Eintrag weiter verarbeiten
Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape
Gespeichert in:
| Zeitschriftentitel: | Bioinformatics |
|---|---|
| Personen und Körperschaften: | , , , , |
| In: | Bioinformatics, 26, 2010, 21, S. 2796-2797 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
|
| Schlagwörter: |
| author_facet |
Pentchev, Konstantin Ono, Keiichiro Herwig, Ralf Ideker, Trey Kamburov, Atanas Pentchev, Konstantin Ono, Keiichiro Herwig, Ralf Ideker, Trey Kamburov, Atanas |
|---|---|
| author |
Pentchev, Konstantin Ono, Keiichiro Herwig, Ralf Ideker, Trey Kamburov, Atanas |
| spellingShingle |
Pentchev, Konstantin Ono, Keiichiro Herwig, Ralf Ideker, Trey Kamburov, Atanas Bioinformatics Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| author_sort |
pentchev, konstantin |
| spelling |
Pentchev, Konstantin Ono, Keiichiro Herwig, Ralf Ideker, Trey Kamburov, Atanas 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btq522 <jats:title>Abstract</jats:title> <jats:p>Summary: Protein–protein interaction detection methods are applied on a daily basis by molecular biologists worldwide. After generating a set of potential interactions, biologists face the problem of highlighting the ones that are novel and collecting evidence with respect to literature and annotation. This task can be as tedious as searching for every predicted interaction in several interaction data repositories, or manually screening the scientific literature. To facilitate the task of evidence mining and novelty assessment of protein–protein interactions, we have developed a Cytoscape plugin that automatically mines publication references, database references, interaction detection method descriptions and pathway annotation for a user-supplied network of interactions. The basis for the annotation is ConsensusPathDB—a meta-database that integrates numerous protein–protein, signaling, metabolic and gene regulatory interaction repositories for currently three species: Homo sapiens, Saccharomyces cerevisiae and Mus musculus.</jats:p> <jats:p>Availability: The ConsensusPathDB plugin for Cytoscape (version 2.7.0 or later) can be installed within Cytoscape on a major operating system (Windows, Mac OS, Unix/Linux) with Sun Java 1.5 or later installed through Cytoscape's Plugin manager (category ‘Network and Attribute I/O’). The plugin is freely available for download on the ConsensusPathDB web site (http://cpdb.molgen.mpg.de).</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> <jats:p>Contact: kamburov@molgen.mpg.de</jats:p> Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape Bioinformatics |
| doi_str_mv |
10.1093/bioinformatics/btq522 |
| facet_avail |
Online Free |
| finc_class_facet |
Biologie Chemie und Pharmazie Mathematik Informatik |
| format |
ElectronicArticle |
| fullrecord |
blob:ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9iaW9pbmZvcm1hdGljcy9idHE1MjI |
| id |
ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9iaW9pbmZvcm1hdGljcy9idHE1MjI |
| institution |
DE-L229 DE-D275 DE-Bn3 DE-Brt1 DE-Zwi2 DE-D161 DE-Gla1 DE-Zi4 DE-15 DE-Pl11 DE-Rs1 DE-105 DE-14 DE-Ch1 |
| imprint |
Oxford University Press (OUP), 2010 |
| imprint_str_mv |
Oxford University Press (OUP), 2010 |
| issn |
1367-4811 1367-4803 |
| issn_str_mv |
1367-4811 1367-4803 |
| language |
English |
| mega_collection |
Oxford University Press (OUP) (CrossRef) |
| match_str |
pentchev2010evidenceminingandnoveltyassessmentofproteinproteininteractionswiththeconsensuspathdbpluginforcytoscape |
| publishDateSort |
2010 |
| publisher |
Oxford University Press (OUP) |
| recordtype |
ai |
| record_format |
ai |
| series |
Bioinformatics |
| source_id |
49 |
| title |
Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_unstemmed |
Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_full |
Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_fullStr |
Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_full_unstemmed |
Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_short |
Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_sort |
evidence mining and novelty assessment of protein–protein interactions with the consensuspathdb plugin for cytoscape |
| topic |
Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| url |
http://dx.doi.org/10.1093/bioinformatics/btq522 |
| publishDate |
2010 |
| physical |
2796-2797 |
| description |
<jats:title>Abstract</jats:title>
