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Geospatial binding for transdisciplinary research in crop science: the GRASPgfs initiative


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The paper retraces the GRASPgfs endeavor (Geospatial Resource for Agricultural Species and Pests with integrated workflow modelling to support Global Food Security) between multiple disciplines around a common objective of facilitating research and model simulations for sustainable food security. Within this endeavor, the geospatial media has been the enabler for multidisciplinary research in crop modelling. Geospatial genetic-trait variations and associations with environmental forecasting were the main focus of the GRASPgfs. Designing the platform achieving this objective generated a transdisciplinary vision of modelling and forecasting for sustainable agriculture. Based on interoperability principles, seamless access as well as sharing for data, metadata and processing models, the design is described in this paper. This geospatial binding facilitates and supports new types of hypotheses and analysis as illustrated in the paper with a landscape genetic case study (bambara groundnut) and a crop disease modelling (eyespot disease). The approach and the eGRASP platform are generic enough to accommodate further complexity into the integrated modelling that this geospatial binding enables.
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O R I G I N A L A R T I C L E Open Access
Geospatial binding for transdisciplinary
research in crop science: the GRASPgfs
Didier G. Leibovici
, Suchith Anand
, Roberto Santos
, Sean Mayes
, Rumiana Ray
, Masoud Al-Azri
Abdul Baten
, Graham King
, Asha S. Karunaratne
, Sayed Azam-Ali
and Mike J. Jackson
The paper retraces the GRASPgfs endeavor (Geospatial Resource for Agricultural Species and Pests with integrated
workflow modelling to support Global Food Security) between multiple disciplines around a common objective of
facilitating research and model simulations for sustainable food security. Within this endeavor, the geospatial media
has been the enabler for multidisciplinary research in crop modelling. Geospatial genetic-trait variations and
associations with environmental forecasting were the main focus of the GRASPgfs. Designing the platform
achieving this objective generated a transdisciplinary vision of modelling and forecasting for sustainable agriculture.
Based on interoperability principles, seamless access as well as sharing for data, metadata and processing models,
the design is described in this paper. This geospatial binding facilitates and supports new types of hypotheses and
analysis as illustrated in the paper with a landscape genetic case study (bambara groundnut) and a crop disease
modelling (eyespot disease). The approach and the eGRASP platform are generic enough to accommodate further
complexity into the integrated modelling that this geospatial binding enables.
Keywords: Agriculture models, Crop modelling, Scientific workflow, Geospatial information, Genetic-trait,
Interoperability, GIS, OGC, Web services
A FAO report of the Commission on Genetic Resources
for Food and Agriculture (CGRFA 13/11) clearly identi-
fied spatial analysis to identify varieties likely to have
climate-adapted traits as an aid to plant breedingas
one of the eight priorities in multidisciplinary research.
In addition, Earth Observation data (EO) has proven the
capacity to provide measurements of key environmental
conditions to predict the production of the healthy crops
and potential disease threats.
Such agricultural modelling and simulations need ac-
cess to elaborated geolocated genetic-trait information
as well as complementary data sources coming from
geospatial data providers and geospatial data hubs,e.g.
soil moisture data, climate data. The BBSRC funded pro-
ject GRASPgfs Geospatial Resource for Agricultural
Species, pests and Pathogens with workflow integrated
modelling to support Global Food Securityinitiated the
design and prototype of an e-infrastructure linking to-
gether (i) a geo-germplasm database, (ii) a dynamic
metadata catalog and (iii) a workflow modelling tool to
enable optimal usage of the geo-genetic-trait informa-
tion. This is desired in various types of simulations for
crop trait variation, forecasts under climate forcing sce-
narios and crop disease epidemics.
This initiative and the prototype of the e-
infrastructure based on open standards is described.
Access to a wide range of information, from rigorous
scientific results to hear-sayfarmersknowledge is be-
coming critical to be able to target efforts in food secur-
ity planning at community or at country levels. Also,
designing scientific and intervention strategies within
changing climates and markets is a fundamental
* Correspondence:;
Nottingham Geospatial Institute, University of Nottingham, Nottingham, UK
Full list of author information is available at the end of the article
Open Geospatial Data,
Software and Standards
© The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
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Leibovici et al. Open Geospatial Data, Software and Standards (2017) 2:20
DOI 10.1186/s40965-017-0034-3
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
challenge. The Plant Genetic Resources for Food and
Agriculture part of the FAOs Global Plan of Action for
plant genetic resources has been established as a world-
wide dynamic mechanism using WIEWS
to foster infor-
mation exchange among members (more than 150
countries) and as an instrument for periodic assess-
The enhanced use of this type of resource and
other germplasm banks with additional contextual infor-
mation is nonetheless still highly desired. In a recent
FAO report
from the Commission on Genetic Re-
sources for Food and Agriculture clearly identified
spatial analysis to identify varieties likely to have
climate-adapted traits as an aid to plant breedingas
one of the eight priorities in multidisciplinary research.
Technologies for the collection and dissemination of
geolocated information, using broad-band mobile com-
munications, sensor platforms, spatial search and perva-
sive computing, are fundamentally changing the access
to and use of location-based data in agriculture [20].
However, the necessary cross-disciplinary research
needed to transform raw data and information into use-
ful intelligence and knowledge to improve the planets
environmental, economic and societal well-being is still
constrained by disciplinary and organizational silos and
legacy concepts. Even if this was already acknowledged
in the 1940s, the geo-location of genetic data in ecology
and agriculture for further spatial analysis: spatial gen-
etic, is still a recent concept [17]. Within the from farm
to forkchain, various heterogeneous data including
genetic-trait information are to be considered as part of
the computational modelling for prevision and forecast;
most of them have a geo-location or spatial component
or would be required to have one to be used from a
plethora of model applications of various complexities.
