Annotation Of Web Services Research Articles

Research and Application of the Internet of Things Service Platform Based on Semantic Network

In order to study the Internet of Things service platform based on semantic Network, a service-oriented clustering labeling method is proposed, firstly, a semantic Web service similarity computing method is proposed to solve the shortcomings of the existing methods. This method describes the designed semantic Web service annotation clustering algorithm based on AP algorithm. The distance matrix and related parameters of the algorithm are calculated and assigned according to the results of similarity calculation. The correctness of preference parameter selection will be compared and verified in the service discovery system. The greater the value of damping coefficient, the more iterations, and the slower the convergence rate. However, when the value of damping coefficient is 0.7, the number of iterations is moderate and the convergence rate is the best, which proves that this method has a better effect on service function matching.

A Topic-Sensitive Method for Mashup Tag Recommendation Utilizing Multi-Relational Service Data

Tagging systems have been widely used as a major way of managing Web service resources. Many portals such as ProgrammableWeb and BioCatalogue allow users to create manual tags annotating Web services and their compositions (e.g., mashups). This is extremely helpful for managing and retrieving enormous Web service data. In the past few years, many tag recommendation approaches have been proposed for Web services that contain few or no tags. Most of them only exploit the textual content or tag service matrix information. Sometimes those approaches suffer from the data sparsity problem, especially when Web services have only few tags or their auxiliary textual contents are hard to be obtained. In real world, a plenty of relationships are available in recommendation systems, e.g., the composition relationship between services and the annotation relationship between mashups and tags. These multi-relational data can be utilized as additional features to improve the recommendation performance. In this paper, we exploit various types of relationships as features and propose a novel topic-sensitive approach based on the Factorization Machines for mashup tag recommendation. Factorization Machines is utilized to model the pair-wise interactions between all features and predict adequate tags for mashups. In this approach, we first obtain the latent topics of all tags as well as the description documents for mashups and APIs based on a novel probabilistic topic model. Then, a multi-relational network by mining various relationships from the Web service data is constructed. Various auxiliary informations are subsequently extracted from the network to train the Factorization Machines. The proposed model is evaluated on three real-world datasets and the experimental results show that it outperforms several state-of-the-art methods.

Optimizing Semantic Annotations for Web Service Invocation

Semantic annotations play an important role in semantics-aware service discovery, recommendation and composition. While existing approaches and tools focus on facilitating the development of semantic annotations on web services, the validation of the quality of annotations is largely overlooked. Meanwhile, the refinement of semantic annotations mostly goes through manual processes, which not only is time-consuming but also requires significant domain knowledge. To enhance the Quality of Semantic Annotation (QoSA), we have developed a technique to incrementally assess and correct semantic annotations of web services. Aiming at supporting web service interoperation, we have formalized the QoSA of input and output parameters. Based on such formalism, test cases are automatically generated to validate service annotations. Learned semantic instances are then accumulated to iteratively validate semantic annotations of other services. Furthermore, a three-phase optimization methodology including local-feedback, global-feedback, and global-propagate is developed to improve the QoSA by incrementally correcting inaccurate annotations. Experiments over a real-world web services repository have demonstrated that our technique can effectively improve QoSA of services, gaining a 78.68 percent improvement in input parameters annotations and identifying 36.47 percent inaccurate output parameters annotations. The proposed technique can be equipped at various service repositories to enhance service discovery and recommendation.

Improving spaCy dependency annotation and PoS tagging web service using independent NER services.

Dependency parsing is often used as a component in many text analysis pipelines. However, performance, especially in specialized domains, suffers from the presence of complex terminology. Our hypothesis is that including named entity annotations can improve the speed and quality of dependency parses. As part of BLAH5, we built a web service delivering improved dependency parses by taking into account named entity annotations obtained by third party services. Our evaluation shows improved results and better speed.

Integrating an Ontology of Radiology Differential Diagnosis with ICD-10-CM, RadLex, and SNOMED CT.

