biopolymer
type: Class
subclass of: organic polymer
description: A biopolymer is an organic polymer that are typically produced by the cells of living organisms.

monomer
type: Class
subclass of: submolecule
description: A monomer is a submolecule that is proper part of some polymer, and is a building block for such polymer.

polymer
type: Class
subclass of: molecule
description: A polymer is a molecule composed of a connected set of monomeric residues.

lipid residue
type: Class
subclass of: organic submolecule
description: A lipid residue is a part of an organic molecule that was derived from a lipid molecule.

data storage device
type: Class
subclass of: device
description: A data storage device is a device that is capable of storing information.

solid state hard drive
type: Class
subclass of: hard disk drive
description: A solid-state drive (SSD) is a data storage device that uses solid-state memory to store persistent data.

hard disk drive
type: Class
subclass of: data storage device
description: A hard disk drive (HDD) is a non-volatile, random access device for digital data. It features rotating rigid platters on a motor-driven spindle within a protective enclosure. Data is magnetically read and written on the platter by read/write heads that float on a film of air above the platters.

sound wave
type: Class
subclass of: wave
description: A sound wave is a mechanical wave that is an oscillation of pressure transmitted through a solid, liquid, or gas, composed of frequencies within the range of hearing.

chemical functional group
type: Class
subclass of: submolecule
alternative: chemical group
description: A chemical functional group is a submolecule that confers specific chemical properties.

wave
type: Class
subclass of: heterogeneous substance
description: A wave is a physical entity that travels through space and time, consist of oscillations or vibrations and may be accompanied by the transfer of energy.

non-protein coding RNA (ncRNA) gene
type: Class
subclass of: gene
alternative: ncRNA gene
description: A non-protein coding RNA (ncRNA) gene is a gene that encodes for a RNA transcript that is not further translated into a protein product.
equivalent to: http://purl.obolibrary.org/obo/SO_0001263

chromosome
type: Class
subclass of: molecular complex
description: A chromosome is a molecular complex of circular or linear DNA and bound proteins.

radio receiver
type: Class
subclass of: communication device
description: A radio receiver is a communication device that receives its input from an antenna, uses electronic filters to separate a wanted radio signal from all other signals picked up by this antenna, amplifies it to a level suitable for further processing, and finally converts through demodulation and decoding the signal into a form usable for the consumer, such as sound, pictures, digital data, measurement values, navigational positions.

telephone
type: Class
subclass of: communication device
description: The telephone is a communications device that transmits and receives sounds, and are minimally composed of a microphone to speak into, a speaker'which reproduces the voice of the other person and a ringer which makes a sound to alert the owner when a call is coming in.

radar
type: Class
subclass of: device
description: A radar is an object-detection system which uses radio waves to determine the range, altitude, direction, or speed of objects.

device
type: Class
subclass of: heterogeneous substance
description: A device is usually a constructed tool.

communication device
type: Class
subclass of: device
description: A communication device is a device that facilitates the transmission of information through encoded in an audio or digital signal between a sender and a receiver.

protein coding gene
type: Class
subclass of: gene
description: A gene that contains an open reading frame which codes for a protein.
equivalent to: http://purl.obolibrary.org/obo/SO_0001217

functional rna coding gene
type: Class
subclass of: rna gene
description: A gene that codes for a functional RNA molecule.

predicted gene
type: Class
subclass of: gene
description: A predicted gene is a gene that was identified through computational method but has not been experimentally validated.

pseudogene
type: Class
subclass of: nucleic acid part
description: A pseudo gene is a region of a nucleic acid that either cannot be transcribed, or its RNA transcript cannot be translated.
equivalent to: http://purl.obolibrary.org/obo/SO_0000336

validated gene
type: Class
subclass of: gene
description: An experimentally validated gene is a gene whose existence has been demonstrated through experimental methods.

sample
type: Class
subclass of: heterogeneous substance
description: A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use.

liquid solution
type: Class
subclass of: heterogeneous substance
description: A liquid solution is a heterogeneous substance in a liquid state.

double stranded DNA
type: Class
subclass of: double stranded nucleic acid
disjoint with: double stranded RNA
description: double stranded nucleic acid is a molecular complex composed of two weakly connected deoxyribonucleic acids.

nucleic acid strand
type: Class
subclass of: nucleic acid
description: A nucleic acid strand is a single-stranded nucleic acid that is part of a double stranded nucleic acid complex.

positive nucleic acid strand
type: Class
subclass of: nucleic acid strand
alternative: forward strand
description: The positive nucleic acid strand refers to the strand that is to be read 5' to 3'.

negative nucleic acid strand
type: Class
subclass of: nucleic acid strand
alternative: reverse strand
description: The negative nucleic acid strand is the strand that is that is complimentary to the forward strand and appears from 3' to 5'.

double stranded nucleic acid
type: Class
subclass of: molecular complex
description: double stranded nucleic acid is a molecular complex composed of two weakly connected nucleic acids.

double stranded RNA
type: Class
subclass of: double stranded nucleic acid
description: double stranded nucleic acid is a molecular complex composed of two weakly connected ribonucleic acids.

ribosomal RNA gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
alternative: rRNA gene
description: A ribosomal RNA gene is a gene that codes for a ribosomal RNA molecule.
equivalent to: http://purl.obolibrary.org/obo/SO_0001637

5' splice site
type: Class
subclass of: splice site
description: The 5' splice site is the terminal region of an exon that is 5' to the intron that is to be excised.

