Colony of thermophilic bacteria at Mickey Hot Springs, Oregon





Bacteria Biotope at BioNLP-ST'13

MEM OntoBiotope - References

OntoBiotope references

State of the art in building habitat ontologies

Concerning the description of bacterial habitats, two main sources

  • 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.

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:

  • 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.