The Experts below are selected from a list of 894 Experts worldwide ranked by ideXlab platform
Peter Em Taschner - One of the best experts on this subject based on the ideXlab platform.
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Open Access A Formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
2013Co-Authors: Jeroen Fj Laros, André Blavier, Peter Em Taschner, Johan Den T Dunnen, Ghent BelgiumAbstract:Background: The use of a standard human sequence variant nomenclature is advocated by the Human Genome Variation Society in order to unambiguously describe genetic variants in databases and literature. There is a clear need for tools that allow the mining of data about human sequence variants and their functional consequences from databases and literature. Existing text mining focuses on the recognition of protein variants and their effects. The recognition of variants at the DNA and RNA levels is essential for dissemination of variant data for diagnostic purposes. Development of new tools is hampered by the complexity of the current nomenclature, which requires processing at the character level to recognize the specific syntactic constructs used in variant descriptions. Results: We approached the gene variant nomenclature as a scientific sublanguage and created two Formal descriptions of the syntax in Extended Backus-Naur Form: one at the DNA-RNA level and one at the protein level. To ensure compatibility to older versions of the human sequence variant nomenclature, previously recommended variant description Formats have been included. The first grammar versions were designed to help build variant description handling in the Alamut mutation interpretation software. The DNA and RNA level descriptions were then updated and used to construct the context-free parser of the Mutalyzer 2 sequence variant nomenclature checker, which has already been used to check more than one million variant descriptions. Conclusions: The Extended Backus-Naur Form provided an overview of the full complexity of the syntax of the sequence variant nomenclature, which remained hidden in the textual Format and the division of the recommendations across the DNA, RNA and protein sections of the Human Genome Variation Society nomenclature websit
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A Formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
BMC Bioinformatics, 2011Co-Authors: Jeroen Fj Laros, André Blavier, Johan T Den Dunnen, Peter Em TaschnerAbstract:Background The use of a standard human sequence variant nomenclature is advocated by the Human Genome Variation Society in order to unambiguously describe genetic variants in databases and literature. There is a clear need for tools that allow the mining of data about human sequence variants and their functional consequences from databases and literature. Existing text mining focuses on the recognition of protein variants and their effects. The recognition of variants at the DNA and RNA levels is essential for dissemination of variant data for diagnostic purposes. Development of new tools is hampered by the complexity of the current nomenclature, which requires processing at the character level to recognize the specific syntactic constructs used in variant descriptions. Results We approached the gene variant nomenclature as a scientific sublanguage and created two Formal descriptions of the syntax in Extended Backus-Naur Form: one at the DNA-RNA level and one at the protein level. To ensure compatibility to older versions of the human sequence variant nomenclature, previously recommended variant description Formats have been included. The first grammar versions were designed to help build variant description handling in the Alamut mutation interpretation software. The DNA and RNA level descriptions were then updated and used to construct the context-free parser of the Mutalyzer 2 sequence variant nomenclature checker, which has already been used to check more than one million variant descriptions. Conclusions The Extended Backus-Naur Form provided an overview of the full complexity of the syntax of the sequence variant nomenclature, which remained hidden in the textual Format and the division of the recommendations across the DNA, RNA and protein sections of the Human Genome Variation Society nomenclature website ( http://www.hgvs.org/mutnomen/ ). This insight into the syntax of the nomenclature could be used to design detailed and clear rules for software development. The Mutalyzer 2 parser demonstrated that it facilitated decomposition of complex variant descriptions into their individual parts. The Extended Backus-Naur Form or parts of it can be used or modified by adding rules, allowing the development of specific sequence variant text mining tools and other programs, which can generate or handle sequence variant descriptions.
Lins, Hertz Wilton De Castro - One of the best experts on this subject based on the ideXlab platform.
