Paleontology Knowledge Graph for Data-Driven Discovery

Abstract

A knowledge graph (KG) is a knowledge base that integrates and represents data based on a graph-structured data model or topology. Geoscientists have made efforts to construct geoscience-related KGs to overcome semantic heterogeneity and facilitate knowledge representation, data integration, and text analysis. However, there is currently no comprehensive paleontology KG or data-driven discovery based on it. In this study, we constructed a two-layer model to represent the ordinal hierarchical structure of the paleontology KG following a top-down construction process. An ontology containing 19 365 concepts has been defined up to 2023. On this basis, we derived the synonymy list based on the paleontology KG and designed corresponding online functions in the OneStratigraphy database to showcase the use of the KG in paleontological research.

Keywords

paleontology knowledge graph / ontology / synonymy list / OneStratigraphy / big data / geology

References

[] Allmon W D, Bottjer D J. . Evolutionary Paleoecology: The Ecological Context of Macroevolutionary Change, 2001 New York Columbia University Press 357,

[] Bottjer D. . Paleoecology: Past, Present and Future, 2016 Chichester John Wiley & Sons 222,

[] Bromley R G. . Trace Fossils: Biology, Taxonomy and Applications, 1996 London Chapman & Hall 361,

[] Brower A V Z, Schuh R T. . Biological Systematics: Principles and Applications, 2021 New York Cornell University Press 328,

[] Buatois L A, Mángano M G. . Ichnology: Organism-Substrate Interaction in Space and Time, 2011 New York Cambridge University Press 358,

[] Cavalier-Smith T. A Revised Six-Kingdom System of Life. Biological Reviews of the Cambridge Philosophical Society, 1998, 73(3): 203-266

[] Chen X J, Jia S B, Xiang Y. A Review: Knowledge Reasoning over Knowledge Graph. Expert Systems with Applications, 2020, 141: 112948,

[] Copeland H F. The Kingdoms of Organisms. The Quarterly Review of Biology, 1938, 13(4): 383-420,

[] Copeland H F. . The Classification of Lower Organisms, 1956 Palo Alto Pacific Books 302,

[] Dash M C. . Fundamentals of Ecology, 2001 New York Tata McGraw-Hill Education 453

[] Dong, S. C., Shi, Y. K., Ran, Y. Z., et al., 2023. Biological Classification System Knowledge Graph and Semi-automatic Construction of Its Invertebrate Fossil Branches. Journal of Earth Science. https://doi.org/10.1007/s12583-023-1941-y

[] Dong S C, Yin H W, Xu G. Heterogeneous Data Searching Based on Geologic Time Ontology. Journal of Geo-Information Science, 2010, 12(2): 2194-2199, in Chinese with English Abstract)

[] Droser M L, Bottjer D J, Sheehan P M. Evaluating the Ecological Architecture of Major Events in the Phanerozoic History of Marine Invertebrate Life. Geology, 1997, 25(2): 167-170,

[] Ehrlinger L, Wöß W. Towards a Definition of Knowledge Graphs. SEMANTiCS, 2016, 48(1–4): 2

[] Fensel D, Şimşek U, Angele K, et al., et al.. Fensel D, Şimşek U, Angele K, et al., et al.. Introduction: What is a Knowledge Graph?. Knowledge Graphs, 2020 Cham, Switzerland Springer 1-10,

[] Foote M, Miller A I. . Principles of Paleontology (Third Edition), 2007 New York W. H. Freeman 354

[] Haeckel E. . Generelle Morphologie der Organismen, 1866 Berlin Reimer 462, in German)

[] Häntzschel W. Teichert C. Trace Fossil and Problematica. Treatise on Invertebrate, 1975 Lawrence Geological Society of America, University of Kansas Press 1-263

[] Hautmann M. What is Macroevolution?. Palaeontology, 2020, 63(1): 1-11,

[] Hu X M, Xu Y W, Ma X G, et al.. Knowledge System, Ontology, and Knowledge Graph of the Deep-Time Digital Earth (DDE): Progress and Perspective. Journal of Earth Science, 2023, 34(5): 1323-1327,

[] Janev V, Graux D, Jabeen H, et al.. . Knowledge Graphs and Big Data Processing, 2020 Switzerland Springer Nature 209,

[] Knaust D. . Atlas of Trace Fossils in Well Core: Appearance, Taxonomy and Interpretation, 2017 Dordrecht Springer International Publishing 209,

[] 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: 31-49,

[] Linnaeus, C., 1735. Systemae Naturae, Sive Regna tria Naturae, Systematics Proposita per Classes, Ordines, Genera & Species. Lugduni Batavorum. 12

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

[] Ma X G, Carranza E J M, Wu C L, et al.. Ontology-Aided Annotation, Visualization, and Generalization of Geological Time-Scale Information from Online Geological Map Services. Computers & Geosciences, 2012, 40: 107-119,

[] 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,

[] Martin R E. . Taphonomy: A Process Approach, 1999 Cambridge Cambridge University Press 524,

