The Experts below are selected from a list of 249 Experts worldwide ranked by ideXlab platform

Stefan A Rensing - One of the best experts on this subject based on the ideXlab platform.

  • reannotation and extended community resources for the genome of the non seed plant physcomitrella patens provide insights into the evolution of plant gene structures and functions
    BMC Genomics, 2013
    Co-Authors: Andreas D Zimmer, Daniel Lang, Karol Buchta, Stephane Rombauts, Tomoaki Nishiyama, Mitsuyasu Hasebe, Yves Van De Peer, Stefan A Rensing
    Abstract:

    The moss Physcomitrella patens as a model species provides an important reference for early-diverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies. The usability of a reference genome greatly depends on the quality of the annotation and the availability of Centralized community resources. Therefore, in the light of accumulating evidence for missing genes, fragmentary gene structures, false annotations and a low rate of functional annotations on the original release, we decided to improve the moss genome annotation. Here, we report the complete moss genome re-annotation (designated V1.6) incorporating the increased transcript availability from a multitude of developmental stages and tissue types. We demonstrate the utility of the improved P. patens genome annotation for comparative genomics and new extensions to the cosmoss.org resource as a Central Repository for this plant “flagship” genome. The structural annotation of 32,275 protein-coding genes results in 8387 additional loci including 1456 loci with known protein domains or homologs in Plantae. This is the first release to include information on transcript isoforms, suggesting alternative splicing events for at least 10.8% of the loci. Furthermore, this release now also provides information on non-protein-coding loci. Functional annotations were improved regarding quality and coverage, resulting in 58% annotated loci (previously: 41%) that comprise also 7200 additional loci with GO annotations. Access and manual curation of the functional and structural genome annotation is provided via the http://www.cosmoss.org model organism database. Comparative analysis of gene structure evolution along the green plant lineage provides novel insights, such as a comparatively high number of loci with 5’-UTR introns in the moss. Comparative analysis of functional annotations reveals expansions of moss house-keeping and metabolic genes and further possibly adaptive, lineage-specific expansions and gains including at least 13% orphan genes.

Ana Maria De Carvalho Moura - One of the best experts on this subject based on the ideXlab platform.

  • metadata to support transformations and data metadata lineage in a warehousing environment
    Lecture Notes in Computer Science, 2004
    Co-Authors: Aurisan Souza De Santana, Ana Maria De Carvalho Moura
    Abstract:

    Data warehousing is a collection of concepts and tools which aim at providing and maintaining a set of integrated data (the data warehouse - DW ) for business decision support within an organization. They extract data from different operational data sources, and after some cleansing and transformation procedures data are integrated and loaded into a Central Repository to enable analysis and mining. Data and metadata lineage are important processes for data analysis. The first allows users to trace warehouse data items back to the original source item from which they were derived and the latter shows which operations have been performed to achieve that target data. This work proposes integrating metadata captured during transformation processes using the CWM metadata standard in order to enable data and metadata lineage. Additionally it presents a tool specially developed for performing this task.

Paula R Williamso - One of the best experts on this subject based on the ideXlab platform.

  • sharing individual participant data from clinical trials an opinion survey regarding the establishment of a Central Repository
    PLOS ONE, 2014
    Co-Authors: Catrin Tudu Smith, Kerry Dwa, Mike Clarke, Richard D Riley, Douglas G Altma, Paula R Williamso
    Abstract:

    Background: Calls have been made for increased access to individual participant data (IPD) from clinical trials, to ensure that complete evidence is available. However, despite the obvious benefits, progress towards this is frustratingly slow. In the meantime, many systematic reviews have already collected IPD from clinical trials. We propose that a Central Repository for these IPD should be established to ensure that these datasets are safeguarded and made available for use by others, building on the strengths and advantages of the collaborative groups that have been brought together in developing the datasets. Objective: Evaluate the level of support, and identify major issues, for establishing a Central Repository of IPD. Design: On-line survey with email reminders. Participants: 71 reviewers affiliated with the Cochrane Collaboration’s IPD Meta-analysis Methods Group were invited to participate. Results: 30 (42%) invitees responded: 28 (93%) had been involved in an IPD review and 24 (80%) had been involved in a randomised trial. 25 (83%) agreed that a Central Repository was a good idea and 25 (83%) agreed that they would provide their IPD for Central storage. Several benefits of a Central Repository were noted: safeguarding and standardisation of data, increased efficiency of IPD meta-analyses, knowledge advancement, and facilitating future clinical, and methodological research. The main concerns were gaining permission from trial data owners, uncertainty about the purpose of the Repository, potential resource implications, and increased workload for IPD reviewers. Restricted access requiring approval, data security, anonymisation of data, and oversight committees were highlighted as issues under governance of the Repository. Conclusion: There is support in this community of IPD reviewers, many of whom are also involved in clinical trials, for storing IPD in a Central Repository. Results from this survey are informing further work on developing a Repository of IPD which is currently underway by our group.

