Find open-source science resources

A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.

250 of 6,234 resources

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The Crystallographic Defect Core Ontology (CDCO) defines the common terminology shared across all types of crystallographic defects, providing a unified framework for data integration in materials science.

Active03 months ago
CC-BY-4.0

Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation.

Active104 months ago
Jupyter Notebook
MIT

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.

Active74 months ago
HTML
NOASSERTION

The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.

Active44 months ago

This ontology integrates cell type markers for cells in the Cell Ontology from various sources along with details of marker context (anatomical context, assay), confidence (where available) and provenance. [from repository]

Active14 months ago
Python

A vocabulary describing subjects taught in German primary and secondary school (not university/hochschulen), such as German, math, and art.

Active44 months ago
CC0-1.0

An _gentle_ implementation of the Unified Foundational Ontology (UFO), which is an upper level ontology like BFO that is concerned with e.g. expressing temporal relationships between events.

Active425 months ago
CC-BY-4.0

Ribocentre is designed to contain comprehensive information of all natural ribozymes.

Active15 months ago
JavaScript

The initial focus of the GS1 Web Vocabulary is consumer-facing properties for clothing, shoes, food beverage/tobacco and properties common to all products. [from homepage]

Active505 months ago
Apache-2.0

MathModDB is a database of mathematical models developed by the Mathematical Research Data Initiative (MaRDI). MathModDB defines a data model with classes (Mathematical Model, Mathematical Formulation, Research Field, Research Problem, Quantity [Kind], Computational Task, Publication), object properties/relations, data properties and annotation properties as an ontology. This ontology is populated with individuals/data from various fields of applied mathematics, making it a knowledge graph. [from homepage]

Active55 months ago
CC-BY-4.0
Active205 months ago
HTML
Active05 months ago
GPL-3.0
Active45 months ago
CC-BY-SA-4.0
Active55 months ago
Python
NOASSERTION

This ontology is a formal representation that captures the fundamental concepts and their relationships to one another in the field of curriculum design and implementation of the German school system.

Idle26 months ago
Makefile

The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR.

Idle96 months ago
Makefile
CC-BY-4.0

The NFDI4Culture Ontology (CTO) is a domain-specific ontology module developed within the Task Area 5 of the NFDI4Culture initiative. (from homepage)

Idle67 months ago
Makefile

The Bibframe vocabulary consists of RDF classes and properties used for the description of items cataloged principally by libraries, but may also be used to describe items cataloged by museums and archives. Classes include the three core classes - Work, Instance, and Item - in addition to many more classes to support description. Properties describe characteristics of the resource being described as well as relationships among resources. For example: one Work might be a "translation of" another Work; an Instance may be an "instance of" a particular Bibframe Work. Other properties describe attributes of Works and Instances. For example: the Bibframe property "subject" expresses an important attribute of a Work (what the Work is about), and the property "extent" (e.g. number of pages) expresses an attribute of an Instance.

Idle547 months ago
Python

An ontology about scholarship

Idle167 months ago
Unlicense

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)

Idle07 months ago
HTML
GPL-3.0

A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)

Idle97 months ago
Python
CC-BY-4.0

A vocabulary describing licenses for data and code

Idle07 months ago
Python
CC0-1.0

An ontology with predicates to formalization of the concept of mentions. The mentions may be either explicit (e.g. as when well stated into an article "Dr. Johnson's groundbreaking research on climate change") or implicit (e.g. such as discussing "seminal studies in the field"). MiTO contains the object property mito:mentions and its inverse mito:isMentionedBy.

Idle28 months ago

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

Idle28 months ago
Makefile

Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.

Idle88 months ago
NOASSERTION

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

Idle08 months ago
Makefile

The Mobilome Ontology describes bacterial mobile genetic elements, their mechanisms, and associated epidemiology.

Idle109 months ago
Makefile
Idle69 months ago
Apache-2.0

The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science.

Idle429 months ago
Shell
CC-BY-4.0

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

Idle09 months ago
HTML
NOASSERTION

SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library.

Idle10510 months ago
Makefile
CC-BY-4.0

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

Idle010 months ago
HTML
NOASSERTION

An ontology of information entities about an individual

Idle010 months ago
HTML
Idle110 months ago
HTML

Assigns identifiers to knowledge graphs (KGs) that are used and/or maintained within any NFDI consortium.

Idle010 months ago
Python
CC0-1.0

openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item.

Idle3510 months ago
Pkl
CC0-1.0
Idle612 months ago
Python

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.

Idle1011 year ago
HTML
NOASSERTION

An ontology of qualifications, distinctions, and certifications that uses the Phenotype And Trait Ontology term quality (PATO:0000001) as a root term.

Idle11 year ago
Python
MIT

A project supporting the DRAO application ontology, a hierarchy of specific research domains and descriptors which imports subsets of terms from over 40 publicly-available terminologies. (from repository)

Idle21 year ago
Makefile
NOASSERTION

The midlevel energy ontology (MENO) is a BFO-based midlevel ontology. It comprises the concepts for energy qualities, energy-based dispositions and energy-driven transformation and transfer processes and their interrelations. It has the goal to provide an upper level structure for these concepts for energy-related domain ontologies.

Idle21 year ago
Shell

The WikiPatwhays Graphical Pathway Markup Language (GPML) vocabulary.

Idle11 year ago
Groovy
Apache-2.0

An open, community-driven registry of conference and event venues. EVR assigns persistent identifiers (PIDs) to make referencing venues FAIR. This is similar to how ORCID assigns PIDs to researchers and ROR assigns PIDs to research organizations. This benefits researchers assembling information about in-person conferences and events by enabling them to refer in an unambiguous way to the venue where it takes place. This repository follows the [Open Data, Open Code, Open Infrastructure (O3) principles](https://www.nature.com/articles/s41597-024-03406-w), meaning that the data and code are all in one repository that anyone can contribute to.

Idle01 year ago
Python
MIT

An ontology encoding the core metadata based on the Intelligent Information Request and Delivery (iiRDS) standard

Idle31 year ago