These are either biophysical, agro-economically based
and more mechanistic or deterministic orientated [6, 13,
14, 19, 30, 36] or more stochastic orientated [2, 5, 12,
23, 42, 48, 52], more rule-based including agent-based
orientated [32, 45, 49] but all contain a combination of
those types. Therefore, a cross-disciplinary expertise
driven from geospatial sciences methodologies appeared
to be needed to develop an integrating framework for
relevant data sources, in order to allow knowledge gath-
ering across all subjects relevant to Food Security.
The objective of the geospatial integration e-
infrastructure framework that GRASPgfs initiative has
proposed to establish is to facilitate the use and reuse of
trait data in crop, animal and microbial species of agri-
cultural importance. The initiative relies on the position
that the geospatial realm, as an entry point and end-
point of this e-infrastructure, enables researchers but
also stakeholders and policy makers to ground their de-
velopment strategies but also to elaborate more easily al-
ternatives [3, 6, 26, 30, 31, 36, 40]. Not only this binding
is conceptual and interdisciplinary but also it has conrete
technical impacts on the e-infrastructure utilizing Open
Geosptial Consortium (OGC) standards. Linked with dy-
namic climate records within the framework capabilities
on scientific workflow modelling, this would allow ad-
dressing food security issues for sustainable agriculture
by enabling predictive modelling with identification and
characterization of new sources of germplasm.
The paper describes the initial overall architecture de-
sign and first results on establishing the eGRASP plat-
form and e-infrastructure. Section 2 concentrates on
expressing the method in defining the approach and ini-
tial challenges for long-term objectives; section 3 high-
lights the bases in designing the eGRASP solution and
architecture along with illustrative examples of initial re-
sults on using such approach.
Targeting global food security issues and sustainable
agriculture, related to crop selection and climate change
needs the development of models integrating a range of
disciplines such as genetic, agro-ecological modelling
and land-climate forecasts. Geospatial science can be the
mediating component of an e-infrastructure enabling
data and processing to be retrieved, integrated and made
available within a geospatial scientific workflow model-
ling interface with uncertainty management.
The main objective of the geospatial integration frame-
work wihin GRASPgfs was to facilitate the use and reuse
of known (and new) sources of crop traits together with
dynamic climate records within the framework capabil-
ities of workflow modelling addressing food security is-
sues concerning sustainable agriculture. Describing
agricultural species germplasm for genotype characteris-
tics with the data ordered by geospatial origin, the
higher-level descriptor being agricultural traithas been
put forward as enabling new way of expressing and ana-
lysing trait variations [34, 41].
Highlighting model complexity for integrated assess-
ments required for global food security, a recent review
of crop models under climate forcing pointed out the
need of generic solution enabling or facilitating the com-
bination of various models together [14]. Figure 1 encap-
sulates the challenges of facilitating the elaboration of
such analysis via an integrated workflow modelling. This
workflow grasping the big pictureand illustrating the
cross-disciplinary expertise required is conceptual and
each data entry or processing task may in fact illustrate
the use of complex data structures and sub-workflows
themselves. The framework to develop would need to fa-
cilitate the integration of the driving key conceptual as-
pects of this model. Following this conceptual approach
and being able to re-use data and models available to in-
stantiate such model would enable new perspectives on
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crop genetic diversity by (i) identifying new sources of
trait variation, (ii) geolocating suitable germplasm, (iii)
planning breeding objectives with the greatest likely im-
pact from the added information of local market and
farmers knowledge [8, 34], and (iv) evaluating the effects
of climate change scenario.
Integrating heterogeneous datasets coming from vari-
ous sources within a generic platform means being able
to access and understand the semantics of these data
and processes in order to allow the platform to present
the data, analyse them, or instantiate a workflow model
using them [9, 25]. Easily integrating various data and
processing resources has considerable advantages in
terms of rapid development of models and their execu-
tion but gives less control on the quality of the results as
various uncertainties coexisting in the components of
the workflow model. Therefore, bounding with uncer-
tainty assessment the outcomes of the models should
also be the aim of the eGRASP platform to allow better
decision-making. Specific capacities are also needed to
integrate information such as genetic-trait encoding and
ontology binding with disparate germplasm data sources.
Pests, pathogens and weeds are encompassed at the crop
information level and in the process themselves as they
are often impacting from interacting with the environ-
mental conditions.
Designing, developping and implementing
The GRASPgfs has therefore focused on designing and
implementing a flexible, interoperable platform based on
open source software
compliant with GEOSS
standards and services for data and processing
capabilities. From delivering a flexible, integrative and
sharing eGRASP web platform based on openess, the ob-
jectives of enabling researchers in crop modelling, agro-
ecological modelling either as developer of new models
or evaluating agriculture strategies (agro-ecomic model-
ling), to seamlessly re-use existing models and specific
data such genetic-trait information will be achieved. For
efficiency and controls on the quality in terms of uncer-
tainty and variability of the outcomes, the design of the
platform allowed functionalities to easily browse and
visualise metadata as well as has to geo-computationally
evaluate workflows output uncertainties [15, 25, 28].
Spatial analysis of the spatial variations either of the pre-
dicted outcomes and their uncertainties were included
in the design to be part of the platform as well. That
way the modelling part and of the decision making part
are interlinked, allowing more flexibility and adaptability.
The approach and the concept of the eGRASP platform
has been the result of multidisciplinary exchanges lead-
ing to a real transdisciplinary vision [4, 21, 38] that is
highlighted in the next section.
