Cell Component Ontology Ontology

Generated: 09-Oct-2015 15:15:36
Contents:

Class Hierarchy


Class Definitions

This section of the HTML version of the ontology contains the class definitions of the ontology. Each class defines a type of entity. A class is defined to have a set of slots, where each slot defines attributes and properties that may be used by an instance of that class.

Slots are inherited by a class from its parent classes. Usually this HTML form of the ontology shows only the names of the slots at each class, with links provided to the full definition of the slot in the slot section of the ontology. However, when the definition of a slot is changed within a class with respect to its parent, the full definition of the slot is shown.

Class: CCO

This class is the root of the Cell Component Ontology.

Superclasses: FRAMES

Subclasses: CCO-SUPER-COMP, CCO-MEMBRANE, CCO-SUBORG-CMPT, CCO-ENVELOPE, CCO-SPACE, CCO-SURFACE-MAT, CCO-ORGANELLE

Slots:

Class: CCO-SUPER-COMP

Superclasses: CCO

Subclasses: CCO-SPORE, CCO-CYTOPLASM

Slots:

Class: CCO-SPORE

Superclasses: CCO-SUPER-COMP

Slots:

Class: CCO-CYTOPLASM

Superclasses: CCO-SUPER-COMP

Slots:

Class: CCO-MEMBRANE

Superclasses: CCO

Subclasses: CCO-ACIDCALC-MEM, CCO-ENDO-MEM, CCO-ER-MEM, CCO-GOLGI-MEM, CCO-LYS-MEM, CCO-MBODY-MEM, CCO-MIT-MEM, CCO-NUC-MEM, CCO-OUTER-MEM, CCO-PLASMA-MEM, CCO-PLASTID-MEM, CCO-THY-MEM, CCO-VAC-MEM, CCO-VESICLE-MEM

Slots:

Class: CCO-ACIDCALC-MEM

Superclasses: CCO-MEMBRANE

Slots:

Class: CCO-ENDO-MEM

Superclasses: CCO-MEMBRANE

Subclasses: CCO-EARLY-ENDO-MEM, CCO-LATE-ENDO-MEM

Slots:

Class: CCO-EARLY-ENDO-MEM

Superclasses: CCO-ENDO-MEM

Slots:

Class: CCO-LATE-ENDO-MEM

Superclasses: CCO-ENDO-MEM

Slots:

Class: CCO-ER-MEM

Superclasses: CCO-MEMBRANE

Subclasses: CCO-RGH-ER-MEM, CCO-SMTH-ER-MEM

Slots:

Class: CCO-RGH-ER-MEM

Superclasses: CCO-ER-MEM

Slots:

Class: CCO-SMTH-ER-MEM

Superclasses: CCO-ER-MEM

Slots:

Class: CCO-GOLGI-MEM

Superclasses: CCO-MEMBRANE

Subclasses: CCO-GOLGI-VES-MEM, CCO-GOLGI-CIST-MEM

Slots:

Class: CCO-GOLGI-VES-MEM

Superclasses: CCO-GOLGI-MEM, CCO-VESICLE-MEM

Slots:

Class: CCO-GOLGI-CIST-MEM

Superclasses: CCO-GOLGI-MEM

Slots:

Class: CCO-LYS-MEM

Superclasses: CCO-MEMBRANE

Slots:

Class: CCO-MBODY-MEM

Superclasses: CCO-MEMBRANE

Subclasses: CCO-GLYCO-MEM, CCO-GLYOX-MEM, CCO-PEROX-MEM

Slots:

Class: CCO-GLYCO-MEM

Superclasses: CCO-MBODY-MEM

Slots:

Class: CCO-GLYOX-MEM

Superclasses: CCO-MBODY-MEM

Slots:

Class: CCO-PEROX-MEM

Superclasses: CCO-MBODY-MEM

Slots:

Class: CCO-MIT-MEM

Superclasses: CCO-MEMBRANE

Subclasses: CCO-MIT-IMEM, CCO-MIT-OMEM

Slots:

Class: CCO-MIT-IMEM

Superclasses: CCO-MIT-MEM

Slots:

Class: CCO-MIT-OMEM

Superclasses: CCO-MIT-MEM

Slots:

Class: CCO-NUC-MEM

some sources use the same term refer to nuclear envelope. We distinguish them. The term nuclear membrane is a classification term for the inner and outer nuclear membranes. It does not include the perinuclear space.

