Data sharing and interoperability from multi-source long term observations: challenges and opportunities in marine biology

Long-term observatories are widely used in marine sciences to monitor marine ecosystems and investigate their evolution. Recently, data from innovative technologies as well as ‘omics-based' approaches is being collected alongside physical, biogeochemical and taxonomic information. Their integration represents a challenging opportunity, pushing for suitable computational approaches to for data retrieval, storage, interoperability, reusability and sharing. Several initiatives are addressing these issues, suggesting the most appropriate and sensitive strategies and protocols. Ensuring interoperability among different sources and providing seamless data access is essential when designing tools to store and share the collected information.Here we present our effort in the development of web-accessible resources for Long-Term Ecosystem Research (LTER), taking into account available protocols and approaching appropriate software solutions for: i) collecting and integrating real-time environmental and biological observations with -omics data; ii) exploiting international established data formats and protocols to expose through RESTful APIs the collected data; iii) accessing the collections through an interactive, web-accessible resource to permit aggregated views.The aim of this effort is to reinforce the leadership of the Stazione Zoologica “Anton Dohrn” as a Mediterranean Sea marine observatory, and to be ready for the next era challenges in marine biology.

Data sharing and interoperability from multi-source long term observations: challenges and opportunities in marine biology

Long-term observatories are widely used in marine sciences to monitor marine ecosystems and investigate their evolution. Recently, data from innovative technologies as well as ‘omics-based' approaches is being collected alongside physical, biogeochemical and taxonomic information. Their integration represents a challenging opportunity, pushing for suitable computational approaches to for data retrieval, storage, interoperability, reusability and sharing. Several initiatives are addressing these issues, suggesting the most appropriate and sensitive strategies and protocols. Ensuring interoperability among different sources and providing seamless data access is essential when designing tools to store and share the collected information.Here we present our effort in the development of web-accessible resources for Long-Term Ecosystem Research (LTER), taking into account available protocols and approaching appropriate software solutions for: i) collecting and integrating real-time environmental and biological observations with -omics data; ii) exploiting international established data formats and protocols to expose through RESTful APIs the collected data; iii) accessing the collections through an interactive, web-accessible resource to permit aggregated views.The aim of this effort is to reinforce the leadership of the Stazione Zoologica “Anton Dohrn” as a Mediterranean Sea marine observatory, and to be ready for the next era challenges in marine biology.

Heredity, evolution and development in their (epistemic) environment at the turn of the nineteenth century

During the early 1870s a young zoologist who worked as a Privatdozent delivering lectures at different Prussian universities invested much of his family wealth and solicited his fellows' contributions to establish a research facility by the sea. The young zoologist happened to be called Anton Dohrn. From the time it opened its doors, the Anton Dohrn Zoological Station – or Naples Zoological Station, as it was originally called – played a crucial role in shaping life sciences as it facilitated research aimed at explaining the mechanics of inheritance. During the last quarter of the nineteenth century and the first decades of the twentieth, zoologists attempted to explain how evolutionary changes occur within a population and become stabilized. In so doing, they looked at developmental processes as well as environmental pressure, coming up with different hypotheses to explain inheritance. In some cases, their research was highly speculative, whereas in other cases they conducted cytological observations to identify the material basis of heredity. Research on evolution and development has been carried out in different places, and zoological stations like the one in Naples have played a major role in this story. However, numerous biological institutions active at the turn of the twentieth century have not received much attention from historians.

Quality assurance in the identification of deep-sea taxa from video and image analysis: response to Henry and Roberts

New high-resolution image data obtained from the Hebrides Terrace Seamount and analysed by ourselves and Henry and Roberts (Henry, L-A., and Roberts, J. M. Recommendations for best practice in deep-sea habitat classification: Bullimore et al. as a case study. ICES Journal of Marine Science, 71: 895–898.), suggested that we may have misidentified Solenosmilia variabilis as either Lophelia pertusa or Madrepora oculata in a previously analysed dataset from the Anton Dohrn Seamount (published in Bullimore et al., 2013). Therefore, we undertook a reanalysis of our entire image data holdings from multiple sample sites and identified possible records of S. variabilis from four sites previously sampled: Anton Dohrn Seamount, Rockall Bank, George Bligh Bank and the Hatton-Rockall Basin. The reanalysis of our image data holdings together with historic data from the wider literature suggests that, in the Northeast Atlantic region, S. variabilis is distributed from 888–2803 m (mean ∼1500 m) with reef habitat present only on Anton Dohrn Seamount. In this paper we discuss the use of video and imagery as a survey and monitoring too and make recommendations of best practice in data acquisition and analysis. We highlight the need for the development of training materials for deep-sea field identification in order to achieve reliable, replicable and comparable datasets among observers, and suggest possible quality assurance procedures.