�ݺ�ߣshows by User: jeliazkova

�ݺ�ߣshows by User: jeliazkova_nina / http://www.slideshare.net/images/logo.gif �ݺ�ߣshows by User: jeliazkova_nina / Sun, 24 Mar 2019 18:58:19 GMT �ݺ�ߣShare feed for �ݺ�ߣshows by User: jeliazkova_nina Making project data avalialble eNanomapper through Database /slideshow/making-project-data-avalialble-enanomapper-through-database/137957524 makingprojectdataavalialbleenanomapperdatabase-190324185819
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]]> Sun, 24 Mar 2019 18:58:19 GMT /slideshow/making-project-data-avalialble-enanomapper-through-database/137957524 jeliazkova_nina@slideshare.net(jeliazkova_nina) Making project data avalialble eNanomapper through Database jeliazkova_nina <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/makingprojectdataavalialbleenanomapperdatabase-190324185819-thumbnail.jpg?width=120&height=120&fit=bounds" />

Making project data avalialble eNanomapper through Database from Nina Jeliazkova

]]> 19 1 https://cdn.slidesharecdn.com/ss_thumbnails/makingprojectdataavalialbleenanomapperdatabase-190324185819-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post

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0 eNanoMapper database, search tools and templates /slideshow/enanomapper-database-search-tools-and-templates/72296024 enanomapperdb-searchtools-templatesclean-170218065655
A webinar given at the NCIP Hub https://nciphub.org/resources/1925 Nanomaterial safety assessment has become an important task following the production growth of engineered nanomaterials (ENMs) and the increased interest for ENMs from various academic, industry and regulatory parties. A number of challenges exist in nanomaterials data representation and integration mainly due to the data complexity and origination of ENM information from diverse sources. We have recently described eNanoMapper database [1] as part of the computational infrastructure for toxicological data management of engineered materials, developed within eNanoMapper project [2]. The eNanoMapper prototype database is publicly available at http://data.enanomapper.net, demonstrating the integration of data from multiple sources, using the common data model and Application Programming Interface. The supported import formats are IUCLID5 files (OECD HT), semantic format (RDF) and custom spreadsheet templates. The latter accommodates the preferred approach for data gathering for the majority of the NanoSafety Cluster projects and is enabled by a configurable parser mapping the the custom spreadsheet organization into the internal eNanoMapper storage components through external configuration file. Import of spreadsheet data and other data formats, generated by a number of NanoSafety Cluster projects is currently ongoing. The export formats have been extended with the new ISA JSON format, following the most recent ISA specification. Defining templates for data gathering is a common activity for most of the NanoSafety Cluster projects usually resulting in modified Excel spreadsheets. In order to help avoiding the incompatibility issues, we present a tool for template generation, based on templates released under open license by JRC under the framework of the NANoREG project [3]. A number of physchem, in-vitro and in-vivo assays are supported and using feedback from users we added and extended existing information about different aspects of nanosafety, e.g. environmental exposure, cell culture assays, cellular and animal models, nanomaterial production features, and nanomaterial ageing. Finally, the data can be accessed programmatically via the application programming interface as well as via user friendly search interface at https://search.data.enanomapper.net. The search application is powered by a free text search engine and eNanoMapper ontology and was improved over the last year based on user feedback.The search function allows now multiple filtering for information. It is possible to stack filters for e.g. nanomaterial type, cell model and assay. eNanoMapper is supported by European Commission 7th Framework Programme for Research and Technological Development Grant (Grant agreement no: 604134). ]]>
A webinar given at the NCIP Hub https://nciphub.org/resources/1925 Nanomaterial safety assessment has become an important task following the production growth of engineered nanomaterials (ENMs) and the increased interest for ENMs from various academic, industry and regulatory parties. A number of challenges exist in nanomaterials data representation and integration mainly due to the data complexity and origination of ENM information from diverse sources. We have recently described eNanoMapper database [1] as part of the computational infrastructure for toxicological data management of engineered materials, developed within eNanoMapper project [2]. The eNanoMapper prototype database is publicly available at http://data.enanomapper.net, demonstrating the integration of data from multiple sources, using the common data model and Application Programming Interface. The supported import formats are IUCLID5 files (OECD HT), semantic format (RDF) and custom spreadsheet templates. The latter accommodates the preferred approach for data gathering for the majority of the NanoSafety Cluster projects and is enabled by a configurable parser mapping the the custom spreadsheet organization into the internal eNanoMapper storage components through external configuration file. Import of spreadsheet data and other data formats, generated by a number of NanoSafety Cluster projects is currently ongoing. The export formats have been extended with the new ISA JSON format, following the most recent ISA specification. Defining templates for data gathering is a common activity for most of the NanoSafety Cluster projects usually resulting in modified Excel spreadsheets. In order to help avoiding the incompatibility issues, we present a tool for template generation, based on templates released under open license by JRC under the framework of the NANoREG project [3]. A number of physchem, in-vitro and in-vivo assays are supported and using feedback from users we added and extended existing information about different aspects of nanosafety, e.g. environmental exposure, cell culture assays, cellular and animal models, nanomaterial production features, and nanomaterial ageing. Finally, the data can be accessed programmatically via the application programming interface as well as via user friendly search