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Geoscience Frontiers 14 (2023) 101521

Contents lists available at ScienceDirect

Geoscience Frontiers
journal homepage: www.elsevier.com/locate/gsf

Research Paper

Construction of a fluvial facies knowledge graph and its application in


sedimentary facies identification
Lei Zhang a,b, Mingcai Hou a,b,⇑, Anqing Chen a,b, Hanting Zhong a,b, James G. Ogg a,b, Dongyu Zheng a,b
a
Key Laboratory of Deep-time Geography and Environment Reconstruction and Applications, MNR & Institute of Sedimentary Geology, Chengdu University of Technology,
Chengdu 610059, China
b
State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation (Chengdu University of Technology), Chengdu 610059, China

a r t i c l e i n f o a b s t r a c t

Article history: Lithofacies paleogeography is a data-intensive discipline that involves the interpretation and compilation
Received 25 July 2022 of sedimentary facies. Traditional sedimentary facies analysis is a labor-intensive task with the added
Revised 15 November 2022 complexity of using unstructured knowledge and unstandardized terminology. Therefore, it is very diffi-
Accepted 29 November 2022
cult for beginners or non-geology scholars who lack a systematic knowledge and experience in sedimen-
Available online 5 December 2022
Handling Editor: M. Santosh
tary facies analysis. These hurdles could be partly alleviated by having a standardized, structured, and
systematic knowledge base coupled with an efficient automatic machine-assisted sedimentary facies
identification system. To this end, this study constructed a knowledge system for fluvial facies and carried
Keywords:
out knowledge representation. Components include a domain knowledge graph for types of fluvial facies
Fluvial facies (meandering, braided and other fluvial depositional environments) and their characteristic features (bed-
Knowledge graph forms, grain size distribution, etc.) with visualization, a method for query and retrieval on a graph data-
Domain ontology base platform, a hierarchical knowledge tree-structure, a data-mining clustering algorithm for machine-
Sedimentary facies identification analysis of publication texts, and an algorithm model for this area of sedimentary facies reasoning. The
Machine-assisted interpretation underlying sedimentary facies identification and knowledge reasoning system is based on expert experi-
ence and synthesis of publications. For testing, 17 sets literature publications data that included details of
sedimentary facies data (bedforms, grain sizes, etc.) were submitted to the artificial intelligence model,
then compared and validated. This testing set of automated reasoning results yielded an interpretation
accuracy of about 90% relative to the published interpretations in those papers. Therefore, the model
and algorithm provide an efficient and automated reasoning technology, which provides a new approach
and route for the rapid and intelligent identification of other types of sedimentary facies from literature
data or direct use in the field.
Ó 2022 China University of Geosciences (Beijing) and Peking University. Published by Elsevier B.V. on
behalf of China University of Geosciences (Beijing). This is an open access article under the CC BY-NC-ND
license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

1. Introduction ‘‘lithology, sedimentary structure, paleontology and mineral, etc.”


can be used to infer the origin and formation environment of sed-
Lithofacies analysis is the description and classification of sedi- imentary rock (Reading, 1978; Selley, 1982), therefore, are impor-
ments, followed by the interpretation of sedimentary processes tant for paleogeographic reconstructions (Hou et al., 2019; Ogg,
and depositional environments that typically is accomplished by 2019; Kontakiotis et al., 2020; Elatrash et al., 2021).
applying a facies model (Anderton, 1985; Kontakiotis et al., Traditionally, subject experts analyze and interpret sedimen-
2020). A facies is the sum of the lithologic and paleontological tary facies based applying their own experience and learning to
characteristics of a sedimentary rock (Moore, 1949; Teichert, observations in a field outcrop section, a seismic profile (Leila
1958; Kiersnowski et al., 1995), and a facie model can be regarded et al., 2022) and/or well log data (Lai et al., 2018). However, the
as a general summary of a specific sedimentary environment acquisition of relevant knowledge, accumulation of geoscience
(Potter, 1959; Walker, 1976). Facies marker data composed of experience, and updating of that knowledge are time-consuming
and might require a lengthy learning curve. The current digital
⇑ Corresponding author at: Key Laboratory of Deep-time Geography and information revolution has produced an exponential growth of
Environment Reconstruction and Applications, MNR & Institute of Sedimentary multi-source heterogeneous distributed data (Lassila and
Geology, Chengdu University of Technology, Chengdu 610059, China. Hendler, 2007; Hendler, 2009). At the same time, the non-
E-mail address: houmc@cdut.edu.cn (M. Hou).

https://doi.org/10.1016/j.gsf.2022.101521
1674-9871/Ó 2022 China University of Geosciences (Beijing) and Peking University. Published by Elsevier B.V. on behalf of China University of Geosciences (Beijing).
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

