Gene Regulation Ontology (GRO)
type: Ontology
version info: 0.5
creator: Vivian Lee
date: April 20, 2010
creator: Elena Beisswanger
description: The Gene Regulation Ontology (GRO) covers gene regulatory processes occurring on the intracellular level and molecular entities participating in these processes.
creator: Jung-jae Kim
creator: Andrea Splendiani
type: Thing
default language: en

reference
type: AnnotationProperty
type: DatatypeProperty
definition: Reference to a similar term in an external database or terminological resource.

synonym
type: AnnotationProperty
type: DatatypeProperty
definition: An exact synonyms of the given ontology term.

definition
type: AnnotationProperty
type: DatatypeProperty
type: FunctionalProperty
definition: GRO definition explaining the meaning of a class or property. If the definition was taken from an external resource a reference is given in brackets.

hasPolarity
type: DatatypeProperty
type: FunctionalProperty
range: DataRange
  one of: negative
  one of: positive
  one of: positive and negative
  one of: unknown

AP2-EREBP-related domain
type: Class
subclass of: DNA binding domain of transcription factor
subclass of: Restriction
  on property: partOf
  some values from: AP2-EREBP related transcription factor
definition: A domain consisting of the AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) related DNA-binding sequence.

AP2-EREBP related transcription factor
type: Class
subclass of: enhancer binding transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: AP2-EREBP-related domain
definition: A transcription factor containing the AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) related DNA-binding domain, which plays a variety of roles throughout the plant life cycle.

acetylation
type: Class
subclass of: modification of molecular entity
definition: A reaction that introduces an acetyl functional group into an organic compound. [http://en.wikipedia.org/wiki/Acetylation]

activation
type: Class
subclass of: regulatory process
subclass of: Restriction
  on property: hasPolarity
  has value: positive
definition: Any process that activates, maintains or increases the frequency, rate or extent of an action.

activation of polymerase
type: Class
equivalent class: Class
  intersection of: activation
  intersection of: Restriction
    on property: hasPatient
    some values from: polymerase activity
  intersection of: Restriction
    on property: hasPatient
    all values from: polymerase activity
definition: Any process that initiates the activity of the inactive enzyme polymerase.

activation of process
type: Class
equivalent class: Class
  intersection of: activation
  intersection of: Restriction
    on property: hasPatient
    some values from: process
  intersection of: Restriction
    on property: hasPatient
    all values from: process
definition: Any process that activates or increases the frequency, rate or extent of a process.

activation of protein
type: Class
equivalent class: Class
  intersection of: activation
  intersection of: Restriction
    on property: hasPatient
    some values from: gene product function
  intersection of: Restriction
    on property: hasPatient
    all values from: gene product function
definition: Any process that initiates the activity of the inactive form of a protein.

activation of transcription regulator activity
type: Class
equivalent class: Class
  intersection of: activation
  intersection of: Restriction
    on property: hasPatient
    some values from: transcription regulator activity
  intersection of: Restriction
    on property: hasPatient
    all values from: transcription regulator activity
definition: Any process that activates or increases the frequency, rate or extent of activity of a transcription regulator, any factor plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor (modified from [GO:0051091, GO:0030528])

affecting
type: Class
subclass of: process

agonist
type: Class
subclass of: ligand
definition: Any molecule that improves the activity of a different molecule; e.g., a hormone, which acts as an agonist when it binds to its receptor, thus triggering a biochemical response. [http://www.combichemistry.com/medical-chemistry-glossary.html]

amino acid
type: Class
subclass of: organic chemical
disjoint with: carbohydrate
disjoint with: gas
disjoint with: inositol phosphate
disjoint with: ion
disjoint with: lipid
disjoint with: nucleoside
disjoint with: second messenger
disjoint with: vitamin
reference: CHEBI:33709 amino acids
definition: Carboxylic acids containing one or more amino groups. [CHEBI:33709]
reference: IMR:0001695 amino acid

antagonist
type: Class
subclass of: ligand
definition: An agent that opposes the action or reduces the physiological activity of another.

antisense RNA
type: Class
subclass of: ncRNA
reference: SO:0000644 antisense_RNA
definition: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. [SO:0000644]

apoenzyme
type: Class
subclass of: protein
definition: a protein that combines with a coenzyme to form an active enzyme [http://wordnet.princeton.edu/perl/webwn?s=apoenzyme]

archaebacterium
type: Class
subclass of: prokaryote
disjoint with: bacterium
definition: Ancient life forms that evolved separately from bacteria and blue-green algae. [http://wordnet.princeton.edu/perl/webwn?s=archaebacterium]
reference: NCBI Taxonomy ID: 2157 Archaea

architectural proteins
type: Class
subclass of: protein
definition: Proteins that bend DNA.

atom
type: Class
subclass of: molecular entity
definition: The smallest part of an element that still has all properties of that element. Its nucleus consists of protons and neutrons and is surrounded by orbiting electrons. [http://www.nsc.org/EHC/guidebks/wippglos.htm]

attenuator
type: Class
subclass of: DNA region
definition: A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. [SO:0000140]
reference: SO:0000140 attenuator

bacterial RNA polymerase promoter
type: Class
subclass of: promoter
subclass of: Restriction
  on property: fromSpecies
  some values from: bacterium
definition: A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. [SO:0000613]
reference: SO:0000613 bacterial RNApol promoter

bacteriophage
type: Class
subclass of: virus
definition: A virus that infects bacteria. Also called a phage. [www.accessexcellence.org/RC/AB/WYW/wkbooks/SFTS/glossary.html]
reference: NCBI Taxonomy ID: 38018 unidentified phage

bacterium
type: Class
subclass of: prokaryote
definition: Any of the unicellular prokaryotic organisms, which vary in terms of morphology, oxygen and nutritional requirements and motility and can exist either as independent (free-living) organisms or as parasites (dependent upon another organism for life).
reference: NCBI Taxonomy ID: 2 Bacteria

basic domain
type: Class
subclass of: DNA binding domain of transcription factor
subclass of: Restriction
  on property: partOf
  some values from: basic domain transcription factor
definition: A domain containing a basic region that mediates sequence-specific DNA-binding.

basic domain transcription factor
type: Class
subclass of: enhancer binding transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: basic domain
definition: A transcription factor containing basic domain.

behavior
type: Class
subclass of: biological process
subclass of: Restriction
  on property: hasAgent
  some values from: organism
reference: GO:0007610 behavior
definition: The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. [GO:0007610]

beta barrel alpha helix domain
type: Class
subclass of: cold shock domain
subclass of: Restriction
  on property: partOf
  some values from: beta-barrel alpha-helix domain transcription factor
definition: A DNA binding domain usual found in the viral protein E2, in which it forms a dimeric beta barrel, with each subunit contributing an anti-parallel 4-stranded beta sheet half-barrel. The topology of each subunit is beta1-1-beta2-beta3-2-beta4. Helix 1 is the recognition helix housing all of the amino acid residues involved in direct DNA sequence specification. Upon dimerisation, strands beta2 and beta4 at the edges of each subunit participate in a continuous hydrogen-bonding network, which results in an 8-stranded beta-barrel. The dimer interface is extensive, made up of hydrogen bonds between subunits and a substantial hydrophobic beta-barrel core. (modified from [InterPro:IPR000427]

beta-barrel alpha-helix domain transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: beta barrel alpha helix domain
definition: A transcription factor containing beta-barrel alpha-helix domain.

beta scaffold domain transcription factor with minor groove contacts
type: Class
subclass of: enhancer binding transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: beta scaffold domain with minor groove contacts
definition: A transcription factor containing beta scaffold domain with minor groove contacts

beta scaffold domain with minor groove contacts
type: Class
subclass of: DNA binding domain of transcription factor
subclass of: Restriction
  on property: partOf
  some values from: beta scaffold domain transcription factor with minor groove contacts
definition: A domain containing beta scaffold structure and usually binding to the DNA minor groove.

bidirectional promoter
type: Class
subclass of: promoter
definition: Promoter sequences between divergently transcribed neighbouring gene pairs that initiate transcription in both directions. [http://www.everythingbio.com/glos/definition.php?word=bidirectional+promoters]

binding
type: Class
subclass of: physical interaction
subclass of: Restriction
  on property: resultsIn
  some values from: physical contact
reference: GO:0005488 binding
definition: The selective, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488]

binding assay
type: Class
subclass of: experimental method
subclass of: Restriction
  on property: resultsIn
  some values from: binding
definition: An analytic procedure in which binding is studied involves the labelling of an expressed protein.

binding of DNA binding domain of protein to DNA
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: DNA binding domain of protein
  intersection of: Restriction
    on property: hasPatient
    some values from: DNA
  intersection of: Restriction
    on property: hasAgent
    all values from: DNA binding domain of protein
  intersection of: Restriction
    on property: hasPatient
    all values from: DNA
definition: Selective interaction of a DNA binding domain of a protein with DNA.

binding of molecular entity
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: molecular entity
  intersection of: Restriction
    on property: hasAgent
    all values from: molecular entity
definition: Selective interaction of a molecule entity with other substance.

binding of protein
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: protein
  intersection of: Restriction
    on property: hasAgent
    all values from: protein
definition: Selective interaction of a protein with other molecules.

binding of protein to DNA
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: protein
  intersection of: Restriction
    on property: hasPatient
    some values from: DNA
  intersection of: Restriction
    on property: hasAgent
    all values from: protein
  intersection of: Restriction
    on property: hasPatient
    all values from: DNA
definition: The selective interaction of a protein or protein complex with a deoxyribonucleotide, any compound consisting of a deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety.

binding of protein to protein binding site of DNA
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: protein
  intersection of: Restriction
    on property: hasPatient
    some values from: protein binding site of DNA
  intersection of: Restriction
    on property: hasAgent
    all values from: protein
  intersection of: Restriction
    on property: hasPatient
    all values from: protein binding site of DNA
definition: Selective interaction of a protein with a specific site on DNA which forms a chemical bond.

binding of protein to protein binding site of protein
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: protein
  intersection of: Restriction
    on property: hasPatient
    some values from: protein binding site of protein
  intersection of: Restriction
    on property: hasAgent
    all values from: protein
  intersection of: Restriction
    on property: hasPatient
    all values from: protein binding site of protein
definition: Selective interaction of a protein with a specific site on other proteins which forms a chemical bond.

binding of RNA polymerase to DNA
type: Class
subclass of: binding
subclass of: Restriction
  on property: hasPatient
  some values from: RNA polymerase binding site of DNA
subclass of: Restriction
  on property: hasAgent
  some values from: RNA
definition: Selective interaction of RNA polymerase with DNA

binding of TF to TF binding site of DNA
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: transcription factor
  intersection of: Restriction
    on property: hasPatient
    some values from: transcription factor binding site of DNA
  intersection of: Restriction
    on property: hasAgent
    all values from: transcription factor
  intersection of: Restriction
    on property: hasPatient
    all values from: transcription factor binding site of DNA
definition: Selective interaction of a transcription factor with a specific site on DNA which forms a chemical bond.

binding of TF to TF binding site of protein
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: transcription factor
  intersection of: Restriction
    on property: hasPatient
    some values from: TF binding site of protein
  intersection of: Restriction
    on property: hasAgent
    all values from: transcription factor
  intersection of: Restriction
    on property: hasPatient
    all values from: TF binding site of protein
definition: Selective interaction of a transcription factor with one or more specific sites on a protein.

binding of transcription activator to enhancer
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: transcription activator
  intersection of: Restriction
    on property: hasPatient
    some values from: enhancer
  intersection of: Restriction
    on property: hasAgent
    all values from: transcription activator
  intersection of: Restriction
    on property: hasPatient
    all values from: enhancer
definition: The selective interaction of a transcription activator with a cis-acting sequence that increases the utilization of (some) eukaryotic promoter.

binding of transcription factor to DNA
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: transcription factor
  intersection of: Restriction
    on property: hasPatient
    some values from: DNA
  intersection of: Restriction
    on property: hasAgent
    all values from: transcription factor
  intersection of: Restriction
    on property: hasPatient
    all values from: DNA
definition: The function of binding to a specific DNA sequence in order to modulate transcription. [GO:0003700]

binding of transcription factor to operator
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: transcription factor
  intersection of: Restriction
    on property: hasPatient
    some values from: operator
  intersection of: Restriction
    on property: hasAgent
    all values from: transcription factor
  intersection of: Restriction
    on property: hasPatient
    all values from: operator
definition: Selective interaction of a transcription factor with an operator

binding of transcription repressor to silencer
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: transcription repressor
  intersection of: Restriction
    on property: hasPatient
    some values from: silencer
  intersection of: Restriction
    on property: hasAgent
    all values from: transcription repressor
  intersection of: Restriction
    on property: hasPatient
    all values from: silencer
definition: Selective interaction of a transcription repressor with a collection of short DNA sequence elements which suppress the transcription of an adjacent gene or genes.

binding of translation initiation complex to RNA
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasAgent
    some values from: translation initiation complex
  intersection of: Restriction
    on property: hasPatient
    some values from: RNA
  intersection of: Restriction
    on property: hasAgent
    all values from: translation initiation complex
  intersection of: Restriction
    on property: hasPatient
    all values from: RNA
synonym: RNA binding of translation initiation complex
definition: Selective interaction of translation initiation complex with RNA which leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site.

binding site of protein
type: Class
subclass of: protein domain
subclass of: Restriction
  on property: patientOf
  some values from: binding to binding site of protein
definition: A region on a protein that forms a chemical bond with other molecules.

binding to binding site of protein
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasPatient
    some values from: binding site of protein
  intersection of: Restriction
    on property: hasPatient
    all values from: binding site of protein
definition: Selective interaction of a molecule with a specific site on a protein which forms a chemical bond.

binding to micro RNA
type: Class
subclass of: binding to RNA
subclass of: Restriction
  on property: hasPatient
  all values from: miRNA
subclass of: Restriction
  on property: hasPatient
  some values from: miRNA
definition: Interacting selectively with microRNA.
synonym: miRNA binding
synonym: microRNA binding

binding to molecular entity
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasPatient
    some values from: molecular entity
  intersection of: Restriction
    on property: hasPatient
    all values from: molecular entity
definition: Interacting selectively with a molecular entity.
synonym: molecular binding

binding to protein
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasPatient
    some values from: protein
  intersection of: Restriction
    on property: hasPatient
    all values from: protein
reference: GO:0005515 protein binding
definition: Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).[GO:0005515]

binding to RNA
type: Class
equivalent class: Class
  intersection of: binding
  intersection of: Restriction
    on property: hasPatient
    some values from: RNA
  intersection of: Restriction
    on property: hasPatient
    all values from: RNA
reference: GO:0003723 RNA binding
definition: Interacting selectively with an RNA molecule or a portion thereof. [GO:0003723]
synonym: RNA binding

biofilm
type: Class
subclass of: physical continuant
subclass of: Restriction
  on property: hasPart
  some values from: microorganism
definition: A slime layer that develops naturally when bacteria congregate on surfaces. [publications.nigms.nih.gov/thenewgenetics/glossary.htm]

biomass
type: Class
subclass of: physical continuant
definition: Total mass of all the organisms of a given type and/or in a given area. (From Concise Dictionary of Biology, 1990) It includes the yield of vegetative mass produced from any given crop. [MeSH:D018533]

