Frequently Asked Questions

How are the papers selected?

Our main interest is to gather information about leaf development. Key publications are selected based on their findings describing altered leaf phenotypes or additional data about genes known to be involved in leaf formation, growth or senescence.

Which papers are annotated?

Our paper library currently contains 435 primary research papers. A detailed list can be found here.

What kinds of statements are curated in LEAFDATA?

The LEAFDATA statements are organized into ten major classes based on the information content. These categories are: Phenotype, Gene expression, Feature, DNA-protein interaction, Protein-protein interaction, Genetic interactions, Process, Regulation of gene expression, Regulation of process and Regulation of phenotype.

How are statements extracted from publications?

Full text papers are manually curated using the Knowtator annotation tool in the Protégé environment. We have created the LeafKnowtator system to optimize data collection. Using LeafKnowtator allowed us to keep text fragments from the original publications and at the same times assign biomedical ontologies to these statements in a structured way. Detailed description of the LeafKnowtator and our annotation method is published in Current Plant Biology.

How should LEAFDATA be cited?

Szakonyi D, Van Landeghem S, Baerenfaller K, Baeyens L, Blomme J, Casanova-Saez R, De Bodt S, Esteve-Bruna D, Fiorani F, Gonzalez N, Gronlund J, Immink RGH, Jover-Gil S, Kuwabara A, Munoz-Nortes T, van Dijk ADJ, Wilson-Sanchez D, Buchanan-Wollaston V, Angenent GC, Van de Peer Y, Inze D, Micol JL, Gruissem W, Walsh S, and Hilson P (2015) The KnownLeaf Literature Curation System Captures Knowledge about Arabidopsis Leaf Growth and Development and Facilitates Integrated Data Mining. CURRENT PLANT BIOLOGY

Is it possible to download LEAFDATA database?

LEAFDATA contains unpublished material therefore free downloads are not available at the moment. Please, contact us for potential collaborations at info@leafdata.org First, smaller version of the manually curated dataset can be found at the official AGRON-OMICS portal.

What does LEAFDATA contain?

Our database contain 15721 individual statements. In details:

For the first LEAFDATA release, we chose to display only the text fragments and links to the original papers. However, the database contains further records and organized biomedical ontologies. These could be used to visualize some of our curated data and merge them with other public database as it was shown in Szakonyi et al 2015.

Is the data in LEAFDATA up-to-date?

The database is continuously expanding and regularly updated. However, manual curation is a time consuming and labor intensive process. In addition, the number of key publications is continuously expanding. Therefore, there is a significant gap between our collection and all the relevant publications. According to our estimate, we have processed approximately 10-20% of the leaf literature.

What kinds of statements are curated in LEAFDATA?

The LEAFDATA statements are organized into ten major classes based on the information content. These categories are: Phenotype, Gene expression, Feature, DNA-protein interaction, Protein-protein interaction, Genetic interactions, Process, Regulation of gene expression, Regulation of process and Regulation of phenotype.

How was the database and website was created?

For text curation and data conversion, we have employed the published LeafKNowtator and KnownLeaf resources. Leafdata runs on sql server database and utilising the Coldfusion development platform. Dataweaver International supports LEAFDATA by providing a hosted environment and implementing the Scientific Intelligence behind the LEAFDATA website as provided by project leader Dr Dora Szakonyi.