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EXECUTIVE SUMMARY

R. Gahbauer, T. Landberg, J. Chavaudra, J. Dobbs, N. Gupta, G. Hanks, J.-C. Horiot, K.-A. Johansson, T. Möller, S. Naudy, J. Purdy, I. Santenac (+2 others)
2004 Journal of the International Commission on Radiation Units and Measurements  
Project: ART -an ontology based tool for preparation of articles Executive Summary This report has two main goals:  To introduce a new formalism for the description of scientific papers CISP (the Core  ...  It makes use of an ontology of experiments EXPO proposed at the University of Wales, Aberystwyth as a core ontology, and DOLCE (a Descriptive Ontology for Linguistic and Cognitive Engineering) developed  ...  Our analysis of papers is based on an ontological representation of investigations. A scientific paper is one of many ways (the most typical) of representing investigations.  ... 
doi:10.1093/jicru/ndh017 pmid:24170787 fatcat:kv5mw5ywgvbqtapnjw2pana2ca

Moving from dataset metadata to semantics in ecological research: a case in translating EML to OWL

Elena Mena-Garcés, Elena García-Barriocanal, Miguel-Angel Sicilia, Salvador Sánchez-Alonso
2011 Procedia Computer Science  
, including the reuse of scientific ontologies to express the observed entities and their characteristics.  ...  The Ecological Metadata Language (EML) is an XML-based metadata specification developed for the description of datasets and their associated context in ecology.  ...  leading to these results has received funding from the European Commission under grant agreement nº 250525 corresponding to project VOA3R (Virtual Open Access Agriculture & Aquaculture Repository: Sharing Scientific  ... 
doi:10.1016/j.procs.2011.04.175 fatcat:vw2b3nvltndo7l4qfhhjwpykii

An ontology for scientific information in a Grid environment: the earth system Grid

L. Pouchard, L. Cinquini, B. Drach, D. Middleton, D. Bernholdt, K. Chanchio, I. Foster, V. Nefedova, D. Brown, P. Fox, J. Garcia, G. Strand (+5 others)
2003 CCGrid 2003. 3rd IEEE/ACM International Symposium on Cluster Computing and the Grid, 2003. Proceedings.  
We present ontology entities and a declarative model that provide the outline for an ontology of scientific information. Relationships between concepts are also given.  ...  This paper describes the increasing role of ontologies in the context of Grid Computing for obtaining, comparing and analyzing data.  ...  For instance, a user may build on the fly a collection of data files based on attributes defined in the ontology.  ... 
doi:10.1109/ccgrid.2003.1199424 dblp:conf/ccgrid/PouchardCDMBCFNBFGSWCKSS03 fatcat:ll7dk6uci5gorlsriin2iiwoxq

A review of ontologies for describing scholarly and scientific documents

Almudena Ruiz-Iniesta, Óscar Corcho
2014 Extended Semantic Web Conference  
Finally, we provide an example of how some of these ontologies can be used for the annotation of a scientific document.  ...  This rich variety of ontologies makes it difficult for those willing to annotate their documents to know which ones they should select for such activity.  ...  CISP metadata makes use of the ontology of experiments EXPO 16 [3] as a core ontology. CISP includes eight key classes that are presented in Table 3 .  ... 
dblp:conf/esws/Ruiz-IniestaC14 fatcat:dh46cyqeunexbhgvagzyc52foy

A Foundational Ontology to Support Scientific Experiments

Sérgio Manuel Serra da Cruz, Maria Luiza Machado Campos, Marta Mattoso
2012 Joint Seminar on Ontology Research in Brazil / International Workshop on Metamodels, Ontologies and Semantic Technologies  
In this paper, we present a well-founded provenance ontology named Open proVenance Ontology (OvO) which takes inspiration on three theories: the lifecycle of in silico scientific experiments, the Open  ...  OvO may act as a reference conceptual model that can be used by researchers to explore the semantics of provenance metadata.  ...  Related Work There are few research initiatives committed with ontology-based models and formalizations of the in silico scientific experiments.  ... 
dblp:conf/ontobras/CruzCM12 fatcat:c3prnqeynrhnzjcl5ibn2yby6a