standardized terminology and unstructured knowledge can make dure provides an optimized knowledge service and lays a solid
novices feel that the process of sedimentary facies analysis and foundation for the future identification of multiple sedimentary
interpretation is complicated, and it can seem mystifying for facies in the field of lithofacies paleogeography.
non-geology scholars who lack a systematic knowledge of sedi-
mentary facies and paleogeography concepts.
2. Materials and methodology
A knowledge graph is a graphical representation of knowledge
(Paulheim, 2017; Fensel et al., 2020), which is essentially a large-
The main steps (Fig. 1) are: (i) Acquiring fluvial facies
scale semantic web (Berners-Lee et al., 2001; Shadbolt et al.,
knowledge. (ii) Designing the fluvial facies knowledge architecture.
2006; Krause et al., 2016; Färber et al., 2018), in which a knowl-
(iii) Constructing a structured, standardized, and systematic
edge base of semantic conceptual terms is composed of entities
fluvial facies knowledge system. (iv) Constructing a knowledge
(nodes) and relationships (edges) (Singhal, 2012; Ehrlinger and
graph for the fluvial facies domain as a structured multi-node
Wöß, 2016; Kejriwal, 2019; Fensel et al., 2020). Knowledge graph
divergent directed graph. (v) Designing a knowledge reasoning
technology applied to clinical medicine (Santos et al., 2022), to bio-
algorithm and sedimentary facies identification model for fast,
diversity (Page, 2016), to materials science (Mrdjenovich et al.,
efficient, and automatic intelligent identification of fluvial
2020), and other disciplines have enabled new breakthroughs
sedimentary facies.
and tools for interpretation.
Knowledge graphs for different domains of geology have been
coupled with computer science, artificial intelligence, and big data 2.1. Fluvial facies knowledge acquisition
technologies (Cheatham et al., 2018; Karpatne et al., 2018; Gil
et al., 2019; Nizzoli et al., 2020; Wang et al., 2021; Zhou et al., The process of extracting relevant information and concepts
2021; Ma, 2022; Zhang et al., 2022). Such geoscience knowledge from authoritative geoscience literature is a critical initial step
graph has been applied to express and solve scientific problems for constructing a knowledge graph (Wang et al., 2018). Geo-
and enable new knowledge discovery (Bergen et al., 2019; Liu science text mining uses the combination of natural language
and Song, 2020). Zircons can be classified into igneous, metamor- processing (NLP) and machine learning to extract such informa-
phic, and hydrothermal origins from cathodoluminescence images tion from unstructured/semi-structured geoscience literature
from similar deep learning methods (Zheng et al., 2022b). Knowl- (Wang and Ma, 2021) and to express that knowledge in a struc-
edge graph built from deep-time knowledge bases and regional tured form. In addition to enabling geoscience knowledge discov-
geologic time standards will improve interoperability of geo- ery (Ma et al., 2022), these methods also provide a text
science data from multiple sources (Ma et al., 2020, 2022). environment for semantic reasoning. In the same way, when
Recent applications to sediment facies interpretation fall into applied to sedimentary facies identification, knowledge acquisi-
four aspects: tion can provide high-quality knowledge services for which the
(i) Lithology: Mishra et al. (2022) conducted an evaluation and precision reflects to a certain extent the level of the knowledge
development of prediction models for geophysical well logs data base and, therefore, directly affect the accuracy of the sedimen-
analysis and reservoir characterization, and applied machine learn- tary facies identification.
ing techniques to lithology prediction. Zheng et al. (2022a) applied In turn, knowledge graphs can be used to assist natural lan-
the machine learning XGBoost algorithm in the identification of guage processing (NLP) and text mining for analysis of Earth
fluvial-lacustrine lithofacies from well logs. Sun et al. (2022) used science literature (Al-Moslmi et al., 2020; Ma, 2022). (i) Named
logging data of backpropagation (BP) neural network for lithology entity recognition (NER) via deep neural networks that no longer
identification. Xu et al. (2022) proposed an intelligent lithology relies on manually defined knowledge and rules (Fan et al.,
recognition method based on deep learning from databases of rock 2020). (ii) An Att-Bi-LSTM-CRF model with geoscience embedding
images and element information. based on a neural network of bidirectional long short term mem-
(ii) Sedimentary structure: Zhan et al. (2022) used a combina- ory conditional random field (Bi-LSTM-CRF) model with attention
tion of stochastic models and deep learning models to identify sed- mechanism (Qiu et al., 2019). (iii) Development of explainable arti-
imentary structures and discussed an inversion framework for ficial intelligence methods for convolutional neural networks
staged-wise stochastic deep learning. Jacq et al. (2020) developed (CNN) in the Earth sciences (Mamalakis et al., 2022).
an automatic detection and identification of sedimentary struc- Fluvial facies knowledge acquisition is to extensively absorb
tures from hyperspectral imaging (HSI) of sediment cores. historical experience and expert knowledge, and extract the
(iii) Paleontology: Based on the fossil image dataset and deep knowledge contained in heterogeneous data sources through a ser-
convolutional neural networks, automatic classification and identi- ies of operations such as identification, integration, and induction,
fication are realized (Liu et al., 2022). Wang et al. (2022) proposed in order to better serve the construction and application of fluvial
the transpose convolutional neural network (TCNN) model to iden- facies knowledge graph. The data sources are unstructured or
tify brachiopod fossils using a new deep convolutional neural net- semi-structured picture-text-table information in typical text-
work (CNN). books, monographs, geological dictionaries, and sedimentological
(iv) Mineral: Long et al. (2022) carried out classification and and paleogeography literature.
visualization research using artificial intelligence technology for But unfortunately, the classification schemes of fluvial facies are
mineral identification. Wu et al. (2022) proposed a deep learning uneven (Smith, 1974; Rust, 1978a,b; Rust, 1979; Walker and Cant,
mineral identification model based on multi-label image 1979; Miall, 1987; Miall, 2014), and therefore inhibit multimodal
classification. acquisition of information for those facies. Neither modern nor
Most of these works have mainly focuses on the identification ancient fluvial sedimentary facies can be explained by a single uni-
of a single specific facies marker (sediment structure, a fossil taxa, fied or universal facies model. Cant and Walker (1976) described
etc.), but the comprehensive reasoning for sedimentary facies fluvial facies types according to ‘‘bedding (sedimentary
interpretation using multiple characteristic facies markers are rare. structure) + facies”, e.g., planar-tabular cross-bedded facies. Miall
Therefore, this study uses fluvial facies a case example to demon- (1985) elaborated ‘‘lithofacies classification” scheme to classify flu-
stration the entire process from the initial construction of fluvial vial facies. Singh and Bhardwaj (1991) proposed the different types
facies knowledge graph through the final application and verifica- of fluvial facies according to ‘‘sedimentary structure + lithology +
tion of sedimentary facies identification. This step-by-step proce- facies”, e.g., trough cross-stratified sandy facies. Bridge (1993)
2
L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

Fig. 1. The life cycle and technical framework of fluvial facies knowledge graph construction and application.