interface at https://search.data.enanomapper.net. The search application is powered by a free text search engine and eNanoMapper ontology and was improved over the last year based on user feedback.The search function allows now multiple filtering for information. It is possible to stack filters for e.g. nanomaterial type, cell model and assay. eNanoMapper is supported by European Commission 7th Framework Programme for Research and Technological Development Grant (Grant agreement no: 604134). ]]> Sat, 18 Feb 2017 06:56:55 GMT /slideshow/enanomapper-database-search-tools-and-templates/72296024 jeliazkova_nina@slideshare.net(jeliazkova_nina) eNanoMapper database, search tools and templates jeliazkova_nina A webinar given at the NCIP Hub https://nciphub.org/resources/1925 Nanomaterial safety assessment has become an important task following the production growth of engineered nanomaterials (ENMs) and the increased interest for ENMs from various academic, industry and regulatory parties. A number of challenges exist in nanomaterials data representation and integration mainly due to the data complexity and origination of ENM information from diverse sources. We have recently described eNanoMapper database [1] as part of the computational infrastructure for toxicological data management of engineered materials, developed within eNanoMapper project [2]. The eNanoMapper prototype database is publicly available at http://data.enanomapper.net, demonstrating the integration of data from multiple sources, using the common data model and Application Programming Interface. The supported import formats are IUCLID5 files (OECD HT), semantic format (RDF) and custom spreadsheet templates. The latter accommodates the preferred approach for data gathering for the majority of the NanoSafety Cluster projects and is enabled by a configurable parser mapping the the custom spreadsheet organization into the internal eNanoMapper storage components through external configuration file. Import of spreadsheet data and other data formats, generated by a number of NanoSafety Cluster projects is currently ongoing. The export formats have been extended with the new ISA JSON format, following the most recent ISA specification. Defining templates for data gathering is a common activity for most of the NanoSafety Cluster projects usually resulting in modified Excel spreadsheets. In order to help avoiding the incompatibility issues, we present a tool for template generation, based on templates released under open license by JRC under the framework of the NANoREG project [3]. A number of physchem, in-vitro and in-vivo assays are supported and using feedback from users we added and extended existing information about different aspects of nanosafety, e.g. environmental exposure, cell culture assays, cellular and animal models, nanomaterial production features, and nanomaterial ageing. Finally, the data can be accessed programmatically via the application programming interface as well as via user friendly search interface at https://search.data.enanomapper.net. The search application is powered by a free text search engine and eNanoMapper ontology and was improved over the last year based on user feedback.The search function allows now multiple filtering for information. It is possible to stack filters for e.g. nanomaterial type, cell model and assay. eNanoMapper is supported by European Commission 7th Framework Programme for Research and Technological Development Grant (Grant agreement no: 604134). <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/enanomapperdb-searchtools-templatesclean-170218065655-thumbnail.jpg?width=120&height=120&fit=bounds" /> A webinar given at the NCIP Hub https://nciphub.org/resources/1925 Nanomaterial safety assessment has become an important task following the production growth of engineered nanomaterials (ENMs) and the increased interest for ENMs from various academic, industry and regulatory parties. A number of challenges exist in nanomaterials data representation and integration mainly due to the data complexity and origination of ENM information from diverse sources. We have recently described eNanoMapper database [1] as part of the computational infrastructure for toxicological data management of engineered materials, developed within eNanoMapper project [2]. The eNanoMapper prototype database is publicly available at http://data.enanomapper.net, demonstrating the integration of data from multiple sources, using the common data model and Application Programming Interface. The supported import formats are IUCLID5 files (OECD HT), semantic format (RDF) and custom spreadsheet templates. The latter accommodates the preferred approach for data gathering for the majority of the NanoSafety Cluster projects and is enabled by a configurable parser mapping the the custom spreadsheet organization into the internal eNanoMapper storage components through external configuration file. Import of spreadsheet data and other data formats, generated by a number of NanoSafety Cluster projects is currently ongoing. The export formats have been extended with the new ISA JSON format, following the most recent ISA specification. Defining templates for data gathering is a common activity for most of the NanoSafety Cluster projects usually resulting in modified Excel spreadsheets. In order to help avoiding the incompatibility issues, we present a tool for template generation, based on templates released under open license by JRC under the framework of the NANoREG project [3]. A number of physchem, in-vitro and in-vivo assays are supported and using feedback from users we added and extended existing information about different aspects of nanosafety, e.g. environmental exposure, cell culture assays, cellular and animal models, nanomaterial production features, and nanomaterial ageing. Finally, the data can be accessed programmatically via the application programming interface as well as via user friendly search interface at https://search.data.enanomapper.net. The search application is powered by a free text search engine and eNanoMapper ontology and was improved over the last year based on user feedback.The search function allows now multiple filtering for information. It is possible to stack filters for e.g. nanomaterial type, cell model and assay. eNanoMapper is supported by European Commission 7th Framework Programme for Research and Technological Development Grant (Grant agreement no: 604134).