Fig. 1 Workflow design of a generic model to be used in food security and sustainability: the Genetic Agro-ecological Sustainability Proposal
model (BPMN diagram)
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Emergence of a transdisciplinary vision
Whilst building up a core collaboration on this topic
from a range of disciplines (within environmental and
human geography, crop science, geospatial information,
and computing science) at the University of Nottingham
by meeting regularly and having small funding for a few
summer internships in 2010, the common vision
expressed in Fig. 1 started to emerge. Later on, thanks
to a 18 months pump prime funding from the BBSRC
the research work could start. The workflow of Fig. 1 en-
capsulates the vision put into the design of the eGRASP
platform as much as it is a template of potential model-
ling scenarios envisioning the various components as
data and processes needed to consider fulfilling our ob-
jectives for GRASPgfs. If at first it may have seemed that
the geospatial sciences brought tools enabling this re-
search within a cross-disciplinary perspective, it trans-
formed rapidly into acting as a media of a more holistic
integrated approach [16], which then expressed itself in
challenging its specific developments within a context
beyond the disciplines involved. In addition to providing
more opportunities for expanding the capabilities and
applications looked for in the first place, this
advancement also created new avenues for interdiscip-
linary research and practices in the use of GIS in agricul-
ture research.
Beyond the global concept and concepts encapsulated
in it, Fig. 1 is a truly transverse vision that not only put
each specialist of a sub-model within a contextual flow
but also enriches the geospatial e-infrastructure model-
ling framework. This resulted from various flow dia-
grams of conceptual information into a technical and
standardised representation using a cross-disciplinary
encoding standard, the BPMN standard (Business
Process Modelling Notation from the OMG standard or-
ganisation). As far as the cross-disciplinary concerns,
Fig. 1 as a BPMN representation is also a scientific geo-
computational model seen from a meta-level description
that can be linked to a workflow engine enabling its
computational execution once instantiated (Fig. 2).
In order to instantiate such models (entire Fig. 1 or
sub-models encapsulated) the design of the eGRASP
platform is based on the Use Case model in Fig. 2, which
translates the requirements exposed earlier. In this figure
only general use cases are presented with different col-
ours to express the different domains or disciplines
Fig. 2 Use case model (UML) for the GRASPgfs platform
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concerned: the green use cases reflect the crop genetic
with genetic-trait information aspects, the yellow use
cases concern geospatial science with visualisation and
selection of environmental constraints, the bleu use
cases are to do with geocomputational modelling and
scientific workflow composition and evaluation, and the
pink use cases concerns crop epidemiology with the risk
factors associate with the crop modelling including pests
and disease risks from pathogens information.
Like UML
(Unified Modelling Language) particu-
larly using class diagrams for object modelling and
use case diagrams such as in Fig. 2, has been enab-
ling cross-disciplinary exchanges from data modelling
[22], the BPMN language establishes a bridge between
the conceptual integrated modelling towards the ef-
fective execution of the models [44]. Facilitating the
composition of such workflows using existing re-
sources is paramount [11].
Crop modelling complexity
Well-known crop modelling approaches such as APSIM
[19], AquaCrop
are considered here as expressing or
being a sub|-model of the trait variation forecast inte-
gration.The purpose of the GRASPgfs is to re-use
directly these established models within a flexible plat-
form; they can be wrapped into OGC web processing
services (WPS) and made available for the platform as
such [10, 35] or via a brokering system [7, 39]. When
the models can be broken down into sub-components, if
required by the crop-trait variation scenario, this can be
made available to the processing service. When possible
the interaction of these models can be complex to set up
and to combine, the BPMN editor is seen as a simplifica-
tion, particularly when a few models are to be combined.
Ultimately it brings interoperability in interfacing het-
erogeneous data and processing models that do not ne-
cessarily impose standardisation for each of them. This
does not preclude of course a good understanding of the
models used, but the goal of the eGRASP platform is to
hide this complexity and to focus on the ability to re-use
the resources within a more macro scenario for global
food security. Models and types of models identified in
introduction can be potentially re-used here and the
platform objectives are also to facilitate their encapsula-
tion as WPS services (Fig. 3).
When looking at trait variation with genotypic infor-
mation, the crop modelling may start with building up a
selection for trait-variation linked to genotype linkage
Fig. 3 The GeoGermPlasmDB schema, an evolution from CropstoreDB
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and environment interaction. This corresponds to the
Trait Hypothesis Constructionprocess task in the gen-
eric workflow. To this end, it is described in Fig. 2
among the other capabilities of the eGRASP platform;
the functionalities associated to this genetic-trait selec-
tion, before performing the crop modeling for example,
are the green part of the use case model. To achieve this
aspect the platform is reusing the CropStoreDB
base, called GeoGermplasmDB in the architecture de-
sign (Fig. 4). The GeoGermplasmDB has an extended
schema in order to record the geometry associated to
few tables using the OGC standard (Fig. 3) and also to
be able to encode the pest and pathogens characteristics
along with model parameters associated to the crop var-
ieties as stipulated in the requirements. The Geogerm-
plasmDB allows users to record genotype information
and trait information with geo-location depending on
the origins of the seeds and the trial sites and imple-
ments the component Bio-genetic Knowledgecompo-
nent of the platform. Geospatial variations associated
with genetic variations can lead to breed selection
programs [18, 33]. An example using the underutilized
crop of the Bambara groundnut (Vigna subterranea)is
detailed in the example section (Fig. 5).
The other aspects of complexity considered here
come on one hand from the interaction of farmers
knowledge with respect to the land races linked to
their strategies to make a living [24, 32] and on the
other hand to the climate forcing interacting with the
current land conditions. Due mostly to aggregation
and topological properties when modelling these
models, the spatial complexity can now be also intro-
duced [26, 47, 51]. Specific models for climate forcing
more often mechanistic can be used to predict future
ground conditions but are usually integrated with
interaction from general land use categories [43, 50].
The eGRASP capacity
The approach pursued in GRASPgfs and for the design
of the eGRASP platform has been as much top-down as
bottom-up from leading disciplines such crop genetics,
geospatial information modelling and crop modelling.
