Wolfgang Müller

FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.

DeepCurate was a CompLS (Computational. Life Sciences) project, funded by the BMBF, the German ministry of Education and Research.

nfdi4health aims to create the most comprehensive inventory of German epidemiological, public health and clinical trial data to date. It builds a centralised data catalogue with elaborate search functionalities, sophisticated data access management, and a data analysis toolbox, while respecting stringent requirements for privacy concerning personal health data. Standardisation services ensure a high degree of interoperability. Use cases covering prototypical study types and areas of research show ...

SDBV group using Hub

MESI-Review 2024

MESI-STRAT: Systems Medicine of Metabolic-Signaling Networks -A New Concept for Breast Cancer Patient Stratification. Breast cancer is a complex disease with high prevalence in the European Union and world-wide. 75%-80 of the patients have estrogen receptor-positive (ER)-positive tumors and are treated with endocrine therapies. Endocrine therapies, which block ER-driven tumor growth, show high efficacy. Yet, a significant proportion of the patients will eventually relapse with metastatic breast ...

MESI-STRAT Review

PoLiMeR is funded through the EU Marie Skłodowska-Curie Innovative Training Network (ITN), which drives scientific excellence and innovation. ITNs bring together universities, research institutes, industry and clinical partners from across the world to train researchers to doctorate level.

Metabolic diseases are a burden on the European population and health care system. It is increasingly recognised that individual differences with respect to history, lifestyle, and genetic make-up affect disease ...

This project bundles information about COVID-19 related studies and tools in Germany. It intends to provide an information hub for the different initiatives, their aims, their processes, standards and study protocols, as well as their available data and metadata. It is initiated by the German National Research Data Infrastructure for Personal Health Data (nfdi4health), a consortium that plans to establish a concept for a federated research data infrastructure for personal health data in Germany. ...

The project "INtegrative COllaborative modeling in systems MEdicine" aims at connecting different heterogenous datasets and individual models within systems medicine.

The GMDS project group bundles activities for health-related FAIR data infrastructures in the fields of biomedical research, clinical data management and medical informatics in Germany. It aims at providing a platform for information exchange about best practice for and implementation of FAIR data management in these fields and constructing a network of FAIR data managements providers in these fields. Through bridging between providers and potential users of such data management platforms within ...

We will contribute to the LiSyM Research Network an open source, freely available and reproducible multiscale model of the human liver from single cell metabolism to whole liver function. The model will be available in existing standards of systems biology, provide standardized interfaces for data integration and be fully annotated to available biological, medical and computational ontologies. All data, models and source code will be shared within the LiSyM Research Network and made available to ...

Here we collect curated data to be integrated into public repositories

Current chemical concept recognition tools have demonstrated significantly lower performance for in full-text articles than in abstracts. Improving automated full-text chemical concept recognition can substantially accelerate manual indexing and curation and advance downstream NLP tasks such as relevant article retrieval. Participating in BioCreative Track NLM-Chem we focus identifying chemicals in full-text articles (i.e. named entity recognition and normalization).

Chemical named entity recognition (NER) is a significant pre-processing task in natural language processing. Identification and extraction of chemical entities from biomedical literature and entities linking to the knowledge base are essential steps for the chemical text-mining pipeline. However, the identification of chemical entities in a biomedical text is a challenging task due to the diverse morphology of chemical entities and the different types of chemical nomenclature. In this work, we ...

The ground truth collection for the BeeProject. Contains 3819 png scans of hanwritten tables in the folder 'LHI_PNG', followed by digital json and excel files in 'LHI_GT'

One example of a ReStoRunT sheet.

This file is part of a tutorial for the Gesellschaft für Ökologie and the NFDI4Biodiversity.

The purpose of this is using it in ModelXChange.

This table validation code is about simplifying validation of templates for end users. The main use case is an experimental scientist Elie sharing data with a Bioinformatician Bob. Elie and Bob agree to use a common template. This code enables Bob to provide Elie with a validator that checks if Elie's data conforms to the template. Making such a template check should be simple, using the checker should be simple, too. We seek to fill both requirements.

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling. The publication for the introduction and analysis of the benchmark problem collection is available at https://academic.oup.com/bioinformatics/article/35/17/3073/5280731.

Report of the Data Management Foundry Workshop, 19th-20th of March, 2012, Vienna, Austria

a test file

Participants of 2nd FAIRDOM PALs meeting in Munich

FAIRDOM User Meeting Introduction

SEEK functionalities presented by Olga Krebs

Talk given by Olga Krebs at EmPowerPutida project meeting in Bruxeles 23rd November 2016

Written and presented by Wolfgang Müller (HITS) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Prepared and presented by Carole Goble (University of Manchester), Wolfgang Mueller (HITS), Dagmar Waltermath (University of Rostock), at the Reproducible and Citable Data and Models Workshop, Warnemünde, Germany. September 14th - 16th 2015.

Presentation of data management concepts for ERASysAPP projects at IMOMESIC kick off meeting on 8 th of May 2015 in Heidelberg. Part I presented by Olga Krebs

Carole Goble's talk at ERASysAPP - EXCHANGE Networking and Info Day for research projects of the first ERASysAPP call (a day before PALs meeting)

Poster presented at SWAT4LS - Semantic web applications and tools for life science- in Berlin at 10 of december 2014 by Olga Krebs

Presentation by Carole Goble at the International Semantic Web Conference 2013 in Sydney Australia about the use of semantic web technology in SEEK and RightField.

The talk presented by Carole Goble and Wolfgang Mueller at the SysMO evaluation conference 2013 in Berlin.

SEEK at ICSB 2012 (presented by Olga Krebs)