Curation Jamboree Sep 2010 - Revision history

Khanspers: removed IRC link

Khanspers — Fri, 29 Jan 2016 22:35:21 GMT

removed IRC link

←Older revision		Revision as of 22:35, 29 January 2016
Line 3:		Line 3:

	Have you always wanted to contribute to WikiPathways but didn't know where to start? Here's your chance! We are organizing our third curation event to improve the quality and extent of our pathways. Curation events are open to all registered WikiPathways users, no prior experience necessary!		Have you always wanted to contribute to WikiPathways but didn't know where to start? Here's your chance! We are organizing our third curation event to improve the quality and extent of our pathways. Curation events are open to all registered WikiPathways users, no prior experience necessary!
-
-
-	~~[[Support_chat_channel\|>>> JOIN THE LIVE CHAT <<<]]~~
-

	* When: September 23-24, 2010		* When: September 23-24, 2010

Khanspers: Added participant list

Khanspers — Tue, 21 Oct 2014 21:27:58 GMT

Added participant list

←Older revision		Revision as of 21:27, 21 October 2014
Line 91:		Line 91:
	* Add the citation to the Bibliography		* Add the citation to the Bibliography
	* [[Pathway:WP339\|Literature example]]		* [[Pathway:WP339\|Literature example]]
		+
		+	== Participants ==
		+	[[User:Mark.scott\|Mark Scott]], [[User:AlexanderPico\|Alexander Pico]], [[User:Khanspers\|Kristina Hanspers]], [[User:Thomas\|Thomas Kelder]], [[User:MartijnVanIersel\|Martijn van Iersel]], [[User:AllanKuchinsky\|Allan Kuchinsky]], [[User:Jildau\|Jildau Bouwman]], [[User:Bassetfrog\|JT. Saito]], [[User:FerryJagers\|Ferry Jagers]], [[User:Mkutmon\|Martina Kutmon]]

AlexanderPico at 20:50, 21 September 2010

AlexanderPico — Tue, 21 Sep 2010 20:50:51 GMT

←Older revision		Revision as of 20:50, 21 September 2010
Line 3:		Line 3:

	Have you always wanted to contribute to WikiPathways but didn't know where to start? Here's your chance! We are organizing our third curation event to improve the quality and extent of our pathways. Curation events are open to all registered WikiPathways users, no prior experience necessary!		Have you always wanted to contribute to WikiPathways but didn't know where to start? Here's your chance! We are organizing our third curation event to improve the quality and extent of our pathways. Curation events are open to all registered WikiPathways users, no prior experience necessary!
		+
		+
		+	[[Support_chat_channel\|>>> JOIN THE LIVE CHAT <<<]]


	* When: September 23-24, 2010		* When: September 23-24, 2010
-	* Support: WikiPathways admins and curators will be available in an online chat channel during the event to answer all your questions~~. [[Support_chat_channel\|Click here to go to the chat channel.]]~~.	+	* Support: WikiPathways admins and curators will be available in an online chat channel during the event to answer all your questions.

Khanspers at 18:34, 8 September 2010

Khanspers — Wed, 08 Sep 2010 18:34:26 GMT

←Older revision		Revision as of 18:34, 8 September 2010
Line 3:		Line 3:

	Have you always wanted to contribute to WikiPathways but didn't know where to start? Here's your chance! We are organizing our third curation event to improve the quality and extent of our pathways. Curation events are open to all registered WikiPathways users, no prior experience necessary!		Have you always wanted to contribute to WikiPathways but didn't know where to start? Here's your chance! We are organizing our third curation event to improve the quality and extent of our pathways. Curation events are open to all registered WikiPathways users, no prior experience necessary!
		+

	* When: September 23-24, 2010		* When: September 23-24, 2010
Line 26:		Line 27:
	# Add a pathway node (using the pathway button on the toolbar) and double click to open the properties dialog		# Add a pathway node (using the pathway button on the toolbar) and double click to open the properties dialog
	# Enter the text of the original label in the 'text label' field.		# Enter the text of the original label in the 'text label' field.
-	# Set '~~biological type~~' to 'Pathway'.	+	# Set 'Biological Type' to 'Pathway'.
-	# Set '~~database~~' to 'WikiPathways'.	+	# Set 'Database' to 'WikiPathways'.
-	# Enter the identifier found in step 2 in the '~~identifier~~' field.	+	# Enter the identifier found in step 2 in the 'Identifier' field.
-	# Click 'ok' to close the dialog and save the pathway.	+	# Click 'Ok' to close the dialog and save the pathway.

