2023, Abstract in atti di convegno, ENG
Filippo Biscarini, Chiara Gini , Latifa Najar, Fabrizio Ceciliani
The sequencing of the 16S subunit of the bacterial rRNA gene is extensively used as marker gene for the identification and quantification of the individual components of microbial communities. This approach, known as metataxonomics, is applied across a wide range of scientific disciplines, from plant and animal science, to human biology and medicine, to ecology. Several bioinformatic pipelines of analysis have been developed to process this type of data; however, this is a relatively recent field, and it is not yet clear how different pipelines compare. In this work, we are comparing five bioinformatic pipelines: QIIME (quantitative insights into microbial ecology) 1 & 2; MICCA (microbial community analysis); VSEARCH and MOTHUR. We have fixed the set of parameters to process 16S sequencing data (e.g. reads filtering criteria), to make the pipelines as comparable as possible, and investigated the use of different versions of the SILVA and RDP reference microbial databases. These different pipelines have been applied to mock communities (3 samples) for which the bacterial composition was known, and to 64 cow milk samples from the EU-PRIMA project MILKQUA (Milk Quality along the Dairy Chain for a Safe and Sustainable Milk; MILKQUA-H2020-PRIMA 2018--Section 2, MIUR -Italian Ministry of Education, University and Research- Decree n. 593, 26/07/2016). The pipelines are being run up to the production of the OTU/ASV table (table of abundances of bacterial taxa per sample). Results are currently in progress and will be compared in terms of: i) for the mock community data, how well they predict the actual composition of bacterial communities; ii) for milk samples data, how much the detected bacterial composition changes as a function of the pipeline+database combination.
2020, Curatela di atti di convegno (conference proceedings), ENG
Ulrich Schwardmann, Christian Boehme, Dora B. Heras, Valeria Cardellini, Emmanuel Jeannot, Antonio Salis, Claudio Schifanella, Ravi Reddy, Manumachu, Dieter Schwamborn, Laura Ricci, Oh Sangyoon, Thomas Gruber, Laura Antonelli, Stephen L. Scott
Euro-Par 2019 International Workshops, Revised Selected Papers
2019, Abstract in atti di convegno, ENG
Vennari C., Casarano D., Marchesini I., Salvati P., Parise M. & Lollino P.
2019, Contributo in atti di convegno, ENG
Angelo Zinzi ; Maria Teresa Melis ; Maria Teresa Brunetti ; Francesco Zucca ; Paolo Giommi
Exploiting data acquired by different instruments with a 3D visualization is recently becoming a mandatory requirement for a great part of space missions (e.g., [1]). In this context, we adapted MATISSE [2] to the needs of the Moon Mapping project [3], by adding to its database observations and high-order outputs coming from Chang'e 1 and Chang'e 2 (in the following CE1 and CE2, respectively) Chinese missions to the Moon. This task required the development of ad hoc software, able to ingest and spatially (re)project the data, mostly which are mostly formatted compliant to the PDS (Planetary Data System) standard. The possibility of analyzing the data with an effective threedimensional perspective added value to their scientific content and at the same time gave also and easy and "smart" access to the data to non-professional users, which is one of the main target of the Moon Mapping project.
2019, Articolo in rivista, ENG
Matarrese P.; Tieri P.; Anticoli S.; Ascione B.; Conte M.; Franceschi C.; Malorni W.; Salvioli S.; Ruggieri A.
Sex dimorphism in cell response to stress has previously been investigated by different research groups. This dimorphism could be at least in part accounted for by sex-biased expression of regulatory elements such as microRNAs (miRs). In order to spot previously unknown miR expression differences we took advantage of prior knowledge on specialized databases to identify X chromosome-encoded miRs potentially escaping X chromosome inactivation (XCI). MiR-548am-5p emerged as potentially XCI escaper and was experimentally verified to be significantly up-regulated in human XX primary dermal fibroblasts (DFs) compared to XY ones. Accordingly, miR-548am-5p target mRNAs, e.g. the transcript for Bax, was differently modulated in XX and XY DFs. Functional analyses indicated that XY DFs were more prone to mitochondria-mediated apoptosis than XX ones. Experimentally induced overexpression of miR548am-5p in XY cells by lentivirus vector transduction decreased apoptosis susceptibility, whereas its down-regulation in XX cells enhanced apoptosis susceptibility. These data indicate that this approach could be used to identify previously unreported sex-biased differences in miR expression and that a miR identified with this approach, miR548am-5p, can account for sex-dependent differences observed in the susceptibility to mitochondrial apoptosis of human DFs.
