TeBactEn (text mining for bacterial enzymes)
TeBactEn is a tool designed to facilitate the retrieval, extraction and annotation of bacterial enzymatic reactions and pathways from the literature.
The system has been developed in the context of the Microme project (http://microme.eu/) and contains three different data collections, namely (a) a compilation of articles derived from the Microme database, i.e. articles (abstracts and full text articles) that had been used for manual annotation of bacterial pathways (Microme set), (b) a set that covers abstracts from the entire PubMed database that are relevant to bacteria (PubMed set) and finally (c) a collection of abstracts and full text articles that are relevant for a list of bacteria of special interest to the Microme project, facilitating a more exhaustive extraction of enzymes particularly for these bacteria (species set).
In case of all three TeBactEn data collections, an exhaustive recognition of mentions of all species and taxonomic entities was carried out.
Microme Project (http://microme.eu/)
TeBactEn covers all the main steps relevant for the automatic extraction and ranking of metabolism relations from the literature and allows enhanced access and annotation of related information: Identification of metabolism relevant articles. Detection of the bio-entities involved in biochemical reactions: enzyme, compounds and organisms. Extraction weighted (ranked) relationships between these bio-entities. An interface to browse this information and to construct a manually curated database of metabolism reactions. Host user-entered annotations. The option to normalize/ground bio-entity mentions to other knowledgebases like UniProt and ChEBI.