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Bio-ontologies: current trends and future directions
2006
Briefings in Bioinformatics
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He has co-chaired the annual bio-ontologies meeting at ISMB for many years and is a co-developer of a highly successful OWL training course. ...
We review this trend and what benefits it might bring to ontologies and their use within biomedicine. interests include terminology, knowledge representation and ontology in the biomedical domain, both ...
Later in the article, the future direction of these current trends will be explored. It is not possible in such an article to do justice to all the resources available. ...
doi:10.1093/bib/bbl027
pmid:16899495
pmcid:PMC1847325
fatcat:iwzoi4hqi5gmze6ekzwyugcfmy
Measuring the level of activity in community built bio-ontologies
2013
Journal of Biomedical Informatics
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Measuring additions, deletions and changes, together with release frequency, appear to be useful metrics of activity and useful pointers towards future behaviour. ...
Overall, we show that it is possible to objectively measure the activity in an ontology and to make some prediction about future activity. by which an OBO Foundry ontology should be built, one of which ...
The authors thank 'girlwithglasses' without whom much work in bio-ontologies would not have happened. ...
doi:10.1016/j.jbi.2012.04.002
pmid:22554701
fatcat:r2u5xdwc3rcujnv25hfq2tv5vi
The Seventh Annual Bio-Ontologies Meeting Moat House Hotel, Glasgow, 30 July 2004
2004
Comparative and Functional Genomics
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Since the advent of the Gene Ontology, which coincided with the first Bio-Ontologies Meeting, we have seen a year-on-year strengthening of the field; bio-ontologies has moved from being dominated by computer ...
The Annual Bio-Ontologies Meeting [1] has now reached its seventh consecutive year, running as a special interest group (SIG) of the much larger ISMB conference. ...
The theme for the panel was to perform a SWOT analysis for bio-ontologies, in which the internal strengths and weaknesses of bio-ontologies are examined alongside the external opportunities and threats ...
doi:10.1002/cfg.433
pmid:18629147
pmcid:PMC2447436
fatcat:i3lrummryrgkvb5bg54hsa3ory
The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology
2008
Zoomorphology
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I suggest basic criteria for developing data standards on grounds of distinguishing content, concept, nomenclatural, and format standards and discuss the role of data bases and their use of bio-ontologies ...
in current activities for data standardization in biology. ...
Acknowledgments I thank Thomas Bartolomaeus and Markus Koch for discussion and valuable suggestions for an earlier draft of this paper. ...
doi:10.1007/s00435-008-0081-5
fatcat:gtxhwfbd5vde5hx7x5pahtt4li
Inductive Reasoning and Machine Learning for the Semantic Web
2014
Semantic Web Journal
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From the speed of the development of initiatives like Linked Open Data or community efforts to integrate various ontological resources like bio-ontologies, we may expect to have, in the near future, access ...
Hence, one may witness a recent trend in the Semantic Web community to propose complementary forms of reasoning, preferably more efficient and noise-tolerant. ...
doi:10.3233/sw-130103
fatcat:5pqeikfjvndslm7vt4luwl7tqi
Biological knowledge management: the emerging role of the Semantic Web technologies
2009
Briefings in Bioinformatics
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Ontologies and Semantic Web technologies revolutionize these efforts. Here, we review the benefits, trends, current possibilities, and the potential this holds for the biosciences. ...
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 ...
Acknowledgements We thank the editors and three anonymous referees for providing constructive suggestions. We also thank Cecilia Rodriguez for preparing the figures. ...
doi:10.1093/bib/bbp024
pmid:19457869
fatcat:qewyihg44fhvrlletzo74xzj6y
Semantic Web Infrastructure for Fungal Enzyme Biotechnologists
2006
Social Science Research Network
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it with other publicly available bio-ontologies. ...
The OntoIQ interface supports users not familiar with writing DL syntax allowing them access to the ontology with expressive description logic and automated reasoning tools. ...
Acknowledgements This work was financed in part through the Genome Quebec funded project Ontologies, the semantic web and intelligent systems for genomics ...
doi:10.2139/ssrn.3199336
fatcat:4ohkyfw3hbhhng4nvuwlwwsw5e
Semantic web infrastructure for fungal enzyme biotechnologists
2006
Journal of Web Semantics
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it with other publicly available bio-ontologies. ...
