scholarly journals BioKEEN: A library for learning and evaluating biological knowledge graph embeddings

2018 ◽  
Author(s):  
Mehdi Ali ◽  
Charles Tapley Hoyt ◽  
Daniel Domingo-Fernández ◽  
Jens Lehmann ◽  
Hajira Jabeen
Keyword(s):  
Knowledge Graph ◽  
Biological Knowledge ◽  
Command Line ◽  
Graph Embeddings ◽  
Command Line Interface ◽  
Software Ecosystem ◽  
Link Type ◽  
Mapping Resource ◽  
Significant Attention

AbstractKnowledge graph embeddings (KGEs) have received significant attention in other domains due to their ability to predict links and create dense representations for graphs’ nodes and edges. However, the software ecosystem for their application to bioinformatics remains limited and inaccessible for users without expertise in programming and machine learning. Therefore, we developed BioKEEN (Biological KnowlEdge EmbeddiNgs) and PyKEEN (Python KnowlEdge EmbeddiNgs) to facilitate their easy use through an interactive command line interface. Finally, we present a case study in which we used a novel biological pathway mapping resource to predict links that represent pathway crosstalks and hierarchies.AvailabilityBioKEEN and PyKEEN are open source Python packages publicly available under the MIT License at https://github.com/SmartDataAnalytics/BioKEEN and https://github.com/SmartDataAnalytics/PyKEEN as well as through PyPI.

scholarly journals BioKEEN: a library for learning and evaluating biological knowledge graph embeddings

2019 ◽  
Vol 35 (18) ◽  
pp. 3538-3540 ◽  
Author(s):  
Mehdi Ali ◽  
Charles Tapley Hoyt ◽  
Daniel Domingo-Fernández ◽  
Jens Lehmann ◽  
Hajira Jabeen
Keyword(s):  
Supplementary Information ◽  
Knowledge Graph ◽  
Biological Knowledge ◽  
Command Line ◽  
Graph Embeddings ◽  
Command Line Interface ◽  
Software Ecosystem ◽  
Mapping Resource ◽  
Significant Attention

Abstract Summary Knowledge graph embeddings (KGEs) have received significant attention in other domains due to their ability to predict links and create dense representations for graphs’ nodes and edges. However, the software ecosystem for their application to bioinformatics remains limited and inaccessible for users without expertise in programing and machine learning. Therefore, we developed BioKEEN (Biological KnowlEdge EmbeddiNgs) and PyKEEN (Python KnowlEdge EmbeddiNgs) to facilitate their easy use through an interactive command line interface. Finally, we present a case study in which we used a novel biological pathway mapping resource to predict links that represent pathway crosstalks and hierarchies. Availability and implementation BioKEEN and PyKEEN are open source Python packages publicly available under the MIT License at https://github.com/SmartDataAnalytics/BioKEEN and https://github.com/SmartDataAnalytics/PyKEEN Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization

2020 ◽  
Author(s):  
Boxiang Liu ◽  
Kaibo Liu ◽  
He Zhang ◽  
Liang Zhang ◽  
Yuchen Bian ◽  
...  
Keyword(s):  
Ad Hoc ◽  
Rapid Analysis ◽  
Supplementary Information ◽  
Command Line ◽  
Command Line Interface ◽  
Link Type ◽  
Global Pandemic ◽  
Fast Pace ◽  
Public Repositories ◽  
Programming Knowledge

AbstractSummaryCOVID-19 has become a global pandemic not long after its inception in late 2019. SARS-CoV-2 genomes are being sequenced and shared on public repositories at a fast pace. To keep up with these updates, scientists need to frequently refresh and reclean datasets, which is ad hoc and labor-intensive. Further, scientists with limited bioinformatics or programming knowledge may find it difficult to analyze SARS-CoV-2 genomes. In order to address these challenges, we developed CoV-Seq, a webserver to enable simple and rapid analysis of SARS-CoV-2 genomes. Given a new sequence, CoV-Seq automatically predicts gene boundaries and identifies genetic variants, which are presented in an interactive genome visualizer and are downloadable for further analysis. A command-line interface is also available for high-throughput processing.Availability and ImplementationCoV-Seq is implemented in Python and Javascript. The webserver is available at http://covseq.baidu.com/ and the source code is available from https://github.com/boxiangliu/[email protected] informationSupplementary information are available at bioRxiv online.

scholarly journals miR2Trait: an integrated resource for investigating miRNA-disease associations

2021 ◽  
Author(s):  
Poornima Babu ◽  
Ashok Palaniappan
Keyword(s):  
Open Source ◽  
Human Health ◽  
Regulatory Networks ◽  
Command Line ◽  
Command Line Interface ◽  
Cascading Effects ◽  
Commercial Use ◽  
Link Type ◽  
Disease Associations

