In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary (...) for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular (...) O/T as a standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed (...) niche in semantic annotation of large amounts of ncRNA biological and clinical data. (shrink)

There is no consensus yet on the definition of semantic information. This paper contributes to the current debate by criticising and revising the Standard Definition of semantic Information (SDI) as meaningful data, in favour of the Dretske‐Grice approach: meaningful and well‐formed data constitute semantic information only if they also qualify as contingently truthful. After a brief introduction, SDI is criticised for providing necessary but insufficient conditions for the definition of semantic information. SDI is incorrect (...) because truth‐values do not supervene on semantic information, and misinformation (that is, false semantic information) is not a type of semantic information, but pseudo‐information, that is not semantic information at all. This is shown by arguing that none of the reasons for interpreting misinformation as a type of semantic information is convincing, whilst there are compelling reasons to treat it as pseudo‐information. As a consequence, SDI is revised to include a necessary truth‐condition. The last section summarises the main results of the paper and indicates some interesting areas of application of the revised definition. (shrink)

This paper has three main goals. First, to motivate a puzzle about how ignorance-expressing terms like maybe and if interact: they iterate, and when they do they exhibit scopelessness. Second, to argue that there is an ambiguity in our theoretical toolbox, and that exposing that opens the door to a solution to the puzzle. And third, to explore the reach of that solution. Along the way, the paper highlights a number of pleasing properties of two elegant semantic theories, explores (...) some meta-theoretic properties of dynamic notions of meaning, dips its toe into some hazardous waters, and offers characterization theorems for the space of meanings an indicative conditional can have. (shrink)

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. (...) Such annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that will (...) support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications. (shrink)

There is no consensus yet on the definition of semantic information. This paper contributes to the current debate by criticising and revising the Standard Definition of semantic Information as meaningful data, in favour of the Dretske-Grice approach: meaningful and well-formed data constitute semantic information only if they also qualify as contingently truthful. After a brief introduction, SDI is criticised for providing necessary but insufficient conditions for the definition of semantic information. SDI is incorrect because (...) truth-values do not supervene on semantic information, and misinformation is not a tyoe of semantic information, but pseudo-information, that is not semantic information at all. This is shown by arguing that none of the reasons for interpreting misinformation as a type of semantic information is convincing, whilst there are compelling reasons to treat it as pseudo-information. As a consequence, SDI is revised to include a necessary truth-condition. The last section summarises the main results of the paper and indicates the important implications of the revised definition for the analysis of the deflationary theories of truth, the standard definition of knowledge and the classic, quantitative theory of semantic information. (shrink)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of (...) data sources, types, models, and modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential (...) in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)

What follows is a contribution to the horizontal integration of warfighter intelligence data as defined in Chairman of the Joint Chiefs of Staff Instruction J2 CJCSI 3340.02AL: -/- Horizontally integrating warfighter intelligence data improves the consumers’ production, analysis and dissemination capabilities. HI requires access (including discovery, search, retrieval, and display) to intelligence data among the warfighters and other producers and consumers via standardized services and architectures. These consumers include, but are not limited to, the combatant commands, Services, (...) Defense agencies, and the Intelligence Community. (shrink)

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of (...) intelligence data, and describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)

Tagging is the phenomenon in which regions of a picture, map, or diagram are annotated with words or other symbols, to provide descriptive information about a depicted object. The interpretive principles that govern tagged images are not well understood, due in part to the difficulty of integrating pictorial and linguistic semantic rules. Rather than directly combining these rules, I propose to use the framework of perspectival feature maps as an intermediary representation of content, in which the outputs of pictorial (...) and linguistic interpretation may be assimilated. The result is a simple and compositional semantics for tagged images. (shrink)

Our aim here is to lay the groundwork for formal tree-ring analysis combining data from dendrochronology with formal techniques from semantics. We will present the basic syntax of, and basic compositional semantics of tree-ring structures.

