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.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.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 fileAn OWL 2 vocabulary for micropublications is available at 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. During the past two decades the ecosystem of biomedical publications has moved from a print-based to a mainly Web-based model. However, this transition brings with it many new problems, in the context of an exponentially increasing, intractable volume of publications,2; of syComputational methods previously proposed as solutions include ontologies; text miSuch a common metadata representation of scientific claims, argument, evidence and annotation in biomedicine should serve as an integrating point for the original publication, subsequent annotations, and all other computational methods, supporting a single framework for activities in the nine point cycle of authoring-publishing-consumption-reuse we discuss in the section on Use Cases. This cycle can be thought of as an information value chain in science. This means that each set of disparately motivated and rewarded activities, carried out by various actors, creates and passes along value to the next, which consumes this value-added product as an input. A metadata representation to support this value chain would need to:•serve as a common Web-friendly nucleus for value-addition and extraction across the biomedical communications ecosystem: understood, operated upon and exchanged by humans and by computers, as supplements to the linear documents they characterize;•enable more powerful use and sharing of information in biomedicine, particularly through integration and mashup to provide the most relevant views for any social unit of researchers;•enable the addition of value to the content while providing a detailed provenance of what was done;•support computational processing in a way that complete papers in un-augmented linear natural language cannot yet integrate well with existing linear textual representations.This paper introduces the micropublications semantic metadata model. The micropublications model is adapted to the Web, and designed for (a) representing the key arguments and evidence in scientific articles, and (b) supporting the “layering” of annotations and various useful formalizations upon the full text paper.This model responds to the nine use cases we present, in which digital summarization of scientific argumentation with its evidence and methodological support is required. These use cases, for the most part, deal directly with the scientific literature, rather than its processed reflection in curated topical databases. They illustrate how and why currently proposed “statement-based” approaches need richer representation and how this model can play such a role.In this paper we present•a Use Case analysis mapped to sets of common activities in the biomedical communications ecosystem, showing the potential value addition and path to implementation of the proposed model for each Use Case;•a formal model of micropublications;•illustrative examples instantiating the model for each Use Case;•notes on an interface to nanopublications and other statement-based formalizations;•discussion on how the model can support reproducibility and verifiability in research; on implementation in software; and relationship to other work; and•our Conclusions about the role of this model in next-generation scientific publishing.We also provide, in three separate files of Additional Material:1. detailed class, predicate and rule definitions;2. a proposed Web-friendly representation, using community ontologies, serialized in the W3C Web Ontology Language, with a set of examples in RDF; and3. a comparison of micropublications to the SWAN model.Statement-based models have been proposed as mechanisms for publishing key facts asserted in the scientific literature or in curated databases in a machine processable form. Examples include: Biological Expression Language (BEL) statements; SWAN, aWhat we mean by “statement-based” is that they confine themselves to modeling statements found in scientific papers or databases, with limited or no presentation of the backing evidence for these statements. Some offer statement backing in the form of other statements in the scientific literature, but none actually has a complete representation of scientific argument including empirical evidence and methods. Of the three examples we mention,•Nanopublications model only the indicated statement;•SWAN models a principal statement, or “hypothesis”, with supporting statements, or “claims”, from the same publication only, and backing references for the supporting statements;•BEL and SWAN model backing statements from other publications in the literature by citing whole publications, leaving the reader to determine precisely where in the cited document a backing statement actually resides;•None of these models provide a means to build claim networks of arbitrary depth.•None of these models provide a means to transitively close claim lineages to underlying empirical evidence – because they do not represent it.Table Figure The intent of statement-based models is to be relatively simple and useful for specific tasks. In the case of nanopublications, this particular model is currently presented  mainly for data integration across chemical and biological databases. For example, in the current nanopublication guidelines, a nanopThe micropublication approach goes beyond statements and their provenance, proposing a richer model in order to account for a more complete and broadly useful view of scientific argument and evidence, beyond that of simple assertions, or assertions supported only by literature references. It is also designed to be readily compatible with assertions coded in BEL or as nanopublications, as these models are considered useful in certain applications and will need to be integrated.in the process of formation, empirical evidence, as well as formal statements and their provenance, must be a part of our model.Empirical evidence is required in scientific publications so that the scientific community may make and debate judgments based on the “interpretation of nature” rather than interpretation of texts. The proAnopheles as malarial vectors has been well-established for over a century . However, previously, in the late nineteenth century, the existence and nature of malarial vectors was an open research question[presentation of evidence to establish a warrant for belief[For example, consider the following “nano-publishable” fact given in,24: “mosquestion. Open reor belief. Thus, fRecent results spotlight concerns with the communication of evidence and its citation. Begley and Ellis recently found that only 11% of research findings they examined from the academic literature could be reproduced in a biopharmaceutical laboratory. Fang etWe have incorporated a number of features in our model to enable presentation of empirical scientific evidence; therefore including data, not just assertions, as information supporting a statement; as well as other required features for scientific discourse.arguments for qualified claims supported by evidence. This evidence consists of citations to the literature, and novel data with supporting methods. Scientific claims “in the wild” are almost always extensively hedged or qualified, based on recognition of their incomplete or tentative nature[As useful as formal language representations may be, any requirement that statements must only be expressed in formal language such as we find in BEL, nanopublications, and some other approaches, is a potential barrier to adoption in the publication ecosystem. We can expect to encounter scientific claims in their native environment, the biomedical literature, as relatively nuanced e nature. Moreovee nature,37, and Consequently the micropublication model must capture the natural language of claims as they appear in the literature. We treat formalization separately as an optional curatorial step. This more comprehensive approach deals with both with scientific statements “in the wild”, and with the evidence that supports them, and is also compatible with statement-based formalization patterns such as nanopublications.Our model is based on understanding scientific publications as arguments, which present a narrative of experiments or observations, the data obtained, and a reasoned interpretation (“finding”) of the data’s meaning. Such ardefeasible[The determination whether or not a finding is correct, is made over time by the community of the researcher’s peers. What claims are considered true, may evolve over time, based on re-examination of evidence and development of new evidence. Assertions may be criticised and refuted. Thus scientific reasoning is efeasible.Toulmin’s classic model of defeasible reasoning, updatedOur model provides a framework to support extensively qualified claims in natural language, as generally presented by researchers in their primary publications. Most fundamentally, it adds support relations to claims in the literature, to assist in resolving primary scientific evidence within a “lineage” of assertions. Support relations, structured as graphs, back up assertions with the data, context and methodological evidence which validates them.Micropublications permit scientific claims to be formulated minimally as any statement with an attribution (basic provenance), and maximally as entire knowledgebases with extensive evidence graphs.Thus micropublications in their minimal form subsume or encompass statement-based models, while allowing presentation of evidential support for statements and natural language assertions as backing for formalisms. This has significant applicability across the lifecycle of biomedical communications.The goal of the micropublication model is to better adapt scientific publications to production and use on the Web, in the context of the new forms either made available or required. The model supports nine main activities  in our analysis, within nine use case requirement sets (e.g. building citable claims).We begin our analysis of the model’s use case applicability by abstracting major activities related to publishing scientific articles, the benchmark of scientific accomplishment within tWithin these we select a set of important but non-exhaustive applications of the model, targeted at responding to specific deficits already identified. For users of scientific publications, these are mostly centered on failures of evidence and reproduciblity,55,59,60Applications of the model begin with its feature of citable claims (use case 1), supported by evidence (use case 2), from which a robust claims network may be automatically or semi-automatcally constructed and analyzed use case 3). These first three use cases respond to the identified problems of mishandled, degraded or fictitious citations. These f,32,62; aWe then provide a use case centered on abstracting single articles (use case 4). This responds to the publication-volume overload issue noted by Cohen and Hunter, and others,63, by fTopic-centric claim networks may be equivalent to domain-centric knowledgebasees, if all claims having common meaning, but