eNanoMapper database, search tools and templates from Nina Jeliazkova

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0 Making the data available with AMBIT cheminformatics platform /slideshow/making-the-data-available-with-ambit-cheminformatics-platform/62650137 201605ambitmioss-160602094135
Recent developments in AMBIT http://ambit.sf.net , presented by Dr. Nickolay Kochev at the EBI Industry workshop on Molecular Informatics Open Source Software (MIOSS) May 18-19 http://www.ebi.ac.uk/industry/workshops]]>
Recent developments in AMBIT http://ambit.sf.net , presented by Dr. Nickolay Kochev at the EBI Industry workshop on Molecular Informatics Open Source Software (MIOSS) May 18-19 http://www.ebi.ac.uk/industry/workshops]]> Thu, 02 Jun 2016 09:41:35 GMT /slideshow/making-the-data-available-with-ambit-cheminformatics-platform/62650137 jeliazkova_nina@slideshare.net(jeliazkova_nina) Making the data available with AMBIT cheminformatics platform jeliazkova_nina Recent developments in AMBIT http://ambit.sf.net , presented by Dr. Nickolay Kochev at the EBI Industry workshop on Molecular Informatics Open Source Software (MIOSS) May 18-19 http://www.ebi.ac.uk/industry/workshops <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/201605ambitmioss-160602094135-thumbnail.jpg?width=120&height=120&fit=bounds" /> Recent developments in AMBIT http://ambit.sf.net , presented by Dr. Nickolay Kochev at the EBI Industry workshop on Molecular Informatics Open Source Software (MIOSS) May 18-19 http://www.ebi.ac.uk/industry/workshops

Making the data available with AMBIT cheminformatics platform from Nina Jeliazkova

