agINFRA Bulletin

A new bi-monthly newsletter from the agINFRA Project

agINFRA in the EC Action Plan to deliver Open Agricultural Data

The G8 International Conference on Open Data in Agriculture launched in Washington D.C from the 29th to the 30th of April 2013. The two day event was attended by four hundred food security specialists, scientists, policymakers and technicians. The summit was designed to guarantee a commitment from nations and relevant stakeholders to promote and invest in policies or projects that championed the ethos of open accessible data. The main crux of the G8 conference was to ensure open data could be accessed by users in Africa and worldwide, to eventually help them manage a sustainable crop yield and set up a better defence mechanism against environmental risk. Through the liberation of data, acceleration in agricultural advances can occur, whilst also galvanising business and entrepreneurial spirit in developing regions.

The specific objectives of the conference were to discuss options for a potential global sharing platform. Other objectives included a guarantee between stakeholders to synchronise and standardise their information, and be willing to share their best practices with food insecure countries, to allow struggling farmers optimisation of their agricultural resources. Importantly, it was paramount that G8 countries promoted and encouraged the use of open data within developing nations themselves. Shining examples include The Kenyan Open Data Initiative which makes data accessible between software developers and the public.

Practices were presented at the conference including the N-Farm organisation. This organisation is an innovative project that sets up a text messaging service via mobile phone technology to allow farmers to access competing market prices on their crops. The project gathers its data from The Family Early Warning System (FEWSNET), which has allowed N-Farm to generate ten years of historic data on crop market process. This dynamic advance has meant that farmers in developing countries can make the transition into calculating businessmen, who can make well informed decisions on which plants to crop given their unpredictable and fluctuating trends in the harvests. Off the bat of the G8 conference has thus been a wide adoption of mobile application technology in agriculture throughout Africa.

The G8 was a hotbed of dialectic between experts, who brainstormed and presented pioneering projects. agINFRA in collaboration with openAgris, agINFRA’s integrated service, were presented at the event by Johannes Keizer from the AIMS community, discussing the general practices and benefits of Open Data and the use of software computing in relation to agricultural innovation. Other participants such as Dr Howard Shapiro of Mars Global, shared progress on genome mapping of crops that would are not commercially viable. Since the G8 event, Marc Global Inc has stamped a large footstep into the African continent. The organisation has recently cooperated with the African Orphan Consortium (AOCC) to make information on plant genomes publicly available. Orphan crops are African crops that have been neglected by researchers because they are not economically important on the food market. This scientific undertaking will gather data on a hundred African crops. Mars Inc. reflects the doctrinal commitments of the G8 conference; that through scientific advances and open data, good nutrition, productivity and climatic adaptability can be achieved in developing areas.

Moreover, responding to the rhetoric of the G8 summit, the US as a significant stakeholder, has backed and invested in a number of projects that have manifested ex-post G8. For example, the superpower backs The Germplasm Resources Information Network; which opens data on germplasm on crops, animals and microbes. Meanwhile, the US has also taken the initiative to set up projects of its own that can contribute with other G8 nation’s own plans, such as which shares data on rural issues, farms, and agriculture across the planet.

agINFRA can help the G8 commitment for food security, by creating the infrastructure that can allow information to be transferred and spread on agricultural issues across Europe. As agINFRA is an FP7 project funded by the European Commission, it can encourage research from international institutions, governments and subjects based repositories across the European continent on alternative agriculture advances, and ensure the data is dispersed worldwide. AgINFRA was included in the European Commission Action Plan, as part of its ongoing commitment to delivering open data to publically funded agricultural data for Africa and worldwide users. This step represents a support in increasing global food security.

agNFRA can also help by addressing the hurdles that obstruct the seamless application of open data that may slow down the G8 commitments. Questions on how to get governments and organisations to be willing to share their discoveries and let go of their ownership, and how to compute open data into cohesive text must be confronted. Many governments still present their data in raw form which search engines find difficult to detect, making location of data for users difficult. Therefore, despite the many advances that have materialized as a result of the G8 conference, stakeholders will have to continue to suggest solutions to associated problems with open data, in order to ensure long term success.

Watch Dr. Johannes Keizer present agINFRA-powered Service 'Open Agris' to the G8 Meeting

D8 Open Data for Agriculture: G8 Side Event at IFPRI -- May 1, 2013 -- Johannes Keizer

what are we working on? agINFRA Germplasm Working Group

agINFRA is now working closely with the Germplasm research community to allow Germplasm researchers and collection holders to effectively use the infrastructure to expose their information, make searches and enhance their research. Germplasm, simply defined, refers to a collection of genetic resources for any organism. Each organism (e.g a plant) is filed in a germplasm collection as an 'acccession' (like a book in a library). Together, a large collection of these entries forms a Germplasm collection such as a 'seed bank' for plants of a 'nusery' for trees.

