The framework

The framework consists of two major components. Firstly, we have developed generic software for Android, EpiCollect, which allows multiple data records to be entered and stored on a mobile phone (text variables, GPS position, photo etc.) and sent to a central web database. Secondly, we have developed a web application, located within www.spatialepidemiology.net that, for a specific project, allows the mapping, visualisation and analysis of data submitted to the central database. A schematic of the two-way connectivity between mobile phone and project database obtained using EpiCollect and spatialepidemiology.net is shown in Figure 1.

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Figure 1. Data collection, collation and visualisation framework using EpiCollect and www.spatialepidemiology.net.

See text for details.

https://doi.org/10.1371/journal.pone.0006968.g001

For a new project, data variables to be collected for each data record (sample) are firstly defined. These variables are then used in three ways. 1) To define the fields in the project-specific central database and the web forms for standard data entry via the project website. 2) To define the interface for text input for each data record within EpiCollect loaded onto a mobile phone. 3) To define the data values or ranges for filtering the data that are displayed at the project website or on the mobile phone.

For each project, the central registration of phones loaded with EpiCollect is undertaken using a curator's interface (Figure 1A), allowing multiple users to submit data centrally to the project database (Figure 1B). The project-specific website provides a public interface that displays all data using Google Maps or Google Earth (Figure 1C). Points on the map can be coloured either by the user (or group of users) who submitted the data, or alternatively, based on a variable submitted to the database. Furthermore, the display of data can be filtered based on the variables collected. For example, filtering allows display of only those samples obtained within a specific range of a variable or within a specific time period, and graphical summaries based on the variables collected are displayed (Figure 1D). Each time a new data record is sent from EpiCollect to the central database a new point appears on the map and the variables become immediately available for filtering. This allows the progress of the project to be monitored in real-time and, furthermore, a central project curator can, while fieldwork is underway, communicate with individual users, or all users, via instant messaging provided by Google Talk.

EpiCollect

When EpiCollect is launched on the mobile phone three options are initially available, ‘New Entry’, ‘List Entries’ and ‘Display Map’ (Figure 2A). Selecting ‘New Entry’ creates a new data record within the phone's on-board database and assigns a unique ID to the record. The latitude, longitude and altitude of the current position of the user is returned from the GPS unit of the phone (Figure 2B). Three new options are now available, ‘Photo’, ‘Data’ and ‘Store’. Selecting photo allows an image to be taken using the phone's camera, which is assigned to the record (Figure 2C). Selecting ‘Data’ displays the data entry screen (Figure 2D), which can contain any standard form field (text fields, list boxes, check boxes etc.). These fields correspond to those created when defining the project database structure. Data can be entered via an on-screen keyboard (using the touch-screen) or via the hardware keyboard should this be part of the phone (e.g. T-Mobile G1). Following data entry, the ‘Confirm’ button returns the view to the Entry screen (Figure 2C). Selecting ‘Store’ saves the current record to the phone's database along with the date and time that the record was created. Subsequently, this process is repeated to create further records.

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Figure 2. The EpiCollect workflow. See text for details.

https://doi.org/10.1371/journal.pone.0006968.g002

The ‘List entries’ option allows all records stored within the phone's database to be viewed and amended if necessary. From this screen, data can be synchronised with the central database with confirmation of successful data transfer (Figure 2E). The ‘Display Map’ option allows all records stored locally on the phone to be displayed on a map using the in-built Google Maps application (Figure 2F). Furthermore, records based on a particular variable (or all records) can be retrieved from the central database and displayed on the phone using Google Maps in conjunction with the locally stored records (Figure 2G). The standard click-drag-zoom interface to the map is available on the phone allowing map navigation and can, using the GPS, instantly zoom to the phone's current location (Figure 2H).

Field Testing

A simple field test of EpiCollect was carried out in which soil samples were taken across Southern England by a single field worker, to obtain isolates of a soil bacterium (Xenorhabdus nematophila) that is pathogenic to insect larvae. At each location, a sample of soil was taken, along with a photograph of the area. Data variables were then recorded and entered into EpiCollect including soil pH, temperature and moisture. Data from each sampling location were then submitted via EpiCollect from the phone to the central database located at http://www.spatialepidemiology.net/epicollect/xenorhabdus.

