Help:Annotation Pipeline - Revision history

DanielRenfro at 20:01, 15 June 2010

2010-06-15T20:01:02Z

← Older revision		Revision as of 20:01, 15 June 2010
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	==See Also==		==See Also==
	* [[Help:Gene Association File]]		* [[Help:Gene Association File]]


			[[Category:Help]]

DanielRenfro at 19:55, 12 May 2010

2010-05-12T19:55:51Z

← Older revision		Revision as of 19:55, 12 May 2010
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	==Overview==		==Overview==
	Each quarter [[EcoliWiki]] incorporates the ''E. coli'' annotations from [[EcoCyc]] into our website. Upon each [[EcoCyc]] release the annotations are parsed and loaded into the wiki using automated scripts. This is reflected in the montly annotation file submitted to the [[Gene Ontology]] each month.		Each quarter [[EcoliWiki]] incorporates the ''E. coli'' annotations from [[EcoCyc]] into our website. Upon each [[EcoCyc]] release the annotations are parsed and loaded into the wiki using automated scripts. This is reflected in the montly annotation file submitted to the [[Help:Gene_ontology\|Gene Ontology]] each month.

	==Detailed Description==		==Detailed Description==
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	:# determines which gene products need annotations removed		:# determines which gene products need annotations removed
	:# visits those pages in the wiki		:# visits those pages in the wiki
	:# finds the annotation to remove from the [[Help:Gene_ontology Gene Ontology]] table		:# finds the annotation to remove from the [[Help:Gene_ontology\|Gene Ontology]] table
	:# saves the page to commit the edit		:# saves the page to commit the edit
	:# does the same steps for adding annotations		:# does the same steps for adding annotations

DanielRenfro: /* Detailed Description */

2010-05-12T19:55:25Z

Detailed Description

← Older revision		Revision as of 19:55, 12 May 2010
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	; Use a script to add/remove annotations from [[EcoliWiki]]		; Use a script to add/remove annotations from [[EcoliWiki]]
	; A [[wikipedia:PHP\|PHP]] script adds and removes the annotations from the wiki based on the file.		: A [[wikipedia:PHP\|PHP]] script adds and removes the annotations from the wiki based on the file.
	: Specifically, does the following things:		: Specifically, does the following things:
	:# looks in the <tt>differences.lost.gaf</tt> file		:# looks in the <tt>differences.lost.gaf</tt> file
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	:# saves the page to commit the edit		:# saves the page to commit the edit
	:# does the same steps for adding annotations		:# does the same steps for adding annotations


	==Known Issues==		==Known Issues==

DanielRenfro at 19:55, 12 May 2010

2010-05-12T19:55:09Z

← Older revision		Revision as of 19:55, 12 May 2010
Line 1:		Line 1:
	==Overview==		==Overview==
	Each quarter [[EcoliWiki]] incorporates the ''E. coli'' annotations from [[EcoCyc]] into our website. Upon each [[EcoCyc]] release the annotations are parsed and loaded into the wiki using automated scripts.		Each quarter [[EcoliWiki]] incorporates the ''E. coli'' annotations from [[EcoCyc]] into our website. Upon each [[EcoCyc]] release the annotations are parsed and loaded into the wiki using automated scripts. This is reflected in the montly annotation file submitted to the [[Gene Ontology]] each month.

	==Detailed Description==		==Detailed Description==
	~~{{NeedsEditing}}~~		; Obtain the latest [[EcoCyc]] release
			: Quarterly annotations are fetched from [[EcoCyc]] and parsed for validity.

	~~A standardized method of loading annotations into [[EcoliWiki]]~~ is in the ~~works~~:		; Calculate the changes
	# ~~remove (to a file) the ecocyc~~.~~removed annotations~~		: The most recent release is compared to the previous release and two files are generated:
	# ~~remove~~ (~~to a file~~) the ~~IEAs that are older than 1 year~~		:# <tt>differences.lost.gaf</tt>
	~~# validate the EcoCyc GAF~~		:# <tt>differences.gained.gaf</tt>
	~~#* send the output and reasoning for the changes back~~ to [[~~EcoCyc~~]] ~~(Markus)~~		: These two files contain the annotatations (in [http://www.geneontology.org/GO.format.gaf-1_0.shtml GAF 1.0] format) that have been lost or gained since the last release, respectively.
	# ~~sort~~ the file on the ~~appropriate columns~~
	# ~~convert~~ to [[~~IFALT~~]]		; Use a script to add/remove annotations from [[EcoliWiki]]
	# ~~collapse~~ the ~~IEAs~~		; A [[wikipedia:PHP\|PHP]] script adds and removes the annotations from the wiki based on the file.
	# ~~add metadata and load into [[EcoliWiki]]~~		: Specifically, does the following things:
			:# looks in the <tt>differences.lost.gaf</tt> file
			:# determines which gene products need annotations removed
			:# visits those pages in the wiki
			:# finds the annotation to remove from the [[Help:Gene_ontology Gene Ontology]] table
			:# saves the page to commit the edit
			:# does the same steps for adding annotations