Expressivists about epistemic modals deny that ‘Jane might be late’ canonically serves to express the speaker’s acceptance of a certain propositional content. Instead, they hold that it expresses a lack of acceptance. Prominent expressivists embrace pragmatic expressivism: the doxastic property expressed by a declarative is not helpfully identified with that sentence’s compositional semantic value. Against this, we defend semantic expressivism about epistemic modals: the semantic value of a declarative from this domain is the property of doxastic attitudes (...) it canonically serves to express. In support, we synthesize data from the critical literature on expressivism—largely reflecting interactions between modals and disjunctions—and present a semantic expressivism that readily predicts the data. This contrasts with salient competitors, including: pragmatic expressivism based on domain semantics or dynamic semantics; semantic expressivism à la Moss [2015]; and the bounded relational semantics of Mandelkern [2019]. (shrink)

Disaster response is a highly collaborative and critical process that requires the involvement of multiple emergency responders (ERs), ideally working together under a unified command, to enable a rapid and effective operational response. Following the 9/11 and 11/13 terrorist attacks and the devastation of hurricanes Katrina and Rita, it is apparent that inadequate communication and a lack of interoperability among the ERs engaged on-site can adversely affect disaster response efforts. Within this context, we present a scenario-based terrorism case study to (...) highlight the challenges of operational disaster command and response. In this article, which is based on the French emergency response doctrine, we outline a semantics-based common operational command system that is designed to guarantee an efficient information flow among ERs. Our focus is on offering to all ERs, a real-time operational picture of the situation in order to enable multilevel coordination among firefighters, police, healthcare units, public authorities, and other stakeholders. Our approach consolidates information to promote timely sharing of data among ERs. The proposed system is based on an ontology that has been developed to represent the different types of knowledge on the part of ERs, providing a shared vocabulary that covers a variety of interoperability concerns. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system (...) is applied to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

Coreferentialism refers to the common assumption in the literature that slurs and descriptors are coreferential expressions with precisely the same extension. For instance, Vallee recently writes that “If S is an ethnic slur in language L, then there is a non-derogatory expression G in L such that G and S have the same extension”. The non-derogatory expression G is commonly considered the nonpejorative correlate of the slur expression S and it is widely thought that every S has a coreferring G (...) that possesses precisely the same extension. Yet here I argue against this widespread assumption by first briefly introducing what slurs are and then considering four sources of supporting evidence showing that slurs and descriptors are in fact not coreferential expressions with precisely the same extension. I argue that since slurs and descriptors differ in their extension they thereby differ in their meaning or content also. This article additionally introduces the notion of a conceptual anchor in order to adequately account for the relationship between slurs and descriptors actually evidenced in the empirical data, and further considers the inadequacy of common dictionary definitions of slurs. This article therefore contributes to the literature on slurs by demonstrating that previous accounts operating on the assumption that slurs and descriptors are coreferential expressions with the same extension, and that they thereby have the same meaning or content, are inconsistent with empirical data and that an alternative account in accord with Croom better fits the facts concerning their actual meaning and use. (shrink)

Semantic interoperability can be defined as the ability of two or more computer systems to exchange information in such a way that the meaning of that information can be automatically interpreted by the receiving system accurately enough to produce useful results to the end users of both systems. Several activities are currently being performed by a variety of stakeholders to achieve semantic interoperability in healthcare. Many of these activities are not beneficial, because they place too great a focus (...) on business aspects and not enough on involvement of the right sorts of researchers, in particular those that are able to see how the data and information relate to the entities of concern on the side of the patient. The lack of a central focus on the patient, and the associated focus on ‘concepts’, have spawned a variety of mutually incompatible terminologies exhibiting non-resolvable overlap. The predominance of the healthcare IT industry in the writing and selection of semantic interoperability standards mitigates against the benefits that standards, when well designed, can bring about. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In (...) our previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

The standard account of modal expressions in natural language analyzes them as quantifiers over a set of possible worlds determined by the evaluation world and an accessibility relation. A number of authors have recently argued for an alternative account according to which modals are analyzed as quantifying over a domain of possible worlds that is specified directly in the points of evaluation. But the new approach only handles the data motivating it if it is supplemented with a non-standard account (...) of attitude verbs and conditionals. It can be shown the the relational account handles the same data equally well if it too is supplemented with a non-standard account of such expressions. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in (...) the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The widely accepted two-dimensional circumplex model of emotions posits that most instances of human emotional experience can be understood within the two general dimensions of valence and activation. Currently, this model is facing some criticism, because complex emotions in particular are hard to define within only these two general dimensions. The present theory-driven study introduces an innovative analytical approach working in a way other than the conventional, two-dimensional paradigm. The main goal was to map and project semantic emotion space (...) in terms of mutual positions of various emotion prototypical categories. Participants (N = 187; 54.5% females) judged 16 discrete emotions in terms of valence, intensity, controllability and utility. The results revealed that these four dimensional input measures were uncorrelated. This implies that valence, intensity, controllability and utility represented clearly different qualities of discrete emotions in the judgments of the participants. Based on this data, we constructed a 3D hypercube-projection and compared it with various two-dimensional projections. This contrasting enabled us to detect several sources of bias when working with the traditional, two-dimensional analytical approach. Contrasting two-dimensional and three-dimensional projections revealed that the 2D models provided biased insights about how emotions are conceptually related to one another along multiple dimensions. The results of the present study point out the reductionist nature of the two-dimensional paradigm in the psychological theory of emotions and challenge the widely accepted circumplex model. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical (...) Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are (...) relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project (...) also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

