Label Mapping
Label Mapping
Label Mapping is the process of linking labels, such as those used in Biigle, to entities in the database. As a brief example, the label, Biota > Porifera sp. would be mapped to a record containing the scientific name Porifera, the common name, Sponges, the Aphia ID (WoRMS) 558, the Hart code 20A. These properties will be searchable in the database, and can be linked to external taxonomic databases. Because the Aphia ID is included, the taxonomic hierarchy can be navigated, allowing aggregate searches of a taxon's parents and children.
Biigle Label Mapping
The Biigle Label Mapping page allows importers to map labels loaded directly from Biigle projects linked to the currently logged in user.
The user can add their Biigle credentials to their profile. You must be a member of the Importer group to see the credential form, so contact us if you don't see it. You will need to enter the email registered to your Biigle account, and a token. Tokens can be created in your Biigle settings panel. Once your Biigle credentials have been set, you can navigate to the Biigle label mapping page and begin.
First, select a project from the project drop-down. The label tree drop-down will then be populated with label trees used in that project. The list of labels from the selected tree will be displayed.
The Show label hierarchy will show the full path of each label, from the root of the containing tree to the label itself. By default, only "leaf" labels are shown -- those that do not have any children. In general, these are the only ones actually used in annotations. The "Show parents" checkbox shows all labels, including parent labels. Leaf labels are shown with an adjacent leaf icon.
Each label is displayed on a single row with its Biigle label ID and the text of the label. A search icon is displayed next to the label. For labels that describe a taxon, select the text of the label and click the button. A table will appear with matches to the text. Click the scientific name, common name, Hart code and/or Aphia ID to place those items in appropriate fields in the row (if they're not already there, they will be created).
Next to the search icon is the Event Type drop-down. This allows the user to assign one of several types of events to the label, including Observation, Habitat, Anthropogenic, etc. These help database users to distinguish between the different types of observations. Note that the event types are not guaranteed to be distinct. For example, if a habitat consists of identifiable organisms, the user must choose which type to assign. All of the fields assignable to an Observation can also be assigned to a Habitat or any other type.
Tags contain information that doesn't fit into a distinct category. Habitats are often labeled as dominant or subdominant, and species with an indeterminate identification may be labeled as yellow. These can go into tags as well. The Life Stage field allows the assignment of life stage information, such as Egg Masses or Dead. Life stage information can, of course be entered as a tag, but using distinct fields makes sorting a little easier. To add either a tag or a life stage, lick the + button next to the field.
The Field Type drop-down contains a list of properties that can be added to the record. When an item is selected, a new field appears in the row, and the drop-down moves to the right. The types are described below.
| Field Type | Type | Description |
|---|---|---|
| Substrate | Drop-down | Substrate types. Inherited from VideoMiner. |
| Bicocover | Drop-down | Biocover types. Inherited from VideoMiner. |
| Coverage | Drop-down | Coverages intended to apply to substrates. Inherited from VideoMiner. |
| Complexity | Drop-down | The complexity of the habitat. Inherited from VideoMiner. |
| Thickness | Drop-down | The thickness of the substrate. Inherited from VideoMiner. |
| Disturbance | Drop-down | A description of the disturbance of the habitat. Inherited from VideoMiner. |
| Relief | Drop-down | Descriptions of the relief of the terrain. Inherited from VideoMiner. |
| Flow | Drop-down | Descriptions of current flow. |
| Abundance | Drop-down | ACFOR abundance levels for species observations. Inherited from VideoMiner. |
| Status Type | Drop-down | Types of events, such as ROV on/off the bottom. |
| Status Detail | Drop-down | Detailed information about the status event. For example, if the status type is Off Transect the detail field can contain more specific detail, e.g., Transiting. This field is admittedly weird and needs a revisit. |
| Image Quality | Drop-down | Image quality information. Inherited from VideoMiner. |
| Observation Confidence | Drop-down | Observation confidence levels, applicable to species observations. Inherited from VideoMiner. |
| Scientific Name | Text field | The scientific name of an organism. Can be automatically added from the search result or manually added. |
| Common Name | Text field | The common, or vernacular, name of an organism. Can be automatically added from the search result or manually added. |
| Description | Text field | General descriptions of anything. |
| OTU | Text field | The Operational Taxonomic Unit used to label indeterminate species identifications or new species. |
| Cf. | Text field | Conferatur -- a taxon to which the observation can be referred for comparison. |
| Aphia ID | Text field | The ID of a taxon in the WoRMS database. |
| iNaturalist ID | Text field | The ID of a taxon in the iNaturalist database. |
| Hart Code | Text field | The Hart code used in DFO databases. |
| Count | Text field | The number of individuals of the observed taxon. |
| Note | Text field | Any notes the user wishes to add. |
When the labels have been mapped, click the Save button at the top to save the label mappings. They will be preserved in the database and applied when annotations are imported. The next time you load a label tree, the label mappings will be pre-populated.
Generic Labels
This is for non-Biigle labels such as those generated from VideoMiner databases. More information is coming.