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0 The eNanoMapper database for nanomaterial safety information: storage and query /slideshow/the-enanomapper-database-for-nanomaterial-safety-information-storage-and-query/53916845 enanomappernn15-151014092454-lva1-app6892
A number of challenges exist in engineered nanomaterials (ENM) data representation and integration mainly due to data complexity and provenance. We have recently described the eNanoMapper database [doi:10.1109/BIBM.2014.699936] as part of the computational infrastructure for toxicological data management of ENM, developed within the EU FP7 eNanoMapper project. The ontology-supported data model is based on an exhaustive review of existing nano-related data models, databases, and nanomaterial related entries in chemical and toxicogenomic databases. We demonstrate how this approach provides a common ground for integration of data represented in diverse formats (ISA-TAB, OECD HT, custom RDF and set of spreadsheet templates used by the EU NanoSafety Cluster projects) and enables uniform approach towards import, storage and searching of ENM physicochemical measurements and biological assay results. A configurable parser enables import of the data stored in spreadsheet templates, accommodating different organization of the data. The configuration metadata is defined in a separate file, mapping the spreadsheet into the internal data model. The demonstration data provided by eNanoMapper partners ((i) NanoWiki, (ii) a literature dataset on protein coronas and (iii) the ModNanoTox project dataset consisting of 86 assays and 100 different endpoints) illustrates the capability of the associated REST API to support a variety of tests and endpoints, recommended by the OECD Working Party of Manufactured Nanomaterials. The API is tightly integrated with a chemical structure search, allowing highlighting the function as a core, coating or functionalisation. The REST API enables graphical summaries of the data and integration in applications such as NanoQSAR modelling via programmatic interaction.]]>
A number of challenges exist in engineered nanomaterials (ENM) data representation and integration mainly due to data complexity and provenance. We have recently described the eNanoMapper database [doi:10.1109/BIBM.2014.699936] as part of the computational infrastructure for toxicological data management of ENM, developed within the EU FP7 eNanoMapper project. The ontology-supported data model is based on an exhaustive review of existing nano-related data models, databases, and nanomaterial related entries in chemical and toxicogenomic databases. We demonstrate how this approach provides a common ground for integration of data represented in diverse formats (ISA-TAB, OECD HT, custom RDF and set of spreadsheet templates used by the EU NanoSafety Cluster projects) and enables uniform approach towards import, storage and searching of ENM physicochemical measurements and biological assay results. A configurable parser enables import of the data stored in spreadsheet templates, accommodating different organization of the data. The configuration metadata is defined in a separate file, mapping the spreadsheet into the internal data model. The demonstration data provided by eNanoMapper partners ((i) NanoWiki, (ii) a literature dataset on protein coronas and (iii) the ModNanoTox project dataset consisting of 86 assays and 100 different endpoints) illustrates the capability of the associated REST API to support a variety of tests and endpoints, recommended by the OECD Working Party of Manufactured Nanomaterials. The API is tightly integrated with a chemical structure search, allowing highlighting the function as a core, coating or functionalisation. The REST API enables graphical summaries of the data and integration in applications such as NanoQSAR modelling via programmatic interaction.]]> Wed, 14 Oct 2015 09:24:54 GMT /slideshow/the-enanomapper-database-for-nanomaterial-safety-information-storage-and-query/53916845 jeliazkova_nina@slideshare.net(jeliazkova_nina) The eNanoMapper database for nanomaterial safety information: storage and query jeliazkova_nina A number of challenges exist in engineered nanomaterials (ENM) data representation and integration mainly due to data complexity and provenance. We have recently described the eNanoMapper database [doi:10.1109/BIBM.2014.699936] as part of the computational infrastructure for toxicological data management of ENM, developed within the EU FP7 eNanoMapper project. The ontology-supported data model is based on an exhaustive review of existing nano-related data models, databases, and nanomaterial related entries in chemical and toxicogenomic databases. We demonstrate how this approach provides a common ground for integration of data represented in diverse formats (ISA-TAB, OECD HT, custom RDF and set of spreadsheet templates used by the EU NanoSafety Cluster projects) and enables uniform approach towards import, storage and searching of ENM physicochemical measurements and biological assay results. A configurable parser enables import of the data stored in spreadsheet templates, accommodating different organization of the data. The configuration metadata is defined in a separate file, mapping the spreadsheet into the internal data model. The demonstration data provided by eNanoMapper partners ((i) NanoWiki, (ii) a literature dataset on protein coronas and (iii) the ModNanoTox project dataset consisting of 86 assays and 100 different endpoints) illustrates the capability of the associated REST API to support a variety of tests and endpoints, recommended by the OECD Working Party of Manufactured Nanomaterials. The API is tightly integrated with a chemical structure search, allowing highlighting the function as a core, coating or functionalisation. The REST API enables graphical summaries of the data and integration in applications such as NanoQSAR modelling via programmatic interaction. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/enanomappernn15-151014092454-lva1-app6892-thumbnail.jpg?width=120&height=120&fit=bounds" /> A number of challenges exist in engineered nanomaterials (ENM) data representation and integration mainly due to data complexity and provenance. We have recently described the eNanoMapper database [doi:10.1109/BIBM.2014.699936] as part of the computational infrastructure for toxicological data management of ENM, developed within the EU FP7 eNanoMapper project. The ontology-supported data model is based on an exhaustive review of existing nano-related data models, databases, and nanomaterial related entries in chemical and toxicogenomic databases. We demonstrate how this approach provides a common ground for integration of data represented in diverse formats (ISA-TAB, OECD HT, custom RDF and set of spreadsheet templates used by the EU NanoSafety Cluster projects) and enables uniform approach towards import, storage and searching of ENM physicochemical measurements and biological assay results. A configurable parser enables import of the data stored in spreadsheet templates, accommodating different organization of the data. The configuration metadata is defined in a separate file, mapping the spreadsheet into the internal data model. The demonstration data provided by eNanoMapper partners ((i) NanoWiki, (ii) a literature dataset on protein coronas and (iii) the ModNanoTox project dataset consisting of 86 assays and 100 different endpoints) illustrates the capability of the associated REST API to support a variety of tests and endpoints, recommended by the OECD Working Party of Manufactured Nanomaterials. The API is tightly integrated with a chemical structure search, allowing highlighting the function as a core, coating or functionalisation. The REST API enables graphical summaries of the data and integration in applications such as NanoQSAR modelling via programmatic interaction.

