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  1. Article ; Online: Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters

    Fotis A. Baltoumas / Evangelos Karatzas / David Paez-Espino / Nefeli K. Venetsianou / Eleni Aplakidou / Anastasis Oulas / Robert D. Finn / Sergey Ovchinnikov / Evangelos Pafilis / Nikos C. Kyrpides / Georgios A. Pavlopoulos

    Frontiers in Bioinformatics, Vol

    2023  Volume 3

    Abstract: Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods ... ...

    Abstract Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.
    Keywords protein clustering ; metagenomes ; metatranscriptomes ; cluster annotation ; biodiversity ; microbial dark matter ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 612
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Establishment of computational biology in Greece and Cyprus

    Anastasia Chasapi / Michalis Aivaliotis / Lefteris Angelis / Anastasios Chanalaris / Ioannis Iliopoulos / Ilias Kappas / Christos Karapiperis / Nikos C Kyrpides / Evangelos Pafilis / Eleftherios Panteris / Pantelis Topalis / George Tsiamis / Ioannis S Vizirianakis / Metaxia Vlassi / Vasilis J Promponas / Christos A Ouzounis

    PLoS Computational Biology, Vol 15, Iss 12, p e

    Past, present, and future.

    2019  Volume 1007532

    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2019-12-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text.

    Evangelos Pafilis / Sune P Frankild / Lucia Fanini / Sarah Faulwetter / Christina Pavloudi / Aikaterini Vasileiadou / Christos Arvanitidis / Lars Juhl Jensen

    PLoS ONE, Vol 8, Iss 6, p e

    2013  Volume 65390

    Abstract: The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient ... ...

    Abstract The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org.
    Keywords Medicine ; R ; Science ; Q
    Subject code 420
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Environmental variability and heavy metal concentrations from five lagoons in the Ionian Sea (Amvrakikos Gulf, W Greece)

    Katerina Vasileiadou / Christina Pavloudi / Ioanna Kalantzi / Eugenia Apostolaki / Giorgos Chatzigeorgiou / Eva Chatzinikolaou / Evangelos Pafilis / Nafsika Papageorgiou / Lucia Fanini / Spyridon Konstas / Nina Fragopoulou / Christos Arvanitidis

    Biodiversity Data Journal, Vol 4, Iss , Pp 1-

    2016  Volume 25

    Keywords environmental variables ; heavy metals ; Amvrakikos Gulf ; lagoons ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2016-11-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)

    Constantinos Varsos / Theodore Patkos / Anastasis Oulas / Christina Pavloudi / Alexandros Gougousis / Umer Ijaz / Irene Filiopoulou / Nikolaos Pattakos / Edward Vanden Berghe / Antonio Fernández-Guerra / Sarah Faulwetter / Eva Chatzinikolaou / Evangelos Pafilis / Chryssoula Bekiari / Martin Doerr / Christos Arvanitidis

    Biodiversity Data Journal, Vol 4, Iss , Pp 1-

    2016  Volume 28

    Keywords Parallel data manipulation ; R ; pbdMPI vegan ; package ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2016-11-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Seqenv

    Lucas Sinclair / Umer Z. Ijaz / Lars Juhl Jensen / Marco J.L. Coolen / Cecile Gubry-Rangin / Alica Chroňáková / Anastasis Oulas / Christina Pavloudi / Julia Schnetzer / Aaron Weimann / Ali Ijaz / Alexander Eiler / Christopher Quince / Evangelos Pafilis

    PeerJ, Vol 4, p e

    linking sequences to environments through text mining

    2016  Volume 2690

    Abstract: Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this ... ...

    Abstract Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.
    Keywords Bioinformatics ; Ecology ; Microbiology ; Genomics ; Sequence analysis ; Text processing ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2016-12-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Polytraits

    Sarah Faulwetter / Vasiliki Markantonatou / Christina Pavloudi / Nafsika Papageorgiou / Kleoniki Keklikoglou / Eva Chatzinikolaou / Evangelos Pafilis / Georgios Chatzigeorgiou / Katerina Vasileiadou / Thanos Dailianis / Lucia Fanini / Panayota Koulouri / Christos Arvanitidis

    Biodiversity Data Journal, Vol 2, Pp 1-

    A database on biological traits of marine polychaetes

    2014  Volume 41

    Abstract: The study of ecosystem functioning – the role which organisms play in an ecosystem – is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to ... ...

