dataesr/scientific-paragraphs-categorization huggingface dataset:
Opportunities to use data and information to address challenges Background: in international agricultural research and development are expanding rapidly. The use of agricultural trial and evaluation data has enormous potential to improve crops and management practices. However, for a number of reasons, this potential has yet to be realized. This paper reports on the experience of the initiative, an effort to build an online database of agricultural trials AgTrials applying principles of interoperability and open access. Our analysis Methods: evaluates what worked and what did not work in the development of the information resource. We analyzed data on our users and their AgTrials interaction with the platform. We also surveyed our users to gauge their perceptions of the utility of the online database.
, 2014; Lobell et al. , 2011) , to understand the drivers of technology adoption, to set research and development priorities and to conduct both ex-ante and ex-post impact analysis  (Badu-Apraku et al. , 2011; Hyman et al. , 2016; Renkow & Byerlee, 2010; Setimela et al. , 2005). One of the most obvious uses of agricultural trial data is to calibrate crop models, for a single location or for spatially explicit models covering countries, regions or the entire globe. Future use of agricultural trial databases will likely be driven by the increased linking of genotype and phenotype to improve selection and use of germplasm, a growing trend driven by advances in molecular biology and site-specific agriculture. These possibilities suggest great potential for the growing "big data" movement in agriculture to use trial data as part of its larger goal to transform the sector.
Combination of agronomic data from field trials with genomic data shows promise for developing next generation breeding and selection tools using models  (Hwang et al. , 2016). However, the dispersion, lack of organization and inaccessibility of agricultural trial data hinder their use and applicability for resolving problems in agriculture. In an effort to make datasets of agricultural trials publicly and widely available, the AgTrials initiative received startup funds from the Gates Foundation to design and populate an online database, mostly the evaluation of crop varieties. We engaged CGIAR centers, their partners and any others carrying out trials or evaluating agricultural technology, with the aim of populating a database and making the data easily accessible to interested data users.
org) was further supported and developed by the Climate Change, Agriculture, and Food Security (CCAFS) Collaborative Research Program of CGIAR, in collaboration with a number of national and international partners. AgTrials provides access to standardized agronomic trial information for the benefit of future climate change analyses, multienvironment trials and research and development in international agriculture, supporting increased collaboration between countries and institutions across the developing world. The AgTrials initiative draws on both recent and legacy data. Programs such as CCAFS required recipients of project funds to upload recent data from ongoing research. However, most of the data is from past research and development programs. For example, the two largest sources of legacy data are the International Maize Improvement Network (IMIN) and the International Bean Yield Adaptation Network (IBYAN).
These multi-environment trials systems have operated over many years, carrying out trial work under a broad range of environmental conditions  (Reynolds et al. , 2012). In other cases, a breeding program shared trials from one or more research stations, trials that were part of their ongoing crop improvement effort. Trials were also shared from fixed-period projects related to particular biotic or abiotic constraints. One of the AgTrials approaches to standardization is to leverage the Crop Ontology Curation Tool (http://www. cropontology. org/).
Amendments from Version 1 This version of the article responds to the suggestions of reviewers. Please review their comments. We have also replied to their comments at the end of the article. Four new paragraphs and three new references were added. In the introduction, we added a paragraph about the strategy of AgTrials, including some information about how we set the whole thing up. This addition is a response to one of the reviewers who wanted to know a little bit more about strategy. A reviewer also wanted to know about the types of data that are in the information resource. We added a paragraph with generic information on this and two prominent examples of source data initiatives that have information in AgTrials. Reviewers also asked us about similar initiatives or links with complementary initiatives.
REVISED AgTrials includes a dynamic link to the Crop Ontology so that traits or variables measured in trials appear with hyperlinks to their definitions in the Crop Ontology. This capacity allows users to search for a variable measured in any trial in the AgTrials database, and combine it with other trials produced by different data providers. For example, two CGIAR Centers, CIAT and IITA, both conduct large numbers of trials on cassava, the former concentrating work in Latin America and Asia, while the latter focuses on sub-Saharan Africa. In a hypothetical example, a researcher working on resistance to green mites may be searching for germplasm tested in both regions by different organizations. et al. , 2014). The link between agricultural trial data providers and the crop modeling community shows the potential for combining initiatives for analysis of crop improvement potential.
