obofoundry | Topic | Ecosyste.ms: Repos

Topic: "obofoundry"

monarch-initiative/ontogpt

LLM-based ontological extraction tools, including SPIRES

Language: Jupyter Notebook - Size: 80.6 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 701 - Forks: 97

DiseaseOntology/HumanDiseaseOntology

Repository for the Human Disease Ontology.

Language: Makefile - Size: 1.07 GB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 367 - Forks: 112

obophenotype/human-phenotype-ontology

Ontology for the description of human clinical features

Language: Makefile - Size: 1.92 GB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 313 - Forks: 55

ontodev/robot

ROBOT is an OBO Tool

Language: Java - Size: 5.32 MB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 275 - Forks: 75

BFO-ontology/BFO

BFO repository including source code and latest documents

Language: HTML - Size: 85.6 MB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 270 - Forks: 45

INCATools/ontology-development-kit

Ontology lifecycle management

Language: Jinja - Size: 5.59 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 260 - Forks: 56

monarch-initiative/mondo

Mondo Disease Ontology

Language: Jupyter Notebook - Size: 11.6 GB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 259 - Forks: 58

geneontology/go-ontology

Source ontology files for the Gene Ontology

Language: Makefile - Size: 1.94 GB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 237 - Forks: 42

althonos/pronto

A Python frontend to (Open Biomedical) Ontologies.

Language: Python - Size: 10.1 MB - Last synced at: 25 days ago - Pushed at: 4 months ago - Stars: 236 - Forks: 48

FoodOntology/foodon

The core repository for the FOODON food ontology project. This holds the key classes of the ontology; larger files and the results of text-mining projects will be stored in other repos.

Language: Python - Size: 327 MB - Last synced at: 2 days ago - Pushed at: 5 days ago - Stars: 198 - Forks: 37

biolink/biolink-model

Schema and generated objects for biolink data model and upper ontology

Language: Python - Size: 307 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 198 - Forks: 78

callahantiff/PheKnowLator

PheKnowLator: Heterogeneous Biomedical Knowledge Graphs and Benchmarks Constructed Under Alternative Semantic Models

Language: Python - Size: 43.5 MB - Last synced at: 27 days ago - Pushed at: about 1 year ago - Stars: 192 - Forks: 32

OBOFoundry/OBOFoundry.github.io

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Language: Python - Size: 52.1 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 178 - Forks: 213

obophenotype/cell-ontology

An ontology of cell types

Language: Makefile - Size: 490 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 178 - Forks: 53

mapping-commons/sssom

Simple Standard for Sharing Ontology Mappings

Language: Python - Size: 16.4 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 168 - Forks: 25

EnvironmentOntology/envo

A community-driven ontology for the representation of environments

Language: Makefile - Size: 109 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 150 - Forks: 53

obophenotype/uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology

Language: Emacs Lisp - Size: 2.03 GB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 142 - Forks: 34

INCATools/ontology-access-kit

Ontology Access Kit: A python library and command line application for working with ontologies

Language: Python - Size: 83.1 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 141 - Forks: 30

biolink/ontobio

python library for working with ontologies and ontology associations

Language: Python - Size: 66.8 MB - Last synced at: 25 days ago - Pushed at: 5 months ago - Stars: 129 - Forks: 32

OBOAcademy/obook

OBO Organized Knowledge: Training materials for becoming an OBO engineer

Language: Makefile - Size: 68.4 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 110 - Forks: 40

The-Sequence-Ontology/SO-Ontologies

Collect of SO Ontologies

Language: Makefile - Size: 33.4 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 100 - Forks: 37

EBISPOT/OLS 📦

Ontology Lookup Service from SPOT at EBI

Language: JavaScript - Size: 28.6 MB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 98 - Forks: 41

oborel/obo-relations

RO is an ontology of relations for use with biological ontologies

Language: Jupyter Notebook - Size: 15 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 95 - Forks: 49

monarch-initiative/curategpt

LLM-driven curation assist tool

Language: Jupyter Notebook - Size: 11.9 MB - Last synced at: 28 days ago - Pushed at: about 1 month ago - Stars: 90 - Forks: 14

callahantiff/OMOP2OBO

OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies

Language: Jupyter Notebook - Size: 92 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 88 - Forks: 12

information-artifact-ontology/IAO

information artifact ontology

Language: Common Lisp - Size: 3.42 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 87 - Forks: 26

obi-ontology/obi

The Ontology for Biomedical Investigations

Language: Python - Size: 52.6 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 85 - Forks: 29

OBOFoundry/purl.obolibrary.org

A system for managing OBO PURLs

Language: Python - Size: 1.7 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 83 - Forks: 130

obophenotype/upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.

