- https://www.linkedin.com/in/brandizi/edit
Feature_updates: User interface: Improved search interface now supporting <em><strong>without-keyword</strong></em> search New <strong>search-modes</strong> implemented for search with gene-list only,... more
Feature_updates: User interface: Improved search interface now supporting <em><strong>without-keyword</strong></em> search New <strong>search-modes</strong> implemented for search with gene-list only, genomic/qtl regions only, and gene-list + region-search in addition to existing keyword-centric search-modes Added pre-loading spinner for KnetMiner search New search interface layout, icons, post-search auto-scrolling and CSS cleanup Updates to species/data <em>release</em> notes, fixes added to network stats displayed in release notes Deployment: New deployment framework implemented using <strong>Docker</strong> <em><strong>Dockerfiles</strong></em> developed to automate building Docker images for <strong>KnetMiner</strong> for AWS and local deployment. Detailed documentation available at knetminer-docker-docs Build scripts implemented to automate species-specific Dockerfile invocation. Ge...
KnetMiner - web application for gene mining and biological knowledge discovery
Key Features <strong>Gene List & Genome Region search are so much better now</strong>. You have a list of genes and no clue what they do? Just paste you gene ids/names into the Gene List box (without any keyword) and KnetMiner... more
Key Features <strong>Gene List & Genome Region search are so much better now</strong>. You have a list of genes and no clue what they do? Just paste you gene ids/names into the Gene List box (without any keyword) and KnetMiner will provide a summary of your genes, their location, enriched linked terms and allow you to view their knowledge network. Genes wont be ranked and only paths from gene to trait and phenotype nodes will initially be shown. If you combine your gene list with keywords, KnetMiner will be able to rank your gene list based on relevance and highlight the most interesting paths of the knowledge network. <strong>Smart Publication filtering</strong>. Some genes are linked to hundreds of papers. KnetMiner will now only show the most recent 20 publications in GeneView (Evidence box) and in NetworkView. This change will help you to get quicker to most recent research papers and has significantly improved the KnetMiner loading time. <strong>Ne...
In recent years, bioscience communities centered on particular areas of study, or groups of technologies, have generated so-called Minimum Information (MI) checklists specifying the data and metadata that should be captured from the... more
In recent years, bioscience communities centered on particular areas of study, or groups of technologies, have generated so-called Minimum Information (MI) checklists specifying the data and metadata that should be captured from the totality of information generated in the course of an investigation. In parallel, ontologies, formats, data capture tools and databases have been developed that can support the collection, validation, archiving and sharing of MI checklist-compliant data sets. In this paper, we discuss our ...
Research Interests:
Research Interests:
Key Features <strong>Better Gene List & Genome Region Search</strong>. You have a list of genes and no clue what they do? Just paste your gene ids/names into the Gene List box (without any keyword) and let KnetMiner provide a... more
Key Features <strong>Better Gene List & Genome Region Search</strong>. You have a list of genes and no clue what they do? Just paste your gene ids/names into the Gene List box (without any keyword) and let KnetMiner provide a summary of all information it has for your genes, their location, enriched linked terms and allow you to view their knowledge network. Genes won't be ranked and only paths from gene to trait and phenotype nodes will initially be shown. If you combine your gene list with keywords, KnetMiner will be able to rank your gene list based on relevance and highlight the most interesting paths of the knowledge network. <strong>New Web API access</strong>. KnetMiner knowledge networks can now be searched and visualized through API calls. For example, check out the MFT gene in araknet, wheatknet or riceknet. Adding a keyword argument to the URL will do some smart filtering and display the most interesting paths connecting genes and keywords (see...
Documentation for the COVID-19 KnetGraph SPARQL and Cypher endpoints
<b>Copyright information:</b>Taken from "The Genopolis Microarray Database"http://www.biomedcentral.com/1471-2105/8/S1/S21BMC Bioinformatics 2007;8(Suppl 1):S21-S21.Published online 8 Mar... more
<b>Copyright information:</b>Taken from "The Genopolis Microarray Database"http://www.biomedcentral.com/1471-2105/8/S1/S21BMC Bioinformatics 2007;8(Suppl 1):S21-S21.Published online 8 Mar 2007PMCID:PMC1885851.ers/groups association has a related list of permissions. Experiments belong to groups. Access rights of a user to an experiment are determined by the combination of user membership and experiment membership.