An ontology offers a human-readable and machine-computable representation of the concepts in a domain and the relationships among them. Mappings between ontologies enable the reuse and interoperability of biomedical knowledge. We sought to map concepts of the Radiology Gamuts Ontology (RGO), an ontology that links diseases and imaging findings to support differential diagnosis in radiology, to terms in three key vocabularies for clinical radiology: the International Classification of Diseases, version 10, Clinical Modification (ICD-10-CM), the Radiological Society of North America's radiology lexicon (RadLex), and the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT). RGO (version 0.7; Jan 2018) incorporated 16,918 terms (classes) for diseases, interventions, and imaging observations linked by 1782 subsumption (class-subclass) relations and 55,569 causal ("may cause") relations. RGO classes were mapped to RadLex (46,656 classes, version 3.15), SNOMED CT (347,358 classes, version 2018AA), and ICD-10-CM (94,645 classes, version 2018AA) using the National Center for Biomedical Ontology (NCBO) Annotator web service. We identified 1275 exact mappings from RGO to RadLex, 5302 to SNOMED CT, and 941 to ICD-10-CM. RGO terms mapped to one ontology (n = 3401), two ontologies (n = 1515), or all three ontologies (n = 198). The mapped ontologies provide additional terms to support data mining from textual information in the electronic health record. The current work builds on efforts to map RGO to ontologies of diseases and phenotypes. Mappings between ontologies can support automated knowledge discovery, diagnostic reasoning, and data mining.

SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes

BackgroundDespite a wide adoption of English in science, a significant amount of biomedical data are produced in other languages, such as French. Yet a majority of natural language processing or semantic tools as well as domain terminologies or ontologies are only available in English, and cannot be readily applied to other languages, due to fundamental linguistic differences. However, semantic resources are required to design semantic indexes and transform biomedical (text)data into knowledge for better information mining and retrieval.ResultsWe present the SIFR Annotator (http://bioportal.lirmm.fr/annotator), a publicly accessible ontology-based annotation web service to process biomedical text data in French. The service, developed during the Semantic Indexing of French Biomedical Data Resources (2013–2019) project is included in the SIFR BioPortal, an open platform to host French biomedical ontologies and terminologies based on the technology developed by the US National Center for Biomedical Ontology. The portal facilitates use and fostering of ontologies by offering a set of services –search, mappings, metadata, versioning, visualization, recommendation– including for annotation purposes. We introduce the adaptations and improvements made in applying the technology to French as well as a number of language independent additional features –implemented by means of a proxy architecture– in particular annotation scoring and clinical context detection. We evaluate the performance of the SIFR Annotator on different biomedical data, using available French corpora –Quaero (titles from French MEDLINE abstracts and EMEA drug labels) and CépiDC (ICD-10 coding of death certificates)– and discuss our results with respect to the CLEF eHealth information extraction tasks.ConclusionsWe show the web service performs comparably to other knowledge-based annotation approaches in recognizing entities in biomedical text and reach state-of-the-art levels in clinical context detection (negation, experiencer, temporality). Additionally, the SIFR Annotator is the first openly web accessible tool to annotate and contextualize French biomedical text with ontology concepts leveraging a dictionary currently made of 28 terminologies and ontologies and 333 K concepts. The code is openly available, and we also provide a Docker packaging for easy local deployment to process sensitive (e.g., clinical) data in-house (https://github.com/sifrproject).

MSeqDR mvTool: A mitochondrial DNA Web and API resource for comprehensive variant annotation, universal nomenclature collation, and reference genome conversion.

Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include the inconsistency in mtDNA nomenclatures, the existence of multiple reference genomes, and a lack of reference population frequency data. Clinicians need a simple bioinformatics tool that is user-friendly, and bioinformaticians need a powerful informatics resource for programmatic usage. Here, we report the development and functionality of the MSeqDR mtDNA Variant Tool set (mvTool), a one-stop mtDNA variant annotation and analysis Web service. mvTool is built upon the MSeqDR infrastructure (https://mseqdr.org), with contributions of expert curated data from MITOMAP (https://www.mitomap.org) and HmtDB (https://www.hmtdb.uniba.it/hmdb). mvTool supports all mtDNA nomenclatures, converts variants to standard rCRS- and HGVS-based nomenclatures, and annotates novel mtDNA variants. Besides generic annotations from dbNSFP and Variant Effect Predictor (VEP), mvTool provides allele frequencies in more than 47,000 germline mitogenomes, and disease and pathogenicity classifications from MSeqDR, Mitomap, HmtDB and ClinVar (Landrum etal., 2013). mvTools also provides mtDNA somatic variants annotations. "mvTool API" is implemented for programmatic access using inputs in VCF, HGVS, or classical mtDNA variant nomenclatures. The results are reported as hyperlinked html tables, JSON, Excel, and VCF formats. MSeqDR mvTool is freely accessible at https://mseqdr.org/mvtool.php.

