NIFT – NeuroImaging Feature Terminology for mining measurable imaging indices from literature

NeuroImage Feature Terminology (NIFT): a controlled terminology for the annotation of brain imaging features

Anandhi Iyappan a,b, Erfan Younesi a, Alberto Radolfi c,d , Henri Vrooman e,  Shashank Khanna a,b, Giovanni B. Frisonid,e, Martin Hofmann-Apitius a,b, Alzheimer's Disease Neuroimaging Initiative

Submitting to Journal of Alzheimer Disease

Terminology file:

Supplementary files:


CSEO – The Cigarette Smoke Exposure Ontology

Erfan Younesi, Sam Ansari, Michaela Guendel, Shiva Ahmadi, Chris Coggins, Julia Hoeng, Martin Hofmann-Apitius, Manuel C. Peitsch

Submitted to the Journal of Biomedical Semantics

Ontology file:

MSO-BFO integrated

An ontology for Multiple Sclerosis automatically retrieves knowledge from PubMed abstracts and electronic health records

Ashutosh Malhotra, Michaela Guendel,Abdul Mateen Rajput, Heinz-Theodor Mevissen,  Albert Saiz,Xavier Pastor,Raimundo Lozano-Rubi, Elena H Martinez-Lapsicina,Bernd Mueller,Ekaterina Kotelnikova, Luca Toldo, Martin Hofmann-Apitius, Pablo Villoslada.

Link to the Multiple Sclerosis disease ontology owl file:


Parkinson's Disease Ontology for Representation and Modeling of the Parkinson's Disease Knowledge Domain

Erfan Younesi, Ashutosh Malhotra, Michaela Gündel, Phil Scordis, Alpha Tom Kodamullil, Jonathan Van Eyll, Matt Page, Bernd Müller, Stephan Springstubbe, Ullrich Wüllner, Dieter Scheller, Martin Hofmann-Apitius

Ontology file: 

PDO ontology

Genome Medicine (additional files)

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer's disease.

Ashutosh Malhotra,Erfan Younesi, Shweta Bagewadi and Martin Hofmann-Apitius. 


A formal ontology for representing the domain knowledge specific to Alzheimer's disease

Ashutosh Malhotra, Erfan Younesi, Michaela Gündel, Bernd Müller, Michael T. Heneka, Martin Hofmann-Apitius

Link to the Alzheimer's disease ontology owl file:


HuPSON: Ontology for Human Physiology Simulation supporting knowledge-driven simulations in biomedicine

Michaela Gündel, Erfan Younesi, Jiali Wang, Ashutosh Malhotra, Hui Li, Bijun Zhang, Bernard de Bono, Heinz-Theodor Mevissen, Martin Hofmann-Apitius.

Submitted to Journal of Biomedical Semantics, 2013 Biomedical Ontology Issue.

Biomarker terminology

Mining biomarker information in biomedical literature

Erfan Younesi, Luca Toldo, Bernd Müller, Christoph M. Friedrich, Natalia Novac, Alexander Scheer, Martin Hofmann-Apitius, Juliane Fluck

Journal: BMC Medical Informatics & Decision Making

Pharmacome Tools

Pharmacome Tools: A Cytoscape Plugin to Filter Large Drug-Protein Networks for Predicting New Drug-Protein Associations.

Authors: Mohammad Shahid, Karl N. Kirschner, and Martin Hofmann-Apitius.

Submitted to Bioinformatics (

The zipped file contains the plugin binaries and sample data for downloading and testing the plugin.

Pharmacome Tools (ZIP-archive, 32 MB)

Scientific reports (Additional files)

Exploring novel mechanistic insights in Alzheimer's disease by assessing reliability of protein interactions

Ashutosh Malhotra, Erfan Younesi, Sudeep Sahadevan, Joerg Zimmermann and Martin Hofmann-Apitius



Computable cause-and-effect models of healthy and Alzheimer´s disease states and their mechanistic differential analysis.

Alpha Tom Kodamullil, Erfan Younesi, Mufassra Naz, Shweta Bagewadi, Martin Hofmann-Apitius
(accepted in – Alzheimer´s & Dementia, 2015)

Download (Zip-archiv)

Epilepsy Knowledge Assembly

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Güldenpfennig, and Martin Hofmann-Apitius (submitted – Oxford Database, 2018)

Download (epilepsy)