	~~Quarterly [[EcoliWiki]] incorporates the recent changes in annotations from [[EcoCyc]]. These changes are reflected in the monthly submission to the [[Gene Ontology]].~~

	==Known Issues==		==Known Issues==
	* ~~Currently~~ [[EcoliWiki]] ~~has not been removing annotations that~~ were ~~removed from [[EcoCyc]].~~		* A number of ''old'' annotations are still in [[EcoliWiki]]. These were added early in the life of [[EcoliWiki]], and were not tagged with the appropriate metadata that allows us to add/delete annotations. These are spurious and do not contribute to the total set of annotations, as these annotations could be out of date or incorrect.
	~~: (<small>A fix is~~ in the ~~works. --~~[[~~User:DanielRenfro\|Daniel~~]] ~~16:34~~, ~~9 March 2010 (UTC)<~~/~~small>)~~

	~~===IEA Collapsing===~~
	~~In order to keep the number of computational~~ annotations ~~rows down to a manageable level (and so they don't overwhelm the tables) EcoliWiki "collapses" these rows~~. ~~This means ''computational'' annotations for any particular product that~~ are ~~assigned~~ to the ~~same GO term will be collapsed into one row.~~

	~~An example~~, these ~~rows are from a gene_associations.ecocyc file that was imported:~~
	EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:hamap\|GO_REF:0000020 IEA HAMAP:MF_01152 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
	EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR012724 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
	EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR008971 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
	EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR003095 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
	EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR002939 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
	EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR001305 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB


	~~Notice that these 5~~ annotations ~~are assigned to only 2 GO terms. After processing (and formatting for EcoliWiki), they look like this:~~
	~~GO:0051082 unfolded protein binding GO_REF:0000002 IEA: Inferred from Electronic Annotation InterPro:IPR001305 F Seeded from EcoCyc 12~~.~~5 complete~~
	~~GO_REF:0000002 InterPro:IPR002939~~
	~~GO_REF:0000002 InterPro:IPR003095~~
	~~GO_REF:0000002 InterPro:IPR008971~~
	~~GO_REF:0000002 InterPro:IPR012724~~
	~~GO_REF:0000020 HAMAP:MF_01152~~
	~~GO_REF:0000002 InterPro:IPR001305~~

	==See Also==		==See Also==
	* [[Help:Gene Association File]]		* [[Help:Gene Association File]]

DanielRenfro: /* Detailed Description */

2010-05-12T19:40:54Z

Detailed Description

← Older revision		Revision as of 19:40, 12 May 2010
Line 15:		Line 15:
	# add metadata and load into [[EcoliWiki]]		# add metadata and load into [[EcoliWiki]]

			Quarterly [[EcoliWiki]] incorporates the recent changes in annotations from [[EcoCyc]]. These changes are reflected in the monthly submission to the [[Gene Ontology]].

	==Known Issues==		==Known Issues==

DanielRenfro at 22:26, 4 May 2010

2010-05-04T22:26:46Z

← Older revision		Revision as of 22:26, 4 May 2010
Line 1:		Line 1:
			==Overview==
			Each quarter [[EcoliWiki]] incorporates the ''E. coli'' annotations from [[EcoCyc]] into our website. Upon each [[EcoCyc]] release the annotations are parsed and loaded into the wiki using automated scripts.

			==Detailed Description==
	{{NeedsEditing}}		{{NeedsEditing}}

	~~==Overview==~~		A standardized method of loading annotations into [[EcoliWiki]] is in the works:
	~~Each quarter~~ [[EcoliWiki]] ~~incorporates~~ the ~~''E~~. ~~coli''~~ annotations ~~from~~ [[EcoCyc]] ~~into our website. Upon each~~ [[~~EcoCyc~~]] ~~release~~ the ~~annotations are parsed~~ and ~~loaded~~ into ~~the wiki using automated scripts.~~		# remove (to a file) the ecocyc.removed annotations
			# remove (to a file) the IEAs that are older than 1 year
			# validate the EcoCyc GAF
			#* send the output and reasoning for the changes back to [[EcoCyc]] (Markus)
			# sort the file on the appropriate columns
			# convert to [[IFALT]]
			# collapse the IEAs
			# add metadata and load into [[EcoliWiki]]



