96 Hits in 3.9 sec

Bio-ontologies: current trends and future directions

O. Bodenreider
2006 Briefings in Bioinformatics  
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

James Malone, Robert Stevens
2013 Journal of Biomedical Informatics  
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

Phillip Lord, Robert Stevens
2004 Comparative and Functional Genomics  
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

Lars Vogt
2008 Zoomorphology  
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

Claudia d'Amato, Nicola Fanizzi, Marko Grobelnik, Agnieszka Lawrynowicz, Vojtech Svatek
2014 Semantic Web Journal  
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

E. Antezana, M. Kuiper, V. Mironov
2009 Briefings in Bioinformatics  
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

Christopher J.O. Baker, Arash Shaban-Nejad, Xiao Su, Volker Haarslev, Greg Butler
2006 Social Science Research Network  
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

Christopher J.O. Baker, Arash Shaban-Nejad, Xiao Su, Volker Haarslev, Greg Butler
2006 Journal of Web Semantics  
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

Shuheng Wu, Besiki Stvilia
2014 Advances in Classification Research Online  
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

S. Kim
2010 Briefings in Bioinformatics  
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

Y.L. Yip
2009 IMIA Yearbook of Medical Informatics  
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

Morten Tønnessen
2003 Sign Systems Studies  
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]

Arash Shaban-Nejad, Volker Haarslev
2009 Studies in Computational Intelligence  
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

Arash Shaban-Nejad, Alexandre Riazanov, Katia M. Charland, Gregory W. Rose, Christopher J.O. Baker, Robyn Tamblyn, Alan J. Forster, David L. Buckeridge
2012 Procedia Computer Science  
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

Alison Callahan, Michel Dumontier, Nigam H Shah
2011 Journal of Biomedical Semantics  
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
« Previous Showing results 1 — 15 out of 96 results