Anatomy ontology - Root node

Fri Apr 23 14:43:18 EDT 2004

Hello,

Here is a draft of the root node, it has only 28 terms, due to the fact
that many of the tissue and cell terms are absent, and will be added in
the next round (once the tissue node is imported to the main anatomy
ontology). There are some discrepancies in the structures due to the
propagation of the children terms under the specific parentage (for
instance, see meristematic zone under the lateral root node). I'll deal
with this soon.

Please send me your comments/suggestions.
Thanks,

Katica

P.S. Pankaj, do you have time to take a quick look at this node before we
talk today?
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Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
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!type: % is_a is a
!type: < part_of part of
!type: ~ develops_from develops from
$root ; PO:0009005
 %adventitious root ; PO:0020129
 %aerial root ; PO:0003006
 %crown root ; PO:0003008
 <differentiation zone ; PO:0020135 ; synonym:maturation zone ; synonym:specialization zone < lateral root ; PO:0020121
 <elongation zone ; PO:0020125 ; synonym:region of cell elongation ; synonym:region of radial enlargement < lateral root ; PO:0020121 < primary root ; PO:0020127
 %haustorial root ; PO:0003004
 %lateral root ; PO:0020121
  <differentiation zone ; PO:0020135 ; synonym:maturation zone ; synonym:specialization zone < root ; PO:0009005
  <elongation zone ; PO:0020125 ; synonym:region of cell elongation ; synonym:region of radial enlargement < primary root ; PO:0020127 < root ; PO:0009005
  <lateral root cap ; PO:0020131 ; synonym:peripheral cells
  <lateral root meristem ; PO:0003013
   <quiescent center ; PO:0020149 < primary root meristem ; PO:0020147
  <maturation zone ; PO:0003003 < primary root ; PO:0020127 < root ; PO:0009005
  <meristematic zone ; PO:0003001 < primary root ; PO:0020127 < root ; PO:0009005
   <primary root meristem ; PO:0020147 ; synonym:promeristem
    <quiescent center ; PO:0020149 < lateral root meristem ; PO:0003013
  <transition zone ; PO:0003000 < primary root ; PO:0020127 < root ; PO:0009005
 <maturation zone ; PO:0003003 < lateral root ; PO:0020121 < primary root ; PO:0020127
 <meristematic zone ; PO:0003001 < lateral root ; PO:0020121 < primary root ; PO:0020127
  <primary root meristem ; PO:0020147 ; synonym:promeristem
   <quiescent center ; PO:0020149 < lateral root meristem ; PO:0003013
 %nodal root ; PO:0003005
 %primary root ; PO:0020127
  <elongation zone ; PO:0020125 ; synonym:region of cell elongation ; synonym:region of radial enlargement < lateral root ; PO:0020121 < root ; PO:0009005
  <maturation zone ; PO:0003003 < lateral root ; PO:0020121 < root ; PO:0009005
  <meristematic zone ; PO:0003001 < lateral root ; PO:0020121 < root ; PO:0009005
   <primary root meristem ; PO:0020147 ; synonym:promeristem
    <quiescent center ; PO:0020149 < lateral root meristem ; PO:0003013
  <root cap ; PO:0020123 < root ; PO:0009005
   <central root cap ; PO:0020130 ; synonym:columella root cap
    <columella root cap cell ; PO:0020132
     <statolith ; PO:0020134
    <columella root cap initial ; PO:0020133
  <root cortex ; PO:0003010
  <specialization zone ; PO:0003002 < root ; PO:0009005
  <stele ; PO:0020124 < root ; PO:0009005
   %root vascular system ; PO:0003011
    %root vascular cylinder ; PO:0003012
  %tap root ; PO:0020089
  <transition zone ; PO:0003000 < lateral root ; PO:0020121 < root ; PO:0009005
 %radicle ; PO:0020031
 <root cap ; PO:0020123 < primary root ; PO:0020127
  <central root cap ; PO:0020130 ; synonym:columella root cap
   <columella root cap cell ; PO:0020132
    <statolith ; PO:0020134
   <columella root cap initial ; PO:0020133
 %seminal root ; PO:0003009
 <specialization zone ; PO:0003002 < primary root ; PO:0020127
 <stele ; PO:0020124 < primary root ; PO:0020127
  %root vascular system ; PO:0003011
   %root vascular cylinder ; PO:0003012
 %stilt root ; PO:0003007
 <transition zone ; PO:0003000 < lateral root ; PO:0020121 < primary root ; PO:0020127
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!
!Gene Ontology definitions
!
term: adventitious root
goid: PO:0020129
definition: Root developing from any plant part other than the radicle (i.e. stem, leaf, older part of a root).
definition_reference: ISBN:0-87893-403-0
comment: see radicle, lateral root, primary root.