In the world today, a number of portals that provide access to germplasm accessions have been established by different providers. However, access to existing accessions is still limited. One key challenge facing wider accessibility of Germplasm data is that different metadata schemas (ways of referencing information similar to those used in a library) are used by the holding organizations to describe their resources. In addition, existing information published on web portals is, in most cases, not accessible in a machine-readable format. Failure to publish information in a machine-readable format severely limits the ability of researchers to conduct data-intensive processes and potentially prevents further advances in research.

The agINFRA Germplasm Working Group has a clear vision to combat this challenge and make a real difference to the everyday lives of Germplasm researchers and collection managers. Our vision is to:

  • Make the various Germplasm databases interoperable
  • Facilitate the construction of Germplasm 'services'
  • Allow collections and researchers to easily exchange their data

To this end, the agINFRA Germplasm Working group will analyse the metadata schemas that are used to describe germplasm resources and define attributes and vocabularies that can be used to expose germplasm resources in common (Linked Data) format.

The key outcome of the working group will be a set of recommendations for the exposure of germplasm resources in Linked Data format. The recommendations will be embedded in the data infrastructure of agINFRA to allow the exposure of germplasm resources as LOD.

To find out more about the working group and get involved, click here

Green Ideas 2013

Friday, June 28th 2013 at 10am

Leoforos Sofokli Venizelou

Heraklion, Crete

The annual Green Ideas workshop and conference is set to be held in Crete, Greece, from the 28th to the 30th of June 2013. The event is hosted by The Natural History Museum of Crete and organised by Agro-Know Technologies. agINFRA will be the main supporter of the Green Ideas event, together with Natural Europe and Herbal Mednet projects. The main aim of the series of interactive and engaging workshops is to explore ways in which green innovation may be empowered by education and technology. Over two and a half days, international and national participants with an interest in green knowledge and environmental protection from the agricultural, biodiversity and rural education fields will come together to discuss, share and apply best practices. Business plans for green entrepreneurs will be proposed at the workshops. Major questions that will arise from the event will include whether medicinal plants are a sustainable business venture and how to promote education via an inquiry based system of learning. World renowned participants will be involved in ‘what if’ scenarios, and will help map and brainstorm model and cultivate ideas. Certain topics within farming such as creating a good harvest and the planting of crop seeds, and how we can improve the productivity of the farmer and his or her crop yield through the use of Open Data under a modern innovative method of precision farming will be discussed. Hydro-biological data sets for environmental protection and the exchange of accessible information will be analysed to see how it can be used in a meaningful and environmentally friendly way.

Participants who register to the event will get a free pass to the Blue Hackathon organised from the 1st to the 2nd of July in Heraklion Greece, and will also focus on the Open Data and environmental innovation.

This event is of importance to agINFRA , which seeks to create an infrastructure for relevant actors and the general public to access large amounts of raw data within databases, and then disseminate information through exchanging and sharing, and ultimately make calculated inferences from the data available to improve or innovate the environment and agricultural sector. Green Ideas will encourage participants to explore the data set infrastructures available on marine biology, in the hope of protecting the environment exposed to risk.

Watch Green Ideas 2012 Speaker & agINFRA Project Partner Nikos Manouselis in Action!

Green Ideas 2012 - Rapid Fire - Prototype - Nikos Manouselis

Meet the Partners - Johannes Keizer

Johannes Keizer is currently Information Systems Officer for the Food and Agriculture Organization of the UN . For the past 10 years, Dr Keizer has led the Agricultural Information Management Standards and Services (AIMS) team.

The AIMS team dedicated to the management and use of data in Agriculture. The AIMS team, under Dr. Keizer's leadership, manage several large-scale initiatives including the multilingual agricultural concept scheme “AGROVOC”, the International Information Systems for Agricultural Science and Technology (AGRIS) and works together with GFAR (Global Forum on Agricultural Research) on the CIARD RING (“Roadmap to Information Nodes and Gateways”). The AIMS website ( has become one of the most important access points for standards, tools and advice in agricultural information management.

Johannes Keizer has a masters degree in biochemistry and biophysics and a PhD in Biology. Before turning his interest to the management of scientific data he worked as a research fellow on eco-toxicological aspects of organo-phosphorous pesticides.

He is member of the Dublin Core Advisory Board. He lives in Rome and Berlin.

