Bio-Ontology Research Group (@bio-ontology-research-group)
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Top repositories

1

machine-learning-with-ontologies

Jupyter Notebook
105
star
2

deepgo

Function prediction using a deep ontology-aware classifier
Python
75
star
3

ontology-tutorial

Ontology Tutorial
Jupyter Notebook
67
star
4

deepgoplus

DeepGO with GOPlus axioms
Python
62
star
5

mowl

mOWL: Machine Learning library with Ontologies
Python
48
star
6

walking-rdf-and-owl

Feature learning over RDF data and OWL ontologies
Python
44
star
7

phenomenet-vp

A phenotype-based tool for variant prioritization in WES and WGS data
Java
34
star
8

opa2vec

Turning Ontologies Plus Annotation Properties into Vectors
Groovy
34
star
9

multi-drug-embedding

Method for drug repurposing from knowledge graphs and literature
Python
31
star
10

el-embeddings

Embeddings for ontologies in the Description Logic EL++
Python
21
star
11

onto2vec

Representation learning for ontologies and their annotations
Groovy
20
star
12

DL2Vec

Convert Description Logic axioms into a graph, and generate embedding representation for the nodes.
Python
20
star
13

unit-ontology

An ontology of units of measurements
Makefile
18
star
14

deepgozero

DeepGO with Fuzzy DL
Python
15
star
15

vec2sparql

SPARQL Endpoint with functions for computing embedding similarities
Java
13
star
16

DeepSVP

Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity
Python
12
star
17

SMUDGE

SmuDGE: Semantic Disease Gene Embeddings
Python
12
star
18

Onto2Graph

Generating graph structures from OWL ontologies
JavaScript
11
star
19

DeepViral

Source code for the DeepViral paper
Python
9
star
20

AberOWL

Ontology repository that provides Reasoning as as Service
Groovy
9
star
21

DeepMOCCA

Graph Neural Network model for survival analysis from multi-omics data
Jupyter Notebook
8
star
22

aberowl-orepo

AberOWL Ontology Repository
JavaScript
7
star
23

pathophenodb

Web application and additional content for PathoPhenoDB
Python
7
star
24

deeppheno

Python
6
star
25

interpretable-learning

Generate interpretable rules from knowledge bases
Python
5
star
26

mowl-tutorial

Jupyter Notebook
5
star
27

padimi

4
star
28

phenogocon

Method to predict phenotypes from functions
Groovy
4
star
29

predCAN

Ontology-based prediction of cancer driver genes
Python
4
star
30

OAEI2016

Ontology Alignment Evaluation Initiative 2016 Campaign
Web Ontology Language
3
star
31

neural-network-plant-trait-classification

Fine-grained trait classification using deep convolutional neural networks
Python
3
star
32

ontology-extension

Combining lexical and context features for automatic ontology extension
Python
3
star
33

aberowlweb

JavaScript
3
star
34

genepheno

this repository contains text mined gene-phenotype data
Perl
3
star
35

UNMIREOT

Tools to identify, diagnose, and semi-automatically repair hidden contradictions in biomedical ontologies
Groovy
2
star
36

whatizit

A dictionary-based Named Entitiy Recognition tool
Java
2
star
37

ai-biomed-summer-school

TeX
2
star
38

aberowl-meta

Install script and sub-directories for AberOWL
Groovy
2
star
39

mo-phenotype-analysis

Model organism phenotypes contribution in predicting gene disease associations
Python
2
star
40

BORD

Python
2
star
41

phenomeweb

Python
1
star
42

icdpheno

Perl
1
star
43

Sparql2OWL

Java
1
star
44

EL2Box_embedding

Python
1
star
45

ddimech

Python
1
star
46

foodontology

Java
1
star
47

pgsim

Similarity mesure analysis
Python
1
star
48

ontology-and-phenotype-tutorial

Information the the tutorial on phenotypes
TeX
1
star
49

DDIEM

DDIEM
Python
1
star
50

tsoe

Task Specific Ontology Evaluation
1
star
51

deepgoweb

JavaScript
1
star
52

hpi-predict

The scripts to reproduce the analysis of the HPI prediction paper
Jupyter Notebook
1
star
53

semantic-haiku

Groovy
1
star
54

metabolitenet

Jupyter Notebook
1
star
55

pmcanalysis

Groovy
1
star
56

semkernel

Java
1
star
57

Random-walk-with-edge-stratification

C++
1
star
58

jcel

Reasoner for the description logic EL+.
Java
1
star
59

phenomeblast

Source for PhenomeNET and related projects
Groovy
1
star
60

similarityonMGI

this repsoitory contanst data ns scripts to evaluate similarity between gene-phenotypes and disease phenotypes on the MGI gene-disease datasets
Groovy
1
star