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Development of an Ontology for an Integrated Image Analysis Platform to enable Global Sharing of Microscopy Imaging Data [article]

Satoshi Kume, Hiroshi Masuya, Yosky Kataoka, Norio Kobayashi
2021 arXiv   pre-print
We translated the XML-based OME metadata into the base concept of RDF schema as a trial of developing microscopy ontology.  ...  To realise this, we applied Resource Description Framework (RDF) to an Open Microscopy Environment (OME) data model, which is the de facto standard to describe optical microscopy images and experimental  ...  The upper-level concepts and the relation graph of RDF-based data model was constructed from current version of OME and the schema is summarized in Fig. 1 .  ... 
arXiv:2110.10407v1 fatcat:j5v36egrhvdg7godnzqtodf7mq

Linking Search Results, Bibliographical Ontologies and Linked Open Data Resources [chapter]

Fabio Ricci, Javier Belmonte, Eliane Blumer, René Schneider
2013 Communications in Computer and Information Science  
This paper describes a lightweight approach to build an environment for scientific research that connects user-selected information resources with domain specific ontologies and the linked open data cloud  ...  Search results are converted into RDF triples to match with ontology subjects in order to derive relevant subjects and to find related documents in external repositories data that are stored in the Linked  ...  A significant enhancement of RODIN's result delivery coverage comes from an added RDF processing component, which accesses further related documents from LOD data sources based on shared subjects extracted  ... 
doi:10.1007/978-3-319-03437-9_7 fatcat:7nnfxs3wjnbqzbmdeca5fu3pa4

linkedISA: semantic representation of ISA-Tab experimental metadata

Alejandra González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
2014 BMC Bioinformatics  
We applied the conversion tool as part of Bio-GraphIIn, a web-based application supporting integration of the semantically-rich experimental descriptions.  ...  In addition, we defined queries over the linkedISA RDF representation and demonstrated its use over the linkedISA conversion of datasets from Nature' Scientific Data online publication.  ...  They also would like to thank Pavlos Georgiou for his contributions to Bio-GraphIIn and the linkedISA RESTful service development.  ... 
doi:10.1186/1471-2105-15-s14-s4 pmid:25472428 pmcid:PMC4255742 fatcat:3tpqrjmvp5hgpafasevv33rx2q

Construction of an Ortholog Database Using the Semantic Web Technology for Integrative Analysis of Genomic Data

Hirokazu Chiba, Hiroyo Nishide, Ikuo Uchiyama, Yoshihiro Yamanishi
2015 PLoS ONE  
In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub.  ...  On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available  ...  Computational resources were provided by the Data Integration and Analysis Facility, National Institute for Basic Biology.  ... 
doi:10.1371/journal.pone.0122802 pmid:25875762 pmcid:PMC4395280 fatcat:ztivbjcq7fftfo7l2ceh366phi

What the semantic web could do for the life sciences

Eric K. Neumann, Eric Miller, John Wilbanks
2004 Drug Discovery Today BIOSILICO  
The effective exchange of data and accompanying interpretation underpin new hypotheses and experimental designs, typically followed by a community-based process of debate and rebuttal.This community-driven  ...  of peer-reviewed knowledge in discovery research.  ...  Finally, there are many RDF-related resources freely available to the public, including information [3] ( TR/rdf-concepts/) and tools (e.g.  ... 
doi:10.1016/s1741-8364(04)02420-5 fatcat:grqq2bxxsjb37gmxjjlbi2vrqm

AlzPharm: integration of neurodegeneration data using RDF

Hugo YK Lam, Luis Marenco, Tim Clark, Yong Gao, June Kinoshita, Gordon Shepherd, Perry Miller, Elizabeth Wu, Gwendolyn T Wong, Nian Liu, Chiquito Crasto, Thomas Morse (+2 others)
2007 BMC Bioinformatics  
Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard  ...  Results: We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure.  ...  The full contents of the supplement are available online at 1471-2105/8?issue=S3.  ... 
doi:10.1186/1471-2105-8-s3-s4 pmid:17493287 pmcid:PMC1892101 fatcat:iot4qgjhnfe4tidgz43b23wkja

Semantic Web meets Integrative Biology: a survey

H. Chen, T. Yu, J. Y. Chen
2012 Briefings in Bioinformatics  
We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration  ...  We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB  ...  The work of the authors is funded by China National Science Foundation (NSFC61070156), and China national 863 program China Cloud Initiative.  ... 
doi:10.1093/bib/bbs014 pmid:22492191 fatcat:n5xm5kbc75ethlnfwfmgwdtnhq

Technologies and Best Practices for Building Bio-Ontologies [chapter]

