title: PhenUMA: a tool for integrating the biomedical relationships among genes and diseases.
abstract: BACKGROUND
  Several types of genetic interactions in humans can be directly or indirectly associated with the causal effects of mutations. These interactions are usually based on their co-associations to biological processes, coexistence in cellular locations, coexpression in cell lines, physical interactions and so on. In addition, pathological processes can present similar phenotypes that have mutations either in the same genomic location or in different genomic regions. Therefore, integrative resources for all of these complex interactions can help us prioritize the relationships between genes and diseases that are most deserving to be studied by researchers and physicians.
  
  
  RESULTS
  PhenUMA is a web application that displays biological networks using information from biomedical and biomolecular data repositories. One of its most innovative features is to combine the benefits of semantic similarity methods with the information taken from databases of genetic diseases and biological interactions. More specifically, this tool is useful in studying novel pathological relationships between functionally related genes, merging diseases into clusters that share specific phenotypes or finding diseases related to reported phenotypes.
  
  
  CONCLUSIONS
  This framework builds, analyzes and visualizes networks based on both functional and phenotypic relationships. The integration of this information helps in the discovery of alternative pathological roles of genes, biological functions and diseases. PhenUMA represents an advancement toward the use of new technologies for genomics and personalized medicine.
authors.affiliation: Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Andalucía Tech, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain. rorodriguez@uma.es.|CIBER de Enfermedades Raras (CIBERER), E-29071, Málaga, Spain. rorodriguez@uma.es.
authors.forename: Rocío
authors.initials: R
authors.lastname: Rodríguez-López
authors.affiliation: Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Andalucía Tech, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain. armando@uma.es.|CIBER de Enfermedades Raras (CIBERER), E-29071, Málaga, Spain. armando@uma.es.
authors.forename: Armando
authors.initials: A
authors.lastname: Reyes-Palomares
authors.affiliation: Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Andalucía Tech, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain. kika@uma.es.|CIBER de Enfermedades Raras (CIBERER), E-29071, Málaga, Spain. kika@uma.es.
authors.forename: Francisca
authors.initials: F
authors.lastname: Sánchez-Jiménez
authors.affiliation: Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Andalucía Tech, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain. medina@uma.es.|CIBER de Enfermedades Raras (CIBERER), E-29071, Málaga, Spain. medina@uma.es.
authors.forename: Miguel Ángel
authors.initials: MÁ
authors.lastname: Medina
mesh_terms: D000592:Amino Acid Metabolism, Inborn Errors / Q000235:genetics; D016208:Databases, Factual; D002658:Developmental Disabilities; D004194:Disease / Q000235:genetics*; D053263:Gene Regulatory Networks; D005796:Genes / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D008954:Models, Biological; D010641:Phenotype; D012984:Software; D050644:Succinate-Semialdehyde Dehydrogenase / Q000172:deficiency / Q000235:genetics; D018511:Systems Integration
chemical_list: D050644:Succinate-Semialdehyde Dehydrogenase