Dataset Information

Methodology for development of a data and knowledge base for learning from existing nature-based solutions in Europe: The CONNECTING Nature project.

ABSTRACT: Within CONNECTING Nature, we are dealing with developing innovative nature-based solutions (NBS) for climate change adaptation, health and well-being, social cohesion and sustainable economic development in European cities. In order to enable "learning by comparing" and "generating new knowledge" from multiple NBS related studies, a novel data and knowledge base is needed which requires a specified methodological approach for its development. This paper provides conceptual and methodological context and techniques for constructing such a data and knowledge base that will systematically support the process of NBS monitoring and assessment:•A methodology presents the comprehensive, multi-step approach to the NBS data and knowledge development that helps to guide work and influence the quality of an information included.•The paper describes the methodology and main steps/phases for developing a large data and knowledge base of NBS that will allow further systematic review.•The suggested methodology explains how to build NBS related databases from the conceptualization and requirements phases through to implementation and maintenance. In this regard, such a methodology is iterative, with extensive NBS stakeholders' and end-user's involvement that are packaged with reusable templates or deliverables offering a good opportunity for success when used by practitioners and other end-users.•The NBS data and knowledge base gathers information about different NBS models and generations into one easy-to-find, easy-to-use place and provides detailed descriptions of each of the 1490 NBS cases from urban centers in Europe.•The data and knowledge base thus helps users identify the best and most appropriated NBS model/type for addressing the particular goals and, at the same time, considers the local context and potential.•The data obtained can be used for the further meta-analysis by applying statistics or searching for specific sample cases and thus enables to generate and expand the knowledge from multiple NBS related studies, in both qualitative and quantitative ways.

SUBMITTER: Dushkova D

PROVIDER: S-EPMC7600359 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Methodology for development of a data and knowledge base for learning from existing nature-based solutions in Europe: The CONNECTING Nature project.

Dushkova Diana D Haase Dagmar D

MethodsX 20201013

Within CONNECTING Nature, we are dealing with developing innovative nature-based solutions (NBS) for climate change adaptation, health and well-being, social cohesion and sustainable economic development in European cities. In order to enable "learning by comparing" and "generating new knowledge" from multiple NBS related studies, a novel data and knowledge base is needed which requires a specified methodological approach for its development. This paper provides conceptual and methodological con ...[more]

PMID: 33163370

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Project description:BACKGROUND: Identification of transcription factors (TFs) involved in a biological process is the first step towards a better understanding of the underlying regulatory mechanisms. However, due to the involvement of a large number of genes and complicated interactions in a gene regulatory network (GRN), identification of the TFs involved in a biology process remains to be very challenging. In reality, the recognition of TFs for a given a biological process can be further complicated by the fact that most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation except for small conserved domains. This poses a significant challenge for identification of the exact TFs involved or ranking the importance of a set of TFs to a process of interest. Therefore, new methods for recognizing novel TFs are desperately needed. Although a plethora of methods have been developed to infer regulatory genes using microarray data, it is still rare to find the methods that use existing knowledge base in particular the validated genes known to be involved in a process to bait/guide discovery of novel TFs. Such methods can replace the sometimes-arbitrary process of selection of candidate genes for experimental validation and significantly advance our knowledge and understanding of the regulation of a process. RESULTS: We developed an automated software package called TF-finder for recognizing TFs involved in a biological process using microarray data and existing knowledge base. TF-finder contains two components, adaptive sparse canonical correlation analysis (ASCCA) and enrichment test, for TF recognition. ASCCA uses positive target genes to bait TFS from gene expression data while enrichment test examines the presence of positive TFs in the outcomes from ASCCA. Using microarray data from salt and water stress experiments, we showed TF-finder is very efficient in recognizing many important TFs involved in salt and drought tolerance as evidenced by the rediscovery of those TFs that have been experimentally validated. The efficiency of TF-finder in recognizing novel TFs was further confirmed by a thorough comparison with a method called Intersection of Coexpression (ICE). CONCLUSIONS: TF-finder can be successfully used to infer novel TFs involved a biological process of interest using publicly available gene expression data and known positive genes from existing knowledge bases. The package for TF-finder includes an R script for ASCCA, a Perl controller, and several Perl scripts for parsing intermediate outputs. The package is available upon request (hairong@mtu.edu). The R code for standalone ASCCA is also available.

Dataset Information

Methodology for development of a data and knowledge base for learning from existing nature-based solutions in Europe: The CONNECTING Nature project.

Publications

Methodology for development of a data and knowledge base for learning from existing nature-based solutions in Europe: The CONNECTING Nature project.

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