Figure 1

Overview of the four perspectives of phenotype information together with existing corresponding solutions. From a generic perspective, the phenome ecosystem can be described according to three main dimensions, in addition to a fourth orthogonal one: (i) representation - providing the mechanisms required to capture phenotype knowledge; (ii) acquisition - providing the tools for acquiring and storing phenotype data and knowledge; (iii) processing - dealing with the use and application of the phenotype knowledge in diverse contexts; and (iv) interoperability - aiming to bridge the different representations and formalisms describing phenotype knowledge. The figure depicts a map of the current solutions corresponding to each of the four dimensions. Two major strands emerge when targeting the representation and acquisition of phenotypes - that is, focusing on pre-composed or post-composed phenotypes. Also, some approaches deal with multiple dimensions at the same time. DECIPHER, Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources; FMA, Foundation Model of Anatomy; FYPO, Worm Phenotype Ontology; hp, human phenotype; MA, Mouse Adult Gross Anatomy Ontology; MGD, Mouse Genome Database; MIPS, Munich Information Center for Protein Sequence; MP, Mouse Phenotype Ontology; NCBO, National Center for Biomedical Ontology; NLP, natural language processing; OMIM, Online Mendelian Inheritance of Man database; OWL, Web Ontology Language; PATO, Phenotype and Trait Ontology; WP, Worm Phenotype Ontology; ZFIN, Zebrafish Information Network.