A pattern-based approach to a cell tracking ontology

被引:4
|
作者
Burek, Patryk [1 ]
Scherf, Nico [2 ,4 ]
Herre, Heinrich [3 ]
机构
[1] Marii Curie Sklodowskiej Univ, Fac Math Phys & Comp Sci, Inst Comp Sci, Pl Marii Curie Sklodowskiej 5, PL-20031 Lublin, Poland
[2] Max Planck Inst Human Cognit & Brain Sci, Stephanstr 1a, D-04103 Leipzig, Germany
[3] Univ Leipzig, Inst Med Informat Stat & Epidemiol, Haertelstr 16-18, D-04107 Leipzig, Germany
[4] Tech Univ Dresden, Inst Med Informat & Biometry, Carl Gustav Carus Fac Med, Fetscherstr 74, D-01307 Dresden, Germany
关键词
Semantic-Based Systems; Knowledge Representation and Management; Semantic annotation of images and videos; Ontologies; VISUALIZATION;
D O I
10.1016/j.procs.2019.09.237
中图分类号
TP18 [人工智能理论];
学科分类号
081104 ; 0812 ; 0835 ; 1405 ;
摘要
Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations. (C) 2019 The Authors. Published by Elsevier B.V.
引用
收藏
页码:784 / 793
页数:10
相关论文
共 50 条
  • [1] OntoCase - A pattern-based ontology construction approach
    Blomqvist, Eva
    [J]. ON THE MOVE TO MEANINGFUL INTERNET SYSTEMS 2007: COOPLS, DOA, ODBASE, GADA, AND IS, PT 1, PROCEEDINGS, 2007, 4803 : 971 - 988
  • [2] PATTERN-BASED ONTOLOGY TRANSFORMATION SERVICE
    Svab-Zamazal, Ondrej
    Svatek, Vojtech
    Scharffe, Francois
    [J]. KEOD 2009: PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON KNOWLEDGE ENGINEERING AND ONTOLOGY DEVELOPMENT, 2009, : 42 - +
  • [3] Experiments on Pattern-based Ontology Design
    Blomqvist, Eva
    Gangemi, Aldo
    Presutti, Valentina
    [J]. K-CAP'09: PROCEEDINGS OF THE FIFTH INTERNATIONAL CONFERENCE ON KNOWLEDGE CAPTURE, 2009, : 41 - 48
  • [4] A Pattern-Based Ontology Engineering Platform
    Janke, Thomas
    [J]. PROCEEDINGS OF THE 12TH EUROPEAN CONFERENCE ON KNOWLEDGE MANAGEMENT, VOLS 1 AND 2, 2011, : 461 - 469
  • [5] A Pattern-Based Approach to Semantic Relation Extraction Using a Seed Ontology
    Al-Yahya, Maha
    Aldhubayi, Luluh
    Al-Malak, Sawsan
    [J]. 2014 IEEE INTERNATIONAL CONFERENCE ON SEMANTIC COMPUTING (ICSC), 2014, : 96 - 99
  • [6] Pattern-based semantic tagging for ontology population
    Inaba, Masumi
    Iida, Takayuki
    Yamasaki, Tomohiro
    Fume, Kosei
    Mizoguchi, Yumiko
    Nagano, Shinichi
    Kawamura, Takahiro
    [J]. SERVICE-ORIENTED COMPUTING: AGENTS, SEMANTICS, AND ENGINEERING, PROCEEDINGS, 2008, 5006 : 45 - 55
  • [7] PATOMAT - VERSATILE FRAMEWORK FOR PATTERN-BASED ONTOLOGY TRANSFORMATION
    Zamazal, Ondrej
    Svatek, Vojtech
    [J]. COMPUTING AND INFORMATICS, 2015, 34 (02) : 305 - 336
  • [8] A Pattern-Based Framework of Change Operators for Ontology Evolution
    Javed, Muhammad
    Abgaz, Yalemisew M.
    Pahl, Claus
    [J]. ON THE MOVE TO MEANINGFUL INTERNET SYSTEMS: OTM 2009 WORKSHOPS, 2009, 5872 : 544 - 553
  • [9] Pattern-Based Ontology Modeling and Reasoning for Emergency System
    Tan, Yue
    Liu, Wei
    Yang, Zhenyu
    Du, Xiaoni
    Liu, Zongtian
    [J]. IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, 2018, E101D (09) : 2323 - 2333
  • [10] TOWARDS PATTERN-BASED REASONING FOR FRIENDLY ONTOLOGY DEBUGGING
    Jarrar, Mustafa
    Heymans, Stijn
    [J]. INTERNATIONAL JOURNAL ON ARTIFICIAL INTELLIGENCE TOOLS, 2008, 17 (04) : 607 - 634