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UCSD Fair Data Informatics Lab - Neuroscience Information Framework

Description

The University of California, San Diego (UCSD) Fair Data and Informatics Laboratory (FDI Lab) supports open science and is home to the Neuroscience Information Framework (NIF). NIF has extensive experience in community engagement, collaborative standards building, effective processes for sharing, federating, and integrating neuroscience data, information, and knowledge.

Roles

[Principal Investigator] Maryann Martone (maryann@ncmir.ucsd.edu)
[Co-Investigator] Jeffrey Grethe (jgrethe@ncmir.ucsd.edu)
[Co-Investigator] Anita Bandrowski (abandrowski@ncmir.ucsd.edu)
[Knowledge Engineer] Tom Gillespie (tom.h.gillespie@gmail.com)

Definitions [Optional]

  • NIFSTD Neuroscience Information Framework (NIF) Standard ontology (NIFSTD) is a neuroscience ontology that maintains an extensive set of terms and concepts important for the domains of neuroscience and biology.
  • InterLex A dynamic lexicon of biomedical terms built on the foundation of NeuroLex

Objectives

  • Develop a semantic framework for annotating and organizing cell level data by maturing community efforts to create a phenotype-based nervous system cell type ontology and phenotype representation
  • Work with the community to develop and implement spatial and semantic standards for managing heterogeneous brain cell census data types

In-scope

  • Create an effective strategy for semantic modeling and classifying neurons
  • Create a comprehensive ontology that represents canonical types (e.g., Purkinje cell), cell classes (e.g., GABAergic neurons) and individuals (Cell X from laboratory Y) based on neuronal properties and phenotypes.
  • Establish a community platform for consortium members and beyond to easily view the ontology and to recommend and provide feedback on terms in the ontology.
  • Provide the neuron ontology and other NIF ontologies covering additional relevant domains, e.g., small molecules, subcellular structures, anatomical structures, techniques, via our open-source terminology/ontology service SciGraph
  • Work with the BICCN community to help ensure that infrastructure and tools conform to best practices for making data FAIR: Findable, Accessible, Interoperable and Reusable
  • Work with the BCDC to develop an information architecture to meet the needs of the BICCN consortium and that interoperates with the larger ontology ecosystem.

Communication

Mailing Lists

NIF Support
Support and information mailing list managed by Zendesk.

Github repositories

NIF Ontology
Repository for the Neuroscience Information Framework (NIF) Standard ontology (NIFSTD). NIFSTD is a neuroscience ontology that maintains an extensive set of terms and concepts important for the domains of neuroscience and biology.

pyontutils
Python utilities for working with ontologies

SciGraph
SciGraph aims to represent ontologies and data described using ontologies as a Neo4j graph. SciGraph reads ontologies with owlapi and ingests ontology formats available to owlapi (OWL, RDF, OBO, TTL, etc).

Documentation

NIF Ontology Documentation
Documentation for the NIF Ontology including neuron specific ontology documentation.

Resources

InterLex

Funding

A Community Resource For Single Cell Data In The Brain