C6 zinc cluster
type: Class
subclass of: zinc-coordinating domain
subclass of: Restriction
  on property: partOf
  some values from: C6 zinc cluster transcription factor
definition: Zinc finger motif of GAL4-type. Six cysteine residues coordinate two zinc ions, i. e. two of the thiol groups coordinate two zinc ions (six cysteines binuclear cluster DNA-binding domain). All GAL4-type proteins possess a single N-terminal zinc finger with an adjacent basic region, which is critical for sequence-specific recognition. Each C3-repeat unit of the structural motif of six cysteines forms short alpha-helical structures separated by a loop with a proline-associated turn. The zinc(II)-binding cluster lies in the DNA major groove and contacts three base pairs. (modified from [TRANSFAC:C0005]

C6 zinc cluster transcription factor
type: Class
subclass of: zinc coordinating domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: C6 zinc cluster
definition: A transcription factor containing C6 zinc cluster domain

carbohydrate
type: Class
subclass of: organic chemical
disjoint with: gas
disjoint with: inositol phosphate
disjoint with: ion
disjoint with: lipid
disjoint with: nucleoside
disjoint with: second messenger
disjoint with: vitamin
definition: A class of organic compounds containing carbon, hydrogen and oxygen and having the general formula Cm(H2O)n. They usually serve as a major energy source in the diet of animals. Example: sugar or starch.
reference: CHEBI:23008 carbohydrate
reference: IMR:0001657 carbohydrate

carbon catabolite
type: Class
subclass of: organic chemical
definition: A carbon compound produced in catabolism.

catabolic pathway
type: Class
subclass of: metabolic pathway
definition: The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. [GO:0009056]
reference: GO:0009056 catabolic process

catalytic activity
type: Class
subclass of: gene product function
definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [GO:0003824]
reference: GO:0003824 catalytic activity

cell
type: Class
subclass of: living entity
subclass of: Restriction
  on property: hasPart
  some values from: cell component
subclass of: Class
  union of: organism
  union of: Restriction
    on property: partOf
    some values from: organism
disjoint with: cell component
disjoint with: molecular entity
definition: The fundamental, structural, and functional units or subunits of living organisms. They are composed of CYTOPLASM containing various ORGANELLES and a CELL MEMBRANE boundary. [MeSH:D002477]

cell adhesion
type: Class
subclass of: cellular process
subclass of: Restriction
  on property: hasAgent
  some values from: cell
subclass of: Restriction
  on property: resultsIn
  some values from: binding
reference: GO:0007155 cell adhesion
definition: The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. [GO:0007155]

cell aging
type: Class
subclass of: cellular process
definition: Progression of the cell from its inception to the end of its lifespan. [GO:0007569]
reference: GO:0007569 cell aging

cell communication
type: Class
subclass of: cellular process
subclass of: Restriction
  on property: hasAgent
  some values from: cell
subclass of: Restriction
  on property: hasParticipant
  on class: cell
  min qualified cardinality: 2
definition: Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. [GO:0007154]
reference: GO:0007154 cell communication

cell component
type: Class
subclass of: physical continuant
subclass of: Restriction
  on property: partOf
  some values from: nucleus
disjoint with: organism
reference: GO:0005575 cellular component
definition: The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. [GO:0005575]

cell cycle
type: Class
subclass of: cellular process
subclass of: Restriction
  on property: hasAgent
  some values from: cell
reference: GO:0007049 cell cycle
definition: The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. [GO:0007049]

cell cycle phase
type: Class
subclass of: cellular process
subclass of: physiological process phase
subclass of: Restriction
  on property: partOf
  some values from: cell cycle
reference: GO:0022403 cell cycle phase
definition: A cell cycle process comprising the steps by which a cell progresses through one of the biochemical and morphological phases and events that occur during successive cell replication or nuclear replication events. [GO:0022403]

cell cycle phase transition
type: Class
subclass of: physiological process phase
definition: Progression from a cell cycle phase to another cell cycle phase.

cell death
type: Class
subclass of: cellular process
subclass of: death
subclass of: Restriction
  on property: hasAgent
  some values from: cell
reference: GO:0008219 cell death
definition: The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. [GO:0008219]

cell differentiation
type: Class
subclass of: cellular developmental process
subclass of: Restriction
  on property: hasAgent
  some values from: cell
reference: GO:0030154 cell differentiation
definition: The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate. [GO:0030154]

cell division
type: Class
subclass of: cell cycle phase
reference: GO:0051301 cell division
definition: The process resulting in the physical partitioning and separation of a cell into daughter cells. [GO:0051301]

cell fate determination
type: Class
subclass of: cellular process
reference: GO:0001709 cell fate determination
definition: Process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment. [GO:0001709]

cell growth
type: Class
subclass of: cellular process
subclass of: growth
subclass of: Restriction
  on property: hasAgent
  some values from: cell
reference: GO:0016049 cell growth
definition: The process by which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. [GO:0016049]

cell homeostasis
type: Class
subclass of: intra cellular process
reference: GO:0019725 cellular homeostasis
definition: The processes involved in the maintenance of an internal equilibrium at the level of the cell. [GO:0019725]

cell motility
type: Class
subclass of: cellular process
subclass of: Restriction
  on property: hasAgent
  some values from: cell
definition: Any process involved in the controlled movement of a cell. [GO:0006928]
reference: GO:0006928 cell motility

cellular component organization and biogenesis
type: Class
subclass of: cellular process
subclass of: Restriction
  on property: hasParticipant
  some values from: cell component
definition: A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a cellular component; includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. [GO:0016043]
reference: GO:0016043 cellular component organization and biogenesis

cellular developmental process
type: Class
equivalent class: Class
  intersection of: developmental process
  intersection of: Restriction
    on property: hasAgent
    some values from: cell
definition: A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. [GO:0048869]
reference: GO:0048869 cellular developmental process

cellular metabolic process
type: Class
subclass of: intra cellular process
reference: GO:0044237 cellular metabolic process
definition: The chemical reactions and pathways by which individual cells transform chemical substances. [GO:0044237]

cellular process
type: Class
equivalent class: Class
  intersection of: biological process
  intersection of: Class
    union of: Restriction
      on property: hasAgent
      some values from: cell
    union of: Restriction
      on property: hasPatient
      some values from: cell
    union of: Restriction
      on property: locatedIn
      some values from: cell
    union of: Restriction
      on property: locatedIn
      some values from: cell component
reference: GO:0009987 cellular process
definition: Processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. [GO:0009987]

chemical
type: Class
subclass of: molecular entity
disjoint with: nucleic acid
disjoint with: protein
disjoint with: protein domain
reference: IMR:0000947 chemical

chromatin
type: Class
subclass of: packed DNA
definition: The material of chromosomes. It is a complex of DNA, histones, and nonhistone proteins found within the nucleus of a cell. [MeSH]

chromatin silencing
type: Class
subclass of: gene silencing
subclass of: negative regulation of transcription
reference: GO:0006342 chromatin silencing
definition: Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin. [GO:0006342]

chromosomal DNA
type: Class
subclass of: DNA molecule
subclass of: Restriction
  on property: partOf
  some values from: chromosome

chromosome
type: Class
subclass of: cell component
subclass of: complex molecular entity
subclass of: Restriction
  on property: partOf
  some values from: nucleus
definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. [GO:0005694]
reference: GO:0005694 chromosome

chronological cell aging
type: Class
subclass of: cell aging
definition: The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state. [GO:0001300]
reference: GO:0001300 chronological cell aging

circadian
type: Class
subclass of: temporal quality
reference: GO:0007623 circadian rhythm
definition: Any biological process in an organism that recurs with a regularity of approximately 24 hours. [GO:0007623]

cleavage
type: Class
subclass of: modification of molecular entity
definition: Covalent bond breakage in a molecule leading to the formation of smaller molecules. [IEV:0002571]

coiled chromosomal DNA
type: Class
subclass of: chromosomal DNA
subclass of: double strand DNA
definition: The tightly coiled DNA contained in chromosome.

cold shock domain
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: cold shock domain transcription factor
definition: ��A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic single-strand nucleic-acid binding proteins. This domain, which is known as the 'cold-shock domain' (CSD)...[InterPro: IPR011129]

cold shock domain transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: cold shock domain
definition: A transcription factor containing cold shock domain.

complex molecular entity
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: hasPart
  on class: molecular entity
  min qualified cardinality: 2
disjoint with: nucleic acid
disjoint with: protein
disjoint with: protein domain
definition: A complex form of molecular entity.

complex of protein and DNA
type: Class
subclass of: complex molecular entity
subclass of: Restriction
  on property: hasPart
  some values from: DNA region
subclass of: Restriction
  on property: hasPart
  some values from: protein
definition: A macromolecular complex containing both protein and DNA molecules. [GO:0032993]
reference: GO:0032993 protein-DNA complex

complex of protein and RNA
type: Class
subclass of: complex molecular entity

complex regulation of transcription
type: Class
subclass of: regulation of transcription
definition: A combination of positive and negative regulation of transcription

conformation
type: Class
subclass of: non physical continuant
disjoint with: direction
disjoint with: double strand DNA
disjoint with: locus
disjoint with: orientation
disjoint with: packed DNA
disjoint with: phenotype
disjoint with: single strand DNA
disjoint with: unpacked DNA
definition: The structural arrangement.

continuant
type: Class
disjoint with: occurrent
definition: Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. [http://www.ifomis.org/bfo/1.1/light/span#Continuant]

copper-fist domain
type: Class
subclass of: DNA binding domain of transcription factor
subclass of: Restriction
  on property: partOf
  some values from: copper fist transcription factor
definition: A domain, similar in structure to metallothionein, undergoing a large conformational change on copper-binding that allows DNA-binding. It contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet. Conserved residues form a basic patch that may be important for DNA binding. (modified from [InterPro: IPR001083])

copper fist transcription factor
type: Class
subclass of: enhancer binding transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: copper-fist domain
definition: Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet. Conserved residues form a basic patch that may be important for DNA binding. [InterPro: IPR001083]

CG island
type: Class
subclass of: DNA region
synonym: CpG island
definition: Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. [SO:0000307]
reference: SO:0000307 CpG_island

DB domain of nuclear receptor
type: Class
subclass of: zinc-coordinating domain
subclass of: Restriction
  on property: partOf
  some values from: nuclear receptor transcription factor
definition: The DNA binding domain of nuclear receptor, a group of proteins function in nuclei to regulate the transcription of target genes in a ligand-responsive manner.

DM domain
type: Class
subclass of: zinc-coordinating domain
subclass of: Restriction
  on property: partOf
  some values from: DM-domain-containing transcription factor
definition: This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans. In D. melanogaste the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences. The NMR analysis of the DSX DM domain revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence. [InterPro: IPR001275]

DM-domain-containing transcription factor
type: Class
subclass of: zinc coordinating domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: DM domain
definition: A transcription factor containing DM domain.

DNA
type: Class
equivalent class: Class
  intersection of: nucleic acid
  intersection of: Restriction
    on property: hasPart
    some values from: deoxynucleotide
disjoint with: RNA
definition: A chain of deoxyribonucleotides.

DNA binding domain of protein
type: Class
subclass of: binding site of protein
subclass of: Restriction
  on property: agentOf
  some values from: binding of DNA binding domain of protein to DNA
definition: Any protein motif that binds to double- or single-stranded DNA with affinity to a specific sequence or set thereof or a general affinity to DNA. [http://en.wikipedia.org/wiki/DNA-binding_domain]

DNA binding domain of transcription factor
type: Class
subclass of: DNA binding domain of protein
subclass of: Restriction
  on property: partOf
  some values from: transcription factor
definition: A domain of a transcription factor that binds DNA.

DNA binding site
type: Class
subclass of: DNA region
definition: A region on a molecule that recognizes and forms a chemical bond with DNA.

DNA fragment
type: Class
subclass of: DNA molecule
definition: A piece of DNA.

DNA modification
type: Class
subclass of: modification of molecular entity
subclass of: Restriction
  on property: hasPatient
  some values from: DNA
reference: GO:0006304 DNA modification
definition: The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. [GO:0006304]

DNA molecule
type: Class
subclass of: DNA
definition: A chain of deoxyribonucleotides as it occures at a whole.

DNA polymerase
type: Class
subclass of: polymerase
definition: An enzyme that catalyses the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA/or RNA template or primer (modified from [GO:0003887, GO:0003964])
reference: GO:0003887 DNA-directed DNA polymerase activity
reference: GO:0003964 RNA-directed DNA polymerase activity

DNA protein interaction
type: Class
equivalent class: Class
  intersection of: physical interaction
  intersection of: Class
    union of: Class
      intersection of: Restriction
        on property: hasAgent
        some values from: DNA
      intersection of: Restriction
        on property: hasPatient
        some values from: protein
    union of: Class
      intersection of: Restriction
        on property: hasAgent
        some values from: protein
      intersection of: Restriction
        on property: hasPatient
        some values from: DNA
  intersection of: Restriction
    on property: hasAgent
    all values from: Class
      union of: DNA
      union of: protein
  intersection of: Restriction
    on property: hasPatient
    all values from: Class
      union of: DNA
      union of: protein
definition: Any complex that forms between a protein molecule and DNA. [http://cancerweb.ncl.ac.uk/cgi-bin/omd?DNA-protein+interaction]

DNA region
type: Class
subclass of: DNA
subclass of: nucleic acid region
definition: A chain of deoxyribonucleotides that is part of a longer chain of deoxyribunucleotides.

ds siRNA
type: Class
subclass of: siRNA
definition: Double-stranded siRNA.

death
type: Class
subclass of: biological process
definition: A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism. [GO:0016265]
reference: GO:0016265 death

decrease
type: Class
subclass of: process
subclass of: Restriction
  on property: hasPolarity
  has value: negative
comment: A process of becoming smaller, less numerous, less important, or less likely.

deoxynucleoside
type: Class
subclass of: nucleoside
subclass of: Restriction
  on property: hasPart
  some values from: deoxyribose
definition: A molecule composed of a nitrogenous base attached to the five-carbon sugar deoxyribose. [http://cancerweb.ncl.ac.uk/cgi-bin/omd?deoxynucleoside]

deoxynucleotide
type: Class
subclass of: nucleotide
subclass of: Restriction
  on property: hasPart
  some values from: deoxyribose
definition: A chemical compound that consists of 3 portions: a nitrogenous base, a sugar, and one or more phosphate groups. In the most common nucleotides the base is a derivative of purine or pyrimidine, and the sugar is deoxyribose. (modified from [http://en.wikipedia.org/wiki/Deoxynucleotide#Nucleotide_structure])

deoxyribose
type: Class
subclass of: ribose
reference: CHEBI:28816 2-deoxy-D-ribose
definition: Deoxyribose is an aldopentose — a monosaccharide containing five carbon atoms, and including an aldehyde functional group in its linear structure. [http://en.wikipedia.org/wiki/Deoxyribose]

destabilization
type: Class
subclass of: regulation of stability
definition: Any process that decreases the stability.

developmental process
type: Class
subclass of: biological process
subclass of: Class
  union of: Restriction
    on property: hasAgent
    some values from: living entity
  union of: Restriction
    on property: hasPatient
    some values from: living entity
definition: A biological process whose specific outcome is the progression of an integrated living unit: a cell, tissue, organ, or organism over time from an initial condition to a later condition. [GO:0032502]
reference: GO:0032502 developmental process

dimerization
type: Class
subclass of: binding of protein to protein binding site of protein
reference: GO:0046983 protein dimerization activity
definition: The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. [GO:0046983]

direction
type: Class
subclass of: non physical continuant
disjoint with: double strand DNA
disjoint with: locus
disjoint with: orientation
disjoint with: packed DNA
disjoint with: phenotype
disjoint with: single strand DNA
disjoint with: unpacked DNA
definition: The spatial relation between one point and another point.

