Hi! Welcome to the OpenBiodiv PhD project by Viktor Senderov at Pensoft as part of the Marie-Curie training network for genomics, bioinformatics, and systematics of the BIG 4 insect groups.
OpenBiodiv is a knowledge management system of biodiversity data. Its components are
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the ontology OpenBiodiv-O
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a semantic graph database storing a LOD dataset (linked open data) populated with informationfrom three sources:
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a web-portal providing a semantic search-and-browse as well as user applications to access the LOD.
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the RDF4R R package for RDF generation
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this repository containing the documentation and bootstrap scripts needed to run an OpenBiodiv instance
More information on what OpenBiodiv is can be found in the draft text of a chapter of my dissertation (Chapter 3).
Please use 2 for citing.
- Senderov, Viktor, Kiril Simov, Nico Franz, Pavel Stoev, Terry Catapano, Donat Agosti, Guido Sautter, Robert A. Morris, and Lyubomir Penev. “OpenBiodiv-O: Ontology of the OpenBiodiv Knowledge Management System.” Journal of Biomedical Semantics 9, no. 1 (January 2018). https://doi.org/10.1186/s13326-017-0174-5.
- Senderov, Viktor, and Lyubomir Penev. “The Open Biodiversity Knowledge Management System in Scholarly Publishing.” Research Ideas and Outcomes 2 (January 11, 2016): e7757. https://doi.org/10.3897/rio.2.e7757.
- Senderov, Viktor, Teodor Georgiev, and Lyubomir Penev. “Online Direct Import of Specimen Records into Manuscripts and Automatic Creation of Data Papers from Biological Databases.” Research Ideas and Outcomes 2 (September 23, 2016): e10617. https://doi.org/10.3897/rio.2.e10617.
- Cardoso, Pedro, Pavel Stoev, Teodor Georgiev, Viktor Senderov, and Lyubomir Penev. “Species Conservation Profiles Compliant with the IUCN Red List of Threatened Species.” Biodiversity Data Journal 4 (September 1, 2016): e10356. https://doi.org/10.3897/BDJ.4.e10356.
- Arriaga-Varela, Emmanuel, Matthias Seidel, Albert Deler-Hernández, Viktor Senderov, and Martin Fikácek. “A Review of the Cercyon Leach (Coleoptera, Hydrophilidae, Sphaeridiinae) of the Greater Antilles.” ZooKeys 681 (June 21, 2017): 39–93. https://doi.org/10.3897/zookeys.681.12522.
- Penev, Lyubomir, Teodor Georgiev, Peter Geshev, Seyhan Demirov, Viktor Senderov, Iliyana Kuzmova, Iva Kostadinova, Slavena Peneva, and Pavel Stoev. “ARPHA-BioDiv: A Toolbox for Scholarly Publication and Dissemination of Biodiversity Data Based on the ARPHA Publishing Platform.” Research Ideas and Outcomes 3 (April 5, 2017): e13088. https://doi.org/10.3897/rio.3.e13088.
- Penev, Lyubomir, Daniel Mietchen, Vishwas Chavan, Gregor Hagedorn, Vincent Smith, David Shotton, Éamonn Ó Tuama, et al. “Strategies and Guidelines for Scholarly Publishing of Biodiversity Data.” Research Ideas and Outcomes 3 (February 28, 2017): e12431. https://doi.org/10.3897/rio.3.e12431.
Select presentations given as part of the OpenBiodiv project are to be found in the presentations directory.
The system is called OpenBiodiv or OBKMS. OBKMS is the older name, but we prefer to call it OpenBiodiv recently.