<b>Copyright information:</b>Taken from "The Genopolis Microarray Database"http://www.biomedcentral.com/1471-2105/8/S1/S21BMC Bioinformatics 2007;8(Suppl 1):S21-S21.Published online 8 Mar 2007PMCID:PMC1885851.tabase.... more
<b>Copyright information:</b>Taken from "The Genopolis Microarray Database"http://www.biomedcentral.com/1471-2105/8/S1/S21BMC Bioinformatics 2007;8(Suppl 1):S21-S21.Published online 8 Mar 2007PMCID:PMC1885851.tabase. We represent data by means of a business objects layer. The representation is consistent with the MIAME recommendations and is similar to MAGE-OM. Respect to this two main simplifications have been introduced. First, we ignore chips manufacturing, since we make use of only one standard platform already described by Affymetrix. Second, we model the experiment design as a tree structure. Although this is not general (for instance, the same stimulus could be applied to two samples) it is a good compromise between flexibility and easy of use. We use controlled vocabulary and protocol classes to manage non free text fields.
KnetMiner - web application for gene mining and biological knowledge discovery
This document describes ISA-TAB, a general purpose framework with which to capture and communicate the complex metadata required to interpret experiments employing combinations of technologies, and the associated data files.
BACKGROUND As the size and complexity of scientific datasets and the corresponding information stores grow, standards for collecting, describing, formatting, submitting and exchanging information are playing an increasingly active role.... more
BACKGROUND As the size and complexity of scientific datasets and the corresponding information stores grow, standards for collecting, describing, formatting, submitting and exchanging information are playing an increasingly active role. Several initiatives occupy strategic positions in the international scenario, both within and across domains. However, the job of harmonising reporting standards is still very much a work in progress; both software interoperability and the data integration remain challenging as things stand. RESULTS The status quo with respect to standardization initiatives is summarized here, with particular emphasis on the motivation for, and the challenges of, ongoing synergistic activities amongst the academic community focused on the creation of truly interoperable standards. CONCLUSIONS Groups generating standards should engage with ongoing cross-domain activities to simplify the integration of heterogeneous data sets to the greatest possible extent.
Research Interests:
Research Interests:
Research Interests:
As the size and complexity of scientific datasets and the corresponding information stores grow, standards for collecting, describing, formatting, submitting and exchanging information are playing an increasingly active role. Several... more
As the size and complexity of scientific datasets and the corresponding information stores grow, standards for collecting, describing, formatting, submitting and exchanging information are playing an increasingly active role. Several initiatives occupy strategic positions in the international scenario, both within and across domains. However, the job of harmonising reporting standards is still very much a work in progress; both software interoperability and the data integration remain challenging as things stand. The status quo with respect to standardization initiatives is summarized here, with particular emphasis on the motivation for, and the challenges of, ongoing synergistic activities amongst the academic community focused on the creation of truly interoperable standards. Groups generating standards should engage with ongoing cross-domain activities to simplify the integration of heterogeneous data sets to the greatest possible extent.
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests: Computer Science, Data Analysis, Medicine, Gene expression, Database Management Systems, and 15 moreBiological Sciences, Mathematical Sciences, BMC Bioinformatics, Dendritic cell, Knowledge base, Computer User Interface Design, Information Storage and Retrieval, Host Parasite Interaction, Controlled Vocabulary, Internet, Database System, Microarray Data, Gene expression profiling, Functional Annotation, and interactive user interface
Research Interests:
Research Interests:
Research Interests:
Microarrays are fundamental tools of nowadays Biology research. While standard formats and software systems have been developed to represent and publicly share information about microarray experiments, limited support is given to the... more
Microarrays are fundamental tools of nowadays Biology research. While standard formats and software systems have been developed to represent and publicly share information about microarray experiments, limited support is given to the representation of the outcomes, experimental hypotheses or conclusions about biological questions that are dealt with in gene expression analysis. We propose an OWL-based model and a Semantic Web-based approach to address the issue. We show that the formalization of microarray-related ...
Abstract. DC-THERA Directory is a web portal to support collaboration, communication and knowledge sharing within DC-THERA, a community focused on immunology. We show how we have faced the problem of representing and managing highly... more
Abstract. DC-THERA Directory is a web portal to support collaboration, communication and knowledge sharing within DC-THERA, a community focused on immunology. We show how we have faced the problem of representing and managing highly heterogeneous and interconnected knowledge. One aspect of the application interface is the search and navigation through web ontologies. Another aspect is the dynamic representation of information entities having variable sets of properties. These results have been achieved ...
Research Interests:
Graph-based modelling is becoming more popular, in the sciences and elsewhere, as a flexible and powerful way to exploit data to power world-changing digital applications. Compared to the initial vision of the Semantic Web, knowledge... more
Graph-based modelling is becoming more popular, in the sciences and elsewhere, as a flexible and powerful way to exploit data to power world-changing digital applications. Compared to the initial vision of the Semantic Web, knowledge graphs and graph databases are becoming a practical and computationally less formal way to manage graph data. On the other hand, linked data based on Semantic Web standards are a complementary, rather than alternative, approach to deal with these data, since they still provide a common way to represent and exchange information. In this paper we introduce rdf2neo, a tool to populate Neo4j databases starting from RDF data sets, based on a configurable mapping between the two. By employing agrigenomicsrelated real use cases, we show how such mapping can allow for a hybrid approach to the management of networked knowledge, based on taking advantage of the best of both RDF and property graphs.