The eNanoMapper database for nanomaterial safety information: storage and query from Nina Jeliazkova

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0 On chemical structures, substances, nanomaterials and measurements /slideshow/on-chemical-structures-substances-nanomaterials-and-measurements/37150154 jcbsymposium-onstructuressubstancesnm-nj-140719055858-phpapp01
"On chemical structures, substances, nanomaterials and measurements" Nina Jeliazkova, Ideaconsult This talk attempts to highlight how I came to recognize the fundamental role of measurements, coming from the realm of data modelling and data analysis. Besides retaining the data provenance it provides insights how do we go beyond chemical structures and address the challenges of representing the identity of chemical substances and nanomaterials (with examples from the latest developments of AMBIT web services and OpenTox API). Finally, supporting the vision of distributed, open, web-like approach towards recording subtle experimental details is essential, not only for the chemists and biologists in the labs, but for all of us using, modelling, storing and querying the data. Presented July 14,2014 in Cambridge , UK Defining the Future for Open Notebook Science – A Memorial Symposium Celebrating the Work of Jean-Claude Bradley http://inmemoriamjcb.wikispaces.com/Jean-Claude+Bradley+Memorial+Symposium]]>
"On chemical structures, substances, nanomaterials and measurements" Nina Jeliazkova, Ideaconsult This talk attempts to highlight how I came to recognize the fundamental role of measurements, coming from the realm of data modelling and data analysis. Besides retaining the data provenance it provides insights how do we go beyond chemical structures and address the challenges of representing the identity of chemical substances and nanomaterials (with examples from the latest developments of AMBIT web services and OpenTox API). Finally, supporting the vision of distributed, open, web-like approach towards recording subtle experimental details is essential, not only for the chemists and biologists in the labs, but for all of us using, modelling, storing and querying the data. Presented July 14,2014 in Cambridge , UK Defining the Future for Open Notebook Science – A Memorial Symposium Celebrating the Work of Jean-Claude Bradley http://inmemoriamjcb.wikispaces.com/Jean-Claude+Bradley+Memorial+Symposium]]> Sat, 19 Jul 2014 05:58:57 GMT /slideshow/on-chemical-structures-substances-nanomaterials-and-measurements/37150154 jeliazkova_nina@slideshare.net(jeliazkova_nina) On chemical structures, substances, nanomaterials and measurements jeliazkova_nina "On chemical structures, substances, nanomaterials and measurements" Nina Jeliazkova, Ideaconsult This talk attempts to highlight how I came to recognize the fundamental role of measurements, coming from the realm of data modelling and data analysis. Besides retaining the data provenance it provides insights how do we go beyond chemical structures and address the challenges of representing the identity of chemical substances and nanomaterials (with examples from the latest developments of AMBIT web services and OpenTox API). Finally, supporting the vision of distributed, open, web-like approach towards recording subtle experimental details is essential, not only for the chemists and biologists in the labs, but for all of us using, modelling, storing and querying the data. Presented July 14,2014 in Cambridge , UK Defining the Future for Open Notebook Science – A Memorial Symposium Celebrating the Work of Jean-Claude Bradley http://inmemoriamjcb.wikispaces.com/Jean-Claude+Bradley+Memorial+Symposium <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/jcbsymposium-onstructuressubstancesnm-nj-140719055858-phpapp01-thumbnail.jpg?width=120&height=120&fit=bounds" /> "On chemical structures, substances, nanomaterials and measurements" Nina Jeliazkova, Ideaconsult This talk attempts to highlight how I came to recognize the fundamental role of measurements, coming from the realm of data modelling and data analysis. Besides retaining the data provenance it provides insights how do we go beyond chemical structures and address the challenges of representing the identity of chemical substances and nanomaterials (with examples from the latest developments of AMBIT web services and OpenTox API). Finally, supporting the vision of distributed, open, web-like approach towards recording subtle experimental details is essential, not only for the chemists and biologists in the labs, but for all of us using, modelling, storing and querying the data. Presented July 14,2014 in Cambridge , UK Defining the Future for Open Notebook Science – A Memorial Symposium Celebrating the Work of Jean-Claude Bradley http://inmemoriamjcb.wikispaces.com/Jean-Claude+Bradley+Memorial+Symposium

