title: MorphoCol: An ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies.
abstract: BACKGROUND
  One of the major concerns of the biomedical community is the increasing prevalence of antimicrobial resistant microorganisms. Recent findings show that the diversification of colony morphology may be indicative of the expression of virulence factors and increased resistance to antibiotic therapeutics. To transform these findings, and upcoming results, into a valuable clinical decision making tool, colony morphology characterisation should be standardised. Notably, it is important to establish the minimum experimental information necessary to contextualise the environment that originated the colony morphology, and describe the main morphological features associated unambiguously.
  
  
  RESULTS
  This paper presents MorphoCol, a new ontology-based tool for the standardised, consistent and machine-interpretable description of the morphology of colonies formed by human pathogenic bacteria. The Colony Morphology Ontology (CMO) is the first controlled vocabulary addressing the specificities of the morphology of clinically significant bacteria, whereas the MorphoCol publicly Web-accessible knowledgebase is an end-user means to search and compare CMO annotated colony morphotypes. Its ultimate aim is to help correlate the morphological alterations manifested by colony-forming bacteria during infection with their response to the antimicrobial treatments administered.
  
  
  CONCLUSIONS
  MorphoCol is the first tool to address bacterial colony morphotyping systematically and deliver a free of charge resource to the community. Hopefully, it may introduce interesting features of analysis on pathogenic behaviour and play a significant role in clinical decision making.
  http://morphocol.org.
authors.affiliation: CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. Electronic address: anamargaridasousa@deb.uminho.pt.
authors.forename: Ana Margarida
authors.initials: AM
authors.lastname: Sousa
authors.affiliation: CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. Electronic address: mopereira@deb.uminho.pt.
authors.forename: Maria Olívia
authors.initials: MO
authors.lastname: Pereira
authors.affiliation: CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain. Electronic address: analia@uvigo.es.
authors.forename: Anália
authors.initials: A
authors.lastname: Lourenço
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000166:cytology*; D064229:Biological Ontologies; D003628:Database Management Systems / Q000458:organization & administration; D016208:Databases, Factual; D020407:Internet; D051188:Knowledge Bases; D009323:Natural Language Processing; D012984:Software; D014584:User-Computer Interface
keywords: Antimicrobial resistance; Colony morphology; Colony morphology ontology; Virulence