disease
type: Class
subclass of: organismal process
definition: A definite pathologic process with a characteristic set of signs and symptoms. It may affect the whole body or any of its parts, and its etiology, pathology, and prognosis may be known or unknown. [MeSH:D004194]

dosage compensation
type: Class
subclass of: regulation of gene expression
reference: GO:0007549 dosage compensation
definition: Compensating for the two-fold variation in X:autosome chromosome ratios between sexes by a global activation or inactivation of all, or most of, genes on one or both of the X chromosomes. [GO:0007549]

double strand DNA
type: Class
subclass of: DNA
disjoint with: locus
disjoint with: orientation
disjoint with: phenotype
disjoint with: single strand DNA
definition: Double stranded DNA molecules

downstream regulatory sequence
type: Class
subclass of: regulatory sequence
definition: A sequence located in the downstream region of a gene that controls the rate or manner in which the gene is expressed.

elongation
type: Class
subclass of: modification

enhancer
type: Class
subclass of: transcription factor binding site of DNA
subclass of: Restriction
  on property: patientOf
  some values from: binding of transcription activator to enhancer
definition: A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. [SO:0000165, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
reference: SO:0000165 enhancer

enhancer binding transcription factor
type: Class
subclass of: positive transcription regulator
definition: A transcription factor selectively interacting with the enhancer

enhancesome
type: Class
subclass of: complex of protein and DNA
subclass of: Restriction
  on property: hasPart
  some values from: regulatory sequence
definition: Regulatory proteins bound to DNA.

enzyme
type: Class
equivalent class: Class
  intersection of: protein
  intersection of: Restriction
    on property: hasFunction
    some values from: catalytic activity
definition: A protein that has catalytic activity.

epigenetic
type: Class
subclass of: quality
definition: Changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence. These changes may remain through cell divisions for the remainder of the cell's life and may also last for multiple generations. Adapted from wikipedia.org/wiki/Epigenetics. [nif_unclassified:nlx_200905_509]

Escherichia coli
type: Class
subclass of: bacterium
synonym: E.coli
reference: NCBI Taxonomy ID: 562 Escherichia coli

euchromatin
type: Class
subclass of: chromatin
definition: Transcriptionally active form of chromatin.

eukaryote
type: Class
subclass of: organism
disjoint with: prokaryote
disjoint with: virus
reference: NCBI Taxonomy ID: 2759 Eukaryota
definition: Organism characterized by the presence of a nucleus. Also other organelles such as mitochondria and/or chloroplasts may be present in eukaryotes. Includes all plants, animals, green algae, and fungi. [http://www.knowledgebank.irri.org/glossary/Glossary/E.htm]

eukaryotic cell
type: Class
subclass of: cell
subclass of: Class
  union of: eukaryote
  union of: Restriction
    on property: partOf
    some values from: eukaryote
definition: A cell containing a nucleus, in which the genes or DNA is housed. The eukaryotic cell has a complex internal structure and is capable of building multicellular organisms. (modified from [http://www.inproteo.com/nwglosde.html and http://www2.wwnorton.com/college/geo/earth2/glossary/e.htm]

eukaryotic gene expression
type: Class
subclass of: gene expression
subclass of: Restriction
  on property: locatedIn
  some values from: eukaryotic cell
subclass of: Restriction
  on property: hasPart
  some values from: nuclear export of mRNA
definition: A process of producing a protein from its gene via transcription and translation in eukaryotes. It is usually controlled at various points in the sequence leading to protein synthesis.

eukaryotic RNA polymerase promoter
type: Class
subclass of: promoter
subclass of: Restriction
  on property: fromSpecies
  some values from: eukaryote
definition: A DNA sequence in eukaryotic DNA to which RNA polymerase binds, to begin transcription. [SO]

exon
type: Class
subclass of: nucleic acid region
definition: A region that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205). [SO:0000147, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
reference: SO:0000147 exon

exon on DNA
type: Class
subclass of: DNA region
subclass of: exon
definition: Any region of DNA within a gene that is transcribed to the final messenger RNA (mRNA) molecule, rather than being spliced out from the transcribed RNA molecule. [http://en.wikipedia.org/wiki/Exon]

exon on RNA
type: Class
subclass of: exon
subclass of: RNA region
definition: The parts of a transcript (i.e. exons) that are spliced together to become mRNA or structural RNA.

experimental intervention
type: Class
subclass of: process

experimental method
type: Class
subclass of: non physical continuant
definition: The use of controlled observations and measurements to test hypotheses. [http://wordnet.princeton.edu/perl/webwn?s=experimental%20method]

expression profiling
type: Class
subclass of: experimental method
subclass of: Restriction
  on property: hasPatient
  some values from: gene expression
definition: The use of high-throughput methods (e.g. DNA microarrays) for evaluating the level and timing of gene expression in a biologic sample (a cell or tissue).

feedback loop
type: Class
subclass of: non physical continuant
definition: The regulatory circuits whereby some proportion of the output signal of a system is passed (fed back) to the input. e.g. repressor and activator proteins in genetic operons are used to create feedback loop.

forkhead/winged-helix domain
type: Class
subclass of: helix-turn-helix domain
subclass of: Restriction
  on property: partOf
  some values from: forkhead/winged-helix transcription factor
definition: The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix'. The fork head domain binds B-DNA as a monomer, but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [InterPro: IPR001766]

forkhead/winged-helix transcription factor
type: Class
subclass of: helix-turn-helix domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: forkhead/winged-helix domain
definition: A transcription factor containing forkhead/winged-helix domain

formation of protein DNA complex
type: Class
subclass of: DNA protein interaction
subclass of: Restriction
  on property: hasAgent
  some values from: protein
subclass of: Restriction
  on property: hasPatient
  some values from: DNA
reference: GO:0065004 protein-DNA complex assembly
definition: The aggregation and bonding together of proteins and DNA molecules to form a protein-DNA complex. [GO:0065004]

formation of transcription factor complex
type: Class
subclass of: binding
subclass of: Restriction
  on property: hasParticipant
  some values from: transcription factor
subclass of: Restriction
  on property: partOf
  some values from: transcription
subclass of: Restriction
  on property: resultsIn
  some values from: transcription factor complex
definition: The joining of transcription factors

formation of transcription initiation complex
type: Class
subclass of: binding
subclass of: Restriction
  on property: hasPatient
  some values from: DNA
subclass of: Restriction
  on property: hasAgent
  some values from: transcription factor
subclass of: Restriction
  on property: partOf
  some values from: transcription initiation
subclass of: Restriction
  on property: resultsIn
  some values from: transcription initiation complex
definition: The process that gives rise to the transcription initiation complex.

formation of translation initiation complex
type: Class
subclass of: binding
subclass of: Restriction
  on property: hasAgent
  some values from: translation factor
subclass of: Restriction
  on property: partOf
  some values from: translation initiation
subclass of: Restriction
  on property: resultsIn
  some values from: translation initiation complex
subclass of: Restriction
  on property: hasPatient
  some values from: RNA
reference: GO:0001732 formation of translation initiation complex
definition: Joining of the large subunit, with release of IF2/eIF2 and IF3/eIF3. This leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site. [GO:0001732]

function
type: Class
subclass of: non physical continuant
disjoint with: physical continuant
definition: Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. [GO:0003674]
reference: GO:0003674 molecular function

fungus
type: Class
subclass of: eukaryote
definition: Any of numerous microorganisms of the kingdom Fungi, which are characterized by the absence of chlorophyll and by the presence of a rigid cell wall composed of chitin, mannans and sometimes cellulose. The kingdom includes the yeasts, molds, smuts, and mushrooms.
reference: NCBI Taxonomy ID: 4751 Fungi

fusion gene
type: Class
subclass of: gene
subclass of: Restriction
  on property: hasPart
  on class: gene
  min qualified cardinality: 2
definition: A hybrid gene formed from two previously separate genes. It can occur as the result of a translocation, interstitial deletion, or chromosomal inversion. The fusion of two genes is often taken as evidence that these genes have related functions [http://en.wikipedia.org/wiki/Fusion_gene]

fusion of DNA regions
type: Class
subclass of: experimental method
subclass of: Restriction
  on property: hasParticipant
  on class: DNA region
  min qualified cardinality: 2
definition: The joining of a two DNA regions.

fusion of gene with regulatory DNA region
type: Class
subclass of: fusion of DNA regions
subclass of: Restriction
  on property: hasParticipant
  some values from: gene
subclass of: Restriction
  on property: hasParticipant
  some values from: regulatory sequence
definition: The joining of a gene and a regulatory DNA region.

fusion of gene with reporter gene
type: Class
subclass of: gene fusion
subclass of: Restriction
  on property: hasPatient
  some values from: gene
subclass of: Restriction
  on property: hasPatient
  some values from: reporter gene
definition: The joining of a gene and a reporter gene

fusion protein
type: Class
subclass of: protein
definition: The joining of two or more genes which originally coded for separate proteins. Translation of this fusion gene results in a single polypeptide with function properties derived from each of the original proteins. [http://en.wikipedia.org/wiki/Fusion_protein]

G1-phase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: partOf
  some values from: interphase
reference: GO:0051318 G1 phase
definition: A cell cycle process comprising the steps by which a cell progresses through G1 phase, one of two 'gap' phases in the cell cycle; G1 is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis. [GO:0051318]

G1-S phase
type: Class
subclass of: cell cycle phase transition
definition: Progression from G1 phase to S phase of cell cycle.

G2-phase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: partOf
  some values from: interphase
definition: A cell cycle process comprising the steps by which a cell progresses through G2 phase, one of two 'gap' phases in the cell cycle; G2 is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis). [GO:0051319]
reference: GO:0051319 G2 phase

G2-M phase
type: Class
subclass of: cell cycle phase transition
definition: Progression from G2 phase to M phase of cell cycle.

GCM domain
type: Class
subclass of: zinc-coordinating domain
subclass of: Restriction
  on property: partOf
  some values from: glia cell missing transcription factors
definition: A domain containing many conserved basic amino acid residues, seven cysteine residues, and four histidine residues. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. (modified from [InterPro:IPR003902])

glia cell missing transcription factors
type: Class
subclass of: zinc coordinating domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: GCM domain
synonym: GCM transcription factor
definition: GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3'. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding. !

gas
type: Class
subclass of: chemical
disjoint with: inositol phosphate
disjoint with: ion
disjoint with: lipid
disjoint with: nucleoside
disjoint with: vitamin
reference: IMR:0001720 gas
definition: The vapor state of matter; nonelastic fluids in which the molecules are in free movement and their mean positions far apart. Gases tend to expand indefinitely, to diffuse and mix readily with other gases, to have definite relations of volume, temperature, and pressure, and to condense or liquefy at low temperatures or under sufficient pressure. [IMR:0001720, MeSH:D005740]

gene
type: Class
subclass of: DNA region
subclass of: Restriction
  on property: partOf
  some values from: DNA
definition: A unit of inheritance; a working subunit of DNA that contributes to phenotype/function and carries a particular set of instructions, usually coding for a particular protein.
reference: SO:0000704 gene

gene expression
type: Class
subclass of: intra cellular process
subclass of: Restriction
  on property: hasPatient
  some values from: gene
subclass of: Restriction
  on property: hasParticipant
  some values from: polymerase
subclass of: Restriction
  on property: hasPart
  some values from: translation
subclass of: Restriction
  on property: hasPart
  some values from: transcription
subclass of: Restriction
  on property: resultsIn
  some values from: gene product
subclass of: Class
  union of: Restriction
    on property: locatedIn
    some values from: cell
  union of: Restriction
    on property: locatedIn
    some values from: cell component
subclass of: Restriction
  on property: hasParticipant
  some values from: promoter
definition: The process by which the information encoded in a gene is converted into protein or some form of RNA. The DNA sequence is first transcribed into RNA and then usually translated into protein. [http://www.homepages.indiana.edu/120800/text/glossary.html]

gene expression regulator
type: Class
subclass of: protein

gene fusion
type: Class
subclass of: fusion of DNA regions
subclass of: Restriction
  on property: resultsIn
  some values from: physical contact
subclass of: Restriction
  on property: resultsIn
  some values from: fusion gene
subclass of: Restriction
  on property: hasParticipant
  on class: gene
  min qualified cardinality: 2
definition: The accidental joining of DNA of two genes, such as can occur in a translocation or inversion. Gene fusions can give rise to hybrid proteins or to the misregulation of the transcription of one gene by the cis regulatory elements (enhancers) of another. [http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-G/gene_fusion.html]

gene mutation
type: Class
subclass of: mutation
subclass of: Restriction
  on property: hasPatient
  some values from: gene
subclass of: Restriction
  on property: resultsIn
  some values from: mutant gene
definition: A change or alteration in a gene.

gene product
type: Class
subclass of: Thing
subclass of: Restriction
  on property: encodedIn
  some values from: gene
subclass of: Class
  union of: protein
  union of: RNA
definition: The biochemical material, either RNA or protein, resulting from expression of a gene. [http://en.wikipedia.org/wiki/Gene_product]

gene product function
type: Class
subclass of: molecular function
subclass of: Restriction
  on property: functionOf
  some values from: protein
reference: GO:0003674 molecular function

gene region
type: Class
subclass of: DNA region
subclass of: Restriction
  on property: partOf
  some values from: gene
definition: A region that harbors a gene.

gene regulation pathway
type: Class
subclass of: signaling pathway
subclass of: Restriction
  on property: hasParticipant
  some values from: gene
definition: A pathway that controls the rate or manner in which a gene is expressed.

gene silencing
type: Class
subclass of: negative regulation of gene expression
subclass of: silencing
reference: GO:0016458 gene silencing
definition: Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation. [GO:0016458]

general transcription factor
type: Class
subclass of: transcription factor
definition: A transcription factor that is required to initiate all transcription events independent of upstream regulatory elements.[PANTHER:MF00228]
synonym: basal transcription factor

genetic imprinting
type: Class
subclass of: regulation of metabolic process
reference: GO:0071514 genetic imprinting
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules by a mechanism that is mediated by DNA, is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. [GO:0071514]

genetic modification
type: Class
subclass of: experimental intervention
subclass of: modification of molecular entity
subclass of: Restriction
  on property: hasPatient
  some values from: nucleic acid

grainy-head transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: grainyhead
definition: A transcription factor containing grainy-head motif.

grainyhead
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: grainy-head transcription factor
definition: A domain of 250 amino acid residues which is required for binding to DNA and a C-terminal dimerization domain. It has a basic helix-loop-helix motif and a isoleucine-rich activation motif.

growth
type: Class
subclass of: biological process
reference: GO:0040007 growth
definition: The increase in size or mass of an entire organism, a part of an organism or a cell. [GO:0040007 ]

HMG
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: HMG-box transcription factor
definition: A DNA-binding domain which in some instances such as HMG1 mediates sequence-unspecific, in other cases such LEF-1 sequence-specific binding to DNA. This domain exhibits a typical L-shaped conformation made up of 3 alpha-helices and an extended N-terminal extension of the first helix. The latter together with helix 1, which contains a kink, form the long arm of the L, whereas helices 1 and 2 form the short arm. Binding to the minor groove induces a sharp bending of the DNA by more than 90 degree, away from the bound protein. The overall topology of the DNA-protein complexes resembles somewhat that of the TBP-TATA box complex. (modified from [TRANSFAC:C0015])

HMG-box transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: HMG
definition: A transcription factor containing high mobility group protein (HMG) box. [PANTHER:MF00226]

HSF domain
type: Class
subclass of: helix-turn-helix domain
subclass of: Restriction
  on property: partOf
  some values from: HSF transcription factor
definition: Heat shock factor (HSF) is a transcriptional activator of heat shock genes: it binds specifically to heat shock promoter elements, which are palindromic sequences rich with repetitive purine and pyrimidine motifs. Under normal conditions, HSF is a homo-trimeric cytoplasmic protein, but heat shock activation results in relocalisation to the nucleus. Each HSF monomer contains one C-terminal and three N-terminal leucine zipper repeats. Point mutations in these regions result in disruption of cellular localisation, rendering the protein constitutively nuclear. Two sequences flanking the N-terminal zippers fit the consensus of a bi- partite nuclear localisation signal (NLS). Interaction between the N- and C-terminal zippers may result in a structure that masks the NLS sequences: following activation of HSF, these may then be unmasked, resulting in relocalisation of the protein to the nucleus. The DNA-binding component of HSF lies to the N-terminus of the first NLS region, a!