On chemical structures, substances, nanomaterials and measurements from Nina Jeliazkova

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0 ISA-TAB and ISA-TAB-Nano overview /slideshow/isatab-and-isatab/32585753 isa-tab-nano-short-140321111301-phpapp01
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]]> Fri, 21 Mar 2014 11:13:01 GMT /slideshow/isatab-and-isatab/32585753 jeliazkova_nina@slideshare.net(jeliazkova_nina) ISA-TAB and ISA-TAB-Nano overview jeliazkova_nina <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/isa-tab-nano-short-140321111301-phpapp01-thumbnail.jpg?width=120&height=120&fit=bounds" />

ISA-TAB and ISA-TAB-Nano overview from Nina Jeliazkova

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0 Hierarchical multi-label classification of ToxCast datasets /slideshow/hierarchical-multilabel-classification-of-toxcast-datasets/13878271 ninajeliazkova-toxcast-epa-15052009-120805123034-phpapp02
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]]> Sun, 05 Aug 2012 12:30:32 GMT /slideshow/hierarchical-multilabel-classification-of-toxcast-datasets/13878271 jeliazkova_nina@slideshare.net(jeliazkova_nina) Hierarchical multi-label classification of ToxCast datasets jeliazkova_nina <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/ninajeliazkova-toxcast-epa-15052009-120805123034-phpapp02-thumbnail.jpg?width=120&height=120&fit=bounds" />

Hierarchical multi-label classification of ToxCast datasets from Nina Jeliazkova

]]> 440 2 https://cdn.slidesharecdn.com/ss_thumbnails/ninajeliazkova-toxcast-epa-15052009-120805123034-phpapp02-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post