	=== Add cellular compartments ===		=== Add cellular compartments ===

Khanspers: /* Add description */

Khanspers — Wed, 08 Sep 2010 18:31:51 GMT

Add description

←Older revision		Revision as of 18:31, 8 September 2010
Line 48:		Line 48:

	=== Add description ===		=== Add description ===
-	* Find pathways with missing descriptions [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags showPathwaysFor=Curation:MissingDescription here]	+	# Find pathways with missing descriptions [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags showPathwaysFor=Curation:MissingDescription here]
-	* A description can be from an outside source (publication, textbook, website) or it can be your own original description. Instructions for how to add descriptions to pathways can be found in the [[Help:Tutorial:Step_10\|tutorial]].	+	# A description can be from an outside source (publication, textbook, website) or it can be your own original description. Instructions for how to add descriptions to pathways can be found in the [[Help:Tutorial:Step_10\|tutorial]].
-	* If you add a description copied from an outside source, please cite the source. Some common sources for descriptions and details on how to cite them are listed below.	+	# If you add a description copied from an outside source, please cite the source. Some common sources for descriptions and details on how to cite them are listed below.
-	* If you add a description for a particular human pathway, consider also adding the description to that same pathway in other species, where appropriate. This may require some editing to change or exclude species names. Please use your own judgment to decide if the description applies to additional species.	+	# If you add a description for a particular human pathway, consider also adding the description to that same pathway in other species, where appropriate. This may require some editing to change or exclude species names. Please use your own judgment to decide if the description applies to additional species.
-	* Once you have added a description to the pathway, remove the [[Template:Curation:MissingDescription\|MissingDescription tag]] from the pathway.	+	# Once you have added a description to the pathway, remove the [[Template:Curation:MissingDescription\|MissingDescription tag]] from the pathway.
		+
		+	==== Sources for descriptions ====
		+	Following are some suggested sources for pathway descriptions.
		+	* [http://en.wikipedia.org/wiki/Main_Page Wikipedia]
		+	* [http://www.pharmgkb.org/ PharmGKB]
		+	* [http://www.reactome.org/ Reactome]
		+	* [http://www.genome.jp/kegg/pathway.html KEGG]
		+	* [http://highwire.stanford.edu/ Scientific literature]
		+
		+	==== Citing sources ====
		+	Citing requirements varies between sources, so it is a good idea to find out the specific requirements for any particular source that you use for descriptions. In general, please cite the source for the description in the actual Descriptions section of the pathway with a direct link to the source (i.e. http://en.wikipedia.org/wiki/TGF_beta_signaling_pathway).
		+	Below are instructions and examples for how to cite specific sources:
		+
		+	===== Wikipedia =====
		+	* Cite Wikipedia in the Description section, and include a link to the relevant page at Wikipedia.
		+	* [[Pathway:WP111\|Wikipedia example]]
		+
		+	===== PharmGKB =====
		+	* Cite PharmGKB in the Description section, and include a link to the relevant pathway page at PharmGKB.
		+	* If the pathway page at PharmGKB indicates that the pathway has been published in the Pharmacogenetics and Genomics journal, review the publication to see if the text used as a description appears in the publication. If so, add the citation to the Bibliography.
		+	* [[Pathway:WP554\|PharmGKB example]]
		+
		+	===== Reactome =====
		+	* Cite Reactome in the Description section, and include a link to the relevant pathway page at Reactome.
		+	* [[Pathway:WP466\|Reactome example]]
		+
		+	===== KEGG =====
		+	* Cite KEGG in the Description section, and include a link to the relevant pathway page at KEGG.
		+	* [[Pathway:WP558\|KEGG example]]
		+
		+	===== Scientific literature =====
		+	* Cite the original publication in the Description section, and if available include a link to open access publications.
		+	* Add the citation to the Bibliography
		+	* [[Pathway:WP339\|Literature example]]

