This document has been written as a BBMRI-ERIC use case description for Research Data<br> A... more This document has been written as a BBMRI-ERIC use case description for Research Data<br> Alliance (RDA) Data Fabric IG (DFIG). References to existing RDA work are minimized on<br> purpose, as it focuses on description of the use case itself. The structure of section complies<br> with the RDA DFIG. The document is intended to be published by RDA among other use cases.
The purpose of this document is to summarize a first set of performance indicators related<br&... more The purpose of this document is to summarize a first set of performance indicators related<br> to the vision, mission, and tasks of BBMRI-ERIC expressed in the BBMRI-ERIC<br> Statutes. It aims at providing ground for further discussions and consensus searching activities<br> within the community and among its various stakeholders. After a consensus is<br> reached, the performance indicators will be adopted and implemented on all levels.
'Biobanks (and Biomolecular Resources Centres)' means collections, repositories and distr... more 'Biobanks (and Biomolecular Resources Centres)' means collections, repositories and distribution centres of all types of human biological samples, such as blood, tissues, cells or DNA and/or related data such as associated clinical and research data, as well as biomolecular resources, including model- and micro-organisms that might contribute to the understanding of the physiology and diseases of humans. BBMRI-ERIC Statutes, Article 1(1)
European journal of human genetics : EJHG, Jan 26, 2015
A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical re... more A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access phenotypic, clinical and other information about samples that are currently stored at biobanks in an integrated manner. However, privacy issues together with heterogeneous information systems and the lack of agreed-upon vocabularies have made specimen searching across multiple biobanks extremely challenging. We describe three case studies where we have linked samples and sample descriptions in order to facilitate global searching of available samples for research. The use cases include the ENGAGE (European Network for Genetic and Genomic Epidemiology) consortium comprising at least 39 cohorts, the SUMMIT (surrogate markers for micro- and macro-vascular hard endpoints for innovative diabetes tools) consortium ...
Management of data to produce scientific knowledge is a key challenge for biological research in ... more Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.
"BBMRI-ERIC associated Expert Centres trusted partners" are building the bridge between... more "BBMRI-ERIC associated Expert Centres trusted partners" are building the bridge between academic and applied research in a public-private partnership model; by integrating pre- competitive research and development endeavours by providing not only access to biological samples and medical data but access also to the broad spectrum of medical and scientific expertise related to the samples, data, and their analysis. BBMRI-ERIC Expert Centres are closely linked to the Vision and Mission strategy of BBMRI-ERIC. This document describes the BBMRI-ERIC Expert Centre public-private-partnership model, the application criteria, the assessment and vote process Adopted by Assembly of Members 27 October 2015.
Biobanks are well-organized resources comprising biological samples and associated information th... more Biobanks are well-organized resources comprising biological samples and associated information that are accessible to scientific investigation. Across Europe, millions of samples with related data are held in different types of collections.While individual collections can be well organized and accessible, the resources are subject to fragmen-tation, insecurity of funding and incompleteness. To address these issues, a Biobanking and BioMolecular Resources Infrastructure (BBMRI) is to be developed across Europe, thereby implementing a European ‘roadmap ’ for research infrastructures that was developed by a forum of EU member states and that has been received by the European Commission. In this review, we describe the work involved in preparing for the construction of BBMRI in a European and global context.
Text clustering divides a set of texts into clusters (parts), so that texts within each cluster a... more Text clustering divides a set of texts into clusters (parts), so that texts within each cluster are similar in content. It may be used to uncover the structure and content of unknown text sets as well as to give new perspectives on familiar ones. The main contributions of this thesis are an investigation of text representation for Swedish and some extensions of the work on how to use text clustering as an exploration tool. We have also done some work on synonyms and evaluation of clustering results. Text clustering, at least such as it is treated here, is performed using the vector space model, which is commonly used in information retrieval. This model represents texts by the words that appear in them and considers texts similar in content if they share many words. Languages differ in what is considered a word. We have investigated the impact of some of the characteristics of Swedish on text clustering. Swedish has more morphological variation than for instance English. We show tha...