HSF transcription factor
type: Class
subclass of: helix-turn-helix domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: HSF domain
definition: Heat shock transcription factor

helix-turn-helix domain
type: Class
subclass of: DNA binding domain of transcription factor
subclass of: Restriction
  on property: partOf
  some values from: helix-turn-helix domain transcription factor
definition: A domain containing two helices connected by a short turn. The second helix binds to DNA with the helix in the major groove, which allows the contact between specific base and residues throughout the protein. The HtH domain is found primarily in gene regulatory proteins and binds DNA in a sequence specific manner.

helix-turn-helix domain transcription factor
type: Class
subclass of: enhancer binding transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: helix-turn-helix domain
definition: A transcription factor containing helix-turn-helix domain.

heterochromatin
type: Class
subclass of: chromatin
definition: Transcriptionally inactive form of chromatin.

heterocyclic base
type: Class
subclass of: chemical
definition: A chemical structure containing a heterocyclic ring. A heterocyclic base unit in each nucleotide (either a pyrimidine or a purine) has nitrogen within the rings so also called a nitrogenous base.

heterodimerization
type: Class
subclass of: dimerization
reference: GO:0046982 protein heterodimerization activity
definition: Interacting selectively with a nonidentical protein to form a heterodimer. [GO:0046982]

histone
type: Class
subclass of: protein
subclass of: Restriction
  on property: agentOf
  some values from: binding of protein to DNA
definition: Any of five related proteins, composed primarily of basic amino acids, which are the scaffold around which DNA is wound to form the chromatin structure of eukaryotic chromosomes [http://www.accessexcellence.org/AE/AEPC/WWC/1994/glossary.html]

histone acetylation
type: Class
subclass of: acetylation
subclass of: DNA modification
reference: GO:0016573 histone acetylation
definition: The modification of histones by addition of acetyl groups. [GO:0016573]

histone fold
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: histone fold transcription factor
definition: A motif consisting of a core of three helices, where the long middle helix is flanked at each end by shorter ones. Proteins displaying this structure include the nucleosome core histones, which form octomers composed of two copies of each of the four histones, H2A, H2B, H3 and H4; archaeal histone, which possesses only the core domain part of eukaryotic histone; and the TATA-box binding protein (TBP)-associated factors (TAF), where the histone fold is a common motif for mediating TAF-TAF interactions. TAF proteins include TAF(II)18 and TAF(II)28, which form a heterodimer, TAF(II)42 and TAF(II)62, which form a heterotetramer similar to (H3-H4)2, and the negative cofactor 2 (NC2) alpha and beta chains, which form a heterodimer. (modified from [InterPro:IPR009072])

histone fold transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: histone fold
definition: A transcription factor containing structure of histone fold.

holoenzyme
type: Class
subclass of: protein
definition: A complete and catalytically active enzyme consisting of all subunits. (i.e. Holoenzyme = Apoenzyme + Cofactor).

homeo box
type: Class
subclass of: helix-turn-helix domain
subclass of: Restriction
  on property: partOf
  some values from: homeobox transcription factor
definition: Three consecutive alpha-helix structures, helix 3 contacts mainly the major groove of the DNA, some contacts at the minor groove are observed as well. Helix 2 and 3 resemble the helix-turn-helix structure of prokaryotic regulators. [TRANSFAC:C0006]

homeobox transcription factor
type: Class
subclass of: helix-turn-helix domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: homeo box
definition: A transcription factor containing the homeobox domain. It is usually involved in the control of gene expression during morphogenesis and development. [PANTHER:MF00038]

homodimerization
type: Class
subclass of: dimerization
reference: GO:0042803 protein homodimerization activity
definition: Interacting selectively with an identical protein to form a homodimer. [GO:0042803]

housekeeping gene
type: Class
subclass of: gene
definition: A gene involved in basic functions needed for the sustenance of the cell. Housekeeping genes are constitutively expressed (they are always turned ON). [http://www.medterms.com/script/main/art.asp?articlekey=24232]

increase
type: Class
subclass of: process
subclass of: Restriction
  on property: hasPolarity
  has value: positive
comment: A process of becoming larger, more numerous, more important, or more likely. [NCI:C25533]
reference: NCI:C25533 Increase

information biopolymer
type: Class
subclass of: molecular entity
definition: Naturally occurring macromolecules that harbor biological information in their structures, e.g. proteins, nucleic acids.

inhibition
type: Class
subclass of: regulatory process
subclass of: Restriction
  on property: hasPolarity
  has value: negative
definition: Any process that stops, prevents or reduces the frequency, rate or extent of an action.

inorganic chemical
type: Class
subclass of: chemical

inositol phosphate
type: Class
subclass of: organic chemical
disjoint with: ion
disjoint with: lipid
disjoint with: nucleoside
disjoint with: vitamin
reference: CHEBI:24846 inositol phosphates

instrument
type: Class
subclass of: physical continuant
definition: A device for measuring, recording, or controlling

insulator
type: Class
subclass of: regulatory sequence
definition: Prevents eukaryotic gene regulatory proteins from influencing distant genes / a trancriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. []
reference: SO:0000627 insulator
synonym: boundary element
synonym: insulator element

interphase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: hasPart
  some values from: G1-phase
subclass of: Restriction
  on property: hasPart
  some values from: G2-phase
subclass of: Restriction
  on property: hasPart
  some values from: S-phase
reference: GO:0051325 interphase
definition: A cell cycle process comprising the steps by which a cell progresses through interphase, the stage of cell cycle between successive rounds of chromosome segregation. Canonically, interphase is the stage of the cell cycle during which the biochemical and physiologic functions of the cell are performed and replication of chromatin occurs. [GO:0051325]

intra cellular process
type: Class
equivalent class: Class
  intersection of: molecular process
  intersection of: Class
    union of: Restriction
      on property: locatedIn
      some values from: cell
    union of: Restriction
      on property: locatedIn
      some values from: cell component
definition: Processes that are carried out within the cell

intracellular transport
type: Class
equivalent class: Class
  intersection of: transport
  intersection of: Restriction
    on property: locatedIn
    some values from: cell
subclass of: intra cellular process
subclass of: Restriction
  on property: hasAgent
  some values from: molecular entity
subclass of: Restriction
  on property: hasAgent
  all values from: molecular entity
subclass of: Restriction
  on property: hasPatient
  some values from: molecular entity
subclass of: Restriction
  on property: hasPatient
  all values from: molecular entity
reference: GO:0046907 intracellular transport
definition: The directed movement of substances within a cell. [GO:0046907]

intra organismal process
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: locatedIn
    some values from: organism
definition: The biological processes occurring inside the organism.

intron
type: Class
subclass of: nucleic acid region
definition: A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. [SO: 0000188, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
reference: SO:0000188 intron

intron on DNA
type: Class
subclass of: DNA region
subclass of: intron
definition: A non-coding segment of DNA; edited out during the transcription process. [http://library.thinkquest.org/17109/glossary.htm]

intron on RNA
type: Class
subclass of: intron
subclass of: RNA region
definition: The parts that are transcribed along with the exons but are removed from the primary gene transcript (pre-RNA) by RNA SPLICING to leave mature RNA.

ion
type: Class
subclass of: chemical
disjoint with: lipid
disjoint with: nucleoside
disjoint with: vitamin
definition: An ion is a molecular entity having a net electric charge. [CHEBI:24870]
reference: CHEBI:24870 ions
reference: IMR:0001658 ion

ligand
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: agentOf
  some values from: binding
definition: Binding to a specific receptor protein and activating intracellular signaling cascades that alter the behavior of the cell. [IMR:0000002, ISBN:0815340729]
reference: IMR:0000002 ligand

lipid
type: Class
subclass of: organic chemical
disjoint with: nucleoside
disjoint with: second messenger
disjoint with: vitamin
definition: A loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. [CHEBI:18059]
reference: CHEBI:18059 lipids
reference: IMR:0000947 lipid

living entity
type: Class
subclass of: physical continuant
definition: An entity of a living organism (a life form).

localization
type: Class
subclass of: process
definition: Any process by which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location. [GO:0051179]
reference: GO:0051179 localization

locus
type: Class
subclass of: non physical continuant
disjoint with: orientation
disjoint with: packed DNA
disjoint with: phenotype
disjoint with: single strand DNA
disjoint with: unpacked DNA
definition: The position of a gene (or other chromosome marker) on a chromosome.

LCR
type: Class
subclass of: regulatory sequence
definition: A region that enhances the expression of linked genes to physiological levels in a tissue-specific and copy number-dependent manner at ectopic chromatin sites. It is required for normal regulation of expression of some genes.
reference: SO:0000037 locus control region
synonym: locus control region

long siRNA
type: Class
subclass of: siRNA

MADS
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: MADS transcription factor
definition: Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box, that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit.!

MADS transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: MADS
definition: A transcription factor containing MADS domain.

maintenance
type: Class
subclass of: affecting

major groove
type: Class
subclass of: three dimensional molecular structure
definition: In a helix, refers to the larger of the unequal grooves that are formed as a result of the double-helical structure of DNA. As a result of the patterns of hydrogen bonding between complementary bases of DNA, the sugar groups stick out at 120 degree angles from each other instead of 180. The major groove is generated by the larger angular distance between sugars. [http://www.sparknotes.com/biology/molecular/structureofnucleicacids/terms/term_11.html]

meiosis
type: Class
subclass of: cell division
reference: GO:0007126 meiosis
definition: 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:0007126]

messenger RNA
type: Class
subclass of: RNA molecule
disjoint with: miRNA
disjoint with: rRNA
definition: A type of RNA that reflects the exact nucleoside sequence of the genetically active DNA. mRNA carries the message of the DNA to the cytoplasm of cells where protein is made in amino acid sequences specified by the mRNA. [http://www.ehsc.orst.edu/outreach/glossary.html]
synonym: mRNA

metabolic pathway
type: Class
subclass of: intra cellular process
subclass of: pathway
subclass of: Restriction
  on property: hasParticipant
  some values from: molecular entity
reference: GO:0008152 metabolic process
definition: Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. [GO:0008152]

methylation
type: Class
subclass of: modification of molecular entity
reference: GO:0032259 methylation
definition: The process by which a methyl group is covalently attached to a molecule. [GO:0032259]

miRNA
type: Class
subclass of: ncRNA
disjoint with: rRNA
definition: Single-stranded RNA molecules of about 21-23 nucleotides in length, which regulate gene expression. miRNAs are encoded by genes that are transcribed from DNA but not translated into protein (non-coding RNA); instead they are processed from primary transcripts known as pri-miRNA to short stem-loop structures called pre-miRNA and finally to functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to downregulate gene expression. [http://en.wikipedia.org/wiki/MicroRNA]
synonym: microRNA

microorganism
type: Class
subclass of: organism
subclass of: Class
  union of: archaebacterium
  union of: bacterium
  union of: fungus
  union of: protist
definition: An organism that can be seen only through a microscope. Microorganisms include bacteria, protozoa, algae, and fungi. Although viruses are not considered living organisms, they are sometimes classified as microorganisms. [http://www.stjude.org/stjude/hospital/med_terms.jsp?medterm=M]

minor groove
type: Class
subclass of: three dimensional molecular structure
definition: In a helix, refers to the smaller of the unequal grooves that are formed as a result of the double-helical structure of DNA. As a result of the patterns of hydrogen bonding between complementary bases of DNA, the sugar groups stick out at 120 degree angles from each other instead of 180. The minor groove is generated by the smaller angular distance between sugars. [http://www.sparknotes.com/biology/molecular/structureofnucleicacids/terms/term_12.html]

mitochondrion
type: Class
subclass of: cell component
definition: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. [GO:0005739]
reference: GO:0005739 mitochondrion

mitosis
type: Class
subclass of: cell division
definition: 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:0007067]
reference: GO:0007067 mitosis

modification
type: Class
subclass of: affecting

modification of molecular entity
type: Class
subclass of: modification
subclass of: molecular process
subclass of: Restriction
  on property: hasPatient
  some values from: molecular entity
definition: A process that causes a change (e.g. covalent alteration or a change of activity) of molecular entity.

molecular binding
type: Class
equivalent class: Class
  union of: binding of molecular entity
  union of: binding to molecular entity
definition: Interacting selectively with molecules

molecular entity
type: Class
subclass of: physical continuant
disjoint with: organism
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. [http://en.wikipedia.org/wiki/Molecular_entity]

molecular function
type: Class
subclass of: function
definition: Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. [GO:0003674]
reference: GO:0003674 molecular function

molecular interaction
type: Class
equivalent class: Class
  intersection of: physical interaction
  intersection of: Restriction
    on property: hasAgent
    some values from: molecular entity
  intersection of: Restriction
    on property: hasPatient
    some values from: molecular entity
  intersection of: Restriction
    on property: hasAgent
    all values from: molecular entity
  intersection of: Restriction
    on property: hasPatient
    all values from: molecular entity
definition: Interaction of a molecule with another molecule.

molecular process
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: hasAgent
    some values from: molecular entity
  intersection of: Restriction
    on property: hasAgent
    all values from: molecular entity
definition: Any processes that are carried out at the molecular level.

molecular structure
type: Class
subclass of: non physical continuant
definition: The arrangement of atoms in a molecule.

motif identification
type: Class
subclass of: experimental method
definition: Identification of motifs using the experimental and computational techniques.

mutant gene
type: Class
subclass of: gene
definition: A gene that has changed (e.g. lost, gained, or exchanged some of the material it received from its parent), affecting the normal transmission and expression of a trait.

mutant protein
type: Class
subclass of: protein

mutant regulatory DNA
type: Class
subclass of: regulatory sequence

mutated protein
type: Class
subclass of: protein
definition: A protein having a change in its amino acid sequence caused by a mutation.

mutation
type: Class
subclass of: process
definition: A permanent change in the DNA sequence of a gene that alters the genetic message carried by that gene.

ncRNA
type: Class
subclass of: RNA molecule
synonym: non-coding RNA

negative regulation
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPolarity
    has value: negative
definition: The process by which a cell decreases the number of a cellular component, such as RNA or protein, in response to an external variable. [http://en.wikipedia.org/wiki/Downregulation]
synonym: down regulation

negative regulation of gene expression
type: Class
equivalent class: Class
  intersection of: regulation of gene expression
  intersection of: Restriction
    on property: hasPolarity
    has value: negative
definition: Any process that stops, prevents or reduces the frequency, rate or extent of gene expression.

