Thursday April 16th, 2015 - Revision history

Cooperl at 18:05, 18 May 2015

2015-05-18T18:05:26Z

← Older revision		Revision as of 18:05, 18 May 2015
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	(will become part of Plant Stress Ontology)		(will become part of Plant Stress Ontology)
	* new undergrad helper working on adding diseases		* new undergrad helper working on adding diseases
	* will also tie into the Panzea dataset as they also have ~~diseaes~~ traits		* will also tie into the Panzea dataset as they also have diseases traits

	* Working with new collaborating Database group [http://www.phi-base.org/ PHI-Base Pathogen] - Host Interaction database- Initiative from Rothamstad in England		* Working with new collaborating Database group [http://www.phi-base.org/ PHI-Base Pathogen] - Host Interaction database- Initiative from Rothamstad in England

Cooperl: /* Next meeting Thursday May 7th */

2015-04-30T16:08:31Z

Next meeting Thursday May 7th

← Older revision		Revision as of 16:08, 30 April 2015
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	Leo has been working with JE and his local Sys Admin to get the SVN access working- maybe fixed by moving to GitHub		Leo has been working with JE and his local Sys Admin to get the SVN access working- maybe fixed by moving to GitHub

	==Next meeting Thursday May ~~7th~~==		==Next meeting Thursday May 21st==

Cooperl: /* E. Other Comments: */

2015-04-23T01:24:33Z

E. Other Comments:

← Older revision		Revision as of 01:24, 23 April 2015
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	==E. Other Comments:==		==E. Other Comments:==
			Leo has been working with JE and his local Sys Admin to get the SVN access working- maybe fixed by moving to GitHub

	==Next meeting Thursday May 7th==		==Next meeting Thursday May 7th==

Cooperl: /* Discussion about storing Ontologies and Associations at GitHub: */

2015-04-23T01:22:15Z

Discussion about storing Ontologies and Associations at GitHub:

← Older revision		Revision as of 01:22, 23 April 2015
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	* '''Question about whether or not we need to maintain the history?''' PJ: Ideally we would keep the history with the ontology files, not so important about the association files.		* '''Question about whether or not we need to maintain the history?''' PJ: Ideally we would keep the history with the ontology files, not so important about the association files.
	* LC: Theoretically this is possible, but it is complicated. On the 4-3 Github call, JE said that he would reorganize the files on the SVN and try importing the history.		* LC: Theoretically this is possible, but it is complicated. On the 4-3 Github call, JE said that he would reorganize the files on the SVN and try importing the history.
	* PJ: Suggest someone should send an email to Github and ask them how best to transfer the SVN history....''~~Whi~~ is doing this??''		* PJ: Suggest someone should send an email to Github and ask them how best to transfer the SVN history....''Who is doing this??''
	* One option would be to maintain the SVN and run a chron job to the Github or visa versa, but this does not solve anything and adds a lot of extra work for maintenance.		* One option would be to maintain the SVN and run a chron job to the Github or visa versa, but this does not solve anything and adds a lot of extra work for maintenance.
	* PJ can ask his contact "GitHub-Justin" if we have questions.		* PJ can ask his contact "GitHub-Justin" if we have questions.

Cooperl: /* Browsing in AmiGO2 */

2015-04-23T01:21:30Z

Browsing in AmiGO2

← Older revision		Revision as of 01:21, 23 April 2015
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	* Need an annotation platform- one idea is a "wiki" type platform		* Need an annotation platform- one idea is a "wiki" type platform
	* May look at GO tool "Noctua", CM can demo on a future call see Link to [[https://github.com/geneontology/noctua Noctua on GitHub]]		* May look at GO tool "Noctua", CM can demo on a future call see Link to [[https://github.com/geneontology/noctua Noctua on GitHub]]
	*

	== C. Update from AISO/BisQue group- Justin Preece:==		== C. Update from AISO/BisQue group- Justin Preece:==

Cooperl: /* Browsing in AmiGO2 */

2015-04-23T01:21:18Z

Browsing in AmiGO2

← Older revision		Revision as of 01:21, 23 April 2015
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	===Browsing in AmiGO2===		===Browsing in AmiGO2===
	* Type term into search box on front page, ~~autofill~~ feature will be useful,		* Type term into search box on front page, auto-fill feature will be useful
	* Column sorting can be customized		* Column sorting can be customized
	* NCBI ids are not displayed correctly as the NCBI tree is not loaded		* NCBI ids are not displayed correctly as the NCBI tree is not loaded
	* Need to check on "Source"- where is it pulling that from?		* Need to check on "Source"- where is it pulling that from? ''It looks like it is using the namespaces from the terms.''