3' splice site
type: Class
subclass of: splice site
description: The 3' splice site is the terminal region of an exon that is 3' to the intron that is to be excised.

amino acid
type: Class
subclass of: organic molecule
description: An amino acid is an organic molecule composed of a carbon bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom. In the case of glycine, the R group is another hydrogen atom.

cis regulatory element
type: Class
subclass of: nucleic acid part
description: A cisregulatory element is a DNA sequence located on the same DNA strand or chromosome as the gene whose expression it affects.

trans-regulatory element
type: Class
subclass of: nucleic acid part
description: A trans-regulatory element is a DNA sequence associated with the regulation of a gene located outside the genomic region supporting the corresponding structural DNA region of the trans-regulatory element (i.e., a different DNA strand or different chromosome).

small cytoplasmic RNA (scRNA) gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
description: A small cytoplasmic RNA (scRNA) gene is a gene that encodes a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins.
equivalent to: http://purl.obolibrary.org/obo/SO_0001266

small nuclear RNA (snRNA) gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
description: A small nuclear RNA (snRNA) gene is a gene that encodes a small niuclear RNA molecule.
equivalent to: http://purl.obolibrary.org/obo/SO_0001268

small nucleolar RNA (snoRNA) gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
description: A small nucleolar RNA (snoRNA) gene is a gene that encodes a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.
equivalent to: http://purl.obolibrary.org/obo/SO_0001267

transfer RNA (tRNA) gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
alternative: solube RNA (sRNA) gene
alternative: tRNA gene
description: A transfer RNA (tRNA) gene is a gene that codes for a tRNA used in the translation of a messenger RNA (mRNA) to produce a protein product.
equivalent to: http://purl.obolibrary.org/obo/SO_0001272

small cytoplasmic RNA (scRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
alternative: scRNA
description: A small cytoplasmic RNA (scRNA) molecule is a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins.

transfer RNA (tRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
alternative: tRNA
description: A transfer RNA (tRNA) is an RNA molecule that aids in the translation of a messenger RNA (mRNA) to produce a protein product.

small nuclear RNA (snRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
alternative: snRNA
description: A small nuclear RNA (snRNA) is a small RNA molecule that is located in the nucleus of a cell.

small nucleolar RNA (snoRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
alternative: snoRNA
description: A small nucleolar RNA (snoRNA) is a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.

non-protein coding RNA (ncRNA)
type: Class
subclass of: RNA transcript
description: A non-protein coding RNA (ncRNA) is a RNA molecular that cannot be used as a template for generating a protein product.

data collection device
type: Class
subclass of: device
description: A data collection device is a device that collects information about one or more objects.

mass spectrometer
type: Class
subclass of: data collection device
description: A mass spectrometer is a device that identifies ions based on their mass to charge ratio using an electromagnetic field.
similar to: http://purl.obolibrary.org/obo/OBI_0000049

microarray device
type: Class
subclass of: data collection device
alternative: microarray platform
description: A microarray device is a device that identifies the binding of a target substance to a physically immobile substrate placed in an array or lattice.
similar to: http://purl.obolibrary.org/obo/OBI_0000052

nmr device
type: Class
subclass of: data collection device
alternative: nuclear magnetic resonance device
description: A nuclear magnetic resonance (NMR) device is a device that applies a magnetic field to perturb nuclei with an odd number of protons and/or of neutrons in order to hav them absort and re-emit electromagnetic radiation.
equivalent to: http://purl.obolibrary.org/obo/OBI_0000566

single nucleotide polymorphism
type: Class
subclass of: nucleotide residue
alternative: SNP
alternative: SNV
alternative: single nucleotide variation
description: a single nucleotide variation (SNV) is a nucleotide residue that is a variant compared to some reference nucleic acid sequence.

epimer
type: Class
subclass of: stereoisomer
description: An epimer is a stereoisomer that differs in configuration at only one stereogenic center.

analyte
type: Class
subclass of: chemical substance
description: an analyte is a substance or chemical constituent of interest in an analytical procedure.

protein domain
type: Class
subclass of: amino acid polymer submolecule
description: A protein domain is a part of a protein that maintains its structure and function independently of the rest of the protein.