different wording, can be made functionally equivalent (use case 5). They are more readily computable, if formalized (use case 6) in languages such as Biological Expression Language (BEL); or nanoPublications must be discussed in the biomedical community. This is a part of their validation. Making online discussion part of the permanent record in a compact way related directly to the claim network of an article, constitutes use case 7, and again responds to the critical “filtration” and flagging of invalid or disputed results,67. Use Lastly, if this model is to be deployed, it must be backward-compatible with the existing communications ecosystem. For this we rely on emerging stand-off web annotation models (use case 9)-88.tool users) in this ecosystem, for important unsatisfied use cases.The use cases in Figure Table Building and using citable claims1. Motivation: Simkin and Roychodhury used mathematical techniques to show that scientific authors only read approximately 10%-20% of the papers they cite, and many of the rest are evidently copied from reference lists,33. GreeUse: Citable claims are a specific remedy for citation distortion by allowing ready comparison of what is cited, to what the citation is claimed to assert.Implementation: Citable claims may be constructed economically at the point where researchers read and take notes upon, or search for backing for their own assertions in, the domain literature of their field.Comments: Any scientific statement with an attribution may be formalized as a citable claim using the micropublication model.Modeling evidence support for claims2. Motivation: Evidence is the basis for assessment and validation of claims in biomedical (and scientific) argument. Greenberg,4 specifUse: Micropublications may be used to represent experimental evidence supporting claims, as they can represent non-statement artifacts such as reagents, images and other data. This function of the model has multiple roles. It adds additional value to citable claims by indicating what claims are actually backed by direct evidence, and what this evidence is. It also provides the ability to trace the association of claims in the literature to specific methods and data, and vice versa.Implementation: As in use case 1, evidence support for claims may be modeled as part of the process of recording bibliographic references. It may also be modeled directly by publishers as supplemental metadata, or by biomedical Web communities as part of a discussion.Producing a digital abstract of a publication3. Motivation: Digital abstracts would be extremely useful supplemental metadata. They would be particularly useful to enable text mining as argued by Gerstein et al..Use: A micropublication could be used to formalize the supporting attribution, central claims, references to literature, scientific data, materials & methods, annotations, comments, and formalizations, of scientific communications.Implementation: They could be provided by publishers or by value-add third parties, or created as part of personal or institutional knowledge bases. Mashing-up digital abstracts can be done by third-party applications, and would be one way to deal with intractable publication volumes, by properly summarizing them in a reliable, computable way.Comments: To enable complete digital abstracting, we define a system of classes for representing biological objects such as reagents, software, datasets and method descriptions, which are not statements in natural language or triples, but are important in documenting the foundational evidence for biomedical claims and arguments, and in making biomedical methods reusable.Claim network analysis of publication sets4. Motivation: As previously noted, it has been shown that the biomedical literature contains a significant proportion of non-reproducible results. These can be made even more problematic as they are repeatedly cited and transformed in claim networks.Use: Claim network analysis can be used to determine the origin of, and compare evidence for, individual and contrasting claims in the literature. Particularly when experiments are being designed based on putative findings of a body of prior research; it seems critical to be able to fully assess the entire background of a set of assertions.Implementation: Micropublications once instantiated, embody individual arguments, which in turn may be composed by resolution of references. This allows us to create extended graphs showing the basis in evidence for claims in the literature, even when they are deeply buried in chains of citations. Claim lineages are chains of citing/cited claims. Lineage visualization is proposed as a tool for readers and reviewers.Representing common meaning using similarity groups5. Motivation: Resolution of references often entails finding a claim in a cited document, which is similar to the claim formulated in the citing document. Further, parallel claims, of equivalent or near-equivalent meaning, may arise from different lines of research, without resolution to a common progenitor study.Similarity groups, a set of claims may be defined as having "sufficient" closeness in meaning to a representative exemplar, or Holotype claim. Their purpose is to allow normalization of diverse sets of statements with essentially the same meaning in the literature, without combinatorial explosion. We term the members of a given equivalence group, “equivalents” of one another.Use: Using Implementation: Holotypes may be defined (a) when a backing statement for a claim is defined, by choosing one or the other as the holotype, or by defining a new “annotator’s version” as a holotype; (b) in a similar way, when a text similarity search on the library of claims detects similar statements in separate claim lineages.similog-holotype model is an empirically based model that allows similar claims to be normalized to a common natural language representation, without dropping necessary qualifiers and hedging. Translations of claims to formal or other natural languages may also be considered similogs to the translated original, based on (sufficient) equivalence of meaning.Comments: The Claim formalization with attribution6. Motivation: Various applications in computing require translation of natural-language claims in the biomedical literature to statements in a formal vocabulary. Biological Expression Language (BEL) and AtteUse: Ideally one would like to be able to trace formalized claims back to their foundational evidence in the literature just as one does with natural language claims. The micropublications model supports formalization of claims.Implementation: At the point a formalized claim is created (modeled) from a base statement in the literature, the creating application may capture its supporting statement using the micropublications model. For example, in the current BEL software, instead of capturing only the Pubmed ID of the publication from which a BEL statement is derived, one might readily capture the backing statement as well, as a micropublication.Comment: Remember that the minimal form of a micropublication is a simple statement, with its attribution, and the attribution of its encapsulating micropublication.Modeling annotation and discussion7. Motivation: Annotation and discussion of scientific literature is increasingly conducted on the Web.Use: Scientific claims and evidence may be annotated in personal or institutional knowledge bases, and may be discussed online in specialized Web portals or communities. Modeling these texts as micropublications, with their backing statements and evidence from the literature, allows them to be exchanged freely between applications in a standard format.Implementation: This may be done by Web or other applications at the time the publications are annotated or discussion is captured.Building and using bipolar claim-evidence networks8. Motivation: Scientific discourse often involves disagreement on the correct interpretation or theoretical model for existing evidence. It is important to know where gaps or disagreements exist because these naturally suggest areas for further research. Support/attack relationships exist in the literature for alternative interpretations, hypotheses and models of biomedical function, structure, disease etiology, pathology, agent toxicity, therapeutic action, etc.Use: We provide an abstract logic representation compatible with much of the current AI literature on argumentation, as well as a description logic presentation modeled in OWL , which backing and warrant as classes; we avoid that, because these concepts become relativized across a large network: one publication’s backing is another’s warrant.While Toulmin and VerhHyper[support, as is the relationship between a statement and the reference cited to justify it. In another context, these might be modelled as disparate properties, say as “interpretation” and “citation”.This relativization suggests a graph structure, which is also compatible with work in unipolar and bipoHyper or SWANHyper. Using aThe micropublications model is a framework which accomodates a spectrum of complexity, from minimal to maximal representations. It can ingest the simplest forms and give room for stepwise elaboration, consistent with the incremental distributed value chain in which we are trying to embed it. The minimal representation is a single identified statement, where attribution is attached to both the statement and the identification. The maximal representation may be as complex as an entire knowledge base. It is worth stressing that despite the richness of this model, using it does not by any means require deploying all of its concepts for any particular scenario.Class, Predicate and Rule Definitions for Micropublications of Additional fileTo introduce the model, we outline the semantic and mathematical models of argument. Next we illustrate examples of how the model may be applied to each of the Use Cases from the preceding analysis, across the cycle of activities depicted in Figure claim, with statements and/or evidence deployed to support it. Its support may also include contrary statements or evidence; and/or the claim may dispute claims made by other arguments. These are called challenges in our model, rebuttal by Toulmin[attacks in the artifical intelligence literature on argumentation frameworks , qualified by a citation of the work from which they were paraphrased. Toulmin calls these paraphrases “warrants” , and the work indicated by a citation is called the “backing”, which would be consulted to validate the warrant.supports relationship between warrant and backing.As we are interested in constructing claim networks, it should be clear that in a network, warrant and backing are relative terms. Furthermore, to contruct such a network, we will need to have backing which resides in another work, available in the form of a single statement, not the entire work. While a citation of an entire article may be acceptable as a temporary measure, reflecting pragmatic boundaries, ultimately we wish to have the full claim network at hand. This sets us up to be able to transitively close the network. To do so we use a Defining this relationship consistently across the model – whether we are dealing with supporting