Data storage and AmiGO2 Working Group - Revision history

Cooperl: /* Participants */

2015-06-02T19:04:54Z

Participants

← Older revision		Revision as of 19:04, 2 June 2015
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	* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI), Seth Carbon		* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI), Seth Carbon
	* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)		* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)

			= Link to [[Data storage and AmiGO 2 Working Group Meetings]]=

Cooperl: /* Participants */

2015-06-02T19:04:32Z

Participants

← Older revision		Revision as of 19:04, 2 June 2015
Line 47:		Line 47:
	* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI), Seth Carbon		* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI), Seth Carbon
	* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)		* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)

	~~[[Data storage and AmiGO 2 Working Group Meetings]]~~

Cooperl: /* Data storage and AmiGO 2 Working Group Meetings: */

2015-06-02T19:02:18Z

Data storage and AmiGO 2 Working Group Meetings:

← Older revision		Revision as of 19:02, 2 June 2015
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	* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)		* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)

	=Data storage and AmiGO 2 Working Group Meetings:=		[[Data storage and AmiGO 2 Working Group Meetings]]
	~~==Data storage and AmiGO 2 call 1-30-15==~~
	* Who: PJ, CM, Seth, EZ, LC, JP, JE
	* Discussion of the planned transition to the AmiGO 2.0 platform
	* JE is working on installing SolR database - View details and progress reports here: [[AmiGO2_install]]

	~~== Data Storage and AmiGO2 call 2-18-15==~~
	* Who: JE, JP, EZ
	* Link to video recording: [[Media:Data_Storage_2-18-15.mp4]]
	* Link to audio recording: [[File:Data Storage Meeting audio only 2-18-15.m4a\|thumbnail\|Data_Storage_Meeting_audio_only_2-18-15.m4a]]


	* Further discussion of AmiGO2 progress and overview of AmiGO2 interface

	~~== Planteome Interface meeting 3-2-15==~~
	~~Who: EZ, LC, JE, PJ ...??~~
	* Link to video recording: [[File:Planteome Interface mtg video 3-2-15.mp4\|thumbnail\|Planteome_Interface_mtg_video_3-2-15.mp4]]
	* Link to audio recording: [[File:Planteome Interface mtg audio 3-2-15.m4a\|thumbnail\|Planteome Interface mtg audio 3-2-15.m4a]]

	* EZ: First thing: focus of the project, speed up queries, data visualization, data organization
	* User Interface: it would be good to see how the users operate and what kinds of questions they would ask.
	* Amigo 2, could build enhanced interface so users could inspect their data and build queries.
	* what functionalities are needed?
	* Questions:
	**How will the users access the interface?
	** How will they use the interface?
	~~===Involvement of other organisms? e.g. viruses, animals, etc===~~
	* Could the tools be expanded to other organisms
	* Crops are interacting with the environment, other organisms
	~~=== AmiGO2 introduction===~~
	* show filtered image
	* Cytoscape Sif file, ontology network
	* bring in other ontologies, Rice Xanthomanas example
	* ontology formats

	~~==Data storage and AmiGO2 Working Group Meeting 4-16-15==~~

	~~Who: EZ, BQ, PJ, JP, LC, JE~~

	* Link to video recording: [[File:Data_storage_and_AmiGO2_video_4-16_15.mp4\|thumbnail\|Data_storage_and_AmiGO2_video_4-16_15.mp4]]
	* Link to audio recording: [[File:Data storage and AmiGO2 audio 4-16 15.m4a\|thumbnail\|Data storage and AmiGO2 audio 4-16 15.m4a]]

	* Introductions

	* Storing code developed on Planteome project on Github

	* posting notes on wiki
	* data visualization aspect within AmiGO2- work with JE on
	* Data annotation- wikipedia style?
	* different levels of access
	* To do: Send link to Eugene and Botong- circulate the developer position ad

	~~==Relevant links:==~~
	* https://github.com/geneontology/amigo
	* Demo: http://amigo.geneontology.org/
	* http://amigo2.berkeleybop.org/ - dev server