genomic sequence variant
type: Class
subclass of: nucleic acid part
description: a genomic sequence variant is part of a nucleic acid which is compositionally different than another reference genomic part.
alternative: variant

protein coding sequence
type: Class
subclass of: gene component
description: A protein coding sequence (CDS) is the region of DNA that is translated to form proteins. The CDS refers to those nucleotides (concatenated exons) that can be divided into codons which are actually translated into amino acids by the ribosomal translation machinery.
alternative: CDS
alternative: coding sequence

biologic
type: Class
subclass of: pharmaceutical drug
description: A biologic, also known as a biologic medical product, biological, or biopharmaceutical, is any pharmaceutical drug product manufactured in, extracted from, or semisynthesized from biological sources.

post-translational modification
type: Class
subclass of: amino acid polymer submolecule
description: a post-translational modification is a part of a protein that was added, removed, or modified as a result of a chemical reaction after synthesis.

carbohydrate
type: Class
subclass of: organic polymer
alternative: oligosaccharide
alternative: saccharide
description: a carbohydrate is an organic molecule composed of two or more monosaccharides.

microRNA (miRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
description: A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression.
alternative: miRNA

chemical salt
type: Class
subclass of: molecular complex
alternative: salt
description: a chemical salt is a molecular complex composed of an ionic assembly of cations and anions.

strong chemical salt
type: Class
subclass of: chemical salt
description: a strong chemical salt is a chemical salt that is composed of strong electrolytes. Strong chemical salts contain Na,K,NH4 or NO3, CIO4, CH3COO.

weak chemical salt
type: Class
subclass of: chemical salt
description: a weak chemical salt is a chemical salt composed of weak eletrolytes.

peptide
type: Class
subclass of: amino acid polymer
description: a peptide is an organic polymer composed of between two and fifty amino acids.

oligopeptide
type: Class
subclass of: amino acid polymer
description: an oligopeptide is an organic polymer composed of fewer than 10 or 15 amino acids.

amino acid polymer
type: Class
subclass of: organic polymer
description: an amino acid polymer is an organic polymer composed of two or more amino acid residues.

ingredient
type: Class
subclass of: chemical substance
description: an ingredient is a chemical substance that forms part of a mixture.

protein isoform
type: Class
subclass of: protein
subclass of: isomer
description: a protein isoform is a protein that is a structural variant (different sequence of amino acids and/or post-translational modifications) of another protein, but encoded by the same gene.

salt
type: Class
subclass of: heterogeneous substance
description: a salt is a heterogeneous substance that is coposed of positively charged ions (cations) and negatively charged ions (anions) held together by electrostatic forces.

chemical entity
type: Class
description: A chemical entity is a material entity that pertains to chemistry.
equivalent to: CHEBI:23367
subset: chemical+
example: atom, ion, molecule, chemical substance,

weak submolecular component
type: Class
subclass of: submolecular entity
disjoint with: strong submolecular component
description: A weak submolecular component is a submolecular component that weakly connects submolecular components.

polypeptide
type: Class
subclass of: amino acid polymer
disjoint with: nucleic acid
description: A polypeptide is an organic polymer composed of amino acid residues, typically of less than 50 amino acids in length.

nucleic acid
type: Class
subclass of: organic polymer
description: A nucleic acid is an organic polymer composed of a sequence of nucleotide residues.

ribonucleic acid
type: Class
subclass of: nucleic acid
disjoint with: deoxyribonucleic acid
description: A ribonucleic acid is an organic polymer composed of a sequence of ribonucleotide residues.

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
description: A deoxyribonucleic acid is an organic polymer composed of a sequence of deoxyribonucleotide residues.

lipid
type: Class
subclass of: organic molecule
description: A lipid is a water-insoluable organic molecule.

submolecular entity
type: Class
subclass of: chemical entity
description: A submolecular entity is a chemical entity that is a part of a molecule.

genetic polymorphism
type: Class
subclass of: nucleic acid part
description: genetic polymorphism is the description of a difference in genetic composition at some location.

monosaccharide
type: Class
subclass of: organic molecule
description: A monosaccharide is an organic molecule that consists of a single polyhydroxy aldehyde or ketone group.

hydrogen bond
type: Class
subclass of: weak submolecular component
description: A hydrogen bond is a weak submolecular interaction formed between a hydrogen atom and a electronegative atom.

cation pi interaction
type: Class
subclass of: ionic interaction
description: A cation pi interaction is an ionic interaction between the localized negative charge of π orbital electrons, located above and below the plane of an aromatic ring, and a positive charge.

gene
type: Class
subclass of: nucleic acid part
description: A gene is part of a nucleic acid that contains all the necessary elements to encode a functional transcript.
equivalent to: biopax:Gene
equivalent to: http://purl.obolibrary.org/obo/SO_0000704

chemical element
type: Class
subclass of: homogeneous substance
description: A chemical element is a (effectively) homogeneous substance composed of one type of atom.

