CommunityCurationProtocol - Revision history

Khanspers: /* Protocol */

2014-10-21T21:30:28Z

Protocol

←Older revision		Revision as of 21:30, 21 October 2014
Line 16:		Line 16:
	** Select them all		** Select them all
	** Group them by pressing CTRL-G, or choosing 'group' in the right-click menu		** Group them by pressing CTRL-G, or choosing 'group' in the right-click menu
-	~~{\|class="prettytable"~~
-	\|-
-	~~!Before~~
-	~~!After~~
-	\|-
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/group_before.png~~
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/group_after.png~~
-	\|}
	* Merge multi line labels		* Merge multi line labels
	** Find labels that span multiple lines or labels that are very long		** Find labels that span multiple lines or labels that are very long
	** If multiple labels are used to represent a single block of text, convert them to a single multi-line label		** If multiple labels are used to represent a single block of text, convert them to a single multi-line label
	** Double click on the label to get the text area where you can type the text over multiple lines		** Double click on the label to get the text area where you can type the text over multiple lines
-	~~{\|class="prettytable"~~
-	\|-
-	~~!Before~~
-	~~!After~~
-	\|-
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label_before.png~~
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label_after.png~~
-	\|}
	* Convert label/shape combination to a label with outline		* Convert label/shape combination to a label with outline
	** Find labels with a shape around them that mimic a label with an outline		** Find labels with a shape around them that mimic a label with an outline
	** Remove the shape		** Remove the shape
	** Set the label outline by choosing 'Rectangle' or 'RoundedRectangle' from the 'Outline' field in the properties panel		** Set the label outline by choosing 'Rectangle' or 'RoundedRectangle' from the 'Outline' field in the properties panel
-	~~{\|class="prettytable"~~
-	\|-
-	~~!Before~~
-	~~!After~~
-	\|-
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/labelshape_before.png~~
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/labelshape_after.png~~
-	\|}
	* Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode		* Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode
	** Create a DataNode for the label		** Create a DataNode for the label
	** Double click the DataNode to fill in the textlabel, identifier and database		** Double click the DataNode to fill in the textlabel, identifier and database
-	~~{\|class="prettytable"~~
-	\|-
-	~~!Before~~
-	~~!After~~
-	\|-
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label2datanode_before.png~~
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label2datanode_after.png~~
-	\|}
	* Replace multiple line segments with a single connector		* Replace multiple line segments with a single connector
	** Choose 'Curved' or 'Elbow' for 'Line type' in the right-click menu to get a multi segment connector.		** Choose 'Curved' or 'Elbow' for 'Line type' in the right-click menu to get a multi segment connector.
	** Drag the blue segment handles to adjust the position of individual segments		** Drag the blue segment handles to adjust the position of individual segments
-	~~{\|class="prettytable"~~
-	\|-
-	~~!Before~~
-	~~!After~~
-	\|-
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/multiple_lines_before.png~~
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/multiple_lines_after.png~~
-	\|}
	* Replace arc/arrowhead combinations with curved connectors		* Replace arc/arrowhead combinations with curved connectors
-	~~{\|class="prettytable"~~
-	\|-
-	~~!Before~~
-	~~!After~~
-	\|-
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/curve_before.png~~
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/curve_after.png~~
-	\|}
-
	* Link lines between elements. You can press CTRL-L to reveal all unlinked line ends.		* Link lines between elements. You can press CTRL-L to reveal all unlinked line ends.
-	~~{\|class="prettytable"~~
-	\|-
-	~~!Before~~
-	~~!After~~
-	\|-
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/link_before.png~~
-	~~\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/link_after.png~~
-	\|}

	== Problems ==		== Problems ==

Khanspers: Added participant list

2014-10-21T21:29:20Z

Added participant list

←Older revision		Revision as of 21:29, 21 October 2014
Line 94:		Line 94:

	If you find any bugs in the software, please report them to our [http://www.bigcat.unimaas.nl/tracprojects/pathvisio bug tracker].		If you find any bugs in the software, please report them to our [http://www.bigcat.unimaas.nl/tracprojects/pathvisio bug tracker].
		+
		+	== Participants ==
		+	[[User:AlexanderPico\|Alexander Pico]], [[User:Khanspers\|Kristina Hanspers]], [[User:Susan\|Susan Coort]], [[User:Pahles\|Patrick Ahles]], [[User:Thomas\|Thomas Kelder]], [[User:Michiel\|Michiel Adriaens]], [[User:MartijnVanIersel\|Martijn van Iersel]], [[User:Ehsiao\|Ed Hsiao]]

