Web Service Application Programming Interface Research Articles

Open-source large language models in action: A bioinformatics chatbot for PRIDE database.

We here present a chatbot assistant infrastructure (https://www.ebi.ac.uk/pride/chatbot/) that simplifies user interactions with the PRIDE database's documentation and dataset search functionality. The framework utilizes multiple Large Language Models (LLM): llama2, chatglm, mixtral (mistral), and openhermes. It also includes a web service API (Application Programming Interface), web interface, and components for indexing and managing vector databases. An Elo-ranking system-based benchmark component is included in the framework as well, which allows for evaluating the performance of each LLM and for improving PRIDE documentation. The chatbot not only allows users to interact with PRIDE documentation but can also be used to search and find PRIDE datasets using an LLM-based recommendation system, enabling dataset discoverability. Importantly, while our infrastructure is exemplified through its application in the PRIDE database context, the modular and adaptable nature of our approach positions it as a valuable tool for improving user experiences across a spectrum of bioinformatics and proteomics tools and resources, among other domains. The integration of advanced LLMs, innovative vector-based construction, the benchmarking framework, and optimized documentation collectively form a robust and transferable chatbot assistant infrastructure. The framework is open-source (https://github.com/PRIDE-Archive/pride-chatbot).

Eclipse web service application programming interface

Objective. Low-coupling seamless integration of multiple systems is the core foundation of smart radiotherapy. Following Service-Oriented Architecture style, a set of named operations (Eclipse Web Service API, EWSAPI) was developed for realizing network call of Eclipse. Approach. Under the guidance of Vertical Slice Architecture, EWSAPI was implemented in the C# language and based on ASP .Net Core 6.0. Each operation consists of three components: Request, Endpoint and Response. Depending on the function, the exchanged data for each operation, as input or output parameters, is the empty or a predefined JSON data. These operations were realized and enriched gradually, layer by layer, with reference to the clinical business classification. The business logic of each operation was developed and maintained independently. In situations where Eclipse Scripting API(ESAPI) was required, constraints of ESAPI were followed. Main results. Selected features of Eclipse TPS were encapsulated as standard web services, which can be invocated by other software through network. Several processes for data quality control and planning were encapsulated into interfaces, thereby extending the functionality of Eclipse. Currently, EWSAPI already covers testing of service interface, quality control of radiotherapy data, automation tasks for plan designing and DICOM RT files’ transmission. All the interfaces support asynchronous invocation. A separate Eclipse context will be created for each invocation, and is released in the end. Significance. EWSAPI which is a set of standard web services for calling Eclipse features through network is flexible and extensible. It is an efficient way to integration of Eclipse and other systems and will be gradually enriched with the deepening of clinical applications.

Loose coupling in future distributed space safety simulations

Distributed simulations play an important role in complex space safety related examinations. Realizing an associated system-of-systems solution with as less software adaptation development effort as possible represents a key challenge in this context. The paper presents a microservice-based approach, considering possibilities of the new Simulation Interoperability Standards Organization (SISO) standard Space Reference Federate Object Model. Different High-Level Architecture (HLA) compliant solutions are conversed, ranging from usage of the HLA evolved standard's web service application programming interface (API) over the implementation of a tightly coupled bridging federate to the exploitation of the future HLA (HLA 4) version's standardized federate protocol. A human-in-the-loop space flight simulator concept use case is presented and discussed.

HumanMine: advanced data searching, analysis and cross-species comparison.

HumanMine (www.humanmine.org) is an integrated database of human genomics and proteomics data that provides a powerful interface to support sophisticated exploration and analysis of data compiled from experimental, computational and curated data sources. Built using the InterMine data integration platform, HumanMine includes genes, proteins, pathways, expression levels, Single nucleotide polymorphism (SNP), diseases and more, integrated into a single searchable database. HumanMine promotes integrative analysis, a powerful approach in modern biology that allows many sources of evidence to be analysed together. The data can be accessed through a user-friendly web interface as well as a powerful, scriptable web service Application programming interface (API) to allow programmatic access to data. The web interface includes a useful identifier resolution system, sophisticated query options and interactive results tables that enable powerful exploration of data, including data summaries, filtering, browsing and export. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other biological entities. HumanMine can be used for integrative multistaged analysis that can lead to new insights and uncover previously unknown relationships. Database URL: https://www.humanmine.org

Automated Data Digitization System for Vehicle Registration Certificates Using Google Cloud Vision API