term: aerial root
goid: PO:0003006
definition: Roots that are formed in and exposed to air, e.g., by epiphytes and hemiepiphytes; in some species, aerial roots grow downward from the tropical tree canopy toward the ground as extremely long, unbranched roots. 
definition_reference: Web:http://www.botgard.ucla.edu/html/botanytextbooks/generalbotany/typesofroots/

term: central root cap
goid: PO:0020130
definition: The central part of a root cap in which the cells are arranged in longitudinal files.
definition_reference: GR:pj

term: crown root
goid: PO:0003008
definition: Root that develops from underground nodes at developing stem.
definition_reference: Web:http://schnablelab.plantgenomics.iastate.edu/research/hypothesis/root.shtml

term: differentiation zone
goid: PO:0020135
definition: The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function.
definition_reference: GR:pj

term: elongation zone
goid: PO:0020125
definition: The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size.
definition_reference: GR:pj

term: haustorial root
goid: PO:0003004
definition: the root of particular parasitic plants that become cemented to the host axis via a sticky attachment disc before the root or sinker intrudes into the tissues of the host.
definition_reference: Web:http://www.botgard.ucla.edu/html/botanytextbooks/generalbotany/typesofroots/

term: lateral root
goid: PO:0020121
definition: Root developed from the pericycle of differentiatied primary root.
definition_reference: ISBN:0122151704
definition_reference: TAIR:KI

term: lateral root cap
goid: PO:0020131
definition: The outer part of a root cap. The cells in this region secrete enormous quantities of mucigel.
definition_reference: ISBN:0-12-215170-4

term: maturation zone
goid: PO:0003003
definition: the portion of the root located behind the specialization zone containing cells that are differentiated into their final form and function. Root hairs are fully elongated in this portion of the root.
definition_reference: Web:http://www.arexdb.org/db/anatomy/browse.jsp?ticlstate=TID0`;pwLoginPanel`;AnatomyPartsTree`treestate`4:t`ec`4:t&oid=36&ot=part

term: meristematic zone
goid: PO:0003001
definition: Upper part of the meristem (which comprises the promeristem and the meristematic zone), above the lower promeristem part, where cells are actively dividing and partially differentiated.
definition_reference: Web:http://www.arexdb.org/db/anatomy/browse.jsp?ticlstate=TID0`;pwLoginPanel`;AnatomyPartsTree`treestate`4:t`ec`4:t&oid=36&ot=part

term: nodal root
goid: PO:0003005
definition: Adventitious roots that form characteristically in rings from stem tissues around a node. 
definition_reference: Web:http://www.botgard.ucla.edu/html/botanytextbooks/generalbotany/typesofroots/

term: primary root
goid: PO:0020127
definition: The primary root is the initial root structure which develops from the embryonic radicle.
definition_reference: ISBN:0-12-215170-4

term: primary root meristem
goid: PO:0020147
definition: Apical, primary, meristem of the root
definition_reference: UMSL:fz

term: quiescent center
goid: PO:0020149
definition: Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap.
definition_reference: ISBN:0-12-215170-4

term: radicle
goid: PO:0020031
definition: The part of an embryo or seedling that gives rise to the root system of the adult plant, sometimes more or less abortive
definition_reference: APWeb:Glossary

term: root
goid: PO:0009005
definition: Commonly thought of as one of the three basic parts of the seed plant body, an axial system which is usually underground and more or less positively geotropic, does not bear leaves and only rarely shoots, is endogenous in origin, indeterminate in growth and often with secondary thickening.
definition_reference: APWeb:Glossary

term: root cap
goid: PO:0020123
definition: A group of cells that covers the apical meristem of the root.
definition_reference: APWeb:Glossary

term: root cortex
goid: PO:0003010
definition: The primary tissue located between the vascular system and the epidermis.
definition_reference: ISBN:0471245208

term: root vascular cylinder
goid: PO:0003012
definition: Vascular region of the root axis.
definition_reference: ISBN:0471245208

term: seminal root
goid: PO:0003009
definition: Develops for th escytelar node in the first days of seedling growth.
definition_reference: Web:http://schnablelab.plantgenomics.iastate.edu/research/hypothesis/root.shtml

term: specialization zone
goid: PO:0003002
definition: The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function. Root hairs are starting to emerge in this zone.
definition_reference: Web:http://www.arexdb.org/db/anatomy/browse.jsp?ticlstate=TID0`;pwLoginPanel`;AnatomyPartsTree`treestate`4:t`ec`4:t&oid=36&ot=part

term: statolith
goid: PO:0020134
definition: Solid cell inclusion of starch containing plastids occurring in root cap cells.
definition_reference: GR:pj

term: stele
goid: PO:0020124
definition: The central column of primary vascular tissue in the root and stem and any tissue that it surrounds.
definition_reference: APWeb:Glossary

term: stilt root
goid: PO:0003007
definition: stilt roots: adventitious roots that develop on a trunk or lower branch that begin as aerial roots (another example; reaching for the water) but eventually grow into a substrate of some type; these roots in some cases seem to provide mechanical support, having either good compression or tensile properties to help support trees at their bases. 
definition_reference: Web:http://www.botgard.ucla.edu/html/botanytextbooks/generalbotany/typesofroots/

term: tap root
goid: PO:0020089
definition: The main, descending root of a plant that has a single, dominant root axis derived from the radicle of the seedling.
definition_reference: APWeb:Glossary
comment: see radicle, primary root.

term: transition zone
goid: PO:0003000
definition: Region between the meristem and the region of rapid elongation. Postmititic isodiametric growth zone.
definition_reference: PMID:Baluska et al 2001