drug
type: Class
subclass of: chemical substance
description: A drug is a chemical substance that contains one or more active ingredients that regulate one or more biological processes.

pharmaceutical drug
type: Class
subclass of: drug
alternative: medicine
description: A pharmaceutical preparation is a chemical substance that is approved for use in the medical diagnosis, cure, treatment, or prevention of disease.

haplotype
type: Class
subclass of: genomic sequence variant
description: A haplotype is one of a set of genomic sequence variants.

protein
type: Class
subclass of: amino acid polymer
description: A protein is an organic polymer that is composed of one or more linear polymers of amino acids.
equivalent to: CHEBI:36080

atom
type: Class
subclass of: chemical entity
description: An atom is composed of a core of protons and/or neutrons which may be surrounded by a cloud of electrons.

base pair
type: Class
subclass of: weak submolecular component
description: A base pair is a weak molecular interaction composed of hydrogen bonds between nucleobases.

strong submolecular component
type: Class
subclass of: submolecular entity
description: A strong submolecular component is a submolecular component that strongly connects submolecular components.

5' untranslated region
type: Class
subclass of: gene component
description: The five prime untranslated region (5' UTR) is a section of messenger RNA (mRNA) and the DNA that codes for it that starts at the +1 position (where transcription begins) and ends one nucleotide before the start codon (usually AUG) of the coding region.

3' untranslated region
type: Class
subclass of: gene component
description: A three prime untranslated region (3'-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon.

organic submolecule
type: Class
subclass of: submolecule
description: An organic submolecule is connected region of a molecule.

organic molecule
type: Class
subclass of: molecule
description: An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur)

open reading frame
type: Class
subclass of: gene component
description: An open reading frame (ORF) is a part of a gene that encodes a protein but does not contain a stop codon.

amino acid residue
type: Class
subclass of: amino acid polymer submolecule
description: An amino acid residue is a submolecule of an amino acid that is part of a larger molecule.

nucleotide residue
type: Class
subclass of: nucleic acid part
description: A nucleotide residue is a part of a molecule that derives from a nucleotide.

poison
type: Class
subclass of: drug
description: A poison is a drug that is harzardous or toxic to an organism when ingested at a certain quantity.

active ingredient
type: Class
subclass of: A pharmaceutical ingredient is a part of a pharmaceutical preparation.
description: An active ingredient is a molecular entity that exhibits biological activity.

operon
type: Class
subclass of: nucleic acid part
description: An operon is a collection of contiguous genes transcribed as a single (polycistronic) mRNA.
similar to: SO:0000178

gene regulatory component
type: Class
subclass of: gene component
description: A gene regulatory component is a gene component that exerts a regulatory function.

gene enhancer
type: Class
subclass of: gene regulatory component
description: A gene enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster.

inactive ingredient
type: Class
subclass of: A pharmaceutical ingredient is a part of a pharmaceutical preparation.
description: Aninactive ingredient is a molecular entity that does not exhibit biological activity.

deoxyribonucleic acid template
type: Class
subclass of: deoxyribonucleic acid
description: A deoxyribonucleic acid template is a deoxyribonucleic acid that provides the template to synthesize a complementary strand of DNA through transcription.

deoxyribonucleic acid primer
type: Class
subclass of: SIO_000779
subclass of: deoxyribonucleic acid
description: A deoxyribonucleic acid primer is a deoxyribonucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation.

RNA transcript component
type: Class
subclass of: nucleic acid part
description: An RNA transcript component is a region of an RNA transcript.

mature mRNA
type: Class
subclass of: messenger RNA
description: A mature RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns.

pre-mRNA
type: Class
subclass of: messenger RNA
description: Precursor mRNA (pre-mRNA) is a single strand of messenger ribonucleic acid (mRNA) that is synthesized from a DNA template throught transcription.

mRNA splice variant
type: Class
subclass of: messenger RNA
description: An mRNA splice variant is an mRNA molecule that varies from another mRNA molecule of the same gene origin but having a different final sequence due to differences in its assembly from splice sites.

messenger RNA
type: Class
subclass of: RNA transcript
description: A messenger RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns.

dna gene
type: Class
subclass of: gene
disjoint with: rna gene
description: A gene that is located on DNA.

rna gene
type: Class
subclass of: gene
description: A gene that is located on RNA.

allele
type: Class
subclass of: gene
description: An allele is one of a set of sequence variants of a gene.

carbohydrate residue
type: Class
subclass of: organic submolecule
description: A carbohydrate residue is a part of a molecule that was derived from a monosaccharide molecule.

nucleic acid part
type: Class
subclass of: organic submolecule
description: A nucleic acid part is a component of a nucleic acid.

deoxyribonucleotide residue
type: Class
subclass of: nucleotide residue
disjoint with: ribonucleotide residue
description: A deoxyribonucleotide residue is a part of a molecule that derives from a deoxyribonucleotide.

ribonucleotide residue
type: Class
subclass of: nucleotide residue
description: A ribonucleotide residue is a part of a molecule that derives from a ribonucleotide.

