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bioRxiv · 10.1101/014134

Building the Ferretome

Dmitrii I Sukhinin·Andreas K Engel·Paul Manger·Claus C Hilgetag
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Abstract

Databases of structural connections of the mammalian brain, such as CoCoMac (cocomac.g-node.org) or BAMS (brancusi.usc.edu), are valuable resources for the analysis of brain connectivity and the modeling of brain dynamics in species such as the non-human primate or the rodent, and have also contributed to the computational modeling of the human brain. Another model species that is widely used in electrophysiological or developmental studies is the ferret; however, no systematic compilation of brain connectivity is currently available for this species. Thus, we have started developing a database of anatomical connections and architectonic features of the ferret brain (the Ferretome, www.ferretome.org). The main goals of this database project are: (1) to assemble structural information on the ferret brain that is currently widely distributed in the literature or in different in-house laboratory databases into a single resource which is open to the scientific community; (2) to try and build an extendable community resource that is beneficial to researchers in neuroinformatics and computational neuroscience, as well as to neuroanatomists, by adding value to their data through algorithms for efficient data representation, analysis and visualization; (3) to create techniques for the representation of quantitative and raw data; and (4) to expand existing database ontologies in order to accommodate further neuroarchitectural information for identifying essential relations between brain structure and connections.\n\nThe Ferretome database has adapted essential features of the CoCoMac methodology and legacy. In particular, its data model is derived from CoCoMac. It also uses a semantic parcellation of ferret brain regions as well as a logical brain maps transformation algorithm (objective relational transformation, ORT). The database is being developed in MySQL and has been populated with literature reports on tract tracing observations in the ferret brain using a custom-designed web interface that allows efficient and validated simultaneous input and proofreading by multiple curators. The database is also equipped with a web interface for generating output data that was designed with non-computer science specialist users in mind. This interface can be extended to produce connectivity matrices in several formats including a graphical representation superimposed on established ferret brain maps. An important feature of the Ferretome database is the possibility to trace back entries in connectivity matrices to the original studies archived in the system.\n\nCurrently, the Ferretome contains 50 reports on connections comprising 20 injection reports with more than 150 labeled source and target areas, the majority reflecting connectivity of subcortical nuclei. We hope that the Ferretome database will become a useful resource for neuroinformatics and neural modeling, and will support studies of the ferret brain as well as facilitate advances in comparative studies of mesoscopic brain connectivity.

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Dmitrii I Sukhinin, Andreas K Engel, Paul Manger, Claus C Hilgetag. 2015-01-22. Building the Ferretome. https://doi.org/10.1101/014134

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