Thomas at 12:36, 24 November 2008

2008-11-24T12:36:44Z

←Older revision		Revision as of 12:36, 24 November 2008
Line 93:		Line 93:
	Please use the [[Talk:CommunityCurationProtocol\|talk page]] to discuss general problems (e.g. how to graphically represent something). For pathway specific problems, please use the talk page of the pathway (by pressing the 'discussion' tab on the pathway page).		Please use the [[Talk:CommunityCurationProtocol\|talk page]] to discuss general problems (e.g. how to graphically represent something). For pathway specific problems, please use the talk page of the pathway (by pressing the 'discussion' tab on the pathway page).

-	If you find any bugs in the software, please report them to our [http://~~ftp2~~.bigcat.unimaas.nl/~~~martijn.vaniersel~~/~~mantis/my_view_page.php~~ bug tracker].	+	If you find any bugs in the software, please report them to our [http://www.bigcat.unimaas.nl/tracprojects/pathvisio bug tracker].

AlexanderPico: /* Protocol */

2008-05-18T08:27:31Z

Protocol

←Older revision		Revision as of 08:27, 18 May 2008
Line 71:		Line 71:
	\|}		\|}
	* Replace arc/arrowhead combinations with curved connectors		* Replace arc/arrowhead combinations with curved connectors
-	~~TODO~~: ~~Example~~	+	{\|class="prettytable"
		+	\|-
		+	!Before
		+	!After
		+	\|-
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/curve_before.png
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/curve_after.png
		+	\|}
		+
	* Link lines between elements. You can press CTRL-L to reveal all unlinked line ends.		* Link lines between elements. You can press CTRL-L to reveal all unlinked line ends.
	{\|class="prettytable"		{\|class="prettytable"
Line 81:		Line 89:
	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/link_after.png		\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/link_after.png
	\|}		\|}
-
-	* ...

	== Problems ==		== Problems ==

AlexanderPico: /* Protocol */

2008-05-17T23:36:04Z

Protocol

←Older revision		Revision as of 23:36, 17 May 2008
Line 72:		Line 72:
	* Replace arc/arrowhead combinations with curved connectors		* Replace arc/arrowhead combinations with curved connectors
	TODO: Example		TODO: Example
-	* Link lines between elements. You can press CTRL-R to reveal all unlinked line ends.	+	* Link lines between elements. You can press CTRL-L to reveal all unlinked line ends.
-	~~TODO~~: ~~Example~~	+	{\|class="prettytable"
		+	\|-
		+	!Before
		+	!After
		+	\|-
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/link_before.png
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/link_after.png
		+	\|}
		+
	* ...		* ...

AlexanderPico: /* Protocol */

2008-05-17T23:21:19Z

Protocol

←Older revision		Revision as of 23:21, 17 May 2008
Line 16:		Line 16:
	** Select them all		** Select them all
	** Group them by pressing CTRL-G, or choosing 'group' in the right-click menu		** Group them by pressing CTRL-G, or choosing 'group' in the right-click menu
-	~~TODO~~: ~~Example~~	+	{\|class="prettytable"
		+	\|-
		+	!Before
		+	!After
		+	\|-
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/group_before.png
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/group_after.png
		+	\|}
	* Merge multi line labels		* Merge multi line labels
	** Find labels that span multiple lines or labels that are very long		** Find labels that span multiple lines or labels that are very long

Thomas at 08:18, 15 May 2008

2008-05-15T08:18:25Z

←Older revision		Revision as of 08:18, 15 May 2008
Line 12:		Line 12:
	Things to look for and change in reviewing and improving a pathway.		Things to look for and change in reviewing and improving a pathway.