	~~==Data storage and AmiGO2 Working Group meeting 5-1-15==~~
	~~Who: PJ, BQ, EZ, CM, JE~~
	* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4\|thumbnail\|Data Storage + AmiGO2 meeting 5-1-15-video.mp4]]
	* Link to audio: [[File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a\|thumbnail\|Data Storage + AmiGO2 meeting 5-1-15-audio.m4a]]

	~~===Demo of GO enrichment tool===~~
	*At the GO website (www.geneontology.org)
	*See how it works there compared to the one at AGRIGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php). See if your NIH proposal work with Yanmin Di overlaps and can be adopted.

	*Set of genes you can get a list of Arabidopsis thaliana genes from the attached file. (email)
	* Gene pages at Gramene e.g. http://archive.gramene.org/db/genes/search_gene?acc=GR:0101175 or elsewhere
	*Start thinking about building a gene database, with different access levels for admins and curators, limited in what fields are allowed to be edited by what level.
	~~This is for building the community gene annotation tools. The annotated data from this database can be synced with the AmiGOdb version that Justin Elser and Chris are working on.~~

	~~I hope this will give Bo, enough width to work until the AMIGO build and datasets mature.~~

	~~BinGO~~
	~~http://bioinformatics.oxfordjournals.org/content/21/16/3448.full~~
	~~AgriGO~~
	~~http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/~~

	~~==Data storage and AmiGO2 Working Group Meeting 5-15-15==~~
	~~Who: PJ, EZ, BQ, JE, CM~~

	*Continue to show how the enrichment analysis tools work(agriGO).
	*Discuss about the language and character problem on the page.
	*Agreed to start with design the requirement specification.
	*Share the old database scheme with EZ and BQ.
	*Show the Annotation database to EZ and BQ (unfinished, need to be continued).

	EZ and BQ will start with analyzing the old database scheme and try to study the enrichment analysis algorithms, the first goal of the group is to show the search result through tables. The next step will be visualize it with Graph.

	~~==Data storage and visualization Working Group Meeting 5-27-15==~~
	~~Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)~~

	~~===Link to recordings (in 2 parts):===~~
	* Audio P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a\|thumbnail\|Planteome_Data_Vis_Mtg_p1_5-27-15-audio_only.m4a]]
	* Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]
	* Audio P.2: [[File:Data_Visualization_5-27-15_audio.m4a\|thumbnail\|Data_Visualization_5-27-15_audio.m4a]]
	* Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4\|thumbnail\|Data_Visualization_5-27-15_part_2.mp4]]

	~~===Intro to Planteome for to new students===~~
	* Explanation of ontologies
	* Overview of older AmiGO browser
	* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology [http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php]
	** Used gene set from planteome.cgrb to demonstrate AgriGO usage

	~~==Data storage and visualization Working Group Meeting 6-2-15==~~

Cooperl: /* Data storage and visualization Working Group Meeting 5-27-15 */

2015-06-02T19:01:46Z

Data storage and visualization Working Group Meeting 5-27-15

← Older revision		Revision as of 19:01, 2 June 2015
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	* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology [http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php]		* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology [http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php]
	** Used gene set from planteome.cgrb to demonstrate AgriGO usage		** Used gene set from planteome.cgrb to demonstrate AgriGO usage

			==Data storage and visualization Working Group Meeting 6-2-15==

Cooperl: /* Data storage and visualization Working Group Meeting 5-27-15 */

2015-06-02T19:01:05Z

Data storage and visualization Working Group Meeting 5-27-15

← Older revision		Revision as of 19:01, 2 June 2015
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	Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)		Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)

	Link to recordings (in 2 parts):		===Link to recordings (in 2 parts):===
	Audio P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a\|thumbnail\|Planteome_Data_Vis_Mtg_p1_5-27-15-audio_only.m4a]]		* Audio P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a\|thumbnail\|Planteome_Data_Vis_Mtg_p1_5-27-15-audio_only.m4a]]
			* Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]
			* Audio P.2: [[File:Data_Visualization_5-27-15_audio.m4a\|thumbnail\|Data_Visualization_5-27-15_audio.m4a]]
			* Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4\|thumbnail\|Data_Visualization_5-27-15_part_2.mp4]]

