PO Developers Guide - Revision history

Cooperl at 21:55, 13 October 2016

2016-10-13T21:55:00Z

Cooperl: /* Relations among PO classes */

2015-09-28T21:54:48Z

Relations among PO classes

Meiera: /* Icons for Relations */

2015-09-28T18:53:14Z

Icons for Relations

Meiera: /* downloading Plant Ontology files */

2015-09-02T21:58:11Z

downloading Plant Ontology files

Meiera: /* References (Dbxrefs) */

2015-09-02T21:57:09Z

References (Dbxrefs)

Meiera: /* Committing changes */

2015-09-02T21:56:28Z

Committing changes

Meiera: /* Icons for Relations */

2015-09-02T21:55:10Z

Icons for Relations

Meiera: /* Renaming and redefining terms */

2015-09-02T21:53:34Z

Renaming and redefining terms

Meiera: /* Merging terms */

2015-09-02T21:50:03Z

Merging terms

Meiera: /* Adding terms */

2015-09-02T21:49:13Z

Adding terms

@@ Line 1: / Line 1: @@
 ''This page is under re-construction''
-As an [http://www.obofoundry.org/ OBO Foundry] candidate ontology, the Plant Ontology Consortium (POC) is guided by the [http://www.obofoundry.org/crit.shtml OBO Foundry principles]. Other standard operating procedures have been developed to insure consistency among curators.
+As an [http://www.obofoundry.org/ OBO Foundry] ontology, the Plant Ontology Consortium (POC) is guided by the [http://www.obofoundry.org/crit.shtml OBO Foundry principles]. Other standard operating procedures have been developed to insure consistency among curators.
 =Plant Ontology Files=

@@ Line 180: / Line 180: @@
 ==Relations among PO classes==
-Under the standard Plant Ontology data structure, terms are allowed to have a limited number of relations. Relations are formally defined in the [http://www.obofoundry.org/ro/ OBO relation ontology].
+Under the standard Plant Ontology data structure, terms are allowed to have a limited number of relations. Relations are formally defined in the [https://github.com/oborel/obo-relations/ OBO relation ontology].
 The PO currently has following term-to-term relation types:

@@ Line 195: / Line 195: @@
 ==Icons for Relations==
-When a new relation is added to the Ontology, an icon should be developed for it and it should be stored on the [https://github.com/Planteome/common-files-for-ref-ontologies/tree/master/icons Github] site.
+When a new relation is added to the Ontology, an icon should be developed for it and it should be stored on the [https://github.com/Planteome/common-files-for-ref-ontologies/tree/master/icons GitHub] site.
 ===Associations and relations===

← Older revision		Revision as of 21:58, 2 September 2015
Line 32:		Line 32:


−	In compliance with [http://www.obofoundry.org/crit.shtml OBO Foundry principles], the PO is "open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers." The live version of this file is available through our ~~SVN~~ repository at https://raw.githubusercontent.com/Planteome/plant-ontology/master/po-release-files/plant_ontology.obo as well as on our web browser at http://plantontology.org/amigo/go.cgi.	+	In compliance with [http://www.obofoundry.org/crit.shtml OBO Foundry principles], the PO is "open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers." The live version of this file is available through our Github repository at https://raw.githubusercontent.com/Planteome/plant-ontology/master/po-release-files/plant_ontology.obo as well as on our web browser at http://plantontology.org/amigo/go.cgi.

	==old file formats:==		==old file formats:==

@@ Line 216: / Line 216: @@
 A '''synonym dbxref''' is the same as a definition dbxref, except that it describes the publication that used the synonym.
-A term may have an ''Xref'' that is not associated with a definition or synonym. This may either refer to an external ontology that has a similar term (and will take the form of the unique identifier for that term in the external ontology), or it may be a link to an image in an external database (including a URL). Other types of xrefs are also possible, such as references to the Source Forge tracker items that discuss terms (OBO_PO_SF).
+A term may have an ''Xref'' that is not associated with a definition or synonym. This may either refer to an external ontology that has a similar term (and will take the form of the unique identifier for that term in the external ontology), or it may be a link to an image in an external database (including a URL). Other types of xrefs are also possible, such as references to the Github issue tracker items that discuss terms (OBO_PO_SF).
 ==Obsoleting and destroying terms==

@@ Line 268: / Line 268: @@
 =Committing changes=
-*Always do a SVN update before editing, to make sure you are using the current version of the file.
+*Always do a <code>git pull</code> before editing, to make sure you are using the current version of the file.
-*As soon as you are finished editing, commit to SVN. Provide a brief description of the changes you made. Details of changes (text of new definitions, reference, etc.) should go on the SourceForge tracker.
+*As soon as you are finished editing, commit to Github. Provide a brief description of the changes you made. Details of changes (text of new definitions, reference, etc.) should go on the Github issue tracker.
 *Record any new terms, obsolete terms, or term name changes on the appropriate "New and Obsolete terms" wiki page for the upcoming release. If you later destroy a new term, or change its name, be sure to update this list. Maintain the list in numerical order, so it is easy to check for completeness.

