Applications of Natural Language Processing in Biodiversity Science

Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if biology is to transform into a data-driven science. A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP) and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters), but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science

Emerging semantics to link phenotype and environment

abstract: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.The final version of this article, as published in PeerJ, can be viewed online at: https://peerj.com/articles/1470

Knowledge Organization Systems (KOS) in the Semantic Web: A Multi-Dimensional Review

Since the Simple Knowledge Organization System (SKOS) specification and its SKOS eXtension for Labels (SKOS-XL) became formal W3C recommendations in 2009 a significant number of conventional knowledge organization systems (KOS) (including thesauri, classification schemes, name authorities, and lists of codes and terms, produced before the arrival of the ontology-wave) have made their journeys to join the Semantic Web mainstream. This paper uses "LOD KOS" as an umbrella term to refer to all of the value vocabularies and lightweight ontologies within the Semantic Web framework. The paper provides an overview of what the LOD KOS movement has brought to various communities and users. These are not limited to the colonies of the value vocabulary constructors and providers, nor the catalogers and indexers who have a long history of applying the vocabularies to their products. The LOD dataset producers and LOD service providers, the information architects and interface designers, and researchers in sciences and humanities, are also direct beneficiaries of LOD KOS. The paper examines a set of the collected cases (experimental or in real applications) and aims to find the usages of LOD KOS in order to share the practices and ideas among communities and users. Through the viewpoints of a number of different user groups, the functions of LOD KOS are examined from multiple dimensions. This paper focuses on the LOD dataset producers, vocabulary producers, and researchers (as end-users of KOS).Comment: 31 pages, 12 figures, accepted paper in International Journal on Digital Librarie

Mental evolution: a review of Daniel Dennett’s From Bacteria to Bach and Back

From Bacteria To Bach and Back is an ambitious book that attempts to integrate a theory about the evolution of the human mind with another theory about the evolution of human culture. It is advertised as a defense of memes, but conceptualizes memes more liberally than has been done before. It is also advertised as a defense of the proposal that natural selection operates on culture, but conceptualizes natural selection as a process in which nearly all interesting parameters are free to vary. This liberal conception of key concepts creates space for philosophical innovation, but occasionally makes the empirical content of the theory difficult to pin down. Nevertheless, the book is full of scientific insight, wit, and humor. It will undoubtedly become a cause of both controversy and inspiration for those interested in naturalistic theories of human culture

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

The Plurality of Daily Digital Health: The Emergence of a New Form of Health Coordination

This article presents the current datafication processes in the field of health as a new form of health coordination. Methodologically, the conceptual foundation of the article is embedded in neopragmatist thinking and mainly informed by the "economics of convention" (EC). At the beginning, it is made clear that the datafication processes in the health system and in people's everyday lives are primarily a future vision that has high hopes for improving and controlling health. The aim of the article is to analyze the current effects of these mobilization processes and to show that with datafication processes, a new coordination mode of a digital daily health is introduced. To this end, the new form of digital daily health is being introduced. For this purpose, its characteristics are described and its relevance for coordination processes is shown. After that, the intersection between the new form of digital daily health and individual health will be analyzed. Finally, the consequences of this new health coordination form will be shown on an individual level as well as on the level of political economy of health

The Role of Consciousness in Memory

Conscious events interact with memory systems in learning, rehearsal and retrieval (Ebbinghaus 1885/1964; Tulving 1985). Here we present hypotheses that arise from the IDA computional model (Franklin, Kelemen and McCauley 1998; Franklin 2001b) of global workspace theory (Baars 1988, 2002). Our primary tool for this exploration is a flexible cognitive cycle employed by the IDA computational model and hypothesized to be a basic element of human cognitive processing. Since cognitive cycles are hypothesized to occur five to ten times a second and include interaction between conscious contents and several of the memory systems, they provide the means for an exceptionally fine-grained analysis of various cognitive tasks. We apply this tool to the small effect size of subliminal learning compared to supraliminal learning, to process dissociation, to implicit learning, to recognition vs. recall, and to the availability heuristic in recall. The IDA model elucidates the role of consciousness in the updating of perceptual memory, transient episodic memory, and procedural memory. In most cases, memory is hypothesized to interact with conscious events for its normal functioning. The methodology of the paper is unusual in that the hypotheses and explanations presented are derived from an empirically based, but broad and qualitative computational model of human cognition

Aerospace Medicine and Biology: A continuing supplement 180, May 1978

This special bibliography lists 201 reports, articles, and other documents introduced into the NASA scientific and technical information system in April 1978

Interactions between visual and semantic processing during object recognition revealed by modulatory effects of age of acquisition

The age of acquisition (AoA) of objects and their names is a powerful determinant of processing speed in adulthood, with early-acquired objects being recognized and named faster than late-acquired objects. Previous research using fMRI (Ellis et al., 2006. Traces of vocabulary acquisition in the brain: evidence from covert object naming. NeuroImage 33, 958–968) found that AoA modulated the strength of BOLD responses in both occipital and left anterior temporal cortex during object naming. We used magnetoencephalography (MEG) to explore in more detail the nature of the influence of AoA on activity in those two regions. Covert object naming recruited a network within the left hemisphere that is familiar from previous research, including visual, left occipito-temporal, anterior temporal and inferior frontal regions. Region of interest (ROI) analyses found that occipital cortex generated a rapid evoked response (~ 75–200 ms at 0–40 Hz) that peaked at 95 ms but was not modulated by AoA. That response was followed by a complex of later occipital responses that extended from ~ 300 to 850 ms and were stronger to early- than late-acquired items from ~ 325 to 675 ms at 10–20 Hz in the induced rather than the evoked component. Left anterior temporal cortex showed an evoked response that occurred significantly later than the first occipital response (~ 100–400 ms at 0–10 Hz with a peak at 191 ms) and was stronger to early- than late-acquired items from ~ 100 to 300 ms at 2–12 Hz. A later anterior temporal response from ~ 550 to 1050 ms at 5–20 Hz was not modulated by AoA. The results indicate that the initial analysis of object forms in visual cortex is not influenced by AoA. A fastforward sweep of activation from occipital and left anterior temporal cortex then results in stronger activation of semantic representations for early- than late-acquired objects. Top-down re-activation of occipital cortex by semantic representations is then greater for early than late acquired objects resulting in delayed modulation of the visual response