We pose two arguments for the view that sentences containing definite descriptions semantically express multiple propositions: a general proposition as Russell suggested, and a singular proposition featuring the individual who uniquely satisfies the description at the world-time of utterance. One argument mirrors David Kaplan's arguments that indexicals express singular propositions through a context-sensitive character. The second argument mirrors Kent Bach's and Stephen Neale's arguments for pluralist views about terms putatively triggering conventional implicatures, appositive, and nonrestrictive relative clauses. After presenting these (...) arguments, we show that rival explanations (appeals to implicature, referential use, presupposition, etc.) do not offer equally compelling explanations of the data, and defend the methodology employed in the arguments against some criticisms. (shrink)

Despite the large number of studies conducted on polysemy, they mostly compare the different methods and techniques to learn a language and establish the extent to which particular sense relations facilitate the learning of second language vocabulary. To our best knowledge, no research has been conducted to determine whether or not polysemy is emphasized in non-native English textbooks. The objective of the present research was to determine the degree to which polysemy is incorporated in English textbooks. Thus, the research question (...) guiding the current study is: To what extent is polysemy incorporated in non-native English textbooks? The study is corpus-based research that used a data set of 500 words, i.e., 250 words from each of the two books, utilizing the Sketch Engine word list tool and concordance. The polysemy of the resulting words in the concordance lines generated was semantically annotated manually using WordNet and English dictionaries. The results indicated that polysemy is barely stressed in the textbooks under investigation. The study’s results have substantial implications for polysemy in particular and second or foreign language teaching in general. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

In this paper we investigate if sentences presented as the result of the application of statistical models and artificial intelligence to large volumes of data – the so-called ‘Big Data’ – can be characterized as semantically true, or as quasi-true, or even if such sentences can only be characterized as probably quasi-false and, in a certain way, post-true; that is, if, in the context of Big Data, the representation of a data domain can be configured as (...) a total structure, or as a partial structure provided with a set of sentences assumed to be true, or if such representation cannot be configured as a partial structure provided with a set of sentences assumed to be true. (shrink)

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common (...) understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

In recent decades, the analysis of phraseology has made use of the exploration of large corpora as a source of quantitative information about language. This paper intends to present the main lines of work in progress based on this empirical approach to linguistic analysis. In particular, we focus our attention on some problems relating to the morpho-syntactic annotation of corpora. The CORIS/CODIS corpus of contemporary written Italian, developed at CILTA – University of Bologna (Rossini Favretti 2000; Rossini Favretti, Tamburini, (...) De Santis in press), is a synchronic 100-million-word corpus and is being lemmatised and annotated with part-of-speech (POS) tags, in order to increase the quantity of information and improve data retrieval procedures (Tamburini 2000). The aim of POS tagging is to assign each lexical unit to the appropriate word class. Usually the set of tags is pre-established by the linguist, who uses his/her competence to identify the different word classes. The very first experiments we made revealed how the traditional part-of-speech distinctions in Italian (generally based on morphological and semantic criteria) are often inadequate to represent the syntactic features of words in context. It is worth noting that the uncertainties in categorisation contained in Italian grammars and dictionaries reflect a growing difficulty as they move from fundamental linguistic classes, such as nouns and verbs, to more complex classes, such as adverbs, pronouns, prepositions and conjunctions. This latter class, that groups together elements traditionally used to express connections between sentences, appears inadequate when describing cohesive relations in Italian. This phenomenon actually seems to involve other elements traditionally assigned to different classes, such as adverbs, pronouns and interjections. Recent studies proposed the class of ‘connectives’, grouping all words that, apart from their traditional word class, have the function of connecting phrases and contributing to textual cohesion. From this point of view, conjunctions can be considered as part of phrasal connectives, that can in turn be included in the wider category of textual connectives. The aim of this study is to identify elements that can be included in the class of phrasal connectives, using quantitative methods. According to Shannon and Weaver’s (1949) observation that words are linked by dependent probabilities, corroborated by Halliday’s (1991) argument that the grammatical “system” (in Firth’s sense of the term) is essentially probabilistic, quantitative data are introduced in order to provide evidence of relative frequencies. Section 2 presents a description of word-class categorisation from the point of view of grammars and dictionaries arguing that the traditional category of conjunctions is inadequate for capturing the notion of phrasal connective. Section 3 examines the notion of ‘connective’ and suggests a truth-function interpretation of connective behaviour. Section 4 describes the quantitative methods proposed for analysing the distributional properties of lexical units, and section 5 comments on the results obtained by applying such methods drawing some provisional conclusions. (shrink)