has rewritten Miall (1992) to give a more detailed description of meandering, braided, anastomosing (Smith, 1976, 1980, 1986)
facies marker attributes for each sub-sedimentary facies type. and straight. For example, the Mississippi is a typical meandering
Browne and Naish (2003) explained and described three types of river (Fig. 2). The sediments of meandering and braided rivers
fluvial facies based on ‘‘lithology + facies” (gravel, sand, and mud are widely distributed, whereas the sediments of ancient straight
facies). Scherer and Lavina (2005) described four different facies rivers are not easily preserved.
associations based on ‘‘sedimentary structure + lithology”, e.g., After completing the data collection, a fluvial facies terminology
horizontally laminated sandstones. set was data pre-processed to ensure that standardized, reliable,
Miall (2013) proposed that fluvial facies are composed of eight traceable and valid data are available for knowledge reasoning
basic 3-D architectural elements: (i) Channels. (ii) Gravel bars and and sedimentary facies identification.
bedforms. (iii) Sandy bedforms. (iv) Foreset macroforms. (v) Lateral The operations for the data pre-processing include:
accretion deposits. (vi) Sediment gravity flow deposits. (vii) Lami- (i) Cleaning and de-noising of fluvial facies data, in order to fil-
nated sand sheets. (viii) Overbank fines. He later put forward a new ter invalid information and remove redundant data.
method based on Microforms, Mesoforms, and Macroforms in (ii) Standardization of fluvial facies concepts and terms, merg-
which: (i) Microforms generate small-scale ripple marks and cur- ing and aligning fluvial facies knowledge (e.g., abbreviations, syn-
rent lineations. (ii) Mesoforms include larger-scale flow-regime onyms, etc.).
bedforms: dunes, sandwaves, minor channels, and unit bars (such (iii) Establing a rule set based on fluvial facies knowledge, and
as linguoid bars, transverse bars, longitudinal bars, and diagonal the constraining and standardization of fluvial facies knowledge
bars). (iii) Macroforms include major channels and larger, com- by means of a data dictionary.
pound bar forms (point bars, side bars, sand flats, and islands).
Miall (2013) classified the fluvial facies styles into: (i) High- 2.2. Design fluvial facies knowledge architecture
Sinuosity rivers. (ii) Low-Sinuosity rivers. (iii) Anastomosed rivers.
(iv) Ephemeral rivers. (v) Floodplain environments. Ribes et al. The design of the underlying logical architecture of fluvial facies
(2015) expounded on the stratal patterns and facies assemblages knowledge is an indispensable condition for the construction of
of 16 lithofacies in the Emirhan mini-basin (as modified from knowledge graph and related applications. The design of the
Miall, 1985). knowledge architecture plays a decisive role in the hierarchy,
In addition to the above, multiple factors can affect the structure, and content filling of the knowledge base, also lays a
accumulation and preservation of sedimentary records of fluvial solid foundation for the decision-making power of sedimentary
systems in geological sections in different spatial and temporal facies identification. The scope of knowledge architecture of fluvial
settings, including watershed lithologies, terrain (mountain or facies is the terminology categories and property feature words of
plain), slope, climatic range, the intensity and depth of river fluvial facies, which mainly includes two parts (Fig. 3):
discharge, the seasonal variations in water and sediment (i) Schema layer (Sedimentary facies layer)
discharges, vegetation coverage, the position within a channel or This module, also known as the ‘‘Conceptual ontology layer”,
edge, remodeling of previous fluvial deposits, the direction and refers to the collection of concepts and terms of fluvial facies
angle of field observations (vertical vs horizontal, local vs regional) knowledge, and is equivalent to the corpus of all the keywords
and other factors. In general, the identification of sedimentary and phrases describing the types of fluvial sedimentary facies. It
facies depends upon the regional environment and even upon includs three hierarchies: ① fluvial facies, ② fluvial subfacies,
the geological time. ③ fluvial suborder facies (Feng, 2019; Mou, 2022).
Therefore, the first step in our research was an attempt to (ii) Data layer (Facies marker layer)
absorb, fuse, integrate and synthesize the diverse views of most Facies marker data is a collection of sedimentary properties
scholars as widely as possible. A classical classification of modern (Potter,1959); therefore, this layer is also called ‘‘Property data
fluvial facies deposition (Cant, 1982) was selected as the data layer”. It consists of the sediment records of various environmental
framework, which is divided into four types of river systems: conditions and a suite of basic elements and identifying symbols
3
L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

Fig. 2. Model of the types of sedimentary settings associated with a meandering river, tributary of the Mississippi River, 37°540 13.8100 N, 87°320 05.9000 W.

Fig. 3. Fluvial facies knowledge architecture consists of sedimentary facies layer and facies marker layer. Sedimentary facies layer is schema layer, including the concept
ontology terms of fluvial facies, the data structure is divided into three levels: fluvial facies, fluvial subfacies, and fluvial suborder facies. Facies marker layer is data layer,
covers all property characteristics and property values of fluvial sedimentary facies, and consists of four parts: lithology, sedimentary structure, paleontology, and mineral.

for sedimentary facies identification. It is mainly divided into four 2.3. Fluvial facies knowledge system
layers: ① lithology, ② sedimentary structure, ③ paleontology,
④ mineral. The Deep-time Digital Earth (DDE) is the first big science pro-
The architecture provides a basic information service for the gram of the International Union of Geological Sciences (IUGS)
construction of the fluvial knowledge system and knowledge (Wang et al., 2018, 2021; Ma et al., 2020, 2022; Zhou et al.,
graph. It also provides the effectial decision support for the text 2021; Ma, 2022;). DDE has initiated and implemented a procedure
mining methods and the design of machine learning data-mining for constructing knowledge systems and knowledge graphs, has
algorithm in the future. established terminology standards, and has provided a platform