[] Noy, N. F., McGuinness, D. L., 2001. Ontology Development 101: A Guide to Creating your First Ontology. Stanford Knowledge Systems Laboratory, Technical Report. 1–25

[] Payne J L, Boyer A G, Brown J H, et al.. Two-Phase Increase in the Maximum Size of Life over 3.5 Billion Years Reflects Biological Innovation and Environmental Opportunity. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106(1): 24-27,

[] Peters S E, Husson J M, Wilcots J. The Rise and Fall of Stromatolites in Shallow Marine Environments. Geology, 2017, 45(6): 487-490,

[] Pignatti, J. S., 2009. Evolutionary Paleontology. In: De Vivo, B., Grasemann, B., Stiwe, K., eds., Geology-Volume II. 342–362

[] Qi H. . The Construction of Ontology-Based Earth Science Knowledge Graph: [Dissertation], 2020 Nanjing Nanjing University 1-66 (in Chinese with English Abstract)

[] Qiu Q J, Wang B, Ma K, et al.. A Practical Approach to Constructing a Geological Knowledge Graph: A Case Study of Mineral Exploration Data. Journal of Earth Science, 2023, 34(5): 1374-1389,

[] Ricklefs R E, Miller G L. . Ecology (Fourth Edition), 1999 New York W. H. Freeman 896

[] Ride W D L, Cogger H G, Dupuis C, et al.. . International Code of Zoological Nomenclature (Fourth Edition), 1999 London International Trust for Zoological Nomenclature 306

[] Ruggiero M A, Gordon D P, Orrell T M, et al.. A Higher Level Classification of all Living Organisms. PLoS One, 2015, 10(4): e0119248,

[] Shen Z, Gong Y M, Ban F M, et al.. Taxonomic Reconsideration of Ammonidium Lister 1970 and Related Species and Its Biostratigraphical and Palaeogeographical Implication. Earth Science, 2022, 47(8): 2985-3004 (in Chinese with English Abstract)

[] Smith F A, Payne J L, Heim N A, et al.. Body Size Evolution across the Geozoic. Annual Review of Earth and Planetary Sciences, 2016, 44: 523-553,

[] Song H J, Tong J N, Chen Z Q. Evolutionary Dynamics of the Permian-Triassic Foraminifer Size: Evidence for Lilliput Effect in the End-Permian Mass Extinction and Its Aftermath. Palaeogeography, Palaeoclimatology, Palaeoecology, 2011, 308(1/2): 98-110,

[] Tarhan L G, Droser M L, Planavsky N J, et al.. Protracted Development of Bioturbation through the Early Palaeozoic Era. Nature Geoscience, 2015, 8: 865-869,

[] Tong J N. . Paleontology (Second Edition), 2021 Beijing Higher Education Press 361 (in Chinese)

[] Turland N J, Wiersema J H, Barrie F R, et al.. International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code). Nineteenth International Botanical Congress, 2018 Shenzhen. Koeltz Botanical Books July 2017

[] Uschold M, Gruninger M. Ontologies: Principles, Methods and Applications. The Knowledge Engineering Review, 1996, 11(2): 93-136,

[] Wang X J, Yao L, Wang X D. Permian Naotic-Dissepimented Rugose Corals in China and Their Palaeoenvironmental Implications. Geological Journal, 2021, 56(12): 6151-6161,

[] Whittaker R H. New Concepts of Kingdoms of Organisms. Science, 1969, 163(3863): 150-160,

[] Woese C R, Fox G E. Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms. Proceedings of the National Academy of Sciences of the United States of America, 1977, 74(11): 5088-5090,

[] Woese C R, Kandler O, Wheelis M L. Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America, 1990, 87(12): 4576-4579,

[] Xi J L, Wu J, Wu M B. Design and Construction of Lightweight Domain Ontology of Tectonic Geomorphology. Journal of Earth Science, 2023, 34(5): 1350-1357,

[] Wu G G, He M Y. . Standards for Resource Description of Invertebrate Fossil Specimens, 2016 Beijing Geological Publishing House 356 (in Chinese with English Abstract)

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

[] Xu H Q, Zhao Y Y, Huang H, et al.. A Comprehensive Construction of the Domain Ontology for Stratigraphy. Geoscience Frontiers, 2023, 14(5): 101461,

[] Xu Y W, Hu X M, Han Z. Carbonate Ontology and Its Application for Integrating Microfacies Data. Journal of Earth Science, 2023, 34(5): 1328-1338,

[] Yao L, Lin W, Aretz M, et al.. Colonial Coral Resilience by Decreasing Size: Reaction to Increased Detrital Influx during Onset of the Late Palaeozoic Ice Age. Proceedings Biological Sciences, 2023, 290: 20230220

[] Zhang L N, Hou Z S, Shen B H, et al.. Paleobiogeographic Knowledge Graph: An Ongoing Work with Fundamental Support for Future Research. Journal of Earth Science, 2023, 34(5): 1339-1349,

[] Zhang Y L, Liu G B, Bian L Z. . Paleontology, 1988 Beijing Geological Publishing House 660 (in Chinese)