Digital Libraries and Educational Resources: the AquaRing Semantic Approach

Giuliano Vivanet, Stefano Bianchi, Gianni Vercelli
2010 International Journal of Emerging Technologies in Learning (iJET)  
Large amounts of scientific digital contents are nowadays held by scientific institutions which collect, produce and store information valuable for dissemination, work, study and research.  ...  In order to achieve these goals, a semantic framework and an educational ontology were developed and implemented.  ...  the educational ontology.  ... 
doi:10.3991/ijet.v5i1.1030 fatcat:znk3t4u46zc6zmzplh3biti3lq

A semantic workflow mechanism to realise experimental goals and constraints

Edoardo Pignotti, Peter Edwards, Gary Polhill, Nick Gotts, Alun Preece
2008 2008 Third Workshop on Workflows in Support of Large-Scale Science  
We have developed a framework based upon use of a number of Semantic Web technologies, including the OWL ontology language and the Semantic Web Rule Language (SWRL), to capture scientist's intent.  ...  Workflow technologies provide scientific researchers with a flexible problem-solving environment, by facilitating the creation and execution of experiments from a pool of available services.  ...  The first one is WSMO (Web Service Modelling Ontology) [26] which provides ontological specifications to describe the core elements of Semantic services and the goals associated with the use of the services  ... 
doi:10.1109/works.2008.4723962 fatcat:qxcj36q5y5h5zgpbczt6ihjdgi

SciData: a data model and ontology for semantic representation of scientific data

Stuart J. Chalk
2016 Journal of Cheminformatics  
of scientific data (and its metadata), upon which discipline specific semantics can be applied.  ...  This paper describes a fundamental data model for scientific data that can be applied to data currently stored in any format, and an associated ontology that affords semantic representation of the structure  ...  Acknowledgements Thanks to Neil Ostlund and Mirek Sopek for comments on the data model.  ... 
doi:10.1186/s13321-016-0168-9 pmid:27795738 pmcid:PMC5064921 fatcat:lw222svkezebpc33c7wcpeytw4

ProvCaRe Semantic Provenance Knowledgebase: Evaluating Scientific Reproducibility of Research Studies

Joshua Valdez, Matthew Kim, Michael Rueschman, Vimig Socrates, Susan Redline, Satya S Sahoo
2018 AMIA Annual Symposium Proceedings  
Scientific reproducibility is critical for biomedical research as it enables us to advance science by building on previous results, helps ensure the success of increasingly expensive drug trials, and allows  ...  We evaluated the ProvCaRe knowledgebase with 28,474 "provenance triples" using hypothesis-driven queries to identify and rank research studies based on the provenance information extracted from published  ...  In this paper, we build on "Rigor and Reproducibility" guidelines to develop the ProvCaRe knowledgebase using a new ontology to formally model provenance metadata designed to enhance efforts at replicating  ... 
pmid:29854241 pmcid:PMC5977728 fatcat:qsxwi5zjrfashfzdk3ovpvnhtm

Modeling the Semantics of Contextual and Content-specific Research Metadata using Ontology Languages: issues on combining CERIF and OWL

Brigitte Jšrg, Jaakko Lappalainen, Kostas Kastrantas
2012 Procedia Computer Science  
Such contextual information is of uttermost importance for the processing of datasets and with the retrieval of scientific documents, providing e.g. the key information on provenance and characteristics  ...  In the context of the expanding initiative of the Web of Linked Data, translating that information into semantic languages enables new ways of querying benefitting from the reuse of domain ontologies.  ...  The research described in this paper had the support of EU FP7 project agINFRA (http://aginfra.eu/), contract number 283770.  ... 
doi:10.1016/j.procs.2012.04.171 fatcat:jkvrdehpmveazgav7jwahjdvoy

