Summary of Changes to PO Jan2011 - Revision history

Cooperl: /* Priorities for this release */

2011-01-15T07:24:20Z

Priorities for this release

Rwalls: /* Mid-level terms */

2011-01-13T19:49:27Z

Mid-level terms

Rwalls: /* Upper-level terms */

2011-01-13T17:23:57Z

Upper-level terms

Rwalls: /* Priorities for this release */

2011-01-13T17:21:01Z

Priorities for this release

Rwalls: /* Overview and general changes */

2011-01-13T17:14:30Z

Overview and general changes

Rwalls: /* Overview and general changes */

2011-01-13T17:12:43Z

Overview and general changes

Rwalls: /* Overview and general changes */

2011-01-13T17:11:42Z

Overview and general changes

Rwalls: /* Overview and general changes */

2011-01-13T17:11:03Z

Overview and general changes

Cooperl: /* Overview and general changes */

2011-01-11T18:08:51Z

Overview and general changes

Cooperl: /* Overview and general changes */

2011-01-11T18:07:30Z

Overview and general changes

@@ Line 38: / Line 38: @@
 Status: All terms requested by Generation Challenge Program (GCP) for Musa spp., have been added, either as new terms or synonyms. Several new terms for legumes have been added, as requested by Austin Mast of Florida State University, as well as several general terms requested by TraitNet and several root terms requested by Rich Zobel. Remaining user requests will be dealt with during the next revision.
-. Add terms to PSO for non-angisperm structures
+. Add terms to PSO for non-angiosperm structures
-Status: New upper level terms have been added: sporangium (PO:0025094), microsporangium (PO:0025202), megasporangium (PO:0025201), gametangium (PO:0025124), antheridium (PO:0025125), and archegonium (PO:0025126). Several more new, specific terms have been added: moss capsule(PO:0025232, moss capsule annulus (PO:0025093, moss capsule valve (0025229, moss capsule columella (PO:0025231), antheridium sperm cell (PO:0025120), pollen sperm cell(PO:0025121, archegonium egg cell (PO:0025122)
+Status: New upper level terms have been added: sporangium (PO:0025094), microsporangium (PO:0025202), megasporangium (PO:0025201), gametangium (PO:0025124), antheridium (PO:0025125), and archegonium (PO:0025126). Several more new, specific terms have been added: moss capsule(PO:0025232, moss capsule annulus (PO:0025093, moss capsule valve (PO:0025229, moss capsule columella (PO:0025231), antheridium sperm cell (PO:0025120), pollen sperm cell(PO:0025121), archegonium egg cell (PO:0025122)
-. Update PGDSO to accomodate a broader range of species
+. Update PGDSO to accommodate a broader range of species
 Status: A new structure for the PGDSO was developed, but it awaits testing and approval. Will be revised and incorporated for next release.

@@ Line 70: / Line 70: @@
 *valve (PO:0000033). Added as a general term for all organ parts that split apart, with children fruit valve (PO:0000033; renamed from old term valve) and new term moss capsule valve (PO:0025229).
-*columella. Made fruit columella (PO:0004540; renamed from old term columella) a child of this, plus new term moss capsule columella (PO:0025231).
+*columella (PO:0025230). Made fruit columella (PO:0004540; renamed from old term columella) a child of this, plus new term moss capsule columella (PO:0025231).
 *stele (PO:0025197). Parent to existing term root stele (PO:0020124), plus new terms shoot axis stele (PO:0025198), branch stele(PO:0025199), and stem stele (PO:0025200).
@@ Line 76: / Line 76: @@
 *sporangium (PO:0025094; added during last release but didn’t have definition), megasporangium (PO:0025201), and microsporangium (PO:0025202). Existing terms nucellus (PO:0020020) and pollen sac (PO:0009070) are children of mega- and microsporangium, respectively.
-*canal, parent of petiole canal
+*canal (PO:0025132), parent of petiole canal (PO:0025133)
 *axil (PO:0025224) as a child of plant anatomical space. Made leaf axil (PO:0009023), branch axil (new) and bract axil (new) children of it.

