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A Framework for Generating Query Language Code from OCL Invariants

Florian Heidenreich, Christian Wende, Birgit Demuth
2007 Electronic Communications of the EASST  
This framework allows for mapping UML models to arbitrary data schemas and for mapping OCL invariants to sentences in corresponding declarative query languages, enforcing semantical data integrity on implementation  ...  However, to preserve also the semantical integrity rules we propose a Query Code Generation Framework that enables Model-Driven Integrity Engineering.  ...  We have developed a pattern catalogue for mapping OCL invariants to equivalent expressions in XQuery (similar to the cataloque for SQL Fig. 4 .  ... 
doi:10.14279/tuj.eceasst.9.108 dblp:journals/eceasst/HeidenreichWD08 fatcat:p3dxa5kwkncdxk3lpc2y7pt6oq

A Framework for Integrating XML Transformations [chapter]

Ce Dong, James Bailey
2006 Lecture Notes in Computer Science  
In this paper, we propose a framework for semi-automatic integration of XSLT programs.  ...  is required to operate over a newly integrated XML database.  ...  Thus, when a template selection pattern is a non-full-absolute XPath expression, we might not sure which mapping rules should be chosen for translating the corresponding template from the initial DTD based  ... 
doi:10.1007/11901181_15 fatcat:h72svxapivcazatg2qcasuhsoi

Saliency-based framework for facial expression recognition

Rizwan Ahmed Khan, Alexandre Meyer, Hubert Konik, Saida Bouakaz
2018 Frontiers of Computer Science  
Section 4 presents the novel framework for automatic facial expression recognition. Section 5 presents results of proposed framework on databases containing adult and children faces.  ...  observer for a particular expression.  ... 
doi:10.1007/s11704-017-6114-9 fatcat:a6ztse6vhnegtnxhz5cpwoy5na

Semantic Based Access over XML Data [chapter]

Nikos Bikakis, Nektarios Gioldasis, Chrisa Tsinaraki, Stavros Christodoulakis
2009 Lecture Notes in Computer Science  
In this paper we describe the SPARQL2XQuery framework, which translates the SPARQL queries to semantically equivalent XQuery queries for accessing XML databases from the Semantic Web environment.  ...  Thus, SPARQL queries may have to be submitted and evaluated against existing XML or relational databases, and the results transferred back to be assembled for further processing.  ...  As a consequence, based on schema level mappings for each mapped ontology class or property, we store a set of XPath expressions ("XPath set" for the rest of this paper) that address all the corres-ponding  ... 
doi:10.1007/978-3-642-04754-1_27 fatcat:wwu2ahis4jhzjiqcl32ic4avju

eMouseAtlas informatics: embryo atlas and gene expression database

Chris Armit, Lorna Richardson, Bill Hill, Yiya Yang, Richard A. Baldock
2015 Mammalian Genome  
This provided a framework (Davidson and Baldock 2001) enabling a database of the spatial expression patterns, not constrained by the current understanding of anatomy, and being able to capture any pattern  ...  anatomical components and for archiving in situ gene expression data in the EMAGE database.  ...  Acknowledgments We would like to thank all members of the mouse atlas group at the MRC Human genetics unit for their contributions to the resource, and we acknowledge the financial support of the Medical  ... 
doi:10.1007/s00335-015-9596-5 pmid:26296321 pmcid:PMC4602050 fatcat:bpj752ol7neyfcmifpaomzlhiq

Querying XML Data with SPARQL [chapter]

Nikos Bikakis, Nektarios Gioldasis, Chrisa Tsinaraki, Stavros Christodoulakis
2009 Lecture Notes in Computer Science  
In this paper we present a framework that bridges the heterogeneity gap and creates an interoperable environment where SPARQL queries are used to access XML databases.  ...  We present the algorithms and the implementation of SPARQL2XQuery framework, which is used for answering SPARQL queries over XML databases.  ...  Thus, based on schema level mappings for each mapped ontology class or property, we store a set of XPath expressions ("XPath set" for the rest of this paper) that address all the corresponding instances  ... 
doi:10.1007/978-3-642-03573-9_32 fatcat:6dxgtqhtbvba5jyscai7echpaq

eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis

Chris Armit, Lorna Richardson, Shanmugasundaram Venkataraman, Liz Graham, Nicholas Burton, Bill Hill, Yiya Yang, Richard A Baldock
2017 Developmental Biology  
We show how mapping of gene expression data onto spatial models delivers a framework for capturing gene expression that enhances our understanding of development, and we review the exploratory tools utilised  ...  by the EMAGE gene expression database as a means of defining co-expression of in situ hybridisation, immunohistochemistry, and lacZ-omic expression patterns.  ...  Acknowledgements We are grateful to our collaborators in the Wellcome-funded Deciphering the Mechanisms of Developmental Disorders (DMDD) programme for support and for provision of Fig. 5a .  ... 
doi:10.1016/j.ydbio.2017.01.023 pmid:28161522 pmcid:PMC5442644 fatcat:3intxwycbbevllxl2jomx76loq

More than a decade of developmental gene expression atlases: where are we now?

