Paleobiogeographic Knowledge Graph: An Ongoing Work with Fundamental Support for Future Research

Abstract

Paleobiogeography investigates geographical distributions of fossil organisms and controlling factors that affect their distributions in geological history, to reveal the macro-evolution and coordinated development of life and the environment. It is a crucial window for understanding the biosphere and the geographical environment. After two centuries of development, paleobiogeographic studies have led to the accumulation of significant amounts of knowledge and data; however, the voluminous outputs present the characteristics of an “isolated island” with a scattered, limited number of authoritative definitions of terminologies and semantic heterogeneity among them. This makes data queries cumbersome, the rate of data reuse low, and data sharing more difficult. A knowledge graph (KG) has the advantage of expressing concepts and their semantic relations, which is an important tool for achieving data organization and fusion, and data mining; further, it is also a key technology for realizing the unrestricted sharing of paleobiogeographic information. Through our efforts over the past two years, a paleobiogeographic KG was developed based on the established construction procedure of the KG, which contains 273 concepts, 172 properties, and 47 rules. Meanwhile, the completion of this KG and the construction of a paleobiogeographic platform for display and analysis are now being carried out.

Keywords

biogeographic unit / knowledge base / artificial intelligence / paleobiogeographic platform / knowledge inference / knowledge graph

References

Ackoff R L. From Data to Wisdom. Journal of Applied Systems Analysis, 1989, 16: 3-9.

Amit S. Introducing the Knowledge Graph, 2012, America: Official Blog of Google

Bizer C, Lehmann J, Kobilarov G, . DBpedia-A Crystallization Point for the Web of Data. Web Semantics: Science, Services and Agents on the World Wide Web, 2009, 7(3): 154-165.

Briggs J C. Biogeography and Plate Tectonics, 1987, Amsterdam: Elsevier

Cecca F. Palaeobiogeography of Marine Fossil Invertebrates: Concepts and Methods, 2002, London and New York: Taylor & Francis

Cecca F, Westermann G E G. Towards a Guide to Palaeobiogeographic Classification. Palaeogeography, Palaeo-climatology, Palaeoecology, 2003, 201: 179-181.

Cox C B, Moore P D, Ladle R. Biogeography: An Ecological and Evolutionary Approach, 2016 9th Edition Oxford: Wiley-Blackwell Publishing

Cox S J D, Richard S M. A Geologic Timescale Ontology and Service. Earth Science Informatics, 2015, 8(1): 5-19.

de Candolle A P. Géographie Botanique. Dictionnaire des Sciences Naturelles, 1820, 18: 359-422.

Elith J, Leathwick J R. Species Distribution Models: Ecological Explanation and Prediction across Space and Time. Annual Review of Ecology, Evolution, and Systematics, 2009, 40: 677-697.

Feng L P, Zhu L J, Jiang Y D. Study on a Method of Building Modular Ontology. New Technology of Library and Information Service, 2010, 6: 53-59. (in Chinese with English Abstract

Fensel D, Şimşek U, Angele K, . Knowledge Graphs: Methodology, Tools and Selected Use Cases, 2020, Switzerland: Springer

Fox M S, Chionglo J F, Fadel F G. A Common-Sense Model of the Enterprise, 1993, New York: IIE Press

Hallam A. Atlas of Palaeobiogeography, 1973, Amsterdam: Elsevier

Hou Z W, Zhu Y Q, Gao Y, . Geologic Time Scale Ontology and Its Applications in Semantic Retrieval. Journal of Geo-Information Science, 2018, 20(1): 17-27. (in Chinese with English Abstract)

Hughes N F. Organisms and Continents through Time: Methods of Assessing Relationships between Past and Present Biologic Distributions and the Positions of Continents: A Symposium Volume of 23 Papers, 1973, London: The Palaeontological Association

Kauffman E C. Hallam A. Cretaceous Bivalvia. Atlas of Paleobiogeography, 1973, Amsterdam: Elsevier

Laxton J, Serrano J J, Tellez-Arenas A. Geological Applications Using Geospatial Standards—An Example from OneGeology-Europe and GeoSciML. International Journal of Digital Earth, 2010, 3(Sup1): 31-49.

