Q-Book Systems Pilote Project

This website is the result of an initiative of Work package 5 of the Q-Collect project.

The basic idea behind the Q-Book systems is to allow any researcher or collection working in quarantine related field to store, manage, analyze and publish data associated to their Biological Material on a freely available platform deeply associated, intermixed with Q-bank and EPPO system. The system would be able to cope with the needs of very small to very large Collections.



Fig. 1. Q-Book systems & associated systems


The new pipeline will include:

1. A mobile application (IOS, Android and Windows Mobile) to collect sample information (pictures, GIS coordinates, time and miscellaneous metadata) directly in the field.

2. A lightweight desktop application that will synchronize with the mobile app and where a complete and extensible set of data will be recordable such as administration, bibliographical, geographical, ecological, chemical, physiological, medical, molecular, links to other specialized repositories (e.g. GenBank, GBIF, etc.) and many more. This application will not only allow the storage of data but also to perform advanced queries, polyphasic identifications and classifications based on any combination of characteristics.

3. Data will be stored in a local light weight database.

4. Data will be shareable using the central Q-Book facility that will be accessible, searchable by anyone or by a selected list of co-workers.

5. An online or web-based tool will also be created allowing the addition, edition and management of strains, specimens or any biological material data that could be used as an alternative to or complementing the lightweight desktop application mentioned above.

6. The Q-Book website will include user-friendly basic and advanced searching facilities, distribution maps, online polyphasic identifications and web services to download data.

7. A publication tool will also be available to produce e-books or to export data in basic data exchange formats.



Fig. 2. Q-Book systems for data capture and edition


Since the Q-Book system would be able to cope with all types of data and organisms, it would be used by a very large panel of researchers and people worldwide. It would be used in many scenarios such as biodiversity management and conservation programs anywhere in the world, quarantine and invasive organisms fight, epidemiology or medical diagnostic. It will be especially beneficial to researchers or collections with no or low financial and technical resources.

There are no such projects proposing to record biodiversity at the unit level (strains, specimens or other biological material). Initiatives such as EOL, Catalogue of Life, Species 2000, IUCN, GenBank, StrainInfo, GCM, BOLD or GBIF are concentrating on species data and are, for some of them, referring to existing and officially recognized museums or culture collections. To our knowledge, there is no complete pipeline that proposes what we are going to initiate here. This ambitious project will be unique and used worldwide. African and lesser-developed countries as well as Collections with no or little resources will certainly be the first to benefit from the proposed system since it will be freely and easily accessible. Most of the African Biodiversity remains unknown and very few African researchers have the ability to buy advanced tools to propose their results to third parties. The Q-Book system will allow them to be visible to the scientific and quarantine problematic community and will inevitably initiate collaborations between research groups that, otherwise, would never know about each other. Since the central database would include a very large range of organisms (from dead material to viruses to higher and large organisms), the diversity and the number of potentially useful data to characterize the biological materials will be huge.

Where possible data deposited in Q-Book will be automatically enriched and linked to existing databases such as Genbank, PubMed or SwissProt (via provided accession numbers) but also, via geographic positioning (latitude, longitude, altitude, etc) to other datasets like climate, soils, agricultural practices, elevation, vegetation or many other environmental parameters such as demographic, socio-economic or cultural aspects.




Fig. 3. Q-Book systems functional schema
Data stored in the Q-Book system will be archived in a coded and a highly structured way and everywhere possible, text data will be avoided to allow descriptive statistics (average, variance, frequencies, etc.) to be easily computed. Each data point will be considered by the system as a programing object and usable by object oriented programing languages. Such a system will allow the statistical tools to analyse large datasets and perform correlation analyses (for example but many more will be possible as well, like factorial analyses). The semantic system included in Q-Book will allow users to navigate through heterogeneous but highly connected datasets and to find biological material that have potential properties in view of specific Q related research. Statistical and semantic tools will be operable via simple user interfaces from either simple desktop applications or web based systems. This would allow non-advanced users to perform basic calculations, statistics or navigate through complex datasets in a simple way.

The proposed facility will create a virtual research environment where users will be able to find, connect, correct, combine, visualize, analyse and interpret new combinations of heterogeneous data that are relevant to address their Q-research areas. A framework for resource integration will be developed, combining the taxonomic backbone for species identification, geo-referenced environmental data, existing systems for observational data, and information on species traits and attributes. These resources will become accessible to users within seconds, by (i) providing searchable metadata that describe the data and its source, (ii) assigning unique identifiers as linkers between data according to accepted standards, (iii) creating interfaces and query systems, and (iv) installing routines for quality control and interpolation of data in space and time. The architecture is modular, flexible and scalable, and will be the first infrastructure in the world specifically designed for the integration of such Q-resources. Innovative new services will be made available, based on an analysis of the common needs of users in the prioritised areas: services to analyse genetic diversity of mixtures: ‘environmental DNA’, services for new observational methods using smart sensor technologies, services for constructing species interaction networks, services to link meta-omics data to ecosystem processes in (micro-) communities, for which physical model ecosystem facilities will be created. This being a service-based e-infrastructure means that users can access resources and computational facilities from any place, but also meet in person with technicians when needed to discuss progress and results: facilitating research collaboration is an integral part of the proposed system. Larger or more advanced collections already having strong CMS will also be able to participate to the project by sharing their data via web services. With their permission, their data will be retrieved through web services and will feed the central Q-Book database allowing to perform queries as well as data analyses on the broadest possible basis (see fig 2).

The Q-Book system will also allow small collections or the ones without an existing data management system to have a complete system allowing to integrate and publish their data using a mobile app, a desktop application or using the web based editor directly accessing their records stored in Q-Book. The development of the Q-Book systems will certainly not be achieved by the collections themselves since this would require advanced programming and databasing skills that are not or almost never available in current culture collections. Subcontractors with the relevant experience will have to be hired to build the wanted systems in close collaboration with collections experts and Q-bank as well as EPPO, but also with the end-users (existing and foreseeable new or potential ones).

The system will be completely free (free mobile and desktop applications) and the Q-Book system will be hosted and maintained by Q-bank and/or EPPO if the needed resources are made available by one or several financing bodies. The problem of sustainability is one of the major issues that need to be tackled in future projects.

Deposit your data

Single record deposit form, here
Download batch deposit form, here

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Coordinator:

Dr. P.J.M. (Peter) Bonants

Dr. Peter Bonants
peter.bonants@wur.nl
Plant Research International (PRI)
the Netherlands

Program manager:

Ir. M.J. (Mariëtte) Edema

Ir. Mariëtte Edema
m.j.Edema@minlnv.nl
National Reference Centre, Netherlands Food and Consumer Product Safety Authority (NVWA)
the Netherlands
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