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0 Linking the silos. Data and predictive models integration in toxicology. /slideshow/linking-the-silos-data-and-predictive-models-integration-in-toxicology/13479876 linkingthesilos-nj-120628030238-phpapp02
Silo storage system are typically designed to store one single type of grain. An information silo is characterized by a rigid design, not allowing easy exchange of information and integration with other systems. Life sciences software systems and those applied in toxicology in particular, are often developed independently and compatibility is rarely perceived as a primary design goal. The traditional approach to the integration challenge is to build data warehouses and custom applications managing all the information under a central authority and storing data in a single database schema. The majority of the existing chemical databases rely on a centralized design, offering data access via unique and incompatible interfaces. Loosely coupled systems, allowing end users to share and integrate data on the fly are increasingly considered more appropriate and actively developed [1], but not yet the mainstream in cheminformatics. Our experience in several past and on-going projects, dealing with data integration of chemical structures and toxicity databases, has been reflected in the architecture of the systems that we have designed (e.g. OpenTox, a set of distributed web services, with semantic representation of resources, including data [2], [3], [4]). The core concepts of the information integration are the web service oriented architecture and a data representation design that includes semantic and provenance information uncoupled from the software code and any proprietary metadata. ]]>
Silo storage system are typically designed to store one single type of grain. An information silo is characterized by a rigid design, not allowing easy exchange of information and integration with other systems. Life sciences software systems and those applied in toxicology in particular, are often developed independently and compatibility is rarely perceived as a primary design goal. The traditional approach to the integration challenge is to build data warehouses and custom applications managing all the information under a central authority and storing data in a single database schema. The majority of the existing chemical databases rely on a centralized design, offering data access via unique and incompatible interfaces. Loosely coupled systems, allowing end users to share and integrate data on the fly are increasingly considered more appropriate and actively developed [1], but not yet the mainstream in cheminformatics. Our experience in several past and on-going projects, dealing with data integration of chemical structures and toxicity databases, has been reflected in the architecture of the systems that we have designed (e.g. OpenTox, a set of distributed web services, with semantic representation of resources, including data [2], [3], [4]). The core concepts of the information integration are the web service oriented architecture and a data representation design that includes semantic and provenance information uncoupled from the software code and any proprietary metadata. ]]> Thu, 28 Jun 2012 03:02:36 GMT /slideshow/linking-the-silos-data-and-predictive-models-integration-in-toxicology/13479876 jeliazkova_nina@slideshare.net(jeliazkova_nina) Linking the silos. Data and predictive models integration in toxicology. jeliazkova_nina Silo storage system are typically designed to store one single type of grain. An information silo is characterized by a rigid design, not allowing easy exchange of information and integration with other systems. Life sciences software systems and those applied in toxicology in particular, are often developed independently and compatibility is rarely perceived as a primary design goal. The traditional approach to the integration challenge is to build data warehouses and custom applications managing all the information under a central authority and storing data in a single database schema. The majority of the existing chemical databases rely on a centralized design, offering data access via unique and incompatible interfaces. Loosely coupled systems, allowing end users to share and integrate data on the fly are increasingly considered more appropriate and actively developed [1], but not yet the mainstream in cheminformatics. Our experience in several past and on-going projects, dealing with data integration of chemical structures and toxicity databases, has been reflected in the architecture of the systems that we have designed (e.g. OpenTox, a set of distributed web services, with semantic representation of resources, including data [2], [3], [4]). The core concepts of the information integration are the web service oriented architecture and a data representation design that includes semantic and provenance information uncoupled from the software code and any proprietary metadata. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/linkingthesilos-nj-120628030238-phpapp02-thumbnail.jpg?width=120&height=120&fit=bounds" /> Silo storage system are typically designed to store one single type of grain. An information silo is characterized by a rigid design, not allowing easy exchange of information and integration with other systems. Life sciences software systems and those applied in toxicology in particular, are often developed independently and compatibility is rarely perceived as a primary design goal. The traditional approach to the integration challenge is to build data warehouses and custom applications managing all the information under a central authority and storing data in a single database schema. The majority of the existing chemical databases rely on a centralized design, offering data access via unique and incompatible interfaces. Loosely coupled systems, allowing end users to share and integrate data on the fly are increasingly considered more appropriate and actively developed [1], but not yet the mainstream in cheminformatics. Our experience in several past and on-going projects, dealing with data integration of chemical structures and toxicity databases, has been reflected in the architecture of the systems that we have designed (e.g. OpenTox, a set of distributed web services, with semantic representation of resources, including data [2], [3], [4]). The core concepts of the information integration are the web service oriented architecture and a data representation design that includes semantic and provenance information uncoupled from the software code and any proprietary metadata.

Linking the silos. Data and predictive models integration in toxicology. from Nina Jeliazkova

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0 Chemical similarity /slideshow/chemical-similarity-9159561/9159561 chemicalsimilarity-110907053821-phpapp01
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]]> Wed, 07 Sep 2011 05:38:19 GMT /slideshow/chemical-similarity-9159561/9159561 jeliazkova_nina@slideshare.net(jeliazkova_nina) Chemical similarity jeliazkova_nina <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/chemicalsimilarity-110907053821-phpapp01-thumbnail.jpg?width=120&height=120&fit=bounds" />