This document has been written as a BBMRI-ERIC use case description for Research Data<br> A... more This document has been written as a BBMRI-ERIC use case description for Research Data<br> Alliance (RDA) Data Fabric IG (DFIG). References to existing RDA work are minimized on<br> purpose, as it focuses on description of the use case itself. The structure of section complies<br> with the RDA DFIG. The document is intended to be published by RDA among other use cases.
The purpose of this document is to summarize a first set of performance indicators related<br&... more The purpose of this document is to summarize a first set of performance indicators related<br> to the vision, mission, and tasks of BBMRI-ERIC expressed in the BBMRI-ERIC<br> Statutes. It aims at providing ground for further discussions and consensus searching activities<br> within the community and among its various stakeholders. After a consensus is<br> reached, the performance indicators will be adopted and implemented on all levels.
'Biobanks (and Biomolecular Resources Centres)' means collections, repositories and distr... more 'Biobanks (and Biomolecular Resources Centres)' means collections, repositories and distribution centres of all types of human biological samples, such as blood, tissues, cells or DNA and/or related data such as associated clinical and research data, as well as biomolecular resources, including model- and micro-organisms that might contribute to the understanding of the physiology and diseases of humans. BBMRI-ERIC Statutes, Article 1(1)
European journal of human genetics : EJHG, Jan 26, 2015
A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical re... more A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access phenotypic, clinical and other information about samples that are currently stored at biobanks in an integrated manner. However, privacy issues together with heterogeneous information systems and the lack of agreed-upon vocabularies have made specimen searching across multiple biobanks extremely challenging. We describe three case studies where we have linked samples and sample descriptions in order to facilitate global searching of available samples for research. The use cases include the ENGAGE (European Network for Genetic and Genomic Epidemiology) consortium comprising at least 39 cohorts, the SUMMIT (surrogate markers for micro- and macro-vascular hard endpoints for innovative diabetes tools) consortium ...
Management of data to produce scientific knowledge is a key challenge for biological research in ... more Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.
"BBMRI-ERIC associated Expert Centres trusted partners" are building the bridge between... more "BBMRI-ERIC associated Expert Centres trusted partners" are building the bridge between academic and applied research in a public-private partnership model; by integrating pre- competitive research and development endeavours by providing not only access to biological samples and medical data but access also to the broad spectrum of medical and scientific expertise related to the samples, data, and their analysis. BBMRI-ERIC Expert Centres are closely linked to the Vision and Mission strategy of BBMRI-ERIC. This document describes the BBMRI-ERIC Expert Centre public-private-partnership model, the application criteria, the assessment and vote process Adopted by Assembly of Members 27 October 2015.
Biobanks are well-organized resources comprising biological samples and associated information th... more Biobanks are well-organized resources comprising biological samples and associated information that are accessible to scientific investigation. Across Europe, millions of samples with related data are held in different types of collections.While individual collections can be well organized and accessible, the resources are subject to fragmen-tation, insecurity of funding and incompleteness. To address these issues, a Biobanking and BioMolecular Resources Infrastructure (BBMRI) is to be developed across Europe, thereby implementing a European ‘roadmap ’ for research infrastructures that was developed by a forum of EU member states and that has been received by the European Commission. In this review, we describe the work involved in preparing for the construction of BBMRI in a European and global context.
Text clustering divides a set of texts into clusters (parts), so that texts within each cluster a... more Text clustering divides a set of texts into clusters (parts), so that texts within each cluster are similar in content. It may be used to uncover the structure and content of unknown text sets as well as to give new perspectives on familiar ones. The main contributions of this thesis are an investigation of text representation for Swedish and some extensions of the work on how to use text clustering as an exploration tool. We have also done some work on synonyms and evaluation of clustering results. Text clustering, at least such as it is treated here, is performed using the vector space model, which is commonly used in information retrieval. This model represents texts by the words that appear in them and considers texts similar in content if they share many words. Languages differ in what is considered a word. We have investigated the impact of some of the characteristics of Swedish on text clustering. Swedish has more morphological variation than for instance English. We show tha...
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