Mikel Egãna Aranguren, Robert Stevens, Erick Antezana, Jesualdo Tomás Fernández-Breis, Martin Kuiper, Vladimir Mironov
2010 Knowledge-Based Bioinformatics  
RDF (resource description framework) RDF ( was designed to represent information about Web resources in the Semantic Web, thus to publish data in a basic machine processable form  ...  RDF is based on a simple model that enables the representation of diverse information with very low computational costs, provided that such information can be captured as a set of subject-predicate-object  ... 
doi:10.1002/9780470669716.ch3 fatcat:zdeay5hmh5ap3g7gesi4ac6xxu

Biological knowledge management: the emerging role of the Semantic Web technologies

E. Antezana, M. Kuiper, V. Mironov
2009 Briefings in Bioinformatics  
New knowledge is produced at a continuously increasing speed, and the list of papers, databases and other knowledge sources that a researcher in the life sciences needs to cope with is actually turning  ...  The adequate management of knowledge is therefore becoming fundamentally important for life scientists, especially if they work with approaches that thoroughly depend on knowledge integration, such as  ...  Currently, it provides some resources in RDF (such as GO), which can, in turn, be loaded in triple-based stores enabling querying.  ... 
doi:10.1093/bib/bbp024 pmid:19457869 fatcat:qewyihg44fhvrlletzo74xzj6y

OILing the way to machine understandable bioinformatics resources

R. Stevens, C. Goble, I. Horrocks, S. Bechhofer
2002 IEEE Transactions on Information Technology in Biomedicine  
Successful exchange and integration of information, however, depends on a shared language for communication (a terminology) and a shared understanding of what the data means (an ontology).  ...  The complex questions and analyses posed by biologists, as well as the diverse data resources they develop, require the fusion of evidence from different, independently developed and heterogeneous resources  ...  The interoperation of information requires a consistent shared understanding of the meaning of that information.  ... 
doi:10.1109/titb.2002.1006300 pmid:12075667 fatcat:2e6hblgahnfm3jwhenzgoctgeu

Biomedical semantics in the Semantic Web

Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano, M Marshall
2011 Journal of Biomedical Semantics  
The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive  ...  Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation?  ...  to this workshop and for their contributions to the advancement of one promising solution to the challenges of the future of biomedical research.  ... 
doi:10.1186/2041-1480-2-s1-s1 pmid:21388570 pmcid:PMC3105493 fatcat:iwbnqzgvqfcojdn4yubjoeskla


Therese Schwarzboeck, Philipp Aschenbrenner, Sarah Muehlbacher, Soenke Szidat, Stefan Spacek, Johann Fellner
2018 Detritus  
The study results suggest that the usage of analysis data together with information from literature is the best option to derive reliable input data (TOX Bio and TOX Fos ) for the aBM (mean deviation from  ...  Within this study, 6 different solid RDFs are investigated and the aBM is applied, whereby the suitability of literature values is compared to own analysis data for TOX Bio and TOX Fos .  ...  Further, the work was partly supported by a large-scale research initiative on anthropogenic resources (Christian Doppler Laboratory for Anthropogenic Resources).  ... 
doi:10.31025/2611-4135/2018.13649 fatcat:au6sqmssv5f6fooschnovfo46e

Mapping subjectivity: performing people-centered vocabulary alignment

Cristina Pattuelli
2011 NASKO  
This paper describes a mapping of linked data vocabularies in the area of person-related information.  ...  Although a work in progress, this investigation would provide support for semantic integration and for knowledge sharing and reuse in the area of personal information representation.  ...  Based on a fairly simple representation framework that includes Resource Description Framework (RDF) as its data model and HTTP Unique Resource Identifiers (URIs) to globally identify entities, linked  ... 
doi:10.7152/nasko.v3i1.12801 fatcat:7qzdwgemdnapvcyqhxynic4ggu

BioGateway: a semantic systems biology tool for the life sciences

Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper
2009 BMC Bioinformatics  
Access to the system and supplementary information (such as a listing of the data sources in RDF, and sample queries) can be found at  ...  We demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data.  ...  Results BioGateway data model RDF-ing the resources A suitable data representation is necessary to share and uniformly query the RDF integrated repository.  ... 
doi:10.1186/1471-2105-10-s10-s11 pmid:19796395 pmcid:PMC2755819 fatcat:r4mmbhi3vrenji3dh5kekdz2ge

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal (+54 others)
2013 Journal of Biomedical Semantics  
Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting  ...  We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization.  ...  Sharing predicates: to relate pieces of information from different data sets to each other, data sets should share as many predicates as possible.  ... 
doi:10.1186/2041-1480-4-6 pmid:23398680 pmcid:PMC3598643 fatcat:fm5xaotu3nbafibe3pm3js4d7u
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