ABSTRACTMicroRNAs are key components of cellular regulatory networks, and breakdown in miRNA function could lead to cascading effects culminating in pathophenotypes. A better understanding of the role of miRNAs in diseases would aid human health. Here, we have devised a method for comprehensively mapping the associations between miRNAs and diseases by merging on a common key between two curated omics databases. The resulting bidirectional resource, miR2Trait, is more detailed than earlier catalogues, uncovers new relationships, and includes analytical utilities to interrogate and extract knowledge from these datasets. The resource could aid in identifying the disease enrichment of a user-given set of miRNAs and analyzing the miRNA profile of a specified diseasome. miR2Trait is available as both a web-server (https://sas.sastra.edu/pymir18) and an open-source command-line interface (https://github.com/miR2Trait) under MIT license for both commercial and non-commercial use. The datasets are available for download at: https://doi.org/10.6084/m9.figshare.8288825.

scholarly journals PrimerServer: a high-throughput primer design and specificity-checking platform

2017 ◽  
Author(s):  
Tao Zhu ◽  
Chengzhen Liang ◽  
Zhigang Meng ◽  
Yanyan Li ◽  
Yayu Wu ◽  
...  
Keyword(s):  
High Throughput ◽  
Molecular Breeding ◽  
Primer Design ◽  
Command Line ◽  
Specific Primers ◽  
Data Presentation ◽  
Medical Testing ◽  
Link Type ◽  
Fast Running

AbstractSummaryDesigning specific primers for multiple sites across the whole genome is still challenging, especially in species with complex genomes. Here we present PrimerServer, a high-throughput primer design and specificity-checking platform with both web and command-line interfaces. This platform efficiently integrates site selection, primer design, specificity checking and data presentation. In our case study, PrimerServer achieved high accuracy and a fast running speed for a large number of sites, suggesting its potential for molecular biology applications such as molecular breeding or medical testing.Availability and ImplementationSource code for PrimerServer is available at https://github.com/billzt/PrimerServer. A demo server is freely accessible at https://primerserver.org, with all major browsers [email protected] or [email protected]

ESIS ON THE WORLD WIDE WEB

1994 ◽  
Vol 05 (05) ◽  
pp. 805-809 ◽  
Author(s):  
SALIM G. ANSARI ◽  
PAOLO GIOMMI ◽  
ALBERTO MICOL
Keyword(s):  
World Wide Web ◽  
Web Application ◽  
World Wide ◽  
Markup Language ◽  
Command Line ◽  
Command Line Interface ◽  
The World ◽  
Hypertext Transfer Protocol ◽  
Hypertext Markup Language ◽  
Near Future

On 3rd November, 1993, ESIS announced its Homepage on the World Wide Web (WWW) to the user community. Ever since then, ESIS has steadily increased its Web support to the astronomical community to include a bibliographic service, the ESIS catalogue documentation and the ESIS Data Browser. More functionality will be added in the near future. All these services share a common ESIS structure that is used by other ESIS user paradigms such as the ESIS Graphical User Interface (Giommi and Ansari, 1993), and the ESIS Command Line Interface. A forms-based paradigm, each ESIS-Web application interfaces to the hypertext transfer protocol (http) translating queries from/to the hypertext markup language (html) format understood by the NCSA Mosaic interface. In this paper, we discuss the ESIS system and show how each ESIS service works on the World Wide Web client.

Knowledge Recommendation System for Human-Robot Collaborative Disassembly Using Knowledge Graph

2021 ◽  
Author(s):  
Yang Hu ◽  
Yiwen Ding ◽  
Feng Xu ◽  
Jiayi Liu ◽  
Wenjun Xu ◽  
...  
Keyword(s):  
Recommendation System ◽  
Industrial Robots ◽  
Knowledge Graph ◽  
Disassembly Process ◽  
Knowledge Based ◽  
Manufacturing Efficiency ◽  
Human Operators ◽  
Traditional Manufacturing ◽  
Human Robot Collaboration

Abstract In recent years, more and more attention has been paid to Human-Robot Collaborative Disassembly (HRCD) in the field of industrial remanufacturing. Compared with the traditional manufacturing, HRCD helps to improve the manufacturing flexibility with considering the manufacturing efficiency. In HRCD, knowledge could be obtained from the disassembly process and then provides useful information for the operator and robots to execute their disassembly tasks. Afterwards, a crucial point is to establish a knowledge-based system to facilitate the interaction between human operators and industrial robots. In this context, a knowledge recommendation system based on knowledge graph is proposed to effectively support Human-Robot Collaboration (HRC) in disassembly. A disassembly knowledge graph is constructed to organize and manage the knowledge in the process of HRCD. After that, based on this, a knowledge recommendation procedure is proposed to recommend disassembly knowledge for the operator. Finally, the case study demonstrates that the developed system can effectively acquire, manage and visualize the related knowledge of HRCD, and then assist the human operator to complete the disassembly task by knowledge recommendation, thus improving the efficiency of collaborative disassembly. This system could be used in the human-robot collaboration disassembly process for the operators to provide convenient knowledge recommendation service.

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