Chemical and Biological Assessment of AfSIS soils
Lead Research Organisation:
Rothamsted Research
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
Generate chemical and biological parameters associated with nutrient bioavailability to crops, animals and humans from archived and fresh African soils. Parameters will include metal sesquioxides, cation exchange and phosphate binding capacities and predictors of biological nutrient cycling and loss from metagenome analysis. Data will be incorporated into the oSDP
Planned Impact
unavailable
People |
ORCID iD |
| Andrew Neal (Principal Investigator) |
Publications
Mathers A
(2017)
Determining the fate of selenium in wheat biofortification: an isotopically labelled field trial study
in Plant and Soil
Von Fromm S
(2020)
Continental-scale controls on soil organic carbon across sub-Saharan Africa
Von Fromm SF
(2024)
Controls on timescales of soil organic carbon persistence across sub-Saharan Africa.
in Global change biology
Wang, P.
(2017)
The Nexus of Soils, Plants, Animals and Human Health
| Description | Fertiliser Optimiser App |
| Amount | £28,132 (GBP) |
| Funding ID | BBS/OS/GC/200014A |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 07/2018 |
| Description | GeoNutrition |
| Amount | $6,000,000 (USD) |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 02/2018 |
| End | 01/2022 |
| Description | Open Soils Data Platform |
| Amount | £82,601 (GBP) |
| Funding ID | BBS/OS/GC/200014B |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 07/2018 |
| Title | AWS open data associated with AfSIS soils |
| Description | This data set contains soil infrared spectral data and paired soil property reference measurements for geo-referenced soil samples that were collected through the Africa Soil Information Service (AfSIS) project, which lasted from 2009 through 2018. In this release, we include data collected during Phase I (2009-2013.) Geo-referenced samples were collected from 19 countries in Sub-Saharan African using a statistically sound sampling scheme, and their soil properties were analyzed using both conventional soil testing methods and spectral methods (infrared diffuse reflectance spectroscopy). The two types of data can be paired to form a training data set for machine learning, such that certain soil properties can be well-predicted through less expensive spectral techniques. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Paired wet and dry chemistry measurements for georeferenced soils collected by the Africa Soil Information Service (AfSIS), stored as CSV and OPUS files. |
| URL | https://registry.opendata.aws/afsis/ |
| Title | AfSISdb |
| Description | This is a database of African Soils data developed by QED with funding mainly from Bill and Melinda Gates foundation but also through BBSRC |
| Type Of Material | Database/Collection of data |
| Year Produced | 2014 |
| Provided To Others? | Yes |
| Impact | New data has been added based on chemical analysis at Rothamsted |
| URL | https://afsisdb.qed.ai/about/ |
| Title | AfSISdb metadata endpoint |
| Description | This is JSON format endpoint providing the schema and metadata for the AfSIS databases. It is used to populate metadata into the open soils data platform. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | It is part of the infrastructure of the oSDP and is a technical result only. |
| URL | https://afsisdb.qed.ai/cabinet/api/schema/ |
| Title | Global Soils metgenomic library |
| Description | collection of over 450 shotgun metagenome data sets collected from various public repositories and generated from pristine and managed soils around the globe. These are being used to assess the diversity of micro-organisms and functions and study the effects of management upon soil communities.Partnerships with Bioplatforms Australia and the African Soils information service is contributing metagenomes from across Australia and sub-Saharan Africa to this database and extending the utility of the resource. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | none yet |
| Title | Open Data on AWS: Africa Soil Information Service (AfSIS) Soil Chemistry |
| Description | This dataset contains soil infrared spectral data and paired soil property reference measurements for georeferenced soil samples that were collected through the Africa Soil Information Service (AfSIS) project, which lasted from 2009 through 2018. Georeferenced samples were collected from 19 countries in Sub-Saharan African using a statistically sound sampling scheme, and their soil properties were analyzed using both conventional soil testing methods and spectral methods (infrared diffuse reflectance spectroscopy). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | The two types of data can be paired to form a training dataset for machine learning, such that certain soil properties can be well-predicted through less expensive spectral techniques. |
| URL | https://registry.opendata.aws/afsis/ |
| Title | Open Soils Data Platform |