Language: Makefile - Size: 38.3 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 79 - Forks: 19

biopragmatics/pyobo

📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures

Language: Python - Size: 24.2 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 70 - Forks: 16

geneontology/obographs

Basic and Advanced OBO Graphs: specification and reference implementation

Language: Java - Size: 13.1 MB - Last synced at: 19 days ago - Pushed at: 7 months ago - Stars: 66 - Forks: 12

EBISPOT/DUO

Ontology for consent codes and data use requirements

Language: Makefile - Size: 6.43 MB - Last synced at: 8 months ago - Pushed at: almost 3 years ago - Stars: 64 - Forks: 15

Planteome/plant-ontology

Repository for the Plant Ontology

Language: Perl - Size: 30.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 62 - Forks: 18

jannahastings/emotion-ontology

Ontology for emotions and affective phenomena

Language: Java - Size: 71.7 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 61 - Forks: 13

pato-ontology/pato

PATO - the Phenotype And Trait Ontology

Language: Makefile - Size: 46.5 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 59 - Forks: 18

AgriculturalSemantics/agro

AgrO describes agronomic practices, techniques, and variables used in agronomic experiments.

Language: Python - Size: 5.62 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 57 - Forks: 18

monarch-initiative/MAxO

Medical action ontology

Language: HTML - Size: 237 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 56 - Forks: 4

mapping-commons/sssom-py

Python toolkit for SSSOM mapping format

Language: Python - Size: 17.5 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 54 - Forks: 13

monarch-initiative/koza

Data transformation framework for LinkML data models

Language: Python - Size: 4.68 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 53 - Forks: 5

evidenceontology/evidenceontology

Evidence & Conclusion Ontology development site: Use ISSUES to request terms. See WIKI for how to request terms. See README for how to cite ECO. Visit our website for more project info.

Language: HTML - Size: 59.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 50 - Forks: 20

monarch-initiative/SEPIO-ontology

Ontology for representing scientific evidence and provenance information

Language: Makefile - Size: 230 MB - Last synced at: 4 months ago - Pushed at: 12 months ago - Stars: 50 - Forks: 10

INCATools/ubergraph

Integrated OBO ontology store

Language: Makefile - Size: 174 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 47 - Forks: 5

Superraptor/GSSO

GSSO is the Gender, Sex, and Sex Orientation ontology, including terms related to gender identity and expression, sexual and romantic identity and orientation, and sexual and reproductive behavior.

Language: HTML - Size: 59 MB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 46 - Forks: 9

ebi-chebi/ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

Size: 10.7 KB - Last synced at: 8 months ago - Pushed at: over 3 years ago - Stars: 46 - Forks: 10

Planteome/plant-trait-ontology

Explore the Plant Trait Ontology on the Planteome site.

Language: Python - Size: 16.9 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 45 - Forks: 13

INCATools/semantic-sql

SQL and SQLite builds of OWL ontologies

Language: Python - Size: 7.67 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 45 - Forks: 5

INCATools/dead_simple_owl_design_patterns

A simple system for specifying OWL class design patterns for OBO-ish ontologies.

Language: Python - Size: 5.51 MB - Last synced at: 1 day ago - Pushed at: over 3 years ago - Stars: 45 - Forks: 5

allysonlister/swo

The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, licences, provenance and associated data.

