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Symbiota Documentation

website·Indexed 35 days ago

https://docs.symbiota.org

User, Editor, and Portal Manager guides for Symbiota versions 3.2 and 3.3, covering taxonomic and geographic thesauri, record management, specimen packet printing, identification keys, and dataset administration.

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What's inside Symbiota

  1. Overview of Symbiota Occurrence Traits

    Occurrence traits are stored in a separate table from the main occurrence data. They are primarily managed via the Traits tab in the Occurrence Editor and can be exported as extended measurementOrFact files. The specific traits available for scoring vary by portal; users should contact their portal administrator to request the development of new traits.

  2. Overview of adding occurrence records in Symbiota 3.3

    In Symbiota version 3.3, editors have three primary methods for adding occurrence records based on their permissions: creating skeletal records, creating full records, or uploading an image to generate a record.

  4. Overview of Symbiota Georeferencing tools

    Symbiota provides several tools to assign coordinates and error radii to textual descriptions of occurrence localities. Available tools include:

    • Mapping tool: Used to view a map, manually place a point on the occurrence location, and assign an error radius.
    • GEOLocate tool: Provides access to multiple map layers (USGS Topo Maps, Open Street Maps, Bing Maps, and Leaflet maps) and offers auto-generated potential georeference points for editing.
    • Coordinate cloning tool: Allows users to search for records with similar or identical locality information and import existing coordinates associated with those localities.
    • Duplicate specimen/locality data import: Enables searching for records with identical or similar collector or locality information to import associated coordinates.
    • Batch georeferencing: A workflow to apply Leaflet maps, GEOLocate, and coordinate cloning tools in batch for groups of specimens with similar locality descriptions.
    • GEOLocate Collaborative Georeferencing (CoGe) Integration: Allows exporting records to the GEOLocate CoGe web client for collaborative georeferencing.

  5. Overview of Symbiota biodiversity data software

    Symbiota is an open-source software designed for managing and mobilizing biodiversity data, supporting natural history collections and occurrence records (specimens or observations). The central source code for version 3.2 is hosted on GitHub.
    GitHub Repository: https://github.com/Symbiota/Symbiota

  6. Overview of the GEOLocate Collaborative Georeference Tool (CoGe)

    The GEOLocate Collaborative Georeference Tool (CoGe) is a central georeferencing platform that can be integrated into a Symbiota portal. It allows multiple users to collaborate on georeferencing tasks outside of the primary portal environment. For detailed operational guidance, users can refer to the official CoGe page, the GEOLocate CoGe Training Course, and the written georeferencing protocol.

  7. Overview of Symbiota biodiversity data management software

    Symbiota is an open-source software designed for managing and mobilizing biodiversity data. It is used by over 2,000 natural history collections to manage over 95 million occurrence records (specimens or observations). The central source code for version 3.3 is hosted on GitHub.
    # Source code repository
https://github.com/Symbiota/Symbiota

  8. Overview of Symbiota biodiversity data software

    Symbiota is an open-source software designed for managing and mobilizing biodiversity data. It is used by over 2,000 natural history collections to manage more than 95 million occurrence records (specimens or observations). The central source code for version 3.4 is hosted on GitHub.
    # Source code available at: https://github.com/Symbiota/Symbiota

  9. Overview of the Collaborative Georeferencing (CoGe) workflow

    The GEOLocate Collaborative Georeference Tool (CoGe) allows multiple users to georeference specimens on a central platform outside of the Symbiota portal.

    There are two primary ways to move data:

    1. Direct Push: Data is pushed from the Symbiota portal to CoGe. Georeferences created in CoGe are automatically applied to records in the Symbiota portal in real-time.
    2. Manual CSV Export: Records are downloaded as a CSV from Symbiota, uploaded to CoGe, downloaded after completion, and re-uploaded to Symbiota.

    The general workflow consists of:

    1. Creating a profile on the CoGe website.
    2. Creating a community on the CoGe website.
    3. Adding members to the CoGe community.
    4. Adding data to the CoGe community from the Symbiota portal.
    5. Georeferencing records via the CoGe web client.

  10. Overview of supported media types in Symbiota 3.2

    Symbiota portals support audiovisual media, specifically images and audio files. Video files are currently not supported. Media resources are associated with records via links stored in database tables. Depending on the portal configuration, media may be hosted locally on the portal's servers (which may incur costs or require a hosting agreement) or linked via external URLs by matching catalog numbers.

  11. Understand and search for traits in Symbiota portals

    In Symbiota portals, traits are measurements or characteristics associated with specific records, such as phenology (e.g., life history stage), height, or mass.

    Key constraints and behaviors:

    • Categorical Only: Symbiota currently only supports categorical traits. Numerical traits (precise measurements like "40 g") are not supported.
    • Availability: Traits are not activated in all portals and must be set up on the back end.
    • Data Presence: A lack of trait data for a record does not necessarily mean the trait is absent or wasn't measured; it only means the data is not present in the portal.
    • Searching: Records with traits can be filtered using the "Traits" box within the public search form.

  12. Manage and utilize Symbiota checklists

    Symbiota checklist tools provide the following capabilities for managing taxonomic data:

    • Visualization: View checklists by scientific names, common names, images from the image library, or a combination of these.
    • Voucher Linking: Link voucher specimens directly from the Symbiota portal.
    • Notes: Manage public or private notes associated with specific taxa.
    • Educational Tools: Create identification keys limited to the checklist taxa and use name recognition/spelling games as study aids.
    • Export: Export lists as spreadsheets or Word documents for field use.