| Description | Our aim has been to develop an open data platform for soil information, combining metadata from a broad range of sources and creating a searchable catalogue based upon a semantic data framework. This will enable linking of activities and outputs via common themes (within controlled vocabularies and semantic search) and links across constituent databases using mappings over standard web interfaces and through application programme interfaces (APIs) to the underlying data. This architecture will be readily extensible to other information resources and databases via continual development using common semantics standards such as PROV-O and SoilML. To make the Phase I subset of AfSIS's soil infrared spectral data and paired soil property reference measurements available for release on AWS's Registry of Open Data (RODA), QED (1) coordinated with multiple parties to gather and organize the necessary assets, and (2) built computational notebooks demonstrating how the data can be used. To carry out the first initiative, data from ICRAF and TanSIS, and Phase I wet chemistry data from CROPNUTS, have been uploaded using QED's AfSIS DB portal that has been online since 2014. Re-analyzed AfSIS Phase I wet chemistry data from Rothamsted was sent to QED by way of spreadsheets, which QED then wrote programs for to automatically parse and upload to AfSIS DB. The data in AfSIS DB (https://afsisdb.qed.ai/about/) was then post-processed by way of Python, merging field-acquired georeferences with lab-acquired measurements, and ensuring that only georeferenced samples with both wet and dry chemistry analyses were retained in the final dataset. To collect sufficient metadata, QED also corresponded with ICRAF, CROPNUTS, and Rothamsted to gather formal SOPs for all methods used in their analyses, and these SOPs are also presented on the RODA. In a related effort for propagating metadata, QED also created an endpoint on AfSIS DB that dynamically generates linked data describing the models stored within, to experiment with semantic web technology. The second initiative, of building computational tutorials, has been not only suggested by existing efforts in AfSIS and oSDP, but is also part of AWS's data quality standards for acceptance of a public dataset. Our tutorial first provides an exposition of the structure of the data, and then demonstrates how to read the data from the S3 bucket and build a simple machine learning model for spectral inference. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | We have implemented a first version of the oSDP metadata integration framework based on CEH's Environmental Observatory Framework. This uses an agreed set of metadata and controlled vocabularies needed for integrating a range of data. These have been taken from the CAB Thesaurus and Global Agricultural Concept Scheme and FAO's AGROVOC systems. Prototype metadata integration for several data collections has been achieved enabling searching of the catalogue for datasets containing related information. Some issues have emerged with access to data from African sources (e.g. OFRA) but discussions are ongoing. Metadata descriptions for the chemical and biological datasets (Objective 3) have been developed. Impact is also derived from the importance of releasing data as an exemplar public dataset on the AWS portal. This puts the data in the hands of a major international community who are able to develop new computational methods to interrogate the data. Practical outcomes at end user level in the agriculture and farming community are not available yet, but the international reach of the AWS portal is a major outcome for the project |
| URL | https://afsisdb.qed.ai/about/ |
| Title | Open-access data on African soils available via Amazon DB |
| Description | iGCRF data relating to African soils were used in the first open-access Amazon DB related to soils information. This was announced in December 2018. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | This data will help develop high resolution, ground-truthed maps covering various African regions related to soil chemistry and fertility |
| Description | GeoNutrition-tackling hidden hunger in sub-Saharan Africa |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | We will perform the wet chemistry (including inductively coupled plasma-mass spectrometry, ICP-MS) to quantify properties influencing mineral bioavailability such as iron sesquioxides, effective cation exchange capacity, phosphate binding capacity. Solid-state MIR and XRF measurements on the same samples will be made in AfSIS labs,providing complementary data on total elements, pH and organic C. Together, these data sets will allow us to determine which soil factors are most important in determining crop metal concentrations and help to identify the mechanisms which control nutrient binding and release. It will enable us to determine if the wet chemical results can be predicted reliably from solid-state measurements that can be performed in Africa |
| Collaborator Contribution | Provision of datasets and expertise |
| Impact | none yet |
| Start Year | 2017 |
| Title | Fertilizer Optimizer App on Google Play Strore |
