ARTICLE | doi:10.20944/preprints202003.0383.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: ontology; disability; Semantic Web
Online: 30 March 2020 (07:21:42 CEST)
At least 15% of the population in the world has some type of disability. Unfortunately, this population has the problem of facing various accessibility barriers, to which technological barriers are also added. One of the most relevant obstacles is the one that arises as a result of the development of the technology itself when using the Information and Communication Technologies (ICT). Therefore, the objective of this article is to review the main uses of the Semantic Web tools and to group them together in order to be able to propose the design and construction of more personalized and flexible systems, which allows to help people with disabilities to perform some type of activity using ICT, in this way, knowledge can be modeled in different domains related to people who have some type of disability, using ontologies, and some ontological models can be reused for various types of disability depending on the case study. The usefulness of this study is to reveal that with the models presented, it is possible to construct a Meta ontology that includes some or all areas of disability.
ARTICLE | doi:10.20944/preprints202201.0254.v1
Subject: Biology, Anatomy & Morphology Keywords: Morphology; insects; biodiversity research; ontology development
Online: 18 January 2022 (11:49:54 CET)
The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the last 250 years, research on insect systematics has generated hundreds of terms for naming and comparing those phenotypes. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Insect Anatomical Structures (MoDIAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of insect phenotypes. We applied the MoDIAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multi-species anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to (1) use controlled vocabularies and create semi-automated computer-parsable insect morphological descriptions; (2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and (3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This system will allow for clear and semantically interoperable integration of insect phenotypes in biodiversity studies.
ARTICLE | doi:10.20944/preprints201903.0205.v3
Subject: Materials Science, General Materials Science Keywords: characterisation; materials; ontology; data; metadata; nanoindentation
Online: 12 April 2019 (20:48:02 CEST)
This paper describes a novel methodology of data management in materials characterisation, which has as starting point the creation and usage of Data Management Plan (DMP) for scientific data in the field of materials science and engineering, followed by the development and exploitation of ontologies for the harnessing of data created through experimental techniques. The case study that is discussed here is nanoindentation, a widely used method for the determination and/or modelling of mechanical properties on a small scale.The same methodology can be applicable to a large number of techniques that produce big amount of raw data, while at the same time it can be invaluable tool for big data analysis and for the creation of an open innovation environment, where data can be accessed freely and efficiently.Aspects covered include the taxonomy and curation of data, the creation of ontology and classification about characterization techniques, the harnessing of data in open innovation environments via database construction along with the retrieval of information via algorithms. The issues of harmonization and standardization of such novel approaches are also critically discussed.Finally, the possible implications for nanomaterial design and the potential industrial impact of the new approach are described and a critical outlook is given.
ARTICLE | doi:10.20944/preprints202208.0305.v1
Subject: Medicine & Pharmacology, Allergology Keywords: drug repurposing; combination therapeutics; PubMed; ChEBI; disease ontology; gene ontology; drug interaction; MeSH terms; COVID-19
Online: 17 August 2022 (05:51:53 CEST)
This paper presents a computational approach designed to construct and query a literature-based knowledge graph for predicting novel drug therapeutics. The main objective is to offer a platform that discovers drug combinations from FDA-approved drugs and accelerates their investigations by domain scientists. Specifically, the paper introduced the following algorithms: (1) an algorithm for constructing the knowledge graph from drug, gene, and disease mentions in the biomedical literature; (2) an algorithm for vetting the knowledge graph from drug combinations that may pose a risk of drug interaction; (3) and two querying algorithms for searching the knowledge graph by a single drug or a combination of drugs. The resulting knowledge graph had 844 drugs, 306 gene/protein features, and 19 disease mentions. The original number of drug combinations generated was 2,001. We queried the knowledge graph to eliminate noise generated from chemicals that are not drugs. This step resulted in 614 drug combinations. When vetting the knowledge graph to eliminate the potentially risky drug combinations, it resulted in predicting 200 combinations. Our domain expert manually eliminated extra 54 combinations which left only 146 combination candidates. Our three-layered knowledge graph, empowered by our algorithms, offered a tool that predicted drug combination therapeutics for scientists who can further investigate from the viewpoint of drug targets and side effects.
Subject: Biology, Other Keywords: Gene expression; Gene Ontology; Enrichment analysis; Transcriptomics
Online: 2 April 2020 (11:51:32 CEST)
Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome data with respect to their fold changes. FSEA identifies GO terms, which are shared by the group of genes with a similar magnitude of response, and assesses these changes. GO terms found by FSEA are fold-change-specifically (e.g. weakly, moderately or strongly) affected by a stimulus under investigation. We demonstrate that many responses to abiotic factors, mutations, treatments and diseases occur in a fold-change-specific manner. FSEA analyses suggest that there are two prevailing responses of functionally-related gene groups, either weak or strong. Notably, some of the fold-change-specific GO terms are invisible by classical algorithms for functional gene enrichment, SEA and GSEA. These are GO terms not enriched compared to the genome background but strictly regulated by a factor within specific fold-change intervals. FSEA analysis of a cancer-related transcriptome suggested that the gene groups with a tightly coordinated response can be the valuable source to search for possible regulators, markers and therapeutic targets in oncogenic processes. Availability and Implementation: FSEA is implemented as the FoldGO Bioconductor R package and a web-server https://webfsgor.sysbio.cytogen.ru/ .
ARTICLE | doi:10.20944/preprints201802.0001.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: domain ontology; semantic analysis; linguistics, text resources
Online: 1 February 2018 (03:08:47 CET)
Ontology is a formalized representation of the problem area (PrA). Representation of the PrA in the form of an domain ontology is often used in the process of development of intelligent software systems and used as a knowledge base. The process of building an ontology is complex and requires an expert in the PrA. A large number of researchers are working to solve this problem. The basis of our approach is the use of a pipeline of different linguistic methods of text analysis. The set of rules developed by us is used to build an ontology based on the content analysis of a text resource. This article describes the method of building a domain ontology based on the linguistic analysis of content of text resources, presents an example of the proposed approach, and also presents the architecture of our pipeline.
ARTICLE | doi:10.20944/preprints202107.0516.v1
Subject: Physical Sciences, Acoustics Keywords: proper time; non-locality; simultaneity; wavefunction; measurement; ontology
Online: 22 July 2021 (12:09:46 CEST)
All the arguments of a wavefunction are defined at the same instant implying a notion of simultaneity. In a somewhat related matter, certain phenomena in quantum mechanics seem to have non-local causal relations. Both concepts are in contradiction with special relativity. We propose to define the wavefunction with respect to the invariant proper time of special relativity instead of standard time. Moreover, we shall adopt the original idea of Schrodinger suggesting that the wavefunction represents an ontological cloud-like object that we shall call ‘individual fabric’ that has a finite density amplitude vanishing at infinity. Consequently, measurement can be assimilated to a confining potential that triggers an inherent non-local mechanism within the individual fabric. It is formalised by multiplying the wavefunction with a localising gaussian as in the GRW theory but in a deterministic manner.
ARTICLE | doi:10.20944/preprints202005.0171.v2
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: COVID-19; coronavirus; case-based reasoning; ontology; natural language processing
Online: 15 June 2020 (11:16:23 CEST)
Coronavirus, also known as COVID-19, has been declared a pandemic by the World Health Organization (WHO). At the time of conducting this study, it had recorded over 1.6 million cases while more than 105,000 have died due to it, with these figures rising on a daily basis across the globe. The burden of this highly contagious respiratory disease is that it presents itself in both symptomatic and asymptomatic patterns in those already infected, thereby leading to an exponential rise in the number of contractions of the disease and fatalities. It is therefore crucial to expedite the process of early detection and diagnosis of the disease across the world. The case-based reasoning (CBR) model is an effective paradigm that allows for the utilization of cases’ specific knowledge previously experienced, concrete problem situations or specific patient cases for solving new cases. This study therefore aims to leverage the very rich database of cases of COVID-19 to solve new cases. The approach adopted in this study employs the use of an improved CBR model for state-of-the-art reasoning task in classification of suspected cases of Covid19. The CBR model leverages on a novel feature selection and semantic-based mathematical model proposed in this study for case similarity computation. An initial population of the archive was achieved with 68 cases obtained from the Italian Society of Medical and Interventional Radiology (SIRM) repository. Results obtained revealed that the proposed approach in this study successfully classified suspected cases into their categories at an accuracy of 97.10%. The study found that the proposed model can support physicians to easily diagnose suspected cases of Covid19 base on their medical records without subjecting the specimen to laboratory test. As a result, there will be a global minimization of contagion rate occasioned by slow testing and as well reduce false positive rates of diagnosed cases as observed in some parts of the globe.
ARTICLE | doi:10.20944/preprints201904.0248.v1
Online: 22 April 2019 (11:58:35 CEST)
The will and intellect have been debated philosophically without resolution for centuries. It is for this reason that this article considers doctrines of the will and intellect of two 17th-century rationalist philosophers, Rene Descartes, and Baruch Spinoza, both of whom were chosen as the focus for analysis because of their prominence and contrasting views. Our objective was to critique the doctrine of the will and intellect to develop an alternate theory that expounds on their previous work. A qualitative exploration was undertaken that compared their respective belief systems of Dualism and Monism. Despite the strengths of their arguments, an analysis of Part V of Spinoza’s Ethics and Discourse on Method and Meditations on First Philosophy by Descartes led the author to determine that both were partially correct in their positions yet consistent with one another. From this conclusion and building upon their work, this article presents the synthesis of the author’s alternate theory regarding the qualitative characteristics of both the will and intellect. An ontological argument against the existence of infinite entities as a corollary with the implication that neither the will, intellect, nor God can be infinite. While the limitation of the conclusions drawn is that they are dependent on the author’s philosophical framework, the originality of this paper is based on the author’s synthesis of one coherent theory from two philosophers espousing contrasting theistic systems and should serve as the foundation for future exploration and debate.
ARTICLE | doi:10.20944/preprints201808.0554.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: intelligent service robot; robotic context query; context ontology
Online: 31 August 2018 (16:12:54 CEST)
Service robots operating in indoor environments should recognize dynamic changes from sensors, such as RGB-D camera, and recall the past context. Therefore, we propose a context query-processing framework, comprising spatio-temporal robotic context query language (ST-RCQL) and spatio-temporal robotic context query-processing system (ST-RCQP), for service robots. We designed them based on the spatio-temporal context ontology. ST-RCQL can query not only the current context knowledge but also the past. In addition, ST-RCQL includes a variety of time operators and time constants, and thus queries can be written very efficiently. The ST-RCQP is a query-processing system equipped with a perception handler, working memory, and backward reasoner for real-time query-processing. Moreover, ST-RCQP accelerates query-processing speed by building a spatio-temporal index in the working memory, where percepts are stored. Through various qualitative and quantitative experiments, we demonstrate the high efficiency and performance of the proposed context query-processing framework.
