PO Release SOP Page - Revision history

Meiera: /* Text (tab-delimited) version files: */

2015-10-12T19:20:48Z

Text (tab-delimited) version files:

2015-10-09T23:21:26Z

Creating it from plant_ontology_assert.obo

2015-10-09T23:19:56Z

If a problem is found that needs to be fixed for the release:

2015-10-09T23:19:46Z

Dev version

2015-10-09T23:19:05Z

OWL versions

2015-10-09T23:10:14Z

OWL versions

2015-10-09T23:01:22Z

Files created for the Release

2015-10-09T22:59:00Z

Preparing Ontology Files for Release:

2015-10-09T22:53:40Z

If a problem is found that needs to be fixed for the release:

2015-10-09T22:51:12Z

plant-ontology-assert.obo

@@ Line 365: / Line 365: @@
 The "obsolete" was added because older versions of OBO-Edit did not let you have two terms with the same primary name. I think it does now, but we still kept the practice, just so people wouldn't accidentally use the obsolete term that has the same name.''
-Note: These are generated from the MySql database directly and not from the obo files.  The perl script used to generate the .txt files is located in the [https://github.com/Planteome/plant-ontology/tree/master/scripts-etc plant-ontology/scripts-etc/ GitHub page]
+The perl script used to generate the .txt files is located in the [https://github.com/Planteome/plant-ontology/tree/master/scripts-etc plant-ontology/scripts-etc/ GitHub page]
 ===plant_ontology.txt (was po_all.tbl)===
@@ Line 379: / Line 380: @@
 ===po_synonyms.txt===
-''what is this file?''
+This file lists the ID and names of all terms in the PO and is generated from the plant_ontology.txt file by moving columns into the correct order, and adding prefixes to the ID, name, and synonyms.
-''This file list all PO:ids with their name, Spanish/Japanese synonyms, and definition.''
+<code>cat plant_ontology.txt | awk -F "\t" '{print "id:"$1,"name:"$2,"synonym:"$4$3}' > snynonyms.txt </code>
 ==Location of tab delimited files==

@@ Line 329: / Line 329: @@
 * Save and check by re-opening OboEdit
-=Creating it from plant_ontology_assert.obo =
+===Creating it from plant_ontology_assert.obo ===
 ** Note: We decided not to generate these for Release#21, but can add later if needed.

← Older revision		Revision as of 23:19, 9 October 2015
Line 146:		Line 146:

	This need be done '''prior''' to the release as plant-ontology-assert.obo is the file loaded onto the AmiGO browser. (see below for details)		This need be done '''prior''' to the release as plant-ontology-assert.obo is the file loaded onto the AmiGO browser. (see below for details)
−
−

	===OWL Version of the editor's plant-ontology file:===		===OWL Version of the editor's plant-ontology file:===

← Older revision		Revision as of 23:19, 9 October 2015
Line 146:		Line 146:

	This need be done '''prior''' to the release as plant-ontology-assert.obo is the file loaded onto the AmiGO browser. (see below for details)		This need be done '''prior''' to the release as plant-ontology-assert.obo is the file loaded onto the AmiGO browser. (see below for details)
		+
		+
		+
		+	===OWL Version of the editor's plant-ontology file:===
		+
		+	* April 2013 (SVN # 1840), a new chron job was initiated that creates a owl file from dev every night.
		+
		+	* Creation is done by executing the command "obolib-obo2owl plant_ontology.obo -o plant_ontology.owl" ''(Is this correct?)''
		+
		+	* This file then needs to be hand edited to include the version info. The following line goes right above the </owl:Ontology> line:
		+
		+	<owl:versioninfo>xml:lang="en" version ##</owl:versioninfo>
		+
		+	where ## is the version number.

	==Files created for the Release==		==Files created for the Release==

← Older revision		Revision as of 23:19, 9 October 2015
Line 377:		Line 377:
	*''As of Aug. 2015 plant-ontology.obo.owl file is located in the [https://github.com/Planteome/plant-ontology Planteome GitHub Repository/plant-ontology]''		*''As of Aug. 2015 plant-ontology.obo.owl file is located in the [https://github.com/Planteome/plant-ontology Planteome GitHub Repository/plant-ontology]''

−	~~'''OWL Version of the editor's plant-ontology file:'''~~
−
−	* April 2013 (SVN # 1840), a new chron job was intiated that creates a owl file from dev every night.
−
−	* Creation is done by executing the command "obolib-obo2owl plant_ontology.obo -o plant_ontology.owl" ''(Is this correct?)''
−
−	* This file then needs to be hand edited to include the version info. The following line goes right above the </owl:Ontology> line:
−
−	~~<owl:versioninfo>xml:lang="en" version ##</owl:versioninfo>~~
−
−	~~where ## is the version number.~~

	'''OWL Version of the Live plant-ontology file (release version):'''		'''OWL Version of the Live plant-ontology file (release version):'''

@@ Line 397: / Line 397: @@
 An OWL version of the ontology file is generated for each release, which is located in the plant-ontology/po-release-files repository at: [https://github.com/Planteome/plant-ontology/tree/master/po-release-files GitHub].
-This file is generated from the plant_ontology.obo file at the time of the release, and subsequently copied to GitHub.
+This file is generated from the plant_ontology-##.obo file at the time of the release, and subsequently copied to GitHub.
 Only the plant_ontology.owl file is moved over to GitHub.

← Older revision		Revision as of 23:01, 9 October 2015
Line 150:		Line 150:

	* The OBO file: "plant-ontology-xy.obo" is based on the 'final' version of plant-ontology.obo, with the release # added to differentiate it.		* The OBO file: "plant-ontology-xy.obo" is based on the 'final' version of plant-ontology.obo, with the release # added to differentiate it.
		+	* For version #21: plant-ontology-21.obo

	* Contains all the relations.		* Contains all the relations.

@@ Line 106: / Line 106: @@
 ==Updating the translations==
 *''As of Aug. 2015 the translations folder is located in the [https://github.com/Planteome/plant-ontology/tree/master/po-release-files/translations Github Plant ontology repository po-release-files folder]''
@@ Line 148: / Line 147: @@
 This need be done '''prior''' to the release as plant-ontology-assert.obo is the file loaded onto the AmiGO browser. (see below for details)
-==Files created for release based on the 'final' version of plant-ontology.obo==
+==Files created for the Release==
-* plant-ontology-assert.obo
+* The OBO file:  "plant-ontology-xy.obo" is based on the 'final' version of plant-ontology.obo, with the release # added to differentiate it.
 Note: These additional files should only be generated once the review process is completed. If an ontology problem is found, these will have to be recreated (see below:)

@@ Line 159: / Line 159: @@
 ==Details of the alternative files for the release==
 ===plant-ontology-assert.obo===
-This version is the same as plant-ontology.obo with all nonredundant implied links asserted (added) by a reasoner,
+This version is the same as plant-ontology-21.obo with all nonredundant implied links asserted (added) by a reasoner,
 * Use the OBO-Release manager  [http://code.google.com/p/owltools/wiki/OBOReleaseManagerGUIDocumentation Oort], as the "assert implied links" panel in OBO-Edit does not work very well.  Go here for more information about [https://code.google.com/p/owltools/wiki/OortOptions configuring Oort]