| Description | The Fertilizer OptimizThe concept behind the CABI Fertilizer Optimizer app is easily transferable to the intermediaries and then to farmers through intensified training. Farmers think about the crops they wish to grow and what they can afford to spend on fertilizer. The app then makes suggestions about the most profitable way to apply the fertilizer. The Fertilizer Optimizer works even at very low levels of investment and help farmers to get the best possible returns."er app is designed to help resource constrained farmers to maximise the return on investment on fertilizer, based on what the farmer can realistically afford. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Impact | CABI is now rolling out a programme of training for additional extension workers on the use of the Fertilizer Optimization Tools (FOT) in with a target to reaching up to 1600 more farmers in Uganda. Across Africa, over 3,000 extension workers have already been empowered to use the FOTs to advise farmers on how to maximise their profits from investments in fertilizers. This is another opportunity to out scale the FOT across Africa. A social media campaign will also be utilised to help promote the mobile app for FOT across 13 African countries - including Ethiopia, Malawi, Tanzania, Ghana and Nigeria. |
| URL | https://play.google.com/store/apps/details?id=org.cabi.ofra |
| Title | Fertilizer Optimizer app |
| Description | The original conceptualization and development of the optimization tool was by the university of Nebraska-Lincoln. Jansen J, Wortmann CS, Stockton MC, Kaizzi CK (2013). Maximizing net returns to financially constrained fertilizer use. Agronomy Journal 105 (3) 573-578. The Fertilizer Optimizer tool was built as part of the Optimising Fertilizer Recommendations in Africa (OFRA) project, led by CABI. The project was a partnership between CABI, the University of Nebraska Lincoln, national governments and agricultural research and extension systems in 13 countries in sub-Saharan Africa. OFRA was supported by the Alliance for a Green Revolution in Africa (AGRA). In this project this spreadsheet-based tool was converted to an Android app and validated against the original spreadsheet version. This included transferring the spreadsheet logic over to an Android app, and providing parameters for crop and the sixty agro-environmental zones. Translation of the interface was completed and as well as English, French and Portuguese are now supported. An upgrade to a mobile phone app now offers farmers across Africa even more benefits and cutting-edge fertilizer use technology. This will help farmers to grow healthier, more productive with increasingly profitable crops, as a result of more informed use of how small amounts of fertilizer impact the crops which they grow. Pilot work on the CABI Fertilizer Optimizer app in Uganda has shown that some farmers realised up to a seven-fold increase in yields. Using funding from the BBSRC Global Challenges Research Fund, the app has now been upgraded to make it easier to use. The new app includes the integrated soil fertility management (ISFM) practices feature, and a calibration tool which helps farmers to apply the right quantity of fertilizer to their crops. The Fertilizer Optimizer app is designed to help resource constrained farmers to maximise the return on investment on fertilizer, based on what the farmer can realistically afford. In the latest version of the Fertilizer Optimizer app it is possible to calibrate the fertilizer recommendation to the planting conditions of a user's field. Version 1 of the app provided users with an amount of fertilizer to use and an application rate (e.g. 5kg per hectare). Now it is possible to enter field measurements, container sizes and preferred application technique and the app will help to evenly distribute the recommended fertilizers across the crop providing actionable information tailored to a particular field. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | The Fertilizer Optimizer has been produced for: Burkina Faso, Ethiopia, Ghana, Kenya, Malawi, Mozambique, Niger, Nigeria, Rwanda, Tanzania, Uganda and Zambia and is available to use in English, French and Portuguese. Impact stories are reported in blog posts attached to this report. The was launched in the Google play store in January and it is too soon to discuss impact. Outreach and marketing campaigns will be undertaken by CABI, the responsible partner for this part of the project. Open Soils Data Platform BBS/OS/GC/200014B We have developed and implemented an Open Soils data Platform that enables the storage and searching of multiple information sources on soils e.g. soil samples and support materials such as reports for sub-Saharan Africa. The platform uses an agreed set of metadata and controlled vocabularies needed for integrating a range of data. Prototype metadata integration for several data collections has been achieved enabling searching of the catalogue for datasets containing related-information on soils information. The architecture developed is easily extensible to other information resources and databases as soon as they become viable http://catalogue.ceh.ac.uk/osdp/documents Issues emerged regarding access to data from African sources e.g OFRA but discussions with these and others are ongoing. The continuing objectives are to engage with stakeholders to populate the catalogue with additional datasets so it becomes a valued repository of data for soil health for Africa |
