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An open annotation ontology for science on web 3.0

Paolo Ciccarese, Marco Ocana, Leyla Garcia Castro, Sudeshna Das, Tim Clark
2011 Journal of Biomedical Semantics  
Results: This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation.  ...  Conclusions: The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web.  ...  We are most grateful for the financial support of these institutes and corporations.  ... 
doi:10.1186/2041-1480-2-s2-s4 pmid:21624159 pmcid:PMC3102893 fatcat:qksypoz7efd3fecj4cgfausmdi

Automatic OpenAPI to Bio.tools Conversion [article]

Egon Willighagen, Jonathan Mélius
2017 bioRxiv   pre-print
This work introduces an interoperability layer between two approaches for FAIR annotation of web services: OpenAPI and bio.tools.  ...  Computation has become a central component of life sciences research. Making computational services FAIR has had a strong interest from the life sciences community in the past 15 years.  ...  Acknowledgments We thank ELIXIR-DK for supporting this project via a bio.tools student http://biotools.readthedocs.io/en/latest/studentships.html .  ... 
doi:10.1101/170274 fatcat:joggbcyqebejlpjxt3spxixkaq

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

Yasset Perez-Riverol, Tobias Ternent, Maximilian Koch, Harald Barsnes, Olga Vrousgou, Simon Jupp, Juan Antonio Vizcaíno
2017 Proteomics  
Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other  ...  We here present the OLS Client as a free, open-source Java library to retrieve information from the new version of the OLS.  ...  Web Ontology Language (OWL)-based ontologies, an increase in the number of ontologies covered, as well as multiple enhancements in its web and programmatic interfaces, and in the underlying backend.  ... 
doi:10.1002/pmic.201700244 pmid:28792687 pmcid:PMC5707441 fatcat:olhbz7l2hzeunbl64p4dpjwdza

FOCIH: Form-Based Ontology Creation and Information Harvesting [chapter]

Cui Tao, David W. Embley, Stephen W. Liddle
2009 Lecture Notes in Computer Science  
Thus, scaling ontology creation and population to the size of the web in an effort to create a web of data-which some see as Web 3.0-is prohibitive.  ...  And we offer a way to semi-automatically harvest data from the current web of pages for a Web 3.0 ontology.  ...  FOCIH provides for semi-automatically annotating information according to any view users want-thus opening a pathway to the envisioned Web 3.0.  ... 
doi:10.1007/978-3-642-04840-1_26 fatcat:zi35uea7h5hg3cqerzsohxzo6e

Social Software Approach To E-Learning 3.0

Anna Nedyalkova, KrassimirNedyalkov, TeodoraBakardjieva
2013 Zenodo  
In the present paper, we-ll explore how social media tools provide an opportunity for new developments of the e-Learning in the context of managing personal knowledge.  ...  Students- Survey of use of web technologies and social networking tools is presented.  ...  ** Use 89% 82% 29% TABLE V V STUDENTS' SURVEY OF WEB 3.0 TECHNOLOGIES Web 3.0 is having a high impact on learning Web 3.0 as real after 2015 Web 3.0- barriers: adoption of learning  ... 
doi:10.5281/zenodo.1058809 fatcat:xygjf6lls5denmvxthz5pwf2xi

The EBI RDF platform: linked open data for the life sciences

S. Jupp, J. Malone, J. Bolleman, M. Brandizi, M. Davies, L. Garcia, A. Gaulton, S. Gehant, C. Laibe, N. Redaschi, S. M. Wimalaratne, M. Martin (+4 others)
2014 Bioinformatics  
Motivation: Resource description framework (RDF) is an emerging technology for describing, publishing and linking life science data.  ...  The EBI RDF platform has been developed to meet an increasing demand to coordinate RDF activities across the institute and provides a new entry point to querying and exploring integrated resources available  ...  This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0/), which permits non-commercial re-use  ... 
doi:10.1093/bioinformatics/btt765 pmid:24413672 pmcid:PMC3998127 fatcat:2jzyexnusfdippfn6kq6mnvxjq

Semantic mashup of biomedical data

Kei-Hoi Cheung, Vipul Kashyap, Joanne S. Luciano, Huajun Chen, Yimin Wang, Susie Stephens
2008 Journal of Biomedical Informatics  
Ted Shortliffe (Editor-in-Chief of JBI) for his editorial review and guidance.  ...  Finally, we thank Janine Burch and Rachel Perry (at the JBI Editorial Offices) for coordinating the paper submission, review, and production process.  ...  An ontology is designed for capturing knowledge for a complex personalized health care scenario.  ... 
doi:10.1016/j.jbi.2008.08.003 pmid:18703163 pmcid:PMC3742004 fatcat:utdd2zyj6zfklh5etnhe4gbwwq

Data management in Systems biology II - Outlook towards the semantic web [article]

Gerhard Mayer
2009 arXiv   pre-print
The problems existing today on the way to a true semantic web are pinpointed, different semantic web standards, tools and development frameworks are overlooked and an outlook towards artificial intelligence  ...  It is presented how ontologies can be used for the semantic enrichment of data and how this can contribute to the vision of the semantic web to become true.  ...  One could speak of such an intelligent web making use of semantic annotations as the web 5.0.  ... 
arXiv:0912.2822v1 fatcat:2sl6qr3f2ve57g55gzxd3v4tpy