Figure 3A shows the project-specific web interface and each of the data points on the map indicate a data record (sampling site) submitted via EpiCollect. All samples submitted are listed to the left of the map (Figure 3B) and, using the click-drag-zoom interface, exploration of the data can be undertaken. Clicking one of the sample points displays an ‘info window’ containing the variables collected (soil pH, temp, moisture, GPS position, date etc) and any photograph associated with the record (Figure 3C). Graphical summaries of the variables collected are displayed to the right of the map (Figure 3D) and a number of options are provided for filtering which of the samples points are displayed (Fig 3E). Time sliders allow filtering of data so that only samples collected within a chosen time window are displayed (Figure 3G).

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Figure 3. Simple field test of EpiCollect with data submitted to a project-specific website.

See text for details.

https://doi.org/10.1371/journal.pone.0006968.g003

As mentioned, the project-specific curator can communicate with the field workers directly from the web interface using the instant messaging tool, Google Talk. Figure 3F illustrates the chat interface seen by the curator (this is not available in the public view of the website). Chat requires that each submitter has a Gmail account and is sent from the website and automatically received on the phone as seen in Figure 3I. Message transcripts are automatically stored within the user's Gmail account for future reference. Figure 3H illustrates the view using Google Maps of data requested via the phone from the central database and Figure 3J shows the same data viewed at the project website using Google Earth.

Subsequently, the isolates of the bacterial pathogen recovered from the soil samples at each sampling point will be genotyped (by multilocus sequence typing; MLST [1]) and these molecular typing data will be added to the database, allowing further display options, such as the geographic distribution of particular X. nematophila genotypes.

Illustrative project involving multiple field workers

The simple field test illustrated the collection and submission of data from one field worker and the ability to view data retrieved from the central database on the phone using Google Maps. However, EpiCollect is designed for situations where multiple field workers submit data via mobile phone to a central database. For example, multiple field workers may submit data on animal deaths (e.g. surveillance of living and dead amphibians), or animal infections (e.g. using simple field diagnostic tests to distinguish infected and non-infected animals), and the web application allows colour-coding (or symbol-based coding) of the data points submitted by phone to the project database by different field workers.

To demonstrate this further, Figure 4 shows the web interface for an illustrative dataset where data from each sampling point have been submitted via mobile phone to the project database by multiple field workers across Europe using EpiCollect. Field tests have been used to identify those animals infected with a specific bacterial pathogen and, as in many real life examples, samples from the infected animals are taken back to a laboratory for strain characterisation (in this case determining the serogroup of the strain and its susceptibility or resistance to an antibiotic). The illustrative data can be explored at http://www.spatialepidemiology.net/epicollect/demo.

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Figure 4. Illustrative dataset showing use of EpiCollect by multiple users.

See text for details.

https://doi.org/10.1371/journal.pone.0006968.g004

Figure 4A shows the overall data summary with each point on the map representing sampling locations across Europe. The points are colour-coded based on whether the pathogen recovered from each of these locations is antibiotic-susceptible (green) or antibiotic-resistant (red). All data points are listed at the top left of the interface and the data variables are graphically represented to the right of the map. The distribution in the total sample of each serogroup, and the extent of resistance to the antibiotic are represented as pie charts, and the estimated ages of the infected animals are represented as a bar chart (<1 year, 1–5 years, >5 years). In Figure 4B the sampling points have been colour-coded based on the individuals who have submitted data from their phones. Using the filtering options shown in Figure 4A we can delimit the data displayed on the map to show only those samples where the animals were infected with serogroup 1 of the pathogen. As seen in Figure 4C, delimiting the data in this way also updates the graphical summaries and shows that all strains of serogroup 1 are antibiotic-resistant and, furthermore, that they are almost always isolated from young animals. In infectious disease epidemiology pathogen isolates are generally characterised at a much finer level than provided by serogrouping using discriminatory molecular typing techniques and, after this has been performed, the geographic distribution and extent of antibiotic resistance of individual genotypes could be displayed on the map. Importantly, these maps can be displayed both on the project website and, by using the filtering options provided by EpiCollect, the same data can be requested and viewed as Google Maps on the mobile phone.