4
L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

of technical service support for disciplinary fields within eral. A property node is a description of the property characteris-
sedimentology, paleogeography, petroleum geology, paleontology, tics (values) of an entity (sedimentary facies term).
stratigraphy, etc. Only by laying a good foundation of (vi) Establish the connection between the sedimentary facies
disciplines can we ensure the steady and healthy development of nodes and the facies marker nodes.
scientific research. Scientific research without the support of Distinguish the relationships between nodes at each hierarchy
validated knowledge systems may be eclipsed in the not-to- and connect concept nodes (sedimentary facies) and property/
distant future. property values nodes (facies marker).
The knowledge system of fluvial facies describes the summation (vii) All of the above sedimentary facies (concept nodes) data
of the characteristic indication (facies markers) used in fluvial and facies marker (property nodes) data are stored, and generate
facies identification and all fluvial facies classification. The experi- a data dictionary of fluvial facies in Markdown format (Supplemen-
ence and knowledge accumulation of geoscience experts provide a tary data, Data S1).
powerful theoretical guidance for the construction of fluvial facies
knowledge system. The compilation of a clear and complete fluvial 2.3.2. Knowledge storage
facies knowledge system is an important component of the suite of For the traditional knowledge stored in the human brain mem-
lithofacies knowledge graphs for the paleogeography domain. ory, the brain capacity is limited. When the amount of data surges,
These will provide an infrastructure for knowledge services and the query performance becomes more critical (Brazier et al., 2010);
reasoning applications. therefore a computer-based system becomes more efficient and
convenient to store knowledge. Computer storage of knowledge
2.3.1. Construction method is convenient for subject experts to add, delete, modify, and check,
fluvial knowledge system is a tree-like logical hierarchical data in order to meet the needs of various scenarios and of applications
model, which clearly shows the logical relationship between all for scientific research. Different types of knowledge storage meth-
hierarchies from the root node to the leaf node, and graphically ods have advantages and disadvantages. We have tried the
shows the association and subordination relationship between resource description framework (RDF) (Fig. 4) and web ontology
terms and properties. The structural design of the entire knowl- language (OWL) (Fig. 5) formats for fluvial knowledge storage
edge system is based on having ‘‘fluvial facies” as the ‘‘root node” and describing the data content contained in terms. RDF is a self-
(starting point, a node without parent node), followed by branches describing logical data resource model written in Extended
from the parent node to the child node until it reaches the leaf Markup Language (XML). An example shown in Fig. 3 illustrates
node (facies marker layer), which is the node in the last layer that the extensive array of information types and their values, including
cannot be subdivided. The tree data structure of fluvial facies the class and subclasses, the node’s (initial) creation time, the
knowledge system is characterized by the rule that each concept node’s definition, code names, labels, references, etc.
node has a finite number of child nodes (n > 0) until the leaf node Protégé-based Web ontology programming languages have
(n = 0), and each child node (except the leaf node) can be subdi- much in common with RDF, but OWL offers a broad vocabulary
vided into multiple disjoint subtrees. and more semantics (Parekh et al., 2004). Protégé is an ontology
Here are the detailed step-by-step instructions for building a editor and framework based on OWL (Protégé, 2000), RDF schema
fluvial facies knowledge system: (RDFs), etc. For constructing ontology-based knowledge systems.
(i) Set the root node. World Wide Web Consortium (W3C) standards meet domain
Add a root node of the hierarchical structure tree, with the knowledge (Ma, 2017), and Protégé fully supports the latest OWL
name ‘‘fluvial facies”, which is a ‘‘concept node”. 2 and RDF specifications from the W3C. Each node has a uniform
(ii) Knowledge clustering of fluvial facies consists of two mod- resource identifier (URI) as a unique identifier in the international-
ules: ‘‘sedimentary facies layer” and ‘‘facies marker layer”. ized resource identifier format (Fig. 6).
Clarify whether each of the two nodes has a subordinate rela-
tionship (parent nodes and child nodes) or a sibling relationship 2.3.3. Knowledge representation
(sibling nodes). Through the above steps, an ordered and structured representa-
(iii) Clarify the hierarchy structure relationships between terms. tion framework of fluvial facies knowledge was obtained to
A: Sedimentary facies layer is divided into three sublayers: describe its hierarchical structure characteristics. We then used
① The first hierarchy consists of four classifications of fluvial Python language and JavaScript to design and write code to gener-
sedimentary facies. ate visual charts of fluvial facies knowledge: a fluvial knowledge
② The second hierarchy is fluvial sedimentary subfacies and its system hierarchy sunburst chart (multi-level pie chart) (Supple-
patterns. mentary data Fig. S1), a radial chart (Supplementary data Fig. S2),
③ The third hierarchy is fluvial sedimentary suborder facies etc. The central diagram in Supplementary data Fig. S1 shows the
and its types. apex of the hierarchy tree (the center of the circle), and farther
B: Facies marker layer includes property data of fluvial facies, out from the center of the tree are the lower levels of the hierarchy.
which are: We also developed a web back-end server for visualization of flu-
① lithology, ② sedimentary structure, ③ paleontology, vial facies knowledge system, which provides dynamic web ser-
④ mineral. vices and application development environment. Users can view,
(iv) Define and fill in the annotation information for all concept refresh and enlarge the visualization results on this web server site.
nodes.
Include the names, definitions, and references of the concept 2.4. Fluvial facies knowledge graph
nodes to ensure that knowledge can be traced back to the source.
Of course, the symbol ‘‘@” can also be added before the reference The construction of fluvial facies knowledge graph can reduce
to distinguish the definition from the reference, making it easier the need for the storage of knowledge in human brain, accelerate
for computers to recognize. the efficiency of knowledge reasoning, sorting and storing of
(v) Fill in property and property values for all sedimentary knowledge in a structured form, and then enable a visual expres-
facies. sion. The graph system can also quickly and efficiently find the
The following five keywords are named ‘‘property node”: facies accurate and effective knowledge needed by the research from
marker, lithology, sedimentary structure, paleontology, and min- the ‘‘ocean of knowledge”, thereby reducing the considerable
5
L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

Fig. 4. List RDF code snippet of three terms: Fluvial Facies, Point bar, and Braided river. The red font ‘‘rdf:about” is used to describe or introduce a resource (terminology
name), and the blue font following ‘‘rdf:about” is the unique resource identifier (URI) for that terminology. The red font ‘‘rdf:resource” is used only for attributes and refers to
the introduction of a subject. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

(ii) Automatic build (Bottom-up)