statements, data, or methods – also allows us to bridge the gap between internal argument structure, and inter-argument structure.Representationa, a class whose subclasses include Sentence, Statement, Claim, Data, and Method. Sentences need not be syntactically complete – they may consist of a phrase, single word, or single meaningful symbol . Declarative Sentences are Statements. Sentences which qualify a Statement are Qualifiers. The principal Statement in an argument is called a Claim. Statements may be supported by other Statements, or by Data. Data in turn may be supported by Method, i.e. a description of how the Data was obtained, in the form of a re-usable recipe (or recipe component). A Procedure or a Material is a Method.We call any element of an argument, a elementsOf of the Micropublication which support its Claim, are in its SupportGraph.Figure Later we will examine various forms of argument formalized as Micropublications, using a closely related set of examples taken from the literature on Alzheimer Disease, for each Use Case.http://purl.org/mp, and detailed definitions are provided in Section A.2 of Additional fileThe basic outlines of our model are given here more systematically. An OWL model corresponding to these definitions is available at 1. Entities, Agents, Artifacts, Activities and Representations.Entities are things which may be discussed, real or imaginary.a. Agent is an Entity that makes, modifies, consumes or uses an Artifact.b. An Person or an Organization is an Agent.c. A Artifact is an Entity produced, modified, consumed or used by an Agent.d. An Activity is a process by an Artifact is produced, modified, consumed or used.e. An Representation is an Artifact which represents something.f. A Sentence, Data, Method, Micropublication, Attribution, or ArticleText.g. A Representation may be a 2. Supports and challenges.supports property is a transitive relation between Representations.a. The challenges property is inferred when a Representation either directlyChallenges another, or indirectlyChallenges it by undercutting  a Representation which supports it.b. The 3. Sentences, Statements, Claims and Qualifiers.Sentence is a well-formed series of symbols intended to convey meaning.a. A Statement is a declarative Sentence.b. A Claim is the single principal Statement arguedBy a Micropublication.c. A Qualifier is a Sentence, which may modify a Statement. References and SemanticQualifiers (tags) are two varieties of Qualifier.d. A 4. Data, Method and Material.e. Data, Method and Material are kinds of Representation.supports a Statement, that Statement is supportedByData. Data may be supportedByMethod if a Method supports it.f. If Data supports any Method of which it is a component.g. A Method is a reusable recipe showing how the Data were obtained; it specifies an Activity, and may refer to some Material as a component of the recipe. A Material 5. MicropublicationsMicropublication is a set of Representations, having supports and/or challenges relations to one another and potentially to those which are an elementOf other Micropublications.a. A Representation is defined as an elementOf a Micropublication if that Micropublication either asserts or quotes it.b. A assertedBy a Micropublication is originally instantiated by that Micropublication.i. A Representation quotedBy a Micropublication is referred to by that Micropublication, after first being instantiated by another Micropublication.ii. A Representation iii. The asserts and quotes notions are simple extensions of concepts from Carroll et al. and Bizer’s work on provenance and trust,97.c. ClaimsarguedBy a Micropublication.i. A Claim is the principal statement supports relationships amongst the Representations in a single Micropublications are structured as a directed acyclic graph (DAG), whose root is the Micropublication’s Claim.ii. The d. Attributionsi. The minimal level of support for any Statement is its Attribution to some Agent.e. Support and Challenge Graphssupports property, and which are elementsOf that Micropublication, constitute its Support Graph, being related to the Micropublication by the property hasSupportGraphElement.i. Representations related to the Claim of a Micropublication by the hasChallengeGraphElement works similarly.Figure ii. The property The class Artifact has, as previously noted, a series of subclasses allowing us to deal relatively homogeneously with experimental methods, materials, data, and language artifacts such as statements.All Statements, as Artifacts, should have an Attribution. The Attribution of a Statement is therefore a part of its SupportGraph. The simplest micropublication would be an instance of the Micropublication class, with its Attribution; arguing a Claim, supported by the Claim’s Attribution.Science, Nature, etc. by an eminent scientist, concerning his or her own principal area of expertise, is typically given more weight than an article in a third-tier journal, or a blog post or tweet from an undergraduate with limited expertise. This is why Attribution is part of the SupportGraph of an Argument. However, Attribution alone is weak support. The critical element of support in science is empirical scientific evidence. Complete Class, Predicate and Rule Definitions for Micropublications are given in Additional fileIn scientific argumentation, a publication in a denote the text of an argument, which in most of our examples will be sections of a scientific article. It may include images and other data as well as text.Let a as a Micropublication.Let MP_a denote the corresponding formalization of a as a micropublication or formalized argument, whereThen MP_a = 〈A_mpa, c, A_c, Φ, R〉 is the representation of a ::= an argument text, represented in a document;• a;•MP_a ::= a micropublication, or formalized argument structure, defined on a as a micropublication;•A_mpa ::= the Attribution of this formalization of a;•c ∈Φ ::= a single Statement, being the principal Claim of •A_c ∈Φ ::= the Attribution of the Claim c; and•Φ is a finite non-empty set of Representations which are elements of the Micropublication;+) and challenges (R-) relations, r; Φ+⊆Φ is the nonempty set of all φi covered by R+; and R+ is a strict partial order over Φ+, whose greatest element is c, the principal Claim of the argument in a.•R ⊆ Φ × Φ; where R is a nonempty disjoint union of supports ". Then •the Claim (C1) is that “rapamycin is an inhibitor of the mTOR pathway”;PSpilman;•the Attribution (A_C1) of this claim is to the Agent qualifiedBy the SemanticQualifiers CHEBI: 9168 and INO_0000736;•the Claim is ,C1), supports }.Figure •the SupportGraph for the claim is the set {supports presented in the argument. This micropublication consists only of literature references. We do not assume a cited reference is necessarily valid – it is a representation which may or may not resolve to a real document. If it can be so resolved, we connect it with a further supports/supportedby relationship, to some unique identifer of that document. If the document has Micropublication metadata associated with it, we can then potentially further resolve the reference, to a specific Statement within the document.Use Case Detail: The base use case for Example 1 is constructing libraries of citable Claims.Use Case: The base use case for Example 2 is to enhance citable Claims with supporting Data and reproducible Methods.Data, and the Methods  by which it was obtained, including pre-observation interventions and observational context.In Figure 2 =•the Claim indicated by C1 in Figure Let aThen for the formalized argument or micropublication MP2, we have•the Claim is C3;PSpilman by the attributionOfAgent property; PSpilman is “Patricia Spilman”;•the Attribution of this claim is A_C3, which in turn is related to the Agent •the Support Graph is a set of relations {supports, supports, supports, supports}.Use Case Details: Citable Claims with supporting data and resources give us the capability of showing the material basis for Claims based on original research in a given work. Also, in the forward-looking case of citable archived data and resources, the claims associated with them might be more easily determined. Citable claims in a personal or institutional “library” or database may “index” the associated data and methods more readily than other forms of metadata. Lastly, methods and materials later found to be flawed might be easily traced to claims based upon them.Use Case: The base use case for Example 3 is digital abstracting of a biomedical article in computable form, based on citable Claims with all supporting Statements, Data and Methods.This more complex form of Micropublication summarizes the principal Claim of an article and the evidence supporting it, again based on, and is 3 =Let a•the Claim indicated by C3 above;•the supporting Statements indicated by S1, S2 and S3; and•the supporting Evidence indicated by D1, M1 and M2.Then for MP3 its micropublication we have•the Claim is C3, “Inhibition of mTOR by rapamycin can slow or block AD progression in a transgenic mouse model of the disease”.;PSpilman as its object via attributionForAgent, as in the previous example;•A_C3 is the Attribution of C3, with supports relations on {A_C3, S1, S2, S3, D1, M1, M2, Ref5, Ref9, Ref10}.•the SupportGraph is a set of Use Case: The base use case for Example 4 is Claim network construction and analysis across publications. This supports the need of researchers to record and see clearly the actual statements and evidence intended to be referenced in a cited publication, as opposed to taking on faith the citation of an entire document treated as a “black box”.Claim C3 in Figure 1. rapamycin inhibits mTOR (taken from the literature);2. PDAPP mice are a good  model of human Alzheimer Disease pathology ; and3. Experimental evidence that PDAPP mice fed rapamycin over time regain some measure of cognitive health.A flaw in any of these elements undercuts Claim C3, which is the essential argument of the publication. So it is worthwhile to examine, in addition to the experimental evidence, whether the two supporting statements from the literature are well-grounded. Careful readers do this for important points – or may have the relevant citations already memorized. Implementation of the present use case allows this information from the literature to be modeled, retained and shared.Suppose that for the supporting literature references in Example 3, and111111, we hThe citing Statements in are now Spilman’s Statement S1 ( “rapamycin … an inhibitor of the mTOR pathway…”) cites in suppoSpilman’s Statement S2  cites, shown aClose inspection of the Backing for S2 shows how valuable it may be to clarify this at a Claim-to-Claim level; and to cite actual reagent catalog numbers as Methods  support relationships between C1.1/S1, and C2.1/S2.In resolving support across Micropublications, we establish a Claims network. However we must ensure we retain localization of responsibility, for what is originally presented in the merged graphs, and what is “imported” from elsewhere. This is done using the Abstract model of the Claim about rapamycin:4 =•Claim C1.1 from Figure Let aThen for MP4, its micropublication, we havegiving us a micropublication model for the rapamycin Claim from.