A pharmaceutical ingredient is a part of a pharmaceutical preparation.
type: Class
subclass of: ingredient
label: pharmaceutical ingredient

chemical complex
type: Class
subclass of: chemical substance
description: A chemical complex is a chemical substance composed of weakly connected molecules and ions in a known stoichiometry.

enzyme
type: Class
subclass of: protein
description: An enzyme is a protein or protein complex that realizes its disposition to covalently modify some molecule during a chemical reaction.

catalyst
type: Class
subclass of: chemical substance
description: A catalyst is a molecule that has the capability to reduce the activation energy of a reaction and hence increase the overall rate of reaction.

organic polymer
type: Class
subclass of: organic molecule
description: An organic polymer is an organic molecule composed of connected set of monomeric units.

product
type: Class
subclass of: molecule

reagent
type: Class
subclass of: heterogeneous substance
description: A reagent is a substance that is added to a system in order to bring about a chemical reaction, or added to see if a reaction occurs.

specimen
type: Class
subclass of: sample
description: A specimen is a portion of material for use in testing, examination, or study.

buffer
type: Class
subclass of: liquid solution component
description: A buffer is a dissolved chemical substance that resists change in pH upon addition of small amounts of acid or base.

solvent
type: Class
subclass of: liquid solution component
description: A solvent is a substance that can dissolve other substances (solutes).

solute
type: Class
subclass of: liquid solution component
description: A solute is a substance that becomes dissolved in a solvent.

antigen
type: Class
subclass of: molecule
description: An antigen is a molecule that can be bound by a major histocompatibility complex (MHC) and presented to a T-cell receptor.

receptor
type: Class
subclass of: signal transducer
description: A receptor molecule is a molecule that has the capability to bind to a signal and propogate a response to that signal.

centrifugation pellet
type: Class
subclass of: centrifugation substance
disjoint with: supernatant
description: A centrifugation pellet is a solid substance that forms as a result of compaction by a centrifuge.

supernatant
type: Class
subclass of: centrifugation substance
description: A supernatent is a liquid substance that remains after centrifugation.

centrifugation substance
type: Class
subclass of: chemical substance
description: A centrifugation substance is a substance that is the target or product of centrifugation.

liquid solution component
type: Class
subclass of: heterogeneous substance
description: A liquid solution component is a part of a liquid solution.

placebo
type: Class
subclass of: heterogeneous substance
description: A placebo is a medically ineffectual treatment for a medical condition intended to deceive the recipient.

ligand
type: Class
subclass of: molecule
description: A ligand is a molecule that is part of a complex by weakly interacting with another molecule.

low barrier hydrogen bond
type: Class
subclass of: hydrogen bond
description: A low barrier hydrogen bond is a shorter, stronger hydrogen bond that is formed between both heteroatoms.

activator
type: Class
subclass of: molecular regulator
description: A molecular activator is a molecular regulator that realizes its disposition to conformationally change a target molecule and increase its functionality.

inhibitor
type: Class
subclass of: molecular regulator
description: A molecular inhibitor is a molecular regulator that realizes its disposition to conformationally change a target molecule and decrease its functionality.

molecular regulator
type: Class
subclass of: molecule
description: A molecular regulator is a molecule that regulates the function of another chemical entity.

signal transducer
type: Class
subclass of: molecule
description: A signal transducer is a molecule that responds to and amplifies a signal in a signalling system.

signal
type: Class
subclass of: molecule
description: A signal is an object that initiates a sequence of events.

messenger
type: Class
subclass of: signal transducer
description: A mesenger is a molecule involved in either signal detection or signal propagation from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus.

second messenger
type: Class
subclass of: messenger
description: A second messenger is a molecule that relay signals from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus.

submolecule
type: Class
subclass of: submolecular entity
description: A submolecule is any part of a molecule.

intron
type: Class
subclass of: gene component
description: An intron is a region of a gene that is removed from the final protein open reading frame.

gene component
type: Class
subclass of: nucleic acid part
description: A gene component is a component of a gene.

exon
type: Class
subclass of: gene component
description: An exon is a nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after introns have been removed by RNA splicing.

gene promoter
type: Class
subclass of: gene regulatory component
description: A gene promoter is a region of DNA that initiates transcription of a particular gene.

start codon
type: Class
subclass of: RNA transcript component
disjoint with: stop codon
description: A start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon is almost always preceded by an untranslated region 5' UTR.

stop codon
type: Class
subclass of: RNA transcript component
description: A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.