<jats:p>Summary: Protein–protein interaction detection methods are applied on a daily basis by molecular biologists worldwide. After generating a set of potential interactions, biologists face the problem of highlighting the ones that are novel and collecting evidence with respect to literature and annotation. This task can be as tedious as searching for every predicted interaction in several interaction data repositories, or manually screening the scientific literature. To facilitate the task of evidence mining and novelty assessment of protein–protein interactions, we have developed a Cytoscape plugin that automatically mines publication references, database references, interaction detection method descriptions and pathway annotation for a user-supplied network of interactions. The basis for the annotation is ConsensusPathDB—a meta-database that integrates numerous protein–protein, signaling, metabolic and gene regulatory interaction repositories for currently three species: Homo sapiens, Saccharomyces cerevisiae and Mus musculus.</jats:p>
<jats:p>Availability: The ConsensusPathDB plugin for Cytoscape (version 2.7.0 or later) can be installed within Cytoscape on a major operating system (Windows, Mac OS, Unix/Linux) with Sun Java 1.5 or later installed through Cytoscape's Plugin manager (category ‘Network and Attribute I/O’). The plugin is freely available for download on the ConsensusPathDB web site (http://cpdb.molgen.mpg.de).</jats:p>
<jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p>
<jats:p>Contact: kamburov@molgen.mpg.de</jats:p> |
| container_issue |
21 |
| container_start_page |
2796 |
| container_title |
Bioinformatics |
| container_volume |
26 |
| format_de105 |
Article, E-Article |
| format_de14 |
Article, E-Article |
| format_de15 |
Article, E-Article |
| format_de520 |
Article, E-Article |
| format_de540 |
Article, E-Article |
| format_dech1 |
Article, E-Article |
| format_ded117 |
Article, E-Article |
| format_degla1 |
E-Article |
| format_del152 |
Buch |
| format_del189 |
Article, E-Article |
| format_dezi4 |
Article |
| format_dezwi2 |
Article, E-Article |
| format_finc |
Article, E-Article |
| format_nrw |
Article, E-Article |
| _version_ |
1792340973848625158 |
| geogr_code |
not assigned |
| last_indexed |
2024-03-01T16:11:48.599Z |
| geogr_code_person |
not assigned |
| openURL |
url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fvufind.svn.sourceforge.net%3Agenerator&rft.title=Evidence+mining+and+novelty+assessment+of+protein%E2%80%93protein+interactions+with+the+ConsensusPathDB+plugin+for+Cytoscape&rft.date=2010-11-01&genre=article&issn=1367-4803&volume=26&issue=21&spage=2796&epage=2797&pages=2796-2797&jtitle=Bioinformatics&atitle=Evidence+mining+and+novelty+assessment+of+protein%E2%80%93protein+interactions+with+the+ConsensusPathDB+plugin+for+Cytoscape&aulast=Kamburov&aufirst=Atanas&rft_id=info%3Adoi%2F10.1093%2Fbioinformatics%2Fbtq522&rft.language%5B0%5D=eng |
| SOLR | |
| _version_ | 1792340973848625158 |
| author | Pentchev, Konstantin, Ono, Keiichiro, Herwig, Ralf, Ideker, Trey, Kamburov, Atanas |
| author_facet | Pentchev, Konstantin, Ono, Keiichiro, Herwig, Ralf, Ideker, Trey, Kamburov, Atanas, Pentchev, Konstantin, Ono, Keiichiro, Herwig, Ralf, Ideker, Trey, Kamburov, Atanas |
| author_sort | pentchev, konstantin |
| container_issue | 21 |
| container_start_page | 2796 |
| container_title | Bioinformatics |
| container_volume | 26 |
| description | <jats:title>Abstract</jats:title> <jats:p>Summary: Protein–protein interaction detection methods are applied on a daily basis by molecular biologists worldwide. After generating a set of potential interactions, biologists face the problem of highlighting the ones that are novel and collecting evidence with respect to literature and annotation. This task can be as tedious as searching for every predicted interaction in several interaction data repositories, or manually screening the scientific literature. To facilitate the task of evidence mining and novelty assessment of protein–protein interactions, we have developed a Cytoscape plugin that automatically mines publication references, database references, interaction detection method descriptions and pathway annotation for a user-supplied network of interactions. The basis for the annotation is ConsensusPathDB—a meta-database that integrates numerous protein–protein, signaling, metabolic and gene regulatory interaction repositories for currently three species: Homo sapiens, Saccharomyces cerevisiae and Mus musculus.</jats:p> <jats:p>Availability: The ConsensusPathDB plugin for Cytoscape (version 2.7.0 or later) can be installed within Cytoscape on a major operating system (Windows, Mac OS, Unix/Linux) with Sun Java 1.5 or later installed through Cytoscape's Plugin manager (category ‘Network and Attribute I/O’). The plugin is freely available for download on the ConsensusPathDB web site (http://cpdb.molgen.mpg.de).</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> <jats:p>Contact: kamburov@molgen.mpg.de</jats:p> |