•the Claim is C1.1, “rapamycin … an inhibitor of the mTOR pathway…”, derived from “Harrison et al.”;•the SupportGraph is the set of support relations {supports, supports};Abstract model of the Claim about PDAPP mice:5 =•Claim C2.1 from Figure Let aThen for MP5 we havegiving us a micropublication model for the PDAPP mice Claim from.•the Claim is C2.1, “… addition of the Swedish FAD mutation to the APP transgene in a second line of mice, further increased synaptic transmission deficits in young APP mice without plaques”., derived from “Hsia et al.”; and•the SupportGraph is the set of support relations on {C2.1, D2.1, M2.1};Abstract model of the Spilman et al. Statements, with Backing resolved:6 =•Claim C3 from Figure Let a•the supporting Statements indicated by S1, S2 and S3.Then for MP6 we have•the Claim is C3, “Inhibition of mTOR by rapamycin can slow or block AD progression in a transgenic mouse model of the disease.”, from Spilman et al.;•the SupportGraph is expanded and now adds connections to C1.1 and C2.1.We call the graphs C1.1 → S1 and C2.1 → S2, Claim lineages, by analogy with biological lineages.similogs of one another. Groups of similar statements are equivalence classes, defined as having "sufficient" closeness in meaning to a representative exemplar, or Holotype Claim.A Holotype, or representative of the genus, is selected as a matter of convenience and exemplification, to stand for the common meaning of the Statements in a similarity group, as shown in Figure It is easy to see that C3 and C1.1 mean the same thing. C3 is derived from C1.1 . We call these Statements In addition to the C1.1 → C1 lineage, we have three other publications,-116, conexpress Statements”, originating with Strawson’s work[b.The group-of-similogs/holotype approach is empirical. It is based on the notion that scientific communications in form and content are a “literary technology”,which men’s work, which csimilogs is itself an assertion. Your “similarity” may not be my “similarity”, depending upon both the particular application (think of this as a kind of “manufacturing tolerance”), or in some cases, professional judgement. We can model such an assertion as a micropublication as shown in Figure Another question now emerges: identification of statements as being In Strawson’s perspective, we cannot assign any explicit ontological status, i.e. material existence, to a Statement. It is an extra-mundane abstract “meaning” – but always reduced to “meaning” as expressed in the language of formal logic, which is thus smuggled in via the back door. This would seem to be highly problematic, and we avoid it, because scientific publications for the most part do not represent their findings in this way. We then incur a translation step, which can do violence to the natural language presentation of the actual publication. In our model, Statements are Statements, i.e. declarations, assertions, truth-bearing Sentences, in some meaning-conveying language, and do have explicit ontological status.Use Case: Relating a formal-language model of the content (meaning) of a Claim using a controlled vocabulary, directly to its Backing in the literature. It can be useful to translate the content of textual Claims in a scientific publication, into a specialized formal language, for specific computational tasks - for example, doing systems biology.The Biological Expression Language (BEL) is one eIn this case, we model the BEL statement itself as a Micropublication. Here, the Argument Source for the BEL statement is a tuple from a relational database, consisting of the statement text and a reference to the source document, its PubMed ID.7 =Let a•{“a(CHEBI:9168) = | kin(p(HGNC:FRAP1))”, “PMID: 12030785”}We refer to the text of the BEL statement as C7, and to “PMID:12030785” as Ref96, for convenience.Then for the corresponding micropublication MP7, we have•the Claim is C7, “(CHEBI: 9168) = | kin(p(HGNC:FRAP1))”, which in ordinary English means that sirolimus  downregulates HUGO: FRAP1 .•A_C7, the Attribution of this Claim, is {“Pratt D, 2013”}, indicating that the Claim was formulated by Dexter Pratt;•the SupportGraph is the support relation on {A_C7, R96}, indicating the reference to Ref 96 describiAs represented in Figure Claim-level resolution to similogs, would result in a BEL statement for the entire Similarity Group, asserting the rapamycin ↔ mTOR inhibition interaction, whose support thus includes original evidence from the Sabatini group’s publication as well as later review information. As the Claim must have been read and interpreted by a researcher to be translated at all, it seems clear that suitable software could embed specific citation to the Claim level at the time the asssociation with the BEL statement is databased.Use case: Annotation is a key general use case that associates personal comments, discussion, semantic tags, or other constructs with scientific communication. Micropublications allow Annotations to be associated with logically explicit Backing, while contextualizing them within the digital content they describe. Readers as well as reviewers and other discussants may – with suitable software support – attach annotations directly to citable claims.Let’s suppose a reader or reviewer of the Spilman et al. article has some notes, comments, or observations to record – for example, about applicability of the Spilman result to drug discovery and development. The reader could then create annotation, modeled as a new, independent micropublication, referencing the original, as shown in Figure Use case: Scientific claims are defeasible. It is critical in evaluating Claims in biomedical research to review critical argumentation which may defeat them. Over time, not only Claims but Methods become established by withstanding such attacks.c.As noted in Example 4, the main Claim of rests on•PDAPP mice are an established model of human Alzheimer Disease.Spilman et al.’s principal Claim is still technically valid regardless of whether this is true or not, because the paper wisely restricts it to an assertion about the PDAPP mice only. But if in fact PDAPP mice do not model human Alzheimer’s Disease well, the principal Claim as most readers would interpret it, is challenged. The whole point of the article is to suggest that rapamycin or its analogs may be worthy of investigation as therapeutic agents for cases of actual human AD.Bryan et al., in theiHow do we model the challenge of Bryan et al. to the argument in Spilman et al.? In the SWAN project, we did There are two main ways the challenge relationship can be modeled, for two specific use cases. The first way (Case 1) is to model the challenges made within a scientific article, against claims of another publication. The second way (Case 2) is to model disagreement of two articles “from the outside”, i.e. from the perspective of a reviewer or annotator. This approach can support as many different views as desired, of the relationships between different publications, and each view can be accorded its own attribution and authorship status, which can be selected for upon retrieval.challenges relationships originate from elements of the SupportGraph of the Micropublication in which they occur. Even challenges initiated elsewhere may be quoted and included, following Toulmin’s approach to what he called rebuttals.Note that Case 1: Micropublication models a Claim in one publication that challenges another.If an author of Publication A explicitly challenges a Claim of Publication B, that is a part of the discourse that can be modeled as part of the micropublication model of Publication A. In such a case, the “external” Claim being argued against will be quoted or summarized within Publication A.8 = Bryan et al.’s review. Then for MP8 its micropublication isLet a•the Claim C11 from as shown•A_C11 is the Attribution of C11;•the SupportGraph is the set of support relations on {C11, R48, R49, R50 };challenges statement S3 from MP3.•the Claim C11 Case 2.This would only be a good representation of Bryant et al., however, if the specific challenge to Spilman’s paper was actually made in Bryant’s text. In this case, it is not. So the observation must be made by a third party. We outline this situation in Case 2: Micropublication models disagreement between two publications “from the outside”.challenge relations, but the curator of a knowledge base (KB) wishes to note the discrepancy.Suppose micropublications MP3 and MP11 are inconsistent, but it is a third party, not the author of either, who takes note of this fact. The initial micropublication summaries do not contain We can create a new micropublication, MP12, as follows.12 =Let a•A (new) textual assertion that MP11:C11 and MP3:S3 are in conflict; with•Summaries of the Claims MP11:C11 and MP3:S3.12 we haveThen for the MP12 formalization of a•the new assertion C12, an annotation by “KB Curator”, stating: “Bryan et al. claim that PDAPP mice tend to have lower body temperatures, which may result in varying degrees of hypothermia during the MWM task, which in turn can produce amnesia in animals. This challenges the validity of PDAPP mice as an AD model, as asserted in Hsia et al.”This form is diagrammed in Figure Use cases: (1) Making micropublications visually and experientially a part of the existing communications ecosystem for scientist users. (2) Reliably mapping micropublication components to the documents from which they were extracted, or on which they were expressed as annotations, while (3) allowing them also to exist and be exchanged independently.Biomedical researchers, and other workers in biomedical communications, spend a lot of time with the domain literature in their field. They read it, write it, discuss it, annotate it, text mine it, give talks and journal clubs about it, and argue about it. Our aim is to enhance and enable these practices, in a way that lets micropublications and other forms of annotation emerge as side-effects from improved practices. This requires (1) the ability to mash up annotations upon the literature they annotate, and (2) the ability to deconstruct annotations by direct reference to segments of existing literature.d. However, the basic principles of these models are roughly the same.We contextualize micropublications using an OWL ontology of annotations, which is orthogonal to the domain ontologies, and to the model of micropublications. Initially we used the Annotation Ontology, AO,86. We hWe have demonstrated, using AO, that annotation created on HTML target documents can be exported as RDF, and referenced independently by a PDF viewer (Utopia),119, whiIn addition to the ontologies for annotation contextualization, which can be used by any application, we understand that useful document annotation tools are needed. Our team developed the Domeo web document annotation toolkit,81,98, nGreenberg’s publications on citation distortion,4 mentio•Cherry picking data, and•Failure to properly describe methods.They do not mention citation distortion, of various kinds, which Greenberg showed remains a common and unaddressed problem.By providing a metadata model that can cite claims directly, micropublications enable citation networks to be constructed using a single common model, which will tend to distribute the costs. This should