MEM OntoBiotope - References
- Zorana Ratkovic, Wiktoria Golik, Pierre Warnier. BioNLP 2011 Task Bacteria Biotope - The Alvis System. BMC Bioinformatics 13(Suppl 11):S3, juin 2012.
- Robert Bossy, Julien Jourde, Alain-Pierre Manine, Philippe Veber, Erick Alphonse, Maarten van de Guchte, Philippe Bessieres, Claire Nédellec. BioNLP Shared Task - The Bacteria Track. BMC Bioinformatics, (Suppl 11):S3, juin 2012.
- Manine A.P., Alphonse E., Bessieres P. (2009). Learning ontological rules to extract multiple relations of genic interactions from text. Int. J. Med. Inform. 78(12):31-38.
- Wiktoria Golik, Pierre Warnier, Claire Nédellec. (2011) Corpus-based extension of termino-ontology by linguistic analysis: a use case in biomedical event extraction. Ontology and Lexicon: new insights. Workshop proceedings of TIA 2011 : 9th International Conference on Terminology and Artificial Intelligence, M. Slodzian et al. ed., Paris.
- Zorana Ratkovic, Wiktoria Golik, Pierre Warnier, Philippe Veber, Claire Nédellec, "BioNLP 2011 Task Bacteria Biotope - The Alvis system", BioNLP workshop joint to ACL, Portland, USA, 2011.
- Robert Bossy, Julien Jourde, Philippe Bessieres, Maarten van de Guchte, Claire Nédellec, "BioNLP shared Tasks 2011 - Bacteria Biotope", BioNLP workshop joint to ACL, Portland, USA, 2011.
Concerning the description of bacterial habitats, two main sources
|State of the art in building habitat ontologies
Other initiatives of interest are retaining our attention, they do not propose formal ontologies but demonstrate the growing interest of the community and illustrate the diversity of the objectives:
- GOLD, for Genomes On Line Database (Liolios et al., 2010), from JGI of DOE (Joint Genome Institute, US Department Of Energy), actually rather a controlled vocabulary typology than an ontology describing and classifying habitats (Ivanova et al., 2010) related to complete genome sequenced organisms into a large table, and more recently, used to describe metagenome sequencing projects;
- EnvO (Environment Ontology project) defined in the context of the recently created GSC consortium (Genomics Standards Consortium) targeting a Minimum Information about a Genome Sequence (MIGS) specification (Field et al., 2008), and related to the Habitat-Lite ontology (Hirschman et al., 2008). It mainly focuses on Eukaryotes.
- one of the first initiatives proposing a description of environmental habitats for bacteria came from people in charge of microbial collections (Floyd et al., 2005) at the ATCC (American Type Collection Culture);
- Plant-Associated Microbe Gene Ontology (PAMGO) lately extended to microbial associations with animal hosts (reviewed in Torto-Alalibo et al., 2010), mainly dedicated to pathogens, and a good example of an effort to complete Gene Ontology (GO) for bacteria annotations;
- EnvDB (Pignatelli et al., 2009), classifying bacteria into habitat classes according to 16S rRNA sequences stored in GenBank (Benson et al., 2011), explicitly resorting to information extraction from scientific texts, including EnvMine (Tamames and de Lorenzo, 2010) dedicated to the identification of habitat physico-chemical properties.