This doctoral thesis examines the phenomenon of Filipinization, specifically understood as the ideological construction of a “Filipino identity” or ‘Filipino subject-consciousness” within the highly determinate context provided by the Filipino ilustrado nationalists such as José Rizal, Marcelo H. del Pilar and their fellow propagandists inasmuch as it leads to the nineteenth (19th) century construction of the modern Philippine nation. Utilizing Jacques Derrida’s deconstructive thinking, this study undertakes a genealogical critique engaged on the concrete historical examination of what is meant by (...) the term “Filipino” across a select historical timeline (1864-1898) and the various notions of Filipino identity implied by the different contexts within which the term “Filipino” has been employed. More specifically, it undertakes a selective philosophical excavation of three seminal texts in the history of Filipinization, viz.: 1) the Manifiesto of Padre Jose Burgos; 2) the writings of the Filipino ilustrados in La Solidaridad; and 3) Jose Rizal’s Annotations on Dr. Antonio de Morga’s Sucesos de las Islas Filipinas. -/- The philosophical claim of this work is the idea that Filipinization, taken as the differential construction of Filipino identity, is the effective translation of the colonial epistemic violence of Eurocentric racism and its consequent “horror of absolutism” into the homo-hegemony of Filipino nationalisms. By fetishizing the notion of a carefully constructed and essential “Filipino-identity,” Filipinization and the current nationalist discourses that utilize them, unwittingly, stands complicit with the same colonial violence and hegemony that they wish to combat. This happens precisely when the very structures of colonial oppression, on the ideological and practical levels, are transmogrified into nationalist ideals that assume legal and political power unto themselves in a self-referential and self-legitimating fashion. -/- Three processes will demonstrate the above thesis: first, by examining historical texts and setting itself against established nationalist historiographies, a genealogical analysis of the term “Filipino” reveals it as a pliable signifier whose semantics have evolved through time. From its originary referent in the Spanish criollo (creole), it has come to refer to people who would have been otherwise entirely alien to this class, viz., the mestizos (both Spanish and Chinese), the principalia (native elite), and eventually, the lowland Catholicized natives themselves. The historical hermeneutic of this identity-discourse in Padre José Burgos’ Manifiesto yields the fact that what gives the term “Filipino” its semantic consistency as a class concept is its essential constitution as a Hispanic and Catholic identity. -/- Second, from this semantic identification of the term “Filipino” as a Hispano-Catholic identity, we proceed to clarify the meaning of Filipinization in terms of the nationalist propaganda carried out by the Filipino ilustrados in the fortnightly periodical La Solidaridad. Here, the specific ilustrado construction of Filipino identity as a Spanish citizen (ciudadano Español) is revealed precisely as a political and legal construct that served as the basis for their own politics of social inclusion/exclusion. Filipinization can only be applied to those who have been hispanized and Christianized and never to those tribes who have resisted and remained outside Spanish colonial authority. Filipinization is thus revealed as a process of Hispanization and Christianization whereby the recipients of Spanish colonial hegemony are transformed into the religiously docile bodies of the Spanish Empire. -/- From this highly determinate context, the study proceeds to examine Rizal’s ontological grounding of collective Filipino-ness in the mythological construction of the pre-hispanic past as the source of a unique Filipino ancestrality. In his work on de Morga’s Sucesos, what is revealed is a mythologization that grounds a native, essential Filipino identity within a past unscathed by the Spanish colonial experience. Such mythologization, however, can only be possible through an anachronistic nationalist interpretation of historical data. Here, Filipinization is revealed as an exclusive prerogative, a nationalist program by which Rizal and the ilustrado class can combat the evils and excesses of the Spanish colonial enterprise. Ironically, though, this same struggle for emancipation also became an instrument by which the ilustrado class can retain their unjustified position of power over those who belonged to the colonial underside, thus, securing the possibility of perpetuating their own ilustrado bourgeois class interests. -/- Such discursive complicity is the essence of the myth of Filipinization: it presents nationalist identity discourse as an anti-colonial enterprise while being underlined by an economy of motives designed to cater primarily to the exclusive interests of the elite and ilustrado class. Thus, instead of securing the genuine, inclusive emancipation of all colonial subjects and a more humane existence for the poor and suffering majority, ilustrado nationalism has, ironically, merely reinforced those operative structures of colonial discrimination and oppression when the ilustrados: 1) grounded their racial theory upon the very same discourse of Eurocentric superiority that they are precisely supposed to question and 2) claimed a patrimony over Filipinas as their exclusive sovereign inheritance. These two factors illustrate how the manifest transfer of power from the Spanish Empire to the Philippine sovereign nation (and later as a nation-state) illustrate how Filipinization merely has transmogrified the face of Spanish colonialism into its new, subtle, and worse form in Filipino nationalism. -/- In this vein, the existence of the 19th century modern Philippine nation merely masked and deferred the crisis that was supposed to transfer power from the Spanish Empire to the multitude of the poor and suffering native indio majority. This crisis became all the more difficult to address be-cause of the duplicitous character of the discourse of Filipinization itself. It has not only effectively transferred power into the hands of the nationalist elite but also captured authentic emancipatory discourse within the identity-trap against which it can only hope to get out. This study concludes with the claim about the impossibility of ever escaping and overcoming the epistemic and practical violence necessarily contained within the historical discourse of colonialism. Or simply, we have no language or discourse that would enable us to overcome the complicity of Filipinization with the very (epistemic) violence against which it has set itself. (shrink)