allow much more clarity to be brought to the question, “on what grounds is this statement made?” Furthermore, the networks may be resolved to purported foundational data and methods, which supply the ultimate evidence supporting a claim.warrant for belief, in addition to any empirical supporting evidence directly presented. In Toulmin’s terminology, the warrant is a purported summary of the backing. In Example 1 this would be the actual document referred to by the citation[The elements of a Claim’s SupportGraph are its citation. If the Greenberg demonstrated that this happens far more frequently than one would like and is a serious defect in the domain literature which he reviewed (amounting to hundreds of papers). Because it is far too laborious to check each and every cited document, searching for the relevant Claim, citable Claims are proposed here as a method to dramatically reduce the labor cost of checking a Claim’s support. With proper software, identifying such Claims may be automated.Citable Claims could be constructed most economically at the point where researchers read and take notes upon, or search for backing for their own assertions in, the domain literature of their field. Today researchers commonly use bibliographic reference managers such as Zotero, EndNote, etc. to record this aspect of reading and note-taking, but the Claim(s) for which they record a bibliographic reference are not captured. Our model allows them to have a standard sharable representation.Figure Lancet Neurology, which removed the “is often stated to” qualifier, upgrading the claim to “fact”, without citation.It can be readily seen that Needham et al.’s claim thGreenberg also notes, in reviewing one of the “foundational” publications from the same laboratory, “major It is true that reagent citation is a more complex problem than simply providing and implementing this model can resolve. It needs urgent action by publishers to require more specificity in textual identification by authors, along with availability of global registries such as those provided by the Neuroscience Information Framework,99,130, Resolution of claims to their support in data and methods, including research reagents, is an important new feature, not provided by our previous SWAN model  its References, which have already been parsed out as computable objects; (b) Data, in the form of images in the article, also already parsed out as computable and annotatable objects; or (c) other micropublication-annotated Statements within the article.We have now also implemented a Micropublications-based annotation functionality as a plugin to Domeo version 2. The user interface (UI) for this plugin is shown in Figure Currently Domeo implements an internal version of the micropublications model which it can serialize and store persistently; this version is currently deployed.One of the key features the micropublications model will provide in the context of pharmaceutical research, is the ability to securely link proprietary internal data as supporting evidence.We proposed this model as a general purpose representation model for claims, evidence and argument in the biomedical and other scientific literature. By design it is not intended to be limited in applicability to a single program. To be most useful, it requires reasonably widespread adoption. In addition to the Domeo implementation we describe above, we suggest two particularly attractive points of uptake to the community at large.1. Any bibliographic management software can implement micropublications. This would enable the scientist user to have a structured library at hand, not only of the references s/he has cited, but also of the particular statements within the referenced material, which are most important.2. Publishers may implement micropublications as value-added annotation to their published content.The main value proposition for implementing this model is to enable individual statements in the literature to be cited and referenced directly both by traditional articles and in web discussions,; linked easily into citation networks; and grounded in their supporting evidence – data and methods. We believe this is a pressing need across the biomedical research and development community, to provide better accountability and to support a culture of greater transparency. A number of poor scholarly practices regarding evidence might also be prevented by widespread adoption of our model, embedded in useful applications. Ultimately we believe it can greatly facilitate data and methods re-usability, improving the reliability and reproducibility of research results.Micropublications enable us to formalize the arguments and evidence in scientific publications. We have shown the need for this kind of formalization in order to meet a number of significant use cases in the biomedical communications ecosystem. We have also demonstrated that purely statement-based models are too underfeatured to deal with scientific controversy and evidentiary requirements, and therefore cannot adequately meet use cases requiring an examination of evidence – which we believe will be the majority of those arising from the primary literature.Our analysis clearly places the Micropublications model, or some near relative, among the required components for next-generation scientific publishing.Nonetheless we believe statement-based models also have an important role in formalizing statements, or at least those which have already been deployed with an adequate set of supporting evidence. Such formalizations should also record the original authors’ textual interpretation of the empirical evidence as the grounds for later formalization. We provide a clear interface to such models.An example of this kind of application would be in drug hunting teams in a pharma or biotech company. Examination of evidence and possible contradiction is absolutely fundamental to the activities of such teams in qualifying targets and leads. At the same time, with adequate evidence chains, there is most certainly a role for statement formalization, and we have provided for this as an important interface in our model.We have also attempted to show how the model not only meets various core use cases, but that it can be applied across a spectrum of complexity, from very simple annotations of the kind researchers make nearly every day using reference management and annotation software, to complex curated knowledgebases. This is a basic requirement for success in adoption: you do not have to buy the whole package. There is a simple entry point beyond which you need go no further. But you may go on, if you so choose.We assume that implementation will be in various kinds of software environments in which the actual detailed construction of micropublications is built into useful activities, where the formal instantiations of micropublications are constructed internally and behind the scenes – but may be shared at will. Our research group has built a micropublications capability into the Domeo web annotation platform as a first step, and an evaluation of the model in this context will be presented in a forthcoming article.As a general point, we expect value to accrue in the use of this model by enabling interoperability and incremental value addition through annotation, by users at various points in the scientific communication’s ecosystem, who receive significant added utility in return for any additional work they put into modeling activities. In use cases such as bibliographic management tools, much of the required modeling work is already done in everyday use of the existing tools. What is added (claim identification in cited works and specification of representative or holotype claims), is certainly going to be useful to the users who implement it.The most promising approaches overall, will generate micropublications as standardized annotation metadata that can be exchanged and accumulated between applications.As pointed out in, when anWe hope that other researchers will see the utility of one or more elements of this model for their own use cases of choice, and apply it. Developers and architects who wish to explore further uses of this model, including modifications and new applications, are invited to contact and discuss with the authors.http://purl.org/mp/. It is made available by the copyright holder, Massachusetts General Hospital, for use under terms of the W3C open source license .The micropublications ontology may be accessed at aClass names in the model are always capitalized, and are italicized on first occurrence. Predicate names are always in lower case and always italicized. When a term such as “claim”, “statement”, or “supports”, is not being used as a formal class or predicate name, it is not capitalized or italicized.bW.V.O. Quine criticized Strawson’s formulation for similar reasons[ reasons.cHowever, note that the author does not actually say “these mice are a good model of AD”.dAll three of the current authors participated in the work of the W3C group, and the second author co-chaired it; overall the W3C Open Annotation Community Group has had the participation of 55 institutions; with 97 participating individuals and representatives at the time of writing.The authors declare no competing interests.TC conducted the research, developed the micropublication use cases and designed the abstract model. He is the primary author of the OWL vocabulary and RDF examples based on the abstract model, and of this publication as a whole. PNC helped to check the consistency of the abstract model, and provided valuable technical guidance in development of the OWL vocabulary and the RDF examples. He also developed the Domeo Micropublications plugin. CAG supervised the research, and critiqued and edited several versions of this publication, including the present one. All authors read and approved the final manuscript.OWL Vocabulary and RDF Examples.Click here for fileClass, Predicate and Rule Definitions for Micropublications.Click here for fileRelationship of Micropublications to the SWAN Model.Click here for file