Khanspers: /* Add literature reference */

Khanspers — Wed, 08 Sep 2010 18:30:36 GMT

Add literature reference

←Older revision		Revision as of 18:30, 8 September 2010
Line 43:		Line 43:

	=== Add literature reference ===		=== Add literature reference ===
-	* Find pathways without literature references [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags&showPathwaysFor=Curation:NeedsReference here]	+	# Find pathways without literature references [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags&showPathwaysFor=Curation:NeedsReference here]
-	* A literature reference can be from a publication or text book. For example, you may be able to find literature references for specific pathways by searching [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] or [http://en.wikipedia.org/wiki/Main_Page Wikipedia]. Instructions for how to add literature references to pathways can be found in the [[Help:Tutorial:Step_9\|tutorial]].	+	# A literature reference can be from a publication or text book. For example, you may be able to find literature references for specific pathways by searching [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] or [http://en.wikipedia.org/wiki/Main_Page Wikipedia]. Instructions for how to add literature references to pathways can be found in the [[Help:Tutorial:Step_9\|tutorial]].
-	* Once you have added at least one literature reference to the pathway, remove the [[Template:Curation:NeedsReference\|NeedsReference tag]] from the pathway.	+	# Once you have added at least one literature reference to the pathway, remove the [[Template:Curation:NeedsReference\|NeedsReference tag]] from the pathway.

	=== Add description ===		=== Add description ===

Khanspers: /* Suggested tasks */

Khanspers — Wed, 08 Sep 2010 18:30:13 GMT

Suggested tasks

←Older revision		Revision as of 18:30, 8 September 2010
Line 18:		Line 18:
	* Add literature references to pathways with no literature reference. [[Curation_Jamboree_Sep_2010#Add literature reference\|Details]]		* Add literature references to pathways with no literature reference. [[Curation_Jamboree_Sep_2010#Add literature reference\|Details]]
	* Add pathway description to pathways with missing description [[Curation_Jamboree_Sep_2010#Add description\|Details]]		* Add pathway description to pathways with missing description [[Curation_Jamboree_Sep_2010#Add description\|Details]]
-

	=== Link pathways ===		=== Link pathways ===

Khanspers: /* Suggested tasks */

Khanspers — Wed, 08 Sep 2010 18:30:00 GMT

Suggested tasks

←Older revision		Revision as of 18:30, 8 September 2010
Line 15:		Line 15:
	* Add pathway links to pathways [[Curation_Jamboree_Sep_2010#Link_pathways\|Details]]		* Add pathway links to pathways [[Curation_Jamboree_Sep_2010#Link_pathways\|Details]]
	* Add new cellular compartments [[Curation_Jamboree_Sep_2010#Add_cellular_compartments\|Details]]		* Add new cellular compartments [[Curation_Jamboree_Sep_2010#Add_cellular_compartments\|Details]]
-	* Update datanode annotation (xrefs) for datanodes with missing or incorrect annotation. [[~~Curation Jamboree 2010~~#~~Update datanode annotation~~\|Details]]	+	* Update datanode annotation (xrefs) for datanodes with missing or incorrect annotation. [[Curation_Jamboree_Sep_2010#Update_datanode_annotation\|Details]]
	* Add literature references to pathways with no literature reference. [[Curation_Jamboree_Sep_2010#Add literature reference\|Details]]		* Add literature references to pathways with no literature reference. [[Curation_Jamboree_Sep_2010#Add literature reference\|Details]]
	* Add pathway description to pathways with missing description [[Curation_Jamboree_Sep_2010#Add description\|Details]]		* Add pathway description to pathways with missing description [[Curation_Jamboree_Sep_2010#Add description\|Details]]

