ifdo integration - Githubissues

The BIIGLE team has expressed interest in using ifdo as data interchange with FathomNet. Discussion is at https://github.com/biigle/core/issues/443. I wrote a proof-of-concept to convert a sample ifdo to FathomNet style CSV at ifdo-to-fathomnet.sc. Sample YAML from BIIGLE:

# General information about the dataset.
image-set-header:
    # UUID, name, handle are mandatory fields of each iFDO.
    image-set-uuid: 2a2360e9-a5ec-4ad2-be04-0ea0b4cbdc58
    image-set-name: SO268-1_21-1_GMR_CAM-23
    # Handles are a superset of DOIs and can be obtained with a Handle server.
    # See: http://handle.net/
    image-set-handle: 20.500.12085/2a2360e9-a5ec-4ad2-be04-0ea0b4cbdc58@data
    # Version must be specified but defaults to v1.0.0 if not present.
    image-set-ifdo-version: v1.0.0
    # List of labels (not annotations) that are used in this dataset.
    image-annotation-labels:
        # Label IDs should be universally unique if possible. It must be unique in this file.
        # The info field can be used for a URL, too.
        - id: urn:lsid:marinespecies.org:taxname:124731
          name: Kolga hyalina
          info: http://www.marinespecies.org/aphia.php?p=taxdetails&id=124731
    # List of persons who created annotations in this dataset.
    image-annotation-creators:
        # ORCID ID can be used as annotator ID, if available.
        - id: 0000-0002-7122-2343
          name: Martin Zurowietz
# List of images of this dataset (list keys are image filenames).
image-set-items:
    SO268-1_21-1_GMR_CAM-23_20190513_131416.jpg:
        # List of annotations on this image.
        image-annotations:
            # Bounding box annotation: x1,y1,x2,y2,x3,y3,x4,y4
            - coordinates: [10,10,10,20,20,20,20,10]
              shape: rectangle
              # An annotation can have one or more labels. Label and annotator are referenced
              # by their ID.
              labels:
                  - label: urn:lsid:marinespecies.org:taxname:124731
                    annotator: 0000-0002-7122-2343

fathomnet / community-feedback

ifdo integration #33