| Title | Open Soils Data Platform portal |
| Description | We have developed and implemented an Open Soils data Platform that enables the storage and searching of multiple information sources on soils e.g. soil samples and support materials such as reports for sub-Saharan Africa. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2018 |
| Impact | This portal can integrate metadata across data collections and enable searching of the catalogue. |
| URL | http://catalogue.ceh.ac.uk/osdp/documents |
| Description | CABI Blog - Fertilizer Optimization Tool helps return son to teacher training school |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | The blog explains the impact of using the Fertiliser optimisation App for one farmer and how it improved his family finances. "I wanted to grow 1 acre of maize and ¾ acre of soybean. He gave me various investment scenarios which showed the amount that can be invested and expected yields and income. I decided to invest UGX80,000 (approx. $22). I didn't even have the money but borrowed UGX 40,000 and gave it to him so he could buy me DAP which I applied at planting. Later I gave him the remaining money and he brought Urea which I applied when the maize was at knee high. "I was able to harvest 7 bags of maize and 1 ½ bags of soybean. Before, I used this technology I used to harvest 7 bags of maize from 3 acres (about 1.5 bags per acre) and 70kg soybean per acre. I was very excited to have achieved such an output. I decided to sell part of the soybean to buy fertilizer for this season. This time I planted 4 acres of maize and ¼ acre of groundnuts and invested UGX120,000 (approx. $32) up from UGX80,000 last season. "I was also able to seek admission for my son at Busikho Teachers' Training College, where he is training as a Grade I teacher. I paid 5 bags of maize to the college to cover part of his starting fees. The rest of the harvest I have left for home consumption." |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://blog.cabi.org/2018/12/07/fertilizer-optimization-tool-helps-return-son-to-teacher-training-s... |
| Description | CABI Blog - Fertilizer Optimization Tool pays dividends for farmers in Uganda |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | The blog was describing a workshop explaining the benefits of the Fertiliser Optimisation tool to a club comprised of five farmer groups, each with about 30 members, who meet weekly. As a club they come together as a whole and meet monthly. During their weekly meetings the farmers take advantage of the opportunity to save and borrow money under the popular co-save program known as Village Savings and Loan Associations (VSLA). Ultimately this is aimed at enhancing financial inclusion. According to one user "When I was introduced to the Fertilizer Optimization Tool by Mr Mawanda, I only had UGX 50,000 (approx. $13). I told him I cannot use fertilizer because I don't have enough money to buy even one bag of fertiliser. One 50kg bag, alone, is sold at UGX150,000 (approx. $40). "He explained that the tool helps to calculate only the fertiliser I need given the amount to invest. The output showed that I needed to buy 10kg of DAP, and 10kg Urea for my ½ acre of maize. I applied the DAP, one bottle top per hole and Urea in bands. As a result, I harvested 700kg compared to 100kg before (or even sometimes less) from the same area." For farmers who used fertilizer before, their appraisal of the tool was based on its ability to recommend only what is required, therefore, avoiding wastage of fertilizers. The common practice for those using fertilizer has been to procure 50kg of fertilizer, commonly, DAP, Urea or TSP and applying according to their own knowledge. This practice, farmers have realised, has a high investment cost attached to it - yet this cost is not necessarily offset by the added production. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://blog.cabi.org/2018/11/23/fertilizer-optimization-tool-pays-dividends-for-farmers-in-kenya/ |
| Description | CABI Press Release - Phone app set to transform how low-income farmers in Africa invest in fertilizer |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | This is was the press release made to announce the release of the Fertiliser optimisation tool in the Google Play Store |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.cabi.org/news-and-media/2019/phone-app-set-to-transform-how-low-income-farmers-in-africa... |
| Description | Fertiliser Optimisation App - Training and User Testing |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | These were training and user feedback sessions on the beta-test version of the Fertiliser Optimisation App... There were a total of 5 sessions held in Uganda. The impact was that future uses (small holder farmers) and advisors were taught about the benefits of the app, they also provided feedback on usability to the UK team in CABI. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Wefarm visit |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | To discuss how WeFarm and Rothamsted could work together |
| Year(s) Of Engagement Activity | 2018 |