GitHub topics: geneontology
geneontology/go-ontology
Source ontology files for the Gene Ontology
Language: Makefile - Size: 2.11 GB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 236 - Forks: 43
geneontology/pathways2GO
Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
Language: Java - Size: 39 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 11 - Forks: 0
kevinrue/GOexpress
Analysies of gene expression data using Gene Ontology
Language: R - Size: 3.47 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 9 - Forks: 2
geneontology/noctua-models
This is the data repository for the models created and edited with the Noctua tool stack for GO.
Language: Makefile - Size: 7.24 GB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 11 - Forks: 3
geneontology/go-site
A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
Language: JavaScript - Size: 14.2 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 47 - Forks: 89
geneontology/go-annotation
This repository hosts the tracker for issues pertaining to GO annotations.
Language: Python - Size: 158 MB - Last synced at: 8 days ago - Pushed at: 14 days ago - Stars: 38 - Forks: 10
geneontology/amigo
AmiGO is the public interface for the Gene Ontology.
Language: JavaScript - Size: 179 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 31 - Forks: 17
geneontology/minerva
Language: Java - Size: 10.7 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 7 - Forks: 9
geneontology/go-shapes
Schema for Gene Ontology Causal Activity Models defined using RDF Shapes
Language: Shell - Size: 144 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 2 - Forks: 0
geneontology/obographs
Basic and Advanced OBO Graphs: specification and reference implementation
Language: Java - Size: 22.1 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 68 - Forks: 14
obophenotype/uberon
An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
Language: Emacs Lisp - Size: 2.04 GB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 141 - Forks: 34
ToledoEM/msigdf Fork of stephenturner/msigdf
Molecular Signatures Database (MSigDB) in a tidy data frame
Language: HTML - Size: 373 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 26 - Forks: 6
geneontology/geneontology.github.io
Repository for storing GO documentation, directly available through the general GO site
Language: SCSS - Size: 17.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 9
geneontology/go-stats
Compute statistics & changes for both the GO ontology and annotations
Language: Python - Size: 142 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
biopatternsg/biopatternsg
This project combines Generative AI and Logic AI to form an integrated process, a pipeline, that retrieves large volumes of scientific information and produces logical models that can be validated and leveraged by human experts. Our goals are to organize and to analyze knowledge with the assistance of AI and other bio-information retrieval tools.
Size: 50.2 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1 - Forks: 1
geneontology/neo
noctua entity ontology
Language: Perl - Size: 3.39 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 9 - Forks: 2
geneontology/helpdesk
The Gene Ontology Helpdesk
Size: 128 KB - Last synced at: 8 days ago - Pushed at: 7 months ago - Stars: 16 - Forks: 6
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: 3 months ago - Pushed at: 3 months ago - Stars: 141 - Forks: 30
INCATools/boomer
Bayesian OWL ontology merging
Language: Scala - Size: 1.42 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 29 - Forks: 2
geneontology/noctua
Graph-based modeling environment for biology, including prototype editor and services
Language: JavaScript - Size: 192 MB - Last synced at: 27 days ago - Pushed at: over 1 year ago - Stars: 40 - Forks: 13
geneontology/go-rhea-boom
Language: Makefile - Size: 12 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 1
geneontology/noctua-landing-page
Language: TypeScript - Size: 99.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0
geneontology/reactome-go-cams
A set of GO-CAMs built automatically from Reactome pathways.
Size: 150 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0
geneontology/wc-gocam-viz
Web component to visualize GO-CAMs
Language: TypeScript - Size: 913 KB - Last synced at: 26 days ago - Pushed at: 6 months ago - Stars: 2 - Forks: 2
geneontology/pipeline
Declarative pipeline for the Gene Ontology.