The AgTrials initiative also made some efforts to link with other agricultural data initiatives or databases. If we can link the phenotypic data from trials carried out in multiple environments to data held in gene banks, gene expression studies could support the analysis of genotype by environment interactions. The variety names in the AgTrials database are also found in gene bank databases. Whereas gene bank data may focus on phenotypic characteristics, the AgTrials data is focused on yield or resistance to environmental constraints. We carried out some successful tests to find these links for some of the cassava trials in the database. The link between evaluation trial data and gene bank data could be explored in greater detail with the Genesys initiative, a portal linking to germplasm accessions in gene banks around the world (https://www.
genesyspgr. org/). AgTrials could also interact with the CGIAR's Integrated Breeding Platform (IBP), an initiative to develop methods and tools for crop improvement (https://www. integratedbreeding. net/). The efforts described above have been explored, but not yet implemented. There are likely a number of other initiatives where these types of information resources could be integrated. The developments of the AgTrials initiative described above have provided us with an initial experience in the construction of an interoperable agricultural trial database. To date, our experience with the AgTrials initiative suggests that research and development advances from using agricultural trial databases will require increased collaboration among and within public and private sectors. The private sector may not share data because their business case depends on not making it widely accessible.
Public sector research and development faces a number of obstacles for increased collaboration. Researchers may refuse to make their data available because they have not yet published their findings, their data is not well organized, or they have no incentive to share. Organizational and access issues include the frequent lack of consistent metadata and standards to enable interoperability, resulting in problems of data integration, which is a key requirement to addressing global agricultural challenges. Thus, our experience to date in the use of agricultural trial data across organizations, countries and continents presents both problems and opportunities. This evaluation assesses the experience of the AgTrials initiative in greater depth, reporting on the results of a survey administered via its network of users.
Methods The objective of our analysis was to understand what worked and what did not in an effort to develop a global database of trials and evaluations of agricultural technology. Our approach was to review user experience in the AgTrials initiative to date, to analyze user interaction and usage data, and to survey users on their experiences. Our analysis includes information from the project website (www. agtrials. org) from mid-2011 to the end of 2016. We reviewed records from the sign-up information provided by users when registering on the website, including their motivation for participation. Statistics reports provided by Google Analytics were used to assess traffic on the website, along with the record of data downloads. The AgTrials website also includes data and statistics on the institutions providing data, the crops for which data is available, the location of trials and the participation of institutions involved in the initiative.
The project team administered a survey in August 2016 to evaluate the perspective of the AgTrials user base (survey results available from https://en. surveymonkey. net/results/SM-YLGDFPQG/) and survey data accompanies this article (Dataset 1;  Hyman et al. , 2017). As an incentive to participate in the survey, users were offered the possibility to enter a draw for a smartphone, an incentive reflected in the 44% response rate of users who received an invitation. 146 of 326 registered and active users took part in the survey; 19 of the survey replies were not fully complete. The survey covered topics on incentives and motivations for providing data, use of data, the potential for a global repository of trial information, and other topics. A copy of the survey questions can be found in Supplementary File 1.
Registered users and the website More than 400 people have registered on the AgTrials website, providing their contact information and their motivation for participation (Figure  1 ). However, 326 of the registered users are considered active, having returned to the site after registration. Between the middle of 2011 and July 2016, the website had 25,648 visits, 64% of these being return visits. Most of the visitors were from Colombia, reflecting the program's outreach from the International Center for Tropical Agriculture (CIAT), which hosts the initiative and is based in Cali, Colombia. Large numbers of visitors were also registered from the United States, Nigeria, Kenya and the Netherlands. Our data users downloaded 1,531 datasets during the analysis period. User motivations. The stated motivations for joining the initiative varied across the more than 400 users from across the world (Figure  1 ), with the following being the most common reasons to look for data in AgTrials: for validating crop models; for studies on genotype by environment interaction; for acquiring daily weather or soil information; or for use in the context of studies on climate change.
Many users were students working on a thesis project. The initiative came to the attention of at least two hackathons -events where coders and developers use API to bring data into their own applications. Some registered users of AgTrials were professionals working on aspects of open data initiatives, interested in data curation, metadata, and how the initiative was set up. Some of these were working with other networks that use agricultural evaluation data, such as the AgMIP (http://www. agmip. org/) and iPlant (rebranded as CyVerse, with the URL http://www. cyverse. org/) initiatives. A few research and development donors and their beneficiaries joined the initiative to share and verify evaluations resulting from their projects. Trial contributions by users. Users of the AgTrials platform contributed over 35,000 records of trial information from locations across the world (Figure  2 ).
