Correction to: An ontological foundation for ocular phenotypes and rare eye diseases.

Professor Michael Larsen, who is a member of the ERN-EYE Ontology Study Group and co-chair of Workgroup on Retinal Rare Eye Diseases (WG1), was inadvertently omitted from the author list in the Acknowledgements section of the original article [1].

An ontological foundation for ocular phenotypes and rare eye diseases.

BACKGROUND: The optical accessibility of the eye and technological advances in ophthalmic diagnostics have put ophthalmology at the forefront of data-driven medicine. The focus of this study is rare eye disorders, a group of conditions whose clinical heterogeneity and geographic dispersion make data-driven, evidence-based practice particularly challenging. Inter-institutional collaboration and information sharing is crucial but the lack of standardised terminology poses an important barrier. Ontologies are computational tools that include sets of vocabulary terms arranged in hierarchical structures. They can be used to provide robust terminology standards and to enhance data interoperability. Here, we discuss the development of the ophthalmology-related component of two well-established biomedical ontologies, the Human Phenotype Ontology (HPO; includes signs, symptoms and investigation findings) and the Orphanet Rare Disease Ontology (ORDO; includes rare disease nomenclature/nosology). METHODS: A variety of approaches were used including automated matching to existing resources and extensive manual curation. To achieve the latter, a study group including clinicians, patient representatives and ontology developers from 17 countries was formed. A broad range of terms was discussed and validated during a dedicated workshop attended by 60 members of the group. RESULTS: A comprehensive, structured and well-defined set of terms has been agreed on including 1106 terms relating to ocular phenotypes (HPO) and 1202 terms relating to rare eye disease nomenclature (ORDO). These terms and their relevant annotations can be accessed in http://www.human-phenotype-ontology.org/ and http://www.orpha.net/ ; comments, corrections, suggestions and requests for new terms can be made through these websites. This is an ongoing, community-driven endeavour and both HPO and ORDO are regularly updated. CONCLUSIONS: To our knowledge, this is the first effort of such scale to provide terminology standards for the rare eye disease community. We hope that this work will not only improve coding and standardise information exchange in clinical care and research, but also it will catalyse the transition to an evidence-based precision ophthalmology paradigm.

A nomenclature and classification for the congenital myasthenic syndromes: preparing for FAIR data in the genomic era.

BACKGROUND: Congenital myasthenic syndromes (CMS) are a heterogeneous group of inherited neuromuscular disorders sharing the common feature of fatigable weakness due to defective neuromuscular transmission. Despite rapidly increasing knowledge about the genetic origins, specific features and potential treatments for the known CMS entities, the lack of standardized classification at the most granular level has hindered the implementation of computer-based systems for knowledge capture and reuse. Where individual clinical or genetic entities do not exist in disease coding systems, they are often invisible in clinical records and inadequately annotated in information systems, and features that apply to one disease but not another cannot be adequately differentiated. RESULTS: We created a detailed classification of all CMS disease entities suitable for use in clinical and genetic databases and decision support systems. To avoid conflict with existing coding systems as well as with expert-defined group-level classifications, we developed a collaboration with the Orphanet nomenclature for rare diseases, creating a clinically understandable name for each entity and placing it within a logical hierarchy that paves the way towards computer-aided clinical systems and improved knowledge bases for CMS that can adequately differentiate between types and ascribe relevant expert knowledge to each. CONCLUSIONS: We suggest that data science approaches can be used effectively in the clinical domain in a way that does not disrupt preexisting expert classification and that enhances the utility of existing coding systems. Our classification provides a comprehensive view of the individual CMS entities in a manner that supports differential diagnosis and understanding of the range and heterogeneity of the disease but that also enables robust computational coding and hierarchy for machine-readability. It can be extended as required in the light of future scientific advances, but already provides the starting point for the creation of FAIR (Findable, Accessible, Interoperable and Reusable) knowledge bases of data on the congenital myasthenic syndromes.

Aquatic Biodiversity in the Amazon: Habitat Specialization and Geographic Isolation Promote Species Richness.

