FAIR semantics and the NVS

The FAIR principles provide guidelines for the publication of digital resources such as datasets, code, workflows, and research objects aiming at making them Findable, Accessible, Interoperable, and Reusable(1). Amongst them, the I of the FAIR promotes interoperability and more specifically principle I2 suggests that metadata should use vocabularies that themselves follow the FAIR principles. Recently, FAIRsFAIR1 project officially published a first iteration of recommendations for making vocabularies FAIR (2). These recommendations include 17 general recommendations aligned with the different FAIR Principles and 10 Best Practice recommendations. The main objective of these recommendations is to provide a set of guidelines for creating a harmonised and interoperable semantic landscape easing the use and reuse of semantic artefacts from multiple different scientific domains

Moving towards FAIR mappings and crosswalks.

Mappings and crosswalks are key elements to ensure semantic interoperability as well as metadata and data integration between different information systems. Designing FAIR compliant systems requires making sure all the elements that constitute the systems are themselves FAIR to support machine-actionability and automation. This paper describes the ongoing European and international effortto build a framework for FAIR Mappings and crosswalks. This framework aims to be generic enough to capture the diverse set of use cases and methodologies across domains and communities. It should be composed of a set of technical recommendations to aid compliance with FAIR principles, a set of models for machine actionable mappings and crosswalks as well as a practical framework with aligned good practices to support the creation of mappings by scientific communities. Developed in the context of FAIR IMPACT, a Horizon Europe project, this work will be pursued within a more international context as a Research Data Alliance Working Group

Converging on a Semantic Interoperability Framework for the European Data Space for Science, Research and Innovation (EOSC)

L’interopérabilité sémantique (IS) est au cœur des principes FAIR et de la conception à grande échelle des infrastructures interdisciplinaires. L’European Open Science Cloud (EOSC) est un effort à l’échelle européenne vers une telle infrastructure, visant à approfondir la collaboration régionale en matière de recherche et à construire un espace de données partagé pour la science, la recherche et l’innovation

Computational Neuroscience Ontology: a new tool to provide semantic meaning to your models

The diversity of modeling approaches in computational neuroscience makes model sharing, retrieval, reuse and reproducibility difficult and even sometimes impossible. To address this problem, standardized languages have been developed by and for the community, such as NeuroML[1], PyNN [2] and NineML (http://software.incf.org/software/nineml). Although these languages enable software interoperability and therefore model reuse and reproducibility, they lack semantic information that would facilitate efficient model sharing and retrieval. In the context of the INCF Multi-Scale Modeling (MSM) program, we have developed an ontology to annotate spiking network models described with NineML and other structured model description languages. Ontologies are formal models of knowledge in a particular domain and composed of classes that represent concepts defining the field as well as the logical relations that link these concepts together [3]. These classes and relations have unique identifiers and definitions that allow unambiguous annotation of digital resources such as web pages or model source code. Implemented in a machine-readable format, these knowledge models can be used to design more efficient and intuitive information retrieval systems for experts in the field. We are proposing the first version of the Computational Neuroscience Ontology or CNO. This ontology is composed of 207 classes representing general concepts related to computational neuroscience organized in a hierarchy of concepts. CNO is currently available on Bioportal (http://bioportal.bioontology.org/ontologies/3003). The design of CNO follows some of the recommendations of the Open Biological and Biomedical Ontologies (OBO) community and is compatible with the ontologies developed and maintained within the Neuroscience Information Framework (NIF, [4]http://www.neuinfo.org). Integration with this large federation of neuroscience ontologies has two main advantages: (1) it allows the linking of models with biological information, creating a bridge between computational and experimental knowledge bases; (2) as ontology development is an iterative process that relies on inputs from the community, NIF has developed NeuroLex (http://neurolex.org), an effective collaborative platform, available for community inputs on the content in CNO. With the further development of CNO based on inputs from the community, we hope CNO will provide a useful framework to federate digital resources in the field of computational neuroscience

NineML: the network interchange for neuroscience modeling language

The growing number of large-scale neuronal network models has created a need for standards and guidelines to ease model sharing and facilitate the replication of results across different simulators. To foster community efforts towards such standards, the International Neuroinformatics Coordinating Facility (INCF) has formed its Multiscale Modeling program, and has assembled a task force of simulator developers to propose a declarative computer language for descriptions of large-scale neuronal networks. The name of the proposed language is "Network Interchange for Neuroscience Modeling Language" (NineML) and its initial focus is restricted to point neuron models. The INCF Multiscale Modeling task force has identified the key concepts of network modeling to be 1) spiking neurons 2) synapses 3) populations of neurons and 4) connectivity patterns across populations of neurons. Accordingly, the definition of NineML includes a set of mathematical abstractions to represent these concepts. NineML aims to provide tool support for explicit declarative definition of spiking neuronal network models both conceptually and mathematically in a simulator independent manner. In addition, NineML is designed to be self-consistent and highly flexible, allowing addition of new models and mathematical descriptions without modification of the previous structure and organization of the language. To achieve these goals, the language is being iteratively designed using several representative models with various levels of complexity as test cases. The design of NineML is divided in two semantic layers: the Abstraction Layer, which consists of core mathematical concepts necessary to express neuronal and synaptic dynamics and network connectivity patterns, and the User Layer, which provides constructs to specify the instantiation of a network model in terms that are familiar to computational neuroscience modelers. As part of the Abstraction Layer, NineML includes a flexible block diagram notation for describing spiking dynamics. The notation represents continuous and discrete variables, their evolution according to a set of rules such as a system of ordinary differential equations, and the conditions that induce a regime change, such as the transition from subthreshold mode to spiking and refractory modes. The User Layer provides syntax for specifying the structure of the elements of a spiking neuronal network. This includes parameters for each of the individual elements (cells, synapses, inputs) and the grouping of these entities into networks. In addition, the user layer defines the syntax for supplying parameter values to abstract connectivity patterns. The NineML specification is defined as an implementation-neutral object model representing all the concepts in the User and Abstraction Layers. Libraries for creating, manipulating, querying and serializing the NineML object model to a standard XML representation will be delivered for a variety of languages. The first priority of the task force is to deliver a publicly available Python implementation to support the wide range of simulators which provide a Python user interface (NEURON, NEST, Brian, MOOSE, GENESIS-3, PCSIM, PyNN, etc.). These libraries will allow simulator developers to quickly add support for NineML, and will thus catalyze the emergence of a broad software ecosystem supporting model definition interoperability around NineML