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OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system

Viktor Senderov, Kiril Simov, Nico Franz, Pavel Stoev, Terry Catapano, Donat Agosti, Guido Sautter, Robert A. Morris, Lyubomir Penev
2018 Journal of Biomedical Semantics  
The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System.  ...  knowledge graph) and enables the creation of the OpenBiodiv Knowledge Management System.  ...  Availability of data and materials A partial dataset from Pensoft's journals has been generated with OpenBiodiv-O and can be found at the SPARQL Endpoint <http://213.145.125. 72:7777/>, select repository  ... 
doi:10.1186/s13326-017-0174-5 pmid:29347997 pmcid:PMC5774086 fatcat:2l6q5qyumzg7flvuqwwznp247a

OpenBiodiv-O Ontology: Bridging the Gap Between Biodiversity Data and Biodiversity Publishing

Mariya Dimitrova, Viktor Senderov, Kiril Simov, Teodor Georgiev, Lyubomir Penev
2019 Biodiversity Information Science and Standards  
The application of OpenBiodiv-O towards a working solution for the biodiversity publishing domain demonstrates the potential of ontology modelling for data organisation and management.  ...  Reusing of existing ontologies within OpenBiodiv-O helps to establish a link between OpenBiodiv-O and other ontologies and facilitates federated querying between OpenBiodiv and other knowledge graphs.  ...  The application of OpenBiodiv-O towards a working solution for the biodiversity publishing domain demonstrates the potential of ontology modelling for data organisation and management.  ... 
doi:10.3897/biss.3.35773 fatcat:cueuufbqvnfr3lf4bnjywoygde

OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science

Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, Kiril Simov
2019 Publications  
The need for a system to store and manage collective biodiversity knowledge in a community-agreed and interoperable open format has evolved into the concept of the Open Biodiversity Knowledge Management  ...  The data from both sources are converted to Resource Description Framework (RDF) and integrated in a graph database using the OpenBiodiv-O ontology and an RDF version of the Global Biodiversity Information  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/publications7020038 fatcat:tuf4vbhydfazzhbd2uj7tk632i

Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph

Mariya Dimitrova, Viktor Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev
2021 Biodiversity Data Journal  
The linked open data is modelled according to the OpenBiodiv-O ontology integrating semantic resource types from recognised biodiversity and publishing ontologies with OpenBiodiv-O resource types, introduced  ...  OpenBiodiv is a biodiversity knowledge graph containing a synthetic linked open dataset, OpenBiodiv-LOD, which combines knowledge extracted from academic literature with the taxonomic backbone used by  ...  Acknowledgements This research received funding from the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie grant agreements BIG4 (No 642241) and IGNITE (No  ... 
doi:10.3897/bdj.9.e67671 pmid:34690512 pmcid:PMC8486731 fatcat:faejgpgxi5hxdkods3q7fykndu

Knowledge-based Biomedical Data Science 2019 [article]

Tiffany J. Callahan, Ignacio J. Tripodi Computational Bioscience Program, Department of Pharmacology, University of Colorado Denver Anschutz Medical Campus
2019 arXiv   pre-print
Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs.  ...  Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine.  ...  ACKNOWLEDGEMENTS The authors have no acknowledgements. SUPPLEMENTAL MATERIAL The full versions of Tables 1-3 are submitted as Supplemental Tables 1-3.  ... 
arXiv:1910.06710v1 fatcat:kvz5k643zvhpdiq67blc2v33wi

A Novel Kuhnian Ontology for Epistemic Classification of STM Scholarly Articles [article]

Khalid M. Saqr, Abdelrahman Elsharawy
2020 arXiv   pre-print
To the best of the authors knowledge, this is the first attempt for creating an ontology for describing scholarly articles based on the Kuhnian paradigmatic view of science.  ...  Here, we adopt the principles of Kuhnian philosophy to construct a novel ontology aims at classifying and evaluating the impact of STM scholarly articles.  ...  Senderov et al 12 proposed OpenBioDiv-O; an ontology that serves as the basis of the OpenBiodiv Knowledge Management System.  ... 
arXiv:2002.03531v1 fatcat:7ge5pbxbzncvdiejtf5lyirbde

