Enabling comparisons of characters using an Xper2 based knowledge-base of fern morphology

Phytotaxa ◽  
2014 ◽  
Vol 183 (3) ◽  
pp. 145 ◽  
Author(s):  
Adèle Corvez ◽  
Anaïs Grand
Keyword(s):  
Missing Data ◽  
Knowledge Base ◽  
Descriptive Data ◽  
Plant Ontology ◽  
Interchange Format ◽  
User Friendly

Ferns comprise both extant and fossil taxa displaying a broad morphological and anatomical disparity. In order to compare their features, we propose a knowledge base of 46 genera, 101 characters and 273 character states with illustrations, bibliographical references and annotations with terms from the Plant Ontology Consortium (amongst others). The knowledge base is designed with the Xper² program. Descriptions are exhaustive (i.e., all the taxa have been given values for every character) thanks to the management of inapplicable and missing data. The Xper² format is compatible with the standard interchange format Structured Descriptive Data (SDD). The user-friendly and intuitive environment provided by Xper2 should help users to take ownership of our conceptualization.

Towards the Development of a Knowledge Base for Realizing User-Friendly Data Mining

2012 ◽  
pp. 121-126
Author(s):  
Roberto Espinosa ◽  
Diego García-Saiz ◽  
Jose Jacobo Zubcoff ◽  
Jose-Norberto Mazón ◽  
Marta Zorrilla
Keyword(s):  
Data Mining ◽  
Knowledge Base ◽  
User Friendly

ITA Expansion, Time, and Costs

2019 ◽  
pp. 113-140
Author(s):  
Susan D. Franck
Keyword(s):  
Missing Data ◽  
Dispute Resolution ◽  
Diffusion Of Innovations ◽  
Sociological Perspective ◽  
Descriptive Data ◽  
Expansion Time ◽  
Legal Costs ◽  
Potential Impact ◽  
Time Required ◽  
Over Time

Chapter 4 initially provides data about the growth of ITA as well as offering a series of frames against which to understand its evolution, including a sociological perspective analyzing changes in ITA’s caseload against Professor Everett’s theory of diffusion of innovations. It next explores other elements of time, namely case length and deliberative delays, by offering descriptive data and testing whether case length has reliably increased over time or whether resolution times vary on the basis of institutions resolving disputes. It then turns to exploring temporal elements related to bifurcation and separate opinions. After providing an explanation of the fiscal costs data particularly related to parties’ legal costs as well as tribunal costs and expenses (and conducting a variety of tests to explore the potential impact of missing data), the last section identifies the reliable relationship between the costs of dispute resolution and the time required to resolve the dispute.

scholarly journals CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Adriano Ferrasa ◽  
Mayara M Murata ◽  
Teresa D C G Cofre ◽  
Juliana S Cavallini ◽  
Gustavo Peron ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Citrus Canker ◽  
Limited Information ◽  
Xanthomonas Citri ◽  
Comprehensive Knowledge ◽  
Genetic Mechanisms ◽  
Serious Disease ◽  
Canker Development ◽  
User Friendly

Abstract Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the CitrusKB knowledge base. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable resource of information on citrus and their interaction with the citrus canker bacterium X. citri. CitrusKB provides tools for a user-friendly web interface to let users search and analyse a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease, with controls and infected plants at different stages of infection by the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue over time by the incorporation of novel annotations and analysis tools. We expect that CitrusKB may substantially contribute to the field of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

scholarly journals Multiple Imputation of Multilevel Missing Data

SAGE Open ◽  
2016 ◽  
Vol 6 (4) ◽  
pp. 215824401666822 ◽  
Author(s):  
Simon Grund ◽  
Oliver Lüdtke ◽  
Alexander Robitzsch
Keyword(s):  
Missing Data ◽  
Multiple Imputation ◽  
Multilevel Models ◽  
R Package ◽  
Data Sets ◽  
Multilevel Data ◽  
Statistical Knowledge ◽  
Multilevel Research ◽  
User Friendly ◽  
High Degree

The treatment of missing data can be difficult in multilevel research because state-of-the-art procedures such as multiple imputation (MI) may require advanced statistical knowledge or a high degree of familiarity with certain statistical software. In the missing data literature, pan has been recommended for MI of multilevel data. In this article, we provide an introduction to MI of multilevel missing data using the R package pan, and we discuss its possibilities and limitations in accommodating typical questions in multilevel research. To make pan more accessible to applied researchers, we make use of the mitml package, which provides a user-friendly interface to the pan package and several tools for managing and analyzing multiply imputed data sets. We illustrate the use of pan and mitml with two empirical examples that represent common applications of multilevel models, and we discuss how these procedures may be used in conjunction with other software.

scholarly journals The 8 Years of Existence of Xper3: State of the art and future developments of the platform

