Find open-source science resources

Research ecosystem for rigorous and trustworthy AI scientists — a protocol and skill bundle that makes autonomous research verifiable, crystallized, and observable through structured, machine-executable research artifacts and five agent skills for research management, compilation, verification, visualization, and publication (ARA-Labs, 447+ stars, MIT License, 2026)

Identifiers in the GTN correspond to training materials in various formats (markdown, slides, video). The users can apply learned concepts directly within the framework via galaxy workflows.

The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database.

Production-grade ETL for transforming complex documents into structured formats, with open-source API

Cheminformatics toolkit

Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]

An Apache-based persistent URL (PURL) service

This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.

A vocabulary used in tandem with SHACL for representing node shapes

Library of descriptors to aid in the data-mining of materials properties, created by the Lawrence Berkeley National Laboratory.

DCAT-AP is a DCAT profile for sharing information about Catalogues containing Datasets and Data Services descriptions in Europe, under maintenance by the SEMIC action, Interoperable Europe. This Application Profile provides a minimal common basis within Europe to share Datasets and Data Services cross-border and cross-domain. [from homepage]

The Data Privacy Vocabulary provides an ontology (classes and properties) and taxonomies of concepts to represent information regarding how personal data is processed in the form of an ontology or a knowledge graph.

This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.

Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.

Parallel Computing and Scientific Machine Learning: MIT 18.337J/6.338J course materials (1.9k+ stars)

A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies).

A representation of variables appearing in models in the environmental research space.

Suite of tools to handle gene annotations in any GTF/GFF format.

An ontology demonstrating rich ontology for rubber extrusion.

BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.

The primary goal of this ontology is to standardize the representation of molecular simulation data, processes, and methodologies across disparate simulation platforms, engines (e.g., GROMACS, AMBER, NAMD), and analysis tools, while ensuring these terms are interoperable with existing life sciences ontologies

An international LGBTQ+ linked data vocabulary

It is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

Large-scale benchmark suite for protein fitness prediction and design, aggregating 200+ deep mutational scanning assays and clinical variant datasets across diverse protein families and taxa, with standardized zero-shot and supervised leaderboards for variant effect prediction, mutation effect prediction, and protein language model evaluation (OATML & Marks Lab, NeurIPS 2023 Spotlight, Datasets & Benchmarks)

The Generative Artificial Intelligence Delegation Taxonomy (GAIDeT) assigns identifiers to contributor roles as an extension to the Contributor Roles Taxonomy (CRediT) to support promoting transparency and accountability in academic publishing when AI contribtors are involved in research. It is operationalized in the [GAIDeT Declaration Generator](https://panbibliotekar.github.io/gaidet-declaration/), an interactive tool for researchers to disclose the delegation of tasks to generative AI (GAI) tools in accordance with the GAIDeT taxonomy.

Webapp for generating conformers

CCSO is an educational ontology acting as a data model for concepts and entities within an academic setting, enabling also the annotation of potentially available resources. The ontology aims to conceptualize educational entities within Curriculum and Syllabus with appropriate coverage and quality, in order to support rich services on top for improving curriculum management and automatically enabling syllabus semantic processes. (from homepage)

HOSO is an ontology of informational entities and processes related to healthcare organizations and services.

HEPRO is an ontology of informational entities and processes related to health procedures and health activities.

An ontology of information entities about an individual

Easily get SRA download links and other information.

Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business.

This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI).

A concept scheme that defines the types of relationships between a learning resource and a node in an educational framework.

BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format.

An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.

An educational ontology for personalised recommendation learning systems that is based on learning path and user profile. It represents the key components for a personalised learning system based on our requirement analysis.

This ontology defines a taxonomy of software functions based on the work of the NSF-funded EarthCube Resource Registry working group. The functions are generally organized by their role in the research process.

This mini-ontology contains classes and instances for each version of the licenses that are commonly used in software projects, particularly open source software projects. The URI's for each are the canonical URI's for that license (where they exist).

TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)

The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces.