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Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications.

Clark T, Ciccarese PN, Goble CA - J Biomed Semantics (2014)

Bottom Line: The institutional "goal" of science is publishing results.At the same time they will add significant value to, and are intentionally compatible with, statement-based formalizations.We suggest that micropublications, generated by useful software tools supporting such activities as writing, editing, reviewing, and discussion, will be of great value in improving the quality and tractability of biomedical communications.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Neurology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA ; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA ; School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK.

ABSTRACT

Background: Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods. They are the essential mediating artifacts in the ecosystem of scientific communications. The institutional "goal" of science is publishing results. The linear document publication format, dating from 1665, has survived transition to the Web. Intractable publication volumes; the difficulty of verifying evidence; and observed problems in evidence and citation chains suggest a need for a web-friendly and machine-tractable model of scientific publications. This model should support: digital summarization, evidence examination, challenge, verification and remix, and incremental adoption. Such a model must be capable of expressing a broad spectrum of representational complexity, ranging from minimal to maximal forms.

Results: The micropublications semantic model of scientific argument and evidence provides these features. Micropublications support natural language statements; data; methods and materials specifications; discussion and commentary; challenge and disagreement; as well as allowing many kinds of statement formalization. The minimal form of a micropublication is a statement with its attribution. The maximal form is a statement with its complete supporting argument, consisting of all relevant evidence, interpretations, discussion and challenges brought forward in support of or opposition to it. Micropublications may be formalized and serialized in multiple ways, including in RDF. They may be added to publications as stand-off metadata. An OWL 2 vocabulary for micropublications is available at http://purl.org/mp. A discussion of this vocabulary along with RDF examples from the case studies, appears as OWL Vocabulary and RDF Examples in Additional file 1.

Conclusion: Micropublications, because they model evidence and allow qualified, nuanced assertions, can play essential roles in the scientific communications ecosystem in places where simpler, formalized and purely statement-based models, such as the nanopublications model, will not be sufficient. At the same time they will add significant value to, and are intentionally compatible with, statement-based formalizations. We suggest that micropublications, generated by useful software tools supporting such activities as writing, editing, reviewing, and discussion, will be of great value in improving the quality and tractability of biomedical communications.

No MeSH data available.


Related in: MedlinePlus

Example 2: Scientific Evidence consisting of Data and Methods supporting C3, a Claim from [67]. D1 is a composite image of graphs produced from the primary data. The Methods M1 (a procedure) and M2 (a transgenic mouse strain), both support D1.
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Figure 8: Example 2: Scientific Evidence consisting of Data and Methods supporting C3, a Claim from [67]. D1 is a composite image of graphs produced from the primary data. The Methods M1 (a procedure) and M2 (a transgenic mouse strain), both support D1.

Mentions: In Figure 8 we abstract and model a Statement from Spilman et al.[27], supported by scientific evidence, i.e., a Representation of Data, and the Methods (= “materials and methods”) by which it was obtained, including pre-observation interventions and observational context.


Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications.

Clark T, Ciccarese PN, Goble CA - J Biomed Semantics (2014)

Example 2: Scientific Evidence consisting of Data and Methods supporting C3, a Claim from [67]. D1 is a composite image of graphs produced from the primary data. The Methods M1 (a procedure) and M2 (a transgenic mouse strain), both support D1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4530550&req=5

Figure 8: Example 2: Scientific Evidence consisting of Data and Methods supporting C3, a Claim from [67]. D1 is a composite image of graphs produced from the primary data. The Methods M1 (a procedure) and M2 (a transgenic mouse strain), both support D1.
Mentions: In Figure 8 we abstract and model a Statement from Spilman et al.[27], supported by scientific evidence, i.e., a Representation of Data, and the Methods (= “materials and methods”) by which it was obtained, including pre-observation interventions and observational context.

Bottom Line: The institutional "goal" of science is publishing results.At the same time they will add significant value to, and are intentionally compatible with, statement-based formalizations.We suggest that micropublications, generated by useful software tools supporting such activities as writing, editing, reviewing, and discussion, will be of great value in improving the quality and tractability of biomedical communications.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Neurology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA ; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA ; School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK.

ABSTRACT

Background: Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods. They are the essential mediating artifacts in the ecosystem of scientific communications. The institutional "goal" of science is publishing results. The linear document publication format, dating from 1665, has survived transition to the Web. Intractable publication volumes; the difficulty of verifying evidence; and observed problems in evidence and citation chains suggest a need for a web-friendly and machine-tractable model of scientific publications. This model should support: digital summarization, evidence examination, challenge, verification and remix, and incremental adoption. Such a model must be capable of expressing a broad spectrum of representational complexity, ranging from minimal to maximal forms.

Results: The micropublications semantic model of scientific argument and evidence provides these features. Micropublications support natural language statements; data; methods and materials specifications; discussion and commentary; challenge and disagreement; as well as allowing many kinds of statement formalization. The minimal form of a micropublication is a statement with its attribution. The maximal form is a statement with its complete supporting argument, consisting of all relevant evidence, interpretations, discussion and challenges brought forward in support of or opposition to it. Micropublications may be formalized and serialized in multiple ways, including in RDF. They may be added to publications as stand-off metadata. An OWL 2 vocabulary for micropublications is available at http://purl.org/mp. A discussion of this vocabulary along with RDF examples from the case studies, appears as OWL Vocabulary and RDF Examples in Additional file 1.

Conclusion: Micropublications, because they model evidence and allow qualified, nuanced assertions, can play essential roles in the scientific communications ecosystem in places where simpler, formalized and purely statement-based models, such as the nanopublications model, will not be sufficient. At the same time they will add significant value to, and are intentionally compatible with, statement-based formalizations. We suggest that micropublications, generated by useful software tools supporting such activities as writing, editing, reviewing, and discussion, will be of great value in improving the quality and tractability of biomedical communications.

No MeSH data available.


Related in: MedlinePlus