2018, Articolo in rivista, ENG
Renna, Massimiliano; Montesano, Francesco F.; Signore, Angelo; Gonnella, Maria; Santamaria, Pietro
Puglia region is particularly rich in agro-biodiversity, representing an example of how local vegetables varieties can still strongly interact with modern horticulture. Unfortunately, the genetic diversity of vegetable crops in this region has been eroded, due to several factors such as abandonment of rural areas, ageing of the farming population, and failure to pass information down the generations. This article summarizes the objectives, methodological approach and results of the project Biodiversity of the Puglia's vegetable crops (BiodiverSO), an integrated project funded by Puglia Region Administration under the 2007-2013 and 2014-2020 Rural Development Program (RDP). Results were reported for each of the eight activities of the project. Moreover, the Polignano carrot (a local variety of Daucus carota L.) was described as a case study, since several tasks have been performed within all eight project activities with the aim of verifying the effectiveness of these actions in terms of safeguarding for this genetic resource strongly linked with local traditions. BiodiverSO is an example of protection and recovery of vegetables at risk of genetic erosion that could help to identify and valorize much of the Puglia's plant germplasm.
2017, Articolo in rivista, ENG
Cumbo F.; Fiscon G.; Ceri S.; Masseroli M.; Weitschek E.
Background: Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types. Results: We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration. Additionally, it supports the conversion in CSV, GTF, JSON, and XML standard formats. Furthermore, TCGA2BED extends TCGA data with information extracted from other genomic databases (i.e., NCBI Entrez Gene, HGNC, UCSC, and miRBase). We also provide and maintain an automatically updated data repository with publicly available Copy Number Variation, DNA-methylation, DNA-seq, miRNA-seq, and RNA-seq (V1,V2) experimental data of TCGA converted into the BED format, and their associated clinical and biospecimen meta data in attribute-value text format. Conclusions: The availability of the valuable TCGA data in BED format reduces the time spent in taking advantage of them: it is possible to efficiently and effectively deal with huge amounts of cancer genomic data integratively, and to search, retrieve and extend them with additional information. The BED format facilitates the investigators allowing several knowledge discovery analyses on all tumor types in TCGA with the final aim of understanding pathological mechanisms and aiding cancer treatments.
2014, Presentazione, ENG
Pio G., Ceci M., Malerba D., D'Elia D.