  • feasibility of establishing a Central Repository for the individual participant data from research studies
    Trials, 2011
    Co-Authors: Catrin Tudu Smith, Kerry Dwa, Mike Clarke, Richard D Riley, Douglas G Altma, Paula R Williamso
    Abstract:

    Meta-analysis of individual participant data (IPD) is widely accepted as the most reliable approach for systematic reviews. Advantages include standardising outcome definition across studies, increased potential to investigate subgroups, reducing bias by analysing on an intention to treat basis, minimising the possibility of within study selective reporting, thorough analyses of time to event outcomes, opportunities to identify unpublished studies through collaboration with the original researchers, and incorporating additional follow-up. IPD provides a rich source of information that allows clinical and methodological developments to extend beyond exploring the main effects that are traditionally of interest in a single trial or systematic review. These opportunities, coupled with the resources required for the IPD approach which are often prohibitive for reviewers, make it essential that as much use as possible is made of IPD that have been collected We propose that a secure Central Repository be established to store previously collected IPD. Restricted access to the Central Repository would only be granted following an approval process that would involve the original reviewers and a nominated committee. The Central Repository would facilitate exploring additional clinical and methodological questions across a range of studies and reviews. To assess the feasibility of developing and managing a Central Repository, we have undertaken an on-line survey of 70 IPD reviewers registered with the Cochrane IPD Meta-analysis Methods Group. We asked about their willingness to provide anonymised IPD from their review and asked about practical issues that this may raise. Non-responders have been reminded about the survey up to three times. Analyses are ongoing and will be presented, along with future plans at the conference.

Germa Rigau - One of the best experts on this subject based on the ideXlab platform.

  • construccion de una base de conocimiento lexico multilingue de amplia cobertura multilingual Central Repository
    Linguamática, 2013
    Co-Authors: Aito Gonzalezagirre, Germa Rigau
    Abstract:

    The use of wide coverage and general domain semantic resources has become a common practice and often necesary by existing systems Natural Language Processing (NLP). WordNet is by far the most widely used semantic resource in NLP. Following the success of WordNet, the EuroWordNet project has designed a multilingual semantic infrastructure to develop wordnets for a set of European languages. In EuroWordNet, these wordnets are interconnected with links stored in the Inter-Lingual Index (ILI). Following the EuroWordNet architecture, the MEANING project has developed the first versions of Multilingual Central Repository (MCR) using WordNet 1.6 as ILI. Thus, maintaining the compatibility between wordnets of different languages ​​and versions. This version of the MCR integrates six different versions of the English WordNet (1.6 to 3.0) and wordnets in Spanish, Catalan, Basque and Italian, along with more than a million semantic relationships between concepts and semantic properties different ontologies. We recently developed a new version of MCR using WordNet 3.0 as ILI. This new version of the MCR integrates wordnets of five different languages: English, Spanish, Catalan, Basque and Galician. The current version of MCR, like the previous one, systematically integrates thousands of semantic relations between concepts. In addition, the MCR is enriched with about 460,000 semantic and ontological properties including Base Level Concepts, Top Ontology, WordNet Domains and AdimenSUMO, providing all ontological consistency the integrated semantic wordnets and resources on it.

  • multilingual Central Repository version 3 0
    Language Resources and Evaluation, 2012
    Co-Authors: Aito Gonzalezagirre, Egoitz Laparra, Germa Rigau
    Abstract:

    This paper describes the upgrading process of the Multilingual Central Repository (MCR). The new MCR uses WordNet 3.0 as Interlingual-Index (ILI). Now, the current version of the MCR integrates in the same EuroWordNet framework wordnets from five different languages: English, Spanish, Catalan, Basque and Galician. In order to provide ontological coherence to all the integrated wordnets, the MCR has also been enriched with a disparate set of ontologies: Base Concepts, Top Ontology, WordNet Domains and Suggested Upper Merged Ontology. The whole content of the MCR is freely available.

  • the meaning multilingual Central Repository
    2004
    Co-Authors: Jordi Atserias, Luis Villarejo, Germa Rigau, Eneko Agirre, Joh M Carroll, Ernardo Magnini, Piek Vosse
    Abstract:

    This paper describes the first version of the Multilingual Central Repository, a lexical knowledge base developed in the framework of the MEANING project. Currently the MCR integrates into the EuroWordNet framework five local wordnets (including four versions of the English WordNet from Princeton), an upgraded version of the EuroWordNet Top Concept ontology, the MultiWordNet Domains, the Suggested Upper Merged Ontology (SUMO) and hundreds of thousand of new semantic relations and properties automatically acquired from corpora. We believe that the resulting MCR will be the largest and richest Multilingual Lexical Knowledge Base in existence.

  • starting up the multilingual Central Repository
    Procesamiento Del Lenguaje Natural, 2003
    Co-Authors: Jordi Atserias, Germa Rigau, Luis Villarejo
    Abstract:

    This paper describes the initial design of the Multilingual Central Repository. The first version of the MCR integrates into the same EuroWordNet framework, five local wordnets (including three versions of the English WordNet from Princeton), the EuroWordNet Top Ontology, MultiWordNet Domains, and hundreds of thousand of new semantic relations and properties automatically acquired from corpora. In fact, the resulting MCR is going to constitute the largest and richest multilingual lexical-knowledge ever build.

Aurisan Souza De Santana - One of the best experts on this subject based on the ideXlab platform.

  • metadata to support transformations and data metadata lineage in a warehousing environment
    Lecture Notes in Computer Science, 2004
    Co-Authors: Aurisan Souza De Santana, Ana Maria De Carvalho Moura
    Abstract:

    Data warehousing is a collection of concepts and tools which aim at providing and maintaining a set of integrated data (the data warehouse - DW ) for business decision support within an organization. They extract data from different operational data sources, and after some cleansing and transformation procedures data are integrated and loaded into a Central Repository to enable analysis and mining. Data and metadata lineage are important processes for data analysis. The first allows users to trace warehouse data items back to the original source item from which they were derived and the latter shows which operations have been performed to achieve that target data. This work proposes integrating metadata captured during transformation processes using the CWM metadata standard in order to enable data and metadata lineage. Additionally it presents a tool specially developed for performing this task.