Xiaoming Hu

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About Xiaoming Hu:

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SEEK ID: https://testing.sysmo-db.org/people/426

Location: Germany

ORCID: Not specified

Joined: 11th Jun 2025

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Programme: Independent Projects

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Xiaoming Test

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Start date: 30th Dec 2018

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SDBV, Heidelberg Institute for Theoretical Studies

ROR ID: https://ror.org/01f7bcy98

Department: SDBV

Country: Germany

City: Heidelberg

Web page: https://www.h-its.org

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A Multiscale Simulation Approach to Compute Protein–Ligand Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics

Xiaoming Test

Abstract

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Authors: Abraham Muñiz-Chicharro, Gaurav K. Ganotra, Rebecca C. Wade

Date Published: 27th Oct 2025

Publication Type: Journal Article

DOI: 10.1021/acs.jcim.5c01488

Citation: J. Chem. Inf. Model. 65(20):11215-11231

Created: 29th Oct 2025 at 16:59

Flexible Metadata Structuring for Research Data Management Through the FAIRDOM-SEEK Platform - Implementing Tailored and Complex Metadata Schemes in SEEK

Xiaoming Test

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Abstract (Expand)

Modern research projects increasingly require hybrid metadata approaches that balance adherence to domain-overarching, as well as domain-specific community standards with flexibility for project- or … resource-specific metadata. The FAIRDOM-SEEK platform [1] is a widely used research data management system designed to support diverse domains, from systems biology to health research data, by integrating standardized metadata models (e.g., the ISA framework [2]) with customizable extensions. To address this need, we introduce the Extended Metadata feature in SEEK, which allows researchers to extend core metadata schemas with user-defined fields, hierarchies, and semantic annotations while ensuring interoperability with domain-specific standards. We demonstrate this capability through two use cases: 1. NFDI4Health Local Data Hubs (LDH) [3],[4]: In the context of the German National Research Data Infrastructure for Personal Health Data (NFDI4Health [5]), we have developed Local Data Hubs (LDH) based on the SEEK platform. These hubs support federated data structuring and sharing for sensitive health data from clinical trials, epidemiological studies, and public health research and allow to connect local platforms to the central metadata repository of NFDI4Health, the German Health Study Hub. Given the complexity of the NFDI4Health metadata schema (MDS) [6], the SEEK-based LDH software utilizes the Extended Metadata feature to fully represent the schema, allowing for flexible project-defined metadata extensions. 2. FAIR Data Station (FAIR-DS) [7]: Based on the ISA-framework, with the addition of Observation units from MIAPPE [8], the FAIR-DS is a web application that enables users to create and manage metadata according to FAIR principles. Using packages and terms configured through the UI, it generates Excel spreadsheets which are then populated to gather the metadata. FAIR-DS is then used to validate the metadata and generates RDF datasets representing the content. SEEK has been updated to allow Extended Metadata and Sample Types to be configured automatically via these RDF datasets, and also the content can be imported, and updated, in a single action. The Extended Metadata feature allows users to define additional metadata attributes to be tailored to specific data types, ensuring compliance with standards. When creating a resource, users can select an Extended Metadata type from a dropdown menu, dynamically triggering the rendering of associated metadata input forms within the web interface. This enables seamless integration of resource-specific metadata (e.g., clinical trial study metadata) alongside core descriptive fields. Currently, only instance administrators can create, manage (enable/disable), and delete additional attributes for specific resource types (e.g., ISA items such as Investigation, Study, Assay, as well as Projects and Models) based on specific schemas (e.g., the NFDI4Health MDS). Attribute types range from simple (e.g., string, text, date, integer, Boolean) to complex (e.g., controlled vocabularies linked to ontologies, nested hierarchical structures), with validation rules for mandatory or optional fields. Regular expressions are introduced to ensure correct input formatting. Metadata schemas can be created through backend seed files, JSON uploads, or FAIR-DS RDF imports. These schemas are programmatically accessible via the SEEK REST API, enabling automated metadata creation and retrieval. This ensures interoperability with external tools while adhering to FAIR data principles.

