Literature Search
Under construction at the moment
Under construction at the moment
In the MDDB, processed data from a sequence read archive (SRA) is stored and integrated such that fungal DNA sequences are directly retrievable from a study source. The Biodiversity and distribution search facilitates the navigation from individual environmental sample deposited in SRA to a larger scale by linking the spatial components of the origins of the samples.
The biodiversity search allows to obtain set of fungal sequences observed in refined world regions (such as countries of a continent) as well as use environmental criterias such as biomes.
Nowadays data linked to research in particular in the biological domain is made available in public repositories. In particular, the NCBI sequence read archive (SRA) repository provides raw high-throughput sequencing (HTS) data generated for specific studies of interest. This archive contains many studies which belong to metabarcoding and it is a very valuable source of information. Unfortunately, biological information from sequence data contained in these studies is not directly retrievable.
The data made available in SRA derives always from a publication. Researchers find it difficult nowadays to explore and select data which is contained in different repositories. Also there seems to still be missing the cross reference of the main repositories such as PubMed and Sequence Read Archives.
The MDDB allows to navigate and search within the main descriptions of a publication and of a study containing the sequence data. The web interface is designed to search within the provenance identifiers of the repositories, but also by using keywords linked to the title, abstract, authors and institution both within the domain spaces of literature and SRA repositories.
The MycoDiversity DataBase (MDDB) has been developed for two main reasons. First, the MDDB facilitates the navigation and search of public fungal metabarcoding studies. Secondly, it increases the usability of metabarcoding data obtained from sequence read archives, in particular from the NCBI SRA.
Data contained from MDDB was obtained by associating data from different public domains: literature repositories, metabarcoding studies, barcoding data and taxonomic reference databases.
The MDDB includes the integration of fungal metabarcoding data of environmental samples to ecology and taxonomy.
The MDDG allows the detection of fungal biodiversity and distribution.
The development of this web interface aims to provide a user friendly navigational tool for fungal barcoding data selection from published HTS data as well as auxiliate research with the understanding of the global fungal diversity and distribution.
The extension of the filtering methods and applications aim to become a supportive source for global scale analyses of patterns in fungal biodiversity and distribution, in addition to assisting evolutionary and ecological research on fungi.