Structured and graphical queries for Drosophila neuroscience data

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Informatics


Disorders of the nervous system account for the single biggest cost to the National Health Service and affect one in three people in the developed world at some point in their life. Designing treatment therapies requires us to understand first how the brain works yet it is the most complex organ known and thus simpler models are essential. The brain of the fruit fly, Drosophila melanogaster, provides an excellent model system for studying how brains function. It is orders of magnitude smaller and simpler than a mammalian brain, yet genetically it is remarkably similar. Moreover, like mammalian brains, is capable of learning and is remodelled in response to experience and environmental context. There is a large history of research into the brain of Drosophila and other insects. This gives a firm foundation to modern studies of the genetic basis of how the Drosophila brain is built and functions. Such studies take advantage of an increasingly powerful array of genetic techniques that allow specific regions, cells and genes to be disrupted thus measuring their function. At the same time, increasingly sophisticated imaging techniques are revealing the structure of the Drosophila brain in ever-finer detail. The sheer volume and microscopic detail of the data being collected poses a problem to researchers wanting to build and communicate coherent models of brain function or to share the tools they use for their experiments. Navigating through the blizzard of new information is made particularly difficult by the varying and often confusing nomenclature that is an inevitable feature of a complicated field with such a long history. We aim to remedy this by building a web-based atlas and search tool - Virtual Fly Brain. Users will be able to navigate by clicking on labelled regions in a 3D reference image of a brain, or by searching and browsing a structured vocabulary which names brain regions and the brain cells which connect them. Users will be able to highlight brain regions in various colours by choosing terms in the vocabulary they find through browsing and searching. Choosing a term will also prompt the display of various information related to that term: links to additional images; written definitions with references to the scientific papers they come from; synonyms and comments to help disambiguate confusing or conflicting usage of terms. Users will be able to use the lists of terms generated by these queries to search for related data stored in FlyBase, the main genetic database of the Drosophila community. This will allow them to find genes expressed in structures on the list or which are known to be involved in the construction or function of these structures. It will also allow them to search for sophisticated genetic reagents which target these structures. Finally, we will provide tools to help new researchers and students to explore and learn how the brain is organised and allow expert users to label their own data using our structured vocabulary and for.

Technical Summary

The amount and complexity of data being produced on the structure, development and connectivity of the Drosophila brain means that biologists will increasingly need tools to help them search, integrate and synthesise this data into models of how the brain works. The neuroanatomical working group is about to agree upon a new set of defined terms and boundaries for the major neuropil of the adult fly brain and presumably will follow with the tract systems and developmental histories. This is an essential first step but these conclusions need to be integrated into a formal ontology that extends the existing whole body/organism ontology currently embedded in FlyBase. Further, the ontology needs to be augmented with the development of appropriate data structures, query tools and visualisation software. Hence, we do not propose a new atlas or database of expression patterns (these already exist, or will be developed by others), rather a means to integrate any such resource with a centralised query system. We will also have to extend the FlyBase anatomy ontology to support neural specific features (particularly connectivity information). This will allow new more complex queries to be developed returning data on information flow in the CNS. The centralised query system will also link terms to phenotypic and gene information within FlyBase as well as images from external databases or atlases that use the ontology terms agreed by the nomenclature working group. We will develop a series of tools for building and visualising queries based on neuroanatomical terms. All software/tools produced will be open-source so that they can be re-used or extended by the community. As part of the study we will also revise and extend the annotation of Drosophila neuroscience studies indexed in FlyBase which is currently lagging behind other areas. Joint with BB/G02233X/1.


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Cantarelli M (2018) Geppetto: a reusable modular open platform for exploring neuroscience data and models. in Philosophical transactions of the Royal Society of London. Series B, Biological sciences

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Knowles-Barley S (2011) Biologically inspired EM image alignment and neural reconstruction. in Bioinformatics (Oxford, England)

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Knowles-Barley S (2010) BrainTrap: a database of 3D protein expression patterns in the Drosophila brain. in Database : the journal of biological databases and curation

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Milyaev N (2012) The Virtual Fly Brain browser and query interface. in Bioinformatics (Oxford, England)

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Osumi-Sutherland D (2012) A strategy for building neuroanatomy ontologies. in Bioinformatics (Oxford, England)

Description The fruit fly Drosophila has a long history as a model organism for studying how nervous systems function in behavior, including in complex tasks such as learning, memory and mating behaviour. The future looks very promising too - massive new data-sets are helping to map the fine details of neuroanatomy and provide extensive toolkits for researchers to finely target neurons for their experiments.

