Transcript Relation types used in CL

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Relation types used in
Hemo_CL
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Cell types
 Cells are

considered independent continuants
Smith, B. et al. Nat. Biotechnol 25, 1251-1255 (2007).
 Genus-differentia
approach
 “an X is a G that D”
 X = independent continuant
 G = independent continuant
 D = relationship + term from CL (rarely) or orthogonal
ontology
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Ontologies & Relationships used in
Differentia
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CL and PATO
Cell phenotype
multinuclear osteoclast is_a
“osteoclast” has_quality “multinucleate” [PATO:0001908]
22 of this type
Cellular component phenotype
basophilic cytoplasm [CP:0000028] is_a
“cytoplasm” [GO:0005737] has_quality “basophilic” [PATO:0002094]
8 of this type
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CL and anatomical ontology
adjacent_to
lymph node subcapsular sinus macrophage is_a:
“lymph node macrophage” adjacent_to “capsule of lymph node” [UBERON:0002194]
2 of these definition types added
part_of
alpha-beta intraepithelial T cell is_a:
“mature alpha-beta T cell” part_of “intestinal epithelium” [UBERON:0001277]
42 of these definition types added
+ CL, PRO, and GO-cellular complex
has_part :
• 22 to CP
• 30 to GO
• 25 to PRO
has_plasma_membrane part:
• 30 to GO
• 304 to PRO
lacks_part:
• 3 to CP
• 8 to GO
• 3 to PRO
lacks_plasma_membrane part:
• 22 to GO
• 374 to PRO
has_high_plasma_membrane_amount:
• 11 to GO
• 45 to PRO
has_low_plasma_membrane_amount:
• 10 to GO
• 52 to PRO
cytotoxic CD56-dim natural killer cell is_a
“mature natural killer cell” has_low_plasma_membrane_amount “neural cell adhesion molecule 1 (CD56)”
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CL and GO-biological process
participates_in (11)
pre-B-I cell is_a:
“precursor B cell” participates_in “immunoglobulin heavy chain V-D-J recombination”
has_completed (9)
class switched memory B cell is_a:
“memory B cell” has_completed “isotype switching”
has_not_completed (5)
immature alpha-beta T cells is_a:
“alpha-beta T cell” has_not_completed “ T cell selection”
+ CL and GO-biological process
Inspired by the Fly anatomy’s “has_function_in”:
“Johnston's organ” has_function_in “detection of mechanical stimulus
involved in sensory perception of wind”
capable_of (157)
T-helper 17 cell is_a:
“CD4-positive helper T cell” capable_of “interleukin 17 production”
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Do we need more than one relationship
to link to GO processes?
capable_of
T-helper 17 cell is_a:
“CD4-positive helper T cell” capable_of “interleukin 17
production”
“alpha-beta intraepithelial T cell” capable_of “mucosal
immune response”
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Do we need more than one relationship
to link to GO processes?
mucosal immune
IIL
response
IIL
IL-17 Production
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part_of
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Th17 cell
alpha-beta IEL
?=
has_function_in
can_function_in
capable_of