Function
type: Class
IAO_0000112: Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law
IAO_0000115: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.

Role
type: Class
IAO_0000112: Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university
IAO_0000115: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.

MaterialEntity
type: Class
IAO_0000115: Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
IAO_0000112: Examples: collection of random bacteria, a chair, dorsal surface of the body

GenericallyDependentContinuant
type: Class
IAO_0000112: Examples: a certain PDF file that exists in different and in several hard drives
IAO_0000115: Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.

GO:RNA_polymerase_activity
type: Class
subclass of: GO:nucleotidyltransferase_activity
IAO_0000412: imported from: Gene Ontology, Version 1.931
IAO_0000118: alternative term: ribonucleic acid transcriptase activity ribonucleic polymerase activity ribonucleic transcriptase activity RNA nucleotidyltransferase activity RNA transcriptase activity transcriptase C ribonucleic acid formation factors C RNA formation factors ribonucleate nucleotidyltransferase activity ribonucleate polymerase activity ribonucleic acid nucleotidyltransferase ribonucleic acid polymerase activity
IAO_0000111: editor preferred term: RNA polymerase activity
IAO_0000115: Definition: Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template.

GO:nucleotidyltransferase_activity
type: Class
subclass of: GO:transferase_activity,_transferring_phosphorus-containing_groups
IAO_0000412: imported from: Gene Ontology, Version 1.931
IAO_0000111: editor preferred term: nucleotidyltransferase activity
IAO_0000115: Definition: Catalysis of the transfer of a nucleotidyl group to a reactant.

CHEBI:ribosomal_RNA
type: Class
subclass of: CHEBI:ribonucleic_acid
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000118: alternative term: rRNA
IAO_0000115: Definition: RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis.

CHEBI:ribonucleic_acid
type: Class
IAO_0000118: alternative term: RNA pentosenucleic acid ribose nucleic acid
disjoint with: CHEBI:deoxyribonucleic_acid
subclass of: CHEBI:nucleic_acid
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000115: Definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
IAO_0000111: editor preferred term: ribonucleic acid

CHEBI:messenger_RNA
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: messenger RNA
IAO_0000118: alternative term: mRNA template RNA
IAO_0000115: Definition: An RNA molecule that transfers the coding information for protein synthesis from the chromosomes to the ribosomes mRNA is formed from a DNA template by transcription. It may be a copy of a single gene or of several adjacent genes (polycistronic mRNA). On the ribosome, the sequence is converted into the programmed amino acid sequence through translation.
subclass of: CHEBI:ribonucleic_acid

polyacrylamide_gel
type: Class
IAO_0000111: editor preferred term: polyacrylamide gel
comment: term imported from: Ontology for Biomedical Investigations, Version 2009-11-06 Philly (aka version 1.0) Release Candidate
IAO_0000117: Definition Editor: Olga-Ximena Giraldo
IAO_0000112: Example Of Usage: Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
subclass of: SEP:gel
IAO_0000115: definition: A Polyacrylamide Gel is a separation matrix used in electrophoresis of biomolecules, such as proteins or DNA fragments. Traditional DNA sequencing techniques such as Maxam-Gilbert or Sanger methods used polyacrylamide gels to separate DNA fragments differing by a single base-pair in length so the sequence could be read.
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Polyacrylamide_gel

SEP:gel
type: Class
IAO_0000119: definition source: Sample processing and separation techniques, Version 1.070708
subclass of: processed_material
IAO_0000115: Definition: A gel is a compund substance which is a colloid in a more solid form than a solution.

amplified_DNA
type: Class
subclass of: processed_material
IAO_0000111: Editor Preferred Term: amplified DNA
IAO_0000112: Example Of Usage: Amplied DNA created by PCR
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000119: Definition Source: Alan Ruttenberg
IAO_0000117: Definition Editor: PERSON: Alan Ruttenberg
IAO_0000115: Definition: DNA that has been produced in an enzymatic amplification process

processed_material
type: Class
subclass of: MaterialEntity
IAO_0000112: Example Of Usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples.
IAO_0000111: Editor Preferred Term: processed material
IAO_0000115: Definition: Is a material entity that is created or changed during material processing.
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000117: Definition Editor: PERSON: Alan Ruttenberg

M4L:3′→5′_exonuclease_(proofreading)_activity
type: Class
IAO_0000115: definition: Proofreading DNA polymerases are accurate due to the 3′→5′ exonuclease activity, which can remove a misincorporated nucleotide from a growing DNA chain.
IAO_0000111: editor preferred term: 3′→5′_exonuclease (proofreading) activity
IAO_0000112: example of usage: enzyme Pfu DNA polymerase. When the amplified product is to be cloned, expressed or used in mutation analysis, Pfu DNA polymerase is a better choice due to its high fidelity.
IAO_0000119: definition source: Promega, Protocols & Applications Guide. http://www.promega.com/paguide/chap1.htm#title4
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: Proofreading DNA polymerase
subclass of: GO:DNA-directed_DNA_polymerase_activity

GO:DNA-directed_DNA_polymerase_activity
type: Class
IAO_0000118: alternative term: delta DNA polymerase activity deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) activity deoxyribonucleic acid duplicase activity deoxyribonucleic duplicase activity deoxyribonucleic polymerase I DNA duplicase activity DNA nucleotidyltransferase (DNA-directed) activity DNA polymerase alpha DNA polymerase beta DNA polymerase gamma DNA polymerase I DNA polymerase II DNA polymerase III DNA polymerase V activity DNA replicase activity DNA-dependent DNA polymerase activity duplicase epsilon DNA polymerase activity eta DNA polymerase activity gamma DNA-directed DNA polymerase activity iota DNA polymerase activity kappa DNA polymerase activity Klenow fragment lambda DNA polymerase activity mu DNA polymerase activity nu DNA polymerase activity sequenase sigma DNA polymerase activity Taq DNA polymerase Taq Pol I Tca DNA polymerase theta DNA polymerase activity zeta DNA polymerase activity alpha DNA polymerase activity beta DNA polymerase activity
IAO_0000111: editor preferred term: DNA-directed DNA polymerase activity
IAO_0000115: Definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and primer.
subclass of: GO:DNA_polymerase_activity
IAO_0000412: imported from: Gene Ontology, Version 1.931

CHEBI:organic_hydroxy_compound
type: Class
subclass of: CHEBI:hydroxides
IAO_0000118: alternative term: hydroxy compounds
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000115: definition: An organic compound having at least one hydroxy group attached to a carbon atom.

CHEBI:hydroxides
type: Class
IAO_0000115: Definition: Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
IAO_0000111: editor preferred term: hydroxides
IAO_0000412: Imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:heteroatomic_molecular_entity

M4L:vinyl_glove
type: Class
IAO_0000119: definition source: Emerald, Professional Protection Products. http://www.emeraldlatexgloves.com/gloves-101.htm
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: Vinyl is the first synthetic material available to consumer, is a material composed of polyvinyl chloride and plasticizers that softens the material. These type of gloves are an economical alternative to latex gloves. These gloves offer great for basic hand