PlutoF – cloud database and computing services supporting biological research
Date
2011-10-04
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Abstract
Doktoritöö eesmärgiks oli luua platvorm, mis võimaldaks üle veebi sisestada, talletada, toimetada ja analüüsida elurikkuse ning sellega seotud metaandmestikku. Töö kitsamaks eesmärgiks oli luua spetsiifilised lahendused seente molekulaarsete andmete (DNA järjestuste) analüüsimiseks ja nende DNA-põhiseks määramiseks.
Paljud seeneliigid ei moodusta määramiseks kasutatavaid viljakehi elades vaid seeneniidistikuna mullas. Seetõttu nende eristamiseks ja kindlakstegemiseks morfoloogilistest ning anatoomilistest tunnustest ei piisa. Viimased viisteist aastat on seeneliikide määramiseks keskkonnaproovidest kasutatud kindla DNA regiooni nukleotiidseid järjestusi. Selliste DNA järjestuste määramiseks tuleb neid võrrelda teadaolevate liikide järjestustega. Viimased pärinevad reeglina eksperdi poolt määratud seene viljakehast või eluskultuurist. Sellise DNA-põhise määramise kitsaskohaks on seni olnud kõrge kvaliteediga määratud DNA järjestuste andmebaasi puudumine, mille vastu uusi järjestusi võrrelda.
Käesoleva töö raames loodi seente viljakehadest pärit kvaliteetseid DNA järjestusi sisaldav andmebaas UNITE (http://unite.ut.ee) koos selle veebiväljundi ja analüüsitarkvaraga seente kiireks ja usaldusväärseks DNA-põhiseks määramiseks. Andmebaas sisaldab DNA järjestusi seente viljakehadest, mis on kogutud oma ala ekspertide poolt üle maailma. Lisaks on võimalik analüüsidesse kaasata ka kõiki rahvusvahelistesse geenipankadesse lisatud keskkonnaproovidest pärit DNA järjestusi, mille metaandmestikku rahvusvahelise uurimisrühma poolt meie süsteemis kontrollitakse ja täiendatakse. Doktoritöö raames loodi mitmed tarkvaralahendused vastavate DNA järjestuste kvaliteedi kontrollimiseks ning veebi-töölaud PlutoF (http://plutof.ut.ee) kogu andmestiku haldamiseks ja analüüsimiseks. Ka UNITE andmebaas asub PlutoF pilves.
PlutoF platvorm võimaldab lisaks eelpool kirjeldatud näitele luua ja hallata mitmesuguseid elurikkuse andmebaase taksonoomiast keskkonnagenoomikani. PlutoF pilve on edukalt kasutatud andmebaaside Eesti eElurikkus ja Eesti Liikide Register loomiseks (http://elurikkus.ut.ee) ning Eesti loodusteaduslike kogude rahvuslike andmebaaside (http://elurikkus.ut.ee/collections.php?lang=est) loomiseks. Erinevad, sh. rahvusvahelised uurimisrühmad kasutavad PlutoF pilve ökoloogiliste uuringute haldamiseks ning molekulaarsete andmete analüüsimiseks.
The aim of this thesis was to develop technologies for managing, editing and analyzing biodiversity data. The main focus was put on developing web-based tools for molecular identification of fungi. Many fungi do not form fruit-bodies which are needed for morphological identification. Instead they live in soil as fungal hyphae. For this reason the identification of fungal species in ecological studies is nowadays most commonly DNA-based – DNA sequences from unknown species are compared against DNA sequences from known species which are often identified by an expert based on fungal fruit-body or living culture. For DNA-based identification the presence of a reference database consisting of correctly identified high-quality DNA sequences for comparison is needed. As a result of this thesis, UNITE – a database storing high-quality fungal DNA sequences generated from fruiting bodies collected and identified by experts together with public web page and analysis tools for fast and reliable identification of fungi was developed (http://unite.ut.ee). In addition to reference dataset there’s also an option to include all fungal DNA sequences deposited in international gene repositories in the identification process. These DNA sequences are stored locally in our system where their quality is checked, identifications verified and metadata complemented. As a result of this thesis, several software tools for checking sequence quality, and a web-based workbench PlutoF (http://plutof.ut.ee) for managing and analyzing these data were developed. PlutoF cloud enables to create and manage various biodiversity databases from taxonomy to environmental genomics. It has been successfully used for creating Estonian eBiodiversity database and Estonian Species Registry (http://elurikkus.ut.ee), and Estonian national databases of natural history collections (http://elurikkus.ut.ee/collections.php?lang=est). Several international workgroups use PlutoF cloud for managing ecological studies and analyzing molecular data.
The aim of this thesis was to develop technologies for managing, editing and analyzing biodiversity data. The main focus was put on developing web-based tools for molecular identification of fungi. Many fungi do not form fruit-bodies which are needed for morphological identification. Instead they live in soil as fungal hyphae. For this reason the identification of fungal species in ecological studies is nowadays most commonly DNA-based – DNA sequences from unknown species are compared against DNA sequences from known species which are often identified by an expert based on fungal fruit-body or living culture. For DNA-based identification the presence of a reference database consisting of correctly identified high-quality DNA sequences for comparison is needed. As a result of this thesis, UNITE – a database storing high-quality fungal DNA sequences generated from fruiting bodies collected and identified by experts together with public web page and analysis tools for fast and reliable identification of fungi was developed (http://unite.ut.ee). In addition to reference dataset there’s also an option to include all fungal DNA sequences deposited in international gene repositories in the identification process. These DNA sequences are stored locally in our system where their quality is checked, identifications verified and metadata complemented. As a result of this thesis, several software tools for checking sequence quality, and a web-based workbench PlutoF (http://plutof.ut.ee) for managing and analyzing these data were developed. PlutoF cloud enables to create and manage various biodiversity databases from taxonomy to environmental genomics. It has been successfully used for creating Estonian eBiodiversity database and Estonian Species Registry (http://elurikkus.ut.ee), and Estonian national databases of natural history collections (http://elurikkus.ut.ee/collections.php?lang=est). Several international workgroups use PlutoF cloud for managing ecological studies and analyzing molecular data.
Description
Väitekirja elektrooniline versioon ei sisalda publikatsioone.
Keywords
metaandmed, andmeanalüüs, seened, DNA-analüüs, määramine, metadata, data analysis, fungi, DNA analysis, determination