A literature survey on the performance evaluation model of semantics enabled web services

Semantically annotating web services is gaining lots of attention as a significant area to support the machine-driven matchmaking and composition of web services. Therefore, the support of ontologies and tools for the semantic annotation of web services is turning into a key concern to assist the dissemination of Semantic Web services. The target of this literature review is to summarise the progress of the annotation of web services and additionally the state-of-art of the performance analysis of such annotated services by providing answers to connected analysis queries. The review identified approaches offered for semantically expanding upon functional and non-functional aspects of web services. However, many of the approaches are either not valid or the validation done lacks quality. It is to be believed that a substantial amount of effort remains to be done to realise the state of research in Semantic Web services and in evaluating the performance of them.

A literature survey on the performance evaluation model of semantics enabled web services

Semantically annotating web services is gaining lots of attention as a significant area to support the machine-driven matchmaking and composition of web services. Therefore, the support of ontologies and tools for the semantic annotation of web services is turning into a key concern to assist the dissemination of Semantic Web services. The target of this literature review is to summarise the progress of the annotation of web services and additionally the state-of-art of the performance analysis of such annotated services by providing answers to connected analysis queries. The review identified approaches offered for semantically expanding upon functional and non-functional aspects of web services. However, many of the approaches are either not valid or the validation done lacks quality. It is to be believed that a substantial amount of effort remains to be done to realise the state of research in Semantic Web services and in evaluating the performance of them.

SERNOTATE: An automated approach for business service description annotation for efficient service retrieval and composition

SummaryBusiness service advertisements are today published online to convey essential information about services to customers. However, current Web search engines are unable to search and combine online service advertisements. Semantic service annotation is important for its ability to enable machines to understand the meaning of services and support in effective service retrieval and service composition. Existing research in the area of semantic service annotation has focused on the annotation of Web services in a semi‐automated approach. It cannot be applied to business service information as it is not in the form of Web Services Description Language but in free text format. Moreover, semi‐automated approaches are inappropriate for annotating a large amount of online service information which changes dynamically and they are therefore not suitable for the timely dissemination of service information to customers. To solve these issues, we propose SERNOTATE, which is an automated approach for business service description annotation for efficient service retrieval and composition. We propose new semantic‐based linking approaches, namely, Extended Case‐based Reasoning, vector‐based, and classification‐based, that automatically annotate business services to relevant service concepts. Each approach assists in the single‐label and multi‐label annotation of service terms to concept terms to provide a better representation of services. The experimental results test and validate the applicability of the proposed approaches to the automatic annotation of business service descriptions to service concepts on a real‐world dataset.

An ontology-based web service framework for construction supply chain collaboration and management

Purpose – The purpose of this paper is to present a framework for integrating construction supply chain in order to resolve the data heterogeneity and data sharing problems in the construction industry. Design/methodology/approach – Standardized web service technology is used in the proposed framework for data specification, transfer, and integration. Open standard SAWSDL is used to annotate web service descriptions with pointers to concepts defined in ontologies. NoSQL database Cassandra is used for distributed data storage among construction supply chain stakeholders. Findings – Ontology can be used to support heterogeneous data transfer and integration through web services. Distributed data storage facilitates data sharing and enhances data control. Practical implications – This paper presents examples of two ontologies for expressing construction supply chain information – ontology for material and ontology for purchase order. An example scenario is presented to demonstrate the proposed web service framework for material procurement process involving three parties, namely, project manager, contractor, and material supplier. Originality/value – The use of web services is not new to construction supply chains (CSCs). However, it still faces problems in channelizing information along CSCs due to data heterogeneity. Trust issue is also a barrier to information sharing for integrating supply chains in a centralized collaboration system. In this paper, the authors present a web service framework, which facilitates storage and sharing of information on a distributed manner mediated through ontology-based web services. Security is enhanced with access control. A data model for the distributed databases is also presented for data storage and retrieval.