This method extracts information from the geoscience litera-
ture, reclassifies, integrates and summarizes the data extracted,
automatically generates the knowledge base semi-automatic or
automatically, and constructs the knowledge graph (Wang et al.,
2018). Knowledge can also be selected from geoscience linked
open data (LOD) to build a knowledge graph (Cheatham et al.,
2018). The model of this method is flexible and changeable, but
the reliability of the automatically extracted knowledge is ques-
tionable, and it needs the intervention of geoscience experts to ver-
ify whether the data is accurate and reasonable.
(iii) Mixing top-down and bottom-up
They do not conflict with each other, but are complementary to
each other. Each exerts its own advantages to build a more reliable
geoscience knowledge graph. Moreover, the more labeled data are
provided by geoscience experts, the better the performance of the
knowledge graph.
Fig. 5. Annotation of ‘‘Braided river” in web ontology language (OWL) format. The In this study, the third hybrid method was used to construct the
terminology’s unique resource identifier (URI), names of subclasses and super-
fluvial facies domain knowledge graph (Abu-Salih, 2021). The
classes, references, code name, terminology generation time, definition, and rdf
shema (rdfs) lable are mentioned.
resulting fluvial facies knowledge graph is a fine-grained, high-
precision, multi-node, divergent, and one-way directed semantic
network graph.
workload for knowledge acquisition, improving the experience of
knowledge search, and enhancing the quality of knowledge retrie- 2.4.1. Domain ontology and triples modeling
val. However, the construction of fluvial facies knowledge graph Knowledge modeling with fluvial facies triples is the process of
itself is an extremely complex process. There are several ways to building the conceptual model of the knowledge graph. The gram-
build a knowledge graph (Kejriwal, 2019; Fensel et al., 2020; Ma, matical structure of a fluvial facies triplet is ‘‘subject-predicate-
2022): object (SPO) ”. An ‘‘node-edge-node” is the skeleton of the fluvial
(i) Manual construction (Top-down) facies triples, and it has two sets of expressions as illustrated by
According to the geological field experience and knowledge the Cypher code:
rules of geological experts, the top-down method first designs a (i) Ontology/Entity-Relationship-ontology/entity
data schema framework manually, fills in the conceptual knowl- (Fluvial_Facies)-[:Classification]->(Meandering_river),
edge from the top level, and gradually refined (Auer et al., 2018) (ii) Ontology/entity-Property-Property values
to form a structured and hierarchical skeleton, and then fills in (Natural_levee)-[:Property]->(Facies_marker5),
the knowledge in sequence. Although the mode of this method is (Facies_marker5)-[:Include]->(Paleontology5),
relatively fixed, but it has a high accuracy data set. (Paleontology5)-[:Include]->(Plant_root5),
6
L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

Fig. 6. Partial URIs of Protege’s OWL ontology, generated by the OWL application programming interface (API). The attribute ‘‘xml:base” be inserted in extensive markup
language (XML) document to specify a base internationalized resource identifier (IRI) format other than the base IRI of the document or external entity. The red font ‘‘rdf:
about” is used to describe an ontology (terminology name), and the blue font after ‘‘rdf:about” is the URI of that ontology. The red font ‘‘rdf:resource” introduces a subject that
is used only to describe attributes. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Then, two parts of sedimentary facies (ontology/entity) and (Miller, 2013), using Cypher graph database query language.
facies marker (property and property values) are filled into this tri- The storage pattern is based on key value (Kemper, 2015),
plet skeleton model to prepare for the generation of fluvial facies which is helpful for queries to use knowledge more conve-
knowledge graph. niently and quickly. This is different from the widely used dis-
Ontology is a set of conceptualized and explicit formal specifi- tributed storage method in table format, because the flexibility
cations (Gruber, 1993; Guarino et al., 2009; Smith, 2012; of traditional table data sets is not good, data is only stored,
Effingham, 2013; Jacquette et al., 2014). Fluvial facies domain data can’t communicate with each other, and there is no con-
ontology refers to concepts and terms related to fluvial sedimen- nection and link between data. Using Neo4j for graph data
tary facies. The entity refers to the ontology plus the instance; modeling of fluvial facies domain knowledge can improve effi-
for example, the sedimentary facies in a specific spatio-temporal ciency and flexibility (Lal, 2015), can write all triples knowledge
range can be called sedimentary facies entity. Ontology terminolo- in one step, also can use comma separated value (CSV) file to
gies are indispensable materials for knowledge reasoning batch import. Especially when the amount of data is large,
(Ehrlinger and Wöß, 2016). Ontology is also the lifeblood of build- the advantages of graph database are more obvious. Moreover,
ing data-driven and model-driven geoscience domain knowledge the code of Cypher is readable, and is described as ‘‘like SQL
graphs (Brewster et al., 2004; Ma et al., 2014; Jain, 2020). The dif- a declarative, textual query language”, while Cypher (Neo4js’s
ference between a knowledge graph and an ontology is that knowl- query language) is more scalable (Kemper, 2015). Meanwhile,
edge graph = ontology + data (Bess, 2020). When the basic logic Neo4j provides well-performing graph algorithms, and it also
rules and the fluvial facies knowledge triples are constructed, the has a certain auxiliary effect on knowledge reasoning and
knowledge is no longer an isolated information point, but becomes knowledge calculation.
a huge semantic web connected by the fluvial facies ontology
terms (nodes) and their association relationships (edges). 2.4.3. Visualization, query, and retrieve
The construction steps of fluvial facies ontology triples are as The code written in Cypher language was run on the Neo4j
follows: graph database platform, and a complete fluvial facies knowledge
graph was generated (Supplementary data Fig. S3). The visualiza-
(i) Describe and define fluvial facies ontologies and entities. tion of fluvial facies knowledge graph based on Neo4j graph data-
(ii) Clarify and customize (or follow existing definitions) rela- base describes the conceptual terms (ontology/entity), properties,
tionships between ontologies and entities. property characteristics (property values) and relationships
(iii) For qualitative data, the properties of ontology and entity (edges) of fluvial facies in a structured form or a multi-
should be set. For quantitative data, the corresponding prop- dimensional visual display. The Neo4j graph database expresses
erty values should be added. fluvial facies knowledge as information that can be understood,
(iv) Create and list the instance. processed and interpreted by computers. The platform also shows
code error feedback so we know what went wrong and can correct
2.4.2. Knowledge storage it. The Neo4j graph database platform provides the ability to query
The processed and refined fluvial facies knowledge triples and retrieve data using Cypher, which can view the query results of
are stored in the native graph database platform Neo4j a graphical knowledge graph and the number of nodes and edges it
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L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

Fig. 7. The graph view of running a MATCH and RETURN command statement to query the node named ‘‘diagonal” on the Neo4j fluvial facies knowledge graph database. The
row of labels starting with the number 260 in gray represents the properties and relationships (and their corresponding quantities) of the fluvial facies knowledge graph, and
the row of colored labels starting with the number 261 in purple represents all the nodes of the fluvial facies knowledge graph and their quantities, with a total of seven layers
of nodes. The bottom part shows that the fluvial facies knowledge graph consists of 261 nodes (ontologies) and 260 edges (relationships) in total. (For interpretation of the
references to color in this figure legend, the reader is referred to the web version of this article.)

