Databases - Revision history

Ivan@dote.ru at 04:13, 2 July 2013

2013-07-02T04:13:28Z

Lan@dote.ru: /* See also */

2013-06-26T08:27:10Z

‎See also

Stan.lo@dote.ru at 05:38, 26 June 2013

2013-06-26T05:38:13Z

Stan.lo@dote.ru: /* Interface */

2013-06-24T07:09:24Z

‎Interface

Stan.lo@dote.ru at 05:31, 24 June 2013

2013-06-24T05:31:47Z

Stan.lo@dote.ru: /* See also */

2013-06-24T05:02:52Z

‎See also

Stan.lo@dote.ru: /* See also */

2013-06-24T04:48:38Z

‎See also

Stan.lo@dote.ru: from the workbench help

2013-06-21T11:20:58Z

from the workbench help

Stan.lo@dote.ru: from the workbench help and GX manual

2013-06-21T09:43:24Z

from the workbench help and GX manual

New page

{{draft}}

Close integration with biological databases containing experimental data is a distinctive feature of BioUML, which is essential for accurate and convenient modeling of biological systems.
For the purpose of working with different kinds of data the database type concept has been introduced. The database type defines:
* data types (gene, protein, RNA, substance, reaction, etc.) that are stored in the database;
* mapping of the database content into diagram elements and diagram types that can be used with the database;
* diagram types that can be used to present the database content as a set of diagrams;
* the query engine to find interacting components of the system; search results can be shown as a graph and edited by the user.

According to their content (data type) biological databases can be divided into several groups as follows (one database can provide several types of data):

{|class="wikitable"
| ||colspan="5" align="center"| '''Data type'''
|-
| ||pathways||gene/protein classification||genome||pathways simulation||transcription factor
|-
|Apoptosis model|| || || || + ||
|-
|[[Biomodels]]|| || || || + ||
|-
|[[Biopath]]|| || || || + ||
|-
|[http://www.ensembl.org/ Ensemble]|| || || + || ||
|-
|[http://www.ncbi.nlm.nih.gov/pubmed/15016385 Geneways]|| + || || || ||
|-
|[http://www.geneontology.org/ GO]|| || + || || ||
|-
|[http://www.biouml.net/vc/gtrd.shtml GTRD]|| || + || || || +
|-
|[http://humancyc.org/ HumanCyc]|| + || + || || ||
|-
|[http://www.genome.jp/kegg/ KEGG]|| || || || + ||
|-
|[http://www.biobase-international.com/product/proteome Proteome (Biobase)]|| || + || || ||
|-
|[http://www.reactome.org/ReactomeGWT/entrypoint.html Reactome]|| + || + || || ||
|-
|[http://www.biobase-international.com/product/transcription-factor-binding-sites Transfac (Biobase)]|| || || || || +
|-
|[http://genexplain.com/transpath-1 TRANSPath (Biobase)]|| + || + || || ||
|-
|[http://genome.ucsc.edu/ UCSC Genome Browser]|| || || + || ||
|-
|[[Virtual Human]]|| || || || + ||
|}

Databases can be installed locally (for the BioUML workbench) or can be accessed via the Internet from the BioUML server, which supports secure access to databases. The server administrator can configure security settings for access to each database installed on the server. The information where a database is installed (locally or on the server side) as well as about its availability is displayed using different icons.

==Interface==
{{draft}}
Repository Pane tab

The icon color indicates where the database is installed and its accessibility:
blue color - database is installed locally, accessible for reading and writing;
yellow - remote public database, accessibility for reading and writing is specified by R and W letters;
red color - remote protected database, user should log-in to get access to the database, accessibility for reading and writing is specified by R and W letters;
green color - remote protected database, user successfully logged in, accessibility for reading and writing is specified by R and W letters;

==See also==
*[[Databases installation]]
*[[Repository pane]]

@@ Line 28: / Line 28: @@
 |[[Gene Ontology database|GO]]|| ||style="background-color:PaleGreen"| + || || ||
 |-
-|[http://www.biouml.net/vc/gtrd.shtml GTRD]|| || + || || || +
+|[[GTRD]]|| || + || || || +
 |-
 |[http://humancyc.org/ HumanCyc]|| + || + || || ||

@@ Line 76: / Line 76: @@
 *[[Repository pane]]
 *[[Search tools]]
-*[[Features]]
+*[[:Category:Databases|List of databases]]
 ==External links==