Khanspers: /* Update datanode annotation */

Khanspers — Wed, 08 Sep 2010 18:29:15 GMT

Update datanode annotation

←Older revision		Revision as of 18:29, 8 September 2010
Line 39:		Line 39:

	=== Update datanode annotation ===		=== Update datanode annotation ===
-	The purpose of this task is to add annotation for datanodes that are unannotated. You can find pathways with missing datanode annotation [[Special:SpecialCurationTags&showPathwaysFor=Curation:MissingXRef\|here]].	+	The purpose of this task is to add annotation for datanodes that are unannotated. You can find pathways with missing datanode annotation [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags&showPathwaysFor=Curation:MissingXRef here].
	# Review the datanode annotations in the DataNodes list at the bottom of the pathway page to identify unannotated datanodes. Instructions for how to update datanode annotation can be found [[Help:Tutorial:Step_3\|here]].		# Review the datanode annotations in the DataNodes list at the bottom of the pathway page to identify unannotated datanodes. Instructions for how to update datanode annotation can be found [[Help:Tutorial:Step_3\|here]].
	# After you have updated the pathways, if all datanodes in the pathway are correctly annotated, remove the [[Template:Curation:MissingXRef\|MissingXRef tag]] from the pathway.		# After you have updated the pathways, if all datanodes in the pathway are correctly annotated, remove the [[Template:Curation:MissingXRef\|MissingXRef tag]] from the pathway.

Khanspers: /* Add datanode annotation */

Khanspers — Wed, 08 Sep 2010 18:28:38 GMT

Add datanode annotation

←Older revision		Revision as of 18:28, 8 September 2010
Line 38:		Line 38:
	# Size and place the new object so that it fits into the pathway where the original graphic is placed, then delete the original and replace it with the new object.		# Size and place the new object so that it fits into the pathway where the original graphic is placed, then delete the original and replace it with the new object.

-	=== ~~Add~~ datanode annotation ===	+	=== Update datanode annotation ===
	The purpose of this task is to add annotation for datanodes that are unannotated. You can find pathways with missing datanode annotation [[Special:SpecialCurationTags&showPathwaysFor=Curation:MissingXRef\|here]].		The purpose of this task is to add annotation for datanodes that are unannotated. You can find pathways with missing datanode annotation [[Special:SpecialCurationTags&showPathwaysFor=Curation:MissingXRef\|here]].
	# Review the datanode annotations in the DataNodes list at the bottom of the pathway page to identify unannotated datanodes. Instructions for how to update datanode annotation can be found [[Help:Tutorial:Step_3\|here]].		# Review the datanode annotations in the DataNodes list at the bottom of the pathway page to identify unannotated datanodes. Instructions for how to update datanode annotation can be found [[Help:Tutorial:Step_3\|here]].

←Older revision		Revision as of 18:30, 8 September 2010
Line 15:		Line 15:
	* Add pathway links to pathways [[Curation_Jamboree_Sep_2010#Link_pathways\|Details]]		* Add pathway links to pathways [[Curation_Jamboree_Sep_2010#Link_pathways\|Details]]
	* Add new cellular compartments [[Curation_Jamboree_Sep_2010#Add_cellular_compartments\|Details]]		* Add new cellular compartments [[Curation_Jamboree_Sep_2010#Add_cellular_compartments\|Details]]
-	* Update datanode annotation (xrefs) for datanodes with missing or incorrect annotation. [[~~Curation Jamboree 2010~~#~~Update datanode annotation~~\|Details]]	+	* Update datanode annotation (xrefs) for datanodes with missing or incorrect annotation. [[Curation_Jamboree_Sep_2010#Update_datanode_annotation\|Details]]
	* Add literature references to pathways with no literature reference. [[Curation_Jamboree_Sep_2010#Add literature reference\|Details]]		* Add literature references to pathways with no literature reference. [[Curation_Jamboree_Sep_2010#Add literature reference\|Details]]
	* Add pathway description to pathways with missing description [[Curation_Jamboree_Sep_2010#Add description\|Details]]		* Add pathway description to pathways with missing description [[Curation_Jamboree_Sep_2010#Add description\|Details]]