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ODM2 Datasets, YODA file & Spreadsheet Ingest

Presenting: Anthony, Steve

ODM2 Datasets

ODM2 Datasets are the primary unit for data from ODM2 to be shared, published and archived, as they:

  • Contain one or more Results, as many as specified by the user
  • Include a Title and Abstract (optional)
  • Can be linked to Authors and Citations
  • Have a Universally Unique Identifier (UUID) for unambiguous provenance.

ODM2 Datasets can contain all of the fields shown in the ODM2 Overview Entity Relationship Diagram

YAML Observation Data Archive (YODA) Profiles

The YAML Observation Data Archive & Exchange (YODA) File Format was developed as a specification for for exchanging a specific type of ODM2 Dataset -- one in which Results are grouped into a single two-dimensional data array similar to how scientists most commonly view their data (e.g. in tables or DataFrames).

YODA Profiles have been developed for common dataset types to define expectations for the data array block and to facilitate data/metadata input forms/templates for the end-user. We have developed three YODA Profiles to date:

  1. Time Series
  2. Specimen Time Series
  3. Specimens (under development)

These YODA Profiles have been implemented in both YAML and Microsoft Excel Spreadsheet representations.

We envision numerous future YODA Profiles.

YODA-Tools Desktop App for Spreadsheet Ingest

The YODA Tools library, which is built upon the ODM2PythonAPI, was developed to ingest datasets from our YODA Excel Templates and load these datasets into ODM2. YODA Tools can also create YODA Files from these Excel Templates or from an operational instance of an ODM2 database, or read YODA Files directly into an ODM2 database.

YODA Tools has a simple desktop application, in addition to providing all functions in Python.

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