Development of an application programming interface to automate downloading and processing of precision livestock data
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PROVIDER: S-EPMC11209544 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:Remotely sensed data - available at medium to high resolution across global spatial and temporal scales - are a valuable resource for ecologists. In particular, products from NASA's MODerate-resolution Imaging Spectroradiometer (MODIS), providing twice-daily global coverage, have been widely used for ecological applications. We present MODISTools, an R package designed to improve the accessing, downloading, and processing of remotely sensed MODIS data. MODISTools automates the process of data downloading and processing from any number of locations, time periods, and MODIS products. This automation reduces the risk of human error, and the researcher effort required compared to manual per-location downloads. The package will be particularly useful for ecological studies that include multiple sites, such as meta-analyses, observation networks, and globally distributed experiments. We give examples of the simple, reproducible workflow that MODISTools provides and of the checks that are carried out in the process. The end product is in a format that is amenable to statistical modeling. We analyzed the relationship between species richness across multiple higher taxa observed at 526 sites in temperate forests and vegetation indices, measures of aboveground net primary productivity. We downloaded MODIS derived vegetation index time series for each location where the species richness had been sampled, and summarized the data into three measures: maximum time-series value, temporal mean, and temporal variability. On average, species richness covaried positively with our vegetation index measures. Different higher taxa show different positive relationships with vegetation indices. Models had high R (2) values, suggesting higher taxon identity and a gradient of vegetation index together explain most of the variation in species richness in our data. MODISTools can be used on Windows, Mac, and Linux platforms, and is available from CRAN and GitHub (https://github.com/seantuck12/MODISTools).
| S-EPMC4278818 | biostudies-literature
Project description:Natural language processing models have emerged that can generate useable software and automate a number of programming tasks with high fidelity. These tools have yet to have an impact on the chemistry community. Yet, our initial testing demonstrates that this form of artificial intelligence is poised to transform chemistry and chemical engineering research. Here, we review developments that brought us to this point, examine applications in chemistry, and give our perspective on how this may fundamentally alter research and teaching.
| S-EPMC8996826 | biostudies-literature
Project description:The 21st Century Cures Act requires that certified health information technology have an application programming interface (API) giving access to all data elements of a patient's electronic health record, "without special effort". In the spring of 2020, the Office of the National Coordinator of Health Information Technology (ONC) published a rule-21st Century Cures Act Interoperability, Information Blocking, and the ONC Health IT Certification Program-regulating the API requirement along with protections against information blocking. The rule specifies the SMART/HL7 FHIR Bulk Data Access API, which enables access to patient-level data across a patient population, supporting myriad use cases across healthcare, research, and public health ecosystems. The API enables "push button population health" in that core data elements can readily and standardly be extracted from electronic health records, enabling local, regional, and national-scale data-driven innovation.
| S-EPMC7678833 | biostudies-literature
Project description:Over 10,000 rare genetic diseases have been identified, and millions of newborns are affected by severe rare genetic diseases each year. A variety of Human Phenotype Ontology (HPO)-based clinical decision support systems (CDSS) and patient repositories have been developed to support clinicians in diagnosing patients with suspected rare genetic diseases. In September 2017, we released PubCaseFinder (https://pubcasefinder.dbcls.jp), a web-based CDSS that provides ranked lists of genetic and rare diseases using HPO-based phenotypic similarities, where top-listed diseases represent the most likely differential diagnosis. We also developed a Matchmaker Exchange (MME) application programming interface (API) to query PubCaseFinder, which has been adopted by several patient repositories. In this paper, we describe notable updates regarding PubCaseFinder, the GeneYenta matching algorithm implemented in PubCaseFinder, and the PubCaseFinder API. The updated GeneYenta matching algorithm improves the performance of the CDSS automated differential diagnosis function. Moreover, the updated PubCaseFinder and new API empower patient repositories participating in MME and medical professionals to actively use HPO-based resources.
| S-EPMC9305291 | biostudies-literature
Project description:BackgroundToxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications.FindingsThis article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources.ConclusionsA novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers.