-	* ~~Identify~~ stacked ~~datanodes and~~ group them (CTRL-G)	+	* Group stacked DataNodes
		+	** Find a group of stacked datanodes
		+	** Select them all
		+	** Group them by pressing CTRL-G, or choosing 'group' in the right-click menu
	TODO: Example		TODO: Example
-	* Find labels that span multiple lines. If multiple labels are used to represent a single block of text, convert them to a single multi-line label	+	* Merge multi line labels
		+	** Find labels that span multiple lines or labels that are very long
		+	** If multiple labels are used to represent a single block of text, convert them to a single multi-line label
		+	** Double click on the label to get the text area where you can type the text over multiple lines
	{\|class="prettytable"		{\|class="prettytable"
	\|-		\|-
Line 22:		Line 28:
	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label_before.png		\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label_before.png
	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label_after.png		\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label_after.png
		+	\|}
		+	* Convert label/shape combination to a label with outline
		+	** Find labels with a shape around them that mimic a label with an outline
		+	** Remove the shape
		+	** Set the label outline by choosing 'Rectangle' or 'RoundedRectangle' from the 'Outline' field in the properties panel
		+	{\|class="prettytable"
		+	\|-
		+	!Before
		+	!After
		+	\|-
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/labelshape_before.png
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/labelshape_after.png
	\|}		\|}
	* Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode		* Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode
		+	** Create a DataNode for the label
		+	** Double click the DataNode to fill in the textlabel, identifier and database
	{\|class="prettytable"		{\|class="prettytable"
	\|-		\|-
Line 33:		Line 53:
	\|}		\|}
	* Replace multiple line segments with a single connector		* Replace multiple line segments with a single connector
		+	** Choose 'Curved' or 'Elbow' for 'Line type' in the right-click menu to get a multi segment connector.
		+	** Drag the blue segment handles to adjust the position of individual segments
	{\|class="prettytable"		{\|class="prettytable"
	\|-		\|-

Thomas at 07:59, 15 May 2008

2008-05-15T07:59:54Z

←Older revision		Revision as of 07:59, 15 May 2008
Line 33:		Line 33:
	\|}		\|}
	* Replace multiple line segments with a single connector		* Replace multiple line segments with a single connector
-	~~TODO~~: ~~Example~~	+	{\|class="prettytable"
		+	\|-
		+	!Before
		+	!After
		+	\|-
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/multiple_lines_before.png
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/multiple_lines_after.png
		+	\|}
	* Replace arc/arrowhead combinations with curved connectors		* Replace arc/arrowhead combinations with curved connectors
	TODO: Example		TODO: Example

Thomas: /* Protocol */

2008-05-15T07:53:34Z

Protocol

←Older revision		Revision as of 07:53, 15 May 2008
Line 15:		Line 15:
	TODO: Example		TODO: Example
	* Find labels that span multiple lines. If multiple labels are used to represent a single block of text, convert them to a single multi-line label		* Find labels that span multiple lines. If multiple labels are used to represent a single block of text, convert them to a single multi-line label
-	~~TODO~~: ~~Example~~	+	{\|class="prettytable"
		+	\|-
		+	!Before
		+	!After
		+	\|-
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label_before.png
		+	\|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label_after.png
		+	\|}
	* Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode		* Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode
	{\|class="prettytable"		{\|class="prettytable"

AlexanderPico at 23:20, 14 May 2008

2008-05-14T23:20:35Z

←Older revision		Revision as of 23:20, 14 May 2008
Line 1:		Line 1:
-	Join us in this Community Curation effort!	+	'''Join us in this Community Curation effort!'''

	During the week of May 19-23, we are going to review all pathways on WikiPathways to make them more robust and amenable to computational analysis. The main improvements we want to make are:		During the week of May 19-23, we are going to review all pathways on WikiPathways to make them more robust and amenable to computational analysis. The main improvements we want to make are:
Line 8:		Line 8:
	Sign-up for particular pathways you would like to review and refer to the protocol below. See the [http://groups.google.com/group/wikipathways-discuss discussion mailing list] for more details about this event.		Sign-up for particular pathways you would like to review and refer to the protocol below. See the [http://groups.google.com/group/wikipathways-discuss discussion mailing list] for more details about this event.

-	* [[Pathways4Curation\|~~Pathways needing curation~~]] - ~~Human pathway archive~~	+	'''--> [[Pathways4Curation\|Pathway Sign-up Table]] <--'''
	== Protocol ==		== Protocol ==
	Things to look for and change in reviewing and improving a pathway.		Things to look for and change in reviewing and improving a pathway.