    Abstract The study of ecosystem functioning – the role which organisms play in an ecosystem – is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http://polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources.
    Keywords Polychaeta ; biological traits ; functional traits ; morphology ; reproduction ; behaviour ; larvae ; life cycle ; life history ; database ; literature ; Biology (General) ; QH301-705.5
    Subject code 333
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases

    Sarah Faulwetter / Evangelos Pafilis / Lucia Fanini / Nicolas Bailly / Donat Agosti / Christos Arvanitidis / Laura Boicenco / Terry Capatano / Simon Claus / Stefanie Dekeyzer / Teodor Georgiev / Aglaia Legaki / Dimitra Mavraki / Anastasis Oulas / Gabriella Papastefanou / Lyubomir Penev / Guido Sautter / Dmitry Schigel / Viktor Senderov /
    Adrian Teaca / Marilena Tsompanou

    Research Ideas and Outcomes, Vol 2, Iss , Pp 1-

    2016  Volume 28

    Abstract: The objective of Workpackage 4 of the European Marine Observation and Data network (EMODnet) is to fill spatial and temporal gaps in European marine species occurrence data availability by carrying out data archaeology and rescue activities. To this end, ...

    Abstract The objective of Workpackage 4 of the European Marine Observation and Data network (EMODnet) is to fill spatial and temporal gaps in European marine species occurrence data availability by carrying out data archaeology and rescue activities. To this end, a workshop was organised in the Hellenic Center for Marine Research Crete (HCMR), Heraklion Crete, (8–9 June 2015) to assess possible mechanisms and guideCorrespondinglines to mobilise legacy biodiversity data. Workshop participants were data managers who actually implement data archaeology and rescue activities, as well as external experts in data mobilisation and data publication. In particular, current problems associated with manual extraction of occurrence data from legacy literature were reviewed, tools and mechanisms which could support a semi-automated process of data extraction were explored and the re-publication of the data, including incentives for data curators and scientists were reflected upon.
    Keywords biodiversity data ; legacy literature ; data arch ; Science ; Q
    Subject code 333
    Language English
    Publishing date 2016-07-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases

    Sarah Faulwetter / Evangelos Pafilis / Lucia Fanini / Nicolas Bailly / Donat Agosti / Christos Arvanitidis / Laura Boicenco / Terry Catapano / Simon Claus / Stefanie Dekeyzer / Teodor Georgiev / Aglaia Legaki / Dimitra Mavraki / Anastasis Oulas / Gabriella Papastefanou / Lyubomir Penev / Guido Sautter / Dmitry Schigel / Viktor Senderov /
    Adrian Teaca / Marilena Tsompanou

    Research Ideas and Outcomes, Vol 2, Iss , Pp 1-

    2016  Volume 28

    Abstract: The objective of Workpackage 4 of the European Marine Observation and Data network (EMODnet) is to fill spatial and temporal gaps in European marine species occurrence data availability by carrying out data archaeology and rescue activities. To this end, ...

    Abstract The objective of Workpackage 4 of the European Marine Observation and Data network (EMODnet) is to fill spatial and temporal gaps in European marine species occurrence data availability by carrying out data archaeology and rescue activities. To this end, a workshop was organised in the Hellenic Center for Marine Research Crete (HCMR), Heraklion Crete, (8–9 June 2015) to assess possible mechanisms and guidelines to mobilise legacy biodiversity data. Workshop participants were data managers who actually implement data archaeology and rescue activities, as well as external experts in data mobilisation and data publication. In particular, current problems associated with manual extraction of occurrence data from legacy literature were reviewed, tools and mechanisms which could support a semi-automated process of data extraction were explored and the re-publication of the data, including incentives for data curators and scientists were reflected upon.
    Keywords biodiversity data ; legacy literature ; data arch ; Science ; Q
    Subject code 333
    Language English
    Publishing date 2016-09-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Engaging the broader community in biodiversity research

    Christos Arvanitidis / Sarah Faulwetter / Georgios Chatzigeorgiou / Lyubomir Penev / Olaf Bánki / Thanos Dailianis / Evangelos Pafilis / Michail Kouratoras / Eva Chatzinikolaou / Lucia Fanini / Aikaterini Vasileiadou / Christina Pavloudi / Panagiotis Vavilis / Panagiota Koulouri / Costas Dounas

    ZooKeys, Vol 150, Iss 0, Pp 211-

    the concept of the COMBER pilot project for divers in ViBRANT

    2011  Volume 229

    Abstract: This paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens’ Network for the Observation of Marine BiodivERsity, http://www.comber.hcmr.gr), which has been initiated under the ViBRANT EU e-infrastructure. It is ...

    Abstract This paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens’ Network for the Observation of Marine BiodivERsity, http://www.comber.hcmr.gr), which has been initiated under the ViBRANT EU e-infrastructure. It is designed and implemented for divers and snorkelers who are interested in participating in marine biodiversity citizen science projects. It shows the necessity of engaging the broader community in the marine biodiversity monitoring and research projects, networks and initiatives. It analyses the stakeholders, the industry and the relevant markets involved in diving activities and their potential to sustain these activities. The principles, including data policy and rewards for the participating divers through their own data, upon which this project is based are thoroughly discussed. The results of the users analysis and lessons learned so far are presented. Future plans include promotion, links with citizen science web developments, data publishing tools, and development of new scientific hypotheses to be tested by the data collected so far.
    Keywords Zoology ; QL1-991
    Subject code 333
    Language English
    Publishing date 2011-11-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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