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j sluka
Flat file for auto loading into the CBO 1.0 version. Individual sections delimited by Heading1 and by new BFO classes
Use <ctrl><tab> to insert the hard tabs needed for Protege4
http://www.ebi.ac.uk/ontology-lookup/
http://bioportal.bioontology.org/
GO, CL and FMA are all OWLs, PRO and CellO are OBOs
BFO uses “Quality”, OPB uses “Property”
Class
1
Comments
External child of
BFO:independent_continuant:
material_entity:object
ExtRefs
Definition
physical_entity_type
2
corpuscular_entity
Not divisible without
fundamental change in character
3
continuous_entity
Divisible without fundamental
change in character
(“portionOf”_
4
Issues
physical_bounded_object
BFO:independent_continuant:
material_entity:object
Object with physical extents.
5
discrete_physical_object
Physical object that is not composed of physical subobjects
6
aggregate_physical_object
Physical object that is composed of physical sub-objects
7
physical_object_quality
8
energy
9
geometrical_properties
10
volume
11
shape
12
13
BFO:...:quality
BFO uses “Quality”, OPB
uses “Property”
Quality and characteristics of physical objects, e.g.,
location, volume, energy etc. BFO uses “Quality”, OPB uses
“Property”
body
anisotropy
directed
14
polarity
15
undirected
16
elongation
17
18
isotropy
19
protrusions
20
position
21
center_of_volume
22
cnter_of_mass
23
orientation
a mathematical point
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Class
Comments
24
surface_area
25
location
26
extent
27
discrete
29
dimensionality
30
1d
31
2d
32
fractal
33
3d
34
texture
35
uniformity
36
pattern
37
gradient
38
39
40
kinetic_properties
mass
mechanical_properties
Deprecated, use OPB
Deprecated, use OPB
Deprecated, use OPB
41
yieldingthreshold
Deprecated, use OPB
42
youngsmodulus
Deprecated, use OPB
43
pressure
Deprecated, use OPB
44
adhesiveproperties
Deprecated, use OPB
45
tension
Deprecated, use OPB
46
stiffness
Deprecated, use OPB
47
poissonratio
Deprecated, use OPB
48
chemicalproperties
Deprecated, use OPB
49
localization
Deprecated, use OPB
50
affinity
Deprecated, use OPB
51
pattern
Deprecated, use OPB
52
53
54
55
gradient
density
electricalproperties
charge
External child of
j sluka
Issues
ExtRefs
Definition
Surface area in three dimensions, length in two dimensions.
continuous
28
p. 2 of 11
Deprecated, use OPB
Deprecated, use OPB
Deprecated, use OPB
Deprecated, use OPB
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Class
Comments
56
voltage
Deprecated, use OPB
57
current
Deprecated, use OPB
58
capacity
Deprecated, use OPB
59
resistance
Deprecated, use OPB
60
conductivity
Deprecated, use OPB
61
gravity
Deprecated, use OPB
62
movementfield
Deprecated, use OPB
63
statisticalproperties
Deprecated, use OPB
64
random
p. 3 of 11
External child of
j sluka
Issues
ExtRefs
Definition
Deprecated, use OPB
65
66
geometrical_entity
67
boundary
68
cell_regions
69
basal_part
70
apical_part
71
lateral_part
72
medial_part
73
Sub-entities
Group with other cell parts?
GO: The region of a cell situated near the base. For
GO:0045178, example, in a polarized epithelial cell, the basal surface
FMA:72558
rests on the basal lamina that separates the epithelium
from other tissue.
organismal_regions
74
dorsal
posterior: but humans vs.
quadripeds are different
Dorsal is a geometric modifier describing parts of an
EFO_0001656
organism relating to or situated near or on the back. For
, FMA:74535
example dorsal fin.
75
ventral
anterior: but humans vs.
quadripeds are different
EFO: Ventral is a geometric modifier describing parts
EFO_0001662 pertaining to the front or anterior of any structure for
example ventral striatum.
76
temporal_entity
77
material_type
78
fluid
79
solute
80
solid
81
gel
82
Sub-entities, use OPB
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Class
Comments
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External child of
83
system
BFO:independent_continuant:
material_entity:object
84
cell
BFO:independent_continuant:
material_entity:object
85
molecule
86
extracellular_matrix
j sluka
Issues
ExtRefs
The “universe” described by the model.
GO:0005623, GO:The basic structural and functional unit of all
CL:0000000, organisms. Includes at least the plasma membrane and the
FMA:68646
cytosol.
