Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph
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 the Global Biodiversity Information Facility. The linked open data is modelled according to the Ope...
Main Authors: | , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Pensoft Publishers
2021-09-01
|
Series: | Biodiversity Data Journal |
Online Access: | https://bdj.pensoft.net/article/67671/download/pdf/ |
id |
doaj-15036ee335ea443e8ef30e1169e38cea |
---|---|
record_format |
Article |
spelling |
doaj-15036ee335ea443e8ef30e1169e38cea2021-09-28T14:14:54ZengPensoft PublishersBiodiversity Data Journal1314-28282021-09-01913110.3897/BDJ.9.e6767167671Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge GraphMariya Dimitrova0Viktor Senderov1Teodor Georgiev2Georgi Zhelezov3Lyubomir Penev4Pensoft PublishersDepartment of Bioinformatics and Genetics, Swedish Museum of Natural HistoryPensoft PublishersPensoft PublishersInstitute of Biodiversity & Ecosystem Research, Bulgarian Academy of SciencesOpenBiodiv 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 the Global Biodiversity Information Facility. 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 to capture the semantics of resources not modelled before.We introduce the new release of the OpenBiodiv-LOD attained through information extraction and modelling of additional biodiversity entities. It was achieved by further developments to OpenBiodiv-O, the data storage infrastructure and the workflow and accompanying R software packages used for transformation of academic literature into Resource Description Framework (RDF). We discuss how to utilise the LOD in biodiversity informatics and give examples by providing solutions to several competency questions. We investigate performance issues that arise due to the large amount of inferred statements in the graph and conclude that OWL-full inference is impractical for the project and that unnecessary inference should be avoided.https://bdj.pensoft.net/article/67671/download/pdf/ |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Mariya Dimitrova Viktor Senderov Teodor Georgiev Georgi Zhelezov Lyubomir Penev |
spellingShingle |
Mariya Dimitrova Viktor Senderov Teodor Georgiev Georgi Zhelezov Lyubomir Penev Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph Biodiversity Data Journal |
author_facet |
Mariya Dimitrova Viktor Senderov Teodor Georgiev Georgi Zhelezov Lyubomir Penev |
author_sort |
Mariya Dimitrova |
title |
Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph |
title_short |
Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph |
title_full |
Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph |
title_fullStr |
Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph |
title_full_unstemmed |
Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph |
title_sort |
infrastructure and population of the openbiodiv biodiversity knowledge graph |
publisher |
Pensoft Publishers |
series |
Biodiversity Data Journal |
issn |
1314-2828 |
publishDate |
2021-09-01 |
description |
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 the Global Biodiversity Information Facility. 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 to capture the semantics of resources not modelled before.We introduce the new release of the OpenBiodiv-LOD attained through information extraction and modelling of additional biodiversity entities. It was achieved by further developments to OpenBiodiv-O, the data storage infrastructure and the workflow and accompanying R software packages used for transformation of academic literature into Resource Description Framework (RDF). We discuss how to utilise the LOD in biodiversity informatics and give examples by providing solutions to several competency questions. We investigate performance issues that arise due to the large amount of inferred statements in the graph and conclude that OWL-full inference is impractical for the project and that unnecessary inference should be avoided. |
url |
https://bdj.pensoft.net/article/67671/download/pdf/ |
work_keys_str_mv |
AT mariyadimitrova infrastructureandpopulationoftheopenbiodivbiodiversityknowledgegraph AT viktorsenderov infrastructureandpopulationoftheopenbiodivbiodiversityknowledgegraph AT teodorgeorgiev infrastructureandpopulationoftheopenbiodivbiodiversityknowledgegraph AT georgizhelezov infrastructureandpopulationoftheopenbiodivbiodiversityknowledgegraph AT lyubomirpenev infrastructureandpopulationoftheopenbiodivbiodiversityknowledgegraph |
_version_ |
1716865846603677696 |