Language: HTML - Size: 9.86 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 44 - Forks: 10

OBOFoundry/COB

An experimental ontology containing key terms from Open Biological and Biomedical Ontologies (OBO)

Language: Makefile - Size: 35.3 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 43 - Forks: 8

vemonet/shapes-of-you

💠 An index for linked open data & standard knowledge descriptions (ontologies, vocabularies, shapes, queries, mappings)

Language: TypeScript - Size: 72.3 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 43 - Forks: 6

rsc-ontologies/rxno

Name Reaction Ontology

Size: 2.26 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 41 - Forks: 12

DiseaseOntology/SymptomOntology

The symptom ontology was designed around the guiding concept of a symptom being: “A perceived change in function, sensation or appearance reported by a patient indicative of a disease”. Understanding the close relationship of Signs and Symptoms, where Signs are the objective observation of an illness, the Symptom Ontology will work to broaden it’s scope to capture and document in a more robust manor these two sets of terms. Understanding that at times, the same term may be both a Sign and a Symptom. The Symptom Ontology is available under CC0 license (https://creativecommons.org/publicdomain/zero/1.0/).

Language: Web Ontology Language - Size: 1.27 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 34 - Forks: 15

EnvironmentOntology/environmental-exposure-ontology

Modular environmental exposures ontology

Language: Makefile - Size: 138 MB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 33 - Forks: 18

ISA-tools/stato

This is the development repository for the STATistics Ontology (STATO). For more information and demonstration on the ontology content, please visit its website:

Language: Java - Size: 11.8 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 33 - Forks: 8

HUPO-PSI/psi-ms-CV

HUPO-PSI mass spectrometry CV

Language: Python - Size: 84.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 31 - Forks: 39

fastobo/fastobo-py

Faultless AST for Open Biomedical Ontologies in Python.

Language: Rust - Size: 2.37 MB - Last synced at: about 1 hour ago - Pushed at: 2 months ago - Stars: 30 - Forks: 4

fastobo/fastobo

Faultless AST for Open Biomedical Ontologies.

Language: Rust - Size: 1.27 MB - Last synced at: 9 days ago - Pushed at: 5 months ago - Stars: 30 - Forks: 3

obophenotype/ncbitaxon

Build for NCBITaxon

Language: Python - Size: 6.49 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 29 - Forks: 7

INCATools/boomer

Bayesian OWL ontology merging

Language: Scala - Size: 1.42 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 29 - Forks: 2

Knowledge-Graph-Hub/kg-obo

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub

Language: Python - Size: 6.12 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 28 - Forks: 2

jannahastings/mental-functioning-ontology

Ontology for all aspects of human mental functioning

Size: 639 KB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 28 - Forks: 13

cmungall/semantic-llama

A knowledge extraction tool that uses a large language model to extract semantic information from text

Language: Python - Size: 1.52 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 28 - Forks: 1

obophenotype/bio-attribute-ontology

source files for OBA (Ontology of Biological Attributes)

Language: Jupyter Notebook - Size: 296 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 27 - Forks: 12

INCATools/dosdp-tools

Utility for working with DOSDP design patterns and OWL ontologies

Language: Scala - Size: 531 KB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 27 - Forks: 5

obo-behavior/behavior-ontology

Neuro Behaviour Ontology: an ontology for human and animal behaviour processes and behaviour phenotypes

Language: Makefile - Size: 88.7 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 25 - Forks: 15

NCI-Thesaurus/thesaurus-obo-edition

OBO Library edition of NCIt

Language: Makefile - Size: 7.62 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 24 - Forks: 8

INCATools/obographviz

Customizable translation of OBO graphs to dot for visualization using graphviz and other tools

Language: JavaScript - Size: 18.4 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 24 - Forks: 6

information-artifact-ontology/ontology-metadata

OBO Metadata Ontology

Language: Makefile - Size: 967 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 23 - Forks: 9

biopragmatics/curies

🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python

Language: Python - Size: 675 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 23 - Forks: 6

OGMS/ogms

Automatically exported from code.google.com/p/ogms

Language: Common Lisp - Size: 2.8 MB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 23 - Forks: 17

OBOFoundry/OBO-Dashboard

Summary Dashboard for Open Biological and Biomedical Ontologies

Language: Python - Size: 393 KB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 22 - Forks: 3

BiodiversityOntologies/bco

Biological Collections Ontology

Language: Makefile - Size: 4.83 MB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 22 - Forks: 3

INCATools/relation-graph

Materialize OWL existential relations

Language: Scala - Size: 606 KB - Last synced at: 9 days ago - Pushed at: 2 months ago - Stars: 21 - Forks: 4

GenEpiO/genepio

The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.

Language: Python - Size: 28.8 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 21 - Forks: 10