Authors: Xiaoming Hu, Stuart Owen, Frank Meineke, Finn Bacall, Carole Goble, Wolfgang Müller, Martin Golebiewski

Date Published: 2025

Publication Type: Conference Paper

DOI: 10.5281/zenodo.16736322

Citation: Zenodo. https://zenodo.org/doi/10.5281/zenodo.16736322.

Created: 11th Nov 2025 at 18:20

A Sample Journal Article

Xiaoming Test

Abstract

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Authors: John Doe, Jane Smith

Date Published: 2024

Publication Type: Journal Article

DOI: 10.1234/example.doi

Citation:

Created: 26th Nov 2025 at 09:59

A Chapter Inside a Book

Xiaoming Test

Abstract

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Author: Charlie Brown

Date Published: 2023

Publication Type: Book Chapter

Citation:

Created: 26th Nov 2025 at 09:59

An Analysis of Example

Xiaoming Test

Abstract

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Authors: John Smith, Jane Doe

Date Published: 1st Jun 2022

Publication Type: Conference Paper

Citation:

Created: 26th Nov 2025 at 10:09

A Conference Paper Example

Xiaoming Test

Abstract

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Author: Sarah Miller

Date Published: 2022

Publication Type: Conference Paper

Citation:

Created: 26th Nov 2025 at 09:59

An Example PhD Thesis

Xiaoming Test

Abstract

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Author: Alex Taylor

Date Published: 2021

Publication Type: PhD Thesis

Citation:

Created: 26th Nov 2025 at 09:59

The Example Book

Xiaoming Test

Abstract

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Author: Douglas Adams

Date Published: 2020

Publication Type: Book

Citation:

Created: 26th Nov 2025 at 09:59

A Technical Report Example

Xiaoming Test

Abstract

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Author: Carol Lee

Date Published: 2019

Publication Type: Report

Citation:

Created: 26th Nov 2025 at 09:59

Miscellaneous Example

Xiaoming Test

Abstract

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Author: Person Unknown

Date Published: 2018

Publication Type: Other

Citation:

Created: 26th Nov 2025 at 09:59

Milton’s Book of Numbers: Book 1 and Its Catalog

Xiaoming Test

Abstract (Expand)

This chapter shows how book 1 of Paradise Lost metaphorically depicts the role of the devil in raising the rebel angels out of their “bottomless perdition,” an act of poetic creation analogous to the …

Author: David Quint

Date Published: 19th Oct 2017

Publication Type: Journal Article

DOI: 10.23943/princeton/9780691161914.003.0002

Citation: Princeton University Press

Created: 22nd Oct 2025 at 18:25, Last updated: 22nd Oct 2025 at 18:25

A Semantics for a Query Language over Sensors, Streams and Relations

Xiaoming Test

Abstract

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Authors: Christian Y. A. Brenninkmeijer, Ixent Galpin, Alvaro A. A. Fernandes, Norman W. Paton

Date Published: 2008

Publication Type: Journal Article

DOI: 10.1007/978-3-540-70504-8_9

Citation: Sharing Data, Information and Knowledge,pp.87-99,Springer Berlin Heidelberg

Created: 22nd Oct 2025 at 16:05, Last updated: 22nd Oct 2025 at 16:05

Sharing Data, Information and Knowledge

Xiaoming Test

Abstract

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Authors: David Hutchison, Takeo Kanade, Josef Kittler, Jon M. Kleinberg, Friedemann Mattern, John C. Mitchell, Moni Naor, Oscar Nierstrasz, C. Pandu Rangan, Bernhard Steffen, Madhu Sudan, Demetri Terzopoulos, Doug Tygar, Moshe Y. Vardi, Gerhard Weikum, Alex Gray, Keith Jeffery, Jianhua Shao