ARTICLE | doi:10.20944/preprints202111.0107.v1
Subject: Life Sciences, Molecular Biology Keywords: Glycan structure; Knowledge representation; Pattern recognition; Ontology; Semantic web
Online: 5 November 2021 (08:34:05 CET)
The level of ambiguity in describing glycan structure has significantly increased with the upsurge of large scale glycomics and glycoproteomics experiments. Consequently, an ontology-based model appears as an appropriate solution for navigating this data. However, navigation is not sufficient and the model should also enable advanced search and comparison. A new ontology with a tree logical structure is introduced to represent glycan structures irrespective of the precision of molecular details. The model heavily relies on the GlycoCT encoding of glycan structures. Its implementation in the GlySTreeM knowledge base was validated with GlyConnect data and benchmarked with the Glycowork library. GlySTreeM is shown to be fast, consistent, reliable and more flexible than existing solutions for matching parts of or whole glycan structures. The model is also well suited to painless future expansion. Availability:https://glyconnect.expasy.org/glystreem/wiki
ARTICLE | doi:10.20944/preprints202108.0101.v1
Subject: Social Sciences, Accounting Keywords: intelligent city; smart city; smart ecosystem; ontology; city smartness
Online: 4 August 2021 (08:38:31 CEST)
The paper is a follow-up of a previous investigation and effort to develop the ontology of the smart city (Komninos, N., Bratsas, C., Kakderi, C., and Tsarchopoulos, P. "Smart city ontologies: Improving the effectiveness of smart city applications". Journal of Smart Cities, vol. 1(1), 1-17. https://www.komninos.eu/wp-content/uploads/2015/07/2015-Smart-City-Ontologies-Published.pdf). Since the publication of this article in 2015, research and literature on smart cities have evolved significantly, as have the technologies for digital spaces and applications that support city functions. These developments are reflected in the present form of the smart city ontology 2.0 we propose. It depicts the building blocks of the smart city ontology (technologies, structure, function, planning), and the object properties and data properties that connect structural blocks and classes. The aim of the SCO 2.0 is to provide a better understanding and description of the smart/intelligent city landscape; identify the main components and processes, the terms used to describe them, their definition and meaning; clarify key processes related to the integration of the different dimensions of the smart city, mainly the physical, social, and digital dimensions. The paper is accompanied by an owl file, developing the ontology through the editor Protégé.
Subject: Life Sciences, Other Keywords: hearing impairment; hearing loss; ontology; data harmonization; meta-analysis
Online: 19 September 2019 (11:37:08 CEST)
Hearing impairment (HI) is a common sensory disorder that is defined as the partial or complete inability to detect sound in one or both ears. This diverse pathology is associated with a myriad of phenotypic expressions and/or syndromes. HI can be caused by various intrinsic, environmental and/or unknown factors. Some ontologies capture some relevant HI forms, phenotypes and syndromes, but there is no comprehensive knowledge portal which includes aspects specific to the HI disease state. This hampers inter-study comparability, integration and interoperability within and across disciplines. This work describes the HI Ontology (HIO) that was developed based on the Sickle Cell Disease Ontology (SCDO) model. This is a collaboratively developed resource built around the 'Hearing Impairment' concept by a group of experts in different aspects of HI and ontologies. HIO is the first comprehensive, standardized, hierarchical and logical representation of existing HI knowledge. HIO allows researchers and clinicians alike to readily access standardized HI-related knowledge in a single location and promote collaborations and HI information sharing, including epidemiological, socio-environmental, biomedical, genetic and phenotypic information. Furthermore, this ontology illustrates the adaptability of the SCDO framework for use in developing a disease-specific ontology.
ARTICLE | doi:10.20944/preprints201704.0111.v1
Subject: Arts & Humanities, Religious Studies Keywords: technology; ontology; will; mastery; Hannah Arendt; George Grant; Iris Murdoch
Online: 18 April 2017 (11:48:02 CEST)
One purported benefit of technology is that it gives humans greater control over how they live their lives. Various technologies are used to protect humans from what are perceived to be the capricious whims of indifferent natural forces. Additionally, technology is used to create circumstances and opportunities that are believed to be preferable because they are more subject to human control. In large measure, the lives of late moderns are effectively constructed and asserted as artifacts of what they will themselves to be. This control is seen prominently at the beginning and end of life. Technology is employed to overcome infertility, prevent illness, disability, and undesirable traits, to select desirable traits and increasingly enhance them. At the end of life, late moderns have a far greater range of options at their disposal than past generations: they can choose to delay death, control pain, or end their lives at the time and with the means of their choosing. The greater control that technology offers helps humans to survive and even flourish, but it comes at a price. One such cost is that it tends to reduce humans to being little more than a will confined within a body. The body is thereby effectively perceived to be an impediment to the will that should be overcome. Is this troubling? Yes. I argue that the purported control technology offers often serves as a distraction or blind spot that may prevent humans from understanding and consenting to their good. In making this argument I draw upon the Christian doctrine of the incarnation as a way of disclosing the creaturely good of finitude against which the will should conform rather than attempting to overcome. I also draw upon Iris Murdoch’s and Simone Weil’s concept of “unselfing” as a way of conforming the will with this good. I revisit issues related to the beginning and end of life to draw-out some of the implications of my argument.