Size: 1.2 MB - Last synced at: 21 days ago - Pushed at: 22 days ago - Stars: 5 - Forks: 5
jn-goe/gruffi
Granular Functional Filtering (Gruffi) to isolate stressed cells
Language: R - Size: 277 KB - Last synced at: 1 day ago - Pushed at: 10 months ago - Stars: 13 - Forks: 5
geneontology/web-gocam
GO-CAM site as an Angular 2+ Application
Language: TypeScript - Size: 5.32 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0
geneontology/noctua-form-base
Language: TypeScript - Size: 144 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1
EdH66/ensembl_to_GO
Conversion of ensembl_id to gene name and gene ontology
Size: 15.6 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
geneontology/wc-ribbon
This repository contains a collection of web components, initially centered on the GO ribbon, a UI tool to visualize a summary of annotations for gene and gene sets.
Language: TypeScript - Size: 265 KB - Last synced at: 8 days ago - Pushed at: 10 months ago - Stars: 2 - Forks: 2
geneontology/noctua_app_stack
Language: HCL - Size: 264 KB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 0 - Forks: 1
dvklopfenstein/goatools_simulation
Stochastic Gene Ontology Enrichment Analyses (GOEA) Simulations in manscript + Multiple-Test Correction Simulations
Language: Python - Size: 92.4 MB - Last synced at: 5 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 1
geneontology/go-announcements
Announcements related to ontology changes that may impact groups using GO, such as obsoletions, merges, etc.
Size: 4.88 KB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 13 - Forks: 1
geneontology/protege-tutorial
Material for GO OWL/Protege Tutorial
Language: Web Ontology Language - Size: 33.1 MB - Last synced at: about 1 year ago - Pushed at: almost 8 years ago - Stars: 55 - Forks: 40
eriklarsen4/RNAseq
Template R code for bioinformatics analysis pipeline of transcriptomic Illumina datasets
Language: HTML - Size: 14 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 0
genescf/GeneSCF
Gene Set Clustering based on Functional annotation
Language: Perl - Size: 4.53 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 5
geneontology/shared-annotation-check
Tools and data for intersections/co-annotation checks in the Gene Ontology.
Language: JavaScript - Size: 30.3 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1
geneontology/go-graphstore
Gene Ontology RDF GraphStore
Language: Makefile - Size: 83 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 4
francescopatane96/RNA-seq_Pipeline
Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last module of the project allows you to use clusterprofiler in order to perform ORA and GSEA analysis (over-representation analysis and gene set enrichment analysis) using GeneOntology (GO), disease ontology (DO), KEGG, reactome eg...
Language: Jupyter Notebook - Size: 31.3 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1
geneontology/noctua-form-legacy
Simple annoton editor workbench for Noctua.
Language: HTML - Size: 2.24 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 3
geneontology/unipathway
Unipathway ontology (inactive)
Language: Jinja - Size: 3.23 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
geneontology/paint
This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
Language: Java - Size: 18.6 MB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 4 - Forks: 4
sinc-lab/Comparison-of-Protein-learning
Comparison of protein learning
Language: Jupyter Notebook - Size: 17.7 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 1
geneontology/gocam-sif-pyexport 📦
Export GO-CAMs to SIF (Python)
Language: Python - Size: 986 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 1
geneontology/curie-util-es5
Javascript Library to translate CURIEs to IRIs and vice versa
Language: JavaScript - Size: 9.77 KB - Last synced at: 30 days ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0
geneontology/gaferencer
Perform annotation deepening and satisfiability checking for GO annotations in GAFs
Language: Scala - Size: 232 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1
geneontology/go-api 📦
Gene Ontology API deployment
Size: 22.5 KB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 5 - Forks: 1
sivkri/gene-info-extractor
Gene Info Extractor: A Python script to extract gene information and annotations from CSV data
Language: Python - Size: 52.7 KB - Last synced at: 6 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
geneontology/ribbon 📦
(DEPRECATED) Short form matrix view of all GO annotations for a given gene
Language: JavaScript - Size: 37.8 MB - Last synced at: 29 days ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 7
geneontology/syngo2lego_data_conversion
A repo for conversion of syngo JSON to GO-CAM OWL
Language: Python - Size: 6.29 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
geneontology/syngo2lego
scala app for converting SynGO JSON to OWL (ttl) for loading into noctua
Language: Scala - Size: 15.4 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1
geneontology/biolink-api Fork of monarch-initiative/biolink-api
API for linked biological knowledge
Language: Python - Size: 1.25 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 1
geneontology/noctua-form
Language: TypeScript - Size: 85.2 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0
geneontology/obo-edit
OBO-Edit is an open source ontology editor written in Java.