	* "Panther Gene Families"- We can customize this and can use our own Inparanoid gene families, as Panther does not have too many plants represented		* "Panther Gene Families"- We can customize this and can use our own Inparanoid gene families, as Panther does not have too many plants represented
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	PJ- Goal is a "Pan-Gene" database - centralized resource for nomenclature and management		PJ- Goal is a "Pan-Gene" database - centralized resource for nomenclature and management
	* Need an annotation platform- one idea is a "wiki" type platform		* Need an annotation platform- one idea is a "wiki" type platform
	* May look at GO tool "Noctua", CM can demo on a future call		* May look at GO tool "Noctua", CM can demo on a future call see Link to [[https://github.com/geneontology/noctua Noctua on GitHub]]
	*		*

Cooperl: /* Test set of annotations loaded */

2015-04-23T01:19:00Z

Test set of annotations loaded

← Older revision		Revision as of 01:19, 23 April 2015
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	\| Plant_Ontology \|\| rice \|\| po_ontology_IMP_gene_oryza_poc.assoc \|\| yes		\| Plant_Ontology \|\| rice \|\| po_ontology_IMP_gene_oryza_poc.assoc \|\| yes
	\|-		\|-
	\| Trait_Ontology \|\| ? \|\| to_diversity_arabidopsis.assoc \|\| yes		\| Trait_Ontology \|\| Arabidopsis \|\| to_diversity_arabidopsis.assoc \|\| yes
	\|-		\|-
	\| Trait_Ontology \|\| ? \|\| to_Protein_association.assoc \|\| no		\| Trait_Ontology \|\| ? \|\| to_Protein_association.assoc \|\| no
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	\|Plant_EO \|\| ? \|\| eo_qtl.assoc \|\| no		\|Plant_EO \|\| ? \|\| eo_qtl.assoc \|\| no
	\|-		\|-
	\|Plant_EO \|\| ~~arabidopsis~~ \|\| eo_diversity_arabidopsis.assoc \|\| no		\|Plant_EO \|\| Arabidopsis \|\| eo_diversity_arabidopsis.assoc \|\| no
	\|-		\|-
	\| Plant_EO \|\| ? \|\| eo_gene.assoc \|\| no		\| Plant_EO \|\| ? \|\| eo_gene.assoc \|\| no

Cooperl: /* Test set of annotations loaded */

2015-04-23T00:46:38Z

Test set of annotations loaded

Cooperl: /* Discussion about storing Ontologies and Associations at GitHub: */

2015-04-21T21:59:23Z

Discussion about storing Ontologies and Associations at GitHub:

← Older revision		Revision as of 21:59, 21 April 2015
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	* One option would be to maintain the SVN and run a chron job to the Github or visa versa, but this does not solve anything and adds a lot of extra work for maintenance.		* One option would be to maintain the SVN and run a chron job to the Github or visa versa, but this does not solve anything and adds a lot of extra work for maintenance.
	* PJ can ask his contact "GitHub-Justin" if we have questions.		* PJ can ask his contact "GitHub-Justin" if we have questions.

			Note from after the call: see this link for [[https://github.com/blog/1986-announcing-git-large-file-storage-lfs Announcing Git Large File Storage (LFS)]]

	====Summary of Goals: ====		====Summary of Goals: ====

Cooperl: /* Discussion about storing Ontologies and Associations at GitHub: */

2015-04-21T18:30:52Z

Discussion about storing Ontologies and Associations at GitHub:

← Older revision		Revision as of 18:30, 21 April 2015
Line 158:		Line 158:
	===Discussion about storing Ontologies and Associations at GitHub:===		===Discussion about storing Ontologies and Associations at GitHub:===
	* Working on plans for moving the ontologies to GitHub, still not completely decided how to do this. See meeting notes [[Ontology_Working_Group_GitHub_Meeting,_Tuesday_April_3rd,_2015\|GitHub Mtg 4-3]]		* Working on plans for moving the ontologies to GitHub, still not completely decided how to do this. See meeting notes [[Ontology_Working_Group_GitHub_Meeting,_Tuesday_April_3rd,_2015\|GitHub Mtg 4-3]]
	* Question about whether or not we need to maintain the history? PJ: Ideally we would keep the history with the .
	* LC Theoretically this is possible, but it is complicated. On the 4-3 Github call, JE said that he would reorganize the files on the SVN		*Re: associations: PJ met a person (another Justin!) from Github on the plane, they are interested in hosting large datasets and offering them through APIs etc
	* PJ: Suggest someone should send an email to Github and ask them how best to transfer the SVN history.
			* '''Question about whether or not we need to maintain the history?''' PJ: Ideally we would keep the history with the ontology files, not so important about the association files.
			* LC: Theoretically this is possible, but it is complicated. On the 4-3 Github call, JE said that he would reorganize the files on the SVN and try importing the history.
			* PJ: Suggest someone should send an email to Github and ask them how best to transfer the SVN history....''Whi is doing this??''
			* One option would be to maintain the SVN and run a chron job to the Github or visa versa, but this does not solve anything and adds a lot of extra work for maintenance.
			* PJ can ask his contact "GitHub-Justin" if we have questions.

