Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Artificial Intelligence
Title: Transforming XML documents to OWL ontologies: A survey
Abstract: The aims of XML data conversion to ontologies are the indexing, integration and enrichment of existing ontologies with knowledge acquired from these sources. The contribution of this paper consists in providing a classification of the approaches used for the conversion of XML documents into OWL ontologies. This classification underlines the usage profile of each conversion method, providing a clear description of the advantages and drawbacks belonging to each method. Hence, this paper focuses on two main processes, which are ontology enrichment and ontology population using XML data. Ontology enrichment is related to the schema of the ontology (TBox), and ontology population is related to an individual (Abox). In addition, the ontologies described in these methods are based on formal languages of the Semantic Web such as OWL (Ontology Web Language) or RDF (Resource Description Framework). These languages are formal because the semantics are formally defined and take advantage of the Description Logics. In contrast, XML data sources are without formal semantics. The XML language is used to store, export and share data between processes able to process the specific data structure. However, even if the semantics is not explicitly expressed, data structure contains the universe of discourse by using a qualified vocabulary regarding a consensual agreement. In order to formalize this semantics, the OWL language provides rich logical constraints. Therefore, these logical constraints are evolved in the transformation of XML documents into OWL documents, allowing the enrichment and the population of the target ontology. To design such a transformation, the current research field establishes connections between OWL constructs (classes, predicates, simple or complex data types, etc.) and XML constructs (elements, attributes, element lists, etc.). Two different approaches for the transformation process are exposed. The instance approaches are based on XML documents without any schema associated. The validation approaches are based on the XML schema and document validated by the associated schema. The second approaches benefit from the schema definition to provide automated transformations with logic constraints. Both approaches are discussed in the text.
Extracted statement — Individual extraction/learning: XML document
Research field: Artificial Intelligence
Title: DTD2OWL: automatic transforming XML documents into OWL ontology
Abstract: DTD and its instance have been considered the standard for data representation and information exchange format on the current web. However, when coming to the next generation of web, the Semantic Web, the drawbacks of XML and its schema are appeared. They mainly focus on the structure level and lack support for data representation. Meanwhile, some Semantic Web applications such as intelligent information services and semantic search engines require not only the syntactic format of the data, but also the semantic content. These requirements are supported by the Web Ontology Language (OWL), which is one of the recent W3C recommendation. But nowadays the amount of data presented in OWL is small in compare with XML data. Therefore, finding a way to utilize the available XML documents for the Semantic Web is a current challenge research. In this work we present an effective solution for transforming XML document into OWL domain knowledge. While keeping the original structure, our work also adds more semantics for the XML document. Moreover, whole of the transformation processes are done automatically without any outside intervention. Further, unlike previous approaches which focus on the schema level, we also extend our methodology for the data level by transforming specific XML instances into OWL individuals. The results in existing OWL syntaxes help them to be loaded immediately by the Semantic Web applications.
Extracted statement — Individual extraction/learning: XML document
Research field: Artificial Intelligence
Title: Transforming XML documents to OWL ontologies: A survey
Abstract: The aims of XML data conversion to ontologies are the indexing, integration and enrichment of existing ontologies with knowledge acquired from these sources. The contribution of this paper consists in providing a classification of the approaches used for the conversion of XML documents into OWL ontologies. This classification underlines the usage profile of each conversion method, providing a clear description of the advantages and drawbacks belonging to each method. Hence, this paper focuses on two main processes, which are ontology enrichment and ontology population using XML data. Ontology enrichment is related to the schema of the ontology (TBox), and ontology population is related to an individual (Abox). In addition, the ontologies described in these methods are based on formal languages of the Semantic Web such as OWL (Ontology Web Language) or RDF (Resource Description Framework). These languages are formal because the semantics are formally defined and take advantage of the Description Logics. In contrast, XML data sources are without formal semantics. The XML language is used to store, export and share data between processes able to process the specific data structure. However, even if the semantics is not explicitly expressed, data structure contains the universe of discourse by using a qualified vocabulary regarding a consensual agreement. In order to formalize this semantics, the OWL language provides rich logical constraints. Therefore, these logical constraints are evolved in the transformation of XML documents into OWL documents, allowing the enrichment and the population of the target ontology. To design such a transformation, the current research field establishes connections between OWL constructs (classes, predicates, simple or complex data types, etc.) and XML constructs (elements, attributes, element lists, etc.). Two different approaches for the transformation process are exposed. The instance approaches are based on XML documents without any schema associated. The validation approaches are based on the XML schema and document validated by the associated schema. The second approaches benefit from the schema definition to provide automated transformations with logic constraints. Both approaches are discussed in the text.