GO:0031012,
FMA:9672
87
interstitial_matrix
GO:0005614
88
basement_lamina
GO:0005605
89
90
91
molecular_field
medium
cell_part
92
nucleus
93
cell_border
94
cell_membrane
95
cell_wall
96
97
cytoplasm
cell_membrane_part
98
membrane_receptor
99
adhesion_molecule
100
tight_junction
101
gap_junction
102
pump
103
ion_channel
104
105
Definition
cell_membrane_local_structu
re
filopodium
Depends on cell, only cell
border and cytosol required
BFO:dependent_continuant:
specifically_dependent_contin
uant
FMA:61764,
Any constituent part of a cell.
GO:The part of the cytoplasm that does not contain
organelles but which does contain other particulate matter,
GO:0005634,
such as protein complexes. FMA: Cell substance which fills
FMA:63840
the cell compartment between the plasma membrane and the
nuclear membrane (for eukaryotes).
Necisary and sufficient
condition for a cell, with
cytosol.
In plants the cell wall is
considered part of the ECM
Necisary and sufficient
condition for a cell, with
cell_border.
Depends on cell_membrane
Depends on cell_membrane
FMA: Cell component which consists of cytosol and
cytoplasmic organelles.
Membrane v.
border?
GO:0044459,
GO: plasma membrane part; Any constituent part of the
plasma membrane, the membrane surrounding a cell that
separates the cell from its external environment. It
consists of a phospholipid bilayer and associated proteins.
FMA:67214
FMA: Cell adhesion molecule
Membrane v.
border?
A thin, stiff protrusion extended by the leading edge of a
motile cell such as a crawling fibroblast or amoeba, or an
axonal growth cone.
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Class
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Comments
j sluka
External child of
Issues
ExtRefs
Definition
106
brush_border
GO: Dense covering of microvilli on the apical surface of
epithelial cells in tissues such as the intestine, kidney,
and choroid plexus; the microvilli aid absorption by
increasing the surface area of the cell.
107
pseudopodium
GO: A temporary protrusion or retractile process of a cell,
associated with flowing movements of the protoplasm, and
serving for locomotion and feeding.
108
cell_type
109
prokaryote
110
eukaryote
111
anuclear
112
virus
Cell_type by broad phyla
Cell without nuclei, e.g.,
platelets and erythrocytes. Not
to be confused with non-nuclear
prokaryotic cells.
Cell without nuclei, e.g., platelets and erythrocytes. Not
to be confused with non-nuclear prokaryotic cells.
MISSING Characteristics: shape, type (CL, ChEBI, GO…) …
terms
Process_tree
From BFO we have “fiat_process_part” for processes without well-defined beginnings and endings (e.g., motility) and “process” which have a specific time referent, like cell division or well
defined beginning and ending time. For now everything put under “process”.
113
114
Class
Comments
BFO Child of
fundamental_physical_process
Generic terms. Cell
has its own subset.
BFO:occurrent:
processual_entity:
process
Issues
Links to
ExtRefs
Definition
occurrent:
processual_entity:
process
movement
115
translation
fiat_process_part
116
rotation
fiat_process_part
117
diffusion
fiat_process_part
118
shape_change
fiat_process_part
119
volume_change
fiat_process_part
120
expansion
fiat_process_part
121
contraction
fiat_process_part
122
creation
123
deletion
124
phenotypic_change
125
barrier_crossing
process
process
Includes molecular
changes such as
ionization
process
process
Includes molecular changes such as ionization
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Class
126
127
128
Comments
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BFO Child of
j sluka
Issues
Links to
ExtRefs
structural_process
cellular_process
Prodcess does not result in a change in the identity of the
Object, but the Object does change in DATA structure
existential_cellular_processes
129
cell_growth
130
cell_division
131
fission
132
mitosis
Volumetric, includes
contraction
For example, bacteria.
fiat_process_part
FMA: The process in which a cell irreversibly increases in size
over time by accretion and biosynthetic production of matter
similar to that already present.
process
GO: The process resulting in the physical partitioning and
separation of a cell into daughter cells.
process
Bacterial cell division.
process
133
meiosis
process
134
cell_division_symmetry
process
GO:0007067,
GO: A cell cycle process comprising the steps by which the
nucleus of a eukaryotic cell divides; the process involves
condensation of chromosomal DNA into a highly compacted form.
Canonically, mitosis produces two daughter nuclei whose
chromosome complement is identical to that of the mother cell.