| S-EPMC3264531 | biostudies-literature
Project description:Tracking technologies offer a way to monitor movement of many individuals over long time periods with minimal disturbances and could become a helpful tool for a variety of uses in animal agriculture, including health monitoring or selection of breeding traits that benefit welfare within intensive cage-free poultry farming. Herein, we present an active, low-frequency tracking system that distinguishes between five predefined zones within a commercial aviary. We aimed to evaluate both the processed and unprocessed datasets against a "ground truth" based on video observations. The two data processing methods aimed to filter false registrations, one with a simple deterministic approach and one with a tree-based classifier. We found the unprocessed data accurately determined birds' presence/absence in each zone with an accuracy of 99% but overestimated the number of transitions taken by birds per zone, explaining only 23% of the actual variation. However, the two processed datasets were found to be suitable to monitor the number of transitions per individual, accounting for 91% and 99% of the actual variation, respectively. To further evaluate the tracking system, we estimated the error rate of registrations (by applying the classifier) in relation to three factors, which suggested a higher number of false registrations towards specific areas, periods with reduced humidity, and periods with reduced temperature. We concluded that the presented tracking system is well suited for commercial aviaries to measure individuals' transitions and individuals' presence/absence in predefined zones. Nonetheless, under these settings, data processing remains a necessary step in obtaining reliable data. For future work, we recommend the use of automatic calibration to improve the system's performance and to envision finer movements.
| S-EPMC8780220 | biostudies-literature
Project description:BACKGROUND: MicroRNAs (miRNAs) are endogenous small RNAs that play a key role in post-transcriptional regulation of gene expression in animals and plants. The number of known miRNAs has increased rapidly over the years. The current release (version 14.0) of miRBase, the central online repository for miRNA annotation, comprises over 10.000 miRNA precursors from 115 different species. Furthermore, a large number of decentralized online resources are now available, each contributing with important miRNA annotation and information. RESULTS: We have developed a software framework, designated here as miRMaid, with the goal of integrating miRNA data resources in a uniform web service interface that can be accessed and queried by researchers and, most importantly, by computers. miRMaid is built around data from miRBase and is designed to follow the official miRBase data releases. It exposes miRBase data as inter-connected web services. Third-party miRNA data resources can be modularly integrated as miRMaid plugins or they can loosely couple with miRMaid as individual entities in the World Wide Web. miRMaid is available as a public web service but is also easily installed as a local application. The software framework is freely available under the LGPL open source license for academic and commercial use. CONCLUSION: miRMaid is an intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources. Furthermore, miRMaid constitutes a basic framework for further programming in which microRNA-interested bioinformaticians can readily develop their own tools and data sources.
| S-EPMC2831003 | biostudies-literature
Project description:Injection molding is a complicated process, and the final part quality depends on many machine and process parameters settings. To increase controllability of the injection molding process, acquisition of the process data is necessary. This paper describes the architecture and development of a prototype of an open application programming interface (API) for injection molding machines (IMMs), which has the potential to be used with different IMMs to log and set the necessary process parameter values. At the moment, the API includes an implementation of EMI data exchange protocol and can be used with ENGEL IMMs with CC300 and RC300 controllers. Data collection of up to 97 machine and process parameters (the number might vary depending on the type of machine at hand), obtained from sensors installed in the machine by the manufacturer is allowed. The API also includes a module for the acquisition of data from additional 3d party sensors. Industrial Raspberry Pi (RevPi) was used to perform analog-to-digital signal conversion and make sensors data accessible via the API prototype. The logging of parameters from the machine and from sensors is synchronized and the sampling frequency can be adjusted if necessary. The system can provide soft real-time communication.
| S-EPMC7924464 | biostudies-literature
Project description:The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems.
| S-EPMC3120779 | biostudies-literature
Project description:An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures are also implemented inside Modelface. The API is a simple batch based application with no memory occupation and is free of charge for academic use. The application is also able to repair missing atom types in the PDB structures making it suitable for many molecular modeling studies such as docking and molecular dynamic simulation. Some successful instances of modeling studies using Modelface are also reported.
| S-EPMC5316258 | biostudies-literature