Awesome Links

[samikanza]

SEMANTIC LINKS

Ontology Lookup Services / Registries / Collections

• NFDI4Cat Terminology Services
• Ontologies in Catalysis
• Mat-Portal
• BioPortal
• OBO Foundry
• OntoBee
• EMBL-EBI

Ontology Mapping Tools

• Simple Standard for Sharing Ontological Mappings (SSSOM) - The Simple Standard for Sharing Ontological Mappings (SSSOM) is a community-driven standard designed to facilitate the exchange and integration of semantic entity mappings.

Generic Ontologies for Publication Data

• schema.org
• DataCite (They don’t officially provide an ontology but an XML schema)
• Dublin Core / DCat
• Mappings between Data Cite & Dublin Core

Scientific Ontologies of Interest

• Voc4Cat - A vocabulary for Catalysis, Voc4Cat, is beeing build up, initiated by NFDI4Cat
• EMMO - Elementary Multiperspective Material Ontology
• Basic Formal Ontology - The Basic Formal Ontology (BFO) is a small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains.
• Experimental Factor Ontology - The scope of EFO is to support the annotation, analysis and visualization of the data handled by the Functional Genomics Team at the EBI. They also add terms for external users when requested.

Linked Data Tools

• JSON-LD Playground - OO-Linked Data Playground
• OO-LD - The Object Oriented Linked Data Schema based on JSON-LD and JSON-SCHEMA
• PyLD for JSON-LD in Python

Semantic Units

• Work on Units in OpenSemanticLab

Semantic Annotation Tools

• DLite - A set of concepts and tools for using data models (aka Metadata) to efficiently describe and work with scientific data.
• CSV to JSON-LD - Library for converting CSV to JSON-LD
• CSV to JSON-LD Convertor - LD-R provides a basic import plugin which allows converting CSV files to JSON-LD RDF format
• CSV-LD - CSV-LD: A CSV-based Serialization for Linked Data
• NOMAD tabular parser
• JSON SubSchema - Tool to check if a new schema is backward-compatible

Semantic Dataset Examples

• SciData - SciData is a data model for scientific data that provides a ontologically defined framework for organizing both the data and metadata from scientific experiments, calculations, and theories.

Data Exchange Formats & ELN Tools

• Ro-Crate
• ELN FileFormat
• OpenSemanticLab - Open Semantic Lab (OSL) is a holistic web platform that can capture all data and ideas and link them precisely (semantically/ontology-based) - no matter if it' s inventory (LIMS), lab notes (ELN), procedures (SOPs) or research (KB).

Semantic ELN Tools

• Schema Registry - A linked schema registry for Knowledge Graph Builders

Metadata Links

• Cedar Workbench - The CEDAR platform provides an easy-to-use solution for creating and reusing FAIR metadata.
• Applying Interoperable Metadata Standards

[scman1]

Reproducibility for Jupyter Notebooks: https://sheeba-samuel.github.io/REPRODUCE-ME/publications.html
There are two tools that generates metadata about execution of jupyter notebooks, each cell is treated as a process. They are backed by the reproduceme ontology https://sheeba-samuel.github.io/REPRODUCE-ME/doc/index-en.html
Intresting to explore if you are considering using notebooks for processing and analysis.