Extracted statement — Input format: XML document
Research field: Artificial Intelligence
Title: DTD2OWL: automatic transforming XML documents into OWL ontology
Abstract: DTD and its instance have been considered the standard for data representation and information exchange format on the current web. However, when coming to the next generation of web, the Semantic Web, the drawbacks of XML and its schema are appeared. They mainly focus on the structure level and lack support for data representation. Meanwhile, some Semantic Web applications such as intelligent information services and semantic search engines require not only the syntactic format of the data, but also the semantic content. These requirements are supported by the Web Ontology Language (OWL), which is one of the recent W3C recommendation. But nowadays the amount of data presented in OWL is small in compare with XML data. Therefore, finding a way to utilize the available XML documents for the Semantic Web is a current challenge research. In this work we present an effective solution for transforming XML document into OWL domain knowledge. While keeping the original structure, our work also adds more semantics for the XML document. Moreover, whole of the transformation processes are done automatically without any outside intervention. Further, unlike previous approaches which focus on the schema level, we also extend our methodology for the data level by transforming specific XML instances into OWL individuals. The results in existing OWL syntaxes help them to be loaded immediately by the Semantic Web applications.
Extracted statement — Input format: XML document
Research field: Artificial Intelligence
Title: Transforming XML documents to OWL ontologies: A survey
Abstract: The aims of XML data conversion to ontologies are the indexing, integration and enrichment of existing ontologies with knowledge acquired from these sources. The contribution of this paper consists in providing a classification of the approaches used for the conversion of XML documents into OWL ontologies. This classification underlines the usage profile of each conversion method, providing a clear description of the advantages and drawbacks belonging to each method. Hence, this paper focuses on two main processes, which are ontology enrichment and ontology population using XML data. Ontology enrichment is related to the schema of the ontology (TBox), and ontology population is related to an individual (Abox). In addition, the ontologies described in these methods are based on formal languages of the Semantic Web such as OWL (Ontology Web Language) or RDF (Resource Description Framework). These languages are formal because the semantics are formally defined and take advantage of the Description Logics. In contrast, XML data sources are without formal semantics. The XML language is used to store, export and share data between processes able to process the specific data structure. However, even if the semantics is not explicitly expressed, data structure contains the universe of discourse by using a qualified vocabulary regarding a consensual agreement. In order to formalize this semantics, the OWL language provides rich logical constraints. Therefore, these logical constraints are evolved in the transformation of XML documents into OWL documents, allowing the enrichment and the population of the target ontology. To design such a transformation, the current research field establishes connections between OWL constructs (classes, predicates, simple or complex data types, etc.) and XML constructs (elements, attributes, element lists, etc.). Two different approaches for the transformation process are exposed. The instance approaches are based on XML documents without any schema associated. The validation approaches are based on the XML schema and document validated by the associated schema. The second approaches benefit from the schema definition to provide automated transformations with logic constraints. Both approaches are discussed in the text.
Extracted statement — RDF Graph: XML document
Research field: Artificial Intelligence
Title: Automatic transforming XML documents into OWL Ontology
Abstract: DTD and its instance have been considered the standard for data representation and information exchange format on the current web. However, when coming to the next generation of web, the Semantic Web, the drawbacks of XML and its schema are appeared. They mainly focus on the structure level and lack support for data representation. Meanwhile, some Semantic Web applications such as intelligent information services and semantic search engines require not only the syntactic format of the data, but also the semantic content. These requirements are supported by the Web Ontology Language (OWL), which is one of the recent W3C recommendation. But nowadays the amount of data presented in OWL is small in compare with XML data. Therefore, finding a way to utilize the available XML documents for the Semantic Web is a current challenge research. In this work we present an effective solution for transforming XML document into OWL domain knowledge. While keeping the original structure, our work also adds more semantics for the XML document. Moreover, whole of the transformation processes are done automatically without any outside intervention. Further, unlike previous approaches which focus on the schema level, we also extend our methodology for the data level by transforming specific XML instances into OWL individuals. The results in existing OWL syntaxes help them to be loaded immediately by the Semantic Web applications.