@@ Line 142: / Line 142: @@
 Since the PO is still actively under development, it is often necessary to make changes to existing terms. This can happen if the curators feel that a term name is not clear, or is not the most commonly used name, or if a definition is found to be incorrect, or if two or more terms are redundant with each other. Curators should use the following guidelines:
-'''Renaming:''' A change in the primary name of a term should be approved by the group, and a tracker item posted on [https://sourceforge.net/tracker/?group_id=76834&atid=835555 Source Forge]. If the name is changed from a less-common to a more-common name, then the term's ID should stay the same, and the original name should be added as a synonym. If the name is changed because the original name was incorrect for the definition, then the term should be obsoleted, and replaced by a new term with the correct name and definition.
+'''Renaming:''' A change in the primary name of a term should be approved by the group, and a tracker item posted on [https://github.com/Planteome/plant-ontology/issues Github]. If the name is changed from a less-common to a more-common name, then the term's ID should stay the same, and the original name should be added as a synonym. If the name is changed because the original name was incorrect for the definition, then the term should be obsoleted, and replaced by a new term with the correct name and definition.
-'''Redefining:''' Any substantive change in the definition of a term, and any change in the definition of an upper-level term (generally 4 or fewer layers into the ontology) should be approved by the group, and a tracker item posted on [https://sourceforge.net/tracker/?group_id=76834&atid=835555 Source Forge].
+'''Redefining:''' Any substantive change in the definition of a term, and any change in the definition of an upper-level term (generally 4 or fewer layers into the ontology) should be approved by the group, and a tracker item posted on [https://github.com/Planteome/plant-ontology/issues Github].
-There is an ongoing effort to convert all text definitions in the PO to the genus-differentia form (see Term definitions, below). If a new genus-differentia definition is for a lower-level ontology term and does change the meaning of the original definition but only uses the new wording format, then a curator may change the definition without posting a tracker item. For example, a change to the definition of epidermis (a term with three levels of ancestors), should be posted on Source Forge, while converting all of the definitions of the different types of epidermis (shoot epidermis, root epidermis, leaf epidermis, etc.) to genus-differentia form does not need a Source Forge tracker item. If the conversion to genus-differentia form changes the meaning of the definition then a tracker item should be posted.
+There is an ongoing effort to convert all text definitions in the PO to the genus-differentia form (see Term definitions, below). If a new genus-differentia definition is for a lower-level ontology term and does change the meaning of the original definition but only uses the new wording format, then a curator may change the definition without posting a tracker item. For example, a change to the definition of epidermis (a term with three levels of ancestors), should be posted on [https://github.com/Planteome/plant-ontology/issues Github], while converting all of the definitions of the different types of epidermis (shoot epidermis, root epidermis, leaf epidermis, etc.) to genus-differentia form does not need a Github Issues tracker item. If the conversion to genus-differentia form changes the meaning of the definition then a tracker item should be posted.
 If the original definition for a term was wrong, and changes to a definition substantially change its meaning, such that a comparison of the original definition and the new definition suggest that they are referring to two different classes, then the original term should be made obsolete, and replaced by a term with the same name but correct definition (see also [http://obofoundry.org/wiki/index.php/Identifiers#Procedure_for_changing_the_definition_of_a_term OBO Foundry principles]). Having a live term and an obsolete term wit the same name will prevent the onotology form loading onto the web browser, so the original, obsolete term should be renamed "obsolete term name", where "term name" is the original name.

@@ Line 88: / Line 88: @@
 ==Merging terms==
-Merging and splitting of terms that have descendents can have broad ripple effects. Such changes will need to be approved by a consensus prior to committing them. Any proposed merges or splits should be posted on the [https://sourceforge.net/tracker/?group_id=76834&atid=835555 Source Forge tracker].
+Merging and splitting of terms that have descendents can have broad ripple effects. Such changes will need to be approved by a consensus prior to committing them. Any proposed merges or splits should be posted on the [https://github.com/Planteome/plant-ontology/issues Github Issue tracker].
 Two or more terms should be merged when the curators determine that they are describing the same class of objects. This often occurs when two ontologies are merged, and there is some overlap of classes between the ontologies. It can also occur if a decision is made only to include a more general class rather than several specific classes. For example, achene, berry and capsule were merged into the term fruit. Finally, merging may be necessary if the curators determine that two classes are redundant, such as when meristemoid was merged with initial cell.

@@ Line 84: / Line 84: @@
 New terms can often be added to the tips of the ontology (leaf terms) without disturbing the structure of the graph. For example, creating a new specific instance of a more general term will not disturb sibling or cousin terms. However, introducing a new root term or a term into the middle of the graph can disturb existing parent/children relationships, and needs to be performed with more care.
-All new terms that are added that are added to the PO should be posted as a request on our [https://sourceforge.net/tracker/?group_id=76834&atid=835555 Source Forge tracker]. This provides an opportunity for all curators and collaborators to comment on the proposed term and its definition and relations. The tracker item also provides a record of the decisions that were made about a term, when those decisions were made, and why.
+All new terms that are added that are added to the PO should be posted as a request on our [https://github.com/Planteome/plant-ontology/issues Github Issues tracker]. This provides an opportunity for all curators and collaborators to comment on the proposed term and its definition and relations. The tracker item also provides a record of the decisions that were made about a term, when those decisions were made, and why.
 ==Merging terms==