2021 ◽  
Vol 5 ◽  
Author(s):  
Adeline Kerner ◽  
Sylvain Bouquin ◽  
Rémy Portier ◽  
Régine Vignes Lebbe
Keyword(s):  
User Interface ◽  
Natural Language ◽  
Knowledge Base ◽  
Knowledge Bases ◽  
Free Access ◽  
Global Biodiversity Information Facility ◽  
Descriptive Data ◽  
Future Developments ◽  
Discriminating Power ◽  
Phenotypic Quality

The Xper3 platform was launched in November 2013 (Saucède et al. 2020). Xper3 is a free web platform that manages descriptive data and provides interactive identification keys. It is a follow-up to Xper (Forget et al. 1986) and Xper2 (Ung et al. 2010). Xper3 is used via web browsers. It offers a collaborative, multi-user interface without local installation. It is compatible with TDWG’s Structured Descriptive Data (SDD) format. Xper3 and its previous version, Xper2, have already been used for various taxonomic groups. In June 2021, 4743 users had created accounts and edited 5756 knowledge bases. Each knowledge base is autonomous and can be published as a free access key link, as a data paper in publications or on websites. The risk of this autonomy and lack of visibility to already existing knowlege bases is possible duplicated content or overlapping effort. Increasingly, users have asked for a public overview of the existing content. A first version of a searching tool is now available online. Explorer lists the databases whose creators have filled in the extended metadata and have accepted the referencing. The user can search by language, taxonomic group, fossil or current, geography, habitat, and key words. New developments of Xper3 are in progress. Some have a first version online, others are in production and the last ones are future projects. We will present an overview of the different projects in progress and for the future. Calculated descriptors are a distinctive feature of Xper3 (Kerner and Vignes Lebbe 2019). These descriptors are automatically computed from other descriptors by using logical operators (Boolean operators). The use of calculated descriptors remains rare. It is necessary to put forward the calculated descriptors to encourage more feedback in order to improve them. The link between Xper3 and Annotate continues to improve (Hays and Kerner 2020). Annotate offers the possibility of tagging images with controlled vocabularies structured in Xper3. Then, an export from Annotate to Xper3, allows automatic filling in of the Xper3 knowledge base with the descriptions (annotations and numerical measures) of virtual specimens, and then comparing specimens to construct species descriptions, etc. Future developments are in progress that will modify the Xper3 architecture in order to have the same functionalities in both local and online versions and to allow various user interfaces from the same knowledge bases. Xper2-specific features, such as merging states, adding notes, adding definitions and/or illustrations in the description tab, having different ways of sorting and filtering the descriptors during an identification (by groups, identification power, alphabetic order, specialist’s choice) have to be added to Xper3. A new tab in Xper3’s interface is being implemented to give an access to various analysis tools, via API (Application Programming Interface), or R programming code: MINSET: minimum list of descriptors sufficient to discriminate all items MINDESCR: minimum set of descriptors to discriminate an item DESCRXP: generating a description in natural language MERGEMOD: proposing to merge states without loss of discriminating power DISTINXP, DISTVAXP: computing similarities between items or descriptors MINSET: minimum list of descriptors sufficient to discriminate all items MINDESCR: minimum set of descriptors to discriminate an item DESCRXP: generating a description in natural language MERGEMOD: proposing to merge states without loss of discriminating power DISTINXP, DISTVAXP: computing similarities between items or descriptors One last project that we would like to implement is an interoperability between Xper3, platforms with biodiversity data (e.g., Global Biodiversity Information Facility, GBIF) and bio-ontologies. An ID field already exists to add Universally Unique IDentifiers (UUID) for taxa. ID fields have to be added for descriptors and states to link them with ontologies e.g., Phenotypic Quality Ontology PATO, Plant Ontology PO. We are interested in discussing future developments to further improve the user interface and develop new tools for the analysis of knowledge bases.

ACMS: a database of alternate conformations found in the atoms of main and side chains of protein structures

2019 ◽  
Vol 52 (4) ◽  
pp. 910-913 ◽  
Author(s):  
R. Santhosh ◽  
P. Chandrasekaran ◽  
Daliah Michael ◽  
K. Rangachari ◽  
Namrata Bankoti ◽  
...  
Keyword(s):  
High Resolution ◽  
Knowledge Base ◽  
Crystal Structures ◽  
Protein Structures ◽  
Protein Molecule ◽  
Data Bank ◽  
Side Chain ◽  
Biological Macromolecules ◽  
Conformational Ensembles ◽  
User Friendly

Proteins are usually dynamic biological macromolecules, thereby exhibiting a large number of conformational ensembles which influence the association with their neighbours and interacting partners. Most of the side-chain atoms and a few main-chain atoms of the high-resolution crystal structures deposited in the Protein Data Bank adopt alternate conformations. This kind of conformational behaviour prompted the authors to explore the relationship, if any, between the alternate conformations and the function of the protein molecule. Thus, a knowledge base of the alternate conformations of the main- and side-chain atoms of protein structures has been developed. It provides a detailed description of the alternate conformations of various residues for more than 60 000 high-resolution crystal structures. The proposed knowledge base is very user friendly and has various flexible options. The knowledge base will be updated periodically and can be accessed at http://iris.physics.iisc.ac.in/acms.

scholarly journals SequencEnG: an Interactive Knowledge Base of Sequencing Techniques

2018 ◽  
Author(s):  
Yi Zhang ◽  
Mohith Manjunath ◽  
Yeonsung Kim ◽  
Joerg Heintz ◽  
Jun S. Song
Keyword(s):  
Knowledge Base ◽  
Educational Resource ◽  
Rapid Progress ◽  
Structured Knowledge ◽  
Ngs Data Analysis ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Acute Challenge

AbstractNext-generation sequencing (NGS) techniques are revolutionizing biomedical research by providing powerful methods for generating genomic and epigenomic profiles. The rapid progress is posing an acute challenge to students and researchers to stay acquainted with the numerous available methods. We have developed an interactive online educational resource called SequencEnG (acronym for Sequencing Techniques Engine for Genomics) to provide a tree-structured knowledge base of 66 different sequencing techniques and step-by-step NGS data analysis pipelines comparing popular tools. SequencEnG is designed to facilitate barrier-free learning of current NGS techniques and provides a user-friendly interface for searching through experimental and analysis methods. SequencEnG is part of the project KnowEnG (Knowledge Engine for Genomics) and is freely available at http://education.knoweng.org/sequenceng/.

Knowledge Interchange in Task-Oriented Architecture: For Space Robot Application

2013 ◽  
Vol 303-306 ◽  
pp. 1774-1781
Author(s):  
Yu Cen ◽  
Wei Jia Zhou
Keyword(s):  
Knowledge Base ◽  
Knowledge Bases ◽  
Space Robot ◽  
Task Completion ◽  
Robot System ◽  
Analysis Task ◽  
Task Processing ◽  
Interchange Format ◽  
Description Task ◽  
Task Oriented

Behaviors of multi-robot system based on task-oriented architecture are intuitional according to the flow of task processing that is obvious to plan and monitor. This paper tables a novel task-oriented architecture for space robot application, which consists of task description, task completion analysis, task compromise. For this architecture, author designed a knowledge interchange mechanism base on KIF (Knowledge Interchange Format) and OKBC (Open Knowledge Base Connectivity). Using this knowledge interchange mechanism, knowledge bases designed by different languages comprehend information transmitted form each other.

scholarly journals CitrusKB: A Comprehensive Knowledge Base for Transcriptome and Interactome of Citrus spp. Infected by Xanthomonas citri subsp. citri at Different Infection Stages

2020 ◽  
Author(s):  
Adriano Ferrasa ◽  
Mayara M. Murata ◽  
Teresa D. C. G. Cofre ◽  
Juliana S. Cavallini ◽  
Gustavo Peron ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Citrus Canker ◽  
Limited Information ◽  
Xanthomonas Citri ◽  
Comprehensive Knowledge ◽  
Genetic Mechanisms ◽  
Serious Disease ◽  
Canker Development ◽  
User Friendly

AbstractCitrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the knowledge base for transcriptome of in vivo citrus interactome, the CitrusKB. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable source of information on citrus and their interaction with the citrus canker bacterium X. citri. The database provides tools for a user-friendly web interface to search and analyze a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease and their interaction, at different stages of infection, with the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue by incorporating annotations and analysis tools. We expect that CitrusKB may substantially contribute to the area of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

scholarly journals mirtronDB: a mirtron knowledge base

2019 ◽  
Vol 35 (19) ◽  
pp. 3873-3874 ◽  
Author(s):  
Bruno Henrique Ribeiro Da Fonseca ◽  
Douglas Silva Domingues ◽  
Alexandre Rossi Paschoal
Keyword(s):  
Knowledge Base ◽  
Current Literature ◽  
Supplementary Information ◽  
Supplementary Data ◽  
The Public ◽  
Knowledge Database ◽  
Group Type ◽  
Access To Knowledge ◽  
User Friendly ◽  
Organism Group

Abstract Motivation Mirtrons arise from short introns with atypical cleavage by using the splicing mechanism. In the current literature, there is no repository centralizing and organizing the data available to the public. To fill this gap, we developed mirtronDB, the first knowledge database dedicated to mirtron, and it is available at http://mirtrondb.cp.utfpr.edu.br/. MirtronDB currently contains a total of 1407 mirtron precursors and 2426 mirtron mature sequences in 18 species. Results Through a user-friendly interface, users can now browse and search mirtrons by organism, organism group, type and name. MirtronDB is a specialized resource that provides free and user-friendly access to knowledge on mirtron data. Availability and implementation MirtronDB is available at http://mirtrondb.cp.utfpr.edu.br/. Supplementary information Supplementary data are available at Bioinformatics online.

Sign in / Sign up

Export Citation Format

Share Document