negative regulation of transcription
type: Class
equivalent class: Class
  intersection of: regulation of transcription
  intersection of: Restriction
    on property: hasPolarity
    has value: negative
definition: Any process that stops, prevents or reduces the frequency, rate or extent of transcription. [GO:0016481]
reference: GO:0016481 negative regulation of transcription

negative regulation of transcription by transcription repressor
type: Class
subclass of: negative regulation of transcription
subclass of: Restriction
  on property: hasAgent
  some values from: transcription
definition: Any process involving transcription repressor activity that stops, prevents or reduces the rate of transcription (modified from [GO:0016481]).

negative regulation of transcription of gene
type: Class
subclass of: regulation of transcription of gene
subclass of: Restriction
  on property: hasPolarity
  has value: negative

negative regulation of translation
type: Class
equivalent class: Class
  intersection of: regulation of translation
  intersection of: Restriction
    on property: hasPolarity
    has value: negative
definition: Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0017148]
reference: GO:0017148 negative regulation of protein biosynthetic process

negative transcription regulator
type: Class
subclass of: transcription regulator
definition: Any transcription regulator that prevents or downregulates transcription.

non physical continuant
type: Class
subclass of: continuant
disjoint with: physical continuant
definition: A non physical continuant is an entity that has no spatial dimension and no mass .

nuclear export of mRNA
type: Class
subclass of: protein targeting
subclass of: Restriction
  on property: hasPatient
  some values from: messenger RNA
subclass of: Restriction
  on property: locatedIn
  some values from: nucleus
reference: GO:0006406 mRNA export from nucleus
definition: The directed movement of mRNA from the nucleus to the cytoplasm. [GO:0006406]

nuclear receptor transcription factor
type: Class
subclass of: transcription coactivator
subclass of: Restriction
  on property: hasPart
  some values from: DB domain of nuclear receptor
definition: A ligand-dependent receptor found in the nucleus of the cell. [GO:0004879]
reference: GO:0004879 ligand-dependent nuclear receptor activity

nucleic acid
type: Class
subclass of: information biopolymer
subclass of: Restriction
  on property: hasPart
  some values from: nucleotide
disjoint with: protein
disjoint with: protein domain
reference: CHEBI:33696 nucleic acids
definition: Macromolecules, the major organic matter of the nuclei of biological cells, made up of nucleotide units, and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. [CHEBI:33696]

nucleic acid molecule
type: Class
subclass of: nucleic acid
definition: A complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses. [http://en.wikipedia.org/wiki/Nucleic_acid]

nucleic acid region
type: Class
subclass of: nucleic acid
definition: A sequence feature of nucleic acids.

nucleoside
type: Class
subclass of: organic chemical
subclass of: Restriction
  on property: hasPart
  some values from: ribose
subclass of: Restriction
  on property: hasPart
  some values from: heterocyclic base
disjoint with: second messenger
disjoint with: vitamin
reference: CHEBI: 33838 nucleosides
reference: IMR:0001697 nucleoside
definition: Ribosyl or deoxyribosyl derivatives of the pyrimidine or purine bases adenine, guanine, xanthine, thymine, cytosine, and uracil. [CHEBI: 33838]

nucleosome
type: Class
subclass of: packed DNA
definition: Spherical sub-units of eukaryotic chromatin that are composed of a core particle consisting of an octamer of histones (two molecules each of histones H2a, H2b, H3 and H4) and 146 nucleotide pairs. [http://www.fao.org/docrep/003/X3910E/X3910E17.htm]

nucleotide
type: Class
subclass of: organic chemical
subclass of: Restriction
  on property: hasPart
  some values from: phosphate group
subclass of: Restriction
  on property: hasPart
  some values from: heterocyclic base
subclass of: Restriction
  on property: hasPart
  some values from: ribose
definition: A nucleotide consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups. Nucleotides can carry chemical energy (e.g. ATP), form coenzymes (e.g. CoA), be used as specific signaling molecules (e.g. cAMP) in the cell. Nucleotides are the subunits of the nucleic acids. [IMR:0001349, ISBN:0815340729]
reference: CHEBI:25608 nucleoside phosphates
reference: IMR:0001349 nucleotide

nucleus
type: Class
subclass of: cell component
definition: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. [GO:0005634]
reference: GO:0005634 nucleus

occurrent
type: Class
definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. [http://www.ifomis.org/bfo/1.1/light/span#Occurrent]

ORF
type: Class
subclass of: DNA region
subclass of: Restriction
  on property: encodes
  some values from: protein
reference: SO:0000236 ORF
definition: The inframe interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. [SO:0000236]
synonym: open reading frame

operator
type: Class
subclass of: transcription factor binding site of DNA
definition: A regulatory element of an operon to which activators or repressors bind hereby effecting translation of genes in that operon. [SO:0000057]
reference: SO:0000057 operator

operon
type: Class
subclass of: DNA region
subclass of: Restriction
  on property: hasPart
  some values from: gene
subclass of: Restriction
  on property: hasPart
  some values from: operator
subclass of: Restriction
  on property: hasPart
  some values from: promoter
definition: A genetic regulatory system in which genes (structural genes) coding for functionally related proteins are clustered along the DNA. The expression of structural genes is controlled by the regulatory elements (operator genes) that respond to environmental cues.
reference: SO:0000178 operon

organic chemical
type: Class
subclass of: chemical

organism
type: Class
subclass of: living entity
definition: An individual living system (such as animal, plant, fungus or micro-organism). In at least some form, all organisms are capable of reacting to stimuli, reproduction, growth and maintenance as a stable whole (after FAO[1]). An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. [http://en.wikipedia.org/wiki/Organism]

organismal process
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Class
    union of: Class
      union of: Restriction
        on property: hasAgent
        some values from: organism
      union of: Restriction
        on property: hasPatient
        some values from: organism
    union of: Restriction
      on property: locatedIn
      some values from: organism
subclass of: biological process
reference: GO:0032501multicellular organismal process
definition: The biological processes, occurring at the level of the organism, pertinent to the function of the organism. [GO:0032501]

orientation
type: Class
subclass of: non physical continuant
disjoint with: packed DNA
disjoint with: phenotype
disjoint with: single strand DNA
disjoint with: unpacked DNA
definition: A position or arrangement of points, relative to one another or other specific directions.

osmotic stress
type: Class
subclass of: stress
definition: An increase or decrease in the concentration of solutes outside the organism or cell (modified from [GO:0006970]).

oxidative stress
type: Class
subclass of: stress
definition: A state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals (modified from [GO:0006979]).

packed DNA
type: Class
subclass of: DNA molecule
subclass of: double strand DNA
disjoint with: phenotype
disjoint with: single strand DNA
disjoint with: unpacked DNA
definition: A packed form of DNA.

paired box
type: Class
subclass of: helix-turn-helix domain
subclass of: Restriction
  on property: partOf
  some values from: paired box transcription factor
definition: A domain consisting of a conserved 124 amino acid N-terminal sequence, found in several developmentally regulated proteins in fruit fly, mouse and human

paired box transcription factor
type: Class
subclass of: helix-turn-helix domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: paired box
definition: A transcription factor containing paired box domain, found in several developmentally regulated proteins in fruit fly, mouse and human

pathway
type: Class
subclass of: molecular process
definition: A series of related biochemical reactions. [http://www.genpromag.com/Glossary.aspx]

peptide
type: Class
subclass of: information biopolymer

phenotype
type: Class
subclass of: non physical continuant
disjoint with: single strand DNA
disjoint with: unpacked DNA
definition: Any observed quality of an organism, such as its morphology, development, or behavior, as opposed to its genotype - the inherited instructions it carries, which may or may not be expressed. [http://en.wikipedia.org/wiki/Phenotype]

phosphate group
type: Class
subclass of: chemical
reference: CHEBI:32958 phosphate group

phosphorylation
type: Class
subclass of: modification of molecular entity
reference: GO:0016310 phosphorylation
definition: The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [GO:0016310]

physical contact
type: Class
subclass of: non physical continuant
definition: Physically touching of two or more objects.

physical continuant
type: Class
subclass of: continuant
definition: A physical continuant is an entity that has spatial dimension. It can either have mass (such as a protein) or no mass (such as DNA minor groove).

physical interaction
type: Class
subclass of: process
subclass of: Restriction
  on property: hasAgent
  all values from: physical continuant
subclass of: Restriction
  on property: hasAgent
  some values from: physical continuant
subclass of: Restriction
  on property: hasPatient
  all values from: physical continuant
subclass of: Restriction
  on property: hasPatient
  some values from: physical continuant
definition: An action that occurs as two or more objects have a physical effect upon one another. (modified from [http://en.wikipedia.org/wiki/Physical_interaction])

biological process
type: Class
subclass of: process
reference: GO:0008150 biological process
definition: Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. [GO:0008150]
synonym: physiological process

physiological process phase
type: Class
subclass of: biological process
subclass of: Restriction
  on property: partOf
  some values from: biological process

plant
type: Class
subclass of: eukaryote
definition: Multicellular, eukaryotic life forms of the kingdom Plantae. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions ( MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alteration of haploid and diploid generations. [MESH:D010944]
reference: NCBI Taxonomy ID:3193 Embryophyta

pocket domain
type: Class
subclass of: DNA binding domain of transcription factor
subclass of: Restriction
  on property: partOf
  some values from: pocket domain
definition: pocket consists of two conserved 'boxes' (A and B) with a less conserved spacer region lying in between

pocket domain transcription factor
type: Class
subclass of: enhancer binding transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: pocket domain
definition: A transcription factor containing pocket domain (e.g. the RB protein).

poly-A signal sequence
type: Class
subclass of: DNA region
reference: SO:0000551 polyA signal sequence
definition: The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. [SO:0000551, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]

polymerase
type: Class
subclass of: enzyme
subclass of: Restriction
  on property: hasFunction
  some values from: polymerase activity
definition: Enzymes that catalyze the synthesis of nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides. [http://www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html#p]

polymerase activity
type: Class
subclass of: gene product function
subclass of: Restriction
  on property: functionOf
  some values from: polymerase
definition: Catalysis of the reaction that synthesizes nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides

positive regulation
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPolarity
    has value: positive
definition: Any process that activates or increases the frequency, rate or extent of a biological process, function or phenomenon.
synonym: up regulation

positive regulation of gene expression
type: Class
equivalent class: Class
  intersection of: regulation of gene expression
  intersection of: Restriction
    on property: hasPolarity
    has value: positive
definition: Any process that activates or increases the frequency, rate or extent of gene expression.

positive regulation of transcription
type: Class
equivalent class: Class
  intersection of: regulation of transcription
  intersection of: Restriction
    on property: hasPolarity
    has value: positive
definition: Any process that activates or increases the frequency, rate or extent of transcription. [GO:0045941]
reference: GO:0045941 positive regulation of transcription

positive regulation of transcription by transcription activator
type: Class
subclass of: positive regulation of transcription
subclass of: Restriction
  on property: hasAgent
  some values from: transcription activator
definition: Any process involving transcription activator activity that activates or increases the frequency, rate or extent of transcription (modified from [GO:0045941]).

positive regulation of transcription of gene
type: Class
subclass of: regulation of transcription of gene
subclass of: Restriction
  on property: hasPolarity
  has value: positive

positive regulation of translation
type: Class
equivalent class: Class
  intersection of: regulation of translation
  intersection of: Restriction
    on property: hasPolarity
    has value: positive
definition: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0045727]
reference: GO:0045727 positive regulation of protein biosynthetic process

positive transcription regulator
type: Class
subclass of: transcription regulator
definition: A transcription regulator activity required for initiation or upregulation of transcription.

posttranscriptional
type: Class
subclass of: temporal quality
definition: Any substance or process that is formed or occurs after the production of a mRNA transcript.

posttranscriptional modification
type: Class
subclass of: intra cellular process
subclass of: modification of molecular entity
subclass of: RNA processing
subclass of: Restriction
  on property: partOf
  some values from: gene expression
subclass of: Restriction
  on property: hasPatient
  some values from: RNA
definition: A genetic process by which, in eukaryotic cells, primary transcript RNA is converted into mature RNA. The three main modifications are 5' capping, 3' polyadenylation, and RNA splicing. (modified from [http://en.wikipedia.org/wiki/Post-transcriptional_modification])

posttranslational
type: Class
subclass of: temporal quality
definition: Any substance or process that is formed or occurs after translation of protein.

posttranslational modification
type: Class
subclass of: protein modification
subclass of: Restriction
  on property: partOf
  some values from: gene expression
reference: GO:0043687 post-translational protein modification
definition: The covalent alteration of one or more amino acids occurring in a protein after the protein has been completely translated and released from the ribosome. [GO:0043687]

pre-miRNA
type: Class
subclass of: miRNA
definition: A stem loop intermediate (60-70 nucleotide) in microRNA production, produced by the nuclear cleavage of a primary miRNA (pri-mRNA) transcript. Pre-microRNAs are transported from the nucleus to the cytoplasm where further cleavage occurs to produce a mature microRNA product (modified from [GO:0035281]).
synonym: pre-microRNA

primary structure
type: Class
subclass of: molecular structure
definition: (Wikipedia, en:) The primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of DNA, RNA or typical intracellular protein), the primary structure is equivalent to specifying the sequence of its monomeric subunits, e.g., the nucleotide or peptide sequence.

