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Leveraging Terminology Services for FAIR Semantic Data Integration across NFDI Domains - How to Integrate Terminology Services Into Other Service Applications

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The National Research Data Infrastructure (NFDI) strives to develop FAIR research data and data services for major scientific disciplines, using terminologies as a key factor for semantic annotations and semantic interoperability of data. Several NFDI consortia provide domain-specific terminologies through Terminology services or registries, offering access, search capabilities, visualization, and downloads. Prioritizing user-friendly access, terminology services seamlessly integrate semantic concepts into applications, often operating in the background to enable smooth semantic annotation and data interoperability. We present exemplary fields of application from selected disciplines and how terminology services support semantic search, user experience, annotation workflows, terminology curation and design.

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URL: https://doi.org/10.5281/zenodo.8342678Communities:

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Data Steward

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Towards a Versatile Terminology Service for Empowering FAIR Research Data: Enabling Ontology Discovery, Design, Curation, and Utilization Across Scientific CommunitiesPresentation of the paper at SEMANTiCS 2023 (https://2023-eu.semantics.cc/)

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PDF

Languages

English

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Presentation

Publication Date

2023-09-15

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5.4 MB

Authors

Philip Strömert

| Vatsal Limbachia

| Pooya Oladazimi

| Philip Strömert

| Vatsal Limbachia

| Pooya Oladazimi

#FAIR #RDM #Ontology #FAIR Research Data Management #OLS #Ontology Curation #Ontology Harmonization #Terminology Services

Keywords

#Data Publication #Repositories #ELN #Minimum Information #Research Data Management (RDM)

Minimum Information Standards in Chemistry: A Call for Better Research Data Management PracticesResearch data management (RDM) is needed to assist experimental advances and data collection in the chemical sciences. Many funders require RDM because experiments are often paid for by taxpayers and the resulting data should be deposited sustainably for posterity. However, paper notebooks are still common in laboratories and research data is often stored in proprietary and/or dead-end file formats without experimental context. Data must mature beyond a mere supplement to a research paper. Electronic lab notebooks (ELN) and laboratory information management systems (LIMS) allow researchers to manage data better and they simplify research and publication. Thus, an agreement is needed on minimum information standards for data handling to support structured approaches to data reporting. As digitalization becomes part of curricular teaching, future generations of digital native chemists will embrace RDM and ELN as an organic part of their research.

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Article

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PDF

Languages

English

Media Type

Text

Publication Date

2022-11-08

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Proprietary

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970 KB

Keywords

Ontologies4Chem: the landscape of ontologies in chemistryFor a long time, databases such as CAS, Reaxys, PubChem or ChemSpider mostly rely on unique numerical identifiers or chemical structure identifiers like InChI, SMILES or others to link data across heterogeneous data sources. The retrospective processing of information and fragmented data from text publications to maintain these databases is a cumbersome process. Ontologies are a holistic approach to semantically describe data, information and knowledge of a domain. They provide terms, relations and logic to semantically annotate and link data building knowledge graphs. The application of standard taxonomies and vocabularies from the very beginning of data generation and along research workflows in electronic lab notebooks (ELNs), software tools, and their final publication in data repositories create FAIR data straightforwardly. Thus a proper semantic description of an investigation and the why, how, where, when, and by whom data was produced in conjunction with the description and representation of research data is a natural outcome in contrast to the retrospective processing of research publications as we know it. In this work we provide an overview of ontologies in chemistry suitable to represent concepts of research and research data. These ontologies are evaluated against several criteria derived from the FAIR data principles and their possible application in the digitisation of research data management workflows.

Learning Resource Type

Article

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PDF

Languages

English

Media Type

Text

Publication Date

2022-03-24

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Size

1.1 MB

Authors

Philip Strömert

| André Castro

| Steffen Neumann

| Philip Strömert

| André Castro

| Steffen Neumann

#terminology #research data #ontology #FAIR data #Cheminformatics #linked data

Keywords

NFDI4Chem: from chemical research data management to digital chemistryThis presentation was held at the GDCh-Wissenschaftsforum (WiFo) "Rethinking Chemistry" 2023 in Leipzig.

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PDF

Languages

English

Media Type

Presentation

Publication Date

2023-09-13

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3.2 MB

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No keywords

NFDI4Chem's Semantic Data Hub: Central Resource for FAIR Chemistry Metadata and MIChIsThis poster illustrates the concept of the NFDI4Chem Semantic Data Hub (SDH), a set of existing and planned NFDI4Chem services that will work together to improve the management and integration of FAIR chemistry research data. It was first presented at the NFDI4Chem Consortium Meeting 5.0 in Halle (Saale).

Learning Resource Type

Poster

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PDF

Languages

English

Publication Date

2024-09-16

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Size

3.1 MB

Keywords

#NFDI4Chem #Chemistry