ARTICLE | doi:10.20944/preprints202109.0102.v1
Subject: Life Sciences, Biotechnology Keywords: abiotic stress; HSFs; genomics; gene ontology; maize breeding; protein 3D structures
Online: 6 September 2021 (13:57:37 CEST)
Heat shock transcription factors (HSFs) participate in regulating many environmental stress responses and biological processes in plants. Maize (Zea mays L.) is a major cash crop that is grown worldwide. However, the growth and yield of maize are affected by several adverse environmental inputs. Therefore, investigating the factors that regulate maize growth and development and resistance to abiotic stress is an essential task for developing stress-resilient maize varieties. Thus, a comprehensive genome-wide identification analysis was performed to identify HSFs in the maize genome. The current study identified 25 ZmHSFs, randomly distributed throughout the maize genome. Phylogenetic analysis revealed that ZmHSFs are divided into three classes and 13 sub-classes. Gene structure and protein motif analysis supported the results obtained through the phylogenetic analysis. Domain analysis showed the DNA-binding domain to be the most conserved region of ZmHSFs. Segmental duplication is shown to be responsible for the expansion of ZmHSFs. Most of the ZmHSFs are localized inside the nucleus, and the ZmHSFs which belong to the same group show similar physio-chemical properties. The 3D structures revealed comparable conserved ZmHSFs protein structures. RNA-seq analysis revealed a major role of class A HSFs including, ZmHSFA-1a and ZmHSFA-2a in all the maize growth stages, i.e., seed, vegetative, and reproductive development. Furthermore, ZmHSFs displayed an obvious spatiotemporal expression. Under abiotic stress conditions (heat, drought, cold, UV, and salinity), members of class A and B ZmHSFs are induced. Gene ontology (GO) annotation analysis indicated a major role of ZmHSFs in resistance to environmental stress and regulation of primary metabolism. Further, the protein-protein interaction analysis showed that ZmHSFs interact with several molecular chaperons and major stress-responsive proteins. To summarize, this study provides novel insights for functional studies on the ZmHSFs in maize breeding programs.
CONCEPT PAPER | doi:10.20944/preprints202010.0161.v1
Subject: Physical Sciences, Acoustics Keywords: preconditions of life; Miller Urey experiment; knowledge representation; ontology log; universality
Online: 7 October 2020 (16:10:50 CEST)
We present an ontology log-OLOG- representation of the classical Miller-Urey experiment, usually considered as a paradigm for spontaneous generation of biomolecules on the prebiotic Earth and also, as a key in understanding the chemical evolution phenomena linked to the origins of life. Ologging The Miler-Urey experiment enables us, through the categorical notion of fibre product or pullback, to define the concept of Biogenic Space, as a space containing low complexity biogenic units subjected to appropriate physical and chemical conditions, facilitating the synthesis of highly complex organic molecules. Also, we characterize the Biogenic Space as a concrete universal object that could be associated with the preconditions for life inside various structures in the universe such as exoplanets and exomoons located in habitable zones, but also in interstellar and intergalactic organic clouds.
ARTICLE | doi:10.20944/preprints202007.0486.v2
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: knowledge representation; curation; biocuration; semantics; systems biology; ontology; user interface; VSM
Online: 29 July 2020 (17:29:20 CEST)
Scientific progress is increasingly dependent on knowledge in computation-ready forms. In the life sciences, among others, many scientists therefore extract and structure knowledge from the literature. In a process called manual curation, they enter knowledge into spreadsheets, or into databases where it serves their and many others' research. Valuable as these curation efforts are, the range and detail of what can practically be captured and shared remains limited, because of the constraints of current curation tools. Many important contextual aspects of observations described in literature simply do not fit in the form defined by these tools, and thus cannot be captured. Here we present the design of an easy-to-use, general-purpose method and interface, that enables the precise semantic capture of virtually unlimited types of information and details, using only a minimal set of building blocks. Scientists from any discipline can use this to convert any complex knowledge into a form that is easily readable and meaningful for both humans and computers. The method VSM forms a universal and high-level language for encoding ideas, and for interacting with digital knowledge.
ARTICLE | doi:10.20944/preprints202007.0557.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: knowledge representation; curation; biocuration; semantics; systems biology; ontology; user interface; VSM
Online: 23 July 2020 (12:23:10 CEST)
ARTICLE | doi:10.20944/preprints202005.0081.v1
Subject: Life Sciences, Genetics Keywords: Lung cancer; biomarker; gene ontology; protein-protein interaction networks; survival analysis
Online: 5 May 2020 (12:28:25 CEST)
Objective: The aim of study is to find key genes and enriched pathways associated with lung cancer. Participants and Methods: Differentially expressed genes (DEGs) data of 54674 genes based on stage, tumor and status of lung cancer was taken from 66 patients of African American (AAs) origin. 2392 DEGs were found based on stage, 13502 DEGs were found based on tumor, 2927 DEGs were found based on status having p value (p<0.05). Results: Total 33 common DEGs were found from stage, tumor and status of lung cancer. Gene ontology (GO) and KEGG pathway enrichment analysis was performed and 49 significant pathways were obtained, out of which 10 pathways were found to be exclusively involved in lung cancer development. Protein-protein interaction (PPI) network analysis found 69 nodes and 324 edges and identified 10 hub genes based on their highest degrees. Module analysis of PPI found that ‘Viral carcinogenesis’, ‘pathways in cancer’, ‘notch signaling pathway’, ‘AMPK signaling pathways’ had a close association with lung cancer. Conclusion: These identified DEGs regulate other genes which play important role in growth of lung cancer. The key genes and enriched pathways identified can thus help in better identification and prediction of lung cancer.
REVIEW | doi:10.20944/preprints202109.0176.v1
Subject: Materials Science, Metallurgy Keywords: Metal alloys; Machine learning; Informatics; Defects; Dislocations; Mechanical deformation; Data science; Ontology
Online: 9 September 2021 (11:22:52 CEST)
In the design and development of novel materials that have excellent mechanical properties, classification and regression methods have been diversely used across mechanical deformation simulations or experiments. The use of materials informatics methods on large data that originate in experiments or/and multiscale modeling simulations may accelerate materials discovery or develop new understanding of materials’ behavior. In this fast-growing field, we focus on reviewing advances at the intersection of data science with mechanical deformation simulations and experiments, with a particular focus on studies of metals and alloys. We discuss examples of applications, as well as identify challenges and prospects.