Extracted statement — Input format: XML instances
Research field: Artificial Intelligence
Title: Ontology enrichment and automatic population from XML data
Abstract: This paper presents a flexible method to enrich and populate an existing OWL ontology from XML data. Basic mapping rules are defined in order to specify the conversion rules on properties. Advanced mapping rules are defined on XML schemas a nd OWL XML schema elements in order to define rules for th e population process. In addition, this flexible method allows u sers to reuse rules for other conversions and populations.
Extracted statement — Input format: XML schema
Research field: Artificial Intelligence
Title: Building ontologies from XML data sources
Abstract: In this paper, we present a tool called X2OWL that aims at building an OWL ontology from an XML datasource. This method is based on XML schema to automatically generate the ontology structure, as well as, a set of mapping bridges. The presented method also includes a refinement step that allows to clean the mapping bridges and possibly to restructure the generated ontology.
Extracted statement — Input format: XML schema
Research field: Artificial Intelligence
Title: Transforming XML schema to OWL using patterns
Abstract: One of the promises of the Semantic Web is to support applications that easily and seamlessly deal with heterogeneous data. Most data on the Web, however, is in the Extensible Markup Language (XML) format, but using XML requires applications to understand the format of each data source that they access. To achieve the benefits of the Semantic Web involves transforming XML into the Semantic Web language, OWL (Ontology Web Language), a process that generally has manual or only semi-automatic components. In this paper we present a set of patterns that enable the direct, automatic transformation from XML Schema into OWL allowing the integration of much XML data in the Semantic Web. We focus on an advanced logical representation of XML Schema components and present an implementation, including a comparison with related work.
Extracted statement — Input format: XML schema
Research field: Artificial Intelligence
Title: An efficient XML to OWL converter
Abstract: XML has become the de-facto standard of data exchange format in E-businesses. Although XML can support syntactic inter-operability, problems arise when data sources represented as XML documents are needed to be integrated. The reason is that XML lacks support for efficient sharing of conceptualization. The Web Ontology Language (OWL) can play an important role here as it can enable semantic inter-operability, and it supports the representation of domain knowledge using classes, properties and instances for applications. In many applications it is required to convert huge XML documents automatically to OWL ontologies, which is receiving a lot of attention. There are some existing converters for this job. Unfortunately they have serious shortcomings, e. g., they do not address the handling of characteristics like internal references, (transitive) import(s), include etc. which are commonly used in XML Schemas. To alleviate these drawbacks, we propose a new framework for mapping XML to OWL automatically. We illustrate our technique on examples to show the efficacy of our approach. We also provide the performance measures of our approach on some standard datasets. We also check the correctness of the conversion process.
Extracted statement — Input format: XML schema
Research field: Biochemistry
Title: Dynamic Impacts of the Inhibition of the Molecular Chaperone Hsp90 on the T-Cell Proteome Have Implications for Anti-Cancer Therapy
Abstract: The molecular chaperone Hsp90-dependent proteome represents a complex protein network of critical biological and medical relevance. Known to associate with proteins with a broad variety of functions termed clients, Hsp90 maintains key essential and oncogenic signalling pathways. Consequently, Hsp90 inhibitors are being tested as anti-cancer drugs. Using an integrated systematic approach to analyse the effects of Hsp90 inhibition in T-cells, we quantified differential changes in the Hsp90-dependent proteome, Hsp90 interactome, and a selection of the transcriptome. Kinetic behaviours in the Hsp90-dependent proteome were assessed using a novel pulse-chase strategy (Fierro-Monti et al., accompanying article), detecting effects on both protein stability and synthesis. Global and specific dynamic impacts, including proteostatic responses, are due to direct inhibition of Hsp90 as well as indirect effects. As a result, a decrease was detected in most proteins that changed their levels, including known Hsp90 clients. Most likely, consequences of the role of Hsp90 in gene expression determined a global reduction in net de novo protein synthesis. This decrease appeared to be greater in magnitude than a concomitantly observed global increase in protein decay rates. Several novel putative Hsp90 clients were validated, and interestingly, protein families with critical functions, particularly the Hsp90 family and cofactors themselves as well as protein kinases, displayed strongly increased decay rates due to Hsp90 inhibitor treatment. Remarkably, an upsurge in survival pathways, involving molecular chaperones and several oncoproteins, and decreased levels of some tumour suppressors, have implications for anti-cancer therapy with Hsp90 inhibitors. The diversity of global effects may represent a paradigm of mechanisms that are operating to shield cells from proteotoxic stress, by promoting pro-survival and anti-proliferative functions. Data are available via ProteomeXchange with identifier PXD000537.