Recent discoveries of semantic compositionality in Japanese tits have enlivened the discussions on the presence of this phenomenon in wild animal communication. Data on semantic compositionality in wild apes are lacking, even though language experiments with captive apes have demonstrated they are capable of semantic compositionality. In this paper, I revisit the study by Boesch (Hum. Evol. 6:81–89, 1991) who investigated drumming sequences by an alpha male in a chimpanzee (_Pan troglodytes_) community in the Taï National (...) Park, Côte d’Ivoire. A reanalysis of the data reveals that the alpha male produced semantically compositional combined messages of travel direction change and resting period initiation. Unlike the Japanese tits, the elements of the compositional expression were not simply juxtaposed but displayed structural reduction, while one of the two elements in the expression coded the meanings of both elements. These processes show relative resemblance to blending and fusion in human languages. Also unlike the tits, the elements of the compositional expression did not have a fixed order, although there was a fixed distribution of drumming events across the trees used for drumming. Because the elements of the expression appear to carry verb-like meanings, the compositional expression also resembles simple verb-verb constructions and short paratactic combinations of two clauses found across languages. In conclusion, the reanalysis suggests that semantic compositionality and phenomena resembling paratactic combinations of two clauses might have been present in the communication of the last common ancestor of chimpanzees and humans, not necessarily in the vocal modality. (shrink)

Miriam Schoenfield argues that moral realism and moral vagueness imply ontic vagueness. In particular, she argues that neither shifty nor rigid semantic accounts of vagueness can provide a satisfactory explanation of moral vagueness for moral realists. This paper constitutes a response. I argue that Schoenfield's argument against the shifty semantic account presupposes that moral indeterminacies can, in fact, be resolved determinately by crunching through linguistic data. I provide different reasons for rejecting this assumption. Furthermore, I argue that (...) Schoenfield's rejection of the rigid semantic account is based on a presupposition that ultimately implies the very same claim that is under dispute: the vagueness of moral predicates in imperfect languages persists in the perfect language, as well. (shrink)

This chapter addresses two questions. First, if knowledge is accounted information, how are we supposed (to apply this analysis in order) to understand perceptual knowledge and knowledge by testimony? In the first part of the chapter, I articulate an answer in terms of a re-interpretation of perception and testimony as data providers rather than full-blown cases of knowledge. Second, if perception and testimony are correctly understood as data providers, how are we supposed (to apply this analysis in order) (...) to understand the semantic value of the data provided by such processes? In the second part of the chapter, I argue in favour of a constructionist hypothesis about how data may become meaningful for human cognitive agents through a process of repurposing of natural data/signals. The conclusion of the chapter is that human agents are natural-born data hackers. (shrink)

Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including (...) models such as archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards. (shrink)

The chapter outlines an abstract theoretical framework that is currently (re-)emerging in the course of a theoretical convergence of several disciplines. In the first section, the fundamental problem of perception theory is formulated, namely, the generation, by the perceptual system, of meaningful categories from physicogeometric energy patterns. In the second section, it deals with basic intuitions and assumptions underlying what can be regarded as the current Standard Model of Perceptual Psychology and points out why this model is profoundly inadequate for (...) dealing with the fundamental problem of perception theory. In the third section, it discusses a level of analysis that promises to be fruitful for dealing, in conformity with established procedures of the natural sciences, with the problem of perceptual “meaning” and the problem of what constitutes a “perceptual object.” In the fourth section, it outlines a theoretical perspective on basic principles of the perceptual system which centers on the notions of complex data types and conceptual forms, and draws an entirely different theoretical picture of the role of the sensory input than traditional accounts. The final section focusses on the issue of material qualities and discusses, within the general theoretical framework outlined, some observations and results on the perception of certain material properties, namely, lustrous and glassy appearances. (shrink)

Double negations are easily recognised in both the so-called “negative literature” and the original texts of some important scientific theories. Often they are not equivalent to the corresponding affirmative propositions. In the case the law of double negation fails they belong to non-classical logic, as first, intuitionist logic. Through a comparative analysis of the theories including them the main features of a new kind of theoretical organization governed by intuitionist logic are obtained. Its arguing proceeds through doubly negated propositions and (...) ad absurdum arguments. Then, the final doubly negated predicate is translated in the corresponding affirmative one, from which all the consequences are deduced in order to test them against reality. According to this model the true formalization of intuitionist logic is Kolmogorov’s 1932 paper. The above analysis also shows that modal words play an auxiliary or substitutive role to intuitionist propositions. In addition, it is shown that Vasiliev’s paraconsistent logic is represented through doubly negated propositions. By means of these three kinds of logic one can attribute a specific kind of logic to each of the three distinct steps of the process of building a scientific theory from the experimental data to its final theoretical system. It is also shown that the definition of negation is of a structural kind, rather than of an objective kind or a subjective kind: it has to be referred to the organization of the theory to which it belongs. (shrink)

Progress in philosophy is difficult to achieve because our methods are evidentially and rhetorically weak. In the last two decades, experimental philosophers have begun to employ the methods of the social sciences to address philosophical questions. However, the adequacy of these methods has been called into question by repeated failures of replication. Experimental philosophers need to incorporate more robust methods to achieve a multi-modal perspective. In this chapter, we describe and showcase cutting-edge methods for data-mining and visualization. Big (...) class='Hi'>data is a useful investigatory tool for moral psychology, and it fits well with the Ramsification method the first author advances in a series of recent papers. The guiding insight of these papers is that we can infer the meaning and structure of concepts from patterns of assertions and inferential associations in natural language. (shrink)

Health Level 7 (HL7) is an international standards development organisation in the domain of healthcare information technology. Initially the mission of HL7 was to enable data exchange via the creation of syntactic standards which supported point-to-point messaging. Currently HL7 sees its mission as one of creating standards for semantic interoperability in healthcare IT on the basis of its flagship “version 3” (v3). Unfortunately, v3 has been plagued by quality and consistency issues, and it has not been able to (...) keep pace with recent developments either in semantics and ontology or in computer science and engineering. HL7’s response has been to develop its “Services-Aware Interoperability Framework” (SAIF), which is intended to provide a foundation for work on all aspects of standardization in HL7 henceforth. We here summarise the major design principles that must be satisfied by a semantic interoperability framework – principles relating both to static semantics and to computational behaviour. We then assess the SAIF in light of these principles. We conclude that the SAIF is not in a position to support the needed reform of the HL7 v3 family of standards. (shrink)

The phenomenon of abbreviation used on Instagram is an interesting thing since the users modify the abbreviation form of expansion words making deviation from the original meaning. The principle of meaning relation between abbreviations and their expansions is used to make a change to the purposes of Instagram users. This research was aimed to describe the principle of abbreviation used in Instagram. An exploitation method was used by the technique of making screenshots and recording the abbreviation data. The results (...) of research indicate that the principle of abbreviation consists of three forms namely inclusion, contact, and complementary. The results of this research can be very effective in understanding as well as how to use abbreviations, especially on Instagram. The Novelty of the study is in investigating the abbreviation used in Instagram. (shrink)

