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Novotný P, Seifert S, Rohn M, Diewald W, Štech M, Triebel D. Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest. Biodivers Data J 2022; 10:e87254. [PMID: 36761603 PMCID: PMC9836605 DOI: 10.3897/bdj.10.e87254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/04/2022] [Indexed: 11/12/2022] Open
Abstract
Background The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the contributing national and regional databases and networks of the neighbouring countries. Careful data transformation between national data providers is essential for understanding distribution patterns and its dynamics for organisms in areas along the national borders. Sharing occurrence data through the international data aggregator Global Biodiversity Information Facility (GBIF) is also complicated and has to consider that the underlying taxonomic concept and geographic information system of each single GBIF dataset might be different. In addition, some regional data providers have a restrictive (non-cc) licensing policy which does not allow data publication via the GBIF network. Therefore, it is necessary to investigate new ways to make data fit for use for a better and comprehensive understanding of the Flora of the Bohemian Forest. New information In this paper, we present a bilateral technical interoperability solution for vascular plant occurrence data for the area between the Czech Republic and Bavaria. We describe the initial state of data providers in both countries and the factual and technical challenges in finding a sustainable concept to establish mutual data sharing. The resulting solution for a functional infrastructure and an agreed data pipeline is described in a step-by-step approach. The new distributed infrastructure allows botanists and other stakeholders from both countries to work within the cross-border context of historical and current plants' distribution.
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Affiliation(s)
- Petr Novotný
- Department of Biology Education, Faculty of Science, Charles University, Praha, Czech RepublicDepartment of Biology Education, Faculty of Science, Charles UniversityPrahaCzech Republic
| | - Stefan Seifert
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB IT Center, Munich, Germany, Munich, GermanyStaatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB IT Center, Munich, GermanyMunichGermany
| | - Martin Rohn
- Babická 2379/1a, Praha, Czech RepublicBabická 2379/1aPrahaCzech Republic
| | - Wolfgang Diewald
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München, Munich, GermanyStaatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung MünchenMunichGermany
| | - Milan Štech
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech RepublicDepartment of Botany, Faculty of Science, University of South BohemiaČeské BudějoviceCzech Republic
| | - Dagmar Triebel
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB IT Center, Munich, Germany, Munich, GermanyStaatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB IT Center, Munich, GermanyMunichGermany
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Lannuzel G, Pouget L, Bruy D, Hequet V, Meyer S, Munzinger J, Gâteblé G. Mining rare Earth elements: Identifying the plant species most threatened by ore extraction in an insular hotspot. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.952439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conservation efforts in global biodiversity hotspots often face a common predicament: an urgent need for conservation action hampered by a significant lack of knowledge about that biodiversity. In recent decades, the computerisation of primary biodiversity data worldwide has provided the scientific community with raw material to increase our understanding of the shared natural heritage. These datasets, however, suffer from a lot of geographical and taxonomic inaccuracies. Automated tools developed to enhance their reliability have shown that detailed expert examination remains the best way to achieve robust and exhaustive datasets. In New Caledonia, one of the most important biodiversity hotspots worldwide, the plant diversity inventory is still underway, and most taxa awaiting formal description are narrow endemics, hence by definition hard to discern in the datasets. In the meantime, anthropogenic pressures, such as nickel-ore mining, are threatening the unique ultramafic ecosystems at an increasing rate. The conservation challenge is therefore a race against time, as the rarest species must be identified and protected before they vanish. In this study, based on all available datasets and resources, we applied a workflow capable of highlighting the lesser known taxa. The main challenges addressed were to aggregate all data available worldwide, and tackle the geographical and taxonomic biases, avoiding the data loss resulting from automated filtering. Every doubtful specimen went through a careful taxonomic analysis by a local and international taxonomist panel. Geolocation of the whole dataset was achieved through dataset cross-checking, local botanists’ field knowledge, and historical material examination. Field studies were also conducted to clarify the most unresolved taxa. With the help of this method and by analysing over 85,000 data, we were able to double the number of known narrow endemic taxa, elucidate 68 putative new species, and update our knowledge of the rarest species’ distributions so as to promote conservation measures.
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Bolduc B, Hodgkins SB, Varner RK, Crill PM, McCalley CK, Chanton JP, Tyson GW, Riley WJ, Palace M, Duhaime MB, Hough MA, Saleska SR, Sullivan MB, Rich VI. The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ 2020. [DOI: 10.7717/peerj.9467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.
