Tools made as a part of the Gkoutos Group / HDR UK Birmingham from current or previous
| Tool | Contributors | Description | DOI |
|---|---|---|---|
| BBCAF Pipeline | labrax | This is a simple pipeline that lets you personalise the settings built on top of caret - it does 5 CV using any number of algorithms configured in caret | https://doi.org/10.1093/eurheartj/ehy815 https://doi.org/10.1371/journal.pmed.1003405 |
| CovidSurg | Risk calculator is based upon data from patients infected with SARS-CoV-2 within the 7-days before to 30-days after surgery | ||
| LCA Clustering and table functions | Generation of different types of clusters, such as LCA, and mixed models | https://doi.org/10.1136/heartjnl-2019-316091 | |
| PGM | azizfurqan | Biomarker prioritisation and power estimation using ensemble gene regulatory network inference | https://doi.org/10.3390/ijms21217886 |
| PowerTools | labrax | A random forest based biomarker discovery and power analysis framework for diagnostics research | https://doi.org/10.1186/s12920-020-00826-6 |
| RNA-seq pipeline | labrax | Pipeline to assist downloading, preparing genome files and then performing analysis on RNA-seq files using either human or mice reference genome | https://dx.doi.org/10.1172%2Fjci.insight.139179 https://heart.bmj.com/content/104/Suppl_6/A95 |
| Vec2SPARQL | coolmaksat, amalic, athro | SPARQL Endpoint with functions for computing embedding similarities | |
| Komenti | reality | Semantic text mining framework | https://doi.org/10.1101/2020.08.04.233049 |
| komenti-guides | reality | Guides for how to use komenti | https://doi.org/10.1101/2020.08.04.233049 |
| komenti-validator | reality | Front-end validation tool for Komenti | https://doi.org/10.1101/2020.08.04.233049 |
| donita | reality | (In development) Provisional term management service for ontologies | |
| generate-patients | reality | Generate noisy patients for semantic similarity experiments | |
| sampledd | reality | Sample patients who will die during their stay in MIMIC-iii, and their associated text records. | |
| add_synonyms | reality | Add a list of synonyms to an OWL ontology | https://doi.org/10.1101/2020.07.10.197541 |
| mimpred | reality | (In development) Reproducible experimental foundation for experiments with MIMIC | |
| mim3val | reality | Test the performance of several negation algorithms over MIMIC-III, and a standalone implementation of komenti-negation | https://doi.org/10.1016/j.compbiomed.2021.104216 |
| mimsim | reality | Tools for performing semantic similarity over MIMIC-III | https://doi.org/10.1101/2021.01.26.428269 |
| ECMO | reality | Extended Clinical Measurement Ontology with additional axiomatisation and connection with HP and MP ontologies | |
| synonym_expansion_validation | reality | Extended HPO and DO vocabularies for use with text mining | https://doi.org/10.1101/2020.07.10.197541 |
| UNMIREOT | reality | Tools for testing the mutual consistency of biomedical ontologies | https://doi.org/10.1186/s12911-020-01336-2 |
| OCIMIDO | sap218 | Ocular Immune-Mediated Inflammatory Diseases Ontology | https://doi.org/10.1016/j.compbiomed.2021.104542 |
| Jabberwocky | sap218 | Toolkit for ontologies: text mining & synonym curation | https://doi.org/10.21105/joss.02168 |