Semantic Publication of Agricultural Scientific Literature Using Property Graphs

Francisco Abad-Navarro, José Antonio Bernabé-Diaz, Alexander García-Castro, Jesualdo Tomás Fernandez-Breis
2020 Applied Sciences  
on semantic annotation, which is facilitated by the inclusion of domain ontologies in the graph.  ...  This workflow consists of (1) RDF generation, including metadata and contents; (2) semantic annotation of the content; and (3) property graph population by adding domain knowledge from ontologies, in addition  ...  It is defined by the OpenBiodiv-O ontology [21] , which integrates bibliographic and biodiversity domain ontologies, such as SPAR ontologies or Treatmen Ontology ( TreatmentOntologies  ... 
doi:10.3390/app10030861 fatcat:4ph46nkc5be3vl5z7kp4oe4xuy

SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC

Markus Stocker, Tina Heger, Artur Schweidtmann, Hanna Ćwiek-Kupczyńska, Lyubomir Penev, Milan Dojchinovski, Egon Willighagen, Maria-Esther Vidal, Houcemeddine Turki, Daniel Balliet, Ilaria Tiddi, Tobias Kuhn (+7 others)
2022 Research Ideas and Outcomes  
In the age of advanced information systems powering fast-paced knowledge economies that face global societal challenges, it is no longer adequate to express scholarly information - an essential resource  ...  It extends the application of the FAIR data principles to scholarly communication practices, hence a more comprehensive coverage of the entire research lifecycle.  ...  The different Communication & dissemination tools and targets, measures to maximise impact and KPIs are outlined in Table 11 .  ... 
doi:10.3897/rio.8.e83789 fatcat:wo7ibzf4xrcqbovdvecip4dczu

Biodiversity Community Integrated Knowledge Library (BiCIKL)

Lyubomir Penev, Dimitrios Koureas, Quentin Groom, Jerry Lanfear, Donat Agosti, Ana Casino, Joe Miller, Christos Arvanitidis, Guy Cochrane, Donald Hobern, Olaf Banki, Wouter Addink (+10 others)
2022 Research Ideas and Outcomes  
knowledge graph &gt; re-use.  ...  through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle.  ...  From 2014-18 he was Governing Board Chair of the Global Biodiversity Information Facility (GBIF), and currently part of the Executive Committee in his role as Budget Committee Chair. management, the chair  ... 
doi:10.3897/rio.8.e81136 fatcat:4owwssl7zzfzna6likizigcv7u

Towards a Semantic Toolbox for Reproducible Knowledge Graph Generation in the Biodiversity Domain - How to Make the Most out of Biodiversity Data

Samira Babalou, David Schellenberger Costa, Jens Kattge, Christine Römermann, Birgitta König-Ries
Knowledge Graphs are widely regarded as one of the most promising ways to manage and link information in the age of Big Data.  ...  In this paper, we propose the creation of a semantic toolbox that will support data owners in transforming their databases into reproducible, dynamically extendable knowledge graphs that can be integrated  ...  Acknowledgments The work described in this paper is conducted in the iKNOW Flexpool project of iDiv, the German Centre for Integrative Biodiversity Research, funded by DFG (Project number 202548816).  ... 
doi:10.18420/informatik2021-044 fatcat:qni3ue6vwngttcr7xft3ls6m6m

Data Science with Scholarly Knowledge Graphs [article]

Kamel Fadel, University, My, Sören Auer, Markus Stocker
This way of scholarly communication severely limits the possibilities to automatically process and reuse scholarly knowledge.  ...  We demonstrate approaches that reuse the ORKG content to draw new insights and build applications and visualizations on top of SKGs data.  ...  The ORKG aims to implement the FAIR principles for scholarly knowledge. This allows for easier reuse in downstream data science of scholarly knowledge published in the literature.  ... 
doi:10.15488/11535 fatcat:zp7dwlo6wnewvb7jw7u5wayjma