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Affiliation(s)
- Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Ruth K. Varner
- Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, NH, USA
- Department of Earth Sciences, College of Engineering and Physical Sciences, University of New Hampshire, Durham, NH, USA
| | - Patrick M. Crill
- Department of Geological Sciences and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Carmody K. McCalley
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Jeffrey P. Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - William J. Riley
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael Palace
- Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, NH, USA
- Department of Earth Sciences, College of Engineering and Physical Sciences, University of New Hampshire, Durham, NH, USA
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Moira A. Hough
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Scott R. Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Virginia I. Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
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Rambold G, Yilmaz P, Harjes J, Klaster S, Sanz V, Link A, Glöckner FO, Triebel D. Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5303972. [PMID: 30715273 PMCID: PMC6354027 DOI: 10.1093/database/baz002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022]
Abstract
With the advent of advanced molecular meta-omics techniques and methods, a new era commenced for analysing and characterizing historic collection specimens, as well as recently collected environmental samples. Nucleic acid and protein sequencing-based analyses are increasingly applied to determine the origin, identity and traits of environmental (biological) objects and organisms. In this context, the need for new data structures is evident and former approaches for data processing need to be expanded according to the new meta-omics techniques and operational standards. Existing schemas and community standards in the biodiversity and molecular domain concentrate on terms important for data exchange and publication. Detailed operational aspects of origin and laboratory as well as object and data management issues are frequently neglected. Meta-omics Data and Collection Objects (MOD-CO) has therefore been set up as a new schema for meta-omics research, with a hierarchical organization of the concepts describing collection samples, as well as products and data objects being generated during operational workflows. It is focussed on object trait descriptions as well as on operational aspects and thereby may serve as a backbone for R&D laboratory information management systems with functions of an electronic laboratory notebook. The schema in its current version 1.0 includes 653 concepts and 1810 predefined concept values, being equivalent to descriptors and descriptor states, respectively. It is published in several representations, like a Semantic Media Wiki publication with 2463 interlinked Wiki pages for concepts and concept values, being grouped in 37 concept collections and subcollections. The SQL database application DiversityDescriptions, a generic tool for maintaining descriptive data and schemas, has been applied for setting up and testing MOD-CO and for concept mapping on elements of corresponding schemas.
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Affiliation(s)
- Gerhard Rambold
- University of Bayreuth, Universitätsstraße 30, Bayreuth, Germany
| | - Pelin Yilmaz
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, Germany
| | - Janno Harjes
- University of Bayreuth, Universitätsstraße 30, Bayreuth, Germany
| | - Sabrina Klaster
- University of Bayreuth, Universitätsstraße 30, Bayreuth, Germany
| | - Veronica Sanz
- University of Bayreuth, Universitätsstraße 30, Bayreuth, Germany.,SNSB IT Center, Menzinger Straße 67, München, Germany
| | - Anton Link
- SNSB IT Center, Menzinger Straße 67, München, Germany
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, Germany.,Jacobs University, Campus Ring 1, Bremen, Germany
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5
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Integration of Web APIs and Linked Data Using SPARQL Micro-Services—Application to Biodiversity Use Cases. INFORMATION 2018. [DOI: 10.3390/info9120310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In recent years, Web APIs have become a de facto standard for exchanging machinereadable data on the Web. Despite this success, however, they often fail in making resource descriptions interoperable due to the fact that they rely on proprietary vocabularies that lack formal semantics. The Linked Data principles similarly seek the massive publication of data on the Web, yet with the specific goal of ensuring semantic interoperability. Given their complementary goals, it is commonly admitted that cross-fertilization could stem from the automatic combination of Linked Data and Web APIs. Towards this goal, in this paper we leverage the micro-service architectural principles to define a SPARQL Micro-Service architecture, aimed at querying Web APIs using SPARQL. A SPARQL micro-service is a lightweight SPARQL endpoint that provides access to a small, resource-centric, virtual graph. In this context, we argue that full SPARQL Query expressiveness can be supported efficiently without jeopardizing servers availability. Furthermore, we demonstrate how this architecture can be used to dynamically assign dereferenceable URIs to Web API resources that do not have URIs beforehand, thus literally “bringing” Web APIs into the Web of Data. We believe that the emergence of an ecosystem of SPARQL micro-services published by independent providers would enable Linked Data-based applications to easily glean pieces of data from a wealth of distributed, scalable, and reliable services. We describe a working prototype implementation and we finally illustrate the use of SPARQL micro-services in the context of two real-life use cases related to the biodiversity domain, developed in collaboration with the French National Museum of Natural History.
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Triebel D, Reichert W, Bosert S, Feulner M, Okach DO, Slimani A, Rambold G. A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4797113. [PMID: 29688348 PMCID: PMC7206647 DOI: 10.1093/database/bax096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/28/2017] [Indexed: 11/14/2022]
Abstract
Database URL http://diversityworkbench.net/Portal/DiversityImageInspector.