@@ Line 52: / Line 52: @@
 ===Upper-level terms===
-There were fewer changes to the upper-level terms during this revision than during the last, but several important new terms were added. The Plant Structure Ontology (PSO) got a new root term: plant anatomical entity (PO:0025131). Plant anatomical entity is now parent to the original root term plant structure (PO:0009011), plus the new terms plant anatomical space (PO:0025117) and portion of plant substance (PO:0025161). Children of plant anatomical space include existing terms like stomatal pore, micropyle and stomium, plus new terms like anther pore (PO:0025118), axil (PO:0025224), and canal (PO:0025132). Cuticle (PO:0000022) is currently the only child of portion of plant substance, but later it could have siblings like latex or xylem sap.
+There were fewer changes to the upper-level of the Plant Structure Ontology (PSO) during this revision than during the last, but several important new terms were added. The PSO got a new root term: plant anatomical entity (PO:0025131). Plant anatomical entity is now parent to the original root term plant structure (PO:0009011), plus the new terms plant anatomical space (PO:0025117) and portion of plant substance (PO:0025161). Children of plant anatomical space include existing terms like stomatal pore, micropyle, and stomium, plus new terms like anther pore (PO:0025118), axil (PO:0025224), and canal (PO:0025132). Cuticle (PO:0000022) is currently the only child of portion of plant substance, but later it could have siblings like latex or xylem sap.
-Also at the upper levels, a new term embryonic plant structure (PO:0025099) was added, as a direct child of plant structure. Analogous to the existing term in vitro plant structure (PO:0000004), embryonic plant structures do not have part_of relationships to whole plant, and remain separate from other, mature, plant structures. Only structures that occur exclusively in embryos are children of embryonic plant structure (e.g., coleoptile, suspensor or embryo proper). Likewise, just as in vitro structures can have derives_from relations to in vivo structures, mature plant structures can have develops_from relations to embryonic plant structures. Plant structures that may be part of either an embryo or an adult plant structure (e.g. hypocotyl, parenchyma) do not go under embryonic plant structure.
+Also at the upper levels, a new term embryonic plant structure (PO:0025099) was added, as a direct child of plant structure. Analogous to the existing term in vitro plant structure (PO:0000004), embryonic plant structures do not have part_of relationships to whole plant. Only structures that occur exclusively in embryos are children of embryonic plant structure (e.g., coleoptile, suspensor, or embryo proper). Likewise, just as ''in vitro'' structures can have derives_from relations to ''in vivo'' structures, mature plant structures can have develops_from relations to embryonic plant structures. Plant structures that may be part of either an embryo or an adult plant structure (e.g. hypocotyl, parenchyma) do not go under embryonic plant structure.
 ===Mid-level terms===

@@ Line 32: / Line 32: @@
 . Compliance with OBO Foundry Principles [is_a parents for all terms, compliance with the Basic Formal Ontology (BFO)]
-Status: All but three terms now have is_a parents. The three remaining terms without parents [imbibition (PO:0007022), seedling growth (PO:0007131), shoot emergence (PO:0007030)] are processes that are part_of seed germination. Since we don't yet have a category for processes (may move to GO), we can't give them is_a parents.
+Status: All terms in the PSO now have is_a parents, as well as al but three terms in the PGDSO. The three remaining terms without parents [imbibition (PO:0007022), seedling growth (PO:0007131), shoot emergence (PO:0007030)] are processes that are part_of seed germination. They will be assigned is_a parents during the next round of revisions, when the PGDSO is restructured. A draft version of a restructured PGDSO that is compliant with BFO criteria was prepared. This will be modified and incorporated into the PO during the next round of revisions.
 . Incorporate user requests
-Status: All terms requested byGeneration Challenge Program (GCP) for Musa spp., have been added, either as new terms or synonyms. Several of terms for legumes have been added, as requested by Austin Mast of Florida State University, as well as several general terms requested by TraitNet and several root terms requested by Rich Zobel. Remaining user requests will be dealt with during future revisions.
+Status: All terms requested by Generation Challenge Program (GCP) for Musa spp., have been added, either as new terms or synonyms. Several new terms for legumes have been added, as requested by Austin Mast of Florida State University, as well as several general terms requested by TraitNet and several root terms requested by Rich Zobel. Remaining user requests will be dealt with during the next revision.
 . Add terms to PSO for non-angisperm structures
-Status: New upper level terms have been added: sporangium, microsporangium, megasporangium, gametangium, antheridium, archegonium. Also, several more specific terms have been added: moss capsule(PO:0025232, moss capsule annulus (PO:0025093, moss capsule valve (0025229, moss capsule columella (PO:0025231), antheridium sperm cell (PO:0025120), pollen sperm cell(PO:0025121, archegonium egg cell (PO:0025122)
+Status: New upper level terms have been added: sporangium (PO:0025094), microsporangium (PO:0025202), megasporangium (PO:0025201), gametangium (PO:0025124), antheridium (PO:0025125), and archegonium (PO:0025126). Several more new, specific terms have been added: moss capsule(PO:0025232, moss capsule annulus (PO:0025093, moss capsule valve (0025229, moss capsule columella (PO:0025231), antheridium sperm cell (PO:0025120), pollen sperm cell(PO:0025121, archegonium egg cell (PO:0025122)
 . Update PGDSO to accomodate a broader range of species
-Status: A new structure for the PGDSO was developed, but it awaits testing and approval. May be incorporated during next release.
+Status: A new structure for the PGDSO was developed, but it awaits testing and approval. Will be revised and incorporated for next release.
 ==Summary of specific changes==