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: hasParticipant
  min cardinality: 1
definition: A process is a collection of molecular events with a defined beginning and end. [GO:0008150]
reference: GO:0008150 biological process

producing
type: Class
subclass of: affecting

prokaryote
type: Class
subclass of: organism
definition: Cell or organism lacking a membrane-bound, structurally discrete nucleus and other subcellular compartments. Bacteria are prokaryotes. [http://www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html#p]

promoter
type: Class
subclass of: regulatory sequence
definition: A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. [SO:0000167]
reference: SO:0000167 promoter

protein
type: Class
subclass of: information biopolymer
subclass of: Restriction
  on property: hasPart
  some values from: amino acid
disjoint with: protein domain
definition: a macromolecule composed of one or several polypeptides. Each polypeptide consists of a chain of amino acids linked together by covalent (peptide) bonds. [http://www.qimr.edu.au/qimr_glossary.html]

protein amplification
type: Class
subclass of: experimental method
subclass of: Restriction
  on property: hasPatient
  some values from: protein
definition: Amplification of protein from a pool of mRNA using technologies such as phage display and Profusion technology.

protein binding site of DNA
type: Class
subclass of: DNA region
subclass of: Restriction
  on property: patientOf
  some values from: binding of protein to protein binding site of DNA
definition: A region on DNA that specifically forms a chemical bond with a protein (or proteins).

protein binding site of protein
type: Class
equivalent class: Class
  intersection of: binding site of protein
  intersection of: Restriction
    on property: patientOf
    some values from: binding of protein to protein binding site of protein
definition: A region on a protein that forms a chemical bond (protein ligands) with other proteins.

protein biosynthesis
type: Class
subclass of: protein metabolism
subclass of: Restriction
  on property: resultsIn
  some values from: protein
subclass of: Restriction
  on property: hasPatient
  some values from: protein
definition: The chemical reactions and pathways resulting in the formation of proteins.

protein catabolism
type: Class
subclass of: catabolic pathway
subclass of: protein metabolism
subclass of: Restriction
  on property: hasPatient
  some values from: protein
reference: GO:0030163 protein catabolic process
definition: The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. [GO:0030163]

protein coding DNA region
type: Class
equivalent class: Class
  intersection of: DNA region
  intersection of: Restriction
    on property: encodes
    some values from: protein
definition: A DNA region that encodes one or more proteins..

protein coding gene
type: Class
subclass of: gene
subclass of: Restriction
  on property: encodes
  some values from: protein
disjoint with: RNA coding gene
definition: A gene that encodes a protein

protein coding region
type: Class
equivalent class: Class
  intersection of: nucleic acid region
  intersection of: Restriction
    on property: encodes
    some values from: protein

protein complex
type: Class
subclass of: complex molecular entity
subclass of: Restriction
  on property: hasPart
  on class: protein
  min qualified cardinality: 2
definition: Any protein group composed of two or more subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups. [GO:0043234]
reference: GO:0043234 protein complex

protein domain
type: Class
subclass of: information biopolymer
subclass of: Restriction
  on property: hasPart
  some values from: amino acid
subclass of: Restriction
  on property: partOf
  some values from: protein
definition: A part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. [http://en.wikipedia.org/wiki/Structural_domain]

protein folding
type: Class
subclass of: protein metabolism
subclass of: Restriction
  on property: hasAgent
  some values from: protein
reference: GO:0006457 protein folding
definition: The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. [GO:0006457]

protein identification
type: Class
subclass of: experimental method
subclass of: Restriction
  on property: hasPatient
  some values from: protein
definition: Identification of proteins using the techniques of electrophoresis, mass spectrometry, etc.

protein maturation
type: Class
subclass of: protein metabolism
subclass of: Restriction
  on property: hasAgent
  some values from: protein
reference: GO:0051604 protein maturation
definition: The process leading to the attainment of the full functional capacity of a protein. [GO:0051604]

protein metabolism
type: Class
subclass of: metabolic pathway
subclass of: Class
  union of: Restriction
    on property: hasAgent
    some values from: protein
  union of: Restriction
    on property: hasPatient
    some values from: protein
reference: GO:0019538 protein metabolic process
definition: The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. [GO:0019538]

protein modification
type: Class
subclass of: modification of molecular entity
subclass of: protein metabolism
subclass of: protein protein interaction
reference: GO:0006464 protein modification process
definition: The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification). [GO:0006464]

protein mutation
type: Class
equivalent class: Class
  intersection of: mutation
  intersection of: Restriction
    on property: resultsIn
    some values from: mutated protein
subclass of: Restriction
  on property: hasPatient
  some values from: protein
definition: A mutation that alters the protein product of a gene.

protein polymerization
type: Class
subclass of: protein metabolism
subclass of: protein protein interaction
subclass of: Restriction
  on property: resultsIn
  some values from: binding
reference: GO:0051258 protein polymerization
definition: The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein. [GO:0051258]

protein protein interaction
type: Class
equivalent class: Class
  intersection of: physical interaction
  intersection of: Restriction
    on property: hasAgent
    some values from: protein
  intersection of: Restriction
    on property: hasPatient
    some values from: protein
  intersection of: Restriction
    on property: hasAgent
    all values from: protein
  intersection of: Restriction
    on property: hasPatient
    all values from: protein
definition: the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks. [http://en.wikipedia.org/wiki/Protein-protein_interaction]

protein subunit
type: Class
subclass of: protein
definition: A single protein molecule that assembles (or coassembles) with other protein molecules to form a multimeric or oligomeric protein. [http://en.wikipedia.org/wiki/Protein_subunit]

protein targeting
type: Class
subclass of: protein transport
subclass of: Restriction
  on property: locatedIn
  some values from: cell
reference: GO:0006605 protein targeting
definition: The process of targeting specific proteins to particular membrane-bound subcellular organelles. Usually requires an organelle specific protein sequence motif. [GO:0006605]

protein transport
type: Class
equivalent class: Class
  intersection of: transport
  intersection of: Restriction
    on property: hasPatient
    some values from: protein
reference: GO:0015031 protein transport
definition: The directed movement of proteins into, out of, within or between cells. [GO:0015031]

protist
type: Class
subclass of: eukaryote
definition: A single-celled, eukaryotic organism that may resemble an animal or a plant. (Allaby 1998) [http://www.oup.com.au/orc/demo_glossary.aspx#P]

quality
type: Class
subclass of: non physical continuant

RHR
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: RHR transcription factor
definition: A DNA binding domain (Rel-type) exhibiting a bipartite subdomain structure, each subdomain comprising a beta-barrel with five loops that form an extensive contact surface to the major groove of the DNA. Particularly, the first loop of the N-terminal subdomain (the highly conserved recognition loop) performs contacts with the recognition element on the DNA, but other loops are involved. The second, C-terminal domain is necessary mainly for protein dimerization. (modified from [TRANSFAC:C0020])

RHR transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: RHR
definition: A transcription factor containing RHR domain

RNA
type: Class
subclass of: nucleic acid
definition: A chain of ribonucleotides.

RNA biosynthesis
type: Class
subclass of: RNA metabolism
subclass of: Restriction
  on property: resultsIn
  some values from: RNA
reference: GO:0032774 RNA biosynthetic process
definition: The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. [GO:0032774]

RNA catabolism
type: Class
subclass of: RNA metabolism
reference: GO:0006401 RNA catabolic process
definition: The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. [GO:0006401]

RNA coding DNA region
type: Class
equivalent class: Class
  intersection of: DNA region
  intersection of: Restriction
    on property: encodes
    some values from: RNA molecule
definition: A region on DNA that encodes RNA.

RNA coding gene
type: Class
subclass of: gene
subclass of: Restriction
  on property: encodes
  some values from: RNA
definition: A gene coding for RNA (tRNA, rRNA, etc.).

RNA coding region
type: Class
equivalent class: Class
  intersection of: nucleic acid region
  intersection of: Restriction
    on property: encodes
    some values from: RNA molecule

RNA elongation
type: Class
subclass of: elongation
subclass of: intra cellular process
subclass of: Restriction
  on property: partOf
  some values from: transcription
reference: GO:0006354 RNA elongation
definition: The extension of an RNA molecule after transcription initiation by the addition of ribonucleotides catalyzed by an RNA polymerase. [GO:0006354]

RNA initiated silencing complex
type: Class
subclass of: complex of protein and RNA
definition: A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation. [GO:0016442]
reference: GO:0016442 RNA-induced silencing complex

RNA interference
type: Class
subclass of: gene silencing
reference: GO:0016246 RNA interference
definition: The process by which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes. [GO:0016246]

RNA metabolism
type: Class
subclass of: metabolic pathway
subclass of: Class
  union of: Restriction
    on property: hasPatient
    some values from: RNA
  union of: Restriction
    on property: resultsIn
    some values from: RNA
reference: GO:0016070 RNA metabolic process
definition: The chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. [GO:0016070]

RNA modification
type: Class
subclass of: modification of molecular entity
subclass of: RNA metabolism
subclass of: Restriction
  on property: hasPatient
  some values from: RNA
reference: GO:0009451 RNA modification
definition: The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically. [GO:0009451]

RNA molecule
type: Class
subclass of: RNA
definition: A chain of ribonucleotides as it occures at a whole.

RNA polymerase
type: Class
equivalent class: Class
  intersection of: polymerase
  intersection of: Restriction
    on property: hasFunction
    some values from: RNA polymerase activity
definition: An enzyme that catalyses the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA or RNA template (modified from [GO:0003899, GO:0003968]).
reference: GO:0003899 DNA-directed RNA polymerase activity
reference: GO:0003968 RNA-directed RNA polymerase activity

RNA polymerase activity
type: Class
subclass of: polymerase activity
subclass of: Restriction
  on property: functionOf
  some values from: RNA polymerase
definition: Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA or RNA template (modified from [GO:0003899, GO:0003968]).
reference: GO:0003899 DNA-directed RNA polymerase activity; GO:0003968 RNA-directed RNA polymerase activity

RNA polymerase binding site of DNA
type: Class
subclass of: DNA binding site
definition: A region on DNA that specifically forms a chemical bond with RNA polymerase.

RNA polymerase II
type: Class
subclass of: RNA polymerase
definition: An enzyme found in eukaryotic cells that catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. Also called RNAP II and Pol II.

RNA polymerase II holoenzyme
type: Class
subclass of: holoenzyme
subclass of: RNA polymerase II
reference: GO:0016591 DNA-directed RNA polymerase II, holoenzyme
definition: Large protein complex composed of the RNA polymerase core complex and a variety of other proteins including transcription factor complexes TFIIA, D, E, F, and H which are required for promoter recognition, and the Mediator subcomplex. Catalyzes the synthesis of eukaryotic pre-mRNA. [GO:0016591]

RNAPolymerase promoter
type: Class
subclass of: promoter
definition: A region (DNA) to which RNA polymerase binds, to begin transcription. [SO:0001203]
reference: SO:0001203 RNA_polymerase_promoter

RNA polymerase III promoter
type: Class
subclass of: RNAPolymerase promoter
subclass of: Restriction
  on property: fromSpecies
  some values from: eukaryote
definition: A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. [SO:0000171]
reference: SO:0000171 RNApol III promoter

RNA polymerase III promoter type 1
type: Class
subclass of: RNA polymerase III promoter
reference: SO:0000617 RNApol_III_promoter_type_1

RNA polymerase III promoter type 2
type: Class
subclass of: RNA polymerase III promoter
reference: SO:0000618 RNApol_III_promoter_type_2

RNA polymerase II promoter
type: Class
subclass of: RNAPolymerase promoter
subclass of: Restriction
  on property: fromSpecies
  some values from: eukaryote
definition: A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. [SO:0000170]
reference: SO:0000170 RNApol II promoter

RNA polymerase I promoter
type: Class
subclass of: RNAPolymerase promoter
subclass of: Restriction
  on property: fromSpecies
  some values from: eukaryote
definition: A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. [SO:0000169]
reference: SO:0000169 RNApol I promoter

RNA processing
type: Class
subclass of: RNA metabolism
subclass of: Restriction
  on property: hasPatient
  some values from: RNA
definition: Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. [GO:0006396]
reference: GO:0006396 RNA processing

RNA protein interaction
type: Class
equivalent class: Class
  intersection of: physical interaction
  intersection of: Class
    union of: Class
      intersection of: Restriction
        on property: hasAgent
        some values from: protein
      intersection of: Restriction
        on property: hasPatient
        some values from: RNA
    union of: Class
      intersection of: Restriction
        on property: hasAgent
        some values from: RNA
      intersection of: Restriction
        on property: hasPatient
        some values from: protein
  intersection of: Restriction
    on property: hasAgent
    all values from: Class
      union of: protein
      union of: RNA
  intersection of: Restriction
    on property: hasPatient
    all values from: Class
      union of: protein
      union of: RNA
reference: GO:0022618 protein-RNA complex assembly
definition: The aggregation and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. [GO:0022618]

RNA region
type: Class
subclass of: nucleic acid region
subclass of: RNA
definition: A chain of ribonucleotides that is part of a longer chain of ribunucleotides.

RNA splicing
type: Class
subclass of: posttranscriptional modification
reference: GO:0008380 RNA splicing
definition: The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. [GO:0008380]

regulation of function
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPatient
    some values from: function
  intersection of: Restriction
    on property: hasPatient
    all values from: function
definition: Any process that modulates the frequency, rate or extent of function.

regulation of gene expression
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPatient
    some values from: gene expression
  intersection of: Restriction
    on property: hasPatient
    all values from: gene expression
definition: Any process that modulates the frequency, rate or extent of gene expression. [GO:0010468]
reference: GO:0010468 regulation of gene expression

regulation of metabolic process
type: Class
subclass of: regulatory process

regulation of modification of molecular entity
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPatient
    some values from: modification of molecular entity
  intersection of: Restriction
    on property: hasPatient
    all values from: modification of molecular entity
definition: Any process that modulates the frequency, rate or extent of modification of molecular entity.

regulation of pathway
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPatient
    some values from: pathway
  intersection of: Restriction
    on property: hasPatient
    all values from: pathway
definition: Any process that modulates the frequency, rate or extent of a pathway

regulation of physical interaction
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPatient
    some values from: physical interaction
  intersection of: Restriction
    on property: hasPatient
    all values from: physical interaction
definition: Any process that modulates the frequency, rate or extent of physical interaction.

regulation of process
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPatient
    some values from: process
  intersection of: Restriction
    on property: hasPatient
    all values from: process
definition: Any process that modulates the frequency, rate or extent of process.

regulation of stability
type: Class
subclass of: regulatory process
definition: Any process that modulates the stability.

regulation of transcriptin by two component regulatory system
type: Class
subclass of: complex regulation of transcription
subclass of: Restriction
  on property: hasAgent
  some values from: two-component regulatory system
definition: Any process that modulates the frequency, rate or extent of transcription by protein components involved in a system responding to environmental changes characterized usually by a sensor kinase in the cell membrane that phosphorylates itself in response to a signal and a response regulator to which the phosphoryl group is transferred.

regulation of transcription
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPatient
    some values from: transcription
  intersection of: Restriction
    on property: hasPatient
    all values from: transcription
subclass of: Restriction
  on property: hasAgent
  some values from: transcription regulator
definition: Any process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0045449]
reference: GO:0045449 regulation of transcription

regulation of transcription of gene
type: Class
subclass of: regulation of transcription
subclass of: Restriction
  on property: hasPatient
  some values from: transcription of gene

regulation of transcription of operon
type: Class
subclass of: regulation of transcription
subclass of: Restriction
  on property: hasPatient
  some values from: transcription of operon
definition: Any process that modulates the frequency, rate or extent of the synthesis of RNA on a template of DNA or DNA on a template of RNA.

regulation of transcription of regulon
type: Class
subclass of: regulation of transcription
subclass of: Restriction
  on property: hasPatient
  some values from: transcription of regulon genes
definition: Any process that modulates the frequency, rate or extent of transcription of regulon

regulation of translation
type: Class
equivalent class: Class
  intersection of: regulatory process
  intersection of: Restriction
    on property: hasPatient
    some values from: translation
  intersection of: Restriction
    on property: hasPatient
    all values from: translation
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0006417]
reference: GO:0006417 regulation of translation

regulation of translational fidelity
type: Class
subclass of: regulation of translation
definition: Any process that modulates the ability of the translational apparatus to interpret the genetic code. [GO:0006450]
reference: GO:0006450 regulation of translational fidelity

regulatory sequence
type: Class
subclass of: DNA region
subclass of: Restriction
  on property: patientOf
  some values from: binding of transcription factor to DNA
definition: A DNA sequence that controls the expression of a gene. [SO:0005836, http://www.genpromag.com/scripts/glossary.asp?LETTER=R] Typically binding sites for proteins required for transcription, such as gene regulatory proteins and polymerases.
reference: SO:0005836 regulatory region
synonym: regulatory DNA
synonym: regulatory DNA region

regulatory process
type: Class
subclass of: affecting
subclass of: process
definition: Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. [GO:0050789]
reference: GO:0050789 regulation of biological process

regulon
type: Class
subclass of: DNA region
subclass of: Restriction
  on property: hasPart
  some values from: gene
subclass of: Restriction
  on property: patientOf
  some values from: transcription of regulon genes
definition: A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. [SO:1001284, ISBN:0198506732]
reference: SO:1001284 regulon

replicative cell aging
type: Class
subclass of: cell aging
reference: GO:0001302 replicative cell aging
definition: The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division. [GO:0001302]

reporter gene
type: Class
subclass of: gene
definition: A transfected gene that encodes an easily assayed product, such as GFP; it is used to monitor gene expression under different conditions; usually to test the activity of a promoter.