ARTICLE | doi:10.20944/preprints202003.0413.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: coronavirus; drug; COVID-19; SARS; MERS; ontology; ChEBI; NDF-RT; DrON; bioinformatics
Online: 29 March 2020 (01:58:40 CET)
Coronavirus-infected diseases have posed great threats to human health. In past years, highly infectious coronavirus-induced diseases, including COVID-19, SARS, and MERS, have resulted in world-wide severe infections. Our literature annotations identified 110 chemical drugs and 26 antibodies effective against at least one human coronavirus infection in vitro or in vivo. Many of these drugs inhibit viral entry to cells and viral replication inside cells or modulate host immune responses. Many antimicrobial drugs, including antimalarial (e.g., chloroquine and mefloquine) and antifungal (e.g., terconazole and rapamycin) drugs as well as antibiotics (e.g., teicoplanin and azithromycin) were associated with anti-coronavirus activity. A few drugs, including remdesivir, chloroquine, favipiravir, and tocilizumab, have already been reported to be effective against SARS-CoV-2 infection in vitro or in vivo. After mapping our identified drugs to three ontologies ChEBI, NDF-RT, and DrON, many features such as roles and mechanisms of action (MoAs) of these drugs were identified and categorized. For example, out of 57 drugs with MoA annotations in NDF-RT, 47 have MoAs of different types of inhibitors and antagonists. A total of 29 anticoronaviral drugs are anticancer drugs with the antineoplastic role. Two clustering analyses, one based on ChEBI-based semantic similarity, the other based on drug chemical similarity, were performed to cluster 110 drugs to new categories. Moreover, differences in physicochemical properties among the drugs were found between those inhibiting viral entry and viral replication. A total of 163 host genes were identified as the known targets of 68 anti-coronavirus drugs, resulting in a network of 428 interactions among these drugs and targets. Chlorpromazine, dasatinib, and anisomycin are the hubs of the drug-target network with the highest number of connected target proteins. Many enriched pathways such as calcium signaling and neuroactive ligand-receptor interaction pathways were identified. These findings may be used to facilitate drug repurposing against COVID-19.
CONCEPT PAPER | doi:10.20944/preprints201910.0366.v1
Subject: Social Sciences, Organizational Economics & Management Keywords: ontology; semantics; safety; security; risk; performance; definitions; concepts; safety science; ISO 31000
Online: 31 October 2019 (09:36:29 CET)
When discussing the concepts of risk, safety, and security, people have an intuitive understanding of what these concepts mean, and, to a certain level, this understanding is universal. However, when delving into the real meaning of these concepts, one is likely to fall into semantic debates and ontological discussions. In industrial parks, it is important that (risk) managers from dierent companies, belonging to one and the same park, have the same understanding of the concepts of risk, safety, and security. It is even important that all companies in all industrial parks share a common understanding regarding these issues. As such, this paper explores the similarities and dierences behind the perceptions of these concepts, to come to a fundamental understanding of risk, safety, and security, proposing a semantic and ontological ground for safety and security science, based on an etymological and etiological study of the concepts of risk and safety. The foundation has been induced by the semantics used in the ISO 31000 risk management guidance standard. Hence, this article proposes a coherent, standardized set of concepts and definitions with a focus on the notion “objectives” that can be used as an ontological foundation for safety and security science, linking “objectives” with the concepts of safety, security, risk, performance and also failure and success, theoretically allowing for an increasingly more precise understanding and measurement of (un)safety across the whole range of individuals, sectors and organizations, or even society as a whole.
ARTICLE | doi:10.20944/preprints201811.0328.v1
Subject: Mathematics & Computer Science, Analysis Keywords: e-learning; automatic test generation; medical ontology; data mining for medical texts
Online: 14 November 2018 (09:45:38 CET)
The Medi-test system we developed was motivated by the large number of resources available for the medical domain, as well as the number of tests needed in this field (during and after the medical school) for evaluation, promotion, certification, etc. Generating questions to support learning and user interactivity has been an interesting and dynamic topic in NLP since the availability of e-book curricula and e-learning platforms. Current e-learning platforms offer increased support for student evaluation, with an emphasis in exploiting automation in both test generation and evaluation. In this context, our system is able to evaluate a student’s academic performance for the medical domain. Using as input medical reference texts and supported by a specially designed medical ontology, Medi-test generates different types of questionnaires for Romanian language. The evaluation includes 4 types of questions (multiple-choice, fill in the blanks, true/false and match), can have customizable length and difficulty and can be automatically graded. A recent extension of our system also allows for the generation of tests which include images. We evaluated our system with a local testing team, but also with a set of medicine students, and user satisfaction questionnaires showed that the system can be used to enhance learning.
ARTICLE | doi:10.20944/preprints201807.0539.v1
Subject: Engineering, General Engineering Keywords: Ontology Model, Context Mashup, Context Type, Context Awareness, Internet of Things (IoT)
Online: 27 July 2018 (12:57:06 CEST)
In an open and dynamic IoT (the Internet of Things) environment, a common context information model is essential for active things to share common knowledge, reason their situations, and support adaptive interoperability with each other. There have been many studies on the IoT context information models based on semantic technology, but most of them have assumed a static situation based on a service-oriented information model suitable for specific applications of the IoT. In the case of applying their models to an open and dynamic IoT environment, two issues have been observed: Most of the models ignore (a) the mashup of the open-world semantics of context information generated by multiple context sources and (b) the reconciliation of the semantic relationships between multiple context entities under dynamic situation changes. Therefore, in this paper, we propose a context information model that is flexible enough to express complex and diverse semantic relationships between context information generated from a variety of context information sources in the IoT. The main background of this proposal is to propose an adaptive context model that can effectively mash up various context classes that use ontology in open and dynamic IoT environments. In this paper, we also show the effectiveness of the proposed model through an adequate verification model and a practical example.