RNA transcript
type: Class
subclass of: ribonucleic acid
description: An RNA transcript is an RNA molecule that is produced from transcription of a nucleic acid template.

splice site
type: Class
subclass of: RNA transcript component
description: A splice site is a region required for the excision of an intron and connection to another exon.

acid
type: Class
subclass of: liquid solution component
description: An acid is a molecular entity in solution capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).

base
type: Class
subclass of: liquid solution component
description: A base is a molecular entity dissolved in a solvent that is capable of accepting a proton (Bronsted base) or forming a covalent bond with a hydron (Lewis base) .

isomer
type: Class
subclass of: molecule
description: An isomer is a molecule that is compositionally identical to another molecule as a result of a different atomic connectivity.

ion
type: Class
subclass of: chemical entity
description: An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge.

cation
type: Class
subclass of: ion
description: An anion is an atom or molecule with a net positive electrical charge.

anion
type: Class
subclass of: ion
description: An anion is an atom or molecule with a net negative electrical charge.

polar solvent
type: Class
subclass of: solvent
disjoint with: nonpolar solvent
description: A polar solvent is a solvent that exhibits a polar quality.

nonpolar solvent
type: Class
subclass of: solvent
description: A non-polar solvent is a solvent that exhibits a non-polar quality.

heterogeneous substance
type: Class
subclass of: chemical substance
disjoint with: homogeneous substance
description: A heterogeneous substance is a chemical substance that is composed of more than one different kind of component.

homogeneous substance
type: Class
subclass of: chemical substance
description: A homogeneous substance is a substance that is composed of a uniform type of entity.

antibody
type: Class
subclass of: protein complex
description: An antibody (also known as immunoglobulins, abbreviated Ig) are gamma globulin proteins that are used by the immune system to identify and neutralize foreign objects. They are typically made of two large heavy chains and two small light chains.

alpha helix
type: Class
subclass of: amino acid polymer submolecule
description: An alpha helix is structural region of a protein that is characterized by 3.6 residues per turn, a translation of 1.5 angstroms along the helical axis in which backbone N-H groups form a hydrogen bond to the backbone carboxyl group of the amino acid four residues prior.

beta strand
type: Class
subclass of: amino acid polymer submolecule
description: A beta strand is structural region of a protein that is characterized by a roughly planar sequence of amino acid residues forming hydrogen bonds between the N-O and the C=O of another part of the peptide and having their side chains perpendicular to the planar axis.

amino acid polymer submolecule
type: Class
subclass of: organic submolecule
description: An amino acid polymer submolecule is a submolecule of an amino acid polymer.

ionic interaction
type: Class
subclass of: weak submolecular component
description: An ionic interaction is a weak submolecular interaction between a charged submolecules.

protein complex
type: Class
subclass of: molecular complex
description: A protein complex is a molecular complex composed of at least two polypeptide chains.

single bond
type: Class
subclass of: covalent bond
description: A single bond is a covalent bond between a pair of atoms in which one pair of electrons are shared.

double bond
type: Class
subclass of: covalent bond
description: A double bond is a covalent bond between a pair of atoms in which two pairs of electrons are shared.

triple bond
type: Class
subclass of: covalent bond
description: A triple bond is a covalent bond between a pair of atoms in which three pairs of electrons are shared.

aromatic bond
type: Class
subclass of: covalent bond
description: An aromatic bond is an interaction between a set of atoms across which pairs of electrons are shared.

disulfide bond
type: Class
subclass of: single bond
description: A disulfide bond is a bond between two sulfur atoms.

dipole-dipole interaction
type: Class
subclass of: weak submolecular component
description: A dipole-dipole interaction is a weak submolecular interaction between strongly electronegative atoms.

van der Waals interaction
type: Class
subclass of: weak submolecular component
description: van der Waals' interaction is an a weak submolecular interaction between an instantaneous dipole and induced dipole.

base stack
type: Class
subclass of: weak submolecular component
description: A base stack is a stabilizing interaction of DNA and RNA between spatially adjacent nucleotides and possibly involving London dispersion, hydrophobic and electrostatic forces.

molecular complex
type: Class
subclass of: chemical complex
description: A molecular complex is a chemical complex composed of at least one weakly interacting molecule.

binary compound
type: Class
subclass of: chemical substance
description: A binary compound is a mereological maximum sum of two kinds of weakly connected entities.

stereoisomer
type: Class
subclass of: isomer
description: A stereoisomer is an isomer in which the atomic connectivity is the same, but differs in its spatial arrangement of atoms.

diastereomer
type: Class
subclass of: stereoisomer
description: A diastereomer is a stereoisomer that is not a mirror image of its isomer.

enantiomer
type: Class
subclass of: stereoisomer
description: An enantiomer is a stereoisomer that is a mirror image of its isomer.

