Abstract
BackgroundIn the post-genomic era, biological databases provide an easy access to a wide variety of scientific data. The vast quantity of literature calls for curated databases where existing knowledge is carefully organized in order to aid novel discoveries. Leaves, the main photosynthetic organs are not only vital for plant growth but also essential for maintaining the global ecosystem by producing oxygen and food. Therefore, studying and understanding leaf formation and growth are key objectives in biology. Arabidopsis thaliana to this date remains the prime experimental model organism in plant science.DescriptionLEAFDATA was created as an easily accessible and searchable web tool to assemble a relevant collection of Arabidopsis leaf literature. LEAFDATA currently contains 13,553 categorized statements from 380 processed publications. LEAFDATA can be searched for genes of interest using Arabidopsis Genome Initiative identifiers, for selected papers by means of PubMed IDs, authors and specific keywords. The results page contains details of the original publications, text fragments from the curated literature grouped according to information types and direct links to PubMed pages of the original papers.ConclusionsThe LEAFDATA database offers access to searchable entries curated from a large number of scientific publications. Due to the unprecedented details of annotations and the fact that LEAFDATA already provides records about approximately 1600 individual loci, this database is useful for the entire plant research community.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-016-0115-9) contains supplementary material, which is available to authorized users.
Highlights
In the post-genomic era, biological databases provide an easy access to a wide variety of scientific data
The LEAFDATA database offers access to searchable entries curated from a large number of scientific publications
Due to the unprecedented details of annotations and the fact that LEAFDATA already provides records about approximately 1600 individual loci, this database is useful for the entire plant research community
Summary
In the post-genomic era, biological databases provide an easy access to a wide variety of scientific data. Studying and understanding leaf formation and growth are key objectives in biology Arabidopsis thaliana to this date remains the prime experimental model organism in plant science. Cell divisions are Szakonyi Plant Methods (2016) 12:15 driven by a great number of cell cycle regulators such as cyclins, cyclin-dependent protein kinases, and inhibitors of cyclin-dependent kinases [9] Many of these factors are key players in DNA endoreduplication crucial for controlling cell size. Cell proliferation drives early stages of leaf development, while cell expansion dominates the later phases of leaf growth During this process, pluripotent initial cells differentiate into the abaxial and adaxial epidermis, the palisade and spongy mesophyll cell layers and the vascular system. Analysis of mutant phenotypes revealed that genes involved in chromatin remodeling, pre-mRNA splicing and processing, protein translation, post-transcriptional regulation via small RNA pathways, proteasome-dependent protein degradation, hormonal signaling, metabolite biosynthesis and numerous other processes are essential for leaf organogenesis [1, 12,13,14,15,16]
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