The DOGRISK questionnaire is an internet-based ongoing study of canine nutrition, living environment, and disease. Here we aim to assess the performance of the questionnaire using data from the first three years in relation to some descriptive and disease variables. We used associated questions, official register records, test-retest repeatability, and email/mail contact with questionnaire respondents.Reliability against an official register of gender, season of birth, breed, and results of hip radiography was tested and Cohen’s Kappa was between 0.95–0.99. Internal consistencies of hypothyroidism status and dog’s age were calculated using Cronbach’s Alpha . Test-retest repeatability of ten variables among 224 participants was analyzed. Gender, season of birth, and born in owner family had Cohen’s Kappa > 0.86, color of coat, vaccination status as an adult, other dogs in household, and vaccination status as a puppy had Cohen’s Kappa between 0.67–0.80, and body condition score under two months of age and tidiness of household, had Cohen’s kappa of 0.45 and 0.42, respectively. In addition, time spent outside had Cohen’s kappa of 0.37. Of the owners contacted by email/mail to confirm their dog’s atopy/allergy (skin symptoms), 8.9 % reported that they had given an incorrect answer , but only 69 % of all reaffirmed positive answers had a diagnosis set by a veterinarian.Our study showed that owners were diligent with basic information and with the status of three diseases. Cohen’s Kappa in the reliability of the test-retest was in most variables at least 0.67. We propose that the descriptive variables and the disease variables be used as such when we generate hypotheses from the DOGRISK data. Internet-based data collection is a cost-effective and simple method to obtain epidemiological data, widely used in human research , 2. Withwww.ruokintakysely.fi) in December 2009, also the internet version was tested on 27 dog owners. This questionnaire is the first to gather a vast information of diseases and diet of dogs meticulously over lifetime. The collected environmental data will be used in later nutritional analyses as adjusting background variables.The Finnish DOGRISK questionnaire is an ongoing, large, internet-based, cross-sectional study of canine nutrition, living environment, and health that contains over 1300 variables. It was launched in December 2009 by the DOGRISK research group of the Department of Equine and Small Animal Medicine, University of Helsinki, Finland. The DOGRISK questionnaire aims to find associations between nutritional, descriptive, and environmental factors and diseases. It is based on the two-page paper-version pilot questionnaire from 2003 that attracted over 1000 answers. To ensure that all important food and diet, environment, and phenotype-related options would be included in the questionnaire, the face and content validity of the questionnaire was checked with veterinary colleagues and people from the dog food and supplement industry, dog breeders, active dog owners, and different dog interest groups. Draft versions were tested on volunteers in the waiting room of the Animal Hospital of the University of Helsinki. A nearly final 14-page version was tested in two clinical trials and during a week in June 2009 among veterinarians, animal nurses, and dog owners in our veterinary hospital waiting room. Before launching the final DOGRISK questionnaire  register. In addition, the reliability was tested through internal consistency by comparing the answers to two related questions within the questionnaire, and by comparing owner-entered information about their dog having skin symptoms with responses to a short email questionnaire sent to owners. The test-retest repeatability was ascertained by using the questionnaires that were filled in twice for the same dog.Eligible respondents were all dog owners who were able to respond to the questionnaire in Finnish. They were recruited by letting dog owners know about the questionnaire at dog fairs, through dog clubs, in dog magazines, by interviews in the media, and later by sending out flyers with a raw food selling vending car. Up to March 23, 2013, a total of 8813 questionnaires had been filled in by Finnish dog owners. The study population consists of 261 different breeds and 1155 mixed-breed dogs (13.1 %) of all age groups, from puppies to senior dogs. The earliest date of birth in the sample was April 8, 1983, as owners of deceased dogs were also allowed to fill in the questionnaire. The study population consists of dogs from all over Finland (northern Europe). Not all questions were mandatory, so the respondents had the opportunity to leave the questions unanswered.From the whole DOGRISK questionnaire study population, 487 dogs with an owner-entered official Finnish Kennel Club (FKC) canine registration number were chosen as a convenience sample, starting from the first dog and moving forward until the 487th. Breed, gender, date of birth, and results of official hip radiographs (if available) were confirmed from the official FKC register and compared with the answers given to the corresponding four questions in the DOGRISK questionnaire. Subject characteristics are shown in Table To assess the internal consistency in the owners’ answers, we compared two answers on the questionnaire that would always be expected to coincide. For this, we chose hypothyroidism, which is a common disease requiring specific diagnostic blood work that is done by veterinarians and that always needs medication. The questionnaire includes a question on whether the dog has the disease or not, and another question on ongoing medication . Cronbach’s Alpha (α) was used to evaluate the reliability of the answers to the owner-reported disease status and medication.The questionnaire also included a question on the dog’s age  and another question on the date of birth. We calculated the difference between the date when the owner filled in the questionnaire and the birth date of the dog, and then recoded it into years: 0.1–0.5 as 0.25 year (puppy), 0.6–1.9 as 1 year (young dog), 2.0–2.9 as 2 years (adult), etc. We then compared this value to the owner’s answer of the dog’s age in years using Cronbach’s Alpha.n = 1354) and asked whether their original answer was correct and whether the condition had been diagnosed by a veterinarian. The owners also had the opportunity to explain their dog’s symptoms more thoroughly.All dog owners who had answered ‘yes’ to the question ‘Does your dog suffer from atopy/allergy (skin symptoms)?’ and had provided either their email address or street address were contacted by email/mail (n = 197) and asked whether their dog suffered from the disease or not. Positive predictive value (PPV) was calculated to evaluate the percentage of true positives of all positive answers of owner-reported disease status of AASS. Here the correct positive answer to the question ‘Does your dog suffer from atopy/allergies (skin symptoms)?’ reaffirmed by the owner by email/mail was used as the ‘golden standard’. From all owner-reaffirmed positive answers, the percentage of dogs with a diagnosis set by a veterinarian was calculated.Additionally, all dog owners who had not ticked an answer ‘yes/no’ to the question on whether their dogs suffered from atopy/allergy (skin symptoms) (AASS) but had answered one or more of the related questions  were also contacted by email/mail . In the consistency between the dog’s age and date of birth the Cronbach’s α was 0.99 (n = 3540).The owner-reported hypothyroidism diagnosis and ongoing hypothyroid medication of the dog were compared and the Cronbach’s α was 0.95 (n = 47). The PPV of the owner-reported disease status of AASS was 0.91. Thirty-seven of the 47 answers were excluded from future analyses as they could not be categorized as atopic nor healthy.Altogether 515 (38 %) of 1354 owners who had responded ‘yes, my dog suffers from atopy/allergy (skin symptoms)’ (AASS) also answered our email/mail. Of these, 457 (89 %) reported having given a correct answer and 58 (11 %) an incorrect answer. All 58 answers reported as incorrect were controlled one by one, and based on the owners’ explanation, 11 were kept as a ‘yes’ and the rest were considered false positives (n = 134), this question was left empty on the questionnaire as these dogs also did not have any answer to the main question of ‘Does your dog suffer from AASS?’.Of the 197 owners who had ticked only one of the AASS-specifying questions , but not the disease question itself, 63 (32 %) answered our email/mail; 49 (78 %) reported that their dog had AASS, while 14 (22 %) reported that their dog did not have AASS. The 49 were recoded as ‘yes’ into the questionnaire data. The 14 ‘no’ answers were controlled one by one, and based on the owners’ explanation, one was recoded into ‘yes’, three were recoded into ‘no’, and ten could not be assigned to either category. For the owners did not answer the email  positive answers remained in the data, with a total of 518 (457 + 11 + 49 + 1) confirmed answers (38 %). In addition, 228 dogs had positive answers without any contact information for the owner. Of the confirmed positive answers, only 69 % had a diagnosis set by a veterinarian.Altogether 244 owners had filled in the questionnaire twice. The time period between the answers varied from 1 day to 38 months. Three variables, i.e. gender, born in owner family, and season of birth, had Cohen’s kappa between 0.86–0.96. Four variables, color of coat, vaccination status as an adult, other dogs in household, and vaccination status as a puppy, had Cohen’s kappa between 0.67–0.80. Two variables, body condition score under two months of age and tidiness of household, had Cohen’s kappa of 0.45 and 0.42, respectively. Time spent outside under two months of age had Cohen’s kappa of 0.37. Results are presented in Table n = 8081). This was expected since hypothyroidism is also a human disease and it can be speculated that people may remember it more easily because of this. It is also always diagnosed from a blood sample at a veterinary clinic, and it invariably requires medication. Discrepant answers to the two questions on diagnosis and medication were very few, but could arise from owners having just visited the clinic and awaiting results, which would have yielded a ‘yes’ for diagnosis but nothing for medication. Another possibility might be that the owner could not remember the name of the disease or the name of the medication, resulting in one of the questions left unanswered.Since we have 43 disease diagnoses  in the DOGRISK questionnaire, it was not feasible to validate them all. However, as we are interested in using different diseases in our future analyses, we chose to validate one medicated disease that could be evaluated easily using a concurrent medication question (hypothyroidism), one diagnosis that could be compared with an external official register , and one disease that even for a specialist is considered difficult to diagnose with 100 % certainty (canine atopic dermatitis or atopy), which in the questionnaire was covered by a wider question: atopy/allergy (skin symptoms)(AASS). The internal consistency for hypothyroidism was excellent . Many dog breed associations in Finland take part in a national hip screening program (PEVISA) [The reliability of the radiographic CHD results was also excellent ((PEVISA)  where do(PEVISA)  at the aAtopy/allergy (skin symptoms) (AASS) is much more difficult to diagnose than hypothyroidism and CHD, and therefore, we expected its reliability to be much lower than for the other two diagnoses. The diagnosing protocol is time-consuming and includes numerous treatment trials, elimination diet trials, blood work, etc. This might be too extensive and expensive for many owners. Thus, many pruritic dogs are incorrectly believed to be atopic by owners or even veterinarians, who sometimes also find it difficult to diagnose atopy and allergies. Some dogs therefore probably have the disease but lack a confirmed diagnosis. The dog’s symptoms also might have disappeared due to environmental or dietary changes, or they may be so mild that the owners think that their dog is healthy. For this validation, we sent a short email/mail questionnaire to the owners to ask about their dogs’ diagnosis. Altogether 31 % of the owners reported that the diagnosis was not verified by a veterinary work-up. However, response consistency