Python Gene-ontology Resources

Ontoseer This document provides documentation for the first version of OntoSeer.OntoSeer is a tool that monitors the ontology development process andp

OntoProtein This is the implement of the paper "OntoProtein: Protein Pretraining With Ontology Embedding". OntoProtein is an effective method that mak

IP-Grabber A tool to generate valid ip addresses of 55 countries. These ip's can be used for OpenBullet. ive added the feature to set the generated ip

Extract gene length based on featureCount calculation gene nonredundant exon length method.

GetTss python Package extract gene TSS site form gencode/ensembl/gencode database GTF file and export bed format file. Install $ pip install GetTss Us

GetTsite python Package extract gene TSS/TES site form gencode/ensembl/gencode database GTF file and export bed format file. Install $ pip install Get

Enabling a developer to use Ontology Web Language (OWL) along with its reasoning capabilities in an Object Oriented Programming (OOP) paradigm, by pro

IMGTgeneDL 0.1.0 Jamie Heather | CCR @ MGH | 2021 This script provides an alternative way to access TCR and IG genes stored in IMGT/GENE-DB. It's prim

Transcription Factor binding predictions with Attention and Transformers A repository with exploration into using transformers to predict DNA ↔ transc

Gauchian: WGS-based GBA variant caller Gauchian is a targeted variant caller for the GBA gene based on a whole-genome sequencing (WGS) BAM file. Gauch

BERTMap: A BERT-based Ontology Alignment System Important Notices The relevant paper was accepted in AAAI-2022. Arxiv version is available at: https:/

Narrative-cartography-ontology This repository contains the map content ontology used in narrative cartography, which is associated with a submission

DeepGeneAnnotator: A tool to annotate the gene in the genome The master thesis of the "Using deep learning to predict gene structures of the coding ge

GENE This is an improved version of GENE. In the original version, the states are generated from the decoder of VAE. We have to check whether the gere

Python wrapper to different clients to determine how a particular term is used.

Production Ontology Merging (PrOM) Framework OWL 2 DL ontology merging framework tailored to the production domain Features preprocessing: translation

Text classification is the task of assigning a set of predefined categories to free text. Text classifiers can be used to organize, structure, and categorize pretty much anything. For example, new articles can be organized by topics, support tickets can be organized by urgency, chat conversations can be organized by language, brand mentions can be organized by sentiment, and so on.

Install vintools To download this package from pypi: pip install vintools Install the development package To download and install the developmen

Enformer - Pytorch (wip) Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch. The original tensorflow

CRISPRanalysis InDels analysis of CRISPR lines by NGS amplicon sequencing technology for a multicopy gene family. In this work, we present a workflow

MUSCO - Multimodal Descriptions of Social Concepts Automatic Modeling of (Highly Abstract) Social Concepts evoked by Art Images This project aims to i

CaLiGraph for Semantic Reasoning Evaluation Challenge This repository contains code and data to use CaLiGraph as a benchmark dataset in the Semantic R

Python module ordered ordered module is the opposite to random - it maintains order in the program. import random x = 5 def increase(): global x

GIANT Code and data for paper "GIANT: Scalable Creation of a Web-scale Ontology" https://arxiv.org/pdf/2004.02118.pdf Please cite our paper if this pr

Markup is an online annotation tool that can be used to transform unstructured documents into structured formats for NLP and ML tasks, such as named-entity recognition. Markup learns as you annotate in order to predict and suggest complex annotations. Markup also provides integrated access to existing and custom ontologies, enabling the prediction and suggestion of ontology mappings based on the text you're annotating.

DeepFRI Deep functional residue identification Citing @article {Gligorijevic2019, author = {Gligorijevic, Vladimir and Renfrew, P. Douglas and Koscio

Trove Trove is a research framework for building weakly supervised (bio)medical named entity recognition (NER) and other entity attribute classifiers