Lieberman B S. aleobiogeography: Using Fossil to Study Global Change, Plate Tectonics, and Evolution, 2000, New York: Kluwer Academic/Plenum Publishers

Lieberman B S. Paleobiogeography: The Relevance of Fossils to Biogeography. Annual Review of Ecology, Evolution, and Systematics, 2003, 34: 51-69.

Lieberman B S. Geobiology and Paleobiogeography: Tracking the Coevolution of the Earth and Its Biota. Palaeogeography, Palaeoclimatology, Palaeoecology, 2005, 219(1/2): 23-33.

Liu Q, Li Y, Duan H, . Knowledge Graph Construction Techniques. Journal of Computer Research and Development, 2016, 53(3): 582-600. (in Chinese with English Abstract)

Ma X G. Knowledge Graph Construction and Application in Geosciences: A Review. Computers & Geosciences, 2022, 161: 105082

Ma X G, Carranza E J M, Wu C L, . A SKOS-Based Multilingual Thesaurus of Geological Time Scale for Interoperability of Online Geological Maps. Computers & Geosciences, 2011, 37(10): 1602-1615.

Ma X G, Ma C, Wang C B. A New Structure for Representing and Tracking Version Information in a Deep Time Knowledge Graph. Computers & Geosciences, 2020, 145 104620

Molles M C, Simon A S. Ecology: Concepts and Applications Eighth Edition, 2018, New York: McGraw-Hill Education

Noy, N., Mcguinness, D., 2001. Ontology Development 101: A Guide to Creating Your First Ontology. Technical Report SMI-2001–0880, Stanford Knowledge Systems Laboratory Technical Report KSL-01–05 and Stanford Medical Informatics

Olson D M, Dinerstein E, Wikramanayake E D, . Terrestrial Ecoregions of the World: A New Map of Life on Earth. BioScience, 2001, 51(11): 933-938.

Qi H. The Construction of Ontology-Based Earth Science Knowledge Graph: [Dissertation], 2020, Nanjing: Nanjing University (in Chinese with English Abstract)

Ross C A. Paleobiogeography. Benchmark Papers in Geology, 1974, Dowden: Hutchingson & Ross, Inc.

Sadava D E, Hillis D M, Heller H C, . Life: The Science of Biology, 2012 10th Edition New York: W. H. Freeman & Co.

Shen S Z, Zhang H, Shi G R, . Early Permian (Cisuralian) Global Brachiopod Palaeobiogeography. Gondwana Research, 2013, 24(1): 104-124.

Shi G R. Multivariate Data Analysis in Palaeoecology and Palaeobiogeography—A Review. Palaeogeography, Palaeoclimatology, Palaeoecology, 1993, 105(3/4): 199-234.

Smith A B. Late Palaeozoic Biogeography of East Asia and Palaeontological Constraints on Plate Tectonic Reconstructions. Philosophical Transactions of the Royal Society of London Series A. Mathematical and Physical Sciences, 1988, 326(1589): 189-227

Rode A L S. The Application of Geographic Information Systems to Paleobiogeography: Implications for the Study of Invasions and Mass Extinctions. The Paleontological Society Papers, 2005, 11 77-88.

Studer R, Benjamins V R, Fensel D. Knowledge Engineering: Principles and Methods. Data & Knowledge Engineering, 1998, 25(1/2): 161-197.

Uschold M, King M, Moralee S, . The Enterprise Ontology. The Knowledge Engineering Review, 1998, 13(1): 31-89.

Wilkinson M D, Dumontier M, Aalbersberg I J, . The FAIR Guiding Principles for Scientific Data Management and Stewardship. Scientific Data, 2016, 3 160018

Woodcock, R., Simons, B., Duclaux, G., et al., 2010. AuScope’s Use of Standards to Deliver Earth Resource Data. EGU General Assembly Conference Abstracts, 1556

Xu Z L, Sheng Y P, He L R, . Review on Knowledge Graph Techniques. Journal of University of Electronic Science and Technology of China, 2016, 45(4): 589-606. (in Chinese with English Abstract)

Yin H F. The Palaeobiogeography of China, 1994, Oxford: Clarendon Press

Zárate M, Braun G, Fillottrani P, . BiGe-Onto: An Ontology-Based System for Managing Biodiversity and Biogeography Data. Applied Ontology, 2020, 15(4): 411-437.

Zhou C H, Wang H, Wang C S, . Geoscience Knowledge Graph in the Big Data Era. Science China Earth Sciences, 2021, 64(7): 1105-1114.