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Especificação e implementação de uma linguagem para transFormação de modelos MOF em repositórios dMOF
Universidade Federal do Rio Grande do Norte, 2014Co-Authors: Lins, Hertz Wilton De CastroAbstract:Este trabalho apresenta a especificação e a implementação de uma linguagem de TransFormações em Modelos definidos segundo a especificação MOF (Meta Object Facility) da OMG (Object Management Group). A especificação utiliza uma abordagem baseada em regras ECA (Event-Condition-Action) e foi feita com base em um conjunto de cenários de uso previamente definidos. O parser responsável por garantir que a estrutura sintática da linguagem está correta foi construído com a ferramenta JavaCC (Java Compiler Compiler) e a descrição da sintaxe da linguagem foi feita com EBNF (Extended Backus-Naur Form). A implementação está dividida em três partes: a criação do programa interpretador propriamente dito em Java, a criação de um executor das ações especificadas na linguagem e sua integração com o tipo de repositório considerado (gerados pela ferramenta DSTC dMOF). Um protótipo final foi desenvolvido e testado nos cenários previamente definidosThis work presents the specification and the implementation of a language of TransFormations in definite Models specification MOF (Meta Object Facility) of OMG (Object Management Group). The specification uses a boarding based on rules ECA (Event-Condition-Action) and was made on the basis of a set of scenes of use previously defined. The Parser Responsible parser for guaranteeing that the syntactic structure of the language is correct was constructed with the tool JavaCC (Java Compiler Compiler) and the description of the syntax of the language was made with EBNF (Extended Backus-Naur Form). The implementation is divided in three parts: the creation of the interpretative program properly said in Java, the creation of an executor of the actions specified in the language and its integration with the type of considered repository (generated for tool DSTC dMOF). A final prototype was developed and tested in the scenes previously define
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Especificação e implementação de uma linguagem para transFormação de modelos MOF em repositórios dMOF
Automação e Sistemas; Engenharia de Computação; Telecomunicações, 2006Co-Authors: Lins, Hertz Wilton De CastroAbstract:This work presents the specification and the implementation of a language of TransFormations in definite Models specification MOF (Meta Object Facility) of OMG (Object Management Group). The specification uses a boarding based on rules ECA (Event-Condition-Action) and was made on the basis of a set of scenes of use previously defined. The Parser Responsible parser for guaranteeing that the syntactic structure of the language is correct was constructed with the tool JavaCC (Java Compiler Compiler) and the description of the syntax of the language was made with EBNF (Extended Backus-Naur Form). The implementation is divided in three parts: the creation of the interpretative program properly said in Java, the creation of an executor of the actions specified in the language and its integration with the type of considered repository (generated for tool DSTC dMOF). A final prototype was developed and tested in the scenes previously definedCoordenação de Aperfeiçoamento de Pessoal de Nível SuperiorEste trabalho apresenta a especificação e a implementação de uma linguagem de TransFormações em Modelos definidos segundo a especificação MOF (Meta Object Facility) da OMG (Object Management Group). A especificação utiliza uma abordagem baseada em regras ECA (Event-Condition-Action) e foi feita com base em um conjunto de cenários de uso previamente definidos. O parser responsável por garantir que a estrutura sintática da linguagem está correta foi construído com a ferramenta JavaCC (Java Compiler Compiler) e a descrição da sintaxe da linguagem foi feita com EBNF (Extended Backus-Naur Form). A implementação está dividida em três partes: a criação do programa interpretador propriamente dito em Java, a criação de um executor das ações especificadas na linguagem e sua integração com o tipo de repositório considerado (gerados pela ferramenta DSTC dMOF). Um protótipo final foi desenvolvido e testado nos cenários previamente definido
Jeroen Fj Laros - One of the best experts on this subject based on the ideXlab platform.