Extracted statement — Material: complex protein network
Research field: Biochemistry
Title: Dynamic Impacts of the Inhibition of the Molecular Chaperone Hsp90 on the T-Cell Proteome Have Implications for Anti-Cancer Therapy
Abstract: The molecular chaperone Hsp90-dependent proteome represents a complex protein network of critical biological and medical relevance. Known to associate with proteins with a broad variety of functions termed clients, Hsp90 maintains key essential and oncogenic signalling pathways. Consequently, Hsp90 inhibitors are being tested as anti-cancer drugs. Using an integrated systematic approach to analyse the effects of Hsp90 inhibition in T-cells, we quantified differential changes in the Hsp90-dependent proteome, Hsp90 interactome, and a selection of the transcriptome. Kinetic behaviours in the Hsp90-dependent proteome were assessed using a novel pulse-chase strategy (Fierro-Monti et al., accompanying article), detecting effects on both protein stability and synthesis. Global and specific dynamic impacts, including proteostatic responses, are due to direct inhibition of Hsp90 as well as indirect effects. As a result, a decrease was detected in most proteins that changed their levels, including known Hsp90 clients. Most likely, consequences of the role of Hsp90 in gene expression determined a global reduction in net de novo protein synthesis. This decrease appeared to be greater in magnitude than a concomitantly observed global increase in protein decay rates. Several novel putative Hsp90 clients were validated, and interestingly, protein families with critical functions, particularly the Hsp90 family and cofactors themselves as well as protein kinases, displayed strongly increased decay rates due to Hsp90 inhibitor treatment. Remarkably, an upsurge in survival pathways, involving molecular chaperones and several oncoproteins, and decreased levels of some tumour suppressors, have implications for anti-cancer therapy with Hsp90 inhibitors. The diversity of global effects may represent a paradigm of mechanisms that are operating to shield cells from proteotoxic stress, by promoting pro-survival and anti-proliferative functions. Data are available via ProteomeXchange with identifier PXD000537.
Extracted statement — Data: critical biological and medical relevance
Research field: Biochemistry
Title: Dynamic Impacts of the Inhibition of the Molecular Chaperone Hsp90 on the T-Cell Proteome Have Implications for Anti-Cancer Therapy
Abstract: The molecular chaperone Hsp90-dependent proteome represents a complex protein network of critical biological and medical relevance. Known to associate with proteins with a broad variety of functions termed clients, Hsp90 maintains key essential and oncogenic signalling pathways. Consequently, Hsp90 inhibitors are being tested as anti-cancer drugs. Using an integrated systematic approach to analyse the effects of Hsp90 inhibition in T-cells, we quantified differential changes in the Hsp90-dependent proteome, Hsp90 interactome, and a selection of the transcriptome. Kinetic behaviours in the Hsp90-dependent proteome were assessed using a novel pulse-chase strategy (Fierro-Monti et al., accompanying article), detecting effects on both protein stability and synthesis. Global and specific dynamic impacts, including proteostatic responses, are due to direct inhibition of Hsp90 as well as indirect effects. As a result, a decrease was detected in most proteins that changed their levels, including known Hsp90 clients. Most likely, consequences of the role of Hsp90 in gene expression determined a global reduction in net de novo protein synthesis. This decrease appeared to be greater in magnitude than a concomitantly observed global increase in protein decay rates. Several novel putative Hsp90 clients were validated, and interestingly, protein families with critical functions, particularly the Hsp90 family and cofactors themselves as well as protein kinases, displayed strongly increased decay rates due to Hsp90 inhibitor treatment. Remarkably, an upsurge in survival pathways, involving molecular chaperones and several oncoproteins, and decreased levels of some tumour suppressors, have implications for anti-cancer therapy with Hsp90 inhibitors. The diversity of global effects may represent a paradigm of mechanisms that are operating to shield cells from proteotoxic stress, by promoting pro-survival and anti-proliferative functions. Data are available via ProteomeXchange with identifier PXD000537.
Extracted statement — Material: Hsp90 family and cofactors themselves