reporter gene construction
type: Class
subclass of: experimental method
subclass of: Restriction
  on property: resultsIn
  some values from: reporter gene
definition: Construction of any gene that encodes an easily assayed product that is used to monitor gene expression under different conditions; usually to test the activity of a promoter.

response process
type: Class
subclass of: process
reference: GO:0050896 response to stimulus
definition: The process of changing state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.), resulting from a stimulus. [GO:0050896] (revised)
synonym: response to chemical stimulus

response to chemical stimulus
type: Class
subclass of: response process
subclass of: Restriction
  on property: hasParticipant
  some values from: molecular entity
definition: A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. [GO:0042221]
reference: GO:0042221 response to chemical stimulus

response to drug
type: Class
subclass of: response to chemical stimulus
definition: A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GO:0042493]
reference: GO:0042493 response to drug

response to protein
type: Class
subclass of: response to chemical stimulus
subclass of: Restriction
  on property: hasParticipant
  some values from: protein
definition: A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a protein stimulus. [GO:0051789]
reference: GO:0051789 response to protein stimulus
synonym: response to protein stimulus

ribose
type: Class
subclass of: carbohydrate
reference: CHEBI:26564 riboses

ribosomal DNA
type: Class
subclass of: DNA molecule
definition: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA. [MeSH:D004275]

ribosomal gene
type: Class
subclass of: gene
definition: Genes encoding ribosomal proteins and rRNAs.

rRNA
type: Class
subclass of: RNA molecule
definition: RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. [SO:0000252, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]
reference: SO:0000252 rRNA

ribosome
type: Class
subclass of: cell component
reference: GO:0005840 ribosome
definition: An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [GO:0005840]

runt like domain
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: runt-like transcription factor
definition: A domain homologous to a defined region within the Drosophila protein Runt. The runt domain contains twelve beta strands, seven of which shape the fold of an immunoglobulin-like beta sandwich (S-type Ig fold) also found in the DNA-binding domains of other transcription factors (NF-kappaB, NFAT, p53, STAT, and the T-domain) that is preceded by an N-terminal alpha helix. The runt domain is responsible for both DNA-binding and heterodimerization which occur at distinct, non-overlapping sites within the domain (modified from [TRANSFAC:C0029]).

runt-like transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: runt like domain
definition: A transcription factor containing runt-like domain.
synonym: runt-domain-like transcription factor

SAND domain
type: Class
subclass of: DNA binding domain of transcription factor
subclass of: Restriction
  on property: partOf
  some values from: SAND domain transcription factor
definition: The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA bindin!

SAND domain transcription factor
type: Class
subclass of: enhancer binding transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: SAND domain
definition: A transcription factor containing SAND domain

SMAD NF-1 transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: SMAD NF 1 domain
definition: A transcription factor containing SMAD NF-1 domain

SMAD NF 1 domain
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: SMAD NF-1 transcription factor
definition: Two DNA binding domains (SMAD and NF1) sharing structural similarity. The SMAD (MH2) domain consists of a sandwich of eleven beta strands in two sheets with Greek key topology. SMAD proteins mediate signaling by the TGF-beta/activin/BMP-2/4 cytokines from receptor Ser/Thr protein kinases at the cell surface to the nucleus. Nuclear factor 1 (NF-1; or CCAAT box-binding transcription factor, CTF) is found in a family of vertebrate nuclear proteins which recognize and bind, as dimers, the palindromic DNA sequence 5'-TGGCANNNTGCCA-3'. The NF-1 proteins have been implicated as regulators of diverse biological processes such as adenovirus replication and transcription of TGF-responsive genes. (modified from [InterPro: IPR008984, IPR000647])

S-phase
type: Class
subclass of: cell cycle phase
subclass of: Restriction
  on property: partOf
  some values from: interphase
reference: GO:0051320 S phase
definition: A cell cycle process comprising the steps by which a cell progresses through S phase, the part of the cell cycle during which DNA synthesis takes place. [GO:0051320]

ss siRNA
type: Class
subclass of: siRNA
definition: Single-stranded siRNA.

STAT
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: STAT transcription factor
definition: The structurally and functionally conserved domains shared by the STAT proteins including: an N-terminal domain that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain that is implicated in protein-protein interactions; a DNA-binding domain with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain. (modified from [InterPro:IPR013801]

STAT transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: STAT
definition: The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT p!

second messenger
type: Class
subclass of: chemical
reference: IMR:0100022 second messenger

selenocysteine incorporation
type: Class
subclass of: translational readthrough
definition: The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine. [GO:0001514]
reference: GO:0001514 selenocysteine incorporation

sequence
type: Class
subclass of: primary structure
definition: The order of nucleotides in RNA or DNA or of amino acids in a polypeptide. [http://www.plantpath.cornell.edu/glossary/Defs_S.htm]

sequence homology analysis
type: Class
subclass of: experimental method
definition: An analytic procedure that compares the similarity of a sequence with other sequences.

sigma factor
type: Class
equivalent class: Class
  intersection of: protein
  intersection of: Restriction
    on property: hasFunction
    some values from: sigma factor activity
definition: A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes. [GO:0016987]

sigma factor activity
type: Class
subclass of: transcription regulator activity
subclass of: Restriction
  on property: functionOf
  some values from: sigma factor
definition: Activity of a sigma factor. A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes. [GO:0016987]
reference: GO:0016987 sigma factor activity

sigma factor antagonist activity
type: Class
subclass of: transcription regulator activity
reference: GO:0016989 sigma factor antagonist activity
definition: The function of binding to a sigma factor and stopping, preventing or reducing the rate of its transcriptional activity. [GO:0016989]

signaling pathway
type: Class
subclass of: pathway
reference: GO:0007165 signal transduction
definition: The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately effecting a change in the functioning of the cell. [GO:0007165]

silencer
type: Class
subclass of: transcription factor binding site of DNA
subclass of: Restriction
  on property: patientOf
  some values from: binding of transcription repressor to silencer
definition: Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes. [SO:0000625, http://www.brunel.ac.uk/depts/bio/project/old_hmg/gloss3.htm]
reference: SO:0000625 silencer

silencing
type: Class
subclass of: inhibition

single strand DNA
type: Class
subclass of: unpacked DNA
definition: DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form. Parvoviridae have a single stranded DNA genome. Single stranded DNA can be produced experimentally by rapidly cooling heat denatured DNA. Heating causes the strands to separate and rapid cooling prevents renaturation. [http://www.biology-online.org/dictionary/Single_stranded_dna]

siRNA
type: Class
subclass of: ncRNA
definition: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. [SO:0000646]
reference: SO:0000646 siRNA
synonym: small interfering RNA

solution
type: Class
subclass of: physical continuant
definition: A solution is a homogeneous mixture composed of two or more substances. In such a mixture, a solute is dissolved in another substance, known as a solvent. [http://en.wikipedia.org/wiki/Solution]

solvent
type: Class
subclass of: physical continuant
definition: A substance (usually a liquid) that dissolves other substances to form a solution

spacer
type: Class
subclass of: DNA region
definition: A region placed between two or more pieces of sequence features (e.g. genes).
todo property: Provides flexibility needed for communication between DNA bound proteins. Not recognized by gene regulatory proteins.

splice enhancer
type: Class
subclass of: regulatory sequence
definition: Region of a transcript that regulates splicing. [SO:0000344]
reference: SO:0000344 splice enhancer

spliceosome
type: Class
subclass of: complex of protein and RNA
subclass of: Restriction
  on property: partOf
  some values from: nucleus
reference: IMR:0000932 spliceosome
definition: The splicing reaction is carried out by the spliceosome, which consists of five small nuclear ribonucleoprotein complexes U1, U2, U4, U5 and U6 snRNPs and a large number of non-snRNP proteins. [IMR:0000932]

splicing
type: Class
subclass of: modification of molecular entity
definition: The process of removing sections of the sequences of a precursor RNA or protein, and joining the remaining sections to form the mature form of RNA or protein.

stabilization
type: Class
subclass of: regulation of stability

starvation
type: Class
subclass of: biological process
definition: Lengthy and continuous deprivation of food. (Stedman, 25th ed) [MeSH: D013217]

stimulon
type: Class
subclass of: DNA region
subclass of: Restriction
  on property: patientOf
  some values from: transcription of stimulon genes
subclass of: Restriction
  on property: hasPart
  some values from: gene
definition: A set of genes/proteins under regulation by the same stimulus

stress
type: Class
subclass of: non physical continuant
definition: MSH2003_2003_05_12A pathological process resulting from the reaction of the body to external forces and abnormal conditions that tend to disturb the organism's homeostasis.

structural domain of transcription activator
type: Class
subclass of: protein domain
definition: A compact, globular sub-structure of a transcription activator.

structural domain of transcription repressor
type: Class
subclass of: protein domain
definition: A compact, globular sub-structure of a transcription repressor.

substrate
type: Class
subclass of: physical continuant
definition: A molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate(s). The substrate binds with the enzyme's active site, and an enzyme-substrate complex is formed. The substrate is broken down into a product and is released from the active site. The active site is now free to accept another substrate molecule. [http://en.wikipedia.org/wiki/Substrate_%28biochemistry%29]

TATA box
type: Class
subclass of: regulatory sequence
subclass of: Restriction
  on property: partOf
  some values from: eukaryotic RNA polymerase promoter
subclass of: Restriction
  on property: fromSpecies
  some values from: eukaryote
definition: A DNA sequence (cis-regulatory element) found in the promoter region of most genes in eukaryotes (also called Goldberg-Hogness box). Considered to be the core promoter sequence, it is the binding site of either transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA polymerase. It has the core DNA sequence 5'-TATAAA-3' or a variant, which is usually followed by three or more adenine bases. The TATA box is usually located 25 base pairs upstream to the transcription site. (modified from [http://en.wikipedia.org/wiki/TATA_box])

TATA-binding protein
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: TBP domain
synonym: TBP
definition: The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins. By contrast, the N-terminal region varies in both length and sequence. [InterPro: IPR000814]

TBP domain
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: TATA-binding protein
definition: A domain within TATA-box binding proteins.

T box domain
type: Class
subclass of: beta scaffold domain with minor groove contacts
definition: A domain defined as the minimal region within the T-box protein that is both necessary and sufficient for sequence-specific DNA binding, all members of the family bind to the DNA consensus sequence TCACACCT. Transcription factors of the T-box family are required both for early cell-fate decisions, such as those necessary for formation of the basic vertebrate body plan, and for differentiation and organogenesis. (modified from [InterPro:IPR001699]

TEA domain
type: Class
subclass of: helix-turn-helix domain
subclass of: Restriction
  on property: partOf
  some values from: TEA domain transcription factor
definition: A domain containing a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. (modified from [InterPro:IPR000818])

TEA domain transcription factor
type: Class
subclass of: helix-turn-helix domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: TEA domain
definition: Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTS domain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism. [InterPro: IPR000818]

TF binding site of protein
type: Class
subclass of: protein binding site of protein
subclass of: Restriction
  on property: patientOf
  some values from: binding of TF to TF binding site of protein
definition: A region on a protein that forms a chemical bond with one or more transcription factors.

TF module
type: Class
subclass of: transcription factor binding site of DNA

temperature
type: Class
subclass of: non physical continuant
definition: A degree of hotness or coldness the can be measured using a thermometer. Temperature is measured in degrees on the Fahrenheit, Celsius, and Kelvin scales. [http://eo.ucar.edu/webweather/glossary.html]

temporal quality
type: Class
subclass of: quality

terminator
type: Class
subclass of: regulatory sequence
reference: SO:0000141 terminator
definition: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. [SO:0000141, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]

three dimensional molecular structure
type: Class
subclass of: molecular structure
definition: 3D structure of a molecule

tissue
type: Class
subclass of: physical continuant
subclass of: Restriction
  on property: partOf
  some values from: organism
subclass of: Restriction
  on property: hasPart
  some values from: cell
definition: A group of similar cells, specialized to perform a particular function (or functions). Examples of tissue include, heart mucslce, skin, bone etc.[http://medicineworld.org/cancer/descriptions.html]

trans-acting siRNA
type: Class
subclass of: siRNA
definition: A form of small interfering RNA (siRNA) that represses gene expression through post-transcriptional gene silencing in land plants. It is transcribed from the genome to form a polyadenylated, double-stranded precursor. Unlike other siRNAs, but like microRNA, ta-siRNA does not require full complementarity to its target RNA to have an effect. [http://en.wikipedia.org/wiki/Trans-acting_siRNA]

transcript
type: Class
subclass of: RNA molecule
definition: An RNA synthesized on a DNA or RNA template by an RNA polymerase. [SO:0000673]
reference: SO:0000673 transcript

transcription
type: Class
subclass of: RNA biosynthesis
subclass of: Restriction
  on property: hasPart
  some values from: RNA elongation
subclass of: Restriction
  on property: hasPart
  some values from: transcription termination
subclass of: Restriction
  on property: hasPart
  some values from: transcription initiation
subclass of: Restriction
  on property: resultsIn
  some values from: RNA
subclass of: Restriction
  on property: hasPatient
  some values from: Class
    union of: gene
    union of: operon
    union of: regulon
    union of: stimulon
subclass of: Restriction
  on property: partOf
  some values from: gene expression
reference: GO:0006350 transcription
definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0006350]

transcription activator
type: Class
equivalent class: Class
  intersection of: positive transcription regulator
  intersection of: Restriction
    on property: hasFunction
    some values from: transcription activator activity
subclass of: Restriction
  on property: hasPart
  some values from: structural domain of transcription activator
definition: A transcription regulator required for initiation of transcription.

transcription activator activity
type: Class
subclass of: transcription regulator activity
subclass of: Restriction
  on property: functionOf
  some values from: transcription activator
definition: Any transcription regulator activity required for initiation or upregulation of transcription. [GO:0016563]
reference: GO:0016563 transcription activator activity

transcription coactivator
type: Class
subclass of: transcription activator
subclass of: transcription cofactor
definition: A transcription cofactor that activates transcription from a RNA polymerase II promoter; it does not bind DNA itself. (modified from [GO:0003713])
reference: GO:0003713 transcription coactivator activity

transcription cofactor
type: Class
equivalent class: Class
  intersection of: transcription regulator
  intersection of: Restriction
    on property: hasFunction
    some values from: transcription cofactor activity
subclass of: Restriction
  on property: hasPart
  some values from: TF binding site of protein
definition: A transcription factor that binds to other transcription factors / the core RNA polymerase II complex but does not bind DNA itself.