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.

Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.

A document processing pipeline for annotating chemical entities in scientific documents.

BackgroundThe recognition of drugs and chemical entities in text is a very important task within the field of biomedical information extraction, given the rapid growth in the amount of published texts (scientific papers, patents, patient records) and the relevance of these and other related concepts. If done effectively, this could allow exploiting such textual resources to automatically extract or infer relevant information, such as drug profiles, relations and similarities between drugs, or associations between drugs and potential drug targets. The objective of this work was to develop and validate a document processing and information extraction pipeline for the identification of chemical entity mentions in text.ResultsWe used the BioCreative IV CHEMDNER task data to train and evaluate a machine-learning based entity recognition system. Using a combination of two conditional random field models, a selected set of features, and a post-processing stage, we achieved F-measure results of 87.48% in the chemical entity mention recognition task and 87.75% in the chemical document indexing task.ConclusionsWe present a machine learning-based solution for automatic recognition of chemical and drug names in scientific documents. The proposed approach applies a rich feature set, including linguistic, orthographic, morphological, dictionary matching and local context features. Post-processing modules are also integrated, performing parentheses correction, abbreviation resolution and filtering erroneous mentions using an exclusion list derived from the training data. The developed methods were implemented as a document annotation tool and web service, freely available at http://bioinformatics.ua.pt/becas-chemicals/.

Using Standardized Lexicons for Report Template Validation with LexMap, a Web-based Application.

An enormous amount of data exists in unstructured diagnostic and interventional radiology reports. Free text or non-standardized terminologies limit the ability to parse, extract, and analyze these report data elements. Medical lexicons and ontologies contain standardized terms for relevant concepts including disease entities, radiographic technique, and findings. The use of standardized terms offers the potential to improve reporting consistency and facilitate computer analysis. The purpose of this project was to implement an interface to aid in the creation of standards-compliant reporting templates for use in interventional radiology. Non-standardized procedure report text was analyzed and referenced to RadLex, SNOMED-CT, and LOINC. Using JavaScript, a web application was developed which determined whether exact terms or synonyms in reports existed within these three reference resources. The NCBO BioPortal Annotator web service was used to map terms, and output from this application was used to create an interactive annotated version of the original report. The application was successfully used to analyze and modify five distinct reports for the Society of Interventional Radiology's standardized reporting project.

Semantic Annotation of SOAP Web Services based on Word Sense Disambiguation Techniques

<p>Un requerimiento clave para materializar la Web semántica involucra la anotación de los recursos y servicios Web con metadatos semánticos. Este procedimiento se ha abordado tradicionalmente como una tarea manual, la cual implica un consumo elevado de tiempo y recursos, así como el conocimiento de formatos de descripción y representaciones formales de conocimiento, como las ontologías. Algunos trabajos de investigación han promovido la generación de mecanismos que automaticen de manera parcial el procedimiento de anotación semántica, sin embargo, en el caso particular de los servicios, estos trabajos prescinden de un análisis del contexto lingüístico de las interfaces o documentos descriptores, que facilite la asignación adecuada de anotaciones semánticas sobre los atributos funcionales de los servicios. En este marco, el presente trabajo, introduce un mecanismo para automatizar la anotación semántica de servicios SOAP, soportada en técnicas de desambiguación del sentido de las palabras (WSD), a partir de las cuales es posible vincular el contexto de los documentos descriptores, al procedimiento de identificación y asociación de entidades ontológicas relacionadas con los atributos del servicio. Este artículo aborda la descripción del mecanismo mencionado, soportándose en un ejemplo, así como los resultados de la evaluación experimental realizada sobre un prototipo que implementa la propuesta.</p>

BioSWR--semantic web services registry for bioinformatics.

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license.