This study aims to develop an automated data digitization system for the Thai vehicle registration certificate. It is the first system developed as a web service Application Programming Interface (API), which is essential for any enterprise to increase its business value. Currently, this system is available on “www.carjaidee.com”. The system involves four steps: 1) an embedded frame aligns a document to be correctly recognised in the image acquisition step; 2) sharpening and brightness filtering techniques to enhance image quality are applied in the pre-processing step; 3) the Google Cloud Vision API receives a prompt to proceed in the recognition step; 4) a specific domain dictionary to improve accuracy rate is developed for the post-processing step. This study defines 92 images for the experiment by counting the correct words and terms from the output. The findings suggest that the proposed method, which had an average accuracy of 93.28%, was significantly more accurate than the original method using only the Google Cloud Vision API. However, the system is limited because the dictionaries cannot automatically recognise a new word. In the future, we will explore solutions to this problem using natural language processing techniques. Doi: 10.28991/CEJ-2022-08-07-09 Full Text: PDF

The Single Page Application architecture when developing secure Web services

The article is devoted to the development of a prototype of a secure single page-application (SPA) web service for automating user information accounting. The relevance of this study is very high due to the use of web services. The article provides a classification of web applications and shows the features of the architecture of a single page application used in the development of the service. Based on a comparative analysis of the architectural styles of the API, the most appropriate style was selected. Considered and taken into account the key points of the development of a secure application programming interface (API), the requirements that must be met by RESTful API services. The work used popular authentication schemes (methods). A comparative characteristic of web frameworks of the Python programming language is given, on the basis of which a tool for implementing a web service is selected. Shows the main advantages of using Python when developing paged web services and the security tools included in the standard package of the Flask web services development framework. Shows how to securely prototype a Python RESTful SPA Web Service API using Flask. An example of using the Swagger tool to describe the specifications of the developed API is given. The process of setting up the application is considered in detail. The main recommendations for securing a web application, setting up a database and a web server are listed. The key points of ensuring the protection of the developed web application are considered. Conclusions are made regarding the choice of the architectural style of the application API, the most suitable tools and technologies for the software implementation of the service.

Caravel: A New Earthworm-Based Open-Source Development for the Italian Seismic Monitoring System

Abstract The Istituto Nazionale di Geofisica e Vulcanologia (INGV) is in charge of earthquake monitoring and surveillance in the Italian territory as a part of the civil protection system. Technological improvements in the last years were taken into account for developing new protocols and software to upgrade all the procedures in the monitoring centers. Real-time earthquake evaluation consists of phase picks, preliminary and automatic hypocenters, local magnitudes and ground-motion parameters. The real-time analysis system presently in use at INGV is the starting point for a new multitier compound system that relies on four main components: an automatic earthquake detection and location system based on Earthworm; a new seismological relational database for parametric data; a full set of new webservices application programming interface specifications to share information and provide data at the application level and; finally, a set of multiplatform interactive revision tools developed to analyze, store, use, and distribute the seismic parameters in real time. These last three components are being completely developed ex-novo at INGV in Rome. Such a system has been engineered to communicate with the International Federation of Digital Seismic Networks standard webservices as well as custom home-made INGV services. Through its custom embedded features Caravel will allow the INGV personnel on duty for seismic surveillance to evaluate and review all automatic estimations before they are communicated to the Italian civil protection agency and then published by external tools through e-mail, SMS, Twitter, and webpages.