Cognitive Approaches for the Semantic Web (Dagstuhl Seminar 12221)

Dedre Gentner, Frank Van Harmelen, Pascal Hitzler, Krzysztof Janowicz, Kai-Uwe Kühnberger, Marc Herbstritt
2012 Dagstuhl Reports  
Cognitive aspects emerge as an essential ingredient for future work on knowledge acquisition, representation, reasoning, and interactions on the Semantic Web.  ...  Essentially, the information stored on the Web is from and for humans.  ...  Sheth, "An Ontological Approach to Focusing Attention and Enhancing Machine Perception on the Web," Applied Ontology, vol. 6(4), pp.345-376, 2011.  ... 
doi:10.4230/dagrep.2.5.93 dblp:journals/dagstuhl-reports/GentnerHHJK12 fatcat:xbh6owcklvcgplcllplbbgvuhe

Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting

Larisa N Soldatova, Susanna-Assunta Sansone, Susie M Stephens, Nigam H Shah
2011 Journal of Biomedical Semantics  
of ontologies and natural language processing for an annotation framework, the generation of textual definitions, and the discovery of gene interaction networks.  ...  and dissemination of knowledge in biomedicine and the life sciences.  ...  This article has been published as part of Journal of Biomedical Semantics Volume 2 Supplement 2, 2011: Proceedings of the Bio-Ontologies Special Interest Group Meeting 2010.  ... 
doi:10.1186/2041-1480-2-s2-i1 pmid:21624154 pmcid:PMC3102888 fatcat:knxc7s6ckzao5jpyoho3bu6xqy

AISO: Annotation of Image Segments with Ontologies

Nikhil Lingutla, Justin Preece, Sinisa Todorovic, Laurel Cooper, Laura Moore, Pankaj Jaiswal
2014 Journal of Biomedical Semantics  
The tool enables researchers and curators to delineate portions of an image into multiple highlighted segments and annotate them with an ontology-based controlled vocabulary.  ...  Therefore, researchers and curators need a tool that can identify and demarcate features in an image plane and allow their annotation with semantically contextual ontology terms.  ...  Stockey at Oregon State University, for their contribution of the paleo-botanical image and subsequent segmentation and annotation, as described in the Case Studies and Figure 3 .  ... 
doi:10.1186/2041-1480-5-50 pmid:25584184 pmcid:PMC4290088 fatcat:77xwkdwl7ragxbvkuj2xywyfja

ABCD 3.0 Ready to Use

David Fichtmueller, Walter G. Berendsohn, Gabriele Droege, Falko Glöckler, Anton Güntsch, Jana Hoffmann, Jörg Holetschek, Mareike Petersen, Fabian Reimeier
2019 Biodiversity Information Science and Standards  
The XML elements are connected to their semantic concepts using the W3C SAWSDL (Semantic Annotation for Web Services Description Language and XML Schema) standard.  ...  The new site is hosted on Github: https://github.com/tdwg/abcd/tree/gh-pages.  ...  The XML elements are connected to their semantic concepts using the W3C SAWSDL (Semantic Annotation for Web Services Description Language and XML Schema) standard.  ... 
doi:10.3897/biss.3.37214 fatcat:avp6dpknsvf7lnvvnscrnq4jqa

Digital Scholarship and Open Science in Psychology and the Behavioral Sciences (Dagstuhl Perpectives Workshop 15302)

Alexander Garcia Castro, Janna Hastings, Robert Stevens, Erich Weichselgartner, Marc Herbstritt
2016 Dagstuhl Reports  
as an integrative platform for e-Science.  ...  This workshop addressed the problem of facilitating the construction of an integrative digital scholarship and open science infrastructure in psychology and the behavioral sciences by utilizing the Web  ...  It is an open tool being engineered for an emerging W3C standard for web annotation.  ... 
doi:10.4230/dagrep.5.7.42 dblp:journals/dagstuhl-reports/CastroHSW15 fatcat:crbhfmhelzhlreiddnm5hxomve

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases [article]

Nuria Queralt Rosinach, Janet Pinero, Alex Bravo Serrano, Ferran Sanz, Laura I Furlong
2015 bioRxiv   pre-print
Motivation: DisGeNET-RDF makes available knowledge on the genetic basis of human diseases in the Semantic Web (SW).  ...  of a rich and fully interconnected Linked Open Data (LOD).  ...  Remarkably, DisGeNET-RDF is integrated in the Open PHACTS Discovery Platform [7] , which is an application for drug discovery based on Semantic Web technology and RDF linked datasets.  ... 
doi:10.1101/032961 fatcat:tbssxfxubvbdth727hypyw6fou

HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0

Kei-Hoi Cheung, Kevin Y. Yip, Jeffrey P. Townsend, Matthew Scotch
2008 Journal of Biomedical Informatics  
Web 2.0 has transformed the Web into an environment that provides richer user experiences by allowing for the combination of disparate information in a variety of data formats, the facilitation of interaction  ...  We then describe Semantic Web, the mainstream Web 3.0 technology that enables more powerful data integration over the Web.  ...  We gratefully acknowledge Mark Gerstein and Carole Goble for suggestions, comments, and views.  ... 
doi:10.1016/j.jbi.2008.04.001 pmid:18487092 pmcid:PMC2933816 fatcat:s7xyuohnv5bm7kzg36dgwy5jpq
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