@@ Line 18: / Line 18: @@
 All terms in the PSO now have is_a parents.
-About 10 terms were made obsolete (see [[New_terms_and_obsolete_terms_for_Jan2011_release]]). These were primarily terms that are sub-celluar components and have been requested in the Gene Ontology (GO), or terms that were incorrectly defined and have been replaced by new terms with the same name but correct definition.
+Eleven terms were made obsolete (see [[New_terms_and_obsolete_terms_for_Jan2011_release]]). These were primarily terms that are sub-celluar components and have been requested in the Gene Ontology (GO), or terms that were incorrectly defined and have been replaced by new terms with the same name but correct definition.
 The defintions of many existing terms were re-written in the genus-differntia form, as well as the definitions for all new terms.
-Several new sub-sets were created: one for TraitNet (general terms need for plant ecology), one for Musa species, and one for angiosperms. The angiosperms subset is still incomplete, but can be added to as revisions progress.
+Several new sub-sets were created: one for TraitNet (general terms need for plant ecology), one for Musa species, and one for angiosperms. The angiosperms subset is still under development, but will be added to as revisions progress. For future releases, subsets for other taxa such as gymnosperms be added.
 The relationship has_part was added to the ontology. For example, inflorescence has_part flower.

@@ Line 14: / Line 14: @@
 The Plant Structure Ontology (PSO) and Plant Growth and Development Stage Ontology (PGDSO) have been merged into one file (plant_ontology.obo), in order to faciliated cross-ontology cross products. The two ontologies still have separate name spaces. The separate files po_anatomy.obo and po_temporal.obo will be maintained for some period of time, but users should try to switch to using the combined file as soon as possible.
-new terms have been added (see [[New_terms_and_obsolete_terms_for_Jan2011_release]]). These include several new top-level terms, a number of mid-level generic terms (such as stele) that were added to provide parents for more specific terms, and a number of bottom- or leaf-level terms. See [[Summary_of_specific_changes]] below for a more detailed description.
+new terms have been added (see [[New_terms_and_obsolete_terms_for_Jan2011_release]]). These include several new top-level terms, a number of mid-level generic terms (such as stele) that were added to provide parents for more specific terms, and a number of bottom- or leaf-level terms. See 'Summary_of_specific_changes' below for a more detailed description.
-All terms in the PSO now have is_a parents, as well as all but three terms in the PGDSO.
+All terms in the PSO now have is_a parents.
-About 10 terms were made obsolete (see [[New_terms_and_obsolete_terms_for_Jan2011_release]]). These were primarily terms that are sub-celluar components and have been requested in the Gene Ontology (GO), or terms that were incorrectly defined and replaced by new terms with the same name but correct definition.
+About 10 terms were made obsolete (see [[New_terms_and_obsolete_terms_for_Jan2011_release]]). These were primarily terms that are sub-celluar components and have been requested in the Gene Ontology (GO), or terms that were incorrectly defined and have been replaced by new terms with the same name but correct definition.
 The defintions of many existing terms were re-written in the genus-differntia form, as well as the definitions for all new terms.

@@ Line 12: / Line 12: @@
 ==Overview and general changes==
-The Plant Structure Ontology (PSO) and Plant Growth and Development Stage Ontology (PGDSO) have been merged into one file (plant_ontology.obo). The two ontologies still have separate name spaces.
+The Plant Structure Ontology (PSO) and Plant Growth and Development Stage Ontology (PGDSO) have been merged into one file (plant_ontology.obo), in order to faciliated cross-ontology cross products. The two ontologies still have separate name spaces. The separate files po_anatomy.obo and po_temporal.obo will be maintained for some period of time, but users should try to switch to using the combined file as soon as possible.
-new terms have been added (see [[New_terms_and_obsolete_terms_for_Jan2011_release]]). These include several new top-level terms, a number of mid-level generic terms (such as stele) that were added to provide parents for more specific terms, and a number of bottom or leaf-level terms. See summary below for a more detailed description.
+new terms have been added (see [[New_terms_and_obsolete_terms_for_Jan2011_release]]). These include several new top-level terms, a number of mid-level generic terms (such as stele) that were added to provide parents for more specific terms, and a number of bottom- or leaf-level terms. See summary below for a more detailed description.
 All terms in the PSO now have is_a parents, as well as all but three terms in the PGDSO.