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XML-based approaches for the integration of heterogeneous bio-molecular data

Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini, David Manset
2009 BMC Bioinformatics  
Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML.  ...  XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources.  ...  networks v.1.1/2006 Uses DTD.  ... 
doi:10.1186/1471-2105-10-s12-s7 pmid:19828083 pmcid:PMC2762072 fatcat:n4tvxjx3ifadjbo4x7jbpx5zfa

XML-Based Approaches for the Integration of Heterogeneous Bio-Molecular Data [chapter]

Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini, David Manset
2011 Recent Advances in Biochemistry  
Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML.  ...  Conclusion: XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources.  ...  networks v.1.1/2006 Uses DTD.  ... 
doi:10.1201/b13131-13 fatcat:ytu7u4pcbzgbflpblij6x3wwky

Integrating and Warehousing Liver Gene Expression Data and Related Biomedical Resources in GEDAW [chapter]

E. Guérin, G. Marquet, A. Burgun, O. Loréal, L. Berti-Equille, U. Leser, F. Moussouni
2005 Lecture Notes in Computer Science  
Data sources include: i) XML records of GENBANK to annotate gene sequence features, integrated using a schema mapping approach, ii) an inhouse relational database that stores detailed experimental data  ...  that provides for each gene its nomenclature, its functional annotation according to Gene Ontology, and its medical annotation according to the UMLS.  ...  BioMeKE-xml document to annotate the ceruloplasmin Gene Fig. 4 . 4 GEDAW UML Conceptual schema Fig. 5 . 5 Example of mapping rules between GENBANK DTD and GEDAW schema Three categories of mapping rules  ... 
doi:10.1007/11530084_14 fatcat:tnruhbrnxnbmpj66c64lcesrwy

Encoding biomedical resources in TEI

Tomaž Erjavec, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun-ichi Tsujii
2003 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine -  
This paper describes a standardised XML tagset (DTD) for annotated biomedical corpora and other resources, which is based on the Text Encoding Initiative Guidelines P4, a general and parameterisable standard  ...  It is well known that standardising the annotation of language resources significantly raises their potential, as it enables re-use and spurs the development of common technologies.  ...  In Figure 1 we define the XML DTD that can be used for encoding biomedical resources, and that we used for GENIA V3.01.  ... 
doi:10.3115/1118958.1118971 dblp:conf/bionlp/ErjavecKOTT03 fatcat:ov3jct3ixvf3tkcl7ptkpumqke

PROMIS: An XML-based metadata framework for proteomics

W. John MacMullen
2005 Proceedings of the American Society for Information Science and Technology  
DTD for use in sharing data sets and their related metadata.  ...  They also use a wide variety of physical instruments and computational methods to perform these analyses.  ...  RDF/XML DTD An RDF/XML document type definition (DTD) is under development for PROMIS.  ... 
doi:10.1002/meet.14504001108 fatcat:3cxpsognizhbzgs4vnaoqa6biy

XML, bioinformatics and data integration

F. Achard, G. Vaysseix, E. Barillot
2001 Bioinformatics  
Motivation: The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably  ...  Additionally, XML and domain specific DTDs are starting to be used to facilitate the transfer and the publication of biological information.  ...  for the description of the molecular functions, biological processes and cellular locations of gene products (Gene Ontology Consortium, 2000) .  ... 
doi:10.1093/bioinformatics/17.2.115 pmid:11238067 fatcat:b66b722fy5b4rl3tvvwsnojiui

Integration of Data Warehouse and Unstructured Business Documents

Ahmad Abdullah Alqarni, Eric Pardede
2012 2012 15th International Conference on Network-Based Information Systems  
schemas and map them to in SQL and XML, this book reveals the true power of semantic data modeling.  ...  XML schema or used in The Library of Congress Subject Headings, in contrast, provide the notion.  ...  An ontology of the DDI 3 data model will be designed by following the ontology to design ontologies on the basis of XML Schemas.  ... 
doi:10.1109/nbis.2012.59 dblp:conf/nbis/AlqarniP12 fatcat:vhvrg3tzujfyrdzgzgc42fuomy

AUTOMATING DATA ACQUISITION INTO ONTOLOGIES FROM PHARMACOGENETICS RELATIONAL DATA SOURCES USING DECLARATIVE OBJECT DEFINITIONS AND XML

DANIEL L. RUBIN, MICHEAL HEWETT, DIANE E. OLIVER, TERI E. KLEIN, RUSS B. ALTMAN
2001 Biocomputing 2002  
Data is imported from the relational source into the ontology using XML, and data integrity is checked by validating the XML submission with an XML schema.  ...  This method uses a declarative interface between the ontology and the data source, and this interface is modeled in the ontology and implemented using XML schema.  ...  a document type definition (DTD) or XML schema.  ... 
doi:10.1142/9789812799623_0009 fatcat:xix2bn4cnfhztluazjzwizjad4