GO:0007126,
GO: A cell cycle process comprising the steps by which a cell
progresses through the nuclear division phase of a meiotic cell
cycle, the specialized nuclear and cell division in which a
single diploid cell undergoes two nuclear divisions following a
single round of DNA replication in order to produce four daughter
cells that contain half the number of chromosomes as the diploid
cell. Meiotic division occurs during the formation of gametes
from diploid organisms and at the beginning of haplophase in
those organisms that alternate between diploid and haploid
generations.
GO: The asymmetric division of cells to produce two daughter
cells with different developmental potentials. It is of
fundamental significance for the generation of cell diversity.
135
symmetric_cell_division
process
136
asymmetric_cell_division
process
GO:0008356,
process
GO:0008219,
137
138
139
140
cell_death
necrosis
apoptosis
autophagic_death
Catch all for cell
death.
process
GO:0006915,
GO: A form of programmed cell death that begins when a cell
receives internal or external signals that trigger the activity
of proteolytic caspases, proceeds through a series of
characteristic stages typically including rounding-up of the
cell, retraction of pseudopodes, reduction of cellular volume
(pyknosis), chromatin condensation, nuclear fragmentation
(karyorrhexis), and plasma membrane blebbing (but maintenance of
its integrity until the final stages of the process), and ends
with the death of the cell.
process
GO:0048102,
GO: A form of programmed cell death that is accompanied by
macroautophagy, which is characterized by the sequestration of
cytoplasmic material within autophagosomes for bulk degradation
by lysosomes. Autophagic cell death is characterized by lack of
chromatin condensation, massive vacuolization of the cytoplasm,
and accumulation of (double-membraned) autophagic vacuoles, with
little or no uptake by phagocytic cells.
GO:0000768,
GO: The formation of a syncytium, a mass of cytoplasm containing
several nuclei enclosed within a single plasma membrane, by the
fusion of the plasma membranes of two or more individual cells.
process
141
cell_fusion
process
142
cell_differentiation
process
143
Definition
cell_environment_process
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Class
144
145
146
147
Comments
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BFO Child of
j sluka
Issues
Links to
cell_import
Via endocytosis, pores
etc.
fiat_process_part
cell_export
exocytosis
fiat_process_part
cell_contact
cell-cell_contact
fiat_process_part
149
cell-noncell_contact
fiat_process_part
150
cell_basement_lamina_contact
fiat_process_part
151
cell_interstitial_matrix _contact
fiat_process_part
cellular_property_process
153
cellular_mechanical_process
154
cellular_kinetic_process
155
geometrical_cellular_process
156
cell_displacement
158
cell_advection
159
chemotaxis
160
haptotaxis
162
fiat_process_part
incompatable
with
GO:0006928
“cell
movement”
cell_movement
157
161
cell_motility
Change in location of
center_of_volume or
center_of_mass
fiat_process_part
fiat_process_part
fiat_process_part
GO:0006935,
GO:0060326
GO: The directed movement of a motile cell or organism, or the
directed growth of a cell guided by a specific chemical
concentration gradient. Movement may be towards a higher
concentration (positive chemotaxis) or towards a lower
concentration (negative chemotaxis).
GO:0048870,
GO: Any process involved in the controlled self-propelled
movement of a cell that results in translocation of the cell from
one place to another.
fiat_process_part
Energy consuming
random cell movement.
Contrast with
chemotaxis, haptotaxis
which are directional.
cell_rotation
fiat_process_part
fiat_process_part
Deprecated. See
cell_growth.
cell_volume_change
164
cell_shape_change
fiat_process_part
165
cell_orientation_change
fiat_process_part
166
cell_adhesion
fiat_process_part
fiat_process_part
167
cell-cell_adhesion
fiat_process_part
168
cell-extracellular_matrix_adhesion
fiat_process_part
cellinterstitial_matrix_adhesion
incompatable with GO:0006928 “cell movement”
fiat_process_part
163
169
Definition
fiat_process_part
148
152
ExtRefs
cell-related_transport
fiat_process_part
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Class
171
172
173
174
Comments
cell-basement_membrane_adhesion
170
BFO Child of
j sluka
Issues
Links to
fiat_process_part
cellular_electrical_process
cellular_chemical_process
cell-cell_process
extracellular_matrix_process
175
interstitual_matrix_process
176
basement_lamina_process
177
molecule_process
used to be
small_molecule_process
178
transport
Catch all class. Cell
has its own set.
179
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interentity_transport
process
process
180
import
process
181
export
process
182
183
intraentity_transport
molecular_targeting
process
ExtRefs
Definition
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CBO Relations
Relation
links
isA
OBO-RO:is_A
has_quality
BFO:inheres_in?