B. A. de Boer, J. M. Ruijter, F. P. J. M. Voorbraak, A. F. M. Moorman
2009 Nucleic Acids Research  
, both for relations as well as for anatomical terms.  ...  A review of these atlases shows that the ideal atlas should be based on a spatial framework, i.e. a series of 3D reference models, which is anatomically annotated using an ontology with sufficient resolution  ...  ACKNOWLEDGEMENTS The authors thank Arie Hasman and Maurice van den Hoff for their valuable suggestions after critically reading the manuscript and Alexandre Soufan for discussions about the 3D gene expression  ... 
doi:10.1093/nar/gkp819 pmid:19822576 pmcid:PMC2794177 fatcat:b42adqur7zd4bewbbxxzg6gjei

SPARQL-RW

Konstantinos Makris, Nikos Bikakis, Nektarios Gioldasis, Stavros Christodoulakis
2012 Proceedings of the 15th International Conference on Extending Database Technology - EDBT '12  
The SPARQL-RW provides a generic method for SPARQL query rewriting, with respect to a set of predefined mappings between ontology schemas.  ...  This paper presents SPARQL-RW (SPARQL-ReWriting), a framework which provides transparent query access over mapped RDF datasets.  ...  Implementation The SPARQL-RW Framework has been implemented using Java 2SE as a software platform, and the Jena framework for SPARQL query manipulation.  ... 
doi:10.1145/2247596.2247678 dblp:conf/edbt/MakrisBGC12 fatcat:ytqddqjuqzg5doc7bp4uvvgzma

More than a decade of developmental gene expression atlases: where are we now?

Bouke A. de Boer, Jan M. Ruijter, Frans P. J. M. Voorbraak, Antoon F. M. Moorman
2010 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors thank Arie Hasman and Maurice van den Hoff for their valuable suggestions after critically reading the manuscript and Alexandre Soufan for discussions about the 3D gene expression  ...  By staining for one of the reference genes, and a gene-of-interest with an unknown expression pattern the gene expression pattern can be mapped to the reference model.  ...  Basically, this framework is used by the Allen Brain Atlas (except for the detailed ontology). The approach involves the mapping of sets of in situ gene expression images to a spatial framework.  ... 
doi:10.1093/nar/gkq070 fatcat:4f3o24bb3jfyljytq6sskrcwem

Mapping RDF Graphs to Property Graphs [article]

Shota Matsumoto, Ryota Yamanaka, Hirokazu Chiba
2018 arXiv   pre-print
Here, we developed a framework based on the Graph to Graph Mapping Language (G2GML) for mapping RDF graphs to property graphs to make the most of accumulated RDF data.  ...  Using this framework, graph data described in the RDF model can be converted to the property graph model and can be loaded to several graph database engines for further analysis.  ...  Here, we developed a framework based on the Graph to Graph Mapping Language (G2GML) for mapping RDF graphs to property graphs.  ... 
arXiv:1812.01801v1 fatcat:us6enoso3nfg7d6jnev3jd4tdm

Developmental Biology and Databases

Chris Armit
2007 Organogenesis  
ontologies, FAte mAps And lineAge: A Common FrAmeworK For developmentAl biology Documenting the being, becoming, and lineage of various embryonic cells/tissues has become an invaluable framework for organising  ...  Such a framework would provide a platform for exploring genotype-phenotype relationships across phyla.  ... 
doi:10.4161/org.3.2.4942 pmid:19279703 pmcid:PMC2649618 fatcat:4bmi4yulg5hrfkmskecm577tla

The 'straight mouse': defining anatomical axes in 3D embryo models

Chris Armit, Bill Hill, S. Venkataraman, Kenneth McLeod, Albert Burger, Richard Baldock
2017 Database: The Journal of Biological Databases and Curation  
Abstract A primary objective of the eMouseAtlas Project is to enable 3D spatial mapping of whole embryo gene expression data to capture complex 3D patterns for indexing, visualization, cross-comparison  ...  For this we have developed a spatio-temporal framework based on 3D models of embryos at different stages of development coupled with an anatomical ontology.  ...  , University of Edinburgh) for providing the OPT Fgf gene expression patterns.  ... 
doi:10.1093/database/bax010 pmid:28365728 pmcid:PMC5467569 fatcat:lr6gakxpgfabpiyhmql5hkcmvm

The QALL-ME Framework: A specifiable-domain multilingual Question Answering architecture ⁎

Óscar Ferrández, Christian Spurk, Milen Kouylekov, Iustin Dornescu, Sergio Ferrández, Matteo Negri, Rubén Izquierdo, David Tomás, Constantin Orasan, Guenter Neumann, Bernardo Magnini, Jose Luis Vicedo
2011 Journal of Web Semantics  
Furthermore, we present a running example to clarify how the framework processes questions as well as a case study that shows a QA application built as an instantiation of the QALL-ME Framework for cinema  ...  This paper presents the QALL-ME Framework, a reusable architecture for building multi-and crosslingual Question Answering (QA) systems working on structured data modelled by an ontology.  ...  into a database of answers, and a collection of pattern mappings stored into a pattern repository containing the minimal question patterns and their corresponding database queries.  ... 
doi:10.1016/j.websem.2011.01.002 fatcat:fjn3vq5rhnbf7doj6nwdelhyea

The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain

Janet Kerwin, Yiya Yang, Paloma Merchan, Subrot Sarma, Jessica Thompson, Xunxian Wang, Juan Sandoval, Luis Puelles, Richard Baldock, Susan Lindsay
2010 Journal of Anatomy  
Human gene expression patterns for genes with characteristic expression in different vertebrates (e.g.  ...  Using MAPaint software, selected gene expression data, gathered using standard methods of in situ hybridisation and immunohistochemistry, are mapped to a representative 3D model for each chosen Carnegie  ...  Using the OPT models as a standard framework enables gene expression patterns to be compared within the same 3D space for each developmental stage in the atlas and database (CS12-CS23).  ... 
doi:10.1111/j.1469-7580.2010.01290.x pmid:20979583 pmcid:PMC2967454 fatcat:rn3odtjyl5a53i6z6trohxc66m
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