or disease repeatability was good: the PPV was 0.91 when comparing the answers in the DOGRISK questionnaire and in the email/mail questionnaire. Therefore, we may consider the owner-reported disease status of AASS quite reliable, bearing in mind the difficulties in diagnosing this disease. Because email/mail was not sent to owners reporting that their dogs did not suffer from AASS, we could not conclude how many true- or false-negatives we had.Owners seemed to be diligent with basic information, as the internal consistency of two questions related to the dog’s age was excellent. Also data on gender, season of birth, and breed matched very well with the official register records. Because all dogs in these analyses were pure bred dogs, the new owner should have received the registration book from the breeder or previous owner in which this information can be verified. In fact, most of our data concerning descriptive information and diseases can be considered good or excellent. Only data for the time before the owner had the dog can be considered slightly more unreliable.n = 3540). Upon comparing self-reported hip osteoarthritis with results of clinical examination, Ratzlaff et al. [Data on web-based questionnaire validity and reliability among human subjects are vast, and a comprehensive review is not feasible in this context. Although between-study comparisons are complicated by differences in the study methods and statistical measures used, the DOGRISK questionnaire appears to compare well with results for humans. The reliability is highly dependent on the exact variable analyzed, as shown by Stanton et al. , who fouf et al.  reportedThe retest population was not a planned repeatability study population, but a subgroup of the group responding to the existing questionnaire twice of their own initiative. Utilizing the responses of the owners who had answered the questionnaire twice was a limitation in our study, as all data will not necessarily be the same. Answers for gender, color of coat, season of birth, and born in owner family are considered stable since they should not change with repeated response, and repeatability in these was indeed high, being very similar to that in Sallander et al. .We provided an option in the questionnaire to save answers midway through the answering process without submitting the questionnaire and to continue answering later. For those that used this option, it probably had a positive effect on the reliability of the answers, as respondents could gather all information before submitting the questionnaire and they could fill in the questionnaire at an optimal time as opposed to completing it in a rush. However, we also had informed respondents who contacted us by email that they could resubmit a totally new questionnaire at will if they received new information about the puppy stage or if conditions changed. As the two answers will then not be similar by default, they will show weaker repeatability. The most logical reasons for why some owners answered the questionnaire twice are because they had reported something incorrectly the first time, because they had forgotten that they had already filled in the questionnaire, because something had changed in their dog’s lives, because they wanted to report extra information about something they had no knowledge of the first time, or because other person in the household had responded to the questionnaire at the second time-point. The questions on body condition score and time spent outside, both covering the period when dogs were under the age of two months, could have been difficult for the owner to report since during this period puppies typically reside with the breeder. Thus, owners likely first provided an “educated guess” on the topic, followed by the actual answer given to them by the breeder, or a second own “educated guess”. This would explain the low repeatability in the answers to these questions, with answers to the question on puppy vaccination being somewhat more reliable, as it is common in Finland to vaccinate all puppies, and this information is usually given in written form (in the passport or vaccination booklet) to new owners if they adopt an older dog.Questions about the environment were also deemed ill-suited to repeated questioning since owners might have moved, taken new pets, stopped smoking, etc., but we nevertheless chose to compare the following non-stable questions: tidiness of household, adult dog’s vaccinations, and other dogs in household. The time factor will be the reason for any discrepancy in the answers here, e.g. tidiness of the household may vary according to the life situation. Also, the number of dogs in the household may vary with time, as old dogs die and new puppies arrive. For the future analyses these variables can still be used but should be interpreted carefully.An epidemiological study, such as the DOGRISK questionnaire, with a large study population can be useful for searching for associations between diseases, nutrition, and descriptive and environmental factors, but the validity and repeatability of the questionnaire must be tested before any conclusions can be drawn. This study validated and tested disease diagnoses and descriptive and environmental factors for reliability; comparing data against that of an official register showed excellent agreement and internal consistency of the questionnaire was very good. The test-retest repeatability was substantial in few questions but good in most of the questions. We propose that the descriptive variables and the disease variables be used as such to generate hypotheses from the DOGRISK data and that second answers be used if owners have answered twice. The food and diet-related questions will be validated in a separate article.


The setting for this study was the Pacific island nation of Vanuatu, an archipelago of 82 islands, located in the South Pacific Ocean. Our objective was to assess the knowledge, attitudes and practices of tuberculosis (TB) patients towards TB.a posteriori inductive categories to draw conclusions.This was a descriptive study using qualitative and quantitative methods. Quantitative analysis was based on the responses provided to closed questions, and we present frequencies to describe the TB patients’ knowledge, attitudes and practice relating to TB. Qualitative analysis was based on open questions permitting fuller explanations. We used thematic analysis and developed kastom” . Most (94%) did not attribute TB to a bacterial cause. However, almost all TB patients (89%) thought that TB was best treated at a hospital with antibiotics. Three quarters (74%) experienced stigma after their TB diagnosis.Thirty five TB patients were interviewed; 22 (63%) were male. They attributed TB to cigarettes, kava, alcohol, contaminated food, sharing eating utensils and “Seeking health care from a traditional healer was common; 54% of TB patients stated that they would first consult a traditional healer for any illness. When seeking a diagnosis for signs and symptoms of TB, 34% first consulted a traditional healer. Patients cited cost, distance and beliefs about TB causation as reasons for first consulting a traditional healer or going to the hospital. Of the TB patients who consulted a traditional healer first, there was an average of two weeks delay before they consulted the health service. In some cases, however, the delay was up to six years.The majority of the TB patients interviewed did not attribute TB to a bacterial cause. Consulting a traditional healer for health care, including while seeking a diagnosis for TB symptoms, was common and may have delayed diagnosis. People require better information about TB to correct commonly held misperceptions about the disease. Traditional healers could also be engaged with the national TB programme, in order to refer people with signs and symptoms of TB to the nearest health service. Tuberculosis (TB) is strongly linked to poverty, and a range of other social, environmental and biological determinants . In the The Pacific Islands region comprises 22 Pacific Island countries and territories with varying levels of income and development, and with different health systems. The highest rates of TB occur in Kiribati, Marshall Islands, Papua New Guinea and Tuvalu  by using the kava cups and sharing cigarettes.”   my food with a kastom leaf and this poison was inside my body, that’s why they can’t get it out of me.” kastom”:Two participants stated that bacteria in food were the cause of their disease. Beliefs about TB causation also extended to stress, overwork, not getting enough rest, hereditary causes and ““A person who usually practice[s] kastom rituals not following his regulations or rules of the specific kastom will be sick of TB.” kastom  to be the local beliefs about TB causation:A quarter  were not aware of local beliefs regarding TB causation but some considered smoking , food and eating utensils , kava and alcohol consumption  and “Yes, I have heard that belief sharing of food and eating utensils may also spread the disease. But things like chewing of kava make it more badly especially our preparation of kava on Tanna.” Just over half  of the participants thought that anyone could contract TB. Others thought that TB affected elderly people , children  and adults . Mothers, people who smoke, and people who work too hard were also considered at risk of developing TB by a few.Just over half were not aware of what might make TB worse , although five people (14%) mentioned that not taking their medicine as prescribed would worsen their disease:“The dangerous thing about TB is that if you don’t take your medication as instructed you could get sicker. This guy from Malakula, he ran away during his treatment, he felt better and decided to go home but he hadn’t finished his treatment. If you go home and feel worse then come back to the hospital for treatment, what will you say to the nurses?” Other factors thought to worsen TB disease were cold, poor nutrition, hard work, kava consumption and smoking.Nearly all of the participants  thought that TB was best treated in the hospital. Almost all participants  believed that TB was curable. When asked about the best treatment for TB, 31 (89%) concluded that western medicine was the best treatment and another four thought that concurrent western and traditional medicine would be the ideal treatment for TB:“I think prayer and the hospital [medicine] but kastom medicine cannot kill the TB bacteria, it can relieve cough but it can’t kill the TB bacteria.” “Western and kastom medicine can help cure TB.” Respondents said that the most harmful thing about TB was that it could kill  while other effects of TB considered harmful were transmissibility, the requirement for medication that must be taken continuously, and stigma. When asked if TB can kill, 31 (89%) said that they believed that it could kill or they had heard about someone who had died from TB.Twenty-six (74%) said that they felt that they were treated differently by other people after being diagnosed with TB, resulting in others avoiding or refusing to eat with them. The participants felt that people avoided them due to concerns about TB transmission. Almost half  said that TB treatment