Superclasses: CCO-MEMBRANE

Subclasses: CCO-NUC-IMEM, CCO-NUC-OMEM

Slots:

Class: CCO-NUC-IMEM

Superclasses: CCO-NUC-MEM

Slots:

Class: CCO-NUC-OMEM

Superclasses: CCO-NUC-MEM

Slots:

Class: CCO-OUTER-MEM

Superclasses: CCO-MEMBRANE

Slots:

Class: CCO-PLASMA-MEM

Superclasses: CCO-MEMBRANE

Subclasses: CCO-PM-ANIMAL, CCO-PM-BACTERIA, CCO-PM-FUNGI, CCO-PM-PLANT

Slots:

Class: CCO-PM-ANIMAL

Superclasses: CCO-PLASMA-MEM

Slots:

Class: CCO-PM-BACTERIA

Superclasses: CCO-PLASMA-MEM

Subclasses: CCO-PM-BAC-POS, CCO-PM-BAC-NEG

Slots:

Class: CCO-PM-BAC-POS

Superclasses: CCO-PM-BACTERIA

Slots:

Class: CCO-PM-BAC-NEG

Superclasses: CCO-PM-BACTERIA

Slots:

Class: CCO-PM-FUNGI

Superclasses: CCO-PLASMA-MEM

Slots:

Class: CCO-PM-PLANT

Superclasses: CCO-PLASMA-MEM

Slots:

Class: CCO-PLASTID-MEM

The term plastid membrane is a classification term for the inner and outer mitochondrial membranes. It does not include the intermembrane space.

Superclasses: CCO-MEMBRANE

Subclasses: CCO-CHROM-MEM, CCO-CHLOR-MEM, CCO-PLAST-OMEM, CCO-PLAST-IMEM

Slots:

Class: CCO-CHROM-MEM

This term does not include the intermembrane space.

Superclasses: CCO-PLASTID-MEM

Subclasses: CCO-CHROM-OMEM, CCO-CHROM-IMEM

Slots:

Class: CCO-CHROM-OMEM

Superclasses: CCO-CHROM-MEM, CCO-PLAST-OMEM

Slots:

Class: CCO-CHROM-IMEM

Superclasses: CCO-CHROM-MEM, CCO-PLAST-IMEM

Slots:

Class: CCO-CHLOR-MEM

This term does not include the intermembrane space.

Superclasses: CCO-PLASTID-MEM

Subclasses: CCO-CHLOR-OMEM, CCO-CHLOR-IMEM

Slots:

Class: CCO-CHLOR-OMEM

Superclasses: CCO-CHLOR-MEM, CCO-PLAST-OMEM

Slots:

Class: CCO-CHLOR-IMEM

Superclasses: CCO-CHLOR-MEM, CCO-PLAST-IMEM

Slots:

Class: CCO-PLAST-OMEM

Superclasses: CCO-PLASTID-MEM

Subclasses: CCO-CHROM-OMEM, CCO-CHLOR-OMEM

Slots:

Class: CCO-CHROM-OMEM

Superclasses: CCO-CHROM-MEM, CCO-PLAST-OMEM

Slots:

Class: CCO-CHLOR-OMEM

Superclasses: CCO-CHLOR-MEM, CCO-PLAST-OMEM

Slots:

Class: CCO-PLAST-IMEM

Superclasses: CCO-PLASTID-MEM

Subclasses: CCO-CHROM-IMEM, CCO-CHLOR-IMEM

Slots:

Class: CCO-CHROM-IMEM

Superclasses: CCO-CHROM-MEM, CCO-PLAST-IMEM

Slots:

Class: CCO-CHLOR-IMEM

Superclasses: CCO-CHLOR-MEM, CCO-PLAST-IMEM

Slots:

Class: CCO-THY-MEM

Superclasses: CCO-MEMBRANE

Subclasses: CCO-CHL-THY-MEM, CCO-THY-MEM-CYA

Slots:

Class: CCO-CHL-THY-MEM

Superclasses: CCO-THY-MEM

Slots:

Class: CCO-THY-MEM-CYA

Superclasses: CCO-THY-MEM

Slots:

Class: CCO-VAC-MEM

Superclasses: CCO-MEMBRANE

Subclasses: CCO-CONTRCTVAC-MEM

Slots:

Class: CCO-CONTRCTVAC-MEM

Superclasses: CCO-VAC-MEM

Slots:

Class: CCO-VESICLE-MEM

Superclasses: CCO-MEMBRANE

Subclasses: CCO-SEC-GRANULE-MEM, CCO-GOLGI-VES-MEM, CCO-ENDOCYT-VES-MEM, CCO-SYN-VES-MEM

Slots:

Class: CCO-SEC-GRANULE-MEM

Superclasses: CCO-VESICLE-MEM

Slots:

Class: CCO-GOLGI-VES-MEM

Superclasses: CCO-GOLGI-MEM, CCO-VESICLE-MEM

Slots:

Class: CCO-ENDOCYT-VES-MEM

Superclasses: CCO-VESICLE-MEM

Slots:

Class: CCO-SYN-VES-MEM

Superclasses: CCO-VESICLE-MEM

Slots:

Class: CCO-SUBORG-CMPT

Superclasses: CCO

Subclasses: CCO-CHLOR-THY, CCO-GOLGI-CIST

Slots:

Class: CCO-CHLOR-THY

Superclasses: CCO-SUBORG-CMPT

Subclasses: CCO-CHL-STKD-THY, CCO-CHL-STR-THY

Slots:

Class: CCO-CHL-STKD-THY

Superclasses: CCO-CHLOR-THY

Slots:

Class: CCO-CHL-STR-THY

Superclasses: CCO-CHLOR-THY

Slots:

Class: CCO-GOLGI-CIST

Superclasses: CCO-SUBORG-CMPT

Subclasses: CCO-GG-MED-CIST, CCO-GG-CIS-CIST, CCO-GG-TR-CIST

Slots:

Class: CCO-GG-MED-CIST

Superclasses: CCO-GOLGI-CIST

Slots:

Class: CCO-GG-CIS-CIST

Superclasses: CCO-GOLGI-CIST

Slots:

Class: CCO-GG-TR-CIST

Superclasses: CCO-GOLGI-CIST

Slots:

Class: CCO-ENVELOPE

Superclasses: CCO

Subclasses: CCO-CE-BAC, CCO-ORGANEL-ENV

Slots:

Class: CCO-CE-BAC

GO definition of cell envelope does not include the cell membrane.

Superclasses: CCO-ENVELOPE

Subclasses: CCO-CE-BAC-NEG, CCO-CE-BAC-POS

Slots:

Class: CCO-CE-BAC-NEG

Superclasses: CCO-CE-BAC

Slots:

Class: CCO-CE-BAC-POS

Superclasses: CCO-CE-BAC

Slots:

Class: CCO-ORGANEL-ENV

Superclasses: CCO-ENVELOPE

Subclasses: CCO-MIT-ENV, CCO-NUC-ENV, CCO-PLASTID-ENV

Slots:

Class: CCO-MIT-ENV

Superclasses: CCO-ORGANEL-ENV

Slots:

Class: CCO-NUC-ENV

Superclasses: CCO-ORGANEL-ENV

Slots:

Class: CCO-PLASTID-ENV

Superclasses: CCO-ORGANEL-ENV

Subclasses: CCO-CHLOR-ENV, CCO-CHROM-ENV

Slots:

Class: CCO-CHLOR-ENV

Superclasses: CCO-PLASTID-ENV

Slots:

Class: CCO-CHROM-ENV

Superclasses: CCO-PLASTID-ENV

Slots:

Class: CCO-SPACE

Superclasses: CCO

Subclasses: CCO-ACIDCALC-LUM, CCO-CYTOSOL, CCO-ENDO-LUM, CCO-ER-LUM, CCO-EXTRACELLULAR, CCO-GOLGI-LUM, CCO-LYS-LUM, CCO-MICRO-LUM, CCO-MIT-IM-SPC, CCO-MIT-LUM, CCO-NUC-LUM, CCO-PERINUC-SPC, CCO-PERIPLASM, CCO-PLAST-IM-SPC, CCO-PLASTID-STR, CCO-THY-LUM, CCO-UNKNOWN-SPACE, CCO-VAC-LUM, CCO-VES-LUM