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Affiliation(s)
- Dagmar Triebel
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80638 München, Germany
| | - Wolfgang Reichert
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80638 München, Germany
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Römbke J, Bernard J, Martin-Laurent F. Standard methods for the assessment of structural and functional diversity of soil organisms: A review. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2018; 14:463-479. [PMID: 29603577 DOI: 10.1002/ieam.4046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/14/2017] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
The lack of standardized methods to study soil organisms prevents comparisons across data sets and the development of new global and regional experiments and assessments. Moreover, standardized methods are needed to evaluate the impact of anthropogenic stressors, such as chemicals, on soil organism communities in the regulatory context. The goal of this contribution is to summarize current methodological approaches to measure structural and functional diversity of soil organisms, and to identify gaps and methodological improvements so as to cross data sets generated worldwide. This is urgently needed because several currently ongoing regional and global soil biodiversity studies are not coordinated with one another in terms of methodology, including database development. Therefore, we evaluated the standard methods to sample, identify, determine, and assess soil organisms currently applied or proposed, using well-accepted criteria such as ecological relevance; practicability of usage in terms of resources, time, and costs; and the level of standardization. Methods addressing both the structure and the functions of soil organisms (populations or communities) are included, with a special focus on new molecular methods based on nucleic acid extraction and further analyses by polymerase chain reaction (PCR)-based approaches for microorganisms and invertebrates. We particularly highlight the activities of the Technical Committee (TC) 190 of the International Organization for Standardization (ISO) because ISO guidelines are legally accredited by many national or international authorities when they put conservation laws and regulations into practice. Finally, we propose detailed recommendations regarding gaps in the available set of standards, in order to identify a list of new methods to be standardized. We propose to organize this whole process under the Global Soil Biodiversity Initiative (GSBI) in order to ensure a truly global approach for the assessment of soil biodiversity. Integr Environ Assess Manag 2018;14:463-479. © 2018 SETAC.
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Affiliation(s)
- Jörg Römbke
- ECT Oekotoxikologie GmbH, Flörsheim, Germany
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8
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Robbertse B, Strope PK, Chaverri P, Gazis R, Ciufo S, Domrachev M, Schoch CL. Improving taxonomic accuracy for fungi in public sequence databases: applying 'one name one species' in well-defined genera with Trichoderma/Hypocrea as a test case. Database (Oxford) 2017; 2017:4553317. [PMID: 29220466 PMCID: PMC5641268 DOI: 10.1093/database/bax072] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 01/18/2023]
Abstract
The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation. Database URL:http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353
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Affiliation(s)
- Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pooja K Strope
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Romina Gazis
- Department of Entomology & Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Stacy Ciufo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Domrachev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
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Fuentes D, Fiore N. The LifeWatch approach to the exploration of distributed species information. Zookeys 2015:133-48. [PMID: 25589865 PMCID: PMC4294304 DOI: 10.3897/zookeys.463.8397] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/28/2014] [Indexed: 11/21/2022] Open
Abstract
This paper introduces a new method of automatically extracting, integrating and presenting information regarding species from the most relevant online taxonomic resources. First, the information is extracted and joined using data wrappers and integration solutions. Then, an analytical tool is used to provide a visual representation of the data. The information is then integrated into a user friendly content management system. The proposal has been implemented using data from the Global Biodiversity Information Facility (GBIF), the Catalogue of Life (CoL), the World Register of Marine Species (WoRMS), the Integrated Taxonomic Information System (ITIS) and the Global Names Index (GNI). The approach improves data quality, avoiding taxonomic and nomenclature errors whilst increasing the availability and accessibility of the information.
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Affiliation(s)
- Daniel Fuentes
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Spain
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Gries C, Gilbert EE, Franz NM. Symbiota - A virtual platform for creating voucher-based biodiversity information communities. Biodivers Data J 2014:e1114. [PMID: 25057252 PMCID: PMC4092327 DOI: 10.3897/bdj.2.e1114] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 06/19/2014] [Indexed: 11/12/2022] Open
Abstract
We review the Symbiota software platform for creating voucher-based biodiversity information portals and communities. Symbiota was originally conceived to promote small- to medium-sized, regionally and/or taxonomically themed collaborations of natural history collections. Over the past eight years the taxonomically diverse portals have grown into an important resource in North America and beyond for mobilizing, integrating, and using specimen- and observation-based occurrence records and derivative biodiversity information products. Designed to mirror the conceptual structure of traditional floras and faunas, Symbiota is exclusively web-based and employs a novel data model, information linking, and algorithms to provide highly dynamic customization. The themed portals enable meaningful access to biodiversity data for anyone from specialist to high school student. Symbiota emulates functionality of modern Content Management Systems, providing highly sophisticated yet intuitive user interfaces for data entry, batch processes, and editing. Each kind of content provision may be selectively accessed by authenticated information providers. Occupying a fairly specific niche in the biodiversity informatics arena, Symbiota provides extensive data exchange facilities and collaborates with other development projects to incorporate and not duplicate functionality as appropriate.
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Affiliation(s)
- Corinna Gries
- University of Wisconsin, Madison, Madison, United States of America
| | | | - Nico M Franz
- Arizona State University, Tempe, United States of America
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Rambold G, Elix JA, Heindl-Tenhunen B, Köhler T, Nash III TH, Neubacher D, Reichert W, Zedda L, Triebel D. LIAS light – Towards the ten thousand species milestone. MycoKeys 2014. [DOI: 10.3897/mycokeys.8.6605] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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12
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Lumbsch T, Boonpragob K, Crittenden P. Lichens: from genome to ecosystems in a changing world. MycoKeys 2013. [DOI: 10.3897/mycokeys.6.4829] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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