Fig. 4 The eGRASP platform architecture design as sub-module of the CropBASE system
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Basically besides strong top-down emphasis on geolo-
cated genetic-trait database (the GeogermplasmDB), and
on a workflow modelling (based on OGC WPS and
BPMN standard), case studies analysis were used to
gather requirements. Mixing these two aspects as well as
envisaging direct use of the top-down elements into the
bottom-up approach, the UML use case diagram of the
required functionalities of the eGRASP platform was ob-
tained (Fig. 2). From the adoption of the use case dia-
gram, disciplinary research took place to refine the case
studies with focus on use case matching and potential
new developments whilst the computing architecture
was design to fit these requirements.
The architecture designed for the eGRASP platform to
enable global spatial data infrastructure functionalities, as
well as the ones described above, is given in Fig. 4. This
viewpoint gives an overview of the different components
without detailing on how specific analytical functionalities
are implemented. The objective for this pump-prime
funding was to establish the design and to demonstrate a
prototype. Therefore, specific functionalities are still to be
developed; further funding is required to pursue these ef-
forts. In Fig. 4, front-end services with their clients are
represented as square boxes and back-end services often
associated with specific information (e.g.,databases, re-
positories) are represented as cylindrical boxes. The
eGRASP system appears in this design as sub-architecture
of the CropBASE
initiative led by CFF (Crops For the
Future), a wiki-knowledge sharing platform integrating
multiple CFF programs also in development.
For the sake of demonstrating the architecture the set
of services implemented and facilities currently avail-
but the platform as well as the CropBASE portal
are not yet operational. The OGC services, for example
using WPS and WFS, can also be used directly in other
clients such as in QGIS (from the OSGeo
the Geovisualisation is supported from QGIS and
from the WMS client provided from the Geoserver
serving the GeogermplasmDB
the Discovery via Metadata Catalogue service (OGC
CSW) is supported by GeoNetwork
, queries on
GEOSS registered catalogue can brings re-usable re-
sources (data or processing services) as well a s local
the GeoWorkflow is supported by a bespoke
specification for OGC services using the jBPM
suite with a web editor and a workflow engine [35].
the GeoGermplasmDB services as well as local
environmental data are served using GeoServer
the results of the simulations or other workflows
can be stored in the local environmental data
a set of ontologies can be used to enrich the data
and processes enabling refined queries via the
metadata catalogue client.
Quality information available for data and processes in
the metadata catalogue are used for uncertainty
Fig. 5 A landscape genetic analysis workflow on bambara groundnut (Vigna subterranea) landraces
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assessmet from the error propagation, by then allowing
better decision-making. This is currently available as
added functionality from the web editor from re-using
the MetaPUnT WPS
service [27, 28] and allowing to
meta-propagate the uncertainties.
First applications
Two illustrative examples are presented here to highlight
the potential of the eGRASP. The first one, a landscape
gentic modelling, uses directly the GeoGermplasmDB
and WFS associated to describe spatially genetic dis-
tances of germplasms. The second one illustrates the
crop disease modelling of the eGRASP facility by design-
ing an examplar wheat eyespot disease model [1]. Both
examples, the landscape genetic association analysis and
the crop disease modelling are using a BPMN scientific
workflow representation, by then demonstrating the
range of modelling situations that eGRASP is intending
to cover.
For the landscape genetic modelling, a glasshouse trial
with 128 plants from 4 repetitions each of 32 landraces
was analysed (Figs. 5 and 6). Here only the genotypic in-
formation was used to retrace geo-location associations
of similar genetic profiles based on 20 microsatellites
molecular markers (SSR) [37, 46]. Five genetic profiles
were identified from k-means on main principal compo-
nents of the SSR response data. In Fig. 6, the green and
red profiles capturing most of the genetic variability are
relatively clustering spatially with an East-west gradient
in the Sahel for the reds and a North-south gradient in
the East and South-East Africa for the greens. Adapta-
tions to similar climatic environment can be though as
explaining these zones with the Sahel zone for the reds
and a more humid tropical zone in the East-Africa for
the greens. Trade routes can be also involved. Further
analysis including the phonologic data with comparison
to local data will be needed to confirm these sorts of
Each task of the workflow in Fig. 5 was performed
from R scripts based on existing packages. These R
scripts are in the process of being encapsulated as WPS
in order to be used and shared from the eGRASP
The second example illustrated in Fig. 7 is a scientific
workflow for crop modelling with potential occurrence
of the eyespot disease. The purpose was to integrate spe-
cific epidemiological disease modelling within a normal
growth simulation model. The Eyespot disease is mod-
elled using few sub-models interfering with the normal
development of the crop:
The inoculation potential model (IPM) determines
the amount of inoculum available for infection of
the host depending on land condition risks and
weather data.
The disease development model (DDM) based on
the inoculation level and key environmental factors
related toinfection and disease developement.
Finally at a key developmental growth stage the
severity of the disease is determined (DSM) and is
based on estimates from the previous two models.
The impact of the severity of disease is then
evaluated iteratively (HRM) at the subsequent
growth stages until the crop has been harvested.
-4 -2 0 2 4 6
Fig. 6 Bambara groundnut (Vigna subterranea) landrace origins classified by genetic distance (bottom: first two principal components and kmeans
classes, top: geo-locations of the sample)
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Each one of the models: IPM, DDM, DSM and HRM
are stochastic models and estimated at the given growth
stages that were identified as crucial during the develop-
ment of the crop on controlled data: GS13, GS32, GS39
and GS65 [1]. The models are to be combined with
physiological based model for crop growth as in the
BPMN representation in Fig. 7. The disease evolution
models have been implemented in R
was chosen as crop growth model. Within APSIM
and using the script manager, R scripts can be ran,
making APSIM the orchestrating engine. Nonehteless,
encapsulating APSIM within a WPS could be a future
solution using the workflow engine wihtin eGRASP.