Chemical similarity from Nina Jeliazkova

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0 Seamless and uniform access to chemical data and tools experience gained in developing the open tox framework /slideshow/seamless-and-uniform-access-to-chemical-data-and-tools-experience-gained-in-developing-the-open-tox-framework/9051292 seamlessanduniformaccesstochemicaldataandtoolsexperiencegainedindevelopingtheopentoxframework-110829024422-phpapp01
The slides summarize the experience gained from the design, implementation and use of a set of distributed web services for predictive toxicology. The OpenTox framework, collaboratively developed by partners of the EU FP7 OpenTox project www.opentox.org, aims at providing unified access to chemicals, toxicity data and predictive models. The framework is based on two technological decisions: a common information model, based on ontologies, and availability of data and methods via a standardized REST web services interface, where every chemical compound, data set, or processing algorithm has a unique web address, used to retrieve information or initiate the calculations. The challenges of designing a distributed system by a distributed team are discussed. A common application programming interface was defined and implemented independently by several partners. Our open source AMBIT REST software package implements a large subset of the OpenTox API (data and processing), and is available both as online services and as a downloadable archive. ]]>
The slides summarize the experience gained from the design, implementation and use of a set of distributed web services for predictive toxicology. The OpenTox framework, collaboratively developed by partners of the EU FP7 OpenTox project www.opentox.org, aims at providing unified access to chemicals, toxicity data and predictive models. The framework is based on two technological decisions: a common information model, based on ontologies, and availability of data and methods via a standardized REST web services interface, where every chemical compound, data set, or processing algorithm has a unique web address, used to retrieve information or initiate the calculations. The challenges of designing a distributed system by a distributed team are discussed. A common application programming interface was defined and implemented independently by several partners. Our open source AMBIT REST software package implements a large subset of the OpenTox API (data and processing), and is available both as online services and as a downloadable archive. ]]> Mon, 29 Aug 2011 02:44:22 GMT /slideshow/seamless-and-uniform-access-to-chemical-data-and-tools-experience-gained-in-developing-the-open-tox-framework/9051292 jeliazkova_nina@slideshare.net(jeliazkova_nina) Seamless and uniform access to chemical data and tools experience gained in developing the open tox framework jeliazkova_nina The slides summarize the experience gained from the design, implementation and use of a set of distributed web services for predictive toxicology. The OpenTox framework, collaboratively developed by partners of the EU FP7 OpenTox project www.opentox.org, aims at providing unified access to chemicals, toxicity data and predictive models. The framework is based on two technological decisions: a common information model, based on ontologies, and availability of data and methods via a standardized REST web services interface, where every chemical compound, data set, or processing algorithm has a unique web address, used to retrieve information or initiate the calculations. The challenges of designing a distributed system by a distributed team are discussed. A common application programming interface was defined and implemented independently by several partners. Our open source AMBIT REST software package implements a large subset of the OpenTox API (data and processing), and is available both as online services and as a downloadable archive. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/seamlessanduniformaccesstochemicaldataandtoolsexperiencegainedindevelopingtheopentoxframework-110829024422-phpapp01-thumbnail.jpg?width=120&height=120&fit=bounds" /> The slides summarize the experience gained from the design, implementation and use of a set of distributed web services for predictive toxicology. The OpenTox framework, collaboratively developed by partners of the EU FP7 OpenTox project www.opentox.org, aims at providing unified access to chemicals, toxicity data and predictive models. The framework is based on two technological decisions: a common information model, based on ontologies, and availability of data and methods via a standardized REST web services interface, where every chemical compound, data set, or processing algorithm has a unique web address, used to retrieve information or initiate the calculations. The challenges of designing a distributed system by a distributed team are discussed. A common application programming interface was defined and implemented independently by several partners. Our open source AMBIT REST software package implements a large subset of the OpenTox API (data and processing), and is available both as online services and as a downloadable archive.

Seamless and uniform access to chemical data and tools experience gained in developing the open tox framework from Nina Jeliazkova

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0 https://cdn.slidesharecdn.com/profile-photo-jeliazkova_nina-48x48.jpg?cb=1706643105 vedina.users.sf.net https://cdn.slidesharecdn.com/ss_thumbnails/makingprojectdataavalialbleenanomapperdatabase-190324185819-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/making-project-data-avalialble-enanomapper-through-database/137957524 Making project data av... https://cdn.slidesharecdn.com/ss_thumbnails/enanomapperdb-searchtools-templatesclean-170218065655-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/enanomapper-database-search-tools-and-templates/72296024 eNanoMapper database, ... https://cdn.slidesharecdn.com/ss_thumbnails/201605ambitmioss-160602094135-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/making-the-data-available-with-ambit-cheminformatics-platform/62650137 Making the data availa...