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Open Access A Formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
2013Co-Authors: Jeroen Fj Laros, André Blavier, Peter Em Taschner, Johan Den T Dunnen, Ghent BelgiumAbstract:Background: The use of a standard human sequence variant nomenclature is advocated by the Human Genome Variation Society in order to unambiguously describe genetic variants in databases and literature. There is a clear need for tools that allow the mining of data about human sequence variants and their functional consequences from databases and literature. Existing text mining focuses on the recognition of protein variants and their effects. The recognition of variants at the DNA and RNA levels is essential for dissemination of variant data for diagnostic purposes. Development of new tools is hampered by the complexity of the current nomenclature, which requires processing at the character level to recognize the specific syntactic constructs used in variant descriptions. Results: We approached the gene variant nomenclature as a scientific sublanguage and created two Formal descriptions of the syntax in Extended Backus-Naur Form: one at the DNA-RNA level and one at the protein level. To ensure compatibility to older versions of the human sequence variant nomenclature, previously recommended variant description Formats have been included. The first grammar versions were designed to help build variant description handling in the Alamut mutation interpretation software. The DNA and RNA level descriptions were then updated and used to construct the context-free parser of the Mutalyzer 2 sequence variant nomenclature checker, which has already been used to check more than one million variant descriptions. Conclusions: The Extended Backus-Naur Form provided an overview of the full complexity of the syntax of the sequence variant nomenclature, which remained hidden in the textual Format and the division of the recommendations across the DNA, RNA and protein sections of the Human Genome Variation Society nomenclature websit
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A Formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
BMC Bioinformatics, 2011Co-Authors: Jeroen Fj Laros, André Blavier, Johan T Den Dunnen, Peter Em TaschnerAbstract:Background The use of a standard human sequence variant nomenclature is advocated by the Human Genome Variation Society in order to unambiguously describe genetic variants in databases and literature. There is a clear need for tools that allow the mining of data about human sequence variants and their functional consequences from databases and literature. Existing text mining focuses on the recognition of protein variants and their effects. The recognition of variants at the DNA and RNA levels is essential for dissemination of variant data for diagnostic purposes. Development of new tools is hampered by the complexity of the current nomenclature, which requires processing at the character level to recognize the specific syntactic constructs used in variant descriptions. Results We approached the gene variant nomenclature as a scientific sublanguage and created two Formal descriptions of the syntax in Extended Backus-Naur Form: one at the DNA-RNA level and one at the protein level. To ensure compatibility to older versions of the human sequence variant nomenclature, previously recommended variant description Formats have been included. The first grammar versions were designed to help build variant description handling in the Alamut mutation interpretation software. The DNA and RNA level descriptions were then updated and used to construct the context-free parser of the Mutalyzer 2 sequence variant nomenclature checker, which has already been used to check more than one million variant descriptions. Conclusions The Extended Backus-Naur Form provided an overview of the full complexity of the syntax of the sequence variant nomenclature, which remained hidden in the textual Format and the division of the recommendations across the DNA, RNA and protein sections of the Human Genome Variation Society nomenclature website ( http://www.hgvs.org/mutnomen/ ). This insight into the syntax of the nomenclature could be used to design detailed and clear rules for software development. The Mutalyzer 2 parser demonstrated that it facilitated decomposition of complex variant descriptions into their individual parts. The Extended Backus-Naur Form or parts of it can be used or modified by adding rules, allowing the development of specific sequence variant text mining tools and other programs, which can generate or handle sequence variant descriptions.
Ap Harrison - One of the best experts on this subject based on the ideXlab platform.
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Evolving Regular Expressions for GeneChip Probe PerFormance Prediction
2010Co-Authors: Wb Langdon, Ap HarrisonAbstract:simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI’s GEO database to indicated the quality of individual HG-U133A probes. Low concordance indicates a poor probe. Regular expressions can be data mined by a Backus-Naur Form (BNF) context-free grammar using strongly typed genetic programming written in gawk and using egrep. The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided.
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Automated DNA Motif Discovery
2010Co-Authors: Wb Langdon, Sanchez Graillet Olivia, Ap HarrisonAbstract:Langdon WB, Sanchez Graillet O, Harrison AP. Automated DNA Motif Discovery. arXiv:1002.0065. 2010.Ensembl’s human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur Form (BNF) grammar for regular expressions is used by genetic programming to ensure the generated strings are legal. The evolved motif suggests the presence of Thymine followed by one or more Adenines etc. early in transcripts indicate a non-protein coding gene
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Evolving DNA motifs to predict GeneChip probe perFormance
'Springer Science and Business Media LLC', 2009Co-Authors: Wb Langdon, Ap HarrisonAbstract:Background: Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe. Results: Regular expressions can be automatically created from a Backus-Naur Form (BNF) context-free grammar using strongly typed genetic programming. Conclusion: The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided. © 2009 Langdon and Harrison; licensee BioMed Central Ltd
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Creating Regular Expressions as mRNA Motifs with GP to Predict Human Exon Splitting
2009Co-Authors: Wb Langdon, J. Rowsell, Ap HarrisonAbstract:Low correlation between mRNA concentrations measured at different locations for the same exon show many current Ensembl exon definitions are incomplete. Automatically created patterns (e.g. TCTTT) in genic DNA sequences identify potential new alternative transcripts. Strongly typed grammar based genetic programming (GP) is used to evolve regular expressions (RE) to classify gene exons with potential alternative mRNA expression from those without. RNAnet gives us correlations between Affymetrix HG-U133 Plus 2 GeneChip probe measurements for the same exon across 2757 Homo Sapiens tissue samples from NCBI’s GEO database. We identify many non-atomic Ensembl exons. I.e. exons with substructure. Biological patterns can be data mined by a Backus-Naur Form (BNF) context-free grammar using a strongly typed GP written in gawk and using egrep. The automatically produced DNA motifs suggest that alternative polyadenylation is not responsible. (Short version in [19].) The training data is available on the internet
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Evolving regular expressions for genechip probe perFormance prediction
'Springer Science and Business Media LLC', 2008Co-Authors: Wb Langdon, Ap HarrisonAbstract:Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low concordance indicates a poor probe. Regular expressions can be data mined by a Backus-Naur Form (BNF) context-free grammar using strongly typed genetic programming written in gawk and using egrep. The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided. © 2008 Springer-Verlag Berlin Heidelberg
André Blavier - One of the best experts on this subject based on the ideXlab platform.