But both the rich history and massive new data-sets also bring serious challenges for researchers. The nomenclature of neurons and brain regions has never been standardised, making it challenging to compare data between papers and even harder to search through large numbers of them for key data. Massive new data-sets bring their own search problems - especially when developed by multiple independent labs.

The Virtual Fly Brain web resource, generated by this project, makes it easy for researchers to search and query across information from hundreds of papers and 10s of thousands of database entries and images to find key data to help them formulate hypotheses and to find the reagents they need to do their experiments. The standard vocabulary that lies at the core of this resource also provides a means for users to mark up their own data in a way that allows them to be easily integrated with data on our site. The new methods for finding groups of neurons that with similar shape and location, developed for this project and available on our site, provide a means for users to make sense of the vast amount of image data now becoming available in this field.
Exploitation Route Virtual Fly Brain (VFB) has emerged as the most prominent community database for fly brain neuroscience research. It is widely used by academic laboratories worldwide for both research and for teaching.

Increasingly VFB is also being used as a data depository and therefore helping research groups full fill their data sharing obligations and promote the re-use of scientific data.
Sectors Digital/Communication/Information Technologies (including Software),Education,Pharmaceuticals and Medical Biotechnology

Description The bulk of the impact to date has been academic. However the resource is accessed and used by biotechnology companies in the field. It is also widely used by students as a learning tool for anatomy.
First Year Of Impact 2012
Sector Pharmaceuticals and Medical Biotechnology
Impact Types Economic

Description Virtual Fly Brain - a global informatics hub for Drosophila neuroscience
Amount £136,310 (GBP)
Funding ID 105023/C/14/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2014 
End 09/2017
Title Braintrap 
Description Braintrap describes a collection of protein-trap strains screened in the Armstrong lab. The brain patters are available to view and scroll through with an intuitive graphical user interface. The protein expression patterns are annotated with provenance provided. 
Type Of Material Database/Collection of data 
Year Produced 2011 
Provided To Others? Yes  
Impact The brain expression patterns are aligned to a common reference volume. This allows proteins to be compared virtually in a simulated brain rather than require ding a new experimental study. 
Title Virtual Fly brain 
Description Virtual Fly Brain acts as a data integration hub for all Drosophila neuroscience. It indexes all the major available datasources and provides a structured front end and advanced query system. 
Type Of Material Database/Collection of data 
Year Produced 2012 
Provided To Others? Yes  
Impact We are now top ranked in Google for Drosophila neuroanatomical terminology We provide a front end for the recently published ontology on Drosophila brain anatomy with revised links to all the previously published literature. We current get around 18000 hits per month. 
Title VirtualFlyBrain v1.5 
Description Virtual Fly Brain acts as a data integration hub for all Drosophila neuroscience. It indexes all the major available datasources and provides a structured front end and advanced query system. This is a new release from follow on funding (Wellcome Trust UK). Original release was 2012, new version released 2016. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact VFB now indexes all Drosophila neuroscience data and is the major data integration site. It also now included (preliminary) larval data as well as adult. 
Description Outdoor Science activities for young people 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact This is an ongoing activity under constant development and delivered approximately 2-3 times per year with young people involved in Scouting primarily aged 13-17 although some activities are being extended to younger age groups. A series of tasks look to develop an awareness of scientific method, how to design experiments, measure accurately, identify and handle sources of noise and handle data. This is only indirectly associated with any specific research funding and more generic in its aim to engage young people in science.
Year(s) Of Engagement Activity 2016,2017
Description School visit Linlithgow 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Schools
Results and Impact We had a lot of interaction with the young people with a lot interest in the work we are doing.

Many took away information packs on the brain, others took away contacts for a junior programming club.
Year(s) Of Engagement Activity 2014