AgTrials user survey User profiles. The AgTrials user survey is based on responses from 146 registered users of the platform who provided information. Nearly 40% of these were from CGIAR Centers, 20% from universities, 14% from government agencies, 6% from NGOs and 8% from the private sector. More than 43% of those surveyed had actually used the data in the context of their original motivation for registering for the platform. For these users, the data was useful for crop modeling and evaluation, genotype by environment interaction studies, phenological studies, as reference data, for data curation of their own databases, for checking weather data, for responding to data requests and for research on data repositories.
AgTrials-relevant data in institutional repositories. The survey asked users how many trials their institution holds that can potentially be part of a global trial repository. 53% of respondents (equivalent to 77 people) indicated that their institution holds between zero and 100 trials that could potentially be part of a database. A total of 16 respondents (11%) suggested they could  provide between 100 and 250 trials. Another 15 respondents (~10%) believed that their institutions can provide between 250 and 50,000 trials. Finally, four respondents indicated that their institutions could provide more than 50,000 trials. When asked to comment on the number of trials that might be part of a repository, there was a range of replies. Several users said that their organization did not have permission to publish trials of farmer partners.
Many of the respondents simply did not know, primarily because they worked in large organizations and didn't have numbers for trials carried out in other departments or other research locations. Barriers to contributing data to AgTrials. The survey also asked users about barriers that discouraged them from contributing data to the AgTrials platform (Table  1 ). Of the 112 respondents to this question, the most common answer given by ~34% of the respondents revolved around their belief that their data was not sufficiently organized for public sharing. 28% indicated that they needed more funding and resources to help them organize and upload data. 27% of the respondents believed that they or their institution simply did not have data to contribute. Another important reason for not wanting to contribute data, offered by 22% of respondents, was that it had not yet been published, and they did not want to share it until they had a chance to publish.
Nearly 17% of respondents said that their data was published on another platform and that they did not want to duplicate efforts. Some respondents (13%) were discouraged from contributing data because they do not know how to upload or make it available. Over 12% of respondents considered that the policies or institutional culture of their institutions discouraged or forbade them from making data available. In about 10% of the responses, users said that donors or partners had asked that data not be made open access. Nearly 10% of the respondents indicated that they did not like the technical and design aspects of the AgTrials platform.
Incentives to encourage contributions to AgTrials. The survey asked users what some incentives might be that would motivate them or their institution to contribute data to the platform (Table  2 ). Over 60 respondents, equivalent to 53%, indicated that the possibility that their data contribution could be cited and acknowledged would be a motivating factor for contributing to the platform. An equal number of users specified that they would be motivated by the possibility that their data could be combined with other datasets, dynamically linked to other platforms to facilitate meta-analyses or linked to larger studies. More than 44% of respondents cited the value of organizing their data in an application specifically designed for managing and sharing agricultural trial data. More than 43% of respondents suggested that they recognize the value of their data and they didn't want it to be lost, but rather remain available and useful to others.
Other incentives and motivating factors for contributing data included being able to comply with their organization or donor's data policy (38%), if they were to receive funding to organize, document and upload the data (29%) and whether recognition of their data contribution could support their institutional or individual performance evaluation (25%). Surveyed users were asked whether they would be willing to provide both metadata and the full dataset, only metadata without the data, or neither data nor metadata. Almost 67% of respondents agreed that they were willing to provide both metadata and the full dataset. More than 27% would be willing to provide metadata only, giving their contact information in order to establish subsequent communication with interested users of their data. In total, 5% of respondents would be unwilling to provide either data or metadata.
Data sources for a global repository. The survey asked users what sources of data should be collected in a global repository. Users indicated that data collected from CGIAR centers (89% of those surveyed) and national agricultural researchers systems (86%) should be included. 81% of those surveyed suggested that trial data from farmer fields carried out through farmer participatory research should be included. Only 59% of those surveyed indicated that data from seed companies or agroindustry should be included in a global trial repository. Users also cited the inclusion of data from agronomic trials that test management practices, environmental and remotely sensed data related to trials and data from breeder trials focus on selecting varieties that perform well.
