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Specification Documentation: Isa-Tab 1.0

Philippe Rocca-Serra, Susanna-Assunta Sansone, Marco Brandizi
2009 Zenodo  
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.
doi:10.5281/zenodo.161355 fatcat:baitbvnbubfbzbc52ztcek4gzm

Specification Documentation: Release Candidate 1, Isa-Tab 1.0

Philippe Rocca-Serra, Susanna-Assunta Sansone, Marco Brandizi
2008 Zenodo  
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.
doi:10.5281/zenodo.161350 fatcat:me5prwg4irfzxgfzpt6rqq3tky

The Genopolis Microarray Database

Andrea Splendiani, Marco Brandizi, Gael Even, Ottavio Beretta, Norman Pavelka, Mattia Pelizzola, Manuel Mayhaus, Maria Foti, Giancarlo Mauri, Paola Ricciardi-Castagnoli
2007 BMC Bioinformatics  
Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood. Public repositories as well as microarray database systems that can be implemented by single laboratories exist. However, there is not yet a tool that can easily support a collaborative environment where different users with different rights of access to data can interact to define a common highly coherent content. The scope of
more » ... Genopolis database is to provide a resource that allows different groups performing microarray experiments related to a common subject to create a common coherent knowledge base and to analyse it. The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions.
doi:10.1186/1471-2105-8-s1-s21 pmid:17430566 pmcid:PMC1885851 fatcat:3niho2pmq5alveexgiuxlzowrm

Organizing knowledge to enable faster data interpretation in COVID-19 research

Joseph Hearnshaw, Marco Brandizi, Ajit Singh, Chris Rawlings, Keywan Hassani-Pak
2021 F1000Research  
., 2006) and provides exports to RDF and tooling to convert RDF to Neo4j (Brandizi et al., 2018b) .  ...  Datasource Data Types Concept Classes URLs 1 (Brandizi et al., 2018a)rmats.It contains data on 27,599 human genes that are present in the KG as "type gene" concepts that are linked to a range of other  ... 
doi:10.12688/f1000research.54071.1 fatcat:ebu5nrjdkng7tgh56oh5i4f4zu

KnetMiner - Intelligent search and visualisation of connected data to explain complex traits and diseases [article]

Keywan Hassani-Pak, Ajit Singh, Marco Brandizi, Joseph Hearnshaw, Andrew L Phillips, John H Doonan, Christopher Rawlings
2020 biorxiv/medrxiv   pre-print
et al., 2018a (Brandizi et al., , 2018b ; Hassani-Pak et al., 2016).  ...  ., 2010) , to publish KGs as standardized and interoperable data based on FAIR principles (Brandizi et al., 2018a) and to visualize biological knowledge networks in an interactive web application (Singh  ... 
doi:10.1101/2020.04.02.017004 fatcat:infoxkiv7fdchcivkmj4nnlpei

Updates to BioSamples database at European Bioinformatics Institute

Adam Faulconbridge, Tony Burdett, Marco Brandizi, Mikhail Gostev, Rui Pereira, Drashtti Vasant, Ugis Sarkans, Alvis Brazma, Helen Parkinson
2013 Nucleic Acids Research  
The BioSamples database at the EBI (http://www. ebi.ac.uk/biosamples) provides an integration point for BioSamples information between technology specific databases at the EBI, projects such as ENCODE and reference collections such as cell lines. The database delivers a unified query interface and API to query sample information across EBI's databases and provides links back to assay databases. Sample groups are used to manage related samples, e.g. those from an experimental submission, or a
more » ... gle reference collection. Infrastructural improvements include a new user interface with ontological and key word queries, a new query API, a new data submission API, complete RDF data download and a supporting SPARQL endpoint, accessioning at the point of submission to the European Nucleotide Archive and European Genotype Phenotype Archives and improved query response times.
doi:10.1093/nar/gkt1081 pmid:24265224 pmcid:PMC3965081 fatcat:lcjgrx5xy5bt5giyidtr2sammq

graph2tab, a library to convert experimental workflow graphs into tabular formats