| doi_str_mv | 10.1093/bioinformatics/btq522 |
| facet_avail | Online, Free |
| finc_class_facet | Biologie, Chemie und Pharmazie, Mathematik, Informatik |
| format | ElectronicArticle |
| format_de105 | Article, E-Article |
| format_de14 | Article, E-Article |
| format_de15 | Article, E-Article |
| format_de520 | Article, E-Article |
| format_de540 | Article, E-Article |
| format_dech1 | Article, E-Article |
| format_ded117 | Article, E-Article |
| format_degla1 | E-Article |
| format_del152 | Buch |
| format_del189 | Article, E-Article |
| format_dezi4 | Article |
| format_dezwi2 | Article, E-Article |
| format_finc | Article, E-Article |
| format_nrw | Article, E-Article |
| geogr_code | not assigned |
| geogr_code_person | not assigned |
| id | ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9iaW9pbmZvcm1hdGljcy9idHE1MjI |
| imprint | Oxford University Press (OUP), 2010 |
| imprint_str_mv | Oxford University Press (OUP), 2010 |
| institution | DE-L229, DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1 |
| issn | 1367-4811, 1367-4803 |
| issn_str_mv | 1367-4811, 1367-4803 |
| language | English |
| last_indexed | 2024-03-01T16:11:48.599Z |
| match_str | pentchev2010evidenceminingandnoveltyassessmentofproteinproteininteractionswiththeconsensuspathdbpluginforcytoscape |
| mega_collection | Oxford University Press (OUP) (CrossRef) |
| physical | 2796-2797 |
| publishDate | 2010 |
| publishDateSort | 2010 |
| publisher | Oxford University Press (OUP) |
| record_format | ai |
| recordtype | ai |
| series | Bioinformatics |
| source_id | 49 |
| spelling | Pentchev, Konstantin Ono, Keiichiro Herwig, Ralf Ideker, Trey Kamburov, Atanas 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btq522 <jats:title>Abstract</jats:title> <jats:p>Summary: Protein–protein interaction detection methods are applied on a daily basis by molecular biologists worldwide. After generating a set of potential interactions, biologists face the problem of highlighting the ones that are novel and collecting evidence with respect to literature and annotation. This task can be as tedious as searching for every predicted interaction in several interaction data repositories, or manually screening the scientific literature. To facilitate the task of evidence mining and novelty assessment of protein–protein interactions, we have developed a Cytoscape plugin that automatically mines publication references, database references, interaction detection method descriptions and pathway annotation for a user-supplied network of interactions. The basis for the annotation is ConsensusPathDB—a meta-database that integrates numerous protein–protein, signaling, metabolic and gene regulatory interaction repositories for currently three species: Homo sapiens, Saccharomyces cerevisiae and Mus musculus.</jats:p> <jats:p>Availability: The ConsensusPathDB plugin for Cytoscape (version 2.7.0 or later) can be installed within Cytoscape on a major operating system (Windows, Mac OS, Unix/Linux) with Sun Java 1.5 or later installed through Cytoscape's Plugin manager (category ‘Network and Attribute I/O’). The plugin is freely available for download on the ConsensusPathDB web site (http://cpdb.molgen.mpg.de).</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> <jats:p>Contact: kamburov@molgen.mpg.de</jats:p> Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape Bioinformatics |
| spellingShingle | Pentchev, Konstantin, Ono, Keiichiro, Herwig, Ralf, Ideker, Trey, Kamburov, Atanas, Bioinformatics, Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| title | Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_full | Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_fullStr | Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_full_unstemmed | Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_short | Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| title_sort | evidence mining and novelty assessment of protein–protein interactions with the consensuspathdb plugin for cytoscape |
| title_unstemmed | Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape |
| topic | Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| url | http://dx.doi.org/10.1093/bioinformatics/btq522 |