Instances: CCO-BOUNDARY, CCO-IN, CCO-MIDDLE, CCO-OUT, CCO-SIDE-1, CCO-SIDE-2

Slots:

Class: CCO-ACIDCALC-LUM

Superclasses: CCO-SPACE

Slots:

Class: CCO-CYTOSOL

Superclasses: CCO-SPACE

Slots:

Class: CCO-ENDO-LUM

Superclasses: CCO-SPACE

Subclasses: CCO-EARLY-END-LUM, CCO-LATE-END-LUM

Slots:

Class: CCO-EARLY-END-LUM

Superclasses: CCO-ENDO-LUM

Slots:

Class: CCO-LATE-END-LUM

Superclasses: CCO-ENDO-LUM

Slots:

Class: CCO-ER-LUM

Superclasses: CCO-SPACE

Subclasses: CCO-RGH-ER-LUM, CCO-SMTH-ER-LUM

Slots:

Class: CCO-RGH-ER-LUM

Superclasses: CCO-ER-LUM

Slots:

Class: CCO-SMTH-ER-LUM

Superclasses: CCO-ER-LUM

Slots:

Class: CCO-EXTRACELLULAR

Superclasses: CCO-SPACE

Slots:

Class: CCO-GOLGI-LUM

Superclasses: CCO-SPACE

Slots:

Class: CCO-LYS-LUM

Superclasses: CCO-SPACE

Slots:

Class: CCO-MICRO-LUM

Superclasses: CCO-SPACE

Subclasses: CCO-GLYCO-LUM, CCO-GLYOX-LUM, CCO-PEROX-LUM

Slots:

Class: CCO-GLYCO-LUM

Superclasses: CCO-MICRO-LUM

Slots:

Class: CCO-GLYOX-LUM

Superclasses: CCO-MICRO-LUM

Slots:

Class: CCO-PEROX-LUM

Superclasses: CCO-MICRO-LUM

Slots:

Class: CCO-MIT-IM-SPC

Superclasses: CCO-SPACE

Slots:

Class: CCO-MIT-LUM

Superclasses: CCO-SPACE

Slots:

Class: CCO-NUC-LUM

Superclasses: CCO-SPACE

Slots:

Class: CCO-PERINUC-SPC

Superclasses: CCO-SPACE

Slots:

Class: CCO-PERIPLASM

Superclasses: CCO-SPACE

Subclasses: CCO-PERI-BAC, CCO-PERI-FUNGI

Slots:

Class: CCO-PERI-BAC

Superclasses: CCO-PERIPLASM

Slots:

Class: CCO-PERI-FUNGI

Superclasses: CCO-PERIPLASM

Slots:

Class: CCO-PLAST-IM-SPC

Superclasses: CCO-SPACE

Subclasses: CCO-CHL-IM-SPC, CCO-CHR-IM-SPC

Slots:

Class: CCO-CHL-IM-SPC

Superclasses: CCO-PLAST-IM-SPC

Slots:

Class: CCO-CHR-IM-SPC

Superclasses: CCO-PLAST-IM-SPC

Slots:

Class: CCO-PLASTID-STR

Superclasses: CCO-SPACE

Subclasses: CCO-CHLOR-STR, CCO-CHROM-STR

Slots:

Class: CCO-CHLOR-STR

Superclasses: CCO-PLASTID-STR

Slots:

Class: CCO-CHROM-STR

Superclasses: CCO-PLASTID-STR

Slots:

Class: CCO-THY-LUM

Superclasses: CCO-SPACE

Subclasses: CCO-CHL-THY-LUM, CCO-THY-LUM-CYA

Slots:

Class: CCO-CHL-THY-LUM

Superclasses: CCO-THY-LUM

Slots:

Class: CCO-THY-LUM-CYA

Superclasses: CCO-THY-LUM

Slots:

Class: CCO-UNKNOWN-SPACE

Superclasses: CCO-SPACE

Slots:

Class: CCO-VAC-LUM

Superclasses: CCO-SPACE

Subclasses: CCO-CONTRCTVAC-LUM

Slots:

Class: CCO-CONTRCTVAC-LUM

Superclasses: CCO-VAC-LUM

Slots:

Class: CCO-VES-LUM

Superclasses: CCO-SPACE

Subclasses: CCO-ENDOCYT-VES-LUM, CCO-SYN-VES-LUM, CCO-SEC-GRANULE-LUM

Slots:

Class: CCO-ENDOCYT-VES-LUM

Superclasses: CCO-VES-LUM

Slots:

Class: CCO-SYN-VES-LUM

Superclasses: CCO-VES-LUM

Slots:

Class: CCO-SEC-GRANULE-LUM

Superclasses: CCO-VES-LUM

Slots:

Class: CCO-SURFACE-MAT

Superclasses: CCO

Subclasses: CCO-EXTRACELL-MAT, CCO-CELLWALL

Slots:

Class: CCO-EXTRACELL-MAT

Superclasses: CCO-SURFACE-MAT

Slots:

Class: CCO-CELLWALL

Superclasses: CCO-SURFACE-MAT

Subclasses: CCO-CW-BAC, CCO-CW-FUNGI, CCO-CW-PLANT

Slots:

Class: CCO-CW-BAC

Superclasses: CCO-CELLWALL

Subclasses: CCO-CW-BAC-NEG, CCO-CW-BAC-POS

Slots:

Class: CCO-CW-BAC-NEG

Superclasses: CCO-CW-BAC

Slots:

Class: CCO-CW-BAC-POS

Superclasses: CCO-CW-BAC

Slots:

Class: CCO-CW-FUNGI

Superclasses: CCO-CELLWALL

Slots:

Class: CCO-CW-PLANT

Superclasses: CCO-CELLWALL

Subclasses: CCO-CW-PL-SEC, CCO-CW-PL-PRIM

Slots:

Class: CCO-CW-PL-SEC

Superclasses: CCO-CW-PLANT

Slots:

Class: CCO-CW-PL-PRIM

Superclasses: CCO-CW-PLANT

Slots:

Class: CCO-ORGANELLE

Superclasses: CCO

Subclasses: CCO-MEM-ORG, CCO-NON-MEM-ORG

Slots:

Class: CCO-MEM-ORG

Superclasses: CCO-ORGANELLE

Subclasses: CCO-ACIDOCALCISOME, CCO-ENDOSOME, CCO-ER, CCO-GOLGI, CCO-LYSOSOME, CCO-MICROBODY, CCO-MIT, CCO-NUCLEUS, CCO-OILBODY, CCO-PLASTID, CCO-THY-CYA, CCO-VACUOLE, CCO-VESICLE

Slots:

Class: CCO-ACIDOCALCISOME

Superclasses: CCO-MEM-ORG

Slots:

Class: CCO-ENDOSOME

Superclasses: CCO-MEM-ORG

Subclasses: CCO-EARLY-ENDO, CCO-LATE-ENDO

Slots:

Class: CCO-EARLY-ENDO

Superclasses: CCO-ENDOSOME

Slots:

Class: CCO-LATE-ENDO

Superclasses: CCO-ENDOSOME

Slots:

Class: CCO-ER

Superclasses: CCO-MEM-ORG

Subclasses: CCO-ROUGH-ER, CCO-SMOOTH-ER

Slots:

Class: CCO-ROUGH-ER

Superclasses: CCO-ER

Slots:

Class: CCO-SMOOTH-ER

Superclasses: CCO-ER

Slots:

Class: CCO-GOLGI

Superclasses: CCO-MEM-ORG

Slots:

Class: CCO-LYSOSOME

Superclasses: CCO-MEM-ORG

Slots:

Class: CCO-MICROBODY

Superclasses: CCO-MEM-ORG

Subclasses: CCO-GLYCOSOME, CCO-GLYOXYSOME, CCO-PEROXISOME

Slots:

Class: CCO-GLYCOSOME

Superclasses: CCO-MICROBODY

Slots:

Class: CCO-GLYOXYSOME

Superclasses: CCO-MICROBODY

Slots:

Class: CCO-PEROXISOME

Superclasses: CCO-MICROBODY

Slots:

Class: CCO-MIT

Superclasses: CCO-MEM-ORG

Slots:

Class: CCO-NUCLEUS

Superclasses: CCO-MEM-ORG

Slots:

Class: CCO-OILBODY

Superclasses: CCO-MEM-ORG

Slots:

Class: CCO-PLASTID

Superclasses: CCO-MEM-ORG

Subclasses: CCO-CHLOROPLAST, CCO-CHROMOPLAST, CCO-ETIOPLAST, CCO-LEUCOPLAST

Slots:

