Details for Planteome Release Version 4.0 October 2020

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The Planteome Project (http://planteome.org/) is pleased to announce the latest release of the annotation database and ontology files. In this Planteome Version 4.0, there are 59,827 ontology terms, 3,060,530 data objects (bioentities) and 19,838,934 associations between bioentities and ontology terms. The Planteome database contains data from 124 plant taxa.

Updates and changes to Annotations:

Gene Ontology annotations based on InterProScan and via orthology from InParanoid were updated to newer versions of the gene sequences. Several new species have been added. The full list is available on the Link to Annotations by Taxa page. Other annotation files were updated if a newer version was available. All annotation files are available on the Planteome SVN Repository.

Links to detailed annotation statistics:

Updates and changes to the Ontologies:

 

Integration of Crop Ontology files with the Plant Trait Ontology.

One new Crop Ontology (https://www.cropontology.org) file has been added- for potato, bringing the total number of integrated trait dictionary files to eleven. These have all been mapped to the Plant Trait Ontology.

 

Summary of changes to ontology files:

 

Plant Ontology:

  • Updated CARO Xrefs on upper level terms and added BFO xrefs

  • Added RO import

  • Fixed property values, parent terms and added PO IDs to existing terms

  • Fixed definition of stolon (PO:0003024), as it can be both aboveground and below

  • Revisions to inflorescence and inflorescence axis terms

  • Definitions of spikelets and its child terms were revised

  • Paraclade terms were revised to match the revisions to inflorescence axes

 

New glossary page for Plant Ontology:

With this release, we have added a searchable glossary table for the Plant Ontology.

Plant Trait Ontology:

New TO Terms Added:

  • grain color trait (TO:0001109): A caryopsis fruit morphology trait (TO:0001079) which is the color of a grain (caryopsis fruit; PO:0030104).

  • spike inflorescence morphology trait (TO:0001110): An inflorescence morphology trait (TO:0000373) which is a quality of a spike inflorescence (PO:0030117).

  • linolenic acid content (TO:1000074): An essential fatty acid (TO:0000604) content which is the amount of a polyunsaturated, 18 carbon long fatty acid, with three double bonds.

  • palmitic acid content (TO:1000075): A fatty acid content (TO:0000604) which is the amount of a straight-chain, sixteen-carbon, saturated long-chain fatty acid in a plant structure.

Revised definitions and/or comment:

  • chlorophyll content(TO:0000495)

  • chlorophyll ratio (TO:0000298)

  • chlorophyll to rubisco ratio (TO:0000320)

  • relative chlorophyll content (TO:0001016)

  • leaf chlorophyll content (TO:0012002)

  • Total water soluble content (TO:0020088)

  • 100-grain weight (TO:0000269)

  • 1000-grain weight (TO:0000382)

  • seed morphology trait (TO:0000184)

  • grain length (TO:0000734)

  • grain length to width ratio (TO:0000411)

  • grain size (TO:0000397)

  • grain length TO:0000734

  • grain shape (TO:0002730)

  • grain shape TO:0002730)

  • polished grain weight (TO:0000593)

  • grain weight to panicle weight ratio (TO:0020002)

  • seed hardness (TO:0000990)

  • phenotypic acceptability (TO:0000322)

  • days to maturity (TO:0000469 )- added synonym 'time to harvest'

  • phenotypic acceptability (TO:0000322)

  • panicle threshability (TO:0000406)

  • seed quality trait (TO:0000931)

  • root quality trait (TO:0001042)

  • fruit quality trait (TO:0002728)

  • adventitious root number (TO:0001006)

  • adventitious root length (TO:0020103)

  • adventitious root thickness (TO:0000475)

  • brittle culm (TO:000020)

  • leaf midvein morphology trait (TO:0000822)

  • root pulling force (TO:0000093)

  • sedge weed response (TO:0000030)

  • momilactone B content (TO:0002671)

  • inflorescence bract development (TO:0006027)

  • root cortical cell length (TO:0020108)

  • spike exsertion (TO:0020069)

  • head drop (TO:0020077)

  • cyanide content (TO:0000955)

  • chlorophyll b content (TO:0000295)- Corrected names (removed hyphens), added hyphenated names as exact synonyms

  • chlorophyll a content (TO:0000293)- Corrected names (removed hyphens), added hyphenated names as exact synonyms

Created definitions that were missing:

  • leaf midrib color (TO:0000720)

  • inflorescence length (TO:0000271) made part_of inflorescence size (TO:0006031)

  • inflorescence circumference (TO:0000680)

  • inflorescence diameter (TO:0000802)

  • spike width (TO:0000638)

  • variegated leaf (TO:0000069)

  • shoot branching (TO:0002639)

  • moisture content trait (TO:0000228)

TO Terms moved to new parent and revised definition:

  • shoot branching (TO:0002639) made is_a shoot axis morphology trait (TO:0000739)

  • lodicule number (TO:0006010) made is_a spikelet floret morphology trait (TO:0000274)

  • milled grain color (TO:0000385) made is_a grain color trait (TO:0001109)

  • fructose content (TO:0006005) made is_a hexose content (TO:0000307)

  • malt-extract percentage (TO:0000611) made is_a brewing quality trait (TO:0001070)

  • metabolized energy of stover (TO:0020081) made is_a: shoot system yield trait (TO:0000327)

  • stover nitrogen content (TO:0020082) made is_a: shoot system yield trait (TO:0000327)

  • exudate sap volume trait (TO:0001020) made is_a: shoot system yield trait (TO:0000327)

  • grain length to width ratio (TO:0002731) and child terms to is_a caryopsis fruit morphology trait (TO:0001079), revised comment

  • inflorescence number (TO:0000582) made is_a reproductive shoot system morphology trait (TO:0000786)

  • inflorescence presence (TO:0000806) made is_a reproductive shoot system morphology trait (TO:0000786)

  • starch yield (TO:0000697) made is_a yield trait (TO:0000371) and part_of grain quality (TO:0000162)

  • curved length of grain with hull (TO:0002763) made a is_a grain curved length ( TO:0002745)

  • rhizome morphology trait (TO:0000549) made is_a shoot axis morphology trait (TO:0000739)

  • rhizome number (TO:0000548) made is_a shoot system morphology trait (TO:0000077)

  • rhizome formation (TO:0002767) made is_a shoot system growth and development trait (TO:0000654)

  • vascular bundle number (TO:0000472) made is_a plant structure morphology trait (TO:0000839)

  • leaf length (TO:0000135) made is_a leaf morphology trait (TO:0000748), and made part_of leaf size (TO:0002637)

  • leaf thickness (TO:0000258) made is_a leaf morphology trait (TO:0000748), and made part_of leaf size (TO:0002637)

  • leaf length to width ratio (TO:0000542) made is_a leaf morphology trait (TO:0000748), and made part_of leaf size (TO:0002637)

  • leaf width (TO:0000370) made is_a leaf morphology trait (TO:0000748), and made part_of leaf size (TO:0002637)

  • colored grain percentage (TO:0000617) made is_a grain color trait (TO:0001109)

  • leaf foliage rating (TO:0000977) made is_a leaf area trait (TO:0000540)

  • seed fertility (TO:0000639) made is_a fertility related trait (TO:0000420), made part_of seed quality (TO:0000931)

  • stem thickness (TO:0000339) made is_a stem morphology trait (TO:0000361), made part_of stem size (TO:0000892), and stem strength (TO:0000051)

  • stomatal complex closure time (TO:0000521) made Is_a plant phenological trait (TO:0000933)

  • flower bract number (TO:0006026) made is_a flower morphology trait (TO:0000499)

Terms renamed and defintion revised:

  • stomatal complex closure rate (TO:0000520)- was stomatal closure rate

  • stomatal complex closure time (TO:0000521)- was stomatal closure time

  • flower bract number (TO:0006026)- was floral bract number

  • wrinkled grain (TO:0000718)- was wrinkled seed, added synonyms: wrinkled kernel (narrow), wrinkled seed (related)

Terms Obsoleted:

  • chlorophyll content in an extract (TO:0012003)- No definition, no annotations. This term was no different than its parent term, chlorophyll content (TO:0000495).

Removed relations causing inconsistency with PATO and RO:

  • nodal rooting TO:0000404

  • pistil number (TO:0002659)

  • rootless (TO:0000198)

 

Plant Experimental Conditions Ontology:

New PECO Terms Added:

  • potassium fertilizer exposure (PECO:0001064): A chemical fertilizer exposure (PECO:0007086) involving the use of potassium fertilizer as a supplement to study plant responses.

  • potassium chloride exposure (PECO:0001065): A potassium fertilizer exposure (PECO:0001064) involving the use of potassium chloride fertilizer as a supplement to study plant responses.

  • nematicide exposure (PECO:0001066): A pesticide exposure (PECO:0007167) involving the application of a nematicide; a chemical entity or mixture of chemical entities to kill plant-parasitic nematodes.

  • castor meal exposure (PECO:0001067): A natural fertilizer exposure (PECO:0007087) which is the application of castor meal. Comment: Castor meal is a by-product of castor oil production from seeds of the Castor (Ricinus communis) plant and has a high nitrogen content.

  • rapeseed meal exposure (PECO:0001068): A natural fertilizer exposure (PECO:0007087) which is the application of rapeseed meal. Comment: Rapeseed meal is a by-product of rapeseed oil production from seeds of the Rapeseed (Brassica napus L.) plant, and has a high protein content.

  • green manure exposure (PECO:0001069): A natural fertilizer exposure (PECO:0007087) which is the application of green manure. Comment: Green manure is created by leaving uprooted or sown crop parts to wither on a field so that they serve as a mulch and soil amendment. The plants used for green manure are often cover crops grown primarily for this purpose.

  • calcium carbonate exposure (PECO:0001070): A salt exposure (PECO:0007185) which is a treatment with calcium carbonate (CHEBI:3311) in order to raise the pH of the growing media. Added synonym: lime exposure (broad)

Revised definitions and/or comment:

  • sand content exposure (PECO:0007051)

  • organic matter content exposure (PECO:0007052)

  • silt content exposure (PECO:0007053)

  • clay content exposure (PECO:0007054)

  • imidazolinone exposure (PECO:0007633)

  • carbohydrate exposure (PECO:0001010)

Created definitions that were missing:

  • bone meal exposure (PECO:0007089)

  • seaweed extract exposure (PECO:0007091)

  • wood ash exposure (PECO:0007092)

  • fish meal exposure (PECO:0007093)