Upcoming agINFRA Sponsored Event: Blue Hackathon 2013

Coming soon in July is the Blue Hackathon 2013, which will take place from the 1st to the 2nd of July in Heraklion Crete. The event is organised by Agro-Know Technologies. agINFRA will again be one of the main supporters of the Hackathon, together with Vibrant - Virtual Biodiversity and iMarine - the data e-infrastructure initiative for fisheries management and conservation of marine living resources. The Hackathon will be hosted by The Hellenic Centre for Marine Research (HCMR). The series of interactive and thought provoking workshops will invite IT developers and hackers, to use their skills and experience to create new ideas for a sustainable and healthier future. The applied ideas that participants will suggest will focus on the multiple benefits of Open Data and APIs that consist of environmental, hydrobiological and oceanographical information. The main crux of the Hackathon is to see how open databases that are focused on marine ecology can contribute to innovations and significant improvements in the sustainability of the environment. The workshops will test out, apply, share and discuss the existing tools used for open data within the marine biological sectors, and see how it can be used in new literature and new disciplines. For this year’s event, a number of open data sets identified by Agro-Know will be worked on by programmers. Some of the data sets suggested include a mobile application that is designed to report animal sightings along ship routes such as fish, dolphins, whales and birds; through the use of GPS mapping. Programmers will investigate how applying and uploading photos by users on to the programme on the hand held device can happen. The British Oceanographic Data Centre (BODC), which deals with biological, chemical, physical and geophysical data with a database that contains measurements of over two thousand different variables, will be looked over by programmers at the event. Moreover, the European Directory of Marine Environmental Data (EDMED), which holds three thousand plus data sets across over six hundred data holding centres in Europe, is just another example of the countless data sets Agro-Know will be showcasing at the Hackathon.

This major event is of importance to agINFRA, as the workshops will closely analyse how open data infrastructures can be used to innovate the environment and solve its many challenges, in this particular case, the marine environment.

For more information please see here.

GBIF database enables global study on thousands of species exposed to climate change

The Global Biodiversity Information Facility (GBIF) is set to begin a global investigation into the effects of climate change on common species. GBIF is a public good with a mandate to assist countries with accessing valuable knowledge on the challenges that impact the survival of biodiversity. The database was set up by governments in 2001 to encourage free and open access to data on biodiversity via the internet. Through an interconnected network consisting of a melange of contributors; GBIF has a greater geographic and thematic spread of participants including academic institutions, scientists, organisations and countries, from bio diverse rice regions. These actors can provide their data for mobilisation, access and discovery in the public domain. The data acquired is then transformed into constructive knowledge as since 2008, nearly eight hundred reviewed papers have cited GBIF mediated data in their own study. Two hundred and thirty GBIF cited papers were published alone in 2012. The online database is a cyber capsule that can capture and indefinitely store information, which is beneficial as much of the generated data on occurrences of organisms are monitored diachronically and across the planet.

Now recently in this month of May, GBIF is set to enable a global study that will analyze fifty thousand plant and wildlife species to assess worldwide losses without urgent need to reduce emissions. It is hoped that temperatures can be reduced to two degrees Celsius rather than four, to buy time of forty years, in order to allow common species to adapt to the remaining two degrees. The hypothesis of the study is that even the diversity of common species will struggle against rising temperature, not just the rare and endangered, which will lead to an impoverished biosphere and ecosystem. Information on current locations of plant and animals, their conditions, museum specimens and from scientific expeditions will be aggregated by a hundred and seventy million individuals who consist of scientists and observational public volunteers. The findings will then be corralled together into the GBIF database. Gathering a global community of researchers and volunteers would not be possible if open data was denied. Information inclusivity can allow one person to contact and access every museum, country, and scientist.

This wide scale collection of open biological data is of importance to agINFRA, as it focuses on how sharing and exchanging results through the use of technology, can help improve global services, development and the protection of the environment.

Upcoming agINFRA-Sponsored Event: Biodiversity Infomatics 2013

Tuesday, Sep. 3rd 2013 at 12pm

Rome, Province of Rome, Italy

Rome, Lazio

Biodiversity Informatics Horizons 2013 (BIH2013) is part of a continuing process that helps to structure and organise the biodiversity informatics community at the European level and beyond.

There have been many successful projects in biodiversity informatics, both at national and supranational level. In Europe this trend has grown under Framework Programmes 5, 6 and 7 and is expected to continue in Horizon 2020. Similar activities have occurred outside Europe, and efforts in biodiversity informatics are increasingly internationally coordinated on the global stage.

To respond to the challenges and priorities of the next decade in biodiversity and ecosystems research, structuring bottom-up and top-down interactions on informatics and cooperating across the community is now an essential activity. Cooperation avoids unnecessary duplication of activity. It helps to maximise and focus effort on building the information resources, tools and infrastructure the scientists and policymakers need. We all know the importance of this as we face environmental, societal and human health challenges on global scale. Science in support of policy to mitigate biodiversity loss due to climate and other man-made changes, to assure food security, and to combat invasive species (to give just a few examples) can only be achieved by full integration of the biodiversity research community through a commonly shared, sustainable einfrastructure across all subdisciplines that reliably serves science and society alike. Hence, the need to coordinate.

