PLAN2L (Plant annotation to literature) is a web tool for integrated text mining and literature-derived bio-entity relation extraction. Although most of the underlying technology could in principle be adapted to other organisms (or bio-topics), we try to provide through PLAN2L a literature mining applications adapted to the needs of researches studying the model organism Arabidopsis thaliana. A more detailed description of the system is provided in the Overview/FAQ section.

You can do PLAN2L literature searches using for instance gene names (APETALA1) or keywords by submitting your query in the search box below.

Reference, reports and presentations:

• Martin Krallinger, Carlos Rodriguez-Penagos, Ashish Tendulkar and Alfonso Valencia: PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucl. Acids Res., Web Server Issue, 2009.
• Report: PLAN2L comment at Faculty of 1000 BIOLOGY
• Presentation of PLAN2L and other bioinformatics infrastructures by Martin Krallinger at: Plant Bioinformatics, Systems and Synthetic Biology Summer School 27-31 July 2009 - University of Nottingham, UK
• Nice online tutorial on PLAN2L provided by the OpenHelix Blog

This system extracts biologically relevant information at various levels, covering the detection and ranking of biological descriptions related to cell cycle, protein interactions, gene regulations, cellular locations as well as developmental processes (flower, root, leave and seed development).
It also provides biological relations between specific bio-entities: gene regulation relations and protein interactions together with the corresponding textual evidence sentences.

Latest news: We have added a protein mutation extraction search option.


If you enter a keyword, term or gene name above you can retrieve the associated literature information.

	Cell cycle: association of sentences/entities according to their relevance for cell cycle information.
	Regulatory information: Regulatory event description (e.g. gene regulation) from sentence classifier/rule based extraction.
	Interaction information: Extraction of interaction information (e.g. PPIs) using a sentence classification system.
	Protein localization: Extraction of subcellular localization information using sentence classifier and keywords.
	Flowering: Relevance for flowering-related processes based on sentence categorization.
	Leaf development: Relevance for leaf develoment and formation based on sentence categorization.
	Root development: Relevance for root develoment and formation based on sentence categorization.
	Seed development: Relevance for seed develoment, seedlings and germination based on sentence categorization.
	BioCreative Metaserver: (BCMS) predictions for gene mentions, normalizations and interactions.

by PLAN2L team 2009, last page update 24th July