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

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          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.

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          Most cited references49

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          A call for transparent reporting to optimize the predictive value of preclinical research.

          The US National Institute of Neurological Disorders and Stroke convened major stakeholders in June 2012 to discuss how to improve the methodological reporting of animal studies in grant applications and publications. The main workshop recommendation is that at a minimum studies should report on sample-size estimation, whether and how animals were randomized, whether investigators were blind to the treatment, and the handling of data. We recognize that achieving a meaningful improvement in the quality of reporting will require a concerted effort by investigators, reviewers, funding agencies and journal editors. Requiring better reporting of animal studies will raise awareness of the importance of rigorous study design to accelerate scientific progress.
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            RAFT1: a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs.

            The immunosuppressants rapamycin and FK506 bind to the same intracellular protein, the immunophilin FKBP12. The FKB12-FK506 complex interacts with and inhibits the Ca(2+)-activated protein phosphatase calcineurin. The target of the FKBP12-rapamycin complex has not yet been identified. We report that a protein complex containing 245 kDa and 35 kDa components, designated rapamycin and FKBP12 targets 1 and 2 (RAFT1 and RAFT2), interacts with FKBP12 in a rapamycin-dependent manner. Sequences (330 amino acids total) of tryptic peptides derived from the 245 kDa RAFT1 reveal striking homologies to the yeast TOR gene products, which were originally identified by mutations that confer rapamycin resistance in yeast. A RAFT1 cDNA was obtained and found to encode a 289 kDa protein (2549 amino acids) that is 43% and 39% identical to TOR2 and TOR1, respectively. We propose that RAFT1 is the direct target of FKBP12-rapamycin and a mammalian homolog of the TOR proteins.
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              High-level neuronal expression of abeta 1-42 in wild-type human amyloid protein precursor transgenic mice: synaptotoxicity without plaque formation.

              Amyloid plaques are a neuropathological hallmark of Alzheimer's disease (AD), but their relationship to neurodegeneration and dementia remains controversial. In contrast, there is a good correlation in AD between cognitive decline and loss of synaptophysin-immunoreactive (SYN-IR) presynaptic terminals in specific brain regions. We used expression-matched transgenic mouse lines to compare the effects of different human amyloid protein precursors (hAPP) and their products on plaque formation and SYN-IR presynaptic terminals. Four distinct minigenes were generated encoding wild-type hAPP or hAPP carrying mutations that alter the production of amyloidogenic Abeta peptides. The platelet-derived growth factor beta chain promoter was used to express these constructs in neurons. hAPP mutations associated with familial AD (FAD) increased cerebral Abeta(1-42) levels, whereas an experimental mutation of the beta-secretase cleavage site (671(M-->I)) eliminated production of human Abeta. High levels of Abeta(1-42) resulted in age-dependent formation of amyloid plaques in FAD-mutant hAPP mice but not in expression-matched wild-type hAPP mice. Yet, significant decreases in the density of SYN-IR presynaptic terminals were found in both groups of mice. Across mice from different transgenic lines, the density of SYN-IR presynaptic terminals correlated inversely with Abeta levels but not with hAPP levels or plaque load. We conclude that Abeta is synaptotoxic even in the absence of plaques and that high levels of Abeta(1-42) are insufficient to induce plaque formation in mice expressing wild-type hAPP. Our results support the emerging view that plaque-independent Abeta toxicity plays an important role in the development of synaptic deficits in AD and related conditions.
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                Author and article information

                Contributors
                Journal
                J Biomed Semantics
                J Biomed Semantics
                Journal of Biomedical Semantics
                BioMed Central
                2041-1480
                2014
                4 July 2014
                : 5
                : 28
                Affiliations
                [1 ]Department of Neurology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
                [2 ]Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
                [3 ]School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
                Article
                2041-1480-5-28
                10.1186/2041-1480-5-28
                4530550
                26261718
                a5fd044d-0534-4447-85a7-5036315c3680
                Copyright © 2014 Clark et al.; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.

                History
                : 12 March 2013
                : 16 June 2014
                Categories
                Research

                Bioinformatics & Computational biology
                argumentation,annotation,data citation,digital abstract,scientific discourse,scientific evidence,methods citation,research reproducibility,nanopublications

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