contains in real time (Fig. 7). The current fluvial facies knowledge 3.1. Reasoning principles and model design
graph contains 261 semantic entities (nodes) and 260 relationships
(edges), in which each node has a unique ID value to avoid node Fluvial sedimentary facies identification is the process of infer-
conflicts. The layout of node position is designed by knowledge ring and predicting ancient depositional environment and sedi-
computation based on the paths of nodes and edges using graph mentary facies by analyzing and interpreting facies marker data.
algorithms. Facies modeling is an important part of facies analysis, which
describes the identification marker (facies marker) such as sedi-
ments and paleontology (Melchor et al., 2012), and uses these to
3. Application of fluvial facies identification and knowledge objectively determine the corresponding facies and deduce the
reasoning deposition process of each sedimentary facies (Anderton, 1985).
The grain size of fluvial sediments varies greatly. With a decrease
Existing, widely accepted methods for sedimentary facies iden- in water energy, the fine suspended matter is gradually deposited,
tification present new constraints and opportunities in the age of and the resulting vertical profile shows a dual structure of lower
coding. Although sedimentary facies identification and prediction coarser (e.g., gravel, sandy) and upper finer (e.g., silt, muddy)
is supported by the knowledge decision of geologists, it, itself, is deposits (He, 2022). The color of rocks partly reflects their compo-
a very complex knowledge reasoning process. Due to the strong sition, structure and origin, and it is one of the important markers
subjectivity of manual identification, the high dimension and high for stratigraphic stratification, correlation and inference of paleo-
unpredictability of facies marker data are inevitably overlooked. geographic conditions.
When multiple factors interfere, the complexity of sedimentary Although the current publications presenting the theoretical
facies interpretation and knowledge prediction increases, and the description and interpretation of facies patterns are reasonable,
identification performance decreases. To try to avoid these compli- they may not be suitable for the derivation of other facies under
cations, this study introduces a novel data-mining clustering algo- spatio-temporal relationships; that is, they are not a universal tem-
rithm that conforms to sedimentological cognition and common plate for understanding the complexity of fluvial facies. The identi-
sense, puts forward a fluvial sedimentary facies knowledge reason- fication and analysis of fluvial sedimentary facies should be
ing model, and designs and develops a sedimentary facies knowl- completed in at least three parts (Miall, 1982): (i) Identification
edge reasoning operating system. Therefore, it provides a and description of major and minor lithofacies components.
practical reference for experts based on sedimentary facies identi- (ii) To determine and study the internal relations of lithofacies
fication and knowledge reasoning. associations. (iii) Geometry and orientation of sedimentary units.
In the final step, the reasoning system is tested and the quality Vertical lithofacies association (profile) has strong cyclicity
of the reasoning results is evaluated. In the following section, we (Visher, 1965; Miall, 1978), which is especially meaningful for
first introduce the background knowledge and methods of fluvial identification. Markov chain (MC) is the best method technique
sedimentary facies identification and prediction, and summarize for vertical sequence analysis (Miall, 1982), the model holds that
the current knowledge reasoning methods and technologies all the past information is stored in the current state, that is, the
(Section 3.1), and then elaborate the theoretical background of state obtained at the n-th transition during the state transition of
data-mining clustering algorithm in detail (Section 3.2). a system, and there is a transition probability, only depends on
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L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

the result of the previous time (the (n–1)-th), and the transition (TransE) series algorithms (Bordes et al., 2013), etc., which can be
probability can be calculated from the previous state, which is used for tasks such as nodes classification and link prediction. (iii)
independent of the original state of the system and the Markov Neural network-based reasoning, for example, Das et al. (2016)
process before the transition (Harbaugh and Bonham-Carter, combined multi-step reasoning based on symbolic logic with
1970). recurrent neural networks (RNN). Socher et al. (2013) introduced
The Markov chain is applied to sedimentary facies identifica- a neural tensor network (NTN) model for reasoning over a large
tion, assuming the sequential state of the probability (P) of the joint knowledge graph. Schlichtkrull et al. (2018) introduced rela-
lithofacies (L) state is: . . .Lt-2, Lt-1, Lt, Lt+1, Lt+2. . ., then the probabil- tional graph convolutional network (R-GCN) and applied them to
ity when Lt+1 depends only on Lt, i.e Eq. (1) link prediction and entity classification tasks. Graph neural net-
work (GNN) have been used to capture structural information
PðLtþ1 j . . . Lt2 ; Lt1 ; Lt Þ ¼ PðLtþ1 jLt Þ ð1Þ
inherently stored in knowledge graph (Arora, 2007).
In summary, we designed the model of fluvial sedimentary The above content analyzes the previous research in this
facies identification and knowledge reasoning (Fig. 8). The reason- research field through the practice of knowledge reasoning based
ing principles of the model are described as follows: on knowledge graph and its related neural network methods and
(i) The probabilities of all the fluvial suborder facies add up to technologies. In this paper, the sedimentary facies identification
100%. method is combined with computer technology and Python and
(ii) The probabilities of each layer are summed up by the prob- other tools. It is found that through the in-depth deduction of
abilities of its subterms. multi-source heterogeneous, multivariate, multi-dimensional,
(iii) The less a single keyword appears in the database, the mixed, random, fuzzy, and spatio-temporal heterogeneous facies
greater the weight of the keyword. marker data, the hypothesis of sedimentary facies can be inferred
(iv) The weight of the fluvial suborder facies is equal to the sum and predicted, and the induction and experiment can be made.
of the weight of the keywords contained in it. Based on the tree logic hierarchy of fluvial facies knowledge and
data-mining clustering algorithm (Song et al., 2018; Portisch
3.2. Reasoning algorithm and system development process et al., 2022), a new data-mining clustering algorithm for sedimen-
tary facies identification was introduced. The aim is to obtain the
To infer the corresponding sedimentary facies from a large corresponding sedimentary facies results as the output data by
amount of facies marker data requires the support of knowledge inputting the facies marker combination data.
reasoning techniques. Knowledge reasoning technology based on First, an initial database is built, the sedimentary facies data sets
knowledge graph has received extensive attention in academia with different hierarchical structures are divided, and the initial
and industry. Generally, there are three kinds of knowledge rea- weight is assigned to each node of the input layer. Then, according
soning methods (Chen et al., 2020a): (i) rule-based reasoning to the tree clustering data structure of the fluvial facies knowledge
(Chen et al., 2020b), in which the algorithm for association rule graph, the correlations between the entity nodes (sedimentary
mining under incomplete evidence (AMIE) was derived from early facies) and the attribute nodes (facies marker) are analyzed. The
inductive logic programming (ILP) system (Galárraga et al., 2013). input feature data (facies marker combination) are read, for which
(ii) Distributed representation learning-based reasoning (Xie et al., the feature data are the input variables used for inference and pre-
2016), of which common methods include: translating embedding diction. The node with the highest matching rate with the input