ARTICLE | doi:10.20944/preprints201801.0290.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: ontology; conceptual model; natural language processing; engineering design; fuzzy hierarchical classifier; clustering
Online: 31 January 2018 (02:44:53 CET)
Software engineers from all over the world solve independently a lot of similar problems. In this condition the problem of code or even better architecture reusing becomes an issue of the day. In this paper two phase approach to determining the functional and structural likenesses of software projects is proposed. This approach combines two methods of artificial intelligence: natural language processing techniques with a novel method for comparing software projects based on ontological representation of their architecture automatically obtained from the projects source code. Additionally several similarity metrics are proposed to estimate similarity between projects.
REVIEW | doi:10.20944/preprints202201.0170.v1
Subject: Mathematics & Computer Science, Other Keywords: significative infrastructure; biological networks; normalized mutual information; recall; pre-cision; modularity; gene ontology
Online: 12 January 2022 (14:17:32 CET)
Abstract: In network science and big data, the concept of finding meaningful infrastructures in networks has emerged as a method of finding groups of entities with similar properties within very complex systems. The whole concept is generally based on finding subnetworks which have more properties (links) amongst nodes belonging to the same cluster than nodes in other groups (A concept presented by Girvan and Newman, 2002). Today meaningful infrastructure identification is applied in all types of networks from computer networks, to social networks to biological networks. In this article we will look at how meaningful infrastructure identification is applied in biological networks. This concept is important in biological networks as it helps scientist discover patterns in proteins or drugs which helps in solving many medical mysteries. This article will encompass the different algorithms that are used for meaningful infrastructure identification in biological networks. These include Genetic Algorithm, Differential Evolution, Water Cycle Algorithm (WCA), Walktrap Algorithm, Connect Intensity Iteration Algorithm (CIIA), Firefly algorithms and Overlapping Multiple Label Propagation Algorithm. These al-gorithms are compared with using performance measurement parameters such as the Mod-ularity, Normalized Mutual Information, Functional Enrichment, Recall and Precision, Re-dundancy, Purity and Surprise, which we will also discuss here.
ARTICLE | doi:10.20944/preprints201911.0024.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: Iranian traditional medicine; Persian medicine; ontology; knowledge-base; Mizaj; temperament; new drug discovery
Online: 3 November 2019 (17:07:50 CET)
Background: Iranian traditional medicine is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unified terminology has been proposed for the concepts of this medicine up to the present time. Considering the extensive use of concepts in the numerous textbooks written by the scholars over centuries, comprehending the totality of the terminology is obviously a very challenging task. To resolve this issue and overcome the obstacles, and code the concepts in a reusable manner, constructing an ontology of the concepts of Iranian traditional medicine seems a necessity.Methods: Makhzan al-Advieh, an encyclopedia of materia medica compiled by Mohammad Hossein Aghili Khorasani, was selected as the resource to create an ontology of Mizaj. The steps followed to accomplish this task included (1) compiling the list of classes for Mizaj; (2) arranging the classes in taxonomy; (3) determining object properties and their cardinalities; (4) specifying annotation properties including codes, labels, synonyms, and definitions for each concept; (5) reviewing the fields pertaining to Mizaj of all monographs in Makhzan al-Advieh. The ontology was created using Protégé with adherence to the principles of ontology development provided by the Open Biological and Biomedical Ontology (OBO) foundry. Results: Mizaj ontology was constructed with a final inclusion of 105 classes, three object properties, and 1078 axioms in the Iranian Traditional Medicine General Ontology database, IrGO, freely available at http://jafarilab.com/irgo/. An indented tree view and an interactive graph view using WebVOWL were used to visualize the ontology. All classes were linked to their instances in the UNaProd database to create a knowledge-base of Mizaj. Conclusion: We constructed an ontology-based knowledge base of ITM concepts of Mizaj in the domain of materia medica to help offer a shared and common understanding of this concept, enable reuse of the knowledge, and make the assumptions explicit. Extending IrGO will bridge the gap between traditional and conventional schools of medicine and help guide future research on new treatment options.
ARTICLE | doi:10.20944/preprints202110.0143.v1
Subject: Engineering, Control & Systems Engineering Keywords: field of professional activity; parsing; educational content; professional requirements; ontology; content markup; intelligent analysis
Online: 8 October 2021 (13:24:14 CEST)
The article explores the task of making higher education more profession-oriented. In this context, we consider the technology of structuring and matching professional activities and content of professional education curricula with the help of ontology. This technology employs intelligent analysis of labor market and educational content matching with the aim to organize educational programs and verify professional competences based on their ontological properties. The article also considers development of a professional training cognitive map that can help design the student’s personalized educational trajectory factoring in the given parameters.
ARTICLE | doi:10.20944/preprints202008.0526.v1
Subject: Mathematics & Computer Science, Other Keywords: SLA; Violation; Adaptive SLA Template; Ontology; Context-aware; Virtual, Dynamic adaptation; Context-Aware Application
Online: 24 August 2020 (10:06:00 CEST)
During recent decades, contextual computing applications have emerged in the field of healthcare and particularly in the field of telemonitoring of patients suffering from chronic obstructive pulmonary disease (COPD). According to WHO rankings, chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide. Various research works are therefore carried out to improve the health of patients and the monitoring of patients in the comfort of their home environment. To this end, several telemonitoring systems are designed to COPD patients. These systems are connected to health center. Emergency physicians follow the patients subscribed to these systems remotely. These systems focus mainly on prediction, decision-making and the requirements of the healthcare profession, and do not address the quality control aspects of services or QoS based on service level agreements (SLAs). This situation can be dangerous for patients in case of extreme exacerbation of COPD patients. For example, the unavailability of the monitoring system can lead to the death of the patient because the emergency physician could not have access to the patient's data in real time in the context of COPD Patient Monitoring. In addition, Remote medical monitoring platforms are manipulating large volumes of data and the risks of data lost or data quality are real. It is therefore important to have the mechanisms to continuously improve the quality of service of these monitoring platforms in general and COPD patients particularly. In this article, we propose an ontology that uses SLA information from COPD monitoring platforms with dynamic data from the patient context. The purpose of this article is to propose a dynamic mechanism model for evaluating SLA violations. This solution allows retrieving knowledge from the main items of the SLA document based on XML and the COPD patient context data dynamically from a COPD SLA ontology. These data retrieved in real time allow the calculation of SLO-based metrics and display a SLA template available on the supplier and consumer interfaces. The information of the SLA violation control Interface changes dynamically depending the context-aware system and SLA document data. The SLA parties can dynamically control their Key Performance Indicators (KPI) Target.