BIH2013 will take place over 3 full days, from lunchtime on Tuesday 3rd September to lunchtime Friday 6th. The venue will be in Rome (awaiting final confirmation).

BIH2013 is sponsored and supported by many existing FP7 projects, including: agINFRA, BioFresh, BIO_SOS, BioVeL, CReATIVEB, eMonocot, ENVRI, EUBON, EUBrazilOpenBio, iMarine, Lifewatch, OpenUp!, PESI, proiBiosphere, and ViBRANT.

Working Focus: Integrating the Infrastructure

agINFRA Infrastructure Deployment & Integration work package (WP3) relies on adaptation of the existing infrastructures, their customization, and the development of new components that will ensure balance in the system and its seamless use. At the lowest level, project hardware resources are organized in Grid (gLite, ARC, dCache and UNICORE technologies) sites and Cloud (CLEVER and Okeanos technologies) resources. On top of these, the layer of Scientific Gateways (SZTAKI's WS-PGRADE/gUSE and Catania SG technologies) provides seamless access to the distributed infrastructures for developers of processing and data management software. User oriented high-level portals (Organic.Edunet, AGRIS, CIARD RING, AgLR-TF) are optimized for orchestration of data generation, provenance, quality assessment, certification, curation, annotation, navigation and management thought the gateways, introducing the agricultural scientific communities into the vision of open and participatory data-intensive science.

2nd agINFRA Training School shows Porting Results

agINFRA recently held our second Technical Training School in Budapest, Hungary. The event, titled 'Porting Data Components over the agINFRA Infrastructure' gave leaners a chance to get hands-on with the infrastructure and to collaborate on the design and rapid prototyping of new agINFRA-powered apps and services. A range of technical experts from different organizations came together to present their ideas to the agINFRA consortium as part of the project meeting. Prototypes included agVivo Grid porting, a Linked Media Framework, a Grid-boosted instance of Green Learning Network and a mobile app version of the agINFRA gLibrary. Stay tuned to the agINFRA website for more exciting events like this in the very near future and catch our team at the Blue Hackathon in Crete!

Friends of agINFRA: SemaGrow

New FP7-Funded Project SemaGrow is carrying out critical work to ensure that Agricultural Data Infrastructures like agINFRA can continue to offer the very best service to data-intensive researchers around the world.

During the last years, the trend to open up data and provide them freely on the Internet has intensified in volume as well as quality and value of the data made available. The linked data community has grasped the opportunity to combine, cross-reference, and analyse unprecedented volumes of high-quality data and to build innovative applications. This effort has caused a tremendous network effect, adding value and creating new opportunities for everybody, including the original data providers.

But most of the low-hanging fruit has been picked and it is time to move on to the next step, combining, cross-indexing and, in general, making the best out of all public data, regardless of their schema, size, and update rate; accepting that some schemas might be better suited to a given dataset and application and that there is no consensus about a "universal" schema or vocabulary for any given application, let alone for the Semantic Web and related initiatives such as the LOD cloud. In other words, we need infrastructure that besides being efficient, real-time responsive and scalable is also flexible and robust enoughto allow data providers to publish in the manner and form that best suits their processes and purposes and data consumers to query in the manner and form that best suits theirs.

To address these challenges, SemaGrow carries out fundamental databases research and develops methods and infrastructure that will be rigorously tested on three large-scale current use cases as well as on their projected data growth beyond project's end: we are laying the foundations for the scalable, efficient, and robust data services needed to take full advantage of the data-intensive and inter-disciplinary Science of 2020.

Meeting of Minds: 4th Project Meeting in Budapest, Hungary

The 4th agINFRA Project meeting took place in late May in the Beautiful surroundings of Budapest, Hungary. The meeting brought together the project partners to discuss their current work, upcoming priorities and the future of agINFRA. Fresh from successful inclusion in the European Commission’s action plan on agricultural data and inclusion in the response of the G8 to agricultural data challenges, agINFRA is perfectly positioned to lead the way in making use of Open Agricultural Data. The UN Food and Agriculture Agency led discussions among the partners about our collective vision for how agINFRA can make a real difference to the daily lives of researchers in agriculture. 21c presented an exciting new strategy to support the project’s recent international exposure and take agINFRA to a wider audience than ever before! Stay tuned for more on agINFRA!

About agINFRA

agINFRA is a FP7 Integrated Infrastructure Initiative (I3) project working to introduce scientific communities in the domain of agriculture to the vision of open and par­ticipatory data-intensive science. agINFRA is designed to remove obstacles blocking open access to scientific information and data in agriculture, as well as improve the preparedness of agricultural scientific communities to face, manage and exploit the abundance of relevant data that is available to support agricultural research. Ultimately, agINFRA will demonstrate how a data infrastructure for agricultural scien­tific communities is set up to facilitate data generation, provenance, quality assessment, certification, curation, annotation, navigation and management.