Deciphering the modular organization of gene regulatory networks is crucial for the understanding of biological processes at a system-wide level. MicroRNAs (miRNAs) represent the largest class of small non-coding RNAs (20-24 nucleotide long (nt)) acting as post-transcriptional regulators of many genes and playing a pivotal role in important biological processes, in almost all organisms and in a large number of human diseases. Computational approaches have been proven to be fundamental in the miRNA research for both gene-specific and large-scale predictions of miRNA targets, for the formulation of new functional hypothesis on their biological role and to guide experimental validations. However, their effectiveness is negatively affected by high uncertainty of miRNA gene target predictions and by the complexity of rules governing miRNA functional targeting whose mechanisms still remain elusive. In order to improve predictions of miRNA targets and to support the elucidation of miRNA functional role in the context of gene regulatory networks, we have recently developed a new two-stepped computational approach. In the first step, a semi-supervised ensemble-based classifier [1] is learned from both experimentally validated interactions (positively labelled examples) and miRNA gene target predictions (MTIs) returned from several prediction algorithms (unlabelled examples). This classifier acts as a meta-classifier of unlabelled examples. As a result of the first step, a unique (meta-)prediction score is available for all possible interactions. In the second step, these prediction scores are used to identify miRNA-gene regulatory networks (MGRNs) through the biclustering algorithm HOCCLUS2 [2]. The effectiveness of the computational approach has been validated on a number of alternative combinations of competitive algorithms for the first and the second step. Both the predicted MTIs and the MGRNs can be queried, retrieved, exported and visualized through the web-based system ComiRNet (http://193.204.187.158:9002/). The system interface facilitates the formulation of complex queries and help the user both in browsing bicluster hierarchies and in visualizing the interaction graph of MRGNs . The hierarchical organization of biclusters improves the interpretability of the results and emphasizes similarities among genes at different granularity levels, allowing ComiRNet users to explore many possible biological scenarios. The functional relationships suggested by miRNAs and target genes in biclusters can help to detect unknown functional similarities or synergies among miRNAs and among target genes, that can enable the discovery of new miRNA and gene functions. Acknowledgements We would like to acknowledge the support of the European Commission through the project MAESTRA - Learning from Massive, Incompletely annotated, and Structured Data (Grant number ICT-2013-612944). This work was also funded by the "PON01 02589 - MicroMap" project and by the flagship project "Interomics". References 1. Pio G, Malerba D, D'Elia D. and Ceci M (2014) Integrating microRNA target predictions for the discovery of gene regulatory networks: a semi-supervised ensemble learning approach, BMC Bioinformatics 15 (S-1): S4. doi:10.1186/1471-2105-15-S1-S4 2. Pio G, Ceci M, D'Elia D, Loglisci C, Malerba D (2013) A novel biclustering algorithm for the discovery of meaningful biological correlations between miRNAs and mRNAs. BMC Bioinformatics,14 (Suppl 7), S8. doi:10.1186/1471-2105-14-S7-S8
2008, Articolo in rivista, ENG
Neubert, Antje; Sturkenboom, Miriam C. J. M.; Murray, Macey L.; Verhamme, Katia M. C.; Nicolosi, Alfredo; Giaquinto, Carlo; Ceci, Adriana; Wong, Ian C. K.
Purpose To identify and describe European health care databases that can be used for pediatric pharmacoepidemiological research. Methods A web-based survey was conducted among all European databases that were listed on the website of the International Society of Pharmacoepidemiology (ISPE) and/or known by an expert group. The survey comprised of questions regarding (a) the nature of the database, (b) database size, (c) demographic, clinical and drug related data provided, (d) cost, and (e) accessibility of the database.
2007, Curatela di atti di convegno (conference proceedings), ENG
Kovács L.; Fuhr N.; Meghini C.
The proceedings contain 72 papers. The topics discussed include: ontology-based question answering for digital libraries; formalizing the get-specific document classification algorithm; trustworthiness analysis of web search results; improved publication scores for online digital libraries via research pyramids; a cooperative-relational approach to digital libraries; lyrics-based audio retrieval and multimodal navigation in music collections; automatic identification of music works through audio matching; roadmap for MultiLingual information access in the European library; a grid-based infrastructure for distributed retrieval; tests, illustrations, and physical objects: the case of ancient shipbuilding treatises; providing context-sensitive access to the earth observation product library; thesaurus-based feedback to support mixed search and browsing environments; and finding related papers in literature digital libraries.
2006, Contributo in atti di convegno, ENG
Bartolini R., Caracciolo C., Giovannetti E., Lenci A., Marchi S., Pirrelli V., Renso C., Spinsanti L.
In this paper we present an original approach to natural language query interpretation which has been implemented within the FuLL (Fuzzy Logic and Language) Italian project of BC S.r.l. In particular, we discuss here the creation of linguistic and ontological resources, together with the exploitation of existing ones, for natural language-driven database access and retrieval. Both the database and the queries we experiment with are Italian, but the methodology we broach naturally extends to other languages.
