Bone tissue definition #27

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wdahdul opened this Issue Aug 3, 2011 · 3 comments

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wdahdul commented Aug 3, 2011

VAO:0000047 : bone tissue
VAO: Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
UBR: The major structural and supportive connective tissue of the body. Osseous tissue forms the rigid part of the bone organs that make up the skeletal system.

CJM-NOTES:Use VAO

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cmungall Aug 3, 2011

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there is also the hierarchy to resolve.

UBR has MI:

....is_a UBERON:0000479 ! tissue
.....is_a UBERON:0002384 ! connective tissue
......is_a UBERON:0002481 ! bone tissue ***
.....is_a UBERON:0004755 ! skeletal tissue
......is_a UBERON:0002481 ! bone tissue ***

and VAO SI:

..is_a VAO:0000017 ! connective tissue
...is_a VAO:0000015 ! skeletal tissue
....is_a VAO:0000047 ! bone tissue ***

UBR should follow VAO here. Will change...

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cmungall commented Aug 3, 2011

there is also the hierarchy to resolve.

UBR has MI:

....is_a UBERON:0000479 ! tissue
.....is_a UBERON:0002384 ! connective tissue
......is_a UBERON:0002481 ! bone tissue ***
.....is_a UBERON:0004755 ! skeletal tissue
......is_a UBERON:0002481 ! bone tissue ***

and VAO SI:

..is_a VAO:0000017 ! connective tissue
...is_a VAO:0000015 ! skeletal tissue
....is_a VAO:0000047 ! bone tissue ***

UBR should follow VAO here. Will change...

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cmungall May 2, 2012

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def has been fixed for some time.

redundant link fixed in next release

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cmungall commented May 2, 2012

def has been fixed for some time.

redundant link fixed in next release

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@cmungall cmungall reopened this Feb 23, 2015

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cmungall Feb 23, 2015

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/ UBERON:0001062 ! anatomical entity
is_a UBERON:0000465 ! material anatomical entity
is_a UBERON:0000061 ! anatomical structure
Reopening this because the distinction between mineralized and mineral-state-neutral bone tissue is not clear:

    is_a UBERON:0010000 ! multicellular anatomical structure
     is_a UBERON:0000479 ! tissue
      is_a UBERON:0002384 ! connective tissue
       is_a UBERON:0004755 ! skeletal tissue
        is_a UBERON:4000013 ! mineralized skeletal tissue
         is_a UBERON:0002481 ! bone tissue
          is_a UBERON:4000115 ! mineralized bone tissue
           is_a UBERON:4000118 ! cellular bone tissue *** 
           is_a UBERON:4000122 ! acellular bone tissue *** 

The def of bone tissue taken from VSAO

def: "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts." [VSAO:0000047, GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170]

already states that it's mineralized. It needs to be clear that this is mineral-state neutral. Or we merge the two terms. Also see the acellular/cellular children.

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cmungall commented Feb 23, 2015

/ UBERON:0001062 ! anatomical entity
is_a UBERON:0000465 ! material anatomical entity
is_a UBERON:0000061 ! anatomical structure
Reopening this because the distinction between mineralized and mineral-state-neutral bone tissue is not clear:

    is_a UBERON:0010000 ! multicellular anatomical structure
     is_a UBERON:0000479 ! tissue
      is_a UBERON:0002384 ! connective tissue
       is_a UBERON:0004755 ! skeletal tissue
        is_a UBERON:4000013 ! mineralized skeletal tissue
         is_a UBERON:0002481 ! bone tissue
          is_a UBERON:4000115 ! mineralized bone tissue
           is_a UBERON:4000118 ! cellular bone tissue *** 
           is_a UBERON:4000122 ! acellular bone tissue *** 

The def of bone tissue taken from VSAO

def: "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts." [VSAO:0000047, GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170]

already states that it's mineralized. It needs to be clear that this is mineral-state neutral. Or we merge the two terms. Also see the acellular/cellular children.

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