Applications of a global agricultural repository. Respondents to the survey also provided information on key applications of an international database of agricultural trials. Several respondents mentioned the use of data for crop modeling, site similarity and other spatial analysis. These applications would evaluate the performance of crop varieties in different places and then estimate where else they might do well, suggesting where a variety release program might focus its activities. Applications of the dataset might examine crop pests and diseases and how their impacts vary with location. Other suggestions considered that the data would be useful in "big data" combinations and analyses of different datasets. For example, one respondent suggested that GPS coordinates from the trials could be used to acquire remote-sensing imagery for each plot, enabling the use of the acquired imagery for phenotyping.
General user reflections. Finally, respondents were asked to reflect on how this type of international trial database initiative could improve, and what direction it might take in the future. Several respondents mentioned the need for technical improvements in the structure of the database and the user interface. A few respondents said that it simply needed more data. Others mentioned the need for capacity building among users in order to be able to use the data more effectively. Many respondents indicated that the combination of this data with other existing datasets needed to be exploited to realize the full potential of the information resource. Several respondents said that the information resource leads to better integration of open data concepts, such as interoperability, metadata and data discovery and sharing.
Discussion Our experience to date in developing an agricultural trial database and the responses to our user survey suggest a number of key topics that need to be considered in the future development of this or similar initiatives. These topics concern the quality and quantity of data, improvements needed in the database and website, possible combinations of this information resource with other information initiatives, open data and data infrastructure issues and institutional arrangements to make this kind of effort succeed. One interesting question surrounding this initiative is what its scope might be in terms of the quantity of data that might be included. Currently there are 35,000 trials in the database, mostly reflecting a large number of CIMMYT maize trials, plus a smaller collection of other crops.
Respondents who said that their organization could potentially contribute more than 50,000 trials were from CGIAR centers. About seven of the CGIAR centers have major breeding programs, and if each of these could contribute 50,000 trials, the total would be 350,000 trials. Many of these CGIAR-reported trials are carried out by national agricultural research institutes and are simply part of larger CGIAR databases. There may be a number of other international organizations that participate in the initiative and could perhaps contribute more than 100,000 trials. There may be no way to know how many trials are carried out by agricultural colleges, universities, NGOs and others around the world. But overall we can speculate that the potential size of this database could be between 500,000 to 1 million agricultural trials.
If a database initiative could reach those kinds of numbers, it is easy to see the potential of this information for all kinds of research and development. Another set of issues related to agricultural trial data concerns the quality of the data and the database itself. It is notable that respondents to the survey said one of the greatest barriers to including data was that their information was not well organized and documented. Our experience has been that data curation efforts have lacked the resources needed to ensure data quality. Data curation is not one of the most exciting tasks, but it is critical for subsequent use of trial result data. Legacy data very often suffers from data quality problems. Therefore, data providers need to use best practices at the moment that data is recorded, as well as curate legacy data to overcome any deficiencies in the original collection of trial information.
Any global trial data and information resource must pay considerable attention to the details of developing quality data that is well documented and an information system that facilitates ease of use in providing or acquiring data. For example, some AgTrials users pointed to the lack of detailed information on experimental design of the trials. Crop modelers typically want as much phenotypic data as possible, but also detailed data on the weather during the trial and the soil conditions of the trial site. For legacy data, it is perhaps unrealistic to expect huge numbers of trials with the full data that a crop modeler might want. But at the very least, data documentation and search mechanisms need to give users a clear picture of the data available in any given trial or set of trials. Therefore in the future of this or similar agricultural trial data resources, developers must make the needed investment to ensure that the data and the interface with the data meet minimum standards for documentation and ease of use.
The open data movement in agriculture is a trend that will surely affect the development of data and information resources like AgTrials. (Stützel et al. , 2016). All of these initiatives point to a growing realization that agricultural data integration can be a very powerful way towards crop improvement  (Reynolds et al. , 2012; Reynolds et al. , 2017). The CGIAR and many of its centers have recently developed new data policies oriented around data sharing and open access. These policies may motivate producers of trial data to participate in AgTrials or similar initiatives as a way to verify their work and share data with stakeholders. However, it will be necessary to emphasize the importance of standardized data initiatives that allow published data to be interoperable. For example, simply uploading data to a system, such as Dataverse, in which providers are not obligated to standardize data, would leave us with datasets that cannot be combined or studied together without a substantial effort by users.