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ASV portal :
ASV portal : an interface to DNA-based biodiversity data in the Living Atlas
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- Prager, Maria (författare)
- Stockholms universitet,Institutionen för ekologi, miljö och botanik,Science for Life Laboratory (SciLifeLab),Stockholm University, Sweden;Karolinska Institutet, Sweden,Stockholm Univ, Dept Ecol Environm & Plant Sci, Sci Life Lab, S-10691 Stockholm, Sweden.;Karolinska Inst, Dept Microbiol Tumor & Cell Biol, S-17177 Stockholm, Sweden.
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- Lundin, Daniel, 1965- (författare)
- Linnéuniversitetet,Institutionen för biologi och miljö (BOM),Vatten,Ctr Ecol & Evolut Microbial Model Syst EEMiS,Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, S-39182 Kalmar, Sweden.
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- Ronquist, Fredrik, 1962- (författare)
- Naturhistoriska riksmuseet,Enheten för bioinformatik och genetik,Fredrik Ronquists grupp
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- Andersson, Anders F. (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,KTH Royal instute of technology, Sweden
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(creator_code:org_t)
- 2023-01-05
- 2023
- Engelska.
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Ingår i: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 24:1
- Relaterad länk:
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https://doi.org/10.1...
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https://lnu.diva-por... (primary) (Raw object)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://urn.kb.se/re...
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http://kipublication...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Background: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited func-tionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Ampli-con Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.Results: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. Conclusion: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.
Ämnesord
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Miljöbioteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Environmental Biotechnology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Nyckelord
- Biodiversity informatics
- Species occurrence
- Darwin core
- Amplicon sequencing
- Metabarcoding
- eDNA
- BLAST
- Ekologi
- Ecology
- Livets mångfald
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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