Details of first results and variables involved in the
IPM, DDM, DSM and HRM model can be seen in [1]
as well as the full validation of the models. Nonethe-
less, despite the capacity of APSIM to run R scripts,
the targetted variables by the disease modelling
couldnt be updated during simulations which led to a
much simpler adaptation of Fig. 7.
For the eGRASP the interest lies in the fact that such
composition and conceptualisation of the models can be
facilitated and controlled, e.g. looking for model ad-
equacy. The interoperability ensures that the models
designed according to the BPMN standard can be then
shared using a standard graphical representation for
better communication but also as XML encoding enab-
ling any workflow engine to run the scientific model
represented as a workflow.
Like UML (Unified Modelling Language) used as a
computing science tool to design of application systems,
leading both to databases and object programing
implementations, the meta-language of the BPMN can
be very rapidly understood from the scientists involved
[22, 29]. This transdisciplinary process enabled to
conceptualise the disease evolution and impact in a
comprehensive way that has been also efficient to put in
practice once each sub-model (tasks in the BPMN
diagram) has been established and fitted.
Future research
Interdisciplinary projects often reduce to cross-
disciplinary spill over; however over a shared building
up initiative to advance on the GRASPgfs concept, a
real transdisciplinary collaboration has been initiated
and experienced. Not only the co-design of the
eGRASP platform with its embryo of capacities has
enabled to envisage new potential research ideas in
each of our disciplines, it also concretised global food
security strategies and analyses. The recent develop-
ment of the GRASPgfs framework along with the
design of the eGRASP was limited as due to the
budget and not all the disciplines firstly envisaged
could be adequately integrated. Whilst in Fig. 1, the
agro-ecologial interaction would derives mostly from
re-using models in landscape genetic and landscape
ecology, as well as the agro-economic would benefit
from models mentioned in the background section,
their data modelling integration represented on the
left hand side of the model has not been yet investi-
gated. For a prototype design this was not crucial as
long as we could still represent its future influence
when composing the models.
Fig. 7 Eyespot disease workflow modelling using APSIM for wheat crop growth simulation
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If some of the services in Fig. 4 are in place the actual
data and processes content is rather small as this was a
proof of concept exercise. Nonetheless PhD students
and recents projects are providing valuable examples
also enhancing the capacity of this platform. The
interoperability principle adopted by the eGRASP,
including its open source and open standard focus, is
the chance for maximum dissemination of this capacity
as a set of cross-platform clients and services. Geospatial
risk assessments in agriculture in relation to species and
pests, can be greatly facilitated from sharing data and
processes which can then reused by the eGRASP.
www.geoportal. org
APSIM: Agricultural Production Systems Simulator; BPMN: Business Process
Modelling Notation; CFF: Crop For the Future; CSW: Catalog Service Web;
DDM: Disease Development Model; DSM: Disease Severity Model; eGRASP:
e-infrastructure for GRASP; FAO: Food and Agriculture Organisation;
GEOSS: Group on Earth Observation System of Systems; GIS: Geographical
Information Science; GRASP: Geospatial Resource for Agricultural Species,
pests and Pathogens; GRASPgfs: GRASP with integrated workflow modelling
to support global food security; GS13: Growth Stage 13; HRM: Harvest
Reduction Model; IPM: Inoculation Potential Model; JBPM: JBoss Business
Process Modelling suite (Java); OGC: Open Geospatial Consortium;
OMG: Object Modelling Group; OSGeo: Open Source Geo; SSR: Simple
sequence repeats; UML: Unifed modelling language; WPS: Web processing
service; XML: eXtended Markup Language
All the co-authors are very grateful to the support and scientific interaction
we had along this initiative with a number of colleagues: Jeremy Morley
now chief geospatial scientist at Ordnance Survey, UK, Sue Walker emeritus
professor in agro-meteorology at the university of the Free State, South
Africa, Charlie Hodgman, honorary professor at the university of Nottingham,
Tim Brailsford, associate professor in computing science at the university of
Nottingham., Thuy Vu, associate professor in geography, at the university
of Nottingham, Malaysian campus and Razlin Azman,now working with
Pr Graham King.
Most of this work has been possible thanks to the funding from the British
Biological Sciences Research Council (BBSRC) grant n° BB/K004034/1 for the
project Geospatial Resource for Agricultural Species, pests and Pathogens
with integrated workflow modelling to support Global Food Security
(GRASPgfs): a prototype.
DL and SA have been leading scientifically the project. DL finalised the
design of the eGRASP and wrote the paper, both based on contributions
from all. Particularly, SM, GK AB, RR, RS, AK provided work, expertise and
information on the database genetic materials. Illustrative examples were
from RS and MA-A whilst MJ and SA-A provided valuable discussions. All
authors read and approved the final manuscript.
Competing interests
The authors declare that they have no competing interests.
Publishers note
Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations.
Author details
Nottingham Geospatial Institute, University of Nottingham, Nottingham, UK.
Plant and Crop Sciences, University of Nottingham, Nottingham, UK.
Sciences, Southern Cross University, Lismore, Australia.
Faculty of Agricultural
Sciences, Sabaragamuwa University, Belihuloya, Sri Lanka.
Crop For the
Future (CFF), Semenyih, Malaysia.
Global Open Data for Agriculture and
Nutrition (GODAN)
Received: 27 January 2017 Accepted: 5 July 2017
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... Experimental datasets for bambara nutritional components have been curated within the CropStoreDB database (Eckes et al. 2017;Leibovici et al. 2017). Development of CDNO involved collaboration and co-development of terms with the Food Ontology (FoodOn) (Dooley et al. 2018). ...
