This repository centralizes biodiversity data mobilization efforts for marine World Heritage sites. See https://iobis.github.io/mwhs-data-mobilization/ for current mobilization status.
This repository is organized as follows:
├── README.md : Description of this repository (this file)
├── index.html : Dataset overview to track mobilization status
├── .gitignore : Files and directories to be ignored by git
|── .gitmodules : Submodule information for git
│
├── datasets
│ ├── site1
│ | ├── dataset1
│ | | ├── raw : Directory containing raw datafiles (PDFs, CSVs, etc.)
│ | | └── processed : Directory containing processed datafiles (OCRed files, saved CSV tables, etc.)
│ | ├── dataset2
│ | └── dataset...
│ ├── site2
│ └── site...
│
├── notebooks
│ ├── site1
│ | ├── dataset1
│ | | ├── dataset.Rproj : R Project file for the dataset
│ | | ├── index.Rmd : R Markdown script for mobilization
│ | | └── index.html : R Markdown HTML document for visualization
│ | ├── dataset2
│ | └── dataset...
│ ├── site2
│ └── site...
|
├── output
│ ├── site1
│ | ├── dataset1
│ | | └── DwC-A.zip : DarwinCore-Archive
│ | ├── dataset2
│ | └── dataset...
│ ├── site2
│ └── site...
|
└── scripts_data
├── pdf_to_tables : Submodule repository of the OCR/table parsing script
└── meta_occurrence_checklist_template.xml : meta.xml file template for Occurrence Core data
- Directory datasets: raw data files and documents organized by site and dataset.
- Directory notebooks: notebooks for bundling individual datasets into a Darwin Core Archive for publishing.
- Directory output: combined Darwin Core Archive output for all sites and datasets.
- Directory scripts_data: shared scripts and template files.
All sites are listed in each of the three major directories, with associated datasets nested under the appropriate site.
Guidelines for mobilizing data are based on A checklist recipe: making species data open and FAIR and associated code: Checklist Recipe
All output will use the biodiversity data standards as outlined in the OBIS manual. The following data fields are highly recommended for all occurrence datasets:
| Field | Description | Darwin Core |
|---|---|---|
| Date | Date of the occurrence. | http://rs.tdwg.org/dwc/terms/eventDate |
| Location | Detailed textual description of the location. | http://rs.tdwg.org/dwc/terms/locality |
| Longitude | Longitude in decimal degrees, point location or centroid for a larger area. | http://rs.tdwg.org/dwc/terms/decimalLongitude |
| Latitude | Latitude in decimal degrees, point location or centroid for a larger area. | http://rs.tdwg.org/dwc/terms/decimalLatitude |
| Coordinate uncertainty | Coordinate uncertainty expressed in meters from the centroid (see fields above). | http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters |
| Scientific name | Scientific name as found in the source. | http://rs.tdwg.org/dwc/terms/scientificName |
| Scientific name identifier | Identifier for the scientific name, preferably a full WoRMS LSID | http://rs.tdwg.org/dwc/terms/scientificNameID |
If a precise coordinates are not available, a spatial polygon can be provided in the footprintWKT field formatted as WKT. Alternatively, a location identifier can be provided in the locationID field, for which we recommend using identifiers from Marine Regions, for example http://marineregions.org/mrgid/26874.
For additional fields, see the OBIS manual or the Darwin Core Quick Reference Guide.