Overview of the Data Model and Schema

The data model for this database is described using an entity-relationship diagram, below (for more on these diagrams, please check out this guide). This diagram shows the structure and organization of the Neurofibromatosis Research Tools Database. Each table (e.g. resource) has a defined set of attributes (e.g. rrid) that will be captured in that table. These tables are often linked to other tables by via primary keys (PKs) and foreign keys (FKs) that define individual records in each table.

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In addition to the data model diagram, a schema for this database is maintained in as a Google spreadsheet and regularly released as machine-readable JSON-LD files. Changes to the schema are tracked both in the Google spreadsheet changelog as well as the release notes.

Implementation of the Data Model

Our current plan is to use the schematic Python package developed by Sage Bionetworks to generate the database tables and data intake spreadsheets (manifests).

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Please feel free to navigate to File → Make a Copy to create a editable copy of these manifests to explore how they work.

Additional Resources

• Source NFTI Data Model Diagram in LucidChart (linked and updated in this document)

  • Description: This is the source diagram of the Data Model for the NF Research Tool Database, generated and maintained in LucidChart (note: please reference the “New Layout Database Schema” sheet). The latest version of this diagram is linked and will be updated in this document . with each update and release of the database schema.

  • Link: https://lucid.app/documents/edit/3a118e5e-8884-48d1-af91-f03987bb0df8/0?callback=close&name=docs&callback_type=back&v=16092&s=612 

• NFTI Database Schema

  • Description: The machine-readable (JSON-LD on Github) and human readable (Google sheet) versions of the schemas encode the data model for the database as well as the dictionary for the attributes used in the database.

  • Link to latest version of schema in Github: https://github.com/nf-osi/nf-research-tools-schema  

  • Link to latest version of schema in shared gdriveGoogle Drive: https://docs.google.com/spreadsheets/d/15fwIhZw7YfhPkzOfQhj6zU_5-_7ywS05-L8qOjMIVdM/edit#gid=0  

• Intake Manifests

  • Description: Draft data intake manifests that use v1.0.1 of the schema:

  • New Cell Line

  • New Animal Model

  • New Genetic Reagent

  • New Antibody

Contact Information

Please feel free to contact Robert Allaway (robert.allaway@sagebase.org) and Ashley Clayton (ashley.clayton@sagebase.org) with any questions or comments related to the NFTI Neurofibromatosis Research Tools Database, data model, or any of the resources linked in this document

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Acknowledgements

Thank you to Brynn Zalmanek, James Eddy, Mialy DeFelice, Milen Nikolov, Kaitlin Throgmorton, and Robert Allaway at Sage Bionetworks for contributions to the development and implementation of the NFTI schemas schema and data model, and to GFF the Gilbert Family Foundation for valuable contributions and feedback.