transcription cofactor activity
type: Class
subclass of: transcription regulator activity
subclass of: Restriction
  on property: functionOf
  some values from: transcription cofactor
reference: GO:0003712 transcription cofactor activity
definition: The function that links a sequence-specific transcription factor to the core RNA polymerase II complex but does not bind DNA itself. [GO:0003712]

transcription corepressor
type: Class
equivalent class: Class
  intersection of: transcription cofactor
  intersection of: transcription repressor
definition: A transcription cofactor that represses transcription from a RNA polymerase II promoter; it does not bind DNA itself. (modified from [GO:0003714])
reference: GO:0003714 transcription corepressor activity

transcription DNA-dependent
type: Class
subclass of: transcription
subclass of: Restriction
  on property: hasPatient
  some values from: DNA
definition: The synthesis of RNA on a template of DNA. [GO:0006351]

transcription during RNA-mediated transposition
type: Class
subclass of: transcription RNA-dependent
subclass of: Restriction
  on property: partOf
  some values from: transcription RNA-dependent
subclass of: Restriction
  on property: hasParticipant
  some values from: RNA
reference: GO:0032199 transcription during RNA-mediated transposition
definition: The synthesis of DNA from an RNA transposon intermediate. [GO:0032199]

transcription factor
type: Class
equivalent class: Class
  intersection of: transcription regulator
  intersection of: Restriction
    on property: hasFunction
    some values from: transcription factor activity
definition: A transcription factor that binds to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein (other transcription factors of cofactors) or protein or macromolecular complex. (modified from [GO:0003700])
synonym: gene regulatory protein

transcription factor activity
type: Class
subclass of: transcription regulator activity
subclass of: Restriction
  on property: functionOf
  some values from: transcription factor
reference: GO:0003700 transcription factor activity
definition: The function of binding to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GO:0003700]

transcription factor binding site of DNA
type: Class
subclass of: protein binding site of DNA
subclass of: regulatory sequence
subclass of: Restriction
  on property: patientOf
  some values from: binding of TF to TF binding site of DNA
definition: A region on DNA that specifically forms a chemical bond with one or more transcription factors.

transcription factor complex
type: Class
subclass of: complex molecular entity
subclass of: Restriction
  on property: hasPart
  some values from: transcription factor
subclass of: Restriction
  on property: hasPart
  on class: transcription regulator
  min qualified cardinality: 2
disjoint with: translation initiation complex
definition: Any protein group composed of two or more transcription factors.

transcription initiation
type: Class
subclass of: intra cellular process
subclass of: Restriction
  on property: partOf
  some values from: transcription
reference: GO:0006352 transcription initiation
definition: Processes involved in the assembly of the RNA polymerase complex at the promoter region of a DNA template resulting in the subsequent synthesis of RNA from that promoter. [GO:0006352]

transcription initiation complex
type: Class
subclass of: complex molecular entity
subclass of: Restriction
  on property: hasPart
  some values from: transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: DNA region
disjoint with: translation initiation complex
definition: The completed assembly of transcription factors and RNA polymerase binding to the promoter.

transcription of gene
type: Class
subclass of: transcription
subclass of: Restriction
  on property: hasPatient
  some values from: gene
reference: GO:0006350 transcription
definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0006350]

transcription of operon
type: Class
subclass of: transcription
subclass of: Restriction
  on property: hasPatient
  some values from: operon
definition: The synthesis of RNA on a DNA template of operon.

transcription of regulon genes
type: Class
subclass of: transcription
subclass of: Restriction
  on property: hasPatient
  some values from: regulon
definition: The synthesis of RNA on the template of regulon genes.

transcription of stimulon genes
type: Class
subclass of: transcription
subclass of: Restriction
  on property: hasPatient
  some values from: stimulon
definition: The synthesis of RNA on the template of stimulon genes.

transcription RNA-dependent
type: Class
subclass of: transcription
subclass of: Restriction
  on property: hasPatient
  some values from: RNA
subclass of: Restriction
  on property: hasPart
  some values from: transcription during RNA-mediated transposition
reference: GO:0006410 transcription RNA-dependent
definition: The synthesis of DNA on a template of RNA. [GO:0006410]

transcription regulator
type: Class
equivalent class: Class
  intersection of: protein
  intersection of: Restriction
    on property: hasFunction
    some values from: transcription regulator activity
subclass of: gene expression regulator
definition: Protein that has transcription regulator activity.

transcription regulator activity
type: Class
subclass of: gene product function
subclass of: Restriction
  on property: functionOf
  some values from: transcription regulator
reference: GO:0030528 transcription regulator activity
definition: Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor. [GO:0030528]

transcription repressor
type: Class
subclass of: negative transcription regulator
subclass of: Restriction
  on property: hasFunction
  some values from: transcription repressor activity
subclass of: Restriction
  on property: hasPart
  some values from: structural domain of transcription repressor
definition: Any transcription regulator that prevents or downregulates transcription.
synonym: transcription inhibitor

transcription repressor activity
type: Class
subclass of: transcription regulator activity
subclass of: Restriction
  on property: functionOf
  some values from: transcription repressor
definition: Any transcription regulator activity that prevents or downregulates transcription. [GO:0016564]
reference: GO:0016564 transcription repressor activity

transcription termination
type: Class
subclass of: intra cellular process
subclass of: Restriction
  on property: partOf
  some values from: transcription
reference: GO:0006353 transcription termination
definition: The process by which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA. [GO:0006353]

transcriptional attenuation
type: Class
subclass of: regulation of transcription
definition: Regulation of transcription through variation in where transcription termination occurs. [GO:0031555]
reference: GO:0031555 transcriptional attenuation

translation
type: Class
subclass of: protein biosynthesis
subclass of: Restriction
  on property: hasPart
  some values from: translation termination
subclass of: Restriction
  on property: hasPart
  some values from: translation initiation
subclass of: Restriction
  on property: partOf
  some values from: gene expression
subclass of: Restriction
  on property: hasPart
  some values from: translation elongation
reference: GO:0006412 translation
definition: The chemical reactions and pathways resulting in the formation of a protein. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein. [GO:0006412]

translation elongation
type: Class
subclass of: elongation
subclass of: intra cellular process
subclass of: Restriction
  on property: partOf
  some values from: translation
reference: GO:0006414 translational elongation
definition: The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. [GO:0006414]

translation factor
type: Class
subclass of: translation regulator
definition: Any of a group of proteins involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.

translation initiation
type: Class
subclass of: intra cellular process
subclass of: Restriction
  on property: partOf
  some values from: translation
reference: GO:0006413 translational initiation
definition: The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA. [GO:0006413]

translation initiation complex
type: Class
subclass of: complex molecular entity
subclass of: Restriction
  on property: hasPart
  some values from: RNA
subclass of: Restriction
  on property: hasPart
  some values from: translation factor
reference: GO:0003743 translation initiation factor activity; IMR:0000901 translation initiation factor
definition: The protein complex that initiates ribosome-mediated translation of mRNA into a polypeptide (modified from [GO:0003743]).

translation regulator
type: Class
subclass of: gene expression regulator
definition: Any substance involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome (modified from [GO:0045182]).
reference: GO:0045182 translation regulator activity

translation termination
type: Class
subclass of: intra cellular process
subclass of: Restriction
  on property: partOf
  some values from: translation
reference: GO:0006415 translational termination
definition: The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). [GO:0006415]

translational attenuation
type: Class
subclass of: regulation of translation
definition: Translational attenuation is a regulatory mechanism analogous to ribosome-mediated transcriptional attenuation. The system requires the presence of a short ORF, called a leader peptide, encoded in the mRNA upstream of the ribosome-binding site and start codon of the gene whose translation is to be regulated. Certain conditions, such as presence of the antibiotic tetracycline in bacteria or amino acid starvation, may cause slowing or stalling of the ribosome translating the leader peptide. The stalled ribosome masks a region of the mRNA and affects which of two alternative mRNA folded structures will form, therefore controlling whether or not a ribosome will bind and initiate translation of the downstream gene. Translational attenuation is analogous to ribosome-mediated transcriptional attenuation, in which mRNA remodeling caused by ribosome stalling regulates transcriptional termination rather than translational initiation. [GO:0031555]
reference: GO:0031555 translational attenuation

translational frameshifting
type: Class
subclass of: regulation of translation
reference: GO:0006452 translational frameshifting
definition: A mechanism whereby different proteins may result from a single mRNA molecule, due to a change in the parsing of three nucleotides per codon relative to an initiating AUG codon. [GO:0006452]

translational readthrough
type: Class
subclass of: regulation of translation
subclass of: translation elongation
reference: GO:0006451 translational readthrough
definition: The continuation of translation beyond a stop codon by the use of a special tRNA that recognizes the UAG and UGA codons as modified amino acids, rather than as termination codons. [GO:0006451]

transport
type: Class
subclass of: localization
subclass of: Restriction
  on property: hasPatient
  some values from: physical continuant
subclass of: Restriction
  on property: hasAgent
  some values from: physical continuant
reference: GO:0006810 transport
definition: The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.[GO:0006810]

transposition
type: Class
subclass of: intra cellular process
definition: Any process involved in mediating the movement of discrete segments of DNA between nonhomolgous sites. [GO:0032196]
reference: GO:0032196 transposition

tryptophan cluster
type: Class
subclass of: helix-turn-helix domain
subclass of: Restriction
  on property: partOf
  some values from: tryptophan cluster transcription factor
definition: A region comprising several tryptophan residues with a spacing of 12-21 amino acid residues; the subclass of myb-type DNA-binding domains typically exhibit a spacing of 19-21 amino acid residues. All IRF family members, except IRF-1 and IRF-2, contain conserved IAD, IRF association domain that is responsible for protein-protein interactions with other IRF family members or with Ets factor PU.1 and/or bHLH factor E47. (modified from [TRANSFAC:C0022])

tryptophan cluster transcription factor
type: Class
subclass of: helix-turn-helix domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: tryptophan cluster
definition: A transcription factor containing tryptophan cluster.

two-component regulatory system
type: Class
subclass of: non physical continuant
definition: System of proteins and other molecular entities responding to environmental changes. Characterized usually by first a sensor kinase in the cell membrane that phosphorylates itself in response to a signal and, second, a response regulator to which the phosphoryl group is transferred. The responder is typically a DNA-binding protein that regulates transcription. Several of these systems are quite complex, involving many proteins in a signaling cascade or contributing to several responses simultaneously. They are involved in a variety processes such as chemotaxis, osmoregulation, magnesium transport, pH tolerance, sporulation, or response of virulent species to host cell's environments.
synonym: phospho-relay system
synonym: phosphorelay system
synonym: two-component sensory transduction system
synonym: two-component signal transduction system
synonym: two-component system

unpacked DNA
type: Class
subclass of: DNA molecule
definition: The DNA that is unpacked from the loosen chromatin and hence get easy access to various enzymes like DNA polymerase or RNA polymerase in replication or transcription of gene.

upstream regulatory sequence
type: Class
subclass of: regulatory sequence
definition: A sequence located in the upstream region of a gene that controls the rate or manner in which the gene is expressed.

virus
type: Class
subclass of: organism
subclass of: Class
  complement of: Restriction
    on property: hasPart
    some values from: cell
definition: A submicroscopic organism that contains genetic information but cannot reproduce itself. To replicate, it must invade another cell and use parts of that cell's reproductive machinery. [http://www.siebelinstitute.com/brewterms/V.html]
reference: NCBI Taxonomy ID: 10239 Viruses

vitamin
type: Class
subclass of: chemical
reference: CHEBI:33229 vitamin
reference: IMR:0001656 vitamin
definition: Organic substances that are required in small amounts for maintenance and growth, but which cannot be manufactured by the human body. [MeSH:D014815]

WRKY domain
type: Class
subclass of: zinc-coordinating domain
subclass of: Restriction
  on property: partOf
  some values from: WRKY transcription factor
definition: The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural stud!

WRKY transcription factor
type: Class
subclass of: zinc coordinating domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: WRKY domain
definition: A transcription factor containing WRKY domain.

X chromosome
type: Class
subclass of: chromosome
reference: GO:0000805 X chromosome
definition: The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males. [GO:0000805]

Y chromosome
type: Class
subclass of: chromosome
definition: The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males. [GO:0000806]
reference: GO:0000806 Y chromosome

zinc-coordinating domain
type: Class
subclass of: DNA binding domain of transcription factor
subclass of: Restriction
  on property: partOf
  some values from: zinc coordinating domain transcription factor
definition: A domain that coordinates one or more zinc atoms. The zinc-coordinating domains show versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein) and are stable scaffolds that have evolved specialized functions.

zinc coordinating domain transcription factor
type: Class
subclass of: enhancer binding transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: zinc-coordinating domain
definition: A transcription factor containing zinc coordinating domain.

3' polyadenylation
type: Class
subclass of: posttranscriptional modification
reference: GO:0006378 mRNA polyadenylation
definition: The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript. [GO:0006378]
synonym: polyadenylation at the 3' end

5' capping
type: Class
subclass of: posttranscriptional modification
reference: GO:0009452 RNA capping
definition: The sequence of enzymatic reactions by which the 5' cap structure, an inverted 7-methylguanosine linked via a 5'-5' triphosphate bridge (m7G(5')ppp(5')X) to the first transcribed residue, is added to a nascent RNA polymerase II transcript. [GO:0009452]

b HLH
type: Class
subclass of: basic domain
subclass of: Restriction
  on property: partOf
  some values from: bHLH transcription factor
definition: The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways. bHLH proteins include MyoD, SREBPs (sterol regulatory element binding proteins), and yeast Pho4 (phosphatase system). In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf. [InterPro: IPR011598]

bHLH transcription factor
type: Class
subclass of: basic domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: b HLH
definition: A transcription factor containing bHLH domain

b HSH
type: Class
subclass of: basic domain
subclass of: Restriction
  on property: partOf
  some values from: bHSH transcription factor
definition: A helix-span-helix domain in the C-terminal region of activator protein-2 (AP-2) transcription factors, which mediates dimerisation and site-specific DNA binding. (modified from [InterPro:IPR013854])

bHSH transcription factor
type: Class
subclass of: basic domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: b HSH
definition: A transcription factor containing bHSH domain

b ZIP
type: Class
subclass of: basic domain
subclass of: Restriction
  on property: partOf
  some values from: bZIP transcription factor
definition: A domain containing a basic region followed by a leucine zipper region, which is required for protein protein interaction.

bZIP transcription factor
type: Class
subclass of: basic domain transcription factor
subclass of: Restriction
  on property: hasPart
  some values from: b ZIP
definition: A transcription factor that contains a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region for protein dimerization.

p 53 like
type: Class
subclass of: beta scaffold domain with minor groove contacts
subclass of: Restriction
  on property: partOf
  some values from: p53-like transcription factor
definition: This domain is found in a number of transcription factors, including p53, NFATC, TonEBP, STAT-1, and NFkappaB, where it is responsible for DNA-binding. These transcription factors play diverse roles in the regulation of cellular functions: the p53 tumour suppressor upregulates the expression of genes involved in cell cycle arrest and apoptosis; NFATC regulates the production of effector proteins involved in coordinating the immune response; TonEBP regulates gene expression induced by osmotic stress and helps regulate intracellular volume during cell growth; STAT-1 plays an important role in B lymphocyte growth and function; and NFkappaB is involved in the inflammatory response. The DNA-binding domain acts to clamp, or in the case of TonEBP, encircle the DNA target in order to stabilize the protein-DNA complex. Protein interactions may also serve to stabilize the protein-DNA complex, for example in the STAT-1 dimer the SH2 (Src homology 2) domain in each monomer is coup!

p53-like transcription factor
type: Class
subclass of: beta scaffold domain transcription factor with minor groove contacts
subclass of: Restriction
  on property: hasPart
  some values from: p 53 like
definition: A transcription factor containing p53-like domain.

tRNA
type: Class
subclass of: RNA molecule
reference: SO:0000253 tRNA
definition: Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. [SO:0000253, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]

DIRECTED-BINARY-RELATION
type: Thing

PAL-CONSTRAINT
type: Thing

Test
type: Thing
type: continuant
has polarity: negative