Language: Java - Size: 335 MB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 7 - Forks: 1
FriedbergLab/debias Fork of parnaljoshi/debias
Language: Python - Size: 10.8 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
geneontology/protege-taxon-constraints
Protégé plugin displaying inferred taxon constraints
Language: Scala - Size: 1.08 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 0
Greco-Lab/FunMappOne
FunMappOne: a tool to summarize and visually navigate functional categories in multiple experiments.
Language: R - Size: 2.71 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 3
geneontology/signor2gocam
Converting Signor pathways to GO-CAM
Language: Python - Size: 135 KB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 2
geneontology/gocamgen
Base repo for constructing GO-CAM model RDF
Language: Python - Size: 295 KB - Last synced at: about 1 month ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
geneontology/termgenie
Web-application for pattern-based ontology class generation
Language: Java - Size: 8.04 MB - Last synced at: about 1 year ago - Pushed at: almost 9 years ago - Stars: 7 - Forks: 6
geneontology/go-opensearch
A self-contained OpenSearch server using BBOP JS and the GOlr backed. Designed to integrate with AmiGO 2.
Language: JavaScript - Size: 4.01 MB - Last synced at: about 1 year ago - Pushed at: almost 12 years ago - Stars: 0 - Forks: 0
geneontology/go-exp
General technique test and test space for Gene Ontology Consortium projects.
Language: JavaScript - Size: 4.38 MB - Last synced at: 23 days ago - Pushed at: about 10 years ago - Stars: 0 - Forks: 1
geneontology/go-ncit
Tracking progress on GO-NCIt integration
Size: 0 Bytes - Last synced at: about 1 year ago - Pushed at: over 9 years ago - Stars: 0 - Forks: 0
geneontology/ec-extractor
Extracts OBO from EC records
Language: Python - Size: 1.95 KB - Last synced at: about 1 year ago - Pushed at: over 9 years ago - Stars: 0 - Forks: 0
geneontology/deep_sea
A repository to discuss addition of terms for deep sea microbial ecology
Size: 0 Bytes - Last synced at: about 1 year ago - Pushed at: over 9 years ago - Stars: 2 - Forks: 0
geneontology/contributor-data-pool
Contributor data pool: an experimental freestanding structured resource for external data contributors
Size: 5.86 KB - Last synced at: about 1 year ago - Pushed at: over 9 years ago - Stars: 1 - Forks: 1
geneontology/contributor-data-services
Contributor data services: experimental scripts and servers to support the mission of the contributor-data-pool.
Size: 1.95 KB - Last synced at: about 1 year ago - Pushed at: over 9 years ago - Stars: 0 - Forks: 0
geneontology/oboedit-bbop
Language: Java - Size: 4.37 MB - Last synced at: about 1 year ago - Pushed at: about 9 years ago - Stars: 0 - Forks: 0
geneontology/training-materials
Training and tutorial materials for the Gene Ontology
Size: 5.86 KB - Last synced at: about 1 year ago - Pushed at: about 9 years ago - Stars: 0 - Forks: 0
geneontology/mybiocaddie Fork of biodatasets/mybiocaddie
Metadata about GO datasets
Language: CSS - Size: 592 KB - Last synced at: about 1 year ago - Pushed at: almost 9 years ago - Stars: 1 - Forks: 0
geneontology/rhea2go
Mapping from RHEA to GO
Language: Perl - Size: 645 KB - Last synced at: about 1 year ago - Pushed at: almost 9 years ago - Stars: 0 - Forks: 0
geneontology/noctua-reasoner
Quick and dirty client-side reasoner for Noctua
Language: JavaScript - Size: 52.7 KB - Last synced at: about 1 year ago - Pushed at: almost 9 years ago - Stars: 5 - Forks: 0
geneontology/autophagy
A site for the GO autophagy project
Size: 9.77 KB - Last synced at: about 1 year ago - Pushed at: almost 9 years ago - Stars: 0 - Forks: 2
geneontology/go-xref-analysis
Language: Prolog - Size: 169 KB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0
geneontology/panther-release-wrangling
All the little chores that need to be done to handle new releases of PANTHER
Language: Java - Size: 7.81 KB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 1
geneontology/panther-enrichment
One of the main uses of the GO is to perform enrichment analysis on gene sets. For example, given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene set.