optical isomer
type: Class
subclass of: stereoisomer
description: An optical isomer is a stereoisomer that rotates the plane of polarization of a beam of plane polarized light.

structural isomer
type: Class
subclass of: isomer
description: A structural isomer is an isomer in which the atoms are joined together in different ways.

ring
type: Class
subclass of: chemical functional group
description: A ring is a submolecule with a circular topology.

aromatic ring
type: Class
subclass of: ring
description: An aromatic ring is a ring in which the electrons are delocalized across all atoms in the ring.

heterocyclic ring
type: Class
subclass of: ring
disjoint with: homocyclic ring
description: A heterocyclic ring is a ring containing a hetero atom.

homocyclic ring
type: Class
subclass of: ring
description: A homocyclic ring is a ring where the atoms are of a single type.

ionic compound
type: Class
subclass of: binary compound
description: An ionic compound is a mereological maximal sum of weakly connected paired positive and negative ions.

allotrope
type: Class
subclass of: chemical element
description: An allotrope is a structural variant of a chemical element.

carbon allotrope
type: Class
subclass of: allotrope
description: A carbon allotrope is a chemical substance composed of carbon.

diamond
type: Class
subclass of: carbon allotrope
description: diamond is a carbon allotrope in which each carbon atom in diamond is covalently bonded to four other carbons in a tetrahedron. These tetrahedrons together form a 3-dimensional network of puckered six-membered rings of atoms.

graphite
type: Class
subclass of: carbon allotrope
description: graphite is an allotrope of carbon which is a conductor, and is the most stable form of solid carbon.

fullerene
type: Class
subclass of: carbon allotrope
description: fullerene is a carbon allotrope which take the form of a hollow sphere, ellipsoid, or tube.

aggregated carbon nanorods
type: Class
subclass of: carbon allotrope
description: aggregate of carbon nanorods is an allotrope of carbon considered to be the least compressible material known, as measured by its isothermal bulk modulus; aggregated diamond nanorods have a modulus of 491 gigapascals (GPa), while a conventional diamond has a modulus of 442 GPa. ADNRs are also 0.3% denser than regular diamond.

amorphous carbon
type: Class
subclass of: carbon allotrope
description: amorphous carbon is an allotrope of carbon that does not have any crystalline structure. As with all glassy materials, some short-range order can be observed, but there is no long-range pattern of atomic positions.

carbon nanofoam
type: Class
subclass of: carbon allotrope
description: carbon nanofoam is an allotrope of carbon that consists of a low-density cluster-assembly of carbon atoms strung together in a loose three-dimensional web. Each cluster is about 6 nanometers wide and consists of about 4000 carbon atoms linked in graphite-like sheets that are given negative curvature by the inclusion of heptagons among the regular hexagonal pattern.

chaoite
type: Class
subclass of: carbon allotrope
description: chaoite is an allotrope of carbon that is slightly harder than graphite with a reflection colour of grey to white.

glassy carbon
type: Class
subclass of: carbon allotrope
description: glassy carbon is an allotrope of carbon which is widely used as an electrode material in electrochemistry, as well as for high temperature crucibles and as a component of some prosthetic devices.

ionsdaleite
type: Class
subclass of: carbon allotrope
description: ionsdaleite is a hexagonal allotrope of the carbon allotrope diamond.