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Open Access A Formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
2013Co-Authors: Jeroen Fj Laros, André Blavier, Peter Em Taschner, Johan Den T Dunnen, Ghent BelgiumAbstract:Background: The use of a standard human sequence variant nomenclature is advocated by the Human Genome Variation Society in order to unambiguously describe genetic variants in databases and literature. There is a clear need for tools that allow the mining of data about human sequence variants and their functional consequences from databases and literature. Existing text mining focuses on the recognition of protein variants and their effects. The recognition of variants at the DNA and RNA levels is essential for dissemination of variant data for diagnostic purposes. Development of new tools is hampered by the complexity of the current nomenclature, which requires processing at the character level to recognize the specific syntactic constructs used in variant descriptions. Results: We approached the gene variant nomenclature as a scientific sublanguage and created two Formal descriptions of the syntax in Extended Backus-Naur Form: one at the DNA-RNA level and one at the protein level. To ensure compatibility to older versions of the human sequence variant nomenclature, previously recommended variant description Formats have been included. The first grammar versions were designed to help build variant description handling in the Alamut mutation interpretation software. The DNA and RNA level descriptions were then updated and used to construct the context-free parser of the Mutalyzer 2 sequence variant nomenclature checker, which has already been used to check more than one million variant descriptions. Conclusions: The Extended Backus-Naur Form provided an overview of the full complexity of the syntax of the sequence variant nomenclature, which remained hidden in the textual Format and the division of the recommendations across the DNA, RNA and protein sections of the Human Genome Variation Society nomenclature websit
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A Formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
BMC Bioinformatics, 2011Co-Authors: Jeroen Fj Laros, André Blavier, Johan T Den Dunnen, Peter Em TaschnerAbstract:Background The use of a standard human sequence variant nomenclature is advocated by the Human Genome Variation Society in order to unambiguously describe genetic variants in databases and literature. There is a clear need for tools that allow the mining of data about human sequence variants and their functional consequences from databases and literature. Existing text mining focuses on the recognition of protein variants and their effects. The recognition of variants at the DNA and RNA levels is essential for dissemination of variant data for diagnostic purposes. Development of new tools is hampered by the complexity of the current nomenclature, which requires processing at the character level to recognize the specific syntactic constructs used in variant descriptions. Results We approached the gene variant nomenclature as a scientific sublanguage and created two Formal descriptions of the syntax in Extended Backus-Naur Form: one at the DNA-RNA level and one at the protein level. To ensure compatibility to older versions of the human sequence variant nomenclature, previously recommended variant description Formats have been included. The first grammar versions were designed to help build variant description handling in the Alamut mutation interpretation software. The DNA and RNA level descriptions were then updated and used to construct the context-free parser of the Mutalyzer 2 sequence variant nomenclature checker, which has already been used to check more than one million variant descriptions. Conclusions The Extended Backus-Naur Form provided an overview of the full complexity of the syntax of the sequence variant nomenclature, which remained hidden in the textual Format and the division of the recommendations across the DNA, RNA and protein sections of the Human Genome Variation Society nomenclature website ( http://www.hgvs.org/mutnomen/ ). This insight into the syntax of the nomenclature could be used to design detailed and clear rules for software development. The Mutalyzer 2 parser demonstrated that it facilitated decomposition of complex variant descriptions into their individual parts. The Extended Backus-Naur Form or parts of it can be used or modified by adding rules, allowing the development of specific sequence variant text mining tools and other programs, which can generate or handle sequence variant descriptions.
