Online Knowledge Base Research Articles

TADKB: Family classification and a knowledge base of topologically associating domains

BackgroundTopologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can obtain family classifications and detailed information about TADs.ResultsWe built an online knowledge base TADKB integrating knowledge for TADs in eleven cell types of human and mouse. For each TAD, TADKB provides the predicted three-dimensional (3D) structures of chromosomes and TADs, and detailed annotations about the protein-coding genes and long non-coding RNAs (lncRNAs) existent in each TAD. Besides the 3D chromosomal structures inferred by population Hi-C, the single-cell haplotype-resolved chromosomal 3D structures of 17 GM12878 cells are also integrated in TADKB. A user can submit query gene/lncRNA ID/sequence to search for the TAD(s) that contain(s) the query gene or lncRNA. We also classified TADs into families. To achieve that, we used the TM-scores between reconstructed 3D structures of TADs as structural similarities and the Pearson’s correlation coefficients between the fold enrichment of chromatin states as functional similarities. All of the TADs in one cell type were clustered based on structural and functional similarities respectively using the spectral clustering algorithm with various predefined numbers of clusters. We have compared the overlapping TADs from structural and functional clusters and found that most of the TADs in the functional clusters with depleted chromatin states are clustered into one or two structural clusters. This novel finding indicates a connection between the 3D structures of TADs and their DNA functions in terms of chromatin states.ConclusionTADKB is available at http://dna.cs.miami.edu/TADKB/.

PP165 Content Instead Of Orders: Experiences Of Launching A Knowledge Base

IntroductionIn Hungary, the procedure for health technology assessment of innovative pharmaceutical products allows 13 assessors 43 calendar days to evaluate reimbursement submissions. These short timelines have created a need for smart capacity building, namely, streamlining the scientific evaluation process while making sure that the quality of the critical appraisals remain high. The objective of this study was to present and evaluate the implementation of an online knowledge base to distill community knowledge, and also for management purposes.MethodsThe scope and the content-, functional-, and technical specification was developed, and information technology security requirements were identified during the pre-implementation phase. An existing platform was chosen for adaptation, ensuring that descriptive follow-up data is available on uptake for monitoring purposes. Both the adaptation and maintenance were carried out internally by the Department of Health Technology Assessment at the National Institute of Pharmacy and Nutrition.ResultsThe key requirements identified when developing the specification were searchability, low maintenance need, low operating costs and attractivity for users. An already existing open-source, flat file content management system was chosen for adaptation. In terms of content, a health technology assessment handbook, process documentation, a news bulletin section was created, and corporate identity elements were added. Since the start of the service in September 2018, the number of total daily page downloads to the knowledge base varied between four and 1,193 (average 205 per day), with the assessment handbook topping the overall page visit statistics.ConclusionsThe implementation of this knowledge base enables the Department of Technology Assessment to rely more on the formalized community knowledge when carrying out critical appraisal, while enabling better knowledge and quality management. Uptake remains an issue on the long run, indicating a need for continuous content development.

The Library Leading: Knowledge Management Supporting Community College Institutional Strategy

abstractThis case study demonstrates how librarians at LaGuardia Community College led a college-wide knowledge management project to implement Ask LaGuardia, an online knowledge base where users can find answers to common questions on navigating this large urban college. Students had been experiencing difficulty receiving clear, correct, and consistent answers to their questions while staff had been challenged by information silos. LaGuardia’s president chose the Library for a leadership role in this initiative supporting a broader strategy of better alignment between Academic and Student Affairs. The Library’s positive reputation and knowledge organization expertise made it a natural fit. Four years in, available data and observations indicate that Ask LaGuardia is meeting its goal of easing students’ difficulties around finding college information while earning campus-wide support in the process. LaGuardia librarians demonstrated one way in which libraries can lead a knowledge management effort, thus, increasing their value to their parent institutions.

Aligning the large-scale ontologies on schema-level for weaving Chinese linked open data

This study purposes a data field and sequence alignment-based ontology mapping architecture, as ontology mapping is an important way to solve the problem of ontology heterogeneous; meanwhile, it also can be considered as a typical scenario on finding the schema-level links in linked open data (LOD). Current researches on LOD is mainly focused on the level of instances so that the task on finding schema-level links between LOD datasets is being ignored. Furthermore, nowadays the knowledge described in Chinese is also an important part of online knowledge base; unfortunately, current Chinese ontology mapping systems have low efficiency and availability, there is still lack of relevant system for large-scale Chinese ontology mapping task in LOD environment. In order to solve this problem, firstly, based on the improved nuclear field-like potential function, we compress the size of unaligned large-scale Chinese ontology. Secondly, we use the sequence alignment algorithm to compute similarity between the concepts. Finally, we compare our system to other typical concept mapping algorithms. Results prove it can reduce the scale of mapping task effectively and also have higher overall performance. This study may have important practical significance for promoting Chinese knowledge sharing, reusing and interoperation.

Scoping the polymer genome: A roadmap for rational polymer dielectrics design and beyond

Abstract The Materials Genome Initiative (MGI) has heralded a sea change in the philosophy of materials design. In an increasing number of applications, the successful deployment of novel materials has benefited from the use of computational methodologies, data descriptors, and machine learning. Polymers have long suffered from a lack of data on electronic, mechanical, and dielectric properties across large chemical spaces, causing a stagnation in the set of suitable candidates for various applications. Extensive efforts over the last few years have seen the fruitful application of MGI principles toward the accelerated discovery of attractive polymer dielectrics for capacitive energy storage. Here, we review these efforts, highlighting the importance of computational data generation and screening, targeted synthesis and characterization, polymer fingerprinting and machine-learning prediction models, and the creation of an online knowledgebase to guide ongoing and future polymer discovery and design. We lay special emphasis on the fingerprinting of polymers in terms of their genome or constituent atomic and molecular fragments, an idea that pays homage to the pioneers of the human genome project who identified the basic building blocks of the human DNA. By scoping the polymer genome, we present an essential roadmap for the design of polymer dielectrics, and provide future perspectives and directions for expansions to other polymer subclasses and properties.

Keynote speakers

Mutually-inversistic machine learning is based on inverse hypothetical inference of mutually-inversistic logic constructed by the author. In mutually-inversistic logic, there are 8 kind of hypothetical inferences, all of which are from the major premise and the minor premise to infer the conclusion. For each hypothetical inference, there are 2 inverse hypothetical inferences, one is from the minor premise and the conclusion to the major premise, the other is from the major premise and the conclusion to the minor premise. Therefore, there are 16 kind of mutually-inversistic machine learning models altogether. FOIL, decision tree learning in inductive learning, rough set learning, genetic algorithm, inverse resolution in inductive logic programming are special cases of mutually-inversistic machine learning.

Molecular fingerprinting of principal neurons in the rodent hippocampus: A neuroinformatics approach

Neurons are often classified by their morphological and molecular properties. The online knowledge base Hippocampome.org primarily defines neuron types from the rodent hippocampal formation based on their main neurotransmitter (glutamate or GABA) and the spatial distributions of their axons and dendrites. For each neuron type, this open-access resource reports any and all published information regarding the presence or absence of known molecular markers, including calcium-binding proteins, neuropeptides, receptors, channels, transcription factors, and other molecules of biomedical relevance. The resulting chemical profile is relatively sparse: even for the best studied neuron types, the expression or lack thereof of fewer than 70 molecules has been firmly established to date. The mouse genome-wide in situ hybridization mapping of the Allen Brain Atlas provides a wealth of data that, when appropriately analyzed, can substantially augment the molecular marker knowledge in Hippocampome.org. Here we focus on the principal cell layers of dentate gyrus (DG), CA3, CA2, and CA1, which together contain approximately 90% of hippocampal neurons. These four anatomical parcels are densely packed with somata of mostly excitatory projection neurons. Thus, gene expression data for those layers can be justifiably linked to the respective principal neuron types: granule cells in DG and pyramidal cells in CA3, CA2, and CA1. In order to enable consistent interpretation across genes and regions, we screened the whole-genome dataset against known molecular markers of those neuron types. The resulting threshold values allow over 6000 very-high confidence (>99.5%) expressed/not-expressed assignments, expanding the biochemical information content of Hippocampome.org more than five-fold. Many of these newly identified molecular markers are potential pharmacological targets for major neurological and psychiatric conditions. Furthermore, our approach yields reasonable expression/non-expression estimates for every single gene in each of these four neuron types with >90% average confidence, providing a considerably complete genetic characterization of hippocampal principal neurons.

Telemedicine in Neonatal Home Care: Identifying Parental Needs Through Participatory Design.

BackgroundFor the majority of preterm infants, the last weeks of hospital admission mainly concerns tube feeding and establishment of breastfeeding. Neonatal home care (NH) was developed to allow infants to remain at home for tube feeding and establishment of breastfeeding with regular home visits from neonatal nurses. For hospitals covering large regions, home visits may be challenging, time consuming, and expensive and alternative approaches must be explored.ObjectiveTo identify parental needs when wanting to provide neonatal home care supported by telemedicine.MethodsThe study used participatory design and qualitative methods. Data were collected from observational studies, individual interviews, and focus group interviews. Two neonatal units participated. One unit was experienced in providing neonatal home care with home visits, and the other planned to offer neonatal home care with telemedicine support. A total of 9 parents with preterm infants assigned to a neonatal home care program and 10 parents with preterm infants admitted to a neonatal unit participated in individual interviews and focus group interviews, respectively.ResultsThree overall themes were identified: being a family, parent self-efficacy, and nurse-provided security. Parents expressed desire for the following: (1) a telemedicine device to serve as a “bell cord” to the neonatal unit, giving 24-hour access to nurses, (2) video-conferencing to provide security at home, (3) timely written email communication with the neonatal unit, and (4) an online knowledge base on preterm infant care, breastfeeding, and nutrition.ConclusionsOur findings highlight the importance of neonatal home care. NH provides parents with a feeling of being a family, supports their self-efficacy, and gives them a feeling of security when combined with nursing guidance. Parents did not request hands-on support for infant care, but instead expressed a need for communication and guidance, which could be met using telemedicine.

A knowledge base for tracking the impact of genomics on population health.

We created an online knowledge base (the Public Health Genomics Knowledge Base (PHGKB)) to provide systematically curated and updated information that bridges population-based research on genomics with clinical and public health applications. Weekly horizon scanning of a wide variety of online resources is used to retrieve relevant scientific publications, guidelines, and commentaries. After curation by domain experts, links are deposited into Web-based databases. PHGKB currently consists of nine component databases. Users can search the entire knowledge base or search one or more component databases directly and choose options for customizing the display of their search results. PHGKB offers researchers, policy makers, practitioners, and the general public a way to find information they need to understand the complicated landscape of genomics and population health.Genet Med 18 12, 1312-1314.

Vehicle Simulator: Virtual Trip Runner (VTR)/ Real Time Recorder (RTR)

This topic is an attempt to develop an open source vehicle simulator for use by anyone needing realistic vehicle data delivered as it would be in a real vehicle. As you probably know, most vehicles nowadays have an On-Board Diagnostic (OBD) connector which is wired up to the car’s internal computer. It is used in many garages where the mechanic can probe the car through the OBD connector and read out parameters onto a display. In an Internet of Things (IoT ) world where the car can be easily connected to the Internet (perhaps via Bluetooth to a smart phone), it could automatically search an online knowledge base and not only report a fault code but also let you know the most likely cause either based on the car’s personal history or on the environment (an expert system could conclude “it is minus 15 degrees Celsius outside, and there is a water leak, and it is likely to be a cracked hose due to the cold temperature – and there was a manufacturer recall notice concerning this hose”). There will be whole sectors of applications such as, safer driver operation of the vehicle, fewer distractions, more automation, safer mechanical performance, better & more timely maintenance warnings, lower cost operation and lower maintenance costs.

Developing a community-based knowledge system: a case study using Sri Lankan agriculture

The Agriculture sector plays a vital role in Sri Lanka’s economy. Not having an agricultural knowledge repository that can be easily accessed by people in agriculture community in Sri Lanka within their own context, is a major problem. As a solution, a large user centred ontology for Sri Lankan farmers was developed to provide required information/knowledge not only in a structured and complete way, but also in a context-specific manner. Since this problem is not only limited to farmers, we extend this for every one working in the agriculture domain. We validate the ontology in terms of accuracy and quality. The online knowledge base based on the ontology with a SPARQL endpoint was created to share and reuse the domain knowledge that can be queried based on user context. A Mobile based application and a Web based application were developed to provide information/knowledge by using this ontology. These applications are also used to evaluate the ontology by getting the feedbacks from users to the knowledge in the ontology. It is very difficult to maintain a large complex ontology. To maintain our ontology, we identified various processes that are required to develop and maintain ontology as a collaborative process. A semi-automatic end-to-end ontology management system was developed to manage the developed ontology and the knowledge base. It provides the facilities to reuse, share, modify, extendand prune the ontology components as required. The facilities to capture users’ information needs and search domain information in user context are also included. In this paper, we present a summary of the overall development process of the ontology including the end-to-end ontology management system.

PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is one of the major causes of female subfertility worldwide and ≈7–10% of women in reproductive age are affected by it. The affected individuals exhibit varying types and levels of comorbid conditions, along with the classical PCOS symptoms. Extensive studies on PCOS across diverse ethnic populations have resulted in a plethora of information on dysregulated genes, gene polymorphisms and diseases linked to PCOS. However, efforts have not been taken to collate and link these data. Our group, for the first time, has compiled PCOS-related information available through scientific literature; cross-linked it with molecular, biochemical and clinical databases and presented it as a user-friendly, web-based online knowledgebase for the benefit of the scientific and clinical community. Manually curated information on associated genes, single nucleotide polymorphisms, diseases, gene ontology terms and pathways along with supporting reference literature has been collated and included in PCOSKB (http://pcoskb.bicnirrh.res.in).

User centered ontology for Sri Lankan farmers

Farmers in Sri Lanka are badly affected by not being able to get vital information required to support their farming activities in a timely manner. Some of the required information can be found in government websites, agriculture department leaflets, and through radio and television programs on agriculture. This knowledge is not reaching the farmers due to its unstructured, incomplete, varied formats, and lack of targeted delivery methods. Thus finding the right information within the context in which information is required in a timely manner is a challenge. The information and knowledge needs to be provided not only in a structured and complete way, but also in a context-specific manner. For instance, farmers need agricultural information within the context of location of their farm land, their economic condition, their interest and beliefs, and available agricultural equipment. To investigate some of the underlying farmer centric research challenges an International Collaborative Research Project to develop mobile based information systems for people in developing countries has been launched. Farmer centered ontology was developed as part of this project. Agricultural information has strong local characteristics in relation to climate, culture, history, languages, and local plant varieties. These local characteristics as well as the need to provide information in a context-specific manner made us develop this user centered ontology for Sri Lankan farmers. Because of the complex nature of the relationships among various concepts we selected an ontological approach that supports description logic to create the knowledge repository. For this we developed a new approach to model the domain knowledge to meet particular access requirements of the farmers in Sri Lanka. Through this approach, we have investigated how to create a knowledge repository of agricultural information to respond to user queries taking into account the context in which information is needed by farmers at various stages of the farming life cycle. The Delphi Method and the OOPS! (web-based tool) were used to validate the ontology. Initial system was trialed with a group of farmers in Sri Lanka. The online knowledge base with a SPARQL endpoint was created to share and reuse the domain knowledge that can be queried based on farmer context.

網上漢字知識庫的構思

網上漢字知識庫的構思

Meta-analysis of human cancers with onconet- An open-access, on-line knowledge base for human cancer gene mutation and expression

Meta-analysis of human cancers with onconet- An open-access, on-line knowledge base for human cancer gene mutation and expression

Trusting the Social Web: issues and challenges

The phenomenon of the Social Web (i.e., the Web of Social Media) has caught the attention of research communities in the last decade. Researchers from diverse disciplines ranging from social and behavioral sciences to computer science have started investigating the issues and challenges in the Social Web. Within computer science, researchers from established research areas such as language technologies, machine learning, and service and cloud computing have started looking into the computational and development challenges brought about by the Social Web. With the continued reports of breach of trust and hoax news spreading from social media to mainstream news, trusting the Social Web has become one of the major challenges that need to be addressed. This special issue focuses on this challenge. In this editorial note, we provide a brief introduction of the Social Web, followed by a discussion on the major challenges in building a trusted Social Web. Finally, we present recent work in trusting the Social Web through a summary of the papers included in this special issue. Social media is increasingly becoming mainstream for a variety of purposes, ranging from online journalism (e.g., blogs), online knowledge bases (e.g., Wikepedia), online marketing (e.g., Twitter), to keeping in touch with friends, family and professional colleagues online (e.g., Facebook, LinkedIn, etc.). These technologies have given rise to a web of social media, also known as the Social Web. The popularity of the Social Web has been overwhelming. It is reported in [8] that 67 % of online adults are connected to one or more social media, and that a large proportion of them first check in to their favorite social media site everyday. This trend is likely to grow as the number of Android-based smartphones shipments alone is expected to reach 1 billion by 2013 [13]. Additionally, the value of social commerce is expected to reach 30 billion dollars within next 5 years. Similarly, 13 % of digital news consumers follow recommendations from Twitter and Facebook. Therefore, the World Wide Web (2015) 18:1–7 DOI 10.1007/s11280-013-0252-2

ICT in Science Education. Exploring the Digital Learning Materials at viten.no

In this paper we focus on students’ learning gains with respect to their understanding of biology and ecological management from the use of a teaching program combining online and offline activities to teach about the socio-scientific controversial issue of wolves in Norway. Gender differences in response to the program and students’ attitudes towards wolves are also investigated. The web-based part of the teaching program consists of an online knowledge base designed to promote discourse and argumentation while working at the computers and in an offline classroom debate. The participants were two Norwegian classes of students age 14-15, who followed the teaching program. A pretest-posttest design with a follow-up four months later was chosen to measure student learning gains. Our results show positive achievement from pretest to posttest and even after four months students continue to demonstrate high levels of retention. Girls have significantly higher scores on posttest and follow-up compared to boys. Our results also show that 2/3 of the students changed their attitudes towards wolves during work with this teaching program.

A comprehensive plan for differentiating the training of teachers of the gifted online at the state, district and university levels in Florida, USA

The training of teachers for a meaningful use of all that contemporary technology offers to developing curriculum requires constant vigilance, experimentation, innovation, revision and updating. The lifestyle of today’s gifted students includes a range of ever-unfolding technologies, such as text messaging, blogging, social networking, personal webpages, video pods, streamed television, online textbooks, online knowledge base, web searching, presentation tools, desktop publishing, graphics infused in word processing, simulations and complex gaming. At the same time, the technology literacy of most teachers is in ‘catch-up mode’ with constant retraining about how to provide curricula that includes webquests, virtual field trips, virtual passports, interactive maps (Google Earth) and webliography (TrackStar), presented in diverse formats. The following questions will be examined in this paper: How do you cross regional boundaries and local educational administration to provide a comprehensive state-wide teacher training system in gifted education? How do you differentiate teacher training in gifted education that uses appropriate methods, strategies and best practices in teaching gifted students? How do you incorporate the daily technology needs and uses of gifted students into training their teachers? How can you provide teacher training that is independent of time and space to reach teachers beyond their classroom yet make it directly applicable? How do you structure a system of accountability that meets state and national standards for gifted education? In the state of Florida, USA, a three-tiered comprehensive approach provides online training and certification to teachers at the state level, through the WOGI (Working on Gifted Issues) project, at the district level that builds on Florida State Training Modules for local relevance, and at the university level that can be incorporated into a graduate Master’s degree with a specialization in gifted education.

FC9 Comprehensive review and field synopsis of genetic associations in cutaneous melanoma

Introduction The genetic susceptibility to melanoma remains the subject of intense research worldwide, focusing on either rare, familial high-penetrance sequence variants, or more common moderate- to low-risk predisposing allele. The number of published data on genetic associations of melanoma has increased immensely over the past years implying a number of putative risk alleles in several genes. Aim To perform a comprehensive field synopsis of all published genetic associations of melanoma and create an on-line database that collects and curates published results in this area. Methods We have collected and catalogued all genetic association studies published in the field of melanoma from 1992 until October 2009, using the PubMed and HuGE PubLit searches and the Melanoma Molecular Map Project (mmmp). We included all relevant case/control studies examining the frequency of risk alleles in melanoma patients and excluded studies of rare (minor allele frequency <0.01), highly penetrant gene mutations. We also included data from large-scale association studies and genome-wide association studies (GWAS). Random-effects meta-analyses using allelic contrasts were carried out for all genetic associations having genotype data in four or more independent case/control studies. Nominally significant results of the meta-analyses were graded for strength of epidemiological evidence based on a grading system developed by HuGENet. A publicly available, online database was created containing the results of our field synopsis and meta-analyses results. Results Our search identified 153 studies in the literature reporting on the association of melanoma risk with 744 polymorphisms in 163 different genes. Apart from 5 recent GWAS, most studies used a candidate gene approach and focused on variants of the MC1R gene (19%), ASIP gene (8%), VDR gene (7%), CDKN2A (7%), and OCA2 gene (6%). We meta-analyzed 78 studies focusing on 37 polymorphisms across 14 different genes. Polymorphisms in several genes (MC1R, ASIP, OCA2, SLC45A2, TYR, VDR and CDKN2A), most of which have been associated with pigmentary traits, showed nominally significant effects with average summary odds ratios of 1.51 (range: 0,361–3,086). Grading of the cumulative evidence by the HuGENet criteria showed that 5 of the significant results (MC1R rs1805007, MC1R rs1805008, MC1R rs1805008 in only Caucasian samples, OCA2 rs1800407 and TYR rs1126809) were characterized as having ‘strong’ epidemiological credibility. Conclusion Our field synopsis and systematic meta-analysis approach offers a powerful tool to assess the current evidence on the genetic susceptibility of melanoma and to track the most viable candidate genes. It also provides an up-to-date on-line knowledge base of the genetic predisposition of melanoma, a prerequisite for the translation of genetic findings into useful applications for disease prevention.

Cartography 2.0: For people who make interactive maps

Cartography 2.0 (http://Cartography2.org) is a free online knowledge base and e-textbook for students and professionals interested in interactive and animated maps. I (Mark) pitched the idea of doing an ‘online textbook’ to my co-authors because I knew that, as teachers, we were all frustrated with the inability of traditional textbooks to keep pace with the constant stream of new Web technologies. Further, we could not find any comprehensive online resources about web-based mapping that provided the same breadth and depth we’ve come to expect from a professionally produced textbook. The kind of knowledge that is needed to make dynamic maps spans many (traditionally separate) fields from computer science to education. While there are great books on all of these fields individually, none offered an answer to the basic question I’ve been asked many times: what’s the important stuff I need to know about making great on-demand/interactive maps?