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Reviving nmrCV or integrating it with CHMO?
Reviving nmrCV or integrating it with CHMO?
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In NFDI4Chem we identified the need for ontology terms that can be used to annotate NMR spectroscopy datasets within repositories such as nmrXiv. Although nmrCV already provides more domain specific terms than the Chemical Methods Ontology (CHMO) which can be reused, it is currently not actively maintained, was deliberately designed as a rather flat controlled vocabulary for the file format nmrML and contains issues to be resolved, especially when considered as a possible ontology module within a larger chemical ontology framework. Given these circumstances we would like to discuss how nmrCV could be revived to add new needed terms and axioms or whether it would be better to integrate it into CHMO. The focus of this discussion will be on the use case requirements of nmrXiv and the NFDI4Chem Terminology Service as possible tools to help manage this process. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI4Chem – Projektnummer 441958208.
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URL: https://doi.org/10.5281/zenodo.10008148Communities:Disciplines:Target Groups:
  • Data Steward
  • Phd Student
Proficiency Levels:
  • Competent

FAIR Ontology Metadata - Crucial Information for Understanding, Evaluation, and Application
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FAIR Ontology Metadata - Crucial Information for Understanding, Evaluation, and ApplicationThis presentation was part of the 2nd Ontologies4Chem Workshop held online 11.-12.10.2023.
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Publication Date
2023-10-12
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Setting up your own ODK ontology repository
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Setting up your own ODK ontology repositoryPresentation given at the Ontology Summit 2023 about how to set up a Git repository with the Ontology Development Kit (ODK).
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Languages
English
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Publication Date
2023-02-09
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CCBY
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1.3 MB
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Ontologies4Chem: the landscape of ontologies in chemistry
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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.
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Article
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Languages
English
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Text
Publication Date
2022-03-24
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CCBYNCND
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1.1 MB
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#terminology#research data#ontology#FAIR data#Cheminformatics#linked data
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NFDI4C* Workshop on synergy & cooperation
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NFDI4C* Workshop on synergy & cooperationA short presentationthat was held in the breakout session "ontologies & metadata" of the NFDI4Chem & NFDI4Cat joint workshop.
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Languages
English
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Presentation
Publication Date
2023-05-05
License
CCBY
Size
4.8 MB
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Keywords
#FAIR data#RDM#Metadaten#metadata#Forschungsdatenmanagement#research data management#repository#FAIR-Prinzipien#ELN#FDM#FAIR principles#FAIRe Daten#Infrastruktur#electronic lab notebook#Chemie#ELB#Elektronisches Laborbuch#Forschungsdateninfrastruktur#HeFDI Data Talk#Repositorium#chemistry#infrastructure#research data infrastructure
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Praktische Probleme der Kernresonanzspektroskopie (PPNMR) 2023: NFDI4Chem: Auf dem Weg zu FAIRen NMR-Daten
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Praktische Probleme der Kernresonanzspektroskopie (PPNMR) 2023: NFDI4Chem: Auf dem Weg zu FAIRen NMR-DatenDie Vision von NFDI4Chem ist die Digitalisierung aller wichtigen Schritte in der chemischen Forschung. Eine zentrale Voraussetzung dafür ist, chemische Forschungsdaten FAIR (Findable, Accessible, Interoperable, Reusable) zu machen. Die NMR-Spektroskopie ist hier ein idealer Anwendungsfall: Sie ist in der chemischen Forschung nahezu allgegenwärtig und hat komplexe Anforderungen an Datenformate für Roh-, verarbeitete und analysierte Daten sowie Metadaten. Um die elektronische Ablage von NMR-Daten von Anfang an zu fördern, setzt NFDI4Chem auf die Nutzung und Entwicklung von NMR-Editoren wie NMRium und ChemSpectra. Sie ermöglichen das Lesen, Verarbeiten und Exportieren der Daten und Metadaten in elektronische Laborjournale (ELNs) und Repositorien. Das ELN Chemotion und das Repositorium nmrXiv (derzeit in der Entwicklung) werden eng aufeinander abgestimmt, um einen nahtlosen Datenfluss durch alle Phasen der Forschung zu gewährleisten. Außerdem arbeiten wir mit den Herausgebern wissenschaftlicher Zeitschriften zusammen, um die Autorenrichtlinien der Verlage bezüglich der Veröffentlichung von NMR-Daten weiterzuentwickeln. In diesem Vortrag möchten wir einen Ausblick auf den Weg geben: Welche Formate und Standards gibt es heute? Was sind geeignete Konzepte für Mindestinformationen, Terminologie und Metadaten? Und welche Werkzeuge stehen zur Verfügung oder werden in Zukunft verfügbar sein?
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English
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Publication Date
2023-03-21
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CCBY
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3.2 MB
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NFDI4Chem Terminology Service: Enabling semantic research data interoperability, discovery and exploitation in chemistry
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NFDI4Chem Terminology Service: Enabling semantic research data interoperability, discovery and exploitation in chemistryNFDI4Chem is an initiative to build an open and FAIR infrastructure for research data management in chemistry. The TS is a central part of the NFDI4Chem infrastructure that is currently in the making and which serves as the single point of access for NFDI4Chem services that use terminologies, controlled vocabularies or ontologies.
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PPTX
Languages
English
Media Type
Presentation
Publication Date
2022-02-08
License
CCBY
Size
5.8 MB
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