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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

Citation distortion: Graph of a claim network from Greenberg 2009 [3] showing citation distortion. The claim presented in this lineage states that amyloid beta deposition in IBM muscle fibers precedes other pathological changes – from which can be inferred that it is the causative factor. The foundational publications, which would be expected to contain supporting data, do not. Needham and Massaglia’s article from Lancet Neurology provides no support at all for Claim C11 at all, treating it as a pure fact. In the Claim network, we assert C11 as a Holotype, or representative Statement, for C12. In fact, that assertion could be made for all Claims in the network.
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Figure 20: Citation distortion: Graph of a claim network from Greenberg 2009 [3] showing citation distortion. The claim presented in this lineage states that amyloid beta deposition in IBM muscle fibers precedes other pathological changes – from which can be inferred that it is the causative factor. The foundational publications, which would be expected to contain supporting data, do not. Needham and Massaglia’s article from Lancet Neurology provides no support at all for Claim C11 at all, treating it as a pure fact. In the Claim network, we assert C11 as a Holotype, or representative Statement, for C12. In fact, that assertion could be made for all Claims in the network.

Mentions: Figure 20 shows an example of citation distortion based on a section of Greenberg’s supplemental data, represented as a micropublication citation network drawn from eight publications[121-128].


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

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

Citation distortion: Graph of a claim network from Greenberg 2009 [3] showing citation distortion. The claim presented in this lineage states that amyloid beta deposition in IBM muscle fibers precedes other pathological changes – from which can be inferred that it is the causative factor. The foundational publications, which would be expected to contain supporting data, do not. Needham and Massaglia’s article from Lancet Neurology provides no support at all for Claim C11 at all, treating it as a pure fact. In the Claim network, we assert C11 as a Holotype, or representative Statement, for C12. In fact, that assertion could be made for all Claims in the network.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 20: Citation distortion: Graph of a claim network from Greenberg 2009 [3] showing citation distortion. The claim presented in this lineage states that amyloid beta deposition in IBM muscle fibers precedes other pathological changes – from which can be inferred that it is the causative factor. The foundational publications, which would be expected to contain supporting data, do not. Needham and Massaglia’s article from Lancet Neurology provides no support at all for Claim C11 at all, treating it as a pure fact. In the Claim network, we assert C11 as a Holotype, or representative Statement, for C12. In fact, that assertion could be made for all Claims in the network.
Mentions: Figure 20 shows an example of citation distortion based on a section of Greenberg’s supplemental data, represented as a micropublication citation network drawn from eight publications[121-128].

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