Verification of Semantic Web Service Annotations Using Ontology-Based Partitioning

Semantic annotation of web services has been proposed as a solution to the problem of discovering services to fit a particular need and reusing them appropriately. While there exist tools that assist human users in the annotation task, e.g., Radiant and Meteor-S, no semantic annotation proposal considers the problem of verifying the accuracy of the resulting annotations. Early evidence from workflow compatibility checking suggests that the proportion of annotations that contain some form of inaccuracy is high, and yet no tools exist to help annotators to test the results of their work systematically before they are deployed for public use. In this paper, we adapt techniques from conventional software testing to the verification of semantic annotations for web service input and output parameters. We present an algorithm for the testing process and discuss ways in which manual effort from the annotator during testing can be reduced. We also present two adequacy criteria for specifying test cases used as input for the testing process. These criteria are based on structural coverage of the domain ontology used for annotation. The results of an evaluation exercise, based on a collection of annotations for bioinformatics web services, show that defects can be successfully detected by the technique.

A framework for evaluating semantic annotations of Web services: A network theory based approach for measuring annotation quality

In the past years various methods have been developed which require semantic annotations of Web services as an input. Such methods typically leverage discovery, match-making, composition and execution of Web services in dynamic settings. At the same time a number of automated Web service annotation approaches have been proposed for enabling application of these methods in settings where it is not feasible to provide the annotations manually. However, lack of effective automated evaluation frameworks has seriously limited proper assessment of the constructed annotations in settings where the overall annotation quality of large quantities of Web services needs to be evaluated. This paper describes an evaluation framework for measuring the quality of semantic annotations for a large number of real-world Web services from heterogeneous application domains. The evaluation framework is generally based on analyzing properties of Web service networks constructed from semantic annotations of the Web services. More specifically, we measure scale-free, small-world and correlation degree properties of the networks to evaluate the overall quality of annotations. The evaluation is demonstrated using annotations constructed semi-automatically for a set of publicly available WSDL documents containing descriptions of about 200 000 Web service operations.

Multilabel Learning for Automatic Web Services Tagging

Recently, some web services portals and search engines as Biocatalogue and Seekda!, have allowed users to manually annotate Web services using tags. User Tags provide meaningful descriptions of services and allow users to index and organize their contents. Tagging technique is widely used to annotate objects in Web 2.0 applications. In this paper we propose a novel probabilistic topic model (which extends the CorrLDA model - Correspondence Latent Dirichlet Allocation-) to automatically tag web services according to existing manual tags. Our probabilistic topic model is a latent variable model that exploits local correlation labels. Indeed, exploiting label correlations is a challenging and crucial problem especially in multi-label learning context. Moreover, several existing systems can recommend tags for web services based on existing manual tags. In most cases, the manual tags have better quality. We also develop three strategies to automatically recommend the best tags for web services. We also propose, in this paper, WS-Portal; An Enriched Web Services Search Engine which contains 7063 providers, 115 sub-classes of category and 22236 web services crawled from the Internet. In WS-Portal, severals technologies are employed to improve the effectiveness of web service discovery (i.e. web services clustering, tags recommendation, services rating and monitoring). Our experiments are performed out based on real-world web services. The comparisons of Precision@n, Normalised Discounted Cumulative Gain (NDCGn) values for our approach indicate that the method presented in this paper outperforms the method based on the CorrLDA in terms of ranking and quality of generated tags.

SELECTION OF ONTOLOGY FOR WEB SERVICE DESCRIPTION LANGUAGE TO ONTOLOGY WEB LANGUAGE CONVERSION

Semantic web is to extend the current human readable web to encoding some of the semantic of resources in a machine processing form. As a Semantic web component, Semantic Web Services (SWS) uses a mark-up that makes the data into detailed and sophi sticated machine readable way. One such language is Ontology Web Language (OWL). Existing conventional web service annotation can be changed to semantic web service by mapping Web Service Description Language (WSDL) with the semantic annotation of OWL-S. In this conversion of WSDL to OWL process, the ontology plays a vital role. Ontology can be stored and retrieved from local rep ository and selecting the appropriate ontology is a complicated process and this can be achieved by Ont ology Searching and Property Matching (OSPM) engine. Ontology is stored in the local repository as ontology document and exact matching of ontology for the requested query can be searched using seman tic similarity ranking method. High ranked classes of ontology will undergo property matching; here reque sted concept will be matched with the resulting property. OSPM engine act as the backbone for selec ting an exact ontology and reduce the conflict that occurs while selecting the ontology for annotation purpose.