Size: 0 Bytes - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 2
geneontology/touchup
for keeping the PAINT GAF files up to date
Language: Java - Size: 74.5 MB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 3
geneontology/go-inca-form
INCA Form (TermGenie2) for GO
Size: 10.7 KB - Last synced at: about 1 year ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0
geneontology/go-notebooks
Jupyter notebooks for GO
Language: Jupyter Notebook - Size: 29.3 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 1
geneontology/gocam-utils
Library for general data access and update of GO-CAMs (www.geneontology.org/gocam)
Size: 2.93 KB - Last synced at: 10 days ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
geneontology/noctua-repl
REPL environment for the Noctua annotation tool
Language: JavaScript - Size: 52.7 KB - Last synced at: 29 days ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0
geneontology/ontobio Fork of biolink/ontobio
python library for working with ontologies and ontology associations
Language: Jupyter Notebook - Size: 2.9 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 0
geneontology/go-mappings
Automated and manual mappings
Language: HTML - Size: 4.1 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
geneontology/gocam-sif-export
Prototype export GO-CAMs to SIF (NodeJS) - favor gocam-sif-pyexport
Language: JavaScript - Size: 115 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
geneontology/activity-flow-editor
Lightweight reusable web component for activity-centric visualizations and edits
Size: 3.91 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
geneontology/molecular_function_refactoring
A repository for the development of patterns and terms for axiomatisation and refactoring of the GO MF branch
Language: Python - Size: 52.7 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1
geneontology/pseudomonas-genome-database Fork of brinkmanlab/pseudomonas-genome-database
Size: 170 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
geneontology/archive-reconstruction
Codes to move various legacy files to the current release.geneontology.org
Language: Python - Size: 1.35 MB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0
geneontology/example-sparql
This contains example SPARQL queries that is accessible by GRLC
Size: 8.79 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
geneontology/noctua-annotation-review
Language: JavaScript - Size: 48.9 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
geneontology/api-gorest
GitHub repository for the NodeJS/Express REST web service go-api-sparql. Used for the front-end www.geneontology.org/gocam.
Language: JavaScript - Size: 130 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
geneontology/gp2term
Language: Python - Size: 14.6 KB - Last synced at: 8 days ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1
geneontology/go-pombase
Code for generating process-centric GO-CAM models from GAFs
Language: Python - Size: 84 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
geneontology/curie-util-py
Python Library to translate CURIEs to IRIs and vice versa
Language: Python - Size: 20.5 KB - Last synced at: 18 days ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
geneontology/noctua-search
Language: JavaScript - Size: 19.7 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
tmsincomb/amigo
Amigo 2 API Wrapper
Language: Python - Size: 5.86 KB - Last synced at: 2 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
tair/ifad-backend
Interactive Functional Annotations Dashboard
Language: TypeScript - Size: 12.3 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1
YoannPa/GOLIAT
GOLIAT - Gene Ontology LInk Analysis Tool.
Language: Python - Size: 6.21 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
Pranavkhade/GOFindBias
The current main function of this project is to help people with .gaf file analysis.
Language: Python - Size: 2.54 MB - Last synced at: 11 days ago - Pushed at: almost 8 years ago - Stars: 1 - Forks: 1
ZeweiChu/GOViewer
gene ontology browser
Language: Java - Size: 4.75 MB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 2 - Forks: 0