Subject: Medicine & Pharmacology, Nutrition Keywords: ontology; nutritional epidemiology; minimal data information; data quality descriptors; study reporting guidelines; Semantic Web
Online: 15 May 2019 (05:51:53 CEST)
1) Background: The use of linked data in Semantic Web are promising approaches to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiologic research; 2) Methods: First, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Second, existing data standards and manuscript reporting guidelines for nutritional epidemiology were converted into ontology, and the terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Third, the ontologies of the nutritional epidemiologic standards, reporting guidelines and the core concepts were gathered in ONE. Three case studies were illustrated for its potential applications. (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts; 3) Results: Ontologies for “food and nutrition” (n=33), “disease and special population” (n=86), “data description” (n=21), “research description” (n=32) and “supplementary (meta) data description” (n=44) were reviewed and listed. ONE consists of 339 classes (79 new classes to describe nutrition data and 24 new classes to describe the content of nutrition manuscripts). The case studies demonstrated the application of ONE. 4) Conclusion: ONE is a resource to automate data integration, searching and browsing, and can be used to assess reporting completeness in nutritional epidemiology.
ARTICLE | doi:10.20944/preprints202111.0179.v1
Subject: Mathematics & Computer Science, Geometry & Topology Keywords: GeoSPARQL; GeoSPARQL 1.1; spatial; geospatial; Semantic Web; RDF; OWL; OGC; Open Geospatial Consortium; standard; ontology.
Online: 9 November 2021 (14:05:34 CET)
In 2012 the Open Geospatial Consortium published GeoSPARQL defining “an RDF/OWL ontology for [spatial] information”, “SPARQL extension functions” for performing spatial operations on RDF data and “RIF rules” defining entailments to be drawn from graph pattern matching. In the 8+ years since its publication, GeoSPARQL has become the most important spatial Semantic Web standard, as judged by references to it in other Semantic Web standards and its wide use for Semantic Web data. An update to GeoSPARQL was proposed in 2019 to deliver a version 1.1 with a charter to: handle outstanding change requests and source new ones from the user community and to “better present” the standard, that is to better link all the standard’s parts and better document & exemplify elements. Expected updates included new geometry representations, alignments to other ontologies, handling of new spatial referencing systems, and new artifact presentation. In this paper, we describe motivating change requests and actual resultant updates in the candidate version 1.1 of the standard alongside reference implementations and usage examples. We also describe the theory behind particular updates, initial implementations of many parts of the standard, and our expectations for GeoSPARQL 1.1’s use.
ARTICLE | doi:10.20944/preprints201611.0092.v2
Subject: Keywords: semantic spatial trajectory; role based access control; Bell-Lapadula model; multi-policy; Web Ontology Language
Online: 17 November 2016 (15:19:51 CET)
With the proliferation of locating devices, more and more raw spatial trajectories are formed, and many works enrich these raw trajectories with semantics, and mine patterns from both raw and semantic trajectories, but access control of spatial trajectories is not considered yet. We present a multi-policy secure model for semantic spatial trajectories. In our model, Mandatory Access Control, Role Based Access Control and Discretionary Access control are all enforced, separately and combined, and we represent the model semi-formally in Ontology Web Language.
ARTICLE | doi:10.20944/preprints202208.0197.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: Deep neural networks; Adversarial Attacks; Poisoning; Backdoors; Trojans; Taxonomy; Ontology; Knowledge Base; Explainable AI; Green AI
Online: 10 August 2022 (09:39:07 CEST)
Deep neural networks (DNN) have successfully delivered a cutting-edge performance in several fields. With the broader deployment of DNN models on critical applications, the security of DNNs becomes an active and yet nascent area. Attacks against DNNs can have catastrophic results, according to recent studies. Poisoning attacks, including backdoor and Trojan attacks, are one of the growing threats against DNNs. Having a wide-angle view of these evolving threats is essential to better understand the security issues. In this regard, creating a semantic model and a knowledge graph for poisoning attacks can reveal the relationships between attacks across intricate data to enhance the security knowledge landscape. In this paper, we propose a DNN Poisoning Attacks Ontology (DNNPAO) that would enhance knowledge sharing and enable further advancements in the field. To do so, we have performed a systematic review of the relevant literature to identify the current state. We collected 28,469 papers from IEEE, ScienceDirect, Web of Science, and Scopus databases, and from these papers, 712 research papers were screened in a rigorous process, and 55 poisoning attacks in DNNs were identified and classified. We extracted a taxonomy of the poisoning attacks as a scheme to develop DNNPAO. Subsequently, we used DNNPAO as a framework to create a knowledge base. Our findings open new lines of research within the field of AI security.
REVIEW | doi:10.20944/preprints202008.0642.v1
Subject: Biology, Plant Sciences Keywords: gene ontology; molecular function; cellular localization; biological function; circadian clock; flowering time; flower development; floral scent
Online: 28 August 2020 (11:42:40 CEST)
GIGANTEA (GI) is a gene involved in multiple biological functions, which were analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling and photoperiodic flowering. The latter function is a central role of GI, as it involves a multitude of pathways, both dependent and independent of the gene CONSTANS(CO) as well as on the basis of interaction with miRNA. The complexity of gene function of GI increases due to the existence of paralogs showing changes in genome structure as well as incidences of sub- and neofunctionalization. We present an updated report of the biological function of GI, integrating late insights into its role in floral initiation, flower development and flower volatile production.
