OpenBiodiv PhD Project

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.

What is OpenBiodiv

OpenBiodiv is a knowledge management system of biodiversity data. Its components are

• the ontology OpenBiodiv-O

• a semantic graph database storing a LOD dataset (linked open data) populated with informationfrom three sources:

  • Pensoft's journals
  • Plazi's Treatment Bank
  • GBIF Taxonomic Backbone

• a web-portal providing a semantic search-and-browse as well as user applications to access the LOD.

• the RDF4R R package for RDF generation

• 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).

Papers that have been published on OpenBiodiv

Please use 2 for citing.

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.

Presentations

Select presentations given as part of the OpenBiodiv project are to be found in the presentations directory.

Visualisation OpenBiodiv Ontology

here

Social Media

• OBKMS Blog
• Twitter

Note

The system is called OpenBiodiv or OBKMS. OBKMS is the older name, but we prefer to call it OpenBiodiv recently.