Fig. 8. Fluvial sedimentary facies identification and knowledge reasoning model. On the right side is the ‘‘Input layer” of the facies mark, knowledge reasoning and knowledge
calculation are carried out in the middle ‘‘Reasoning layer”, and the system displays the corresponding fluvial facies results in the ‘‘Output layer”.

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L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

data and the closest reasoning path was found through knowledge (viii) Convert the sedimentary suborder facies weights to prob-
calculation. The two adjacent sedimentary facies nodes are clus- abilities, as Eq. (4)
tered and merged from bottom to top in turn until the root node.
Fig. 9 shows the flow chart of sedimentary facies identification W mi
Pmi ¼ Pn ð4Þ
and knowledge reasoning for a specific example demo. i¼1 W mi
The following sections describe in detail the development pro-
where Pmi is the probability of the i-th sedimentary suborder facies.
cess of the knowledge reasoning system, the mathematical formula
(ix) Upward inference computes the probability of the upper
derivation process, and the actual calculation methods and steps:
layer, and the probability of each layer is the sum of the probabil-
(i) Create a new embedded local database (using SQLite) named
ities of its sublayers.
‘‘initDB” in Python language.
(ii) A ‘‘DB operation” module was built with the data of sedimen-
tary layer and facies marker layer of fluvial facies, which can be 3.3. Reasoning results and quality assessment
used to create, read (retrieve), update, and delete fluvial facies
data, and query sub-nodes. In order to further verify the reliability of the fluvial sedimen-
(iii) Input keywords in the fluvial facies knowledge graph rea- tary facies identification and knowledge reasoning algorithm, it is
soning model, separated by English commas ’,’. For example, used in practical application scenarios, and the correctness of the
‘‘Gravel, Massive, Sand”. algorithm and program is verified by comparing with the results
(iv) Keywords spotting (k1 , k2 , k3 . . . kn ). of literature (Supplementary data Table S1). First, the facies labeled
(v) Search the database to find out how many times all the key- data from the test data set were input into the sedimentary facies
words (C k1 , C k2 , C k3 . . . C kn ) appear in the model. inference model, and the inference system read the keywords, car-
(vi) The weight of each keyword ki is calculated, and the weight ried out relevant numerical calculations on the obtained sedimen-
of the keyword is inversely proportional to the number of times the tary facies reasoning results, and arranged in hierarchical
keyword appears in the database as Eq. (2) descending order (Supplementary data Fig. S4). The sedimentary
facies reasoning model is then calculated and verified by program-
Qn
i¼1 C ki ming and experiment.
W ki ¼ ð2Þ
C ki Experimental verification:
For example, enter the following keywords in the reasoning
where W ki is the weight of the i-th keyword, and C ki is the number system: ‘‘Fine sandstone, Scour erosional fill, Medium-scale cross
of occurrences of the i-th keyword in the database. bedding, Small-scale cross bedding, Horizontal bedding”. The
(vii) Calculate the weight of the sedimentary suborder facies, reasoning system will then automatically calculate the knowledge.
which is equal to the sum of the keyword weights contained in this Supplementary data Table S2 Supplementary data Table S1 details
sedimentary suborder facies, as Eq. (3) the specific calculation value and the deduced position of the sed-
Xn imentary facies in each layer. The predicted best interpretation of
W mi ¼ i¼1
C wi W ki ð3Þ fluvial facies is then compared with known sedimentary facies
intepretation as explained by experts in the literature. The calcula-
where W mi is the total weight of the i-th suborder facies, C wi is the tion process of the reasoning system for three hierarchies [Fluvial
number of occurrences of the i-th keyword in the suborder facies facies (first hierarchy), Fluvial subfacies (second hierarchy), and
characteristic sign (0 or 1). Fluvial suborder facie (second hierarchy)] of sedimentary facies

Fig. 9. Example of fluvial facies identification and knowledge algorithm flow. Do a demo demonstration to explain, gives the mathematical formula derivation procedure and
the actual numerical calculation process. ‘‘a, b, and c” represent facies marker data, ‘‘A, B, and C” represent fluvial suborder facies, and ‘‘AA” and ‘‘BB” represent fluvial
subfacies.

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L. Zhang, M. Hou, A. Chen et al. Geoscience Frontiers 14 (2023) 101521

