ossification expansion and restructuring

[gocentral]

GO_REF:0000034 -- Phenoscape Skeletal Anatomy Jamboree

Brian K. Hall (Dalhousie University), Matthew Vickaryous (Ontario Veterinary College, University of Guelph), David Blackburn, University of Kansas; Wasila Dahdul, University of South Dakota and NESCent; Alexander Diehl, Mouse Genome Informatics (MGI); Melissa Haendel, Oregon Health & Science University; John G. Lundberg, Department of Ichthyology, Academy of Natural Sciences, Philadelphia; Paula Mabee, Department of Biology, University of South Dakota; Martin Ringwald, Mouse Genome Informatics (MGI); Erik Segerdell, Oregon Health Sciences University; Ceri Van Slyke, Zebrafish Information Network (ZFIN); Monte Westerfield, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon., 2010.

---

Proposed new hierarchy:

GO:0001503 ossification --i-GO:new direct ossification ----i-GO:0001957 intramembranous ossification ----narrow syn dermal ossification ------i-GO:new perichondral ossification ----i-GO:new metaplastic ossification ---------------related synonym metaplasia --i-GO:new replacement ossification ------------exact synonym indirect ossification ----i-GO:0001958 endochondral ossification --i-GO:new ligamentous ossification --i-GO:new intratendonous ossification --i-GO:0043931 ossification involved in bone maturation --i-GO:0043932 ossification involved in bone remodeling --p-GO:0001649 osteoblast differentiation

---

Definitions: GO:0001503 'ossification' Current def: The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. (No change needed)

GO:new 'direct ossification'
def: Ossification that does not require the replacement of preexisting tissues.

GO:new 'replacement ossification' def: Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation. [exact synonym: Indirect ossification]

GO:new 'ligamentous ossification'
def: Ossification wherein bone tissue forms within ligamentous tissue. COMMENT: Ligamentous ossification may occur via replacement ossification or metaplastic ossification or both in any one instance.

GO:new ‘intratendonous ossification’ def: Ossification wherein bone tissue forms within tendonous tissue. COMMENT: Tendonous ossification may occur via replacement ossification or metaplastic ossification or both in any one instance.

GO:0001958 'endochondral ossification'
Current def: The formation of bone by the replacement of cartilage tissue with mineralized bone. New definition: Replacement ossification wherein bone tissue replaces cartilage.

GO:0001957 'intramembranous ossification' current definition: The formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified. Intramembranous ossification is the way flat bones and the shell of a turtle are formed. New definition: Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells. [Narrow synonym: dermal ossification] COMMENT: an instance of intramembranous ossification may also be classified as metaplastic. The former classifies based on tissue type location, and the latter based on mechanism/cell division.

GO:new 'metaplastic ossification'
Def: Direct ossification in which bone formation occurs as result of the direct transformation of non-bone cells into bone cells without cell division. COMMENT: an instance of intramembranous ossification may also be classified as metaplastic. The former classifies based on tissue type location, and the latter based on mechanism/cell division.

GO:new 'perichondral ossification'
def: Intramembranous ossification from the surface of a cartilage element as the perichondrium becomes a periosteum, without replacement of cartilage.

GO:0043931 'ossification involved in bone maturation' current def: The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state. (No change) [Narrow synonym: ossification involved in bone modeling] - because bone modeling is part of normal bone development and maturation.

GO:0043932 'ossification involved in bone remodeling' current def: The formation of bone involved in the continuous turnover of bone matrix and mineral. New def: The formation or growth of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in response to injury or other physical, physiological or environmental stressors.

GO:0001649 'osteoblast differentiation' current def: The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, the mesodermal cell that gives rise to bone. New def: The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.

Note a few things:

1. related closed ticket: http://sourceforge.net/tracker/index.php?func=detail&aid=3454347&group\_id=36855&atid=440764

2. We may wish to update this XP: id: GO:0001503 ! ossification intersection_of: GO:0032502 ! developmental process intersection_of: OBO_REL:results_in_formation_of UBERON:0001474 ! bone

because not all ossification is developmental (perhaps use GO:0032501! multicellular organismal process)

3. Can also add the two following XPs, more to come when there are more uberon classes in place:

id: GO:new ! intratendonous ossification intersection_of: GO:0032501! multicellular organismal process intersection_of: occurs_in UBERON:0000043 ! tendon

id: GO:new ! ligamentous ossification intersection_of: GO:0032501! multicellular organismal process intersection_of: occurs_in UBERON:0000211 ! ligament

(Thanks in advance for your help implementing all this -Melissa)

Reported by: mellybelly

Original Ticket: geneontology/ontology-requests/9048

[gocentral]

• assigned_to: nobody --> rfoulger

Original comment by: rebeccafoulger

[gocentral]

Thanks for all the details Melissa. I've updated the definitions, comments and relationships as suggested, and your new terms are:

direct ossification ; GO:0036072 perichondral ossification ; GO:0036073 metaplastic ossification ; GO:0036074 replacement ossification ; GO:0036075 ligamentous ossification ; GO:0036076 intratendonous ossification ; GO:0036077

In scratch/xps, I've updated the XP for GO:0001503 ! ossification, and added in XPs for: ligamentous ossification ; GO:0036076 intratendonous ossification ; GO:0036077

Let me know if I've missed anything, thanks, Becky

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-accepted

Original comment by: rebeccafoulger