The Neotropical freshwater ichthyofauna has among the highest species richness and density of any vertebrate fauna on Earth, with more than 5,600 species compressed into less than 12% of the world's land surface area, and less than 0.002% of the world's total liquid water supply. How have so many species come to co-exist in such a small amount of total habitat space? Here we report results of an aquatic faunal survey of the Fitzcarrald region in southeastern Peru, an area of low-elevation upland (200-500 m above sea level) rainforest in the Western Amazon, that straddles the headwaters of four large Amazonian tributaries; the Juruá (Yurúa), Ucayali, Purús, and Madre de Dios rivers. All measures of fish species diversity in this region are high; there is high alpha diversity with many species coexisting in the same locality, high beta diversity with high turnover between habitats, and high gamma diversity with high turnover between adjacent tributary basins. Current data show little species endemism, and no known examples of sympatric sister species, within the Fitzcarrald region, suggesting a lack of localized or recent adaptive divergences. These results support the hypothesis that the fish species of the Fitzcarrald region are relatively ancient, predating the Late Miocene-Pliocene (c. 4 Ma) uplift that isolated its several headwater basins. The results also suggest that habitat specialization (phylogenetic niche conservatism) and geographic isolation (dispersal limitation) have contributed to the maintenance of high species richness in this region of the Amazon Basin.

A new species of Gymnotus (Gymnotiformes: Gymnotidae) from the Fitzcarrald Arch of southeastern Peru

Herein Gymnotus chaviro is described from the Alto Yuruá (upper rio Juruá) of southeastern Peru, where it is locally abundant in terra firme streams and floodplain oxbow lakes, and occurs sympatrically and syntopically with the type species of the genus G. carapo. The new species is diagnosed by a unique combination of morphometric, meristic, and osteological traits, and a characteristic color pattern in which the dark band-pairs are unbranched and incompletely separated, and the pale inter-bands rarely reach to the dorsal mid-line on the anterior half of the body, being crescent-shaped in abdominal area. Gymnotus chaviro is a member of the G. carapo species group, with which it shares the presence of two pores in the dorsolateral portion of the preopercle, dark pigment bands with wavy margins that become broken and/or loose contrast with the ground color through growth, a clear patch at the caudal end of an otherwise darkly pigmented anal fin, and more than four arrowhead-shaped (anteroposteriorly compressed) teeth in the anterior portion of the dentary. Gymnotus chaviro is most similar in external appearance to G. curupira of lowland Western Amazonia in possessing a slender lateral profile (mean body depth less than 9 percent total length), a similar color pattern (median number of bands 19 with bands less distinct on dorsum), a large inter-orbital distance (mean greater than 41 percent head length), a broad head (mean head width greater than 65 percent head length) and a large mouth (mean mouth width greater than 43 percent head length). This new species can also be distinguished from G. curupira by the configuration of the preopercular pores, and by several meristic traits of squamation and fin rays. This is the first gymnotiform species described from the interior of the Fitzcarrald Arch, and the only gymnotiform species known to date that is endemic to this upland region of the western Amazon.(AU)

En el presente trabajo se describe Gymnotus chaviro de Alto Yuruá (parte alta del Río Juruá) en el sureste de Peru. Esta especie es abundante en arroyos de tierra firme y llanuras con lagos en herradura, ocurre de manera sintópica y simpátrica con la especie tipo del genero, G. carapo. La nueva especie se diagnostica por una combinación única de rasgos morfométricos, merísticos y osteológicos, así como un patrón característico de bandas pares obscuras no ramificadas e incompletamente separadas, alternando con bandas claras que raramente alcanzan el centro de la línea dorsal en la mitad anterior del cuerpo adquiriendo forma de media luna en la parte abdominal. Gymnotus chaviro es un miembro del grupo de especies de G. carapo, con quien comparte la presencia de dos poros en la porción dorso lateral del preopérculo, bandas con pigmentos obscuros con márgenes ondulados que se parten y/o pierden el contraste con el color de fondo a medida que crece, aleta anal obscura con un claro parche de un pigmento obscuro en borde caudal y más de cuatro dientes en forma de punta de flecha (anteroposteriormente comprimidos) en la porción anterior del dentario. Gymnotus chaviro es más parecido en apariencia externa a G. curupira de las planicies del Oeste Amazonia por tener un perfil lateral esbelto (media de la profundidad del cuerpo es menor al 9 por ciento del largo total), un patrón de color similar (promedio de 19 bandas con otras menos notables en el dorso) una distancia inter-orbital grande (media mayor al 41 por ciento de longitud de cabeza), cabeza ancha (media mayor al 65 por ciento de la longitud de cabeza) una boca grande (media del ancho mayor al 43 por ciento de la longitud de cabeza). Esta especie también se diferencia de G. curupira por la configuración de los poros pre-operculares y por varios rasgos en las escamas y numero de radios en las aletas. Esta es la primera especie de gymnotiforme descrita del interior del Arco de Fitzcarrald ...(AU)