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The Molecule Pages database.

Saunders B, Lyon S, Day M, Riley B, Chenette E, Subramaniam S, Vadivelu I - Nucleic Acids Res. (2007)

Bottom Line: The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function.The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer.The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

View Article: PubMed Central - PubMed

Affiliation: San Diego Supercomputer Center San Diego, La Jolla, CA 92093, Nature Publishing Group, 25 First Street, Cambridge, MA 02141, USA.

ABSTRACT
The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

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Example function for Adenylyl cyclase type 5 (A000001).
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Figure 3: Example function for Adenylyl cyclase type 5 (A000001).

Mentions: To illustrate the depth of the author-entered data, we choose Adenylyl cyclase type 5 (SGMP ID A000001). Because this is a published Molecule Page, the user first arrives at the ‘Abstract’ section, which gives information on the author (Carmen W. Dessauer), gives a summary of the role of Adenylyl cyclase type 5, lists the names and synonyms provided by the author and the editors, indicates that A000001 molecule has 32 enzyme functions, exists in 33 states, has 96 transitions between these states, and shows a miniature version of the network map of these transitions. The ‘Full Text’ section contains a textual description—with published references—of protein function, regulation, interactions, subcellular localization, expression, phenotypes, splice variants and antibodies. The ‘States’ section lists each defined functional state, with links to a constituent list and a transition graph (if applicable) to indicate all the transitions that lead to the state. A protein state is defined by the principal proteins interactions with other protein partners, covalent modifications on all protein components, association with small molecule ligands and cellular location. The ‘Transitions’ section shows a list of the defined transitions, with a link to detailed information on each transition—with initial and final state information, the change that occurred in the transition, process information, other comments and citations (Figure 1). A transition is defined as a biological process that causes the conversion of a protein from one state to another. The ‘Network Map’ gives a graphical representation of all the states, and the transitions between them, defined by the author for A000001 (Figure 2). The ‘Functions’ section shows that A000001 acts as an enzyme, catalyzing the conversion of Mg-ATP to cyclic AMP and pyrophosphate. Each state that catalyzes the reaction is listed, with a link to the detailed state information, and a link to detailed function information with reaction information, comments and citations (Figure 3). The ‘Protein Classes’ section shows classes defined by the author to aid in data entry and display—a class is defined as a group of three or more proteins that behave identically in a particular state.Figure 1.


The Molecule Pages database.

Saunders B, Lyon S, Day M, Riley B, Chenette E, Subramaniam S, Vadivelu I - Nucleic Acids Res. (2007)

Example function for Adenylyl cyclase type 5 (A000001).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238911&req=5

Figure 3: Example function for Adenylyl cyclase type 5 (A000001).
Mentions: To illustrate the depth of the author-entered data, we choose Adenylyl cyclase type 5 (SGMP ID A000001). Because this is a published Molecule Page, the user first arrives at the ‘Abstract’ section, which gives information on the author (Carmen W. Dessauer), gives a summary of the role of Adenylyl cyclase type 5, lists the names and synonyms provided by the author and the editors, indicates that A000001 molecule has 32 enzyme functions, exists in 33 states, has 96 transitions between these states, and shows a miniature version of the network map of these transitions. The ‘Full Text’ section contains a textual description—with published references—of protein function, regulation, interactions, subcellular localization, expression, phenotypes, splice variants and antibodies. The ‘States’ section lists each defined functional state, with links to a constituent list and a transition graph (if applicable) to indicate all the transitions that lead to the state. A protein state is defined by the principal proteins interactions with other protein partners, covalent modifications on all protein components, association with small molecule ligands and cellular location. The ‘Transitions’ section shows a list of the defined transitions, with a link to detailed information on each transition—with initial and final state information, the change that occurred in the transition, process information, other comments and citations (Figure 1). A transition is defined as a biological process that causes the conversion of a protein from one state to another. The ‘Network Map’ gives a graphical representation of all the states, and the transitions between them, defined by the author for A000001 (Figure 2). The ‘Functions’ section shows that A000001 acts as an enzyme, catalyzing the conversion of Mg-ATP to cyclic AMP and pyrophosphate. Each state that catalyzes the reaction is listed, with a link to the detailed state information, and a link to detailed function information with reaction information, comments and citations (Figure 3). The ‘Protein Classes’ section shows classes defined by the author to aid in data entry and display—a class is defined as a group of three or more proteins that behave identically in a particular state.Figure 1.

Bottom Line: The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function.The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer.The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

View Article: PubMed Central - PubMed

Affiliation: San Diego Supercomputer Center San Diego, La Jolla, CA 92093, Nature Publishing Group, 25 First Street, Cambridge, MA 02141, USA.

ABSTRACT
The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

Show MeSH