The combined effects of climate change, increase in world population and dependence on a relatively small selection of crops, are threating the global food security. Despite their limited promotion amongst farmers, seed companies and researchers, underutilised crops could provide alternative sources of nutritionally dense foods and aid in the quest for food production due to their resilience and natural adaptation to marginal environments that could be too harsh for staple crops. Bambara groundnut (Vigna subterranea (L.) Verdc.) is a protein-rich underutilised legume which has also long been recognised to be drought-resistant, capable of fixing atmospheric nitrogen and producing yield in marginal soils. As a consequence of the rapid development of genomic technologies and their current accessibility, in this chapter we share the current progress in genomics using molecular tools, an overview of the genome sequence of bambara groundnut, future work incorporating next-generation sequencing technologies and bioinformatics, as well as an example that showcases the importance of linking trait data to the genome to benefit future breeding programmes.KeywordsBambara groundnutUnderutilisedGenomeMolecular markersBreedingFood security
... Experimental datasets for Bambara nutritional components have been curated within the CropStoreDB database (Eckes et al., 2017;Leibovici et al., 2017). Development of CDNO involved collaboration and co-development of terms with the Food Ontology (FoodOn) (Dooley et al., 2018). ...
Bambara groundnut (Vigna subterranea (L) Verdc) is an underutilised African legume commonly known for its resistance to harsh environmental conditions such as drought, and equally known for its high protein content, and thus, having the potential to aid in the pursuit of food security as the climate is constantly changing. As an underutilised crop, Bambara groundnut has been relatively poorly researched in comparison to other more conventional crops such as maize, wheat, soybean, or rice. To help Bambara groundnut farmers and breeding programs achieve the development of varieties with better agronomical potential, a better understanding of the physiological and genetic mechanisms, in relationship to drought resistance, is needed. A series of experiments under controlled glasshouse conditions were conducted in order to gain a better understanding of the responses of Bambara groundnut to drought. Drought is defined as when the level of water content in the soil is below a healthy threshold for plants to continue normal physiological and biochemical processes. A selection of genotypes was assessed over a period of three years, in 10 L pots, and an Association Genetics Panel was assessed over one season in 5 L pots. Additionally, the transcriptome of a sub-set of 4 genotypes was studied through RNA-sequence, and a genome wide association study was conducted over the association genetics panel. A combination of these approaches allowed to have a better understanding on a series of physiological mechanisms where two main approaches were detected, such as, drought tolerance and drought avoidance. For drought tolerance, several genotypes, such as DodR, S19-3, and TN, showed a higher conservation of their canopy, their efficiency of the photosystem II, relative water content in leaves, and a warmer canopy under drought conditions. Additionally, genes related to several osmo-protectant compounds, and cuticular waxes were differently expressed in response to drought. For drought avoidance, several genotypes, such as UnisR, Kano2, Kano3, and Gresik, showed a faster and higher rate of leaf senescence, lower efficiency of the photosystem II, lower percentage of relative water content in leaves, and a cooler canopy temperature. However, the recovery rate when irrigation was re-introduced, was significantly higher than the drought tolerant genotypes. Additionally, in the case of Gresik, genes related to stomatal conductance were differently expressed in response to drought. These findings will help stepping forward in the Bambara groundnut research by narrowing research objectives in future efforts through a selection of specific physiological traits and genes, and subsequent adaptation into breeding programs by marker assistant selection, or gene editing.
... The reference CDNO OWL file and the source code are available from Github CDNO repository (14). Additional database tables were added to the core CropStoreDB MySQL schema (28) to manage different nutritional data sources, along with an 'ontology register' lookup table to CDNO, FoodOn, ChEBI, NCBI taxon (29) and Plant Ontology (PO) (30) terms. ...
Full-text available
Informed policy and decision-making for food systems, nutritional security, and global health would benefit from standardization and comparison of food composition data, spanning production to consumption. To address this challenge, we present a formal controlled vocabulary of terms, definitions, and relationships within the Compositional Dietary Nutrition Ontology (CDNO, that enables description of nutritional attributes for material entities contributing to the human diet. We demonstrate how ongoing community development of CDNO classes can harmonize trans-disciplinary approaches for describing nutritional components from food production to diet.
... Various database platforms have been developed (19,20), with an increasing number compatible with BrAPI (4), contributing to interoperability. CropStoreDB is a relational schema for explicit management of data and metadata relating to plant experimental genetic resources, traits, trials and associated genetic information (21,22). This database has been used within the interoperable InterStoreDB for linking crop genetic and genomic information (22) and underpins the interactive Brassica Information Portal (23), for which the API has some BrAPI compatibility. ...
Full-text available
Crop phenotypic data underpin many pre-breeding efforts to characterize variation within germplasm collections. Although there has been an increase in the global capacity for accumulating and comparing such data, a lack of consistency in the systematic description of metadata often limits integration and sharing. We therefore aimed to understand some of the challenges facing findable, accesible, interoperable and reusable (FAIR) curation and annotation of phenotypic data from minor and underutilized crops. We used bambara groundnut (Vigna subterranea) as an exemplar underutilized crop to assess the ability of the Crop Ontology system to facilitate curation of trait datasets, so that they are accessible for comparative analysis. This involved generating a controlled vocabulary Trait Dictionary of 134 terms. Systematic quantification of syntactic and semantic cohesiveness of the full set of 28 crop-specific COs identified inconsistencies between trait descriptor names, a relative lack of cross-referencing to other ontologies and a flat ontological structure for classifying traits. We also evaluated the Minimal Information About a Phenotyping Experiment and FAIR compliance of bambara trait datasets curated within the CropStoreDB schema. We discuss specifications for a more systematic and generic approach to trait controlled vocabularies, which would benefit from representation of terms that adhere to Open Biological and Biomedical Ontologies principles. In particular, we focus on the benefits of reuse of existing definitions within pre- and post-composed axioms from other domains in order to facilitate the curation and comparison of datasets from a wider range of crops. Database URL:
... mainly focus on genome data dissemination via CropStore and the Brassica Genome Database (BrassicaDB). The Brassica CropStore was initially developed to collate and disseminate information from crop research communities [201,202] as well as provide data information for Brassica phenotypic and genetic maps from different projects [203,204]. CropStore is an integral part of InterStoreDb which provides a platform for the utilization of a set of interlinked databases to assist linking phenotype to QTL regions for a particular trait. ...
