GeneNet - Revision history

Lan@dote.ru: +Category:Software

2013-06-19T09:38:40Z

+Category:Software

Lan@dote.ru: +Category:BioUML history

2013-06-14T04:36:29Z

+Category:BioUML history

Lan@dote.ru: /* User interface */

2013-06-03T09:58:53Z

‎User interface

Lan@dote.ru at 09:54, 3 June 2013

2013-06-03T09:54:27Z

Lan@dote.ru: Links rectified

2013-06-03T09:52:14Z

Links rectified

Lan@dote.ru: TRRD linked /* Formalized description */

2013-06-03T09:15:37Z

TRRD linked - ‎Formalized description

Stan.lo@dote.ru: info added from BGRS2000 article

2013-05-31T08:19:17Z

info added from BGRS2000 article

Stan.lo@dote.ru: /* User interface */

2013-05-30T11:46:40Z

‎User interface

Stan.lo@dote.ru: /* User interface */

2013-05-30T11:46:01Z

‎User interface

Stan.lo@dote.ru: /* User interface */

2013-05-30T11:42:31Z

‎User interface

← Older revision		Revision as of 09:38, 19 June 2013
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	[[Category:BioUML history]]		[[Category:BioUML history]]
		+	[[Category:Software]]

← Older revision		Revision as of 04:36, 14 June 2013
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	*[http://bioinformatics.oxfordjournals.org/content/15/7/713.full.pdf KOLPAKOV F.A.,ANANKO E.A. ''Interactive Data Input into the GeneNet Database''.Bioinformatics Oxford Journal, Volume 15, Issue 7, 1999]		*[http://bioinformatics.oxfordjournals.org/content/15/7/713.full.pdf KOLPAKOV F.A.,ANANKO E.A. ''Interactive Data Input into the GeneNet Database''.Bioinformatics Oxford Journal, Volume 15, Issue 7, 1999]
	* [http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/2000/bgrs2000_1_049.pdf Ananko E.A., Kolpakov F.A., Kolchanov N.A. ''GeneNet DATABASE: A TECHNOLOGY FOR A FORMALIZED DESCRIPTION OF GENE NETWORKS.'' BGRS thesis, 2000]		* [http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/2000/bgrs2000_1_049.pdf Ananko E.A., Kolpakov F.A., Kolchanov N.A. ''GeneNet DATABASE: A TECHNOLOGY FOR A FORMALIZED DESCRIPTION OF GENE NETWORKS.'' BGRS thesis, 2000]
		+
		+	[[Category:BioUML history]]

@@ Line 76: / Line 76: @@
 # references explaining the type of information described in the field;
 # cross-references within the GeneNet database; and
-# the references to other databases ([[EMBL]], [[SWISS-PROT]], [[TRRD]], {{TRANSFAC}}, and {{EPD}}).
+# the references to other databases ([[EMBL]], [http://www.uniprot.org/ SWISS-PROT], [[TRRD]], {{TRANSFAC}}, and {{EPD}}).
 The system enables coordinated work for several experts on shared data - at any moment only one expert can edit an entry. It also enables informing experts about any changes in  their data automatically by email.

@@ Line 76: / Line 76: @@
 # references explaining the type of information described in the field;
 # cross-references within the GeneNet database; and
-# the references to other databases ([[EMBL]], [[SWISS-PROT]], [[TRRD]], {{TRANSFAC}}, and [http://epd.vital-it.ch/ EPD]).
+# the references to other databases ([[EMBL]], [[SWISS-PROT]], [[TRRD]], {{TRANSFAC}}, and {{EPD}}).
 The system enables coordinated work for several experts on shared data - at any moment only one expert can edit an entry. It also enables informing experts about any changes in  their data automatically by email.

@@ Line 76: / Line 76: @@
 # references explaining the type of information described in the field;
 # cross-references within the GeneNet database; and
-# the references to other databases ([[EMBL]], [[SWISS-PROT]], <span class="plainlinks">[http://wiki.biouml.org/index.php/TRRD_viewer TRRD]</span>, [http://en.wikipedia.org/wiki/TRANSFAC TRANSFAC], and [http://epd.vital-it.ch/ EPD]).
+# the references to other databases ([[EMBL]], [[SWISS-PROT]], [[TRRD]], {{TRANSFAC}}, and [http://epd.vital-it.ch/ EPD]).
 The system enables coordinated work for several experts on shared data - at any moment only one expert can edit an entry. It also enables informing experts about any changes in  their data automatically by email.