The OntoIQ interface supports users not familiar with writing DL syntax allowing them access to the ontology with expressive description logic and automated reasoning tools. ...
Acknowledgements This work was financed in part through the Genome Quebec funded project Ontologies, the semantic web and intelligent systems for genomics ...
doi:10.1016/j.websem.2006.05.001
fatcat:5jk2zvky3ng6bfmxhtmhouvvhu
Exploring the Development and Maintenance Practices in the Gene Ontology
2014
Advances in Classification Research Online
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The Gene Ontology (GO) is one of the most widely used and successful bio-ontologies in biomedicine and molecular biology. ...
The study found that GO has developed various tools and mechanisms to gain expert feedback and engage various communities in developing and maintaining the Ontology in an efficient and less expensive way ...
Among many of the current bio-ontologies, the Gene Ontology (GO) is one of the most successful, and has been widely used for text mining and information extraction (Blaschke, Hirschman, & Valencia, 2002 ...
doi:10.7152/acro.v24i1.14675
fatcat:w7yq5zxnb5hlrbsxrrtuqvlzd4
Knowledge-Based Bioinformatics - From analysis to interpretation. * Edited by Gil Alterovitz and Marco Ramoni
2010
Briefings in Bioinformatics
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At the end of the book, trends on current bioinformatics and conclusions are briefly mentioned. ...
Chapter 11 reviews types of commonly conducted molecular network analysis and their applications, and their challenges/future directions. ...
doi:10.1093/bib/bbq070
fatcat:af44dwyq2ndqrem5rmqwf6eh2y
Accelerating Knowledge Discovery through Community Data Sharing and Integration
2009
IMIA Yearbook of Medical Informatics
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Advances in systems biology, bio-ontologies and text-ming can also be noted. ...
Conclusions Current biomedical research gradually evolves towards an environment characterized by intensive collaboration and more sophisticated knowledge processing activities. ...
Acknowledgement I would like to acknowledge the support of Martina Hutter and the reviewers in the selection process of the IMIA Yearbook. ...
doi:10.1055/s-0038-1638650
fatcat:dmird6o2g5buldu7pnhbfirvoi
Umwelt ethics
2003
Sign Systems Studies
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These include ontological niche, common-Umwelt, total Umwelt and bio-ontological monad. I then present an Uexküllian reading of the deep ecology platform. ...
The current trend towards loss of worlds is not likely to be reversed until some fundamental measures are taken. ...
"bio-ontology", see Tønnessen 2001: 684) . ...
doi:10.12697/sss.2003.31.1.13
fatcat:nqbonglqqzguvo5wjmmok4aihm
Bio-medical Ontologies Maintenance and Change Management
[chapter]
2009
Studies in Computational Intelligence
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In this chapter, we survey and review state of the art change management in bio-ontologies as well as some of the available tools and techniques in this area. ...
Words change, meanings and context change. ...
reusing some existing bio-ontologies, such as GO and TAMBIS (Baker et al. 1998) . ...
doi:10.1007/978-3-642-02193-0_6
fatcat:4lwfhekchnfj3cnto2tqgxwv6m
HAIKU: A Semantic Framework for Surveillance of Healthcare-Associated Infections
2012
Procedia Computer Science
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The considerable effort required for discovery and integration of relevant data from multiple sources limits the current effectiveness of HAI surveillance. ...
Healthcare-Associated Infections (HAI) impose a substantial health and financial burden. Surveillance for HAI is essential to develop and evaluate prevention and control efforts. ...
The paper concludes a discussion of the implications of our study and possible future work directions. Fig. 1 . ...
doi:10.1016/j.procs.2012.06.151
pmid:32288895
pmcid:PMC7129430
fatcat:kyo65lx3effqhf7dbbv32a36bm
HyQue: evaluating hypotheses using Semantic Web technologies
2011
Journal of Biomedical Semantics
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Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. ...
Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. ...
, where the event types are derived from shared bio-ontologies such as the Gene Ontology. ...
doi:10.1186/2041-1480-2-s2-s3
pmid:21624158
pmcid:PMC3102892
fatcat:xd64wxf45za7vjqms7g446hqbq
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