Community data collection, citizen scientists and further uses of EpiCollect

As the name implies, EpiCollect has been designed to allow the collection of epidemiological data. However, there are many other situations where this kind of two-way communication between mobile phones and a central database could be utilised; for example, biodiversity research, where multiple researchers record details (and photograph) the presence and distribution of a particular species. This approach is exemplified by the Zoological Society of London's EDGE of existence programme which is the only global initiative to focus specifically on threatened species (http://www.edgeofexistence.org).

Increasingly, the potential for ‘citizen scientists’ to collect data for community projects within the biological sciences is being exploited. For example, The Open Air Laboratories (OPAL) network (http://www.opalexplorenature.org) encourages anyone with an interest in nature to explore, study, enjoy and protect their local environment, by undertaking animal and plant surveys (such as earthworms found in gardens) with subsequent web-based data submission. Further examples are provided by FrogLife, which encourages the public submission of back-garden amphibian distributions to aid studies in species decline (http://www.froglife.org), the Evolution MegaLab, which encourages the recording of banding patterns of snails so that members of the public can see ‘evolution in their own back-yards’ (http://www.evolutionmegalab.org) and the RSPB's annual ‘Big Garden Birdwatch’ which requests members of the public to record all species of birdlife seen in back-gardens or parks and submit the data for central collation (http://www.rspb.org.uk/birdwatch). These initiatives involve people recording data in notebooks and then either faxing the data or entering them at the website used for the community project. The use of EpiCollect would allow individuals to directly submit their data to the project database from their mobile phone and could significantly increase the collection and collation of data for these types of community projects, especially amongst the young where the mobile phone is the natural way of transferring information.

We are currently exploring the use of EpiCollect for data submission to molecular epidemiological databases (http://www.mlst.net) and for submissions by field workers to a central database being used to catalogue the world-wide prevalence of the disease caused by the emerging amphibian fungal pathogen, Batrachochytrium dendrobatidis, for which we have developed the web application (http://www.spatialepidemiology.net/bd-maps).

Potential Issues and Further Developments

EpiCollect has been designed for projects that range from epidemiology and ecology to community data collection in developed and middle income countries, but a major potential use is for field surveys in resource-limited settings that collect key information for economic and public health decisions and resource allocation. There are a number of issues centred on cost and mobile data network availability that currently could limit the use of systems such as EpiCollect in these settings – for example in parts of sub-Saharan Africa. GPS satellites, in theory, cover the entire globe and obtaining map co-ordinates for data points entered into a phone using EpiCollect should be possible even in remote areas of resource-limited countries. However, the submission of data from EpiCollect to a central database relies on connectivity with mobile data networks. Mobile phone network coverage in Africa is good in some countries but mobile data networks are much less widely available. The global coverage of such networks can be easily accessed (http://www.gsmworld.com/) and is likely to increase considerably in the next few years. Importantly, data collection and storage within EpiCollect is not reliant on data network connectivity, as data records are stored in the phone's database. Data stored in the phone's database while in remote areas can then be synchronised with the central database after returning to an area that does have data connectivity. However, the major limiting factor for current use of EpiCollect and similar applications in many resource-limited countries is adequate access to data networks and the availability and cost of suitable smartphones. Further progress in the penetration of mobile phone technology may remove these limitations in such areas.

A further general issue is maintaining battery power for mobile phones in remote areas but this can now easily be solved by using solar-powered mobile phone chargers, which are now widely available at low cost.

We chose to develop EpiCollect for Android due to its open-source nature and the provision of suitable multiple phones by different network providers (e.g. T-Mobile, Vodafone and Orange). However, we envision that, similarly to Desktop software that is provided for Windows, Macintosh and Linux, versions will eventually be provided for other smartphone operating systems such as Windows mobile and Palm webOS and an iPhone version of EpiCollect will soon be available.

The generic nature of EpiCollect allows it to be used to submit data to any online database, not just those we host at www.spatialepidemiology.net. We provide EpiCollect as free software and will be further developing the tool to allow on-line project definition of variables for the immediate download of versions of the software tailored to specific needs. We encourage those interested in using EpiCollect within their own projects to contact us, so that we can provide software (and an associated website if required) adapted for use in their projects.