Full-text available
Interspecific hybridization is widespread in nature, where it can lead to either the production of new species or to the introgression of useful adaptive traits between species. In agricultural systems, there is also great potential to take advantage of this process for targeted crop improvement. In the Brassica genus, several crop species share close relationships: rapeseed (Brassica napus) is an ancestral hybrid between turnip (B. rapa) and cabbage (B. oleracea), and mustard species B. juncea, B. carinata and B. nigra share genomes in common. This close relationship, plus the abundance of wild relatives and minor crop species in the wider Brassiceae tribe which readily hybridize with the Brassica crop species, makes this genus an interesting example of the use of interspecific hybridization for crop improvement. In this review we introduce the Brassica crop species and their wild relatives, barriers to interspecific and intergeneric hybridization and methods to overcome them, summarize previous successful and unsuccessful attempts at the use of interspecific hybridization for crop improvement in Brassica, and provide information about resources available to breeders wishing to take advantage of this method in the Brassica genus.
Abstract Over the last twenty-five years, the evolution of geospatial standards has followed the practices in scientific and industry communities, while the sharing of data online became more and more efficient. However, adoption of the standards does not come without challenges that enable the standards to develop: (1) the cross disciplinary integration including geoprocessing, requiring synergy between domains, (2) compatibility between national, regional and international e-infrastructures and (3) efforts required to make possible data conflation from heterogeneous sources including crowdsourcing. The agriculture domain is used to illustrate these aspects of geospatial standard adoption throughout the discussion as a representative domain where applications of the standards address a multidisciplinary community. The agriculture domain is also a very dynamic domain with future challenges for geospatial standards arising from rapid developments of new technologies and practices used at different stakeholder levels such as smart farming, cloud computing and virtual research environments. The three big challenges described above can represent barriers or opportunities within each specific domain as well as for the standards in use themselves. It is hoped the chapter will make the reader see them as opportunities for agriculture research, e.g. monitoring or forecasting applications. Keywords geospatial standard; spatial data integration; data harmonization; metadata; geoprocessing workflow; cloud computing
Full-text available
This chapter provides an overview of the various physical experimental and reference data resources available in the public domain to support evolutionary, comparative and functional analysis of Brassica napus genomes, and that underpin pre-breeding R&D and breeding activities for canola and related oilseed crops. Many of these resources have become available as a result of international cooperation through the Multinational Brassica Genome Project (MBGP). The role and establishment of nomenclature and other standards for Brassica species is outlined. Specific plant resources and their use in mutant screening, mapping and genome-wide association studies are described, along with genomic tools such as genetic marker and transcriptome platforms. The range of current genomic data, information resources, bioinformatics tools and analysis pipelines for B. napus are introduced, together with the available dedicated B. napus-specific genome browsers and related online sites. In addition, databases dedicated to managing phenotypic trait, trial and related data are described, and future requirements are identified for enabling greater integration of phenotypic and genotypic information and tools to collate and navigate increasingly complex data sets. Due to rapidly changing genomic technologies and funding support, the coverage of resources described here is unlikely to be comprehensive. However, many additional details are to be found either hosted at or linked from the website on behalf of the MBGP. The Brassica database (BRAD) maintained at also continues to provide a valuable set of reference information.
Full-text available
The Brassica Information Portal (BIP) is a centralised repository for brassica phenotypic data. The site hosts trait data associated with brassica research and breeding experiments conducted on brassica crops, that are used as oilseeds, vegetables, livestock forage and fodder and for biofuels. A key feature is the explicit management of meta-data describing the provenance and relationships between experimental plant materials, as well as trial design and trait descriptors. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for researchers, breeders and other end-users. BIP opens up the opportunity to apply integrative, cross-project analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.
Full-text available
Sharing and reusing data in research is a welcome and encouraged practice since it maximises the scientific outcomes given limited financial, material and human resources. Interdisciplinary research is considered to benefit from this practice, uniting researchers and data from two or more disciplines to advance fundamental understanding or tackle problems whose solution is beyond the limit of an individual body of knowledge. Here we discuss the challenges of combining data across disciplines, focusing in particular on associating geographic location data with genetic data in the context of a project involving Crop Science and Geospatial Information Science disciplines. This project aims to improve understanding of how geographical, environmental and anthropogenic factors affect the genetic variation in a neglected and underutilised crop called Bambara groundnut.
Full-text available
Sharing and reusing data in research is a welcome and encouraged practice since it maximises the scientific outcomes given limited financial, material and human resources. Interdisciplinary research is considered to benefit from this practice, uniting researchers and data from two or more disciplines to advance fundamental understanding or tackle problems whose solution is beyond the limit of an individual body of knowledge. Here we discuss the challenges of combining data across disciplines, focusing in particular on associating geographic location data with genetic data in the context of a project involving Crop Science and Geospatial Information Science disciplines. This project aims to improve understanding of how geographical, environmental and anthropocentric factors affect the genetic variation in a neglected and underutilised crop called Bambara groundnut.
Conference Paper
Full-text available
In this short keynote paper, I will briefly explore the current state of research and practice surrounding the BPMN standard. On basis of this analysis I will offer a personal outlook into the key emerging areas where I believe more research will be required to further understand BPMN, its premise and promise, and how we can shape - and join together - the landscape of BPMN practice and development in academia and industry.