boron atom
type: Class
subclass of: atom

carbon atom
type: Class
subclass of: atom

hydrogen atom
type: Class
subclass of: atom

helium atom
type: Class
subclass of: atom

lithium atom
type: Class
subclass of: atom

beryllium atom
type: Class
subclass of: atom

nitrogen atom
type: Class
subclass of: atom

oxygen atom
type: Class
subclass of: atom

fluorine atom
type: Class
subclass of: atom

neon atom
type: Class
subclass of: atom

sodium atom
type: Class
subclass of: atom

magnesium atom
type: Class
subclass of: atom

aluminium atom
type: Class
subclass of: atom

silicon atom
type: Class
subclass of: atom

phosphorus atom
type: Class
subclass of: atom

sulfur atom
type: Class
subclass of: atom

chlorine atom
type: Class
subclass of: atom

argon atom
type: Class
subclass of: atom

potassium atom
type: Class
subclass of: atom

calcium atom
type: Class
subclass of: atom

scandium atom
type: Class
subclass of: atom

titanium atom
type: Class
subclass of: atom

vanadium atom
type: Class
subclass of: atom

chromium atom
type: Class
subclass of: atom

manganese atom
type: Class
subclass of: atom

iron atom
type: Class
subclass of: atom

cobalt atom
type: Class
subclass of: atom

nickel atom
type: Class
subclass of: atom

copper atom
type: Class
subclass of: atom

zinc atom
type: Class
subclass of: atom

gallium atom
type: Class
subclass of: atom

germanium atom
type: Class
subclass of: atom

arsenic atom
type: Class
subclass of: atom

selenium atom
type: Class
subclass of: atom

bromine atom
type: Class
subclass of: atom

krypton atom
type: Class
subclass of: atom

rubidium atom
type: Class
subclass of: atom

strontium atom
type: Class
subclass of: atom

yttrium atom
type: Class
subclass of: atom

zirconium atom
type: Class
subclass of: atom

niobium atom
type: Class
subclass of: atom

molybdemum atom
type: Class
subclass of: atom

technetium atom
type: Class
subclass of: atom

ruthenium atom
type: Class
subclass of: atom

rhodium atom
type: Class
subclass of: atom

palladium atom
type: Class
subclass of: atom

silver atom
type: Class
subclass of: atom

cadmium atom
type: Class
subclass of: atom

indium atom
type: Class
subclass of: atom

tin atom
type: Class
subclass of: atom

antimony atom
type: Class
subclass of: atom

tellurium atom
type: Class
subclass of: atom

iodine atom
type: Class
subclass of: atom

xenon atom
type: Class
subclass of: atom

caesium atom
type: Class
subclass of: atom

barium atom
type: Class
subclass of: atom

lanthanum atom
type: Class
subclass of: atom

hafnium atom
type: Class
subclass of: atom

tantalum atom
type: Class
subclass of: atom

tungsten atom
type: Class
subclass of: atom

rhenium atom
type: Class
subclass of: atom

osmium atom
type: Class
subclass of: atom

iridium atom
type: Class
subclass of: atom

platinum atom
type: Class
subclass of: atom

gold atom
type: Class
subclass of: atom

mercury atom
type: Class
subclass of: atom

thallium atom
type: Class
subclass of: atom

lead atom
type: Class
subclass of: atom

bismuth atom
type: Class
subclass of: atom

polonium atom
type: Class
subclass of: atom

astatine atom
type: Class
subclass of: atom

radon atom
type: Class
subclass of: atom

francium atom
type: Class
subclass of: atom

radium atom
type: Class
subclass of: atom

actinium atom
type: Class
subclass of: atom

rutherfordium atom
type: Class
subclass of: atom

dubnium atom
type: Class
subclass of: atom

seaborgium atom
type: Class
subclass of: atom

bohrium atom
type: Class
subclass of: atom

hassium atom
type: Class
subclass of: atom

meitnerium atom
type: Class
subclass of: atom

darmstadtium atom
type: Class
subclass of: atom

roentgenium atom
type: Class
subclass of: atom

copernicium atom
type: Class
subclass of: atom

unutrium atom
type: Class
subclass of: atom

ununquadium atom
type: Class
subclass of: atom

ununpentium atom
type: Class
subclass of: atom

ununhexium atom
type: Class
subclass of: atom

ununseptium atom
type: Class
subclass of: atom

ununoctium atom
type: Class
subclass of: atom

cerium atom
type: Class
subclass of: atom

praseodymium atom
type: Class
subclass of: atom

neodymium atom
type: Class
subclass of: atom

promethium atom
type: Class
subclass of: atom

samarium atom
type: Class
subclass of: atom

europium atom
type: Class
subclass of: atom

gadolinium atom
type: Class
subclass of: atom

terbium atom
type: Class
subclass of: atom

dysprosium atom
type: Class
subclass of: atom

holmium atom
type: Class
subclass of: atom

erbium atom
type: Class
subclass of: atom

thulium atom
type: Class
subclass of: atom

ytterbium atom
type: Class
subclass of: atom

lutetium atom
type: Class
subclass of: atom

thorium atom
type: Class
subclass of: atom

protactinium atom
type: Class
subclass of: atom

uranium atom
type: Class
subclass of: atom

neptunium atom
type: Class
subclass of: atom

plutonium atom
type: Class
subclass of: atom

americium atom
type: Class
subclass of: atom

curium atom
type: Class
subclass of: atom

berkelium atom
type: Class
subclass of: atom

californium atom
type: Class
subclass of: atom

einsteinium atom
type: Class
subclass of: atom

fermium atom
type: Class
subclass of: atom

mendelevium atom
type: Class
subclass of: atom

nobelium atom
type: Class
subclass of: atom

lawrencium atom
type: Class
subclass of: atom

covalent bond
type: Class
subclass of: strong submolecular component
description: A covalent bond is a strong submolecular interaction between atoms.

molecule
type: Class
subclass of: chemical entity
description: A molecule is a single chemical entity composed of fully covalently bonded atoms.

chemical substance
type: Class
subclass of: chemical entity
alternative: mixture
description: A chemical substance is a chemical entity composed of two or more weakly (non-covalently) interacting chemical entities.

sio.owl
version info: sio-subset-chemical.owl
version IRI: sio-subset-chemical.owl