lessened the stigma, but 11 (31%) people said that TB-related stigma does not change:“Communities in Vanuatu are afraid of people who have TB. At first we didn’t have diabetes, AIDS and cancer, not even TB, but today they say TB is the most dangerous. People tend to avoid those who have TB because they are scared of catching TB. But if there is awareness about TB people will know and be proud that TB can be treated.” The participants were asked a range of questions about their general health-seeking behaviour. To put this into context they were also asked about their perception of the usual health-seeking practices in their community.Over half of the participants  reported that they would usually seek health care from a traditional healer when seeking medical care for any kind of illness, Table , and the“Like I said people don’t go to the hospital first, only when the traditional healer’s medicine is no longer helping that we think of referring to the hospital. They don’t usually go to the hospital first, only pray and leaf medicine.” “If what I have is a kastom sickness then I go to the traditional healer. But when it’s a hospital sickness, I go to the hospital for fever, cough, TB and some others as well.” When participants were asked about the health-seeking behaviour of people in their community they said that most people 21, 60%) would visit a traditional healer first, however 11 people thought that it would depend on the type of illness and the person’s individual circumstances “I go to a traditional healer because if I go to see him he’ll make me better but if it doesn’t work I’ll go to the hospital.” Many  did not answer questions on the cost of hospital and traditional treatment but 17 (49%) agreed that cost was a factor and many also talked about the distance they needed to travel to get to a hospital  and the convenience of seeing a traditional healer who is often close by:“Cost might be a reason because the hospital is far from where we are so to get transport to a hospital it’s 6000 Vatu [63USD] and when some can’t afford it they go to a traditional healer.” “…distance is too far and [it is] expensive to pay for transport and also paying the outpatient department fee.” However, others thought that a person’s belief about illness causation and cure rather than cost was the factor that determined where people first sought care when sick:“I don’t think that the hospital cost is high, it comes down to people’s beliefs, they believe that if they go to a traditional healer they’ll be cured when that doesn’t work, go well then they go to the hospital and realise that they should have gone to the hospital in the first place. It’s just a strong belief that they have.” short wind”  and their own pathways to a TB diagnosis. “Short wind” was most often interpreted by the participants as asthma, or sometimes influenza.Participants were asked a series of questions about “short wind”, almost half of the respondents said that a healer would not be consulted . Forty percent of respondents stated that people with “short wind” may self-refer to a hospital after they had tried “kastom” medicine when it had provided no relief from symptoms.When asked if people would consult a healer for “When seeking a diagnosis for signs and symptoms of TB, 20 (57%) first consulted the hospital and 12 (34%) a healer. The mean time between consulting a healer and the hospital was 1.9 weeks (or 13 days) for the 12 who first consulted a healer “…women would be given the leaf juice while the men chew the leaf.” Participants accurately described hospital treatment and felt for the most part that the treatment was working well. However, a minority of patients said that they thought the treatment was working slowly. One patient stated:“Yes, we drink medicine and [do] I think is it working slow or fast? The medicine works slow but in the end it will kill the TB bacteria.” In addition, it was clear that a small number of patients (i.e. five) had initially been provided with inappropriate treatment including oral rehydration solution, paracetamol, and antibiotics that are not effective in curing TB (i.e. amoxycillin).The impacts of TB were mainly physical in nature and related to the effects of TB symptoms, neglect of regular duties , isolation from family due to hospitalisation and the effects of TB related stigma:“The main problem I had with TB was that my lungs hurt and I had shortness of breath.” “When I was sick, I didn’t go to the nakamal, meetings and church because of my cough.” Participants were asked what they thought was most feared about TB. The fact that TB is a transmissible disease was something to fear, as was the stigma that relates to TB and the potentially fatal nature of TB:“People think that TB is dangerous because they fear that they may catch it and financially they wouldn’t be able to afford it.” “That people will be afraid of them, that people and families would not like them to sleep, share food and share spoons and forks and plates…That society, people and family will not accept him as a family [member] and friend anymore. That they will lose friends and will lose the support from their families.” Most participants were hopeful that their lives would improve once their TB was treated and cured. The participants noted that they would be able to resume their regular duties , reassess their workload to reduce the likelihood of overworking and experience an alleviation of their TB symptoms. In addition, many of the respondents stated that they would change behaviours by reducing their alcohol and kava intake, quitting cigarette and cannabis smoking, and modifying other behaviours that are perceived to be anti-social :“I know that my life will change now. I’m quitting kava, cigarettes and alcohol.” “I change from going to see different women, having sex all about, working so hard and stealing. Now I have stopped.” kastom”. These findings are consistent with studies from many African countries in which beliefs about TB causation include witchcraft, smoking, sharing eating utensils, and heavy labour [We attempted to better understand the knowledge, attitudes and behaviours of a group of TB patients in Vanuatu. The patients were aware of TB and other diseases in their communities and could describe their symptoms. They were generally not aware of the bacterial cause of TB and thought that TB could be caused by a range of factors including shared food and eating utensils, kava and alcohol, cigarettes, hereditary causes and “y labour ,10,43. Ay labour ,24,27,44y labour ,23,45,46Three quarters of our study patients experienced and were troubled by stigmatisation. Despite national and international efforts to lessen TB related stigma, patients described feelings of fear, shame and embarrassment when diagnosed with TB ,18,47,48Approximately one third of participants reported that they first consulted a traditional healer when seeking a TB diagnosis. In communities where there is a strong tradition of traditional healers and spiritual causation of illness, seeking health care from traditional healers is the norm. In studies of TB patients’ health-seeking behaviour in other low income countries, consultation with a traditional healer as the first point of TB care is commonly reported ,10,22. Ipikinini”), equating to USD 2.20 and USD 1.10 respectively (Current Gross Domestic Product is $3037 USD per capita) [In our study, some patients visited a traditional healer due to the lower cost of doing so or the geographical proximity of the healer. There are approximately 200 known traditional healers in Vanuatu  ; each vi capita) . The cos capita) ,46,51-53 capita) . Distanc capita) .Seeking care from the hospital and a healer concurrently was reported infrequently in our study. In other settings, however, seeking treatment from the hospital system and traditional healers is common ,19,54.The study used a convenience sample. Therefore, the findings may not be generalisable to all of Vanuatu. However, we gained insights into what TB patients believe about TB, in order to assess some of their knowledge about TB and better understand their self-reported health-seeking behaviours. Many of those interviewed had successfully completed TB treatment and therefore may have had a positive experience with western TB treatment. We were not able to interview people who were unable to access this treatment (people whose TB had never been diagnosed) or members of the general community. However, this study was complemented by a study on traditional healers to assess their knowledge, attitudes and self-reported behaviours towards TB. Bias may have been introduced by the type of interviewer chosen. All interviewers were TB nurses employed by the Ministry of Health, and participants may have wanted to please the TB nurses with their answers. However, it was explained that participation in this study would not affect TB treatment or the attitudes of the TB staff towards them, the response rate was very high and many reported contact with traditional healers. In addition, our findings were very similar to other studies, suggesting bias was not significant.This study highlights some of the challenges in delivering TB care in Vanuatu. The majority of TB patients interviewed did not attribute TB to a bacterial cause. Many patients experienced TB related stigma and frequently consulted a traditional healer. Long diagnostic delays were reported by almost a quarter of the patients. Improved education for communities about TB signs and symptoms and where to seek care for signs and symptoms of TB may reduce these delays. Engaging traditional healers may have the added benefit of strengthening the links between western and traditional medicine in Vanuatu and may be helpful for people with TB and other health conditions. Our study provides new evidence on TB knowledge and involvement of traditional healers in TB management in Vanuatu, which can potentially be used to enhance TB services and to better engage traditional healers in TB management.DHS: Demographic and health survey; KV: Kerri Viney; MT: Markleen Tagaro; NTP: National tuberculosis programme; PJ: Penelope Johnson; TB: Tuberculosis; USD: United States Dollars; WHO: World Health Organization.The authors declare that they have no competing interests.KV conceived and designed the study, analysed the data and drafted the first version of the paper. PJ designed the study, advised on data analysis and interpretation and drafted the manuscript. NNL assisted with the study design, provided input into data interpretation and revised the manuscript. MT conceived the concept of the study, assisted with the study design, co-ordinated data collection, and assisted with analysis and interpretation of the data, and revising the manuscript. SF collected data and assisted with data interpretation and revising the manuscript. AS provided advice on data analysis and interpretation and revised the manuscript. DH provided advice on data analysis and interpretation, and revised the manuscript. PK also provided advice on study design, assisted with the funding and ethics applications, provided advice on data analysis and interpretation and revised the manuscript. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2458/14/467/prepub