Arguments from disagreement often take centre stage in debates between competing semantic theories. This paper explores the theoretical basis for arguments from disagreement and, in so doing, proposes methodological principles which allow us to distinguish between legitimate arguments from disagreement and dialectically ineffective arguments from disagreement. In the light of these principles, I evaluate Cappelen and Hawthorne's [2009] argument from disagreement against relativism, and show that it fails to undermine relativism since it is dialectically ineffective. Nevertheless, I argue that (...) an alternative challenge to relativism based on disagreement is available. More generally, I argue that semantic theory is not answerable to data stemming from ‘loaded’ philosophical principles regarding the nature of disagreement. Rather, semantic theorists will exhaust their dialectical responsibilities regarding disagreement if they can demonstrate consistency with a minimal account of the concept. (shrink)

Although the view that sees proper names as referential singular terms is widely considered orthodoxy, there is a growing popularity to the view that proper names are predicates. This is partly because the orthodoxy faces two anomalies that Predicativism can solve: on the one hand, proper names can have multiple bearers. But multiple bearerhood is a problem to the idea that proper names have just one individual as referent. On the other hand, as Burge noted, proper names can have predicative (...) uses. But the view that proper names are singular terms arguably does not have the resources to deal with Burge’s cases. In this paper I argue that the Predicate View of proper names is mistaken. I first argue against the syntactic evidence used to support the view and against the predicativist’s methodology of inferring a semantic account for proper names based on incomplete syntactic data. I also show that Predicativism can neither explain the behaviour of proper names in full generality, nor claim the fundamentality of predicative names. In developing my own view, however, I accept the insight that proper names in some sense express generality. Hence I propose that proper names—albeit fundamentally singular referential terms—express generality in two senses. First, by being used as predicates, since then they are true of many individuals; and second, by being referentially related to many individuals. I respond to the problem of multiple bearerhood by proposing that proper names are polyreferential, and also explain the behaviour of proper names in light of the wider phenomenon I called category change, and show how Polyreferentialism can account for all uses of proper names. (shrink)

The Galilean explanatory style is characterized by the search for the underlying structure of phenomena, the positing of "deep" explanatory principles, and a view of the relation between theory and data, on which the search for "crucial data" is of primary importance. In this paper, I trace the dynamics of adopting the Galilean style, focusing on the science of episodic memory. I argue that memory systems, such as episodic and semantic memory, were posited as underlying competences producing (...) the observable phenomena of memory. Considered in idealized isolation from other systems, episodic memory was taken to underlay the ability of individuals to remember events from their personal past. Yet, in reality, memory systems regularly interact, standing in many-to-many relations to actual memory tasks and experiences. Upon this backdrop, I explore a puzzle about the increasing prominence of the notion of autonoetic consciousness in Tulving's theory of episodic memory. I argue that, contrary to widespread belief, the prominence is not best explained by the purported essential link between autonoetic consciousness and episodic memory. Rather, it is explained by the fact that autonoetic consciousness, hypothesized to uniquely accompany episodic retrieval, was considered a source of crucial data, predictable only from theories positing a functionally distinct episodic memory system. However, with the emergence of a new generation of theories, positing wider memory systems for remembering and imagination, the question of the relation between episodic memory and autonoetic consciousness has been reopened. This creates a pressing need for de-idealization, triggering a new search for crucial data. (shrink)

The orbital debris problem presents an opportunity for inter-agency and international cooperation toward the mutually beneficial goals of debris prevention, mitigation, remediation, and improved space situational awareness (SSA). Achieving these goals requires sharing orbital debris and other SSA data. Toward this, I present an ontological architecture for the orbital debris and broader SSA domain, taking steps in the creation of an orbital debris ontology (ODO). The purpose of this ontological system is to (I) represent general orbital debris and SSA (...) domain knowledge, (II) structure, and standardize where needed, orbital data and terminology, and (III) foster semantic interoperability and data-sharing. In doing so I hope to (IV) contribute to solving the orbital debris problem, improving peaceful global SSA, and ensuring safe space travel for future generations. (shrink)