Research Interests:
Enormous volumes of COVID-19 research data have been published and this continues to increase daily. This creates challenges for researchers to interpret, prioritize and summarize their own findings in the context of published literature,... more
Enormous volumes of COVID-19 research data have been published and this continues to increase daily. This creates challenges for researchers to interpret, prioritize and summarize their own findings in the context of published literature, clinical trials, and a multitude of databases. Overcoming the data interpretation bottleneck is vital to help researchers to be more efficient in their quest to identify COVID-19 risk factors, potential treatments, drug side-effects, and much more. As a proof of concept, we have organized and integrated a range of COVID-19 and human biomedical data and literature into a knowledge graph (KG). Here we present the datasets we have integrated so far and the content of the KG which consists of 674,969 biological concepts and over 1.6 million relationships between them. The COVID-19 KG is available via KnetMiner, an interactive online platform for gene discovery and knowledge mining, or via RDF and Neo4j graph formats which can be searched programmatical...
Research Interests:
ABSTRACTGenerating new ideas and scientific hypotheses is often the result of extensive literature and database reviews, overlaid with scientists’ own novel data and a creative process of making connections that were not made before. We... more
ABSTRACTGenerating new ideas and scientific hypotheses is often the result of extensive literature and database reviews, overlaid with scientists’ own novel data and a creative process of making connections that were not made before. We have developed a comprehensive approach to guide this technically challenging data integration task and to make knowledge discovery and hypotheses generation easier for plant and crop researchers. KnetMiner can digest large volumes of scientific literature and biological research to find and visualise links between the genetic and biological properties of complex traits and diseases. Here we report the main design principles behind KnetMiner and provide use cases for mining public datasets to identify unknown links between traits such grain colour and pre-harvest sprouting in Triticum aestivum, as well as, an evidence-based approach to identify candidate genes under an Arabidopsis thaliana petal size QTL. We have developed KnetMiner knowledge graphs ...
The speed and accuracy of new scientific discoveries - be it by humans or artificial intelligence - depends on the quality of the underlying data and on the technology to connect, search and share the data efficiently. In recent years, we... more
The speed and accuracy of new scientific discoveries - be it by humans or artificial intelligence - depends on the quality of the underlying data and on the technology to connect, search and share the data efficiently. In recent years, we have seen the rise of graph databases and semi-formal data models such as knowledge graphs to facilitate software approaches to scientific discovery. These approaches extend work based on formalised models, such as the Semantic Web. In this paper, we present our developments to connect, search and share data about genome-scale knowledge networks (GSKN). We have developed a simple application ontology based on OWL/RDF with mappings to standard schemas. We are employing the ontology to power data access services like resolvable URIs, SPARQL endpoints, JSON-LD web APIs and Neo4j-based knowledge graphs. We demonstrate how the proposed ontology and graph databases considerably improve search and access to interoperable and reusable biological knowledge ...
Research Interests:
ABSTRACTGenerating new ideas and scientific hypotheses is often the result of extensive literature and database reviews, overlaid with scientists’ own novel data and a creative process of making connections that were not made before. We... more
ABSTRACTGenerating new ideas and scientific hypotheses is often the result of extensive literature and database reviews, overlaid with scientists’ own novel data and a creative process of making connections that were not made before. We have developed a comprehensive approach to guide this technically challenging data integration task and to make knowledge discovery and hypotheses generation easier for plant and crop researchers. KnetMiner can digest large volumes of scientific literature and biological research to find and visualise links between the genetic and biological properties of complex traits and diseases. Here we report the main design principles behind KnetMiner and provide use cases for mining public datasets to identify unknown links between traits such grain colour and pre-harvest sprouting in Triticum aestivum, as well as, an evidence-based approach to identify candidate genes under an Arabidopsis thaliana petal size QTL. We have developed KnetMiner knowledge graphs ...
Research Interests:
The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other... more
The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories. Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.org Contact: isatools@googlegroups.com
Research Interests:
Research Interests:
Abstract. DC-THERA Directory is a web portal to support collaboration, communication and knowledge sharing within DC-THERA, a community focused on immunology. We show how we have faced the problem of representing and managing highly... more
Abstract. DC-THERA Directory is a web portal to support collaboration, communication and knowledge sharing within DC-THERA, a community focused on immunology. We show how we have faced the problem of representing and managing highly heterogeneous and interconnected knowledge. One aspect of the application interface is the search and navigation through web ontologies. Another aspect is the dynamic representation of information entities having variable sets of properties. These results have been achieved ...