	====Summary of Goals: ====		====Summary of Goals: ====

← Older revision		Revision as of 00:46, 23 April 2015
Line 75:		Line 75:
	* Load times seem much better than the old AmiGO, at least for these annotations		* Load times seem much better than the old AmiGO, at least for these annotations
	* Problems were found in some of the files, specifically coming from the col 16- annotation extensions and also in column 5 (ontology ID), where spaces are causing problems		* Problems were found in some of the files, specifically coming from the col 16- annotation extensions and also in column 5 (ontology ID), where spaces are causing problems
	* JE corrected the issues he found in the files, but these revised files need to be committed back to the SVN		* JE corrected the issues he found in the files, but these revised files need to be committed back to the SVN- ''Done''

	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Ontology !! Species !! filename		! Ontology !! Species !! filename !! Issues?
	\|-		\|-
	\| PO-Anatomy \|\|rice \|\| po_anatomy_gene_oryza_gramene.assoc		\| PO-Anatomy \|\|rice \|\| po_anatomy_gene_oryza_gramene.assoc \|\| no
	\|-		\|-
	\| PO-Anatomy \|\| rice \|\| po_anatomy_gene_oryza_poc.assoc		\| PO-Anatomy \|\| rice \|\| po_anatomy_gene_oryza_poc.assoc \|\| yes
	\|-		\|-
	\| PO-Anatomy \|\| rice \|\| po_anatomy_qtl_oryza_gramene.assoc		\| PO-Anatomy \|\| rice \|\| po_anatomy_qtl_oryza_gramene.assoc \|\| no
	\|-		\|-
	\| PO-Anatomy \|\| maize \|\| po_anatomy_gene_zea_MaizeGDB.assoc		\| PO-Anatomy \|\| maize \|\| po_anatomy_gene_zea_MaizeGDB.assoc \|\| no
	\|-		\|-
	\| PO-Anatomy \|\| grape \|\| po_anatomy_gene_vitis_poc.assoc		\| PO-Anatomy \|\| grape \|\| po_anatomy_gene_vitis_poc.assoc \|\| yes
	\|-		\|-
	\| PO-Anatomy \|\| maize \|\|po_anatomy_stock_zea_MaizeGDB.assoc		\| PO-Anatomy \|\| maize \|\|po_anatomy_stock_zea_MaizeGDB.assoc \|\| no
	\|-		\|-
	\| PO_Growth_Stage \|\| rice \|\| po_growth_gene_oryza_gramene.assoc		\| PO_Growth_Stage \|\| rice \|\| po_growth_gene_oryza_gramene.assoc \|\| no
	\|-		\|-
	\| PO_Growth_Stage \|\| rice \|\| po_growth_qtl_oryza_gramene.assoc		\| PO_Growth_Stage \|\| rice \|\| po_growth_qtl_oryza_gramene.assoc \|\| no
	\|-		\|-
	\| PO_Growth_Stage \|\| grape \|\| po_growth_gene_vitis_poc.assoc		\| PO_Growth_Stage \|\| grape \|\| po_growth_gene_vitis_poc.assoc \|\| yes
	\|-		\|-
	\| Plant_Ontology \|\| rice \|\| po_ontology_IMP_gene_oryza_poc.assoc		\| Plant_Ontology \|\| rice \|\| po_ontology_IMP_gene_oryza_poc.assoc \|\| yes
	\|-		\|-
	\| Trait_Ontology \|\| ? \|\| to_diversity_arabidopsis.assoc		\| Trait_Ontology \|\| ? \|\| to_diversity_arabidopsis.assoc \|\| yes
	\|-		\|-
	\| Trait_Ontology \|\| ? \|\| to_Protein_association.assoc		\| Trait_Ontology \|\| ? \|\| to_Protein_association.assoc \|\| no
	\|-		\|-
	\| Trait_Ontology \|\| ? \|\| to_QTL_association.assoc		\| Trait_Ontology \|\| ? \|\| to_QTL_association.assoc \|\| no
	\|-		\|-
	\| Trait_Ontology \|\| Rice \|\| to_diversity_rice.assoc		\| Trait_Ontology \|\| Rice \|\| to_diversity_rice.assoc \|\| no
	\|-		\|-
	\| Trait_Ontology \|\| ? \|\| to_Gene_association.assoc		\| Trait_Ontology \|\| ? \|\| to_Gene_association.assoc \|\| no
	\|-		\|-
	\| Plant_EO \|\| ? \|\| eo_protein.assoc		\| Plant_EO \|\| ? \|\| eo_protein.assoc \|\| no
	\|-		\|-
	\| Plant_EO \|\| rice \|\| eo_diversity_rice.assoc		\| Plant_EO \|\| rice \|\| eo_diversity_rice.assoc \|\| no
	\|-		\|-
	\|Plant_EO \|\| ? \|\| eo_qtl.assoc		\|Plant_EO \|\| ? \|\| eo_qtl.assoc \|\| no
	\|-		\|-
	\|Plant_EO \|\| arabidopsis \|\| eo_diversity_arabidopsis.assoc		\|Plant_EO \|\| arabidopsis \|\| eo_diversity_arabidopsis.assoc \|\| no
	\|-		\|-
	\| Plant_EO \|\| ? \|\| eo_gene.assoc		\| Plant_EO \|\| ? \|\| eo_gene.assoc \|\| no
	\|-		\|-
	\| Gene_Ontology \|\| rice \|\| go_gramene_oryza.assoc		\| Gene_Ontology \|\| rice \|\| go_gramene_oryza.assoc \|\| no
	\|}		\|}