REVIEW | doi:10.20944/preprints202007.0466.v1
Subject: Life Sciences, Genetics Keywords: Alternative Splicing; RNA-Seq; Machine Learning; Deep Learning; Recommender Systems; Multiple Instance Learning; mRNA Isoforms; Gene Ontology
Online: 20 July 2020 (10:53:23 CEST)
Multiple mRNA isoforms of the same gene are produced via alternative splicing, a biological mechanism that regulates protein diversity while maintaining genome size. Alternatively spliced mRNA isoforms of the same gene may sometimes have very similar sequence, but they can have significantly diverse effects on cellular function and regulation. The products of alternative splicing have important and diverse functional roles, such as response to environmental stress, regulation of gene expression, human heritable and plant diseases. The mRNA isoforms of the same gene, such as the apoptosis associated CASP3 gene, can have dramatically different functions. The shorter mRNA isoform product CASP3-S inhibits apoptosis, while the longer CASP3-L mRNA isoform promotes apoptosis. Despite the functional importance of mRNA isoforms, very little has been done to annotate their functions. The recent years have however seen the development of several computational methods aimed at predicting mRNA isoform level biological functions. These methods use a wide array of proteo-genomic data to develop machine learning-based mRNA isoform function prediction tools. In this review, we discuss the computational methods developed for predicting the biological function at the individual mRNA isoform level.
ARTICLE | doi:10.20944/preprints201907.0140.v1
Subject: Life Sciences, Molecular Biology Keywords: PlGF; PGF; blood-retinal barrier; RNA Seq; HREC; gene ontology; fastQC; Trimmomatic; KEGG; pentose phosphate pathway; TGF-β
Online: 10 July 2019 (07:48:20 CEST)
Placental growth factor (PlGF or PGF) is a member of the VEGF family, which is known to play a critical role in pathological angiogenesis, inflammation, and endothelial cell barrier function. However, the molecular mechanisms by which PlGF mediates its effects in non-proliferative diabetic retinopathy (DR) remain elusive. In this study, we performed transcriptome-wide profiling of differential gene expression for human retinal endothelial cells (HRECs) treated with PlGF antibody. The effect of antibody treatment on the samples was validated using trans-endothelial electric resistance (TEER), and western blot. A total of 3760 genes (1750 upregulated and 2010 downregulated) were found to be differentially expressed between the control and PlGF antibody treatment group. These differentially expressed genes (DEGs) were used for gene ontology and enrichment analysis to identify gene function, signal pathway, and interaction networks. The gene ontology results revealed that catalytic activity (GO:0003824) of molecular function, cell (GO:0005623) of the cellular component, and cellular process (GO:0009987) were among the most enriched biological processes. Pathways such as TGF-β, VEGF-VEGFR2, p53, apoptosis, pentose phosphate pathway, and ubiquitin-proteasome pathway, were among the most enriched, and TGF-β1 was identified as a primary upstream regulator. These data provide new insights into the underlying molecular mechanisms of PlGF in mediating biological functions, in relation to DR.
ARTICLE | doi:10.20944/preprints201803.0256.v1
Subject: Physical Sciences, General & Theoretical Physics Keywords: quantum ontology; sub-quantum dynamics; micro-constituents; emergent space-time; emergent quantum gravity; entropic gravity; black hole thermodynamics
Online: 30 March 2018 (05:57:25 CEST)
In this work it is acknowledged that important attempts to devise an emergent quantum (gravity) theory require space-time to be discretized at the Planck scale. It is therefore conjectured that reality is identical to a sub-quantum dynamics of ontological micro-constituents that are connected by a single interaction law. To arrive at a complex system-based toy-model identification of these micro-constituents, two strategies are combined. First, by seeing gravity as an entropic phenomenon and generalizing the dimensional reduction of the associated holographic principle, the universal constants of free space are related to assumed attributes of the micro-constituents. Second, as the effective field dynamics of the micro-constituents must eventually obey Einstein’s field equations, a sub-quantum interaction law is derived from a solution of these equations. A Planck-scale origin for thermodynamic black hole characteristics and novel views on entropic gravity theory result from this approach, which eventually provides a different view on quantum gravity and its unification with the fundamental forces.
REVIEW | doi:10.20944/preprints201612.0027.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: chatbot technology; ontology-based systems; expert systems; diagnosis; conversational agents; robotics; human-robot interaction; physician-patient relationship; intelligent agents
Online: 6 December 2016 (04:46:32 CET)
Access to medical care is a global issue. Technology-aided approaches have been applied in addressing this. Interventions have however not focused on medical diagnosis as a fully automated procedure and available applications employ mainly text-based inputs rather than conversation in natural language. We explored the utility of ontology-based chatbot technology for the design of intelligent agents for medical diagnosis through a systematic review of the most recent related literature. English articles published in 2011-2016 returned 233 hits which yielded 11 relevant articles after a 3-stage screening. Findings showed that the creation of expert systems had been the focus of many the studies which utilize the physician-system-patient framework with system training based mostly on expert knowledge for designing web- or mobile phone-based applications that serve assistive purposes. Findings further indicated gaps in the design and evaluation of more effective systems deployable as standalone applications, for example, on an embodied robotic system. The need for technology supporting the physical examination part of diagnosis, connection to data sources on patients’ vitals and medical history are also indicated in addition to the need for more qualitative work on natural language-based interaction. The system should be one that is continuously learning. Future works should also be directed towards the building of more robust knowledge base as well as evaluation of theory-based diagnostic methodological options