@@ Line 31: / Line 31: @@
 * regulatory event, that is, the effect of an entity on a certain reaction.
-Each class of gene network components is described in its own format in a separate table. The table CELL contains the information on the cell types and lineages. Tissues and organs are also described in this table. The table GENE includes the data on the genes and their regulatory features based on the information from the TRRD. The data on proteins and protein complexes are collected in the table PROTEIN; on nonprotein regulatory substances and metabolites, in the table SUBSTANCE; on the physiological processes and the organismic state during the gene network functioning, in the table STATE. Relations between the gene network components are described in the separate table RELATION. The database is supplemented with two additional tables: SCHEME, which contains the description of the gene network graphs, and LITER with references to the original papers.
+Each class of gene network components is described in its own format in a separate table. The table CELL contains the information on the cell types and lineages. Tissues and organs are also described in this table. The table GENE includes the data on the genes and their regulatory features based on the information from the [[TRRD]]. The data on proteins and protein complexes are collected in the table PROTEIN; on nonprotein regulatory substances and metabolites, in the table SUBSTANCE; on the physiological processes and the organismic state during the gene network functioning, in the table STATE. Relations between the gene network components are described in the separate table RELATION. The database is supplemented with two additional tables: SCHEME, which contains the description of the gene network graphs, and LITER with references to the original papers.
 The formalized description of elementary events is based on application of several informative line codes.
@@ Line 63: / Line 63: @@
 </pre>
 Similarly, any other elementary event may be described in the terms of GeneNet, for instance, mRNA translation, enzyme catalysis, multimerization, etc.
-−
 ==User interface==

@@ Line 1: / Line 1: @@
-{{draft}}
-The object-oriented database GeneNet was developed for accumulating information regarding regulation of gene expression, signal transduction pathways, peculiarities of gene networks organization and mechanisms of their functioning.
+The object-oriented database GeneNet was developed for accumulating information regarding regulation of gene expression, signal transduction pathways, peculiarities of [http://en.wikipedia.org/wiki/Gene_network gene networks] organization and mechanisms of their functioning.
 The GeneNet is a part of [[GeneExpress]], an intellectual system for analysis of genomic regulatory sequences, developed at the [http://www.bionet.nsc.ru/en/ Institute of Cytology and Genetics], [http://www.nsc.ru/en/ Siberian Branch of the Russian Academy of Sciences].
 The GeneNet system is bipartite and includes: (1) a database containing information on gene networks and (2) a Java program for automated construction of the gene network diagrams based on their formalized description in the database.
+[[File:GNdescribed_networks.png|thumb|Informational content of GeneNet database (April,1, 2000)]]
 The GeneNet Java GUI (GeneNet Viewer) provides automated generation of gene network diagrams and allows for visualization and exploration of the database via the Internet. To ensure rapid data accumulation in the database, the interface was supplemented with tools for data input by independent experts having remote access to it.
 The work was supported by the State Science and Technology Program "The Human Genome" of the Russian State Committee for Science and Technology, the Russian Foundation for Basic Research (grants 96-04-50006, 97-04-49740, 97-07-90309, 98-04-49479, 99-07-90203), and Integration Program of the Siberian Branch of the Russian Academy of Sciences.
@@ Line 13: / Line 15: @@
 [[File:GN_DBstructure.png|thumb|Structure of the GeneNet database with references to other databases.]]
 Experimental data from original papers are formalized and collected in the GeneNet database. Using the object-oriented approach, the following components are distinguished in the description of the gene network:
-entities (any material objects),
+* entities (any material objects),
-relations between the entities, and processes occurring in them (for example, viral infection, anemia, etc.).
+* relations between the entities, and processes occurring in them (for example, viral infection, anemia, etc.).
 Four classes of entities are distinguished:
@@ Line 28: / Line 32: @@
 Each class of gene network components is described in its own format in a separate table. The table CELL contains the information on the cell types and lineages. Tissues and organs are also described in this table. The table GENE includes the data on the genes and their regulatory features based on the information from the TRRD. The data on proteins and protein complexes are collected in the table PROTEIN; on nonprotein regulatory substances and metabolites, in the table SUBSTANCE; on the physiological processes and the organismic state during the gene network functioning, in the table STATE. Relations between the gene network components are described in the separate table RELATION. The database is supplemented with two additional tables: SCHEME, which contains the description of the gene network graphs, and LITER with references to the original papers.
 ==User interface==
 [[File:GNDiagram_construction.png|thumb|Example of automated construction of the diagram representing the gene network of the antiviral response at the cell level]]
 The GeneNet Viewer, which is a Java applet, includes means for automated generation of the gene network diagram and a system of filters as well as means for data navigation including interactive images on diagrams, on-line help, interactive cross-references within the GeneNet database and references to other databases.
 All images on diagrams are interactive, i.e. if the user clicks on an image, the textual description of the corresponding entry in the GeneNet database is displayed in a special text window under the diagram. Double clicking on a gene image starts the [[TRRD viewer]], developed using [[Molecular Genetics Library]], and the regulatory map of the gene is visualized.
-The text window contains a formatted text with hypertext references of three types: (1) references explaining the type of information described in the field; (2) cross-references within the GeneNet database; and (3) the references to other databases (EMBL, SWISS-PROT, TRRD, TRANSFAC, and EPD).
+The text window contains a formatted text with hypertext references of three types:
 The system enables coordinated work for several experts on shared data - at any moment only one expert can edit an entry. It also enables informing experts about any changes in  their data automatically by email.

@@ Line 30: / Line 30: @@
 ==User interface==
-[[File:GN_Diagram_construction|thumb|Example of automated construction of the diagram representing the gene network of the antiviral response at the cell level]]
+[[File:GNDiagram_construction|thumb|Example of automated construction of the diagram representing the gene network of the antiviral response at the cell level]]
 The GeneNet Viewer, which is a Java applet, includes means for automated generation of the gene network diagram and a system of filters as well as means for data navigation including interactive images on diagrams, on-line help, interactive cross-references within the GeneNet database and references to other databases.