@@ Line 22: / Line 22: @@
 |[[Biopath]]|| || || ||style="background-color:PaleGreen"| + ||
 |-
-|[[Ensemble]]|| || ||style="background-color:PaleGreen"| + || ||
+|[[Ensembl]]|| || ||style="background-color:PaleGreen"| + || ||
 |-
 |[[Geneways]]||style="background-color:PaleGreen"| + || || || ||
@@ Line 79: / Line 79: @@
 ==External links==
-* [http://www.ensembl.org/ Ensemble official website]
+* [http://www.ensembl.org/ Ensembl official website]
 * [http://www.geneontology.org/ Gene Ontology official website]
 * [http://www.ncbi.nlm.nih.gov/pubmed/15016385 Abstract on the Geneways database at NCBI website]
 * [http://www.reactome.org/ReactomeGWT/entrypoint.html Reactome official website]

@@ Line 68: / Line 68: @@
 **[[File:PublicDB_icon.png]] Remote protected (commercial) database with read access (valid license).
 Databases are [[Repository pane|handled like any other]] data collection in the repository pane with the exception that databases cannot be removed. When a database is selected its description is displayed in the [[Information box| property inspector]] below.
 ==See also==

@@ Line 16: / Line 16: @@
 | ||pathways||gene/protein classification||genome||pathways simulation||transcription factor
 |-
-|Apoptosis model|| || || ||style="background-color:PaleGreen"| + ||
+|[[Apoptosis model]]|| || || ||style="background-color:PaleGreen"| + ||
 |-
 |[[Biomodels]]|| || || ||style="background-color:PaleGreen"| + ||
@@ Line 22: / Line 22: @@
 |[[Biopath]]|| || || ||style="background-color:PaleGreen"| + ||
 |-
-|[http://www.ensembl.org/ Ensemble]|| || ||style="background-color:PaleGreen"| + || ||
+|[[Ensemble]]|| || ||style="background-color:PaleGreen"| + || ||
 |-
-|[http://www.ncbi.nlm.nih.gov/pubmed/15016385 Geneways]||style="background-color:PaleGreen"| + || || || ||
+|[[Geneways]]||style="background-color:PaleGreen"| + || || || ||
 |-
-|[http://www.geneontology.org/ GO]|| ||style="background-color:PaleGreen"| + || || ||
+|[[Gene Ontology database|GO]]|| ||style="background-color:PaleGreen"| + || || ||
 |-
 |[http://www.biouml.net/vc/gtrd.shtml GTRD]|| || + || || || +
@@ Line 36: / Line 36: @@
 |[http://www.biobase-international.com/product/proteome Proteome (Biobase)]|| || + || || ||
 |-
-|[http://www.reactome.org/ReactomeGWT/entrypoint.html Reactome]||style="background-color:PaleGreen"| + ||style="background-color:PaleGreen"| + || || ||
+|[[Reactome]]||style="background-color:PaleGreen"| + ||style="background-color:PaleGreen"| + || || ||
 |-
 |[http://www.biobase-international.com/product/transcription-factor-binding-sites Transfac (Biobase)]|| || || || || +
@@ Line 58: / Line 58: @@
 **[[File:LocalDB_icon.png]] Local database;
 * yellow - remote public database, accessibility for reading and writing is specified by R and W letters:
-**[[File:ProtectedDB_R_icon.png]] Protected database with read access enabled,
+**[[File:ProtectedDB_R_icon.png]] Public database with read access enabled,
 **[[File:PublicDB_R_icon.png]] Public database with read access, write access disabled,
 **[[File:PublicDB_W_icon.png]] Public database with read access, write access enabled,
 **[[File:PublicDB_RW_icon.png]] Public database with read and write access;
 * red color - remote protected database, the user must log-in to get access to the database, accessibility for reading and writing is specified by R and W letters:
-**[[File:RemoteDB_R_icon.png]] Remote protected read-only database (no access),
+**[[File:RemoteDB_R_icon.png]] Remote protected (commercial) read-only database (no access),
-**[[File:RemoteDB_RW_icon.png]] Remote protected read-and-write database (no access);
+**[[File:RemoteDB_RW_icon.png]] Remote protected (commercial) read-and-write database (no access);
 * green color - remote protected database, the user successfully logged in, accessibility for reading and writing is specified by R and W letters:
-**[[File:PublicDB_icon.png]] Public database with read access.
+**[[File:PublicDB_icon.png]] Remote protected (commercial) database with read access (valid license).
 Databases are [[Repository pane|handled like any other]] data collection in the repository pane with the exception that databases cannot be removed. When a database is selected its description is displayed in the [[Information box| property inspector]] below.
@@ Line 75: / Line 75: @@
 *[[Search tools]]
 *[[Features]]

