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Biomedical semantics in the Semantic Web.

Splendiani A, Burger A, Paschke A, Romano P, Marshall MS - J Biomed Semantics (2011)

Bottom Line: Is biomedical information too complex to benefit from simple interlinked representations?What are the implications of adopting a new paradigm for knowledge representation?What are the incentives for the adoption of the Semantic Web, and who are the facilitators?

View Article: PubMed Central - HTML - PubMed

Affiliation: Rothamsted Research, AL5 J2Q, Harpenden, UK. andrea.splendiani@bbsrc.ac.uk.

ABSTRACT
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 areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences?We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20th.

No MeSH data available.


Number of papers in Pubmed which contain the keyword “Semantic Web”, and related keywords, published during the years 2001-2010. Numbers of papers in Pubmed from 2001 to 2010 which contain in the title or abstract the keywords “Semantic Web”, “Website”, “Internet”, “Relational database”, “XML”, “Ontology”. The number of papers for 2010 is linearly extrapolated from the total number of papers published until November 2010. The numbers reported are first normalized by the total number of papers published in Pubmed per year (multiplied by a factor of 105 for readability). They are then divided by the following ratio: (total numbers of papers published in category X between 2001-2010)/(total numbers of papers published in category “Semantic Web” between 2001-2010)
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Figure 1: Number of papers in Pubmed which contain the keyword “Semantic Web”, and related keywords, published during the years 2001-2010. Numbers of papers in Pubmed from 2001 to 2010 which contain in the title or abstract the keywords “Semantic Web”, “Website”, “Internet”, “Relational database”, “XML”, “Ontology”. The number of papers for 2010 is linearly extrapolated from the total number of papers published until November 2010. The numbers reported are first normalized by the total number of papers published in Pubmed per year (multiplied by a factor of 105 for readability). They are then divided by the following ratio: (total numbers of papers published in category X between 2001-2010)/(total numbers of papers published in category “Semantic Web” between 2001-2010)

Mentions: It is perhaps surprising, then, that the number of papers which explicitly mention the term “Semantic Web” in Pubmed has shown a decline in the last two years. Figure 1 shows the trend over the period from 2001 to 2010, in comparison with a few other keywords representing related technologies. While the terms “website”, “internet” and “ontology” are appearing more and more in abstracts, the term “Semantic Web” which ought to encompass them, is not. Could this be due to a general preference for the terms that refer to particular aspects of the Semantic Web such as “ontology” and “linked data"? Clearly, Figure 1 is only a weak and imprecise indication of the impact of a technology, as seen through the frequency of its related terms in literature. Nevertheless, this observation calls for some thoughts on why we do not see more of Semantic Web in life sciences.


Biomedical semantics in the Semantic Web.

Splendiani A, Burger A, Paschke A, Romano P, Marshall MS - J Biomed Semantics (2011)

Number of papers in Pubmed which contain the keyword “Semantic Web”, and related keywords, published during the years 2001-2010. Numbers of papers in Pubmed from 2001 to 2010 which contain in the title or abstract the keywords “Semantic Web”, “Website”, “Internet”, “Relational database”, “XML”, “Ontology”. The number of papers for 2010 is linearly extrapolated from the total number of papers published until November 2010. The numbers reported are first normalized by the total number of papers published in Pubmed per year (multiplied by a factor of 105 for readability). They are then divided by the following ratio: (total numbers of papers published in category X between 2001-2010)/(total numbers of papers published in category “Semantic Web” between 2001-2010)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105493&req=5

Figure 1: Number of papers in Pubmed which contain the keyword “Semantic Web”, and related keywords, published during the years 2001-2010. Numbers of papers in Pubmed from 2001 to 2010 which contain in the title or abstract the keywords “Semantic Web”, “Website”, “Internet”, “Relational database”, “XML”, “Ontology”. The number of papers for 2010 is linearly extrapolated from the total number of papers published until November 2010. The numbers reported are first normalized by the total number of papers published in Pubmed per year (multiplied by a factor of 105 for readability). They are then divided by the following ratio: (total numbers of papers published in category X between 2001-2010)/(total numbers of papers published in category “Semantic Web” between 2001-2010)
Mentions: It is perhaps surprising, then, that the number of papers which explicitly mention the term “Semantic Web” in Pubmed has shown a decline in the last two years. Figure 1 shows the trend over the period from 2001 to 2010, in comparison with a few other keywords representing related technologies. While the terms “website”, “internet” and “ontology” are appearing more and more in abstracts, the term “Semantic Web” which ought to encompass them, is not. Could this be due to a general preference for the terms that refer to particular aspects of the Semantic Web such as “ontology” and “linked data"? Clearly, Figure 1 is only a weak and imprecise indication of the impact of a technology, as seen through the frequency of its related terms in literature. Nevertheless, this observation calls for some thoughts on why we do not see more of Semantic Web in life sciences.

Bottom Line: Is biomedical information too complex to benefit from simple interlinked representations?What are the implications of adopting a new paradigm for knowledge representation?What are the incentives for the adoption of the Semantic Web, and who are the facilitators?

View Article: PubMed Central - HTML - PubMed

Affiliation: Rothamsted Research, AL5 J2Q, Harpenden, UK. andrea.splendiani@bbsrc.ac.uk.

ABSTRACT
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 areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences?We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20th.

No MeSH data available.