Marco Brandizi, Natalja Kurbatova, Ugis Sarkans, Philippe Rocca-Serra
2012 Computer applications in the biosciences : CABIOS  
Motivations: Spreadsheet-like tabular formats are ever more popular in the biomedical field as a mean for experimental reporting. The problem of converting the graph of an experimental workflow into a table-based representation occurs in many such formats and is not easy to solve. Results: We describe graph2tab, a library that implements methods to realise such a conversion in a size-optimised way. Our solution is generic and can be adapted to specific cases of data exporters or data converters
more » ... that need to be implemented. Availability and Implementation: The library source code and documentation are available at http://github.com/ISA-tools/ graph2tab.
doi:10.1093/bioinformatics/bts258 pmid:22556367 pmcid:PMC3371871 fatcat:urvjq67w5zdqhcwfawq64ir35i

Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach

Marco Brandizi, Ajit Singh, Christopher Rawlings, Keywan Hassani-Pak
2018 Journal of Integrative Bioinformatics  
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
more » ... r 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 (i.e. the FAIRness data principles).
doi:10.1515/jib-2018-0023 pmid:30085931 pmcid:PMC6340125 fatcat:mjpm2gtx75dkxn5opunpiun7ta

Towards interoperable reporting standards for omics data: hopes and hurdles

Susanna-Assunta Sansone, Philippe Rocca-Serra, Dawn Field, Chris F Taylor, Weida Tong, Marco Brandizi, Eamonn Maguire, Nataliya Sklyar
2009 Summit on translational bioinformatics  
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
more » ... g 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.
pmid:21347181 pmcid:PMC3041584 fatcat:jfzbyzy76rglni4gkgq42mbuvi

ArrayExpress update—simplifying data submissions

Nikolay Kolesnikov, Emma Hastings, Maria Keays, Olga Melnichuk, Y. Amy Tang, Eleanor Williams, Miroslaw Dylag, Natalja Kurbatova, Marco Brandizi, Tony Burdett, Karyn Megy, Ekaterina Pilicheva (+6 others)
2014 Nucleic Acids Research  
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository for data supporting peer-reviewed publications. It contains data from over 7000 public sequencing and 42 000 array-based studies comprising over 1.5 million assays in total. The proportion of sequencing-based submissions has grown significantly over the last few
more » ... ars and has doubled in the last 18 months, whilst the rate of microarray submissions is growing slightly. All data in ArrayExpress are available in the MAGE-TAB format, which allows robust linking to data analysis and visualization tools and standardized analysis. The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold. In the near future, Annotare will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines. ArrayExpress is a stable and highly accessed resource. Our future tasks include automation of data flows and further integration with other EMBL-EBI resources for the representation of multiomics data.
doi:10.1093/nar/gku1057 pmid:25361974 pmcid:PMC4383899 fatcat:c4fvlffcnfcpde7agoxjir4beu

Sequence-specific Recognition of DNA by the C-terminal Domain of Nucleoid-associated Protein H-NS

Marco Sette, Roberto Spurio, Edoardo Trotta, Cinzia Brandizi, Anna Brandi, Cynthia L. Pon, Gaetano Barbato, Rolf Boelens, Claudio O. Gualerzi
2009 Journal of Biological Chemistry  
The molecular determinants necessary and sufficient for recognition of its specific DNA target are contained in the C-terminal domain (H-NSctd) of nucleoid-associated protein H-NS. H-NSctd protects from DNaseI cleavage a few short DNA segments of the H-NS-sensitive hns promoter whose sequences closely match the recently identified H-NS consensus motif (tCG(t/a)T(a/t)AATT) and, alone or fused to the protein oligomerization domain of phage CI repressor, inhibits transcription from the hns
more » ... in vitro and in vivo. The importance of H-NS oligomerization is indicated by the fact that with an extended hns promoter construct (400 bp), which allows protein oligomerization, DNA binding and transcriptional repression are highly and almost equally efficient with native H-NS and H-NSctd::CI and much less effective with the monomeric H-NSctd. With a shorter (110 bp) construct, which does not sustain extensive protein oligomerization, transcriptional repression is less effective, but native H-NS, H-NSctd::CI, and monomeric H-NSctd have comparable activity on this construct. The specific H-NS-DNA interaction was investigated by NMR spectroscopy using monomeric H-NSctd and short DNA duplexes encompassing the H-NS target sequence of hns (TCCTTACATT) with the best fit (8 of 10 residues) to the H-NSbinding motif. H-NSctd binds specifically and with high affinity to the chosen duplexes via an overall electropositive surface involving four residues (Thr 109 , Arg 113 , Thr 114 , and Ala 116 ) belonging to the same protein loop and Glu 101 . The DNA target is recognized by virtue of its sequence and of a TpA step that confers a structural irregularity to the B-DNA duplex. . 2 The abbreviations used are: C-domain, C-terminal domain; HSQC, heteronuclear single quantum coherence; NOESY, nuclear Overhauser effect spectroscopy.
doi:10.1074/jbc.m109.044313 pmid:19740756 pmcid:PMC2781600 fatcat:3fvi6afazbejdev7xxaevzqmw4

KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species

Keywan Hassani-Pak, Ajit Singh, Marco Brandizi, Joseph Hearnshaw, Jeremy D Parsons, Sandeep Amberkar, Andrew L Phillips, John H Doonan, Chris Rawlings
2021 Plant Biotechnology Journal  
et al., 2018a (Brandizi et al., , 2018b ; Hassani-Pak et al., 2016).  ...  ., 2010) , to publish KGs as standardized and interoperable data based on FAIR principles (Brandizi et al., 2018a) and to visualize biological knowledge networks in an interactive web application (Singh  ... 
doi:10.1111/pbi.13583 pmid:33750020 fatcat:xsjgscimlncdvolkd5c5wvnsrq

DC-THERA Directory, a Knowledge Management System for the support of the European Dendritic Cell Immunology Community

Marco Brandizi, Michaela Gündel, Ciro Scognamiglio, Andrea Splendiani
2009 Workshop on Semantic Web Applications and Tools for Life Sciences  
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
more » ... adopting a modelling approach that combines traditional object-oriented modelling with a triple-based knowledge representation. We discuss advantages of such an approach, especially for what concerns the possible future integration of other information sources.
dblp:conf/swat4ls/BrandiziGSS09 fatcat:4cg47mh4cjd2jgwujgpcc54oqa

Orchestrating differential data access for translational research: a pilot implementation

Marco Brandizi, Olga Melnichuk, Raffael Bild, Florian Kohlmayer, Benedicto Rodriguez-Castro, Helmut Spengler, Klaus A. Kuhn, Wolfgang Kuchinke, Christian Ohmann, Timo Mustonen, Mikael Linden, Tommi Nyrönen (+3 others)
2017 BMC Medical Informatics and Decision Making  
Translational researchers need robust IT solutions to access a range of data types, varying from public data sets to pseudonymised patient information with restricted access, provided on a case by case basis. The reason for this complication is that managing access policies to sensitive human data must consider issues of data confidentiality, identifiability, extent of consent, and data usage agreements. All these ethical, social and legal aspects must be incorporated into a differential
more » ... ent of restricted access to sensitive data. Methods: In this paper we present a pilot system that uses several common open source software components in a novel combination to coordinate access to heterogeneous biomedical data repositories containing open data (open access) as well as sensitive data (restricted access) in the domain of biobanking and biosample research. Our approach is based on a digital identity federation and software to manage resource access entitlements. Results: Open source software components were assembled and configured in such a way that they allow for different ways of restricted access according to the protection needs of the data. We have tested the resulting pilot infrastructure and assessed its performance, feasibility and reproducibility. Conclusions: Common open source software components are sufficient to allow for the creation of a secure system for differential access to sensitive data. The implementation of this system is exemplary for researchers facing similar requirements for restricted access data. Here we report experience and lessons learnt of our pilot implementation, which may be useful for similar use cases. Furthermore, we discuss possible extensions for more complex scenarios.
doi:10.1186/s12911-017-0424-6 pmid:28330491 pmcid:PMC5363029 fatcat:aigfcw4jjzdipnhtkwwatpik4u

The First RSBI (ISA-TAB) Workshop: "Can a Simple Format Work for Complex Studies?"

Susanna-Assunta Sansone, Philippe Rocca-Serra, Marco Brandizi, Alvis Brazma, Dawn Field, Jennifer Fostel, Andrew G. Garrow, Jack Gilbert, Federico Goodsaid, Nigel Hardy, Phil Jones, Allyson Lister (+8 others)
2008 Omics  
This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6-8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating
more » ... and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC). The OMICS Standards Scenario *See the RSBI and ISA-TAB Websites for a complete list of contributors. Web URL: http://www.mged.org/Workgroups/rsbi and
doi:10.1089/omi.2008.0019 pmid:18447634 fatcat:gzla7xafjvhl7afdidn2fyju3e
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