← Older revision		Revision as of 04:48, 24 June 2013
Line 73:		Line 73:
	*[[Databases installation]]		*[[Databases installation]]
	*[[Repository pane]]		*[[Repository pane]]
		+	*[[Features]]

@@ Line 1: / Line 1: @@
-{{draft}}
+{{stub}}
 Close integration with biological databases containing experimental data is a distinctive feature of BioUML, which is essential for accurate and convenient modeling of biological systems.
@@ Line 8: / Line 8: @@
 * the query engine to find interacting components of the system; search results can be shown as a graph and edited by the user.
-According to their content (data type) biological databases can be divided into several groups as follows (one database can provide several types of data):
+According to their content (data type) biological databases can be divided into several groups as follows (one database can provide several types of data; the green colour indicates that the database is freely available in BioUML web edtion):
 {|class="wikitable"
 | ||colspan="5" align="center"| '''Data type'''
@@ Line 15: / Line 16: @@
 | ||pathways||gene/protein classification||genome||pathways simulation||transcription factor
 |-
-|Apoptosis model|| || || || + ||
+|Apoptosis model|| || || ||style="background-color:PaleGreen"| + ||
 |-
-|[[Biomodels]]|| || || || + ||
+|[[Biomodels]]|| || || ||style="background-color:PaleGreen"| + ||
 |-
-|[[Biopath]]|| || || || + ||
+|[[Biopath]]|| || || ||style="background-color:PaleGreen"| + ||
 |-
-|[http://www.ensembl.org/ Ensemble]|| || || + || ||
+|[http://www.ensembl.org/ Ensemble]|| || ||style="background-color:PaleGreen"| + || ||
 |-
-|[http://www.ncbi.nlm.nih.gov/pubmed/15016385 Geneways]|| + || || || ||
+|[http://www.ncbi.nlm.nih.gov/pubmed/15016385 Geneways]||style="background-color:PaleGreen"| + || || || ||
 |-
-|[http://www.geneontology.org/ GO]|| || + || || ||
+|[http://www.geneontology.org/ GO]|| ||style="background-color:PaleGreen"| + || || ||
 |-
 |[http://www.biouml.net/vc/gtrd.shtml GTRD]|| || + || || || +
@@ Line 31: / Line 32: @@
 |[http://humancyc.org/ HumanCyc]|| + || + || || ||
 |-
-|[http://www.genome.jp/kegg/ KEGG]|| || || || + ||
+|[http://www.genome.jp/kegg/ KEGG]|| || || ||style="background-color:PaleGreen"| + ||
 |-
 |[http://www.biobase-international.com/product/proteome Proteome (Biobase)]|| || + || || ||
 |-
-|[http://www.reactome.org/ReactomeGWT/entrypoint.html Reactome]|| + || + || || ||
+|[http://www.reactome.org/ReactomeGWT/entrypoint.html Reactome]||style="background-color:PaleGreen"| + ||style="background-color:PaleGreen"| + || || ||
 |-
 |[http://www.biobase-international.com/product/transcription-factor-binding-sites Transfac (Biobase)]|| || || || || +
@@ Line 43: / Line 44: @@
 |[http://genome.ucsc.edu/ UCSC Genome Browser]|| || || + || ||
 |-
-|[[Virtual Human]]|| || || || + ||
+|[[Virtual Human]]|| || || ||style="background-color:PaleGreen"| + ||
 |}
@@ Line 50: / Line 52: @@
 ==Interface==
-{{draft}}
+[[File:DBview_in_repository.png|thumb|Available databases in the repository pane of BioUML web edition]]
-Repository Pane tab
-The icon color indicates where the database is installed and its accessibility:
+All the available databases are listed under the '''Databases''' tab in the [[repository pane]]. The icon color indicates location and accessibility of the database:
-blue color - database is installed locally, accessible for reading and writing;
+* blue color - the database is installed locally, accessible for reading and writing:
-yellow - remote public database, accessibility for reading and writing is specified by R and W letters;
+**[[File:LocalDB_icon.png]] Local database;
-red color - remote protected database, user should log-in to get access to the database, accessibility for reading and writing is specified by R and W letters;
+* yellow - remote public database, accessibility for reading and writing is specified by R and W letters:
-green color - remote protected database, user successfully logged in, accessibility for reading and writing is specified by R and W letters;
+**[[File:ProtectedDB_R_icon.png]] Protected database with read access enabled,
 ==See also==
 *[[Databases installation]]
 *[[Repository pane]]