SPECIES: Supporting big-data-driven research

SPECIES (Stephens et al. 2019) is a tool to explore spatial correlations in biodiversity occurrence databases. The main idea behind the SPECIES project is that the geographical correlations between the distributions of taxa records have useful information. The problem, however, is that if we have thousands of species (Mexico's National System of Biodiversity Information has records of around 70,000 species) then we have millions of potential associations, and exploring them is far from easy. Our goal with SPECIES is to facilitate the discovery and application of meaningful relations hiding in our data. The main variables in SPECIES are the geographical distributions of species occurrence records. Other types of variables, like the climatic variables from WorldClim (Hijmans et al. 2005), are explanatory data that serve for modeling. The system offers two modes of analysis. In one, the user defines a target species, and a selection of species and abiotic variables; then the system computes the spatial correlations between the target species and each of the other species and abiotic variables. The request from the user can be as small as comparing one species to another, or as large as comparing one species to all the species in the database. A user may wonder, for example, which species are usual neighbors of the jaguar, this mode could help answer this question. The second mode of analysis gives a network perspective, in it, the user defines two groups of taxa (and/or environmental variables), the output in this case is a correlation network where the weight of a link between two nodes represents the spatial correlation between the variables that the nodes represent. For example, one group of taxa could be hummingbirds (Trochilidae family) and the second flowers of the Lamiaceae family. This output would help the user analyze which pairs of hummingbird and flower are highly correlated in the database. SPECIES data architecture is optimized to support fast hypotheses prototyping and testing with the analysis of thousands of biotic and abiotic variables. It has a visualization web interface that presents descriptive results to the user at different levels of detail. The methodology in SPECIES is relatively simple, it partitions the geographical space with a regular grid and treats a species occurrence distribution as a present/not present boolean variable over the cells. Given two species (or one species and one abiotic variable) it measures if the number of co-occurrences between the two is more (or less) than expected. If it is more than expected indicates a signal of a positive relation, whereas if it is less it would be evidence of disjoint distributions. SPECIES provides an open web application programming interface (API) to request the computation of correlations and statistical dependencies between variables in the database. Users can create applications that consume this 'statistical web service' or use it directly to further analyze the results in frameworks like R or Python. The project includes an interactive web application that does exactly that: requests analysis from the web service and lets the user experiment and visually explore the results. We believe this approach can be used on one side to augment the services provided from data repositories; and on the other side, facilitate the creation of specialized applications that are clients of these services. This scheme supports big-data-driven research for a wide range of backgrounds because end users do not need to have the technical know-how nor the infrastructure to handle large databases. Currently, SPECIES hosts: all records from Mexico's National Biodiversity Information System (CONABIO 2018) and a subset of Global Biodiversity Information Facility data that covers the contiguous USA (GBIF.org 2018b) and Colombia (GBIF.org 2018a). It also includes discretizations of environmental variables from WorldClim, from the Environmental Rasters for Ecological Modeling project (Title and Bemmels 2018), from CliMond (Kriticos et al. 2012), and topographic variables (USGS EROS Center 1997b, USGS EROS Center 1997a). The long term plan, however, is to incrementally include more data, specially all data from the Global Biodiversity Information Facility. The code of the project is open source, and the repositories are available online (Front-end, Web Services Application Programming Interface, Database Building scripts). This presentation is a demonstration of SPECIES' functionality and its overall design.

Low-Cost, Open-Source, and Low-Power: But What to Do With the Data?

There are now many ongoing efforts to develop low-cost, open-source, low-power sensors and datalogging solutions for environmental monitoring applications. Many of these have advanced to the point that high quality scientific measurements can be made using relatively inexpensive and increasingly off-the-shelf components. With the development of these innovative systems, however, comes the ability to generate large volumes of high-frequency monitoring data and the challenge of how to log, transmit, store, and share the resulting data. This paper describes a new web application that was designed to enable citizen scientists to stream sensor data from a network of Arduino-based dataloggers to a web-based Data Sharing Portal. This system enables registration of new sensor nodes through a Data Sharing Portal website. Once registered, any Internet connected data-logging device (e.g., connected via cellular or Wi-Fi) can then post data to the portal through a web service application programming interface (API). Data are stored in a back-end data store that implements Version 2 of the Observations Data Model (ODM2). Live data can then be viewed using multiple visualization tools, downloaded from the Data Sharing Portal in a simple text format, or accessed via WaterOneFlow web services for machine-to-machine data exchange. This system was built to support an emerging network of open-source, wireless water quality monitoring stations developed and deployed by the EnviroDIY community for do-it-yourself environmental science and monitoring, initially within the Delaware River Watershed. However, the architecture and components of the ODM2 Data Sharing Portal are generic, open-source, and could be deployed for use with any Internet connected device capable of making measurements and formulating an HTTP POST request.

Integration of Building Information Modeling and Web Service Application Programming Interface for assessing building surroundings in early design stages

Many studies and green building rating systems have addressed the social and environmental importance of site planning. Tools based on BIM and Location Based Services (LBSs) have been developed to estimate energy consumption for material transportation and the surrounding density of the sites. However, the tools are not programmable and limited by their serving phases. This requires solutions that have the flexibility to run site analysis on social surroundings and the compatibility of user programming in the early design stage. Integrating visual programming and web service Application Programming Interface (API) can fulfill the requirements of evaluating publicly available diverse uses of sites and custom coding. This study introduces the method for integrating Dynamo BIM and Amap web service APIs for the evaluations of publicly available diverse uses and transportations. Additionally, implementations of use cases are demonstrated including assessments of Access to Quality Transit and Diverse Uses in LEED v4. Results from the integrated tool are analyzed and validated with survey results. The analysis of results indicates that the integration method introduced in this paper is effective. The limitations, potentials, and future developments are also discussed. The integration of Dynamo BIM and web service APIs might be useful for site assessments in the early design stage or even earlier.

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator.