Data integration and visualization system for enabling conceptual biology

P. V. Gopalacharyulu, E. Lindfors, C. Bounsaythip, T. Kivioja, L. Yetukuri, J. Hollmen, M. Oresic
2005 Bioinformatics  
The biological entities and the distances between them are mapped for the purpose of visualization into the lower dimensional space using the Sammon's mapping.  ...  The system implementation is based on a multi-tier architecture using a native XML database and a software tool for querying and visualizing complex biological networks.  ...  Go to step (4). (3) If the document structures have been defined using DTD then convert the DTD to W3C Schema.  ... 
doi:10.1093/bioinformatics/bti1015 pmid:15961455 fatcat:ozhwui4ynvanvll3fc2bsna23e

GeneClinics: A Hybrid Text/Data Electronic Publishing Model Using XML Applied to Clinical Genetic Testing

P. Tarczy-Hornoch, P. Shannon, P. Baskin, M. Espeseth, R. A. Pagon
2000 JAMIA Journal of the American Medical Informatics Association  
The joint profile/ biological schema DTD is used.  ...  The code that renders the HTML uses the data model specified by the XML DTD to determine order and hierarchy for display of data elements.  ... 
doi:10.1136/jamia.2000.0070267 pmid:10833163 pmcid:PMC61429 fatcat:q7asedxuzvhipmqeiu3ellttbm

Bio-Ontology and text: bridging the modeling gap

C. Friedman, T. Borlawsky, L. Shagina, H. R. Xing, Y. A. Lussier
2006 Bioinformatics  
Moreover, PGschema can be realized automatically in an XML format by using natural language techniques to process the text.  ...  Motivation-Natural language processing (NLP) techniques are increasingly being used in biology to automate the capture of new biological discoveries in text, which are being reported at a rapid rate.  ...  An example of a few specifications of the XML representation is shown in Figure 1 in the form of a document type definition (DTD).  ... 
doi:10.1093/bioinformatics/btl405 pmid:16870928 pmcid:PMC2879055 fatcat:ya5hv7j275ebdoaxfrnomqtntq

Using semantic Web technology to automate data integration in grid and Web service architectures

M. Szomszor, T.R. Payne, L. Moreau
2005 CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.  
To achieve this, we have developed a mapping language which can be used to annotate XML data structures with OWL concepts and properties, a Mapping Language Engine to implement this language, and a Dynamic  ...  While the Grid and Web Services have helped us support heterogeneous resource access through the use of service oriented architectures, they have not addressed the issue of heterogeneous data representation  ...  Mapping Language Our mapping language can be used to specify two types of mapping: ontology concept instances to XML and XML to ontology concept instances.  ... 
doi:10.1109/ccgrid.2005.1558553 dblp:conf/ccgrid/SzomszorPM05 fatcat:z3t7u5ncbzd4tfsjnli6nj4kq4

Changes in Scholarly Communication and the Potential Impact on Biocuration

Philip Bourne
2009 Nature Precedings  
term-mapping databases • Incorporate a more sophisticated term recognition approach into the add-in Challenges • Author use -Familiarity with ontologies, terms -Agreement between co-authors  ...  • End-use of semantically enriched manuscript -Combine with NLM XML standard • Article Authoring Add-in Author Use With such semantic tagging of the literature consider how it might be integrated  ... 
doi:10.1038/npre.2009.3229 fatcat:msh6kzk55fc6phgvntlbue4xxu

Changes in Scholarly Communication and the Potential Impact on Biocuration

Philip Bourne
2009 Nature Precedings  
term-mapping databases • Incorporate a more sophisticated term recognition approach into the add-in Challenges • Author use -Familiarity with ontologies, terms -Agreement between co-authors  ...  • End-use of semantically enriched manuscript -Combine with NLM XML standard • Article Authoring Add-in Author Use With such semantic tagging of the literature consider how it might be integrated  ... 
doi:10.1038/npre.2009.3229.1 fatcat:dlgevrecljcbxpp6s46iylrpla

An extensible application for assembling annotation for genomic data

J. Zhang, V. Carey, R. Gentleman
2003 Bioinformatics  
The unified mapping was then used as the base to process the LocusLink and Gene Ontology data and generate the XML files (http://www.bioconductor.org/ datafiles/dtds/annotate.dtd) for annotation.  ...  Nonstandard Data Structures The Gene Ontology Consortium provides a standardized nomenclature for subcategories of the basic ontological categories molecular function, biological process and cellular component  ... 
doi:10.1093/bioinformatics/19.1.155 pmid:12499308 fatcat:77lyxzz5gncwxg2kqvow2cdo7m
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