	~~Video P.1: [[File:~~Planteome ~~Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]~~		===Intro to Planteome for to new students===
			* Explanation of ontologies
	~~Audio P.2: [[File:Data_Visualization_5-27-15_audio.m4a\|thumbnail\|Data_Visualization_5-27-15_audio.m4a]]~~

	~~Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4\|thumbnail\|Data_Visualization_5-27-15_part_2.mp4]]~~


	* Explanation of ontologies ~~to new students~~
	* Overview of older AmiGO browser		* Overview of older AmiGO browser
	* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php		* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology [http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php]
	* Used gene set from ~~above~~ to ~~show~~ AgriGO usage		** Used gene set from planteome.cgrb to demonstrate AgriGO usage

Elserj at 23:29, 27 May 2015

2015-05-27T23:29:13Z

← Older revision		Revision as of 23:29, 27 May 2015
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	Who: PJ, BQ, EZ, CM, JE		Who: PJ, BQ, EZ, CM, JE
	* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4\|thumbnail\|Data Storage + AmiGO2 meeting 5-1-15-video.mp4]]		* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4\|thumbnail\|Data Storage + AmiGO2 meeting 5-1-15-video.mp4]]
	* Link to ~~video~~: [[File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a\|thumbnail\|Data Storage + AmiGO2 meeting 5-1-15-audio.m4a]]		* Link to audio: [[File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a\|thumbnail\|Data Storage + AmiGO2 meeting 5-1-15-audio.m4a]]

	===Demo of GO enrichment tool===		===Demo of GO enrichment tool===

Elserj at 23:28, 27 May 2015

2015-05-27T23:28:22Z

← Older revision		Revision as of 23:28, 27 May 2015
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	Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]		Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]

			Audio P.2: [[File:Data_Visualization_5-27-15_audio.m4a\|thumbnail\|Data_Visualization_5-27-15_audio.m4a]]

	Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4\|thumbnail\|Data_Visualization_5-27-15_part_2.mp4]]		Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4\|thumbnail\|Data_Visualization_5-27-15_part_2.mp4]]

Elserj at 23:26, 27 May 2015

2015-05-27T23:26:23Z

← Older revision		Revision as of 23:26, 27 May 2015
Line 144:		Line 144:

	Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]		Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]

			Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4\|thumbnail\|Data_Visualization_5-27-15_part_2.mp4]]

Cooperl: /* Data storage and visualization Working Group Meeting 5-27-15 */

2015-05-27T21:41:13Z

Data storage and visualization Working Group Meeting 5-27-15

@@ Line 139: / Line 139: @@
 ==Data storage and visualization Working Group Meeting 5-27-15==
 Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)
 * Explanation of ontologies to new students
@@ Line 144: / Line 150: @@
 * Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php
 * Used gene set from above to show AgriGO usage

Cooperl: /* Data storage and visualization Working Group Meeting 5-27-15 */

2015-05-27T21:40:33Z

Data storage and visualization Working Group Meeting 5-27-15

← Older revision		Revision as of 21:40, 27 May 2015
Line 146:		Line 146:

	Link to recordings (in 2 parts):		Link to recordings (in 2 parts):
			Audio P.1:
			[[File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a\|thumbnail\|Planteome_Data_Vis_Mtg_p1_5-27-15-audio_only.m4a]]

			Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]

← Older revision		Revision as of 23:28, 27 May 2015
Line 144:		Line 144:

	Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]		Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4\|thumbnail\|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]

			Audio P.2: [[File:Data_Visualization_5-27-15_audio.m4a\|thumbnail\|Data_Visualization_5-27-15_audio.m4a]]

	Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4\|thumbnail\|Data_Visualization_5-27-15_part_2.mp4]]		Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4\|thumbnail\|Data_Visualization_5-27-15_part_2.mp4]]