SummarySecond use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical data, but not very suitable for clinical text annotation. In order to add new functionalities to the NCBO Annotator without hosting or modifying the original Web service, we have designed a proxy architecture that enables seamless extensions by pre-processing of the input text and parameters, and post processing of the annotations. We have then implemented enhanced functionalities for annotating and indexing free text such as: scoring, detection of context (negation, experiencer, temporality), new output formats and coarse-grained concept recognition (with UMLS Semantic Groups). In this paper, we present the NCBO Annotator+, a Web service which incorporates these new functionalities as well as a small set of evaluation results for concept recognition and clinical context detection on two standard evaluation tasks (Clef eHealth 2017, SemEval 2014).Availability and implementationThe Annotator+ has been successfully integrated into the SIFR BioPortal platform—an implementation of NCBO BioPortal for French biomedical terminologies and ontologies—to annotate English text. A Web user interface is available for testing and ontology selection (http://bioportal.lirmm.fr/ncbo_annotatorplus); however the Annotator+ is meant to be used through the Web service application programming interface (http://services.bioportal.lirmm.fr/ncbo_annotatorplus). The code is openly available, and we also provide a Docker packaging to enable easy local deployment to process sensitive (e.g. clinical) data in-house (https://github.com/sifrproject).Supplementary information Supplementary data are available at Bioinformatics online.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.

Use of Radiology Procedure Codes in Health Care: The Need for Standardization and Structure.

Radiology procedure codes are a fundamental part of most radiology workflows, such as ordering, scheduling, billing, and image interpretation. Nonstandardized unstructured procedure codes have typically been used in radiology departments. Such codes may be sufficient for specific purposes, but they offer limited support for interoperability. As radiology workflows and the various forms of clinical data exchange have become more sophisticated, the need for more advanced interoperability with use of standardized structured codes has increased. For example, structured codes facilitate the automated identification of relevant prior imaging studies and the collection of data for radiation dose tracking. The authors review the role of imaging procedure codes in radiology departments and across the health care enterprise. Standards for radiology procedure coding are described, and the mechanisms of structured coding systems are reviewed. In particular, the structure of the RadLex™ Playbook coding system and examples of the use of this system are described. Harmonization of the RadLex Playbook system with the Logical Observation Identifiers Names and Codes standard, which is currently in progress, also is described. The benefits and challenges of adopting standardized codes-especially the difficulties in mapping local codes to standardized codes-are reviewed. Tools and strategies for mitigating these challenges, including the use of billing codes as an intermediate step in mapping, also are reviewed. In addition, the authors describe how to use the RadLex Playbook Web service application programming interface for partial automation of code mapping. © RSNA, 2017.

An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry.

The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs). Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS), which also provides a web service API (Application Programming Interface) for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.

The disease and gene annotations (DGA): an annotation resource for human disease

Disease and Gene Annotations database (DGA, http://dga.nubic.northwestern.edu) is a collaborative effort aiming to provide a comprehensive and integrative annotation of the human genes in disease network context by integrating computable controlled vocabulary of the Disease Ontology (DO version 3 revision 2510, which has 8043 inherited, developmental and acquired human diseases), NCBI Gene Reference Into Function (GeneRIF) and molecular interaction network (MIN). DGA integrates these resources together using semantic mappings to build an integrative set of disease-to-gene and gene-to-gene relationships with excellent coverage based on current knowledge. DGA is kept current by periodically reparsing DO, GeneRIF, and MINs. DGA provides a user-friendly and interactive web interface system enabling users to efficiently query, download and visualize the DO tree structure and annotations as a tree, a network graph or a tabular list. To facilitate integrative analysis, DGA provides a web service Application Programming Interface for integration with external analytic tools.

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes >1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in >250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements.

The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

The Mouse Genome Database (MGD, http://www.informatics.jax.org) is the international community resource for integrated genetic, genomic and biological data about the laboratory mouse. Data in MGD are obtained through loads from major data providers and experimental consortia, electronic submissions from laboratories and from the biomedical literature. MGD maintains a comprehensive, unified, non-redundant catalog of mouse genome features generated by distilling gene predictions from NCBI, Ensembl and VEGA. MGD serves as the authoritative source for the nomenclature of mouse genes, mutations, alleles and strains. MGD is the primary source for evidence-supported functional annotations for mouse genes and gene products using the Gene Ontology (GO). MGD provides full annotation of phenotypes and human disease associations for mouse models (genotypes) using terms from the Mammalian Phenotype Ontology and disease names from the Online Mendelian Inheritance in Man (OMIM) resource. MGD is freely accessible online through our website, where users can browse and search interactively, access data in bulk using Batch Query or BioMart, download data files or use our web services Application Programming Interface (API). Improvements to MGD include expanded genome feature classifications, inclusion of new mutant allele sets and phenotype associations and extensions of GO to include new relationships and a new stream of annotations via phylogenetic-based approaches.