Find open-source science resources

Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications.

A controlled vocabulary to support the study of transcription in the developing mouse brain

A controlled vocabulary to support the study of transcription in the human brain

A terminology for the skills necessary to make data FAIR and to keep it FAIR.

An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)

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).

This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases.

Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone.

The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page).

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

The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research).

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.

The NFDI4DataScience ontology (nfdi4dso) is an ontology describing various resources all resources (datasets, data providers, persons, projects and other entities) within the domain of NFDI4DataScience. nfdi4dso is a module that builds upon the [NFDIcore Ontology](https://ise-fizkarlsruhe.github.io/nfdicore/2.0.0/) and maintains alignment with the Basic Formal Ontology (BFO). [adapted from homepage]

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

DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects.

A controlled vocabulary to support the study of transcription in the primate brain

The AOPO provides classes and relationships for the semantic representation of the Adverse Outcome Pathway framework.

MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a data repository and associated data standard designed to describe biosynthetic gene clusters involved in the production of specialized metabolites. It also stores data on measured biological activities and links to other resources such as NCBI, NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and training dataset for machine learning.

MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012

OntoDM-core defines the most essential data mining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. (from abstract)

A controlled vocabulary for education levels, such as primary eduation, secondary education, and post-secondary education

This is a vocabulary for educational sectors as used in the OER World Map (https://oerworldmap.org)

This SKOS vocabulary describes types of primary and secondary schools in Germany, such as Grundschule, Gymnasium, and Realschule. This does not include post-secondary education such as universities or hochschulen.

This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins.

The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.

The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response.

The Science Data Discovery Ontology (sddo) is being developed to provide a semantic foundation for the discovery of information managed by NASA's Science Mission Directorate. This information spans many scientific disciplines, fields and subfields, including heliophysics, earth science, planetary science, astrophysics, biology, astrobiology, and physical science. [from repository]

A vocabulary of university course subjects

Algorithm Metadata Vocabulary is a vocabulary for capturing and storing the metadata about the algorithms (a procedure or a set of rules that is followed step-by-step to solve a problem, especially by a computer). There are uncountable algorithms present in every area (e.g., Computer Science, Mathematics), which makes it hard for specialists, academicians, application engineers, and so forth to discover, distinguish, select, and reuse them. [from repository]