are as follows: The probabilities of the first hierarchy: Meandering (ii) Standardize knowledge:
river (0.917), Anastomosed river (0.083). The probabilities of the Due to the different data sources and data formats of scholars
second hierarchy: Bank deposit (0.833), Floodplain (0.042), Oxbow from different countries, the classification, definition, and descrip-
lake (0.042), Anastomosed channel (0.042), Channel wetland tion of the data generated are also different, thereby resulting in
(0.041). The output results [(Fluvial suborder facie (second hierar- some inconsistencies for knowledge representation. To some
chy)] of the above keywords were ‘‘Crevasse splay (0.667), Natural extent, this ‘‘noise” can be reduced by establishing rule sets and
levee (0.667), Overbank (0.042), Channel-fill (0.042), Multiple by standardized processing.
channels (0.042), Peatland (0.04)”, in descending order of propor- (iii) Version iteration and knowledge update:
tion, and according to the reasoning principle just devised, the Progressive enhancements of knowledge systems and knowl-
sum of each layer of sedimentary facies is 1, while the sedimentary edge graphs should be indicated as version 1.0, 2.0, etc., to avoid
faces results explained by the known expert experience knowledge user confusion. This also applies to improved machine learning
in the literature is ‘‘Crevasse channel” (the keywords entered by algorithms and adjustment of parameters.
the expert are: ‘‘Sandstone, often fine upwards with scoured bases. (iv) Version control (multilingual):
Can be massive, cross-bedded (tough or planar), horizontally bedded, Multi-language versions of the domain knowledge graph can be
ripple cross-laminated”). The results of the experimental verifica- established through exchanges of international scholars, which
tion are good. will also enhance the performance of the data dictionary.
The results show that the output sedimentary facies of the rea-
soning model prediction results closely match the literature inter- 4.2. Methodology layer
pretation results as given in the literature (Miall, 1985; Smith,
1987; Ribes et al, 2015; Wainman and McCabe, 2020), and these (i) Construction method:
results are not only applicable to this suborder facies, but also The top-down construction of knowledge graph based only on
are widely applicable to fluvial facies. As described in Supplemen- domain reference textbooks and legacy publications does not
tary data Table S1, the results from the reasoning system can meet encompass the whole knowledge base. It is necessary to apply
the accuracy requirements of fluvial sedimentary facies identifica- aspects of the bottom-up building of the knowledge graph through
tion, and the interpretation accuracy rate of the results is as high as data-mining techniques using machine reading of literature, com-
90% (Supplementary data Table S2 Supplementary data Table S3). bined with expert intervention, error correction, and inclusion of
It also shows that the reasoning algorithm and model can approx- new knowledge in order to enhance and improve the knowledge
imately describe the process and concepts of fluvial sedimentary graph.
facies identification, which also confirms the reliability of the rea- (ii) Reasoning method:
soning program of fluvial sedimentary facies identification. In addi- In the future, one should consider applying low-dimensional
tion, the operating system has the important features of being fast vector representation methods (Abu-Salih et al., 2021) of word
and convenient for experts to use, which also accelerates the speed embedding or entity embedding for knowledge reasoning, such
of knowledge reasoning and improves the efficiency of knowledge as Trans series models, and to explore neural network knowledge
computing. reasoning, such as graph neural network for knowledge reasoning.
Even through the fluvial sedimentary facies identification and It will also be necessary to solve the knowledge reasoning problem
knowledge reasoning shows a high matching rate when compared of multiple knowledge graphs.
with the interpretations of classic publications, it is not yet a one-
to-one mapping relationship. We can never make a 100% accurate
4.3. Application layer
assessment because sedimentary facies identification itself is char-
acterized by data confounding and high dimensionality, but we can
(i) Interoperability:
provide enough knowledge to give a good assessment. In addition,
To improve interoperability, knowledge revision and audits
one complication is the heterogeneity of data. The data and the
need to be jointly built and shared through coordinated manage-
definition and understanding of concepts are different among the
ment and multi-person collaborative online editing.
dates of publications and the studied region. Lowering this barrier
(ii) Interoperability:
or differences is a goal for an improved knowledge graph. Another
To facilitate public access to applications of the knowledge
factor is the need to complete bottom-up literature data input. In
graph, we developing an online service and web application soft-
the future, we intend to expand and standardize the classification
ware that integrates the knowledge system, knowledge graph,
of various fluvial sedimentary facies according to the author or
knowledge query, knowledge reasoning, and data visualization.
publication date.
(iii) Human vocal interactions:
A user-voice question/answering system for interrogating
4. Discussion
and learning from the intelligent reasoning system for deposi-
tional environments involves data modeling, recognition, and
The general process that was used to prepare the fluvial facies
storage, as well as the design of speech dialogue model train-
knowledge graph can be extended to the identification and inter-
ing modules. The operating system collects and preprocesses
pretation of other sedimentary facies in the field of paleogeogra-
the user’s speech dialogue data (Supplementary data
phy. However, there additional considerations and enhancements
Table S3), then rewrite and matche the existing data packets
are required in order to improve the scalability and general appli-
(data sets) for appropriate response to them. Such a
cability of knowledge graphs in this field.
question-answering system is very important for human-
machine understanding and judging the interpretation of sedi-
4.1. Knowledge layer
mentary facies.
(i) Knowledge completion:
As the basis for any knowledge graph construction, it is neces- 5. Conclusions
sary to enhance the knowledge base of the domain through the
method of knowledge completion in order to update the data Open-source sofeware and shared knowledge architecture are
and pattern layers, and to enrich the semantic ontology model. key factors to drive future knowledge discovery and knowledge
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Declaration of Competing Interest Effingham, N., 2013. An introduction to ontology. Cambridge, UK, Cambridge
University Press.
The authors declare that they have no known competing finan- Ehrlinger, L., Wöß, W., 2016. Towards a definition of knowledge graphs. In: Joint
Proceedings of the Posters and Demos Track of 12th International
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Germany pp. 1-4.
Elatrash, A.M., Abdelwahhab, M.A., Wanas, H.A., El-Naggar, S.I., Elshayeb, H.M.,
Acknowledgements
2021. Multi-disciplinary approach to sedimentary facies analysis of Messinian
Salinity Crisis tectono-sequences (South-Mansoura Area, Nile Delta): incised-
This study was supported by the IUGS Deep-time Digital Earth valley fill geological model reconstruction and petroleum geology-reservoir
(DDE) Big Science Program, National Natural Science Foundation element delineation. J. Petrol. Explor. Prod. 11 (4), 1643–1666. https://doi.org/
10.1007/s13202-021-01124-2.
of China (Grant No. 42050104). The authors want to thank Xian- Fan, R., Wang, L., Yan, J., Song, W., Zhu, Y., Chen, X., 2020. Deep learning-based
kang Hu for providing technical support. We would like to thank named entity recognition and knowledge graph construction for geological
Prof. Chao Ma for his constructive discussions and useful sugges- hazards. ISPRS Int. J. Geo Inf. 9, 15. https://doi.org/10.3390/ijgi9010015.
Färber, M., Bartscherer, F., Menne, C., Rettinger, A., 2018. Linked data quality of
tions. Many thanks are also given to the anonymous reviewers DBpedia, Freebase, OpenCyc, Wikidata, and YAGO. Semantic Web. 9 (1), 77–129.
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