Calling on a million minds for community annotation in WikiProteins (2008)
Mons, Barend, Ashburner, Michael, Chichester, Christine, Van Mulligen, Erik, Weeber, Marc, Den Dunnen, Johan, ...
Abstract WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data...
Reactome - a knowledgebase of human biological pathways (2007)
Peter D'Eustachio, David Croft, Bernard De Bono, Gopal Gopinath, Marc Gillespie, Bijay Jassal, ...
Pathway curation is a powerful tool for systematically associating gene products with functions. Reactome (www.reactome.org) is a manually curated human pathway knowledgebase describing a wide range...
Reactome: a knowledge base of biologic pathways and processes (2007)
Vastrik, Imre, D'Eustachio, Peter, Schmidt, Esther, Joshi-Tope, Geeta, Gopinath, Gopal, Croft, David, ...
Abstract Reactome http://www.reactome.org , an online curated resource for human pathway data, provides infrastructure for computation across the biologic reaction network. We use Reactome to infer...
Reactome: An integrated expert model of human molecular processes and access toolkit (2007)
De Bono, Bernard, Vastrik, Imre, D´Eustachio, Peter, Schmidt, Esther, Gopinath, Gopal, Croft, David, ...
The behaviour of pervasive molecular processes in human biology can be studied through the large-scale modeling of the molecular events that define them. Constructing detailed models of such extent...
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes (2006)
Mark Yandell, Chris J. Mungall, Chris Smith, Simon Prochnik, Joshua Kaminker, George Hartzell, ...
We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences...
An Evaluation of Ontology Exchange Languages for Bioinformatics (2000)
Robin Mcentire, Peter Karp, Neil Abernethy, David Benton, Gregg Helt, Matt Dejongh, ...
Ontologies are specifications of the concepts in a given field, and of the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those...
Kopczynski, Casey C., Noordermeer, Jasprina N., Serano, Thomas L., Chen, Wei-Yu, Pendleton, John D., Lewis, Suzanna, ...
Secreted and transmembrane proteins play an essential role in intercellular communication during the development of multicellular organisms. Because only a small number of these genes have been...
The Generic Genome Browser: A Building Block for a Model Organism System Database
Stein, Lincoln D., Mungall, Christopher, Shu, ShengQiang, Caudy, Michael, Mangone, Marco, Day, Allen, ...
The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser...
BioViews: Java-Based Tools for Genomic Data Visualization
Helt, Gregg A., Lewis, Suzanna, Loraine, Ann E., Rubin, Gerald M.
Visualization tools for bioinformatics ideally should provide universal access to the most current data in an interactive and intuitive graphical user interface. Since the introduction of Java, a...
Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster
Mi, Huaiyu, Vandergriff, Jody, Campbell, Michael, Narechania, Apurva, Majoros, William, Lewis, Suzanna, ...
The functional classification of genes on a genome-wide scale is now in its infancy, and we make a first attempt to assess existing methods and identify sources of error. To this end, we compared two...
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes
Yandell, Mark, Mungall, Chris J, Smith, Chris, Prochnik, Simon, Kaminker, Joshua, Hartzell, George, ...
We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences...
Kopczynski, Casey C., Noordermeer, Jasprina N., Serano, Thomas L., Chen, Wei-Yu, Pendleton, John D., Lewis, Suzanna, ...
Secreted and transmembrane proteins play an essential role in intercellular communication during the development of multicellular organisms. Because only a small number of these genes have been...
The Generic Genome Browser: A Building Block for a Model Organism System Database
Stein, Lincoln D., Mungall, Christopher, Shu, ShengQiang, Caudy, Michael, Mangone, Marco, Day, Allen, ...
The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser...
BioViews: Java-Based Tools for Genomic Data Visualization
Helt, Gregg A., Lewis, Suzanna, Loraine, Ann E., Rubin, Gerald M.
Visualization tools for bioinformatics ideally should provide universal access to the most current data in an interactive and intuitive graphical user interface. Since the introduction of Java, a...
Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster
Mi, Huaiyu, Vandergriff, Jody, Campbell, Michael, Narechania, Apurva, Majoros, William, Lewis, Suzanna, ...
The functional classification of genes on a genome-wide scale is now in its infancy, and we make a first attempt to assess existing methods and identify sources of error. To this end, we compared two...
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes
Yandell, Mark, Mungall, Chris J, Smith, Chris, Prochnik, Simon, Kaminker, Joshua, Hartzell, George, ...
We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences...
Reactome: a knowledge base of biologic pathways and processes
Vastrik, Imre, D'Eustachio, Peter, Schmidt, Esther, Joshi-Tope, Geeta, Gopinath, Gopal, Croft, David, ...
Reactome, an online curated resource for human pathway data, can be used to infer equivalent reactions in non-human species and as a tool to aid in the interpretation of microarrays and other...
Calling on a million minds for community annotation in WikiProteins
Mons, Barend, Ashburner, Michael, Chichester, Christine, Van Mulligen, Erik, Weeber, Marc, Den Dunnen, Johan, ...
WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from...