2003, Articolo in rivista
Pontieri Luigi,Ursino Domenico,Zumpano Ester
In this paper we propose an approach for the extensional integration of data sources with heterogeneous representation formats. The proposed approach is based on the exploitation of a new model, called E-SDR-Network, for representing and handling, at the extensional level, heterogeneous data sources, ranging from databases to XML documents, OEM graphs and other semi-structured data. Due to the specific features of E-SDR-Network, the proposed extensional integration methodology is capable of: (i) easily handling null or unknown values, (ii) producing consistent query answers from possibly inconsistent data and (iii) reconstructing, at the extensional level, the content of each data source involved in the integration task. Finally, we show that E-SDR-Network and the proposed extensional integration algorithm are the counterpart, at the extensional level, of the SDR-Network conceptual model and the associated intensional integration algorithm, already proposed in the literature. Therefore, in the whole, we obtain a complete approach consisting of two components performing synergically both the intensional and the extensional integration of data sources having heterogeneous data representation formats.
2003, Articolo in rivista, ITA/ENG
Marinelli R.
Over the last few years there has been much discussion about the relation between types of data, storage devices and system requirements for the preservation of data. This work carried out for the reorganization of the magnetic Archive of the Institute of Computational Linguistics (ILC), is an example of interaction between data management and recovery methods, as well as between data recording system development and evolution of storage devices. Data structure has also been affected by the technological evolution. It has been necessary to rely on an efficient, well-structured and tested data-base management system. Thus a computerized system was implemented for the joint management of normalized cataloguing files and bibliographic data, using the Information Retrieval System CDS/ISIS. A suitable description corresponding to standard criteria is necessary for a reliable tracing of the documents. The correct use of international standards like ISO to process traditional bibliographic information assures the accessibility, readability and consistency of the data.
2001, Articolo in rivista, ENG
Giannotti F.; Manco G.; Nanni M.; Pedreschi D.
We consider in this paper an extension of Datalog with mechanisms for temporal, nonmonotonic, and nondeterministic reasoning, which we refer to as Datalog++. We show, by means of examples, its flexibility in expressing queries concerning aggregates and data cube. Also, we show how iterated fixpoint and stable model semantics can be combined to the purpose of clarifying the semantics of Datalog++ programs and supporting their efficient execution. Finally, we provide a more concrete implementation strategy on which basis the design of optimization techniques tailored for Datalog++ is addressed.
2000, Articolo in rivista, ENG
M. Attimonelli*, N. Altamura1, R. Benne2, A. Brennicke3, J. M. Cooper4, D. D'Elia5, A. de Montalvo6, B. de Pinto1, M. De Robertis, P. Golik7, V. Knoop3, C. Lanave1, J. Lazowska7, F. Licciulli5, B. S. Malladi8, F. Memeo, M. Monnerot7, R. Pasimeni, S. Pilbout7, A. H. V. Schapira9, P. Sloof2 and, C. Saccone
MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbas e.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.
1997, Articolo in rivista, ENG
Formica, A; Missikoff, M
An object-oriented database (OODB) schema is represented by a collection of types (or class definitions), each of which consists of a set of typed attributes. A schema is generally organised according to an inheritance hierarchy, where subtypes are defined incrementally with respect to their supertypes. Along this hierarchy, subtypes inherit the characteristics of the supertypes. Despite the great variety of proposals in the literature, it is widely recognised that, in presence of inheritance, the object-oriented data model should guarantee, at extensional level, the following properties: (i) substitutiuity of instances; (ii) set inchsion of extensions. The former property guarantees that whenever an object of a given type is required (e.g., as a parameter in a function call) any subtype object can be used instead, without causing a type-check error. The latter property assures that the extension of a subtype is always (i.e., in any legal database) included in the extension of its supertypes. An object-oriented data model that complies with the two above points guarantees several desirable properties for the database schemas such as, for example, absence of run-time type errors [8]. Substitutivity and set inclusion semantics are difficult to be enforced without introducing strong limitations on the model, such as avoiding multiple inheritance or full recursion in the structure of the types.