	==Known Issues==		==Known Issues==
	* Currently [[EcoliWiki]] has not been removing annotations that were removed from [[EcoCyc]].		* Currently [[EcoliWiki]] has not been removing annotations that were removed from [[EcoCyc]].
	: (<small>A fix is in the works. --[[User:DanielRenfro\|Daniel]] 16:34, 9 March 2010 (UTC)</small>)		: (<small>A fix is in the works. --[[User:DanielRenfro\|Daniel]] 16:34, 9 March 2010 (UTC)</small>)


	~~==Detailed Description==~~

	===IEA Collapsing===		===IEA Collapsing===
	* In order to keep the number of computational annotations rows down to a manageable level (and so they don't overwhelm the tables) EcoliWiki "collapses" these rows. This means ''computational'' annotations for any particular product that are assigned to the same GO term will be collapsed into one row.		In order to keep the number of computational annotations rows down to a manageable level (and so they don't overwhelm the tables) EcoliWiki "collapses" these rows. This means ''computational'' annotations for any particular product that are assigned to the same GO term will be collapsed into one row.

	An example, these rows are from a gene_associations.ecocyc file that was imported:		An example, these rows are from a gene_associations.ecocyc file that was imported:
Line 31:		Line 41:
	GO_REF:0000020 HAMAP:MF_01152		GO_REF:0000020 HAMAP:MF_01152
	GO_REF:0000002 InterPro:IPR001305		GO_REF:0000002 InterPro:IPR001305














	==See Also==		==See Also==
	* [[Help:Gene Association File]]		* [[Help:Gene Association File]]

DanielRenfro at 16:34, 9 March 2010

2010-03-09T16:34:38Z

← Older revision		Revision as of 16:34, 9 March 2010
Line 1:		Line 1:
	{{NeedsEditing}}		{{NeedsEditing}}

			==Overview==
			Each quarter [[EcoliWiki]] incorporates the ''E. coli'' annotations from [[EcoCyc]] into our website. Upon each [[EcoCyc]] release the annotations are parsed and loaded into the wiki using automated scripts.

			==Known Issues==
			* Currently [[EcoliWiki]] has not been removing annotations that were removed from [[EcoCyc]].
			: (<small>A fix is in the works. --[[User:DanielRenfro\|Daniel]] 16:34, 9 March 2010 (UTC)</small>)


			==Detailed Description==

			===IEA Collapsing===
			* In order to keep the number of computational annotations rows down to a manageable level (and so they don't overwhelm the tables) EcoliWiki "collapses" these rows. This means ''computational'' annotations for any particular product that are assigned to the same GO term will be collapsed into one row.

			An example, these rows are from a gene_associations.ecocyc file that was imported:
			EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:hamap\|GO_REF:0000020 IEA HAMAP:MF_01152 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
			EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR012724 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
			EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR008971 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
			EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR003095 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
			EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR002939 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB
			EcoCyc EG10240-MONOMER DnaJ GO:0051082 GOA:interpro\|GO_REF:0000002 IEA InterPro:IPR001305 F chaperone with DnaK; heat shock protein dnaJ\|groP\|grpC\|b0015\|ECK0015 protein taxon:511145 20091214 UniProtKB


			Notice that these 5 annotations are assigned to only 2 GO terms. After processing (and formatting for EcoliWiki), they look like this:
			GO:0051082 unfolded protein binding GO_REF:0000002 IEA: Inferred from Electronic Annotation InterPro:IPR001305 F Seeded from EcoCyc 12.5 complete
			GO_REF:0000002 InterPro:IPR002939
			GO_REF:0000002 InterPro:IPR003095
			GO_REF:0000002 InterPro:IPR008971
			GO_REF:0000002 InterPro:IPR012724
			GO_REF:0000020 HAMAP:MF_01152
			GO_REF:0000002 InterPro:IPR001305

DanielRenfro at 23:57, 8 March 2010

2010-03-08T23:57:57Z

← Older revision		Revision as of 23:57, 8 March 2010
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	{{NeedsEditing}}		{{NeedsEditing}}



			==See Also==
			* [[Help:Gene Association File]]

DanielRenfro: Created page with '{{NeedsEditing}}'

2010-03-08T23:57:20Z

Created page with '{{NeedsEditing}}'

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