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A Global crop production is affected by seasonal and climatic variations in temperature, rainfall patterns or intensity and the occurrence of abiotic and biotic stresses. Climate change can alter pest and pathogen populations as well as pathogen complexes that pose an enormous risk to crop yields and future food security. Eyespot disease caused by Oculimacula yallundae and O. acuformis is associated with yield losses in UK wheat estimated in 1998 at £24 million. Crop simulation models have been validated as an important tool for the development of more resilient agricultural systems and improved decision making for growers. The Agricultural Production Systems Simulator (APSIM) is a software tool that enables sub-models to be incorporated for simulation of production in diverse agricultural systems. APSIM-wheat simulates crop growth and development, soil and management options. Modification of APSIM to incorporate epidemiological disease model for crop growth and yield under different disease intensities has not yet been undertaken in UK or elsewhere. Thus, the objective of this work was to develop epidemiological model for eyespot disease and incorporate it within APSIM for crop simulation under a range of disease and environmental conditions. Historical climatic data combined with 8 years of observed disease (2004-2012) data on incidence and severity of eyespot in UK field trials was used to develop epidemiological model, combining infection and severity, for the prediction of disease development in relation to crop growth stages. Crop growth characteristics, biomass and yield were measured separately and employed for eyespot yield loss or biomass reduction model in wheat based on disease severity. Current work is focused on modifying APSIM to simulate crop loss through the incorporation of the epidemiological disease and yield reduction components and further validation to confirm that empirical data were accurately simulated.
Simulation models are an established method used to investigate processes and solve practical problems in a wide variety of disciplines. Central to the concept of this second edition is the idea that environmental systems are complex, open systems. The authors present the diversity of approaches to dealing with environmental complexity and then encourage readers to make comparisons between these approaches and between different disciplines. Environmental Modelling: Finding Simplicity in Complexity 2nd edition is divided into four main sections: An overview of methods and approaches to modelling. State of the art for modelling environmental processes. Tools used and models for management. Current and future developments. The second edition evolves from the first by providing additional emphasis and material for those students wishing to specialize in environmental modelling. This edition: Focuses on simplifying complex environmental systems. Reviews current software, tools and techniques for modelling. Gives practical examples from a wide variety of disciplines, e.g. climatology, ecology, hydrology, geomorphology and engineering. Has an associated website containing colour images, links to WWW resources and chapter support pages, including data sets relating to case studies, exercises and model animations. This book is suitable for final year undergraduates and postgraduates in environmental modelling, environmental science, civil engineering and biology who will already be familiar with the subject and are moving on to specialize in the field. It is also designed to appeal to professionals interested in the environmental sciences, including environmental consultants, government employees, civil engineers, geographers, ecologists, meteorologists, and geochemists.
Bambara groundnut is an indigenous African legume grown mainly in sub-Saharan Africa; it is an important source of protein to the rural majority. There are no established varieties and subsistence farmers grow locally adapted landraces which are generally low yielding. Bambara groundnut is a predominantly self-pollinating crop and is expected to exist as non-identical inbred lines, although the previous lack of co-dominant markers has prevented a formal assessment of heterozygosity within bambara groundnut genotypes. A total set of 75 microsatellites that were characterised in this study were used to investigate the genetic diversity of a set of 24 bambara groundnut landraces, to provide an evaluation of the markers for polymorphism and provide a link with DArT marker data that were previously analysed. Sixty eight microsatellites were identified that were found to be consistent and reproducible, from which a set of markers were selected and used for genetic variability studies of bambara groundnut, to compare the use of molecular markers with morphological markers, and to investigate using SSR markers in pure line selection. The genetic diversity of bambara groundnut was assessed based on morphological characters for two seasons; in a glasshouse experiment at the University of Nottingham, Sutton Bonington Campus, UK and in a field experiment that was conducted at the Botswana College of Agriculture (Notwane farm), Gaborone in a randomised block design with three replicates. The landraces were characterised for 24 quantitative and 13 qualitative characters. The results indicated considerable variation for quantitative characters, while significant morphological differences were also recorded for most characters. Multivariate data analysis was conducted using principal component analysis, cluster analysis and heritability estimates were developed. The low cost, simplicity and agricultural relevance of morphological characterisation makes it an important tool in germplasm genetic variation studies. Thirty four lines from field experiments were investigated for genetic diversity based on 20 microsatellites. The expected heterozygosity (He) had an average of 1 in agreement with the fact that bambara groundnut is predominantly self-pollinating. Both cluster analysis and principle component analysis (PCoA) grouped landraces based mainly on their areas of origin. A thorough molecular analysis of genetic and morphological variation in bambara groundnut was conducted to investigate the relationship between the two assessment techniques. This comparison will assist in breeders making informed decisions as to which approach is best to use in germplasm characterisation and plant breeding and how best to apply such knowledge in practical situations. DNA markers could then aid with the selection of germplasm for breeding, quality control within breeding programmes and, potentially, direct selection via Marker Assisted Selection (MAS). Euclidean distance estimates for morphological data and (Nei’s 1972) genetic distance estimates for SSR data were strongly correlated (r = 0.7; P < 0.001) in the agronomy bay and (r = 0.6; P< 0.001) in the controlled growth room. These results suggest the two approaches are generating the same pattern of genetic diversity, and as such can be used as a surrogate for each other.
Environmental science needs to better link to real-world policy application and simulation-based policy-support systems (PSS) are an appropriate way to do so. Policy-support systems (PSS) are an extension of the ubiquitous and highly variable decision-support systems (DSS). These support systems are targeted at making sophisticated descriptions of process, state and change accessible in a dynamic way to support decision-making, or the testing and design of policies. Recent years have seen considerable growth in research at the water-energy-environment-food (WEEF) nexus and there is much interest in scientific policy support for this from the international development, conservation and governmental policy communities. This demand is focused particularly in the areas of water, biofuels and food, water management for urban supply and hydropower and maintaining ecosystem services. WaterWorld is a spatial policy-support system focused on the hydrological baseline of an area and the impact of land use, land management, and climate change.