Class: CCO-CHLOROPLAST

Superclasses: CCO-PLASTID

Slots:

Class: CCO-CHROMOPLAST

Superclasses: CCO-PLASTID

Slots:

Class: CCO-ETIOPLAST

Superclasses: CCO-PLASTID

Slots:

Class: CCO-LEUCOPLAST

Superclasses: CCO-PLASTID

Subclasses: CCO-AMYLOPLAST, CCO-ELAIOPLAST, CCO-PROT-PLAST

Slots:

Class: CCO-AMYLOPLAST

Superclasses: CCO-LEUCOPLAST

Slots:

Class: CCO-ELAIOPLAST

Superclasses: CCO-LEUCOPLAST

Slots:

Class: CCO-PROT-PLAST

Superclasses: CCO-LEUCOPLAST

Slots:

Class: CCO-THY-CYA

Superclasses: CCO-MEM-ORG

Slots:

Class: CCO-VACUOLE

Superclasses: CCO-MEM-ORG

Subclasses: CCO-CENTRAL-VACUOLE, CCO-STORAGE-VAC, CCO-SENESC-VACUOLE, CCO-CONTRACTILE-VACUOLE

Slots:

Class: CCO-CENTRAL-VACUOLE

Superclasses: CCO-VACUOLE

Slots:

Class: CCO-STORAGE-VAC

Superclasses: CCO-VACUOLE

Slots:

Class: CCO-SENESC-VACUOLE

Superclasses: CCO-VACUOLE

Slots:

Class: CCO-CONTRACTILE-VACUOLE

Superclasses: CCO-VACUOLE

Slots:

Class: CCO-VESICLE

Superclasses: CCO-MEM-ORG

Subclasses: CCO-ENDOCYT-VES, CCO-SYN-VES, CCO-SEC-GRANULE, CCO-GOLGI-VES

Slots:

Class: CCO-ENDOCYT-VES

Superclasses: CCO-VESICLE

Slots:

Class: CCO-SYN-VES

Superclasses: CCO-VESICLE

Slots:

Class: CCO-SEC-GRANULE

Superclasses: CCO-VESICLE

Slots:

Class: CCO-GOLGI-VES

Superclasses: CCO-VESICLE

Subclasses: CCO-ER-GOLGI-VES, CCO-GOLGI-ER-VES, CCO-INTER-GOLGI-VES, CCO-TR-GOLGI-VES

Slots:

Class: CCO-ER-GOLGI-VES

Superclasses: CCO-GOLGI-VES

Slots:

Class: CCO-GOLGI-ER-VES

Superclasses: CCO-GOLGI-VES

Slots:

Class: CCO-INTER-GOLGI-VES

Superclasses: CCO-GOLGI-VES

Slots:

Class: CCO-TR-GOLGI-VES

Superclasses: CCO-GOLGI-VES

Slots:

Class: CCO-NON-MEM-ORG

Superclasses: CCO-ORGANELLE

Subclasses: CCO-CELL-PROJECTION, CCO-CYTOSKELETON, CCO-NUCLEOID, CCO-NUCLEOLUS, CCO-RIBOSOME

Slots:

Class: CCO-CELL-PROJECTION

Superclasses: CCO-NON-MEM-ORG

Subclasses: CCO-FLAGELLUM, CCO-PILUS

Slots:

Class: CCO-FLAGELLUM

Superclasses: CCO-CELL-PROJECTION

Slots:

Class: CCO-PILUS

We consider fimbrae to fall under the definition of pili.

Superclasses: CCO-CELL-PROJECTION

Slots:

Class: CCO-CYTOSKELETON

Superclasses: CCO-NON-MEM-ORG

Slots:

Class: CCO-NUCLEOID

Superclasses: CCO-NON-MEM-ORG

Subclasses: CCO-BAC-NUCLEOID, CCO-MIT-NUCLEOID, CCO-PLAST-NUCLEOID

Slots:

Class: CCO-BAC-NUCLEOID

Superclasses: CCO-NUCLEOID

Slots:

Class: CCO-MIT-NUCLEOID

Superclasses: CCO-NUCLEOID

Slots:

Class: CCO-PLAST-NUCLEOID

Superclasses: CCO-NUCLEOID

Slots:

Class: CCO-NUCLEOLUS

Superclasses: CCO-NON-MEM-ORG

Slots:

Class: CCO-RIBOSOME

Superclasses: CCO-NON-MEM-ORG

Slots:

Instance Definitions

Instance: CCO-BOUNDARY

Types: CCO-SPACE

Slots:

Instance: CCO-IN

Types: CCO-SPACE

Slots:

Instance: CCO-MIDDLE

Types: CCO-SPACE

Slots:

Instance: CCO-OUT

Types: CCO-SPACE

Slots:

Instance: CCO-SIDE-1

Types: CCO-SPACE

Slots:

Instance: CCO-SIDE-2

Types: CCO-SPACE

Slots:


Slot Definitions

This section of the HTML version of the ontology contains the slot definitions of the ontology. Each slot itself has several properties such as documentation about that slot, a cardinality (specifying the number of values that the slot may have), a value type (specifying the data type of slot values), and a domain (specifying the class(es) in which the slot is used).

Slot NameDocumentationProperties
COMMON-NAME The primary name by which an object is known to scientists. Typically the name will be a standard name, or a widely used and familiar name. In some cases arbitrary choices must be made when picking the Common-Name. COMMON-NAME: Common-Name
QUERYABLE?: T
DOMAIN: SLOTS, THING
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
MAXIMUM-CARDINALITY: 1
COMPONENT-OF This slot specifies an object that contains this object as a smaller part. For example, this slot can link a polypeptide or a small molecule to macromolecular complex that contains it.

See the documentation of slot Components for more details.

COMMON-NAME: Component-Of
QUERYABLE?: T
DOMAIN: Chemicals, Polymer-Segments, CCO
VALUE-TYPE: THING
INVERSE: COMPONENTS
COMPONENTS This slot lists the components of some physical assembly:

1. The subunits of a protein complex, a protein-RNA complex, and a
protein-small-molecule complex 2. The genes within a genetic element, or the contigs of a genetic element 3. The genes and other DNA-Segments within a transcription unit 4. Entities witin the cell component ontology 5. The ion constituents in salts

The coefficient of each component (when known) is listed as an annotation of the component value under the label coefficient.

When a modified protein is created to reflect a chemically modified alternative form of the protein, if that protein is a complex, its subunit structure need not be mirrored in the modified-protein frame. The subunit structure should be defined only once, for the frame that represents the unmodified form of the protein.

COMMON-NAME: Components
QUERYABLE?: T
DOMAIN: Salts, Genetic-Elements, Transcription-Units, Complexes, CCO
VALUE-TYPE: THING
INVERSE: COMPONENT-OF
DEFINITION This slot contains the official definition for a Gene Ontology term. COMMON-NAME: Definition
QUERYABLE?: T
DOMAIN: CCO, Gene-Ontology-Terms
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
MAXIMUM-CARDINALITY: 1
GOID The Gene Ontology term that best corresponds to this cell component term. The value of this slot should be a string starting with "GO:" and followed by a set of digits. COMMON-NAME: GO-ID
DOMAIN: CCO
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
MAXIMUM-CARDINALITY: 1
SENSU Restricts the cellular compartment to organisms that match one of the values of this slot. COMMON-NAME: Sensu
QUERYABLE?: T
DOMAIN: CCO
VALUE-TYPE: Organisms
SURROUNDED-BY SURROUNDED-BY is used to describe topological relationships between cellular compartments. We say X SURROUNDED-BY Y in two typical cases: where a space Y is surrounded by a membrane X (example: the bacterial cytosol is surrounded by the plasma membrane of the cell), and where a membrane Y is surrounded by a space X (example: the bacterial inner membrane is surrounded by the bacterial periplasmic space). COMMON-NAME: Surrounded-By
DOMAIN: CCO
VALUE-TYPE: THING
INVERSE: SURROUNDS
SURROUNDS SURROUNDS is used to describe topological relationships between cellular compartments. We say X SURROUNDS Y in two typical cases: where a membrane X encloses a space Y (example: the plasma membrane of a bacterial cell surrounds the cytosol), and where a space X encloses a membrane Y (example: the bacterial periplasmic space encloses the bacterial inner membrane). COMMON-NAME: Surrounds
DOMAIN: CCO
VALUE-TYPE: THING
INVERSE: SURROUNDED-BY