OPB:hasProperty?
Func Sym
Inv
Trans ASym Refl Irrefl
Func
X
OWL markup Definition
X
quality_of
quality_of
has_part
Domain Range Inverse†
“cell” hasQuality “volume”, “point” hasQuality “location”
has_quality
OBO-RO
X
has_proper_part OBO-RO
X
has_integral_part OBO-RO
X
part_of
OBO-RO
X
proper_part_of
OBO-RO
X
integral_part_of
OBO-RO
X
contained_in
OBO-RO
contains
contains
OBO-RO
contained_in
located_in
OBO-RO
X
X
location_of
location_of
OBO-RO
X
X
located_in
instance_of
OBO-RO
CBO
model_of
† Inverse may be different between classes versus instances.
X
part_of
proper_part_of
has_part with the additional restriction that C<>Ci
X
integral_part_of
The defining part of C. “Cell” has_Integral_Part
“cell_membrane”.
X
has_part
has_proper_part
X
has_integral_part
Difference between contains and located?
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OWL Properties represent relationships. There are two main types of properties, Object properties and Datatype properties. Object properties are relationships between two individuals. Object
properties link an individual to an individual. OWL also has a third type of property – Annotation properties. Annotation properties can be used to add information (metadata — data about data)
to classes, individuals and object/datatype properties. Figure 4.12 depicts an example of each type of property.
CBO dataProperty
dataProperty
hasFloatValue
hasIntValue
hasUnit
Functional
Domains
Equivalent
Super
Disjoint
Ranges
(intersections)
Properties Properties Properties
OWL markup
Definition
X
X
X
CBO objectProperty are relationships between two individuals
objectProperty
hasLocation
hasVolume
hasEnergy
Func
Inv
Func
Trans
Sym
ASym
Refl
Irrefl
Domains
Ranges
(intersections) (intersections)
Equivalent
Super
Inverse
Disjoint Property
Object
Properties Properties Properties Chains
Properties
OWL markup
X
X
X
http://www.berkeleybop.org/ontologies/owl/PATO for units and some shapes?
http://forge.morfeo-project.org/wiki_en/index.php/Units_of_measurement_ontology for a discussion of the problem of assigning values and units.
:weight a owl:DatatypeProperty ;
rdfs:label "Weight" .
:weightInKilograms rdfs:subPropertyOf :weight ;
rdfs:label "Weight measured in Kilograms" ;
Definition
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:measuredIn ucum:kilograms .
:weightInPounds rdfs:subPropertyOf :weight ;
rdfs:label "Weight measured in Pounds" ;
:measuredIn ucum:pounds .
CBO annotationProperties
OWL also has a third type of property – Annotation properties. Annotation properties can be used to add information (metadata — data about data) to classes, individuals and object/datatype
properties.
See http://www.w3.org/TR/rdf-primer/ ?
DC:http://dublincore.org/documents/dces/ (Dublin Core)
RDFS:http://www.w3.org/TR/rdf-schema/
annotationProperties
description
creator
Type
Defined In
^^PlainLiteral
DC
DC
DC:description
DC:creator
date
^^Date ?
DC
DC:date
comment
^^PlainLiteral
RDFS
rdfs:comment
discussion
label
xref
versionInfo
^^PlainLiteral
RDFS
rdfs:label
OWL
owl:versionInfo
DC
DC:source
source
^^PlainLiteral
^^PlainLiteral
Definition
An account of the resource. Description may include but is not limited to: an abstract, a table of
contents, a graphical representation, or a free-text account of the resource.
An entity primarily responsible for making the resource.
A point or period of time associated with an event in the lifecycle of the resource. Date may be
used to express temporal information at any level of granularity. Recommended best practice is to
use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF].
Used to provide a human-readable description of a resource.
A textual comment helps clarify the meaning of RDF classes and properties. Such in-line
documentation complements the use of both formal techniques (Ontology and rule languages) and
informal (prose documentation, examples, test cases). A variety of documentation forms can be
combined to indicate the intended meaning of the classes and properties described in an RDF
vocabulary. Since RDF vocabularies are expressed as RDF graphs, vocabularies defined in other
namespaces may be used to provide richer documentation.
Used to provide a human-readable version of a resource's name.
A related resource from which the described resource is derived. The described resource may be
derived from the related resource in whole or in part. Recommended best practice is to identify
the related resource by means of a string conforming to a formal identification system.
OWL markup