at fixed sites during the 2019 bleaching event in the Main Hawaiiian Islands. A 10x10m or 12m diameter circular plot was visually established. 3-4 ground control points (GCPs) were placed within the plot for scale. White balance settings were adjusted in situ using a 15% gray card. JPEG images were collected using a Nikon SL2 digital camera in an underwater housing with a dome port. Images were collected at each site by swimming in a back-and-forth or circular motion 1m above the substrate capturing images continuously to achieve a 60-80% overlap. (Citation: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649)
  • Images for each site were evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. The Structure from Motion (SfM) approach produces an accurately scaled, two-dimensional (2D) orthomosaic model created from the overlapping imagery. Raw imagery was imported into Agisoft Metashape software where images were aligned and used to build 3D dense point clouds (DPCs) following parameters described by Rodriguez et al. (2021). DPCs were then imported into Viscore, a visualization software (Petrovic et al., 2014) where they were scaled and oriented using the GCP information. The ground sample distance (GSD) of the scaled DPC, which estimates the resolution per pixel by measuring the size of each pixel on the ground, ranged from 2-4 mm/pix. A geometrically accurate 2D projection of the DPC (orthoprojection) and scale grid are exported from Viscore and uploaded into ArcGIS Pro for annotation. (Citation: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649)
  • In ArcGIS Pro, each site was set up for annotation by scaling the orthoprojection using the scale grid exported from Viscore, manually digitizing quadrats as a shapefile, and setting up the attribute table in a geodatabase. To record and extract data from the orthoprojection image, each coral colony patch >= 5cm was annotated. Each patch was measured by digitizing a line across the maximum diameter of the colony. Coral ID (to lowest taxonomic level), morphology, and bleaching extent and severity were recorded. During annotation, the original JPEG imagery was viewed alongside the orthoprojection with the Agisoft or Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthoprojection (e.g. under ledges). Following Rodriguez et al. (2021), if a coral species per site was found less than 10 times in the first 10 quadrats, the species was subsequently not recorded in future analyzed quadrats. Therefore, this data should be carefully analyzed and species density should not be calculated for these species with low sample size. If a species had low density at a given site, 20-40 patches were annotated. If a species was abundant at the site, at least 40 patches were annotated. See Rodriguez et al. (2021) for further information. (Citation: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649)
  • Annotations created in ArcGIS Pro were quality controlled using a multi-stage process. Data were exported from ArcMap and quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, data in incorrect columns, bleaching >100%).
5.1.1. If data at different stages of the workflow, or products derived from these data, are subject to a separate data management plan, provide reference to other plan:
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5.2. Quality control procedures employed
(describe or provide URL of description):

Prior to generating the 3D dense point clouds and 2D orthroprojections , the JPEG imagery was evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. During annotation in ArcMap, the original JPEG imagery was viewed alongside the orthoprojection using Agisoft or Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthoprojection. Annotations created in ArcMap were quality controlled using a multi-stage process. Data were quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing segments, data in incorrect columns, % bleaching >100%).

6. Data Documentation

The EDMC Data Documentation Procedural Directive requires that NOAA data be well documented, specifies the use of ISO 19115 and related standards for documentation of new data, and provides links to resources and tools for metadata creation and validation.

6.1. Does metadata comply with EDMC Data Documentation directive?
No
Notes: All required DMP fields must be populated and valid to comply with the directive.
6.1.1. If metadata are non-existent or non-compliant, please explain:

Missing/invalid information:

  • 1.7. Data collection method(s)
Notes: Required DMP fields that are not populated or invalid are listed here.
6.2. Name of organization or facility providing metadata hosting:
NMFS Office of Science and Technology
Always listed as "NMFS Office of Science and Technology"
6.2.1. If service is needed for metadata hosting, please indicate:
Always left blank
6.3. URL of metadata folder or data catalog, if known:
Always listed as the URL to the InPort Data Set record
6.4. Process for producing and maintaining metadata
(describe or provide URL of description):
Metadata produced and maintained in accordance with the NOAA Data Documentation Procedural Directive: https://nosc.noaa.gov/EDMC/DAARWG/docs/EDMC_PD-Data_Documentation_v1.pdf
Always listed with the above statement

7. Data Access

NAO 212-15 states that access to environmental data may only be restricted when distribution is explicitly limited by law, regulation, policy (such as those applicable to personally identifiable information or protected critical infrastructure information or proprietary trade information) or by security requirements. The EDMC Data Access Procedural Directive contains specific guidance, recommends the use of open-standard, interoperable, non-proprietary web services, provides information about resources and tools to enable data access, and includes a Waiver to be submitted to justify any approach other than full, unrestricted public access.

7.1. Do these data comply with the Data Access directive?
Yes
7.1.1. If the data are not to be made available to the public at all, or with limitations, has a Waiver (Appendix A of Data Access directive) been filed?
No
7.1.2. If there are limitations to public data access, describe how data are protected from unauthorized access or disclosure:

None

7.2. Name of organization of facility providing data access:
National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD)
Taken From: Support Roles (Distributor) | Organization
Notes: The name of the Organization of the most recent Support Role of type "Distributor" is used. The support role must be in effect. This information is not required if an approved access waiver exists for this data.
7.2.1. If data hosting service is needed, please indicate:
Taken From: Data Management | If data hosting service is needed, please indicate
Notes: This field is required if a Distributor has not been specified.
7.2.2. URL of data access service, if known:
Taken From: Distribution Info | Download URL
Notes: All URLs listed in the Distribution Info section will be included. This field is required if applicable.
7.3. Data access methods or services offered:

Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

7.4. Approximate delay between data collection and dissemination:
Unknown
7.4.1. If delay is longer than latency of automated processing, indicate under what authority data access is delayed:

8. Data Preservation and Protection

The NOAA Procedure for Scientific Records Appraisal and Archive Approval describes how to identify, appraise and decide what scientific records are to be preserved in a NOAA archive.

8.1. Actual or planned long-term data archive location:
(Specify NCEI-MD, NCEI-CO, NCEI-NC, NCEI-MS, World Data Center (WDC) facility, Other, To Be Determined, Unable to Archive, or No Archiving Intended)
NCEI_MD
8.1.1. If World Data Center or Other, specify:
Taken From: Data Management | Actual or planned long-term data archive location
Notes: This field is required if archive location is World Data Center or Other.
8.1.2. If To Be Determined, Unable to Archive or No Archiving Intended, explain:
Taken From: Data Management | If To Be Determined, Unable to Archive or No Archiving Intended, explain
Notes: This field is required if archive location is To Be Determined, Unable to Archive, or No Archiving Intended.
8.2. Data storage facility prior to being sent to an archive facility (if any):
Pacific Islands Fisheries Science Center - Honolulu, HI
Taken From: Physical Location | Organization, City, State, Location Description
Notes: Physical Location Organization, City and State are required, or a Location Description is required.
8.3. Approximate delay between data collection and submission to an archive facility:
Unknown
8.4. How will the data be protected from accidental or malicious modification or deletion prior to receipt by the archive?
Discuss data back-up, disaster recovery/contingency planning, and off-site data storage relevant to the data collection

NOAA IRC and NOAA Fisheries ITS resources and assets.

9. Additional Line Office or Staff Office Questions

Line and Staff Offices may extend this template by inserting additional questions in this section.

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