Quantification, Negation, and Focus: Challenges at the Conceptual-Intentional Semantic Interface Tista Bagchi National Institute of Science, Technology, and Development Studies (NISTADS) and the University of Delhi Since the proposal of Logical Form (LF) was put forward by Robert May in his 1977 MIT doctoral dissertation and was subsequently adopted into the overall architecture of language as conceived under Government-Binding Theory (Chomsky 1981), there has been a steady research effort to determine the nature of LF in language in light of (...) structurally diverse languages around the world, which has ultimately contributed to the reinterpretation of LF as a Conceptual-Intentional (C-I) interface level between the computational syntactic component of the faculty of language and one or more interpretive faculties of the human mind. While this has opened up further possibilities of research in phenomena such as quantifier scope and scope interactions between negation, quantification, and focus, it has also given rise to a few real challenges to linguistic theory as well. Some of these are: (i) the split between lexical meaning – a matter supposedly belonging to the phase-wise selection of lexical arrays – and issues of semantic interpretation that arise purely from binding and scope phenomena (Mukherji 2010); (ii) partially relatedly, the level at which theta role assignment can be argued to take place, an issue that is taken up by me in Bagchi (2007); and (iii) how supposedly “pure” scopal phenomena relating to quantifiers, negation, and emphasizing expressions such as only and even (comparable to, e.g., Urdu/Hindi hii and bhii, Bangla –i and –o) also have dimensions of both focus and discourse reference. While recognizing all of these challenges, this talk aims to highlight particularly challenge (iii), both in terms of scholarship in the past and for the rich prospects for research on languages of south Asia with the semantics of quantification, negation, and focus in view. The scholarship of the past that I seek to relate this issue to is where, parallel to (and largely independently of) the research on LF that had been happening, Barwise and Cooper were developing their influential view of noun phrases as generalized quantifiers, culminating in their key 1981 article “Generalized Quantifiers and Natural Language” while, independently, McCawley, in his 1981 book Everything that Linguists have Always Wanted to Know about Logic, established through argumentation that all noun phrases semantically behave like generalized quantified expressions (further elaborated by him in the second – 1994 – revised edition of his book). I seek to demonstrate, based on limited data analysis from selected languages of south Asia, that our current understanding of quantification, negation, and focus under the Minimalist view owes something significant to the two major, but now largely marginalized, works of scholarship, and that for the way forward it is essential to adopt a more formal-semantic approach as adopted by them and also by later works such as Denis Bouchard’s (1995) The Semantics of Syntax, Mats Rooth’s work on focus (e.g., Rooth 1996, “Focus” in Shalom Lappin’s Handbook of Contemporary Semantic Theory), Heim and Kratzer’s Semantics in Generative Grammar (1998), and Yoad Winter’s (2002) Linguistic Inquiry article on semantic number, to cite just a few instances. (shrink)

Shared conceptualization, in the sense we take it here, is as recent a notion as the Semantic Web, but its relevance for a large variety of fields requires efficient methods of extraction and representation for both quantitative and qualitative data. This notion is particularly relevant for the investigation into, and construction of, semantic structures such as knowledge bases and taxonomies, but given the required large, often inaccurate, corpora available for search we can get only approximations. We see (...) fuzzy description logic as an adequate medium for the representation of human semantic knowledge and propose a means to couple it with fuzzy semantic networks via the propositional Łukasiewicz fuzzy logic such that these suffice for decidability for queries over a semantic-knowledge base such as “to what degree of sharedness does it entail the instantiation C(a) for some concept C” or “what are the roles R that connect the individuals a and b to degree of sharedness ε.” . (shrink)

Lexical semantics has a problem. As Allesandro Lenci put it, the problem is that it cannot distinguish semantic from non-semantic relationships within its data. (2008, 2014). The data it relies on are patterns of co-occurrence of lexemes within linguistic corpora. But patterns of co-occurrence can reflect either our knowledge of what the world is like or our knowledge of what words mean -- matters of fact or matters of meaning. -/- In this essay, I develop a (...) semantic theory which draws this distinction in a way which makes it discernible in lexical semantics and cognitive science research. In doing so, this theory unifies truth-functional and structuralist approaches to semantics, and provides an integrated explanation of meaning and reference. -/- I base this semantic theory on linguistic dispositions to pair words with words, and to pair words with things, both based on learned patterns of association. These dispositions manifest themselves in verbal behavior, and (in Part 2) I propose a new neurophysical model to account for these dispositions which underlie both the intensional and extensional patterns in that behavior. (shrink)