An ontology-centric architecture for extensible scientific data management systems

Yuan-Fang Li, Gavin Kennedy, Faith Ngoran, Philip Wu, Jane Hunter
2013 Future generations computer systems  
Data management has become a critical challenge faced by a wide array of scientific disciplines in which the provision of sound data management is pivotal to the achievements and impact of research projects  ...  The open and semantic nature of ontology languages also makes this architecture amenable to greater data reuse and interoperability.  ...  We also wish to acknowledge the support of the NCRIS funded Australian Phenomics Network. Finally we wish to thank Dr Xavier Sirault and Dr Kai Xu for their assistance in developing the domain models.  ... 
doi:10.1016/j.future.2011.06.007 fatcat:xswbe7m46nfq7hyrvvmc3czjgu

From Scientific Workflow Patterns to 5-star Linked Open Data

Alban Gaignard, Hala Skaf-Molli, Audrey Bihouée
2016 Workshop on the Theory and Practice of Provenance  
In this paper, we propose PoeM, a lightweight framework for mining provenance in scientific workflows. PoeM allows to produce linked in silico experiment reports based on workflow runs.  ...  Factor Ontology).  ...  In this experiment, a usage scenario for the produced Linked Experiment Report would consists in retrieving Galaxy datasets with SPARQL queries based on the underlying scientific hypothesis/claims, or  ... 
dblp:conf/tapp/GaignardSB16 fatcat:ygbcgyve5fdnreeikcpjoc4awu

oreChem ChemXSeer

Na Li, Leilei Zhu, Prasenjit Mitra, Karl Mueller, Eric Poweleit, C. Lee Giles
2010 Proceedings of the 10th annual joint conference on Digital libraries - JCDL '10  
We show how paragraphs containing experiment information in chemistry papers can be extracted and tagged based on a chemistry ontology with 470 classes, and then represented in ORE along with other document-related  ...  We were also able to model new types of metadata easily. For example, chemists are especially interested in finding information related to experiments in documents.  ...  The ORE model is a graph model based on Named Graphs [4] that are extensions of RDF graphs. Named Graphs consist of nodes and arcs within a node set.  ... 
doi:10.1145/1816123.1816160 dblp:conf/jcdl/LiZMMPG10 fatcat:llshttcnozhj7adhfrnuylo5im

An ontology for a Robot Scientist

L. N. Soldatova, A. Clare, A. Sparkes, R. D. King
2006 Bioinformatics  
Results: We demonstrate the utility of developing an ontology for our new Robot Scientist. This ontology is based on a general ontology of experiments.  ...  The ontology aids the curation and annotating of the experimental data and metadata, and the equipment metadata, and supports the design of database systems to hold the data and metadata.  ...  The work was funded by the BBSRC and the Royal Commission for the Great Exhibition of 1851.  ... 
doi:10.1093/bioinformatics/btl207 pmid:16873508 fatcat:ngkrzfonqvg5fgwa2imlz52u5y

Selected papers from the 12th annual Bio-Ontologies meeting

Larisa N Soldatova, Phillip Lord, Susanna-Assunta Sansone, Susie M Stephens, Nigam H Shah
2010 Journal of Biomedical Semantics  
The author integrates CiTO with several existing formalisms, such as the Dublin Core metadata, FRBR, and the Semantic Web Applications in Neuroscience (SWAN) ontology.  ...  of heterogeneous data sources with the use of a core ontology [5] .  ...  This article has been published as part of Journal of Biomedical Semantics Volume 1 Supplement 1, 2010: Proceedings of the Bio-Ontologies Special Interest Group Meeting 2009: Knowledge in Biology.  ... 
doi:10.1186/2041-1480-1-s1-i1 pmid:20626920 pmcid:PMC2903719 fatcat:rh62wecfifdnxgdrb2kx2v77xe
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