Details for Planteome Release Version 3.0 September 2018

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The Planteome Project (http://planteome.org/) is pleased to announce the latest release of the database and ontology files. In this Planteome Version 3.0, there are 59,189 ontology terms, 2,057,205 data objects (bioentities) and 21,400,874 associations between bioentities and ontology terms. The Planteome database contains data from 95 plant taxa.

        

Links to detailed annotation statisitics:

Summary of changes to ontology files:

The Plant Environment Ontology (EO) has been renamed the Plant Experimental Conditions Ontology (PECO), and all the identifiers have been changed from EO to PECO.  The old EO ids have been retained as alternate ids. All the terms with ‘treatment’ in the name have been renamed as “exposures”,  for example, the root term plant treatment (EO:0001001) has been renamed: plant exposure (PECO:0001001). Introduction of design patterns to facilitate automation.

 

Plant Ontology:

  • 22 new terms to describe the different types of inflorescences
  • Three terms, and two revised ones, to describe different types of pedicels
  • Extensive revisions to inflorescence axis and branch terms
  • New terms to describe parts of the metaxylem vessel
  • Taxon constraint added at root level

 

Plant Ontology Metrics- Sept. 2018 Release
  PO Anatomy PSDS
Number of terms (w/o) obsoletes 1651 1355 296
Number of obsoletes 135 93 42
number of relationships/properties 13 + is_a    
Maximum depth* 10    
Maximum number of children* 65    
Average number of children* 3    
Classes with a single child* 126    
Classes with more than 25 children* 4    

* From bioportal: https://bioportal.bioontology.org/ontologies/PO

 

Plant Trait Ontology:

  • 35 new terms for various morphological traits of different fruit types, including grain (caryopsis fruit) traits, as well as two new terms to describe fruit shattering
  • 51 new terms to describe mineral content in root systems and shoot systems
  • Revisions to the quality branch which include three new new terms for traits associated with processing, cooking and brewing qualities
  • Ten new traits of roots and root systems, including subterranean shoot axis tubers, such as potatoes and yam
  • Ten new terms for inflorescence traits, with four specifically related to the characters of a panicle inflorescence
  • Introduction of design patterns for almost half the terms in the ontology

Two new Crop Ontology files have been added- for sorghum and yam, bringing the total number of  CO files to ten. These have all been mapped to the TO.

  • Yam
  • Sorghum
  • Rice
  • Maize
  • Wheat
  • Cassava
  • Soybean
  • Sweet potato
  • Pigeon pea
  • Lentil

 

 

Details of Changes to the Plant Ontology:

  • New terms to describe the different types of inflorescences:

raceme inflorescence (PO:0030115)

compound raceme inflorescence (PO:0030116)

spike inflorescence (PO:0030117)

compound spike inflorescence (PO:0030118)

catkin inflorescence (PO:0030119)

spadix inflorescence (PO:0030120)

capitulum inflorescence (PO:0030121)

compound capitulum inflorescence (PO:0030122)

panicle inflorescence (PO:0030123)

corymb inflorescence (PO:0030124)

anthela inflorescence (PO:0030125)

cyme inflorescence (PO:0030126)

indeterminate thyrse inflorescence (PO:0030127)

determinate thyrse inflorescence (PO:0030128)

umbel inflorescence (PO:0030129)

compound umbel inflorescence (PO:0030130)

rhipidium inflorescence (PO:0030131)

cincinnus inflorescence (PO:0030132)

compound cincinnus inflorescence (PO:0030133)

bostryx inflorescence (PO:0030134)

drepanium inflorescence (PO:0030135)

compound drepanium inflorescence (PO:0030136)

 

  • Pedicel terms:

New Terms:

  • pedicel (PO:0030112): A shoot axis (PO:0025029) that bears only a flower (PO:0009046) or a fruit (PO:0009001).
  • flower pedicel (PO:0030113): A pedicel (PO:0030112) that bears a flower (PO:0009046).
  • fruit pedicel (PO:0030114): A pedicel (PO:0030112) that bears a fruit (PO:0009001).

Revised terms:

New name Previous name PO:ID
inflorescence flower pedicel flower pedicel PO:0009052
infructescence fruit pedicel fruit pedicel PO:0004536

 

  • Revisions to Inflorescence Branch & Axis terms: 

New name Previous name PO:ID
higher order inflorescence axis inflorescence branch PO:0009081
second order inflorescence axis primary inflorescence branch PO:0006321
third order inflorescence axis second order inflorescence branch PO:0006322
fourth order inflorescence axis third order inflorescence branch PO:0025105
fifth order inflorescence axis fourth order inflorescence branch PO:0025106
sixth order inflorescence axis fifth order inflorescence branch PO:0025107
seventh order inflorescence axis sixth order inflorescence branch PO:0025108
eighth order inflorescence axis seventh order inflorescence branch PO:0025109
ninth order inflorescence axis eighth order inflorescence branch PO:0025110
tenth or higher order inflorescence axis ninth or higher order inflorescence branch PO:0025111

 

 

Other New PO terms:

  • metaxylem vessel (PO:0025620):A primary xylem vessel (PO:0025450) which is part of the metaxylem (PO:0000372).
  • metaxylem tracheid (PO:0025621):A primary xylem tracheid (PO:0025446) that is part of the metaxylem (PO:0000372).
  • metaxylem vessel member (PO:0025622): A primary xylem vessel member (PO:0025448) that is part of the metaxylem (PO:0000372).
  • branch apex (PO:0028004): A shoot axis apex (PO:0000037) that is part of a branch (PO:0025073)
  • gametophyte coma (PO:0028005): A collective plant organ structure (PO:0025007) which is a cluster of gametophore branches (PO:0030021) or non-vascular leaves (PO:0025075) at the top of the gametophore axis (PO:0030020), forming a tuft.
  •  

Changes to the Plant Trait Ontology:

 New Terms added:

  • flag leaf area (TO:0000996): A flag leaf anatomy and morphology trait (TO:0000832) which is the area of the flag leaf (PO:0020103).
  • polished grain length (TO:0000997) : A grain length (TO:0000734) measured on a dehulled, polished grain.
  • polished grain width (TO:0000998): A grain width (TO:0000975) which is the width of the dehulled, polished grain.
  • polished grain length to width ratio (TO:0000999): A grain length to width ratio (TO:0002731) measured on a dehulled, polished grain.
  • root hair density (TO:0001051): A root morphology trait (TO:0000043) which is the number of root hairs (GO:0035618) in a given surface area of a root (PO:0009005).
  • root cortex cross-sectional area (TO:0001052): A portion of plant tissue morphology trait (TO:0000843) which is the cross-sectional area of the root cortex (PO:0000258).
  • subterranean shoot axis tuber length (TO:0001053): A subterranean shoot axis tuber morphology trait (TO:0000742) which is the length of a subterranean shoot axis tuber (PO:0004547).
  • root stele cross-sectional area (TO:0001054): A cardinal organ part morphology trait (TO:0000754) which is the cross-sectional area of the root stele (PO:0020124).
  • root aerenchyma cross-sectional area (TO:0001055): A portion of plant tissue morphology trait (TO:0000843) which is the cross-sectional area of the root aerenchyma (PO:0006213).
  • root cross sectional area (TO:0001056): A root morphology trait (TO:0000043) which is the cross sectional area of a root (PO:0009005).
  • root system width (TO:0001057): A root system morphology trait (TO:0000985) which is the width of the root system (PO:0025025).
  • root system depth (TO:0001058): A root system morphology trait (TO:0000985) which is the depth of the root system (PO:0025025).
  • root system width to depth ratio (TO:0001059): A root system morphology trait (TO:0000985) which is the ratio of the root system width (TO:0001057) to root system depth (TO:0001058).
  • subterranean shoot axis tuber width (TO:0001060): A subterranean shoot axis tuber morphology trait (TO:0000742) which is the width of a subterranean shoot axis tuber (PO:0004547).
  • inflorescence axis thickness (TO:0001061): An inflorescence axis morphology trait (TO:0000782) which is the thickness of an inflorescence axis (PO:0020122).
  • number of panicle internodes (TO:0001062): A panicle inflorescence morphology trait (TO:0000847) which is the number of inflorescence axis internodes (PO:0006326) in a panicle inflorescence (PO:0030123).
  • panicle inflorescence internode length (TO:0001063): A panicle inflorescence morphology trait (TO:0000847) which is the length of the inflorescence axis internodes (PO:0006326) in a panicle inflorescence (PO:0030123).
  • number of panicle inflorescence branches per internode (TO:0001064): A panicle inflorescence morphology trait (TO:0000847) which is the average number of branches per inflorescence axis internode (PO:0006326) in a panicle inflorescence (PO:0030123).
  • panicle inflorescence terminal primary branch length (TO:0001065): A panicle inflorescence morphology trait (TO:0000847) which is the length of a terminal primary branch in a panicle inflorescence (PO:0030123).
  • number of metaxylem vessels (TO:0001066): A vascular tissue morphology trait (TO_0000470) which is the number of metaxylem vessels (PO:0025620).
  • days to booting (TO:0001067): A flowering time trait (TO:0002616) which is the length of time for a plant or group of plants to reach booting stage (PO:0007014).
  • processing quality trait (TO:0001068): A plant quality trait (TO:0000597) that is the utility of a plant, plant structure (PO:0009011) or plant product for post-harvest chemical, biological or mechanical transformation into a desired end product.
  • cooking quality trait (TO:0001069): A processing quality trait (TO:0001068) that is the utility of a plant, plant structure (PO:0009011) or plant product for a food cooking process (FOODON:03450002).
  • brewing quality trait (TO:0001070): A processing quality trait (TO:0001068) that is the utility of a plant, plant structure (PO:0009011) or plant product for post-harvest brewing of fermented endproducts.
  • shoot axis tuber yield (TO:0001071): A shoot system yield trait (TO:0000327) which is the yield of shoot axis tubers (PO:0004543).
  • inflorescence axis length (TO:0001072): An inflorescence axis morphology trait (TO:0000782) which is the length of an inflorescence axis (PO:0020122).
  • fruit shattering (TO:0001073): A fruit senescing quality trait (TO:0002729) that is the tendency of a fruit (PO:0009001) to dehisce, releasing one or more seed(s) (PO:0009001).
  • legume fruit shattering (TO:0001074): A fruit shattering trait (TO:0001073) that is the tendency of a legume fruit (PO:0030100) to dehisce, releasing one or more seed(s) (PO:0009001).
  • pulvinus size (TO:0001075): A cardinal organ part morphology trait (TO:0000754) which is the size of a pulvinus (PO:0009000).
  • infructescence development trait (TO:0001076): A shoot system growth and development trait (TO:0000654) that is a quality of infructescence (PO:0006342) development

Terms for fruit types:

  • berry fruit morphology trait (TO:0001077)
  • capsule fruit morphology trait (TO:0001078)
  • caryopsis fruit morphology trait (TO:0001079)
  • drupe fruit morphology trait (TO:0001080)
  • follicle fruit morphology trait (TO:0001081)
  • legume fruit morphology trait (TO:0001082)
  • nut fruit morphology trait (TO:0001083)
  • samara fruit morphology trait (TO:0001084)
  • TO:0001085- schizocarp fruit morphology trait
  • TO:0001086- silique fruit morphology trait
  • TO:0001087- achene fruit weight
  • TO:0001088- berry fruit weight
  • TO:0001089- capsule fruit weight
  • TO:0001090- drupe fruit weight
  • TO:0001091- follicle fruit weight
  • TO:0001092- legume fruit weight
  • TO:0001093- nut fruit weight
  • TO:0001094- samara fruit weight
  • TO:0001095- schizocarp fruit weight
  • TO:0001096- silique fruit weight
  • TO:0001097- achene fruit morphology trait
  • TO:0001098- pepo fruit morphology trait
  • TO:0001099- pome fruit morphology trait
  • TO:0001100- circumscissile capsule fruit morphology trait
  • TO:0001101- utricle capsule fruit morphology trait
  • TO:0001102- coccarium capsule fruit morphology trait
  • TO:0001103- loculicidal capsule fruit morphology trait
  • TO:0001104- poricidal capsule fruit morphology trait
  • TO:0001105- septicidal capsule fruit morphology trait
  • TO:0001106- loment fruit morphology trait
  • TO:0001107- hesperidium fruit morphology trait
  • TO:0001108- grain volume trait

 

Terms for mineral contents in shoot and root systems:

  • root system aluminium content  TO:1000025
  • root system arsenic content TO:1000026
  • root system boron content TO:1000027
  • root system barium content TO:1000028
  • root system calcium content TO:1000029
  • root system cadmium content TO:1000030
  • root system cobalt content TO:1000031
  • root system chromium content TO:1000032
  • root system copper content TO:1000033
  • root system iron content TO:1000034
  • root system iodine content TO:1000035
  • root system potassium content TO:1000036
  • root system lithium content TO:1000037
  • root system magnesium content TO:1000038
  • root system manganese content TO:1000039
  • root system molybdenum content TO:1000040
  • root system sodium content TO:1000041
  • root system nickel content TO:1000042
  • root system phosphorus content TO:1000043
  • root system lead content TO:1000044
  • root system rubidium content TO:1000045
  • root system sulfur content TO:1000046
  • root system selenium content TO:1000047
  • root system silicon content TO:1000048
  • root system strontium content TO:1000049
  • root system zinc content TO:1000050
  • shoot system aluminium content TO:1000051
  • shoot system arsenic content TO:1000052
  • shoot system boron content TO:1000053
  • shoot system barium content TO:1000054
  • shoot system calcium content TO:1000055
  • shoot system cadmium content TO:1000056
  • shoot system cobalt content TO:1000057
  • shoot system chromium content TO:1000058
  • shoot system copper content TO:1000059
  • shoot system iron content TO:1000060
  • shoot system iodine content TO:1000061
  • shoot system lithium content TO:1000062
  • shoot system magnesium content TO:1000063
  • shoot system manganese content TO:1000064
  • shoot system molybdenum content TO:1000065
  • shoot system nickel content TO:1000066
  • shoot system lead content TO:1000067
  • shoot system rubidium content TO:1000068
  • shoot system sulfur content TO:1000069
  • shoot system selenium content TO:1000070
  • shoot system silicon content TO:1000071
  • shoot system strontium content TO:1000072
  • shoot system zinc content TO:1000073
  •