A survey on knowledge representation in materials science and engineering: An ontological perspective

The possible roles of materials ontology are defined in a hierarchical structure.The comparison criteria for materials ontologies are proposed.The most widely referred nine ontologies are reviewed.We compare the reviewed ontologies by the proposed comparison criteria and roles.The future challenges of materials ontology are presented. Informatics in materials science and engineering is playing more and more important role in contemporary society. Intelligent applications such as new materials discovery, materials selection, life prediction, and failure analysis heavily depend on diverse materials information and knowledge. However, most of the existing materials information scatters in different heterogeneous sources without proper interconnections. Therefore, the integration of materials information from heterogeneous sources and transforming them into materials knowledge are of great significance. For this reason, some materials ontologies have emerged, although they may have different motivations and application scenarios. In this paper, we survey the representation of materials knowledge in recent decade especially from an ontological perspective. For better investigation, the possible roles that materials ontology may play are defined in a hierarchical structure, and comparison criteria for the survey are given, which primarily focuses on ontological aspects and materials application aspects, respectively. Then, we review nine selected materials ontologies, and analyze the main features of them. Afterwards, the surveyed materials ontologies are further discussed and compared according to the comparison criteria and roles definition presented by this paper. Finally, the future challenges of materials ontology development and application are discussed.

[1]  Jens Lehmann,et al.  DBpedia: A Nucleus for a Web of Open Data , 2007, ISWC/ASWC.

[2]  Tim Berners-Lee,et al.  Linked Data - The Story So Far , 2009, Int. J. Semantic Web Inf. Syst..

[3]  Giulio Petrucci,et al.  Information Extraction for Learning Expressive Ontologies , 2015, ESWC.

[4]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[5]  Martin Hepp,et al.  GoodRelations: An Ontology for Describing Products and Services Offers on the Web , 2008, EKAW.

[6]  Uğur Güdükbay,et al.  MaterialVis: material visualization tool using direct volume and surface rendering techniques. , 2014, Journal of molecular graphics & modelling.

[7]  Xiaoming Zhang,et al.  Semantic Data Integration in Materials Science Based on Semantic Model , 2007, Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007).

[8]  Miloslav Konopík,et al.  SWSNL: Semantic Web Search Using Natural Language , 2013, Expert Syst. Appl..

[9]  Emmanuel Pietriga,et al.  Visualizing Populated Ontologies with OntoTrix , 2010, ISWC Posters&Demos.

[10]  Rafael Valencia-García,et al.  Ontology learning from biomedical natural language documents using UMLS , 2011, Expert Syst. Appl..

[11]  Ju Li,et al.  AtomEye: an efficient atomistic configuration viewer , 2003 .

[12]  Phillip B. Messersmith,et al.  Bioinspired antifouling polymers , 2005 .

[13]  Paul N. Schofield,et al.  The Units Ontology: a tool for integrating units of measurement in science , 2012, Database J. Biol. Databases Curation.

[14]  Robert Arp,et al.  Function, Role and Disposition in Basic Formal Ontology , 2008 .

[15]  Isabel F. Cruz,et al.  The role of ontologies in data integration , 2005 .

[16]  Thomas Ertl,et al.  VOWL 2: User-Oriented Visualization of Ontologies , 2014, EKAW.

[17]  Jack C. Wileden,et al.  A semantic knowledge management system for laminated composites , 2014, Adv. Eng. Informatics.

[18]  Joseph Glick,et al.  Ontologies and Databases – Knowledge Engineering for Materials Informatics , 2013 .

[19]  Francky Trichet,et al.  Axiom-based ontology matching , 2005, K-CAP '05.

[20]  Hans-Helmut Over,et al.  Approaches in Using MatML As a Common Language for Materials Data Exchange , 2008, Data Sci. J..

[21]  Barry Smith,et al.  The environment ontology: contextualising biological and biomedical entities , 2013, Journal of Biomedical Semantics.

[22]  Michele Dassisti,et al.  ONTO-PDM: Product-driven ONTOlogy for Product Data Management interoperability within manufacturing process environment , 2012, Adv. Eng. Informatics.

[23]  L. Stein,et al.  OWL Web Ontology Language - Reference , 2004 .

[24]  Gary D. Bader,et al.  Cytoscape.js: a graph theory library for visualisation and analysis , 2015, Bioinform..

[25]  Michael Kifer,et al.  RIF Overview (Second Edition) , 2013 .

[26]  Gunther H. Weber,et al.  Augmented Topological Descriptors of Pore Networks for Material Science , 2012, IEEE Transactions on Visualization and Computer Graphics.

[27]  Antonio De Nicola,et al.  A software engineering approach to ontology building , 2009, Inf. Syst..

[28]  Stefano Spaccapietra,et al.  Modular Ontologies: Concepts, Theories and Techniques for Knowledge Modularization , 2009, Modular Ontologies.

[29]  David Maier,et al.  The Theory of Relational Databases , 1983 .

[30]  C. Steinbeck,et al.  The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web , 2011, PloS one.

[31]  Jeremy G Frey,et al.  Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance , 2013, Wiley interdisciplinary reviews. Computational molecular science.

[32]  Zoran Budimac,et al.  An overview of ontologies and data resources in medical domains , 2014, Expert Syst. Appl..

[33]  Jens Lehmann,et al.  LinkedGeoData: Adding a Spatial Dimension to the Web of Data , 2009, SEMWEB.

[34]  Toshihiro Ashino,et al.  Materials Ontology: An Infrastructure for Exchanging Materials Information and Knowledge , 2010, Data Sci. J..

[35]  Huajun Chen,et al.  OWL reasoning over big biomedical data , 2013, 2013 IEEE International Conference on Big Data.

[36]  Fabien L. Gandon,et al.  RDF 1.1 XML Syntax , 2014 .

[37]  Krzysztof Janowicz,et al.  An Ontology Pattern for Oceanographic Cruises: Towards an Oceanographer's Dream of Integrated Knowledge Discovery , 2014 .

[38]  Amit P. Sheth,et al.  SemMat: Federated Semantic Services Platform for Open materials Science and Engineering , 2017 .

[39]  Dimitri Gagliardi,et al.  A Guide to the Development and Use of Standards-Compliant Data Formats for Engineering Materials Test Data , 2010 .

[40]  Lorena Otero-Cerdeira,et al.  Ontology matching: A literature review , 2015, Expert Syst. Appl..

[41]  Freddy Lécué,et al.  Distributed and Scalable OWL EL Reasoning , 2015, ESWC.

[42]  Xiaoming Zhang,et al.  Semantic Query on Materials Data Based on Mapping MatML to an OWL Ontology , 2009, Data Sci. J..

[43]  Martin Hepp,et al.  BauDataWeb: the Austrian building and construction materials market as linked data , 2013, I-SEMANTICS '13.

[44]  H. Lan,et al.  SWRL : A semantic Web rule language combining OWL and ruleML , 2004 .

[45]  Hafedh Mili,et al.  IBM WebSphere ILOG JRules , 2011 .

[46]  Thomas R. Gruber,et al.  A translation approach to portable ontology specifications , 1993, Knowl. Acquis..

[47]  Sanjay Ghemawat,et al.  MapReduce: simplified data processing on large clusters , 2008, CACM.

[48]  Rafael Valencia-García,et al.  BioOntoVerb: A top level ontology based framework to populate biomedical ontologies from texts , 2012, Knowl. Based Syst..

[49]  Sanjay Ghemawat,et al.  MapReduce: Simplified Data Processing on Large Clusters , 2004, OSDI.

[50]  Hamish Cunningham,et al.  FREyA: An Interactive Way of Querying Linked Data Using Natural Language , 2011, ESWC Workshops.

[51]  Jens Lehmann,et al.  LinkedGeoData: A core for a web of spatial open data , 2012, Semantic Web.

[52]  Juana María Ruiz-Martínez,et al.  ONTOLOGY POPULATION : AN APPLICATION FOR THE E-TOURISM DOMAIN , 2011 .

[53]  Flavius Frasincar,et al.  Ontology population from web product information , 2014, WWW '14 Companion.

[54]  Steffen Staab,et al.  On-To-Knowledge Methodology (OTKM) , 2004, Handbook on Ontologies.

[55]  Johanna Völker,et al.  Acquisition of OWL DL Axioms from Lexical Resources , 2007, ESWC.

[56]  Robert Stevens,et al.  Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology , 2008, BMC Bioinformatics.

[57]  Olivier Bodenreider,et al.  Bio-ontologies: current trends and future directions , 2006, Briefings Bioinform..

[58]  Michel Dumontier,et al.  Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration , 2011, J. Cheminformatics.

[59]  O Bodenreider,et al.  Biomedical ontologies in action: role in knowledge management, data integration and decision support. , 2008, Yearbook of medical informatics.

[60]  Ana Carolina Salgado,et al.  Improving User Interaction on Ontology-based Peer Data Management Systems , 2014 .

[61]  Carole A. Goble,et al.  Ontology-based Knowledge Representation for Bioinformatics , 2000, Briefings Bioinform..

[62]  Jens Lehmann,et al.  DBpedia - A crystallization point for the Web of Data , 2009, J. Web Semant..

[63]  Diego Calvanese,et al.  The Description Logic Handbook: Theory, Implementation, and Applications , 2003, Description Logic Handbook.

[64]  Aldo Gangemi,et al.  Ontology Design Patterns , 2005 .

[65]  Gerhard Weikum,et al.  WWW 2007 / Track: Semantic Web Session: Ontologies ABSTRACT YAGO: A Core of Semantic Knowledge , 2022 .

[66]  Paolo Bouquet,et al.  Asking and answering semantic queries , 2004 .

[67]  A Kokalj,et al.  XCrySDen--a new program for displaying crystalline structures and electron densities. , 1999, Journal of molecular graphics & modelling.

[68]  E. F. Codd,et al.  The Relational Model for Database Management, Version 2 , 1990 .

[69]  Mark A. Musen,et al.  Applications of Ontology Design Patterns in Biomedical Ontologies , 2012, AMIA.

[70]  Milton Borsato,et al.  Bridging the gap between product lifecycle management and sustainability in manufacturing through ontology building , 2014, Comput. Ind..

[71]  Toshihiro Ashino,et al.  Seminar Cum Meeting Report: Codata Task Group for Exchangeable Material Data Representation to Support Research and Education , 2008, Data Sci. J..

[72]  P. E. van der Vet,et al.  Ontologies for very large knowledge bases in materials science: a case study , 1995 .

[73]  Andrea Westerinen,et al.  Semantic Web and Big Data meets Applied Ontology - The Ontology Summit 2014 , 2014, Appl. Ontology.

[74]  Daniel L. Rubin,et al.  Biomedical ontologies: a functional perspective , 2007, Briefings Bioinform..

[75]  Gang Feng,et al.  Disease Ontology: a backbone for disease semantic integration , 2011, Nucleic Acids Res..

[76]  Pascal Hitzler,et al.  Distributed OWL EL Reasoning: The Story So Far , 2014, SSWS@ISWC.

[77]  Miguel Ángel Rodríguez-García,et al.  ONLI: An ontology-based system for querying DBpedia using natural language paradigm , 2015, Expert Syst. Appl..

[78]  Krzysztof Janowicz,et al.  The Stimulus-Sensor-Observation Ontology Design Pattern and its Integration into the Semantic Sensor Network Ontology , 2010, SSN.

[79]  Ian Horrocks,et al.  Experiencing OptiqueVQS: a multi-paradigm and ontology-based visual query system for end users , 2015, Universal Access in the Information Society.

[80]  Jörg Leukel,et al.  Supply chain management ontology from an ontology engineering perspective , 2014, Comput. Ind..

[81]  Kalina Bontcheva,et al.  Improving habitability of natural language interfaces for querying ontologies with feedback and clarification dialogues , 2013, J. Web Semant..

[82]  H. Sofia Pinto,et al.  Ontologies: How can They be Built? , 2004, Knowledge and Information Systems.

[83]  Diego Calvanese,et al.  The description logic handbook: theory , 2003 .

[84]  Cesare Romagnoli,et al.  Open Biomedical Ontologies applied to prostate cancer , 2009, Appl. Ontology.

[85]  Michel Dumontier,et al.  Semantic Web integration of Cheminformatics resources with the SADI framework , 2011, J. Cheminformatics.

[86]  Michael J. Witbrock,et al.  An Introduction to the Syntax and Content of Cyc , 2006, AAAI Spring Symposium: Formalizing and Compiling Background Knowledge and Its Applications to Knowledge Representation and Question Answering.

[87]  Gerhard Weikum,et al.  Knowledge harvesting in the big-data era , 2013, SIGMOD '13.

[88]  Yu Lin,et al.  Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns , 2015, J. Biomed. Semant..

[89]  Oliver Kutz,et al.  Modularity in ontologies , 2012, Appl. Ontology.

[90]  H. Herre General Formal Ontology (GFO): A Foundational Ontology for Conceptual Modelling , 2010 .

[91]  Akrivi Katifori,et al.  Ontology visualization methods—a survey , 2007, CSUR.

[92]  Marie-Francine Moens,et al.  Global machine learning for spatial ontology population , 2015, J. Web Semant..

[93]  Adam Pease,et al.  Towards a standard upper ontology , 2001, FOIS.

[94]  Changquan Calvin Sun Materials science tetrahedron--a useful tool for pharmaceutical research and development. , 2009, Journal of pharmaceutical sciences.

[95]  William R. Hogan,et al.  Natural Language Processing methods and systems for biomedical ontology learning , 2011, J. Biomed. Informatics.

[96]  Jane Hunter,et al.  MatSeek: An Ontology-Based Federated Search Interface for Materials Scientists , 2009, IEEE Intelligent Systems.

[97]  Peter Haase,et al.  Learning Expressive Ontologies , 2008, Ontology Learning and Population.

[98]  N. F. Noy,et al.  Ontology Development 101: A Guide to Creating Your First Ontology , 2001 .

[99]  Hajo Rijgersberg,et al.  Ontology of units of measure and related concepts , 2013, Semantic Web.

[100]  Amit P. Sheth,et al.  The SSN ontology of the W3C semantic sensor network incubator group , 2012, J. Web Semant..

[101]  J. Ågren,et al.  CALPHAD, first and second generation – Birth of the materials genome , 2014 .

[102]  Jos de Bruijn,et al.  GenTax: A Generic Methodology for Deriving OWL and RDF-S Ontologies from Hierarchical Classifications, Thesauri, and Inconsistent Taxonomies , 2007, ESWC.

[103]  Frederico T. Fonseca,et al.  Using Ontologies for Integrated Geographic Information Systems , 2002, Trans. GIS.

[104]  Krishna Rajan,et al.  Materials informatics: Facilitating the integration of data-driven materials research with education , 2008 .

[105]  Nicolaas J. I. Mars,et al.  Structured system of concepts for storing, retrieving, and manipulating chemical information , 1993, J. Chem. Inf. Comput. Sci..

[106]  Ferdinando Villa,et al.  GrOWL: A tool for visualization and editing of OWL ontologies , 2007, J. Web Semant..

[107]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[108]  Jérôme Euzenat,et al.  Ontology Matching: State of the Art and Future Challenges , 2013, IEEE Transactions on Knowledge and Data Engineering.

[109]  J. Euzenat,et al.  Ontology Matching , 2007, Springer Berlin Heidelberg.

[110]  Vojtech Svátek,et al.  Roadmapping and Navigating in the Ontology Visualization Landscape , 2014, EKAW.

[111]  Asunción Gómez-Pérez,et al.  METHONTOLOGY: From Ontological Art Towards Ontological Engineering , 1997, AAAI 1997.

[112]  Manoj Bhat,et al.  PREMΛP: Knowledge Driven Design of Materials and Engineering Process , 2013 .

[113]  Robert Meersman,et al.  Ontology Engineering - The DOGMA Approach , 2008, Advances in Web Semantics I.

[114]  Alejandra Cechich,et al.  Ontology-driven geographic information integration: A survey of current approaches , 2009, Comput. Geosci..

[115]  Huajun Chen,et al.  The Semantic Web , 2011, Lecture Notes in Computer Science.

[116]  Jens Lehmann,et al.  Sorry, i don't speak SPARQL: translating SPARQL queries into natural language , 2013, WWW.

[117]  Nicola Guarino,et al.  Sweetening Ontologies with DOLCE , 2002, EKAW.

[118]  Krishna Rajan,et al.  Visualization in Materials Research: Rendering Strategies of Large Data Sets , 2013 .

[119]  Rosario Girardi,et al.  A domain-independent process for automatic ontology population from text , 2014, Sci. Comput. Program..

[120]  Aparna S. Varde,et al.  MatML: XML for information exchange with materials property data , 2006, DMSSP '06.

[121]  RamakrishnanSivakumar,et al.  A study on development of cognitive support features in recent ontology visualization tools , 2014 .

[122]  Christian de Sainte Marie,et al.  The ONTORULE Project : Where Ontology Meets Business Rules , 2011, RR.

[123]  Krzysztof Janowicz,et al.  A Geo-ontology Design Pattern for Semantic Trajectories , 2013, COSIT.

[124]  Huajun Chen,et al.  Semantic Web meets Integrative Biology: a survey , 2013, Briefings Bioinform..

[125]  Nicolaas J. I. Mars,et al.  Bottom-Up Construction of Ontologies , 1998, IEEE Trans. Knowl. Data Eng..

[126]  Dieter Fensel,et al.  Knowledge Engineering: Principles and Methods , 1998, Data Knowl. Eng..

[127]  David M. Mark,et al.  An Ontology Design Pattern for Surface Water Features , 2014, GIScience.

[128]  Ian Horrocks,et al.  OWL Web Ontology Language Reference-W3C Recommen-dation , 2004 .

[129]  Barry Smith,et al.  SNAP and SPAN: Towards Dynamic Spatial Ontology , 2004, Spatial Cogn. Comput..

[130]  Steffen Staab,et al.  DILIGENT: Towards a fine-grained methodology for Distributed, Loosely-controlled and evolving Engineering of oNTologies , 2004, ECAI.

[131]  Jeffrey Heer,et al.  prefuse: a toolkit for interactive information visualization , 2005, CHI.

[132]  Franz Baader,et al.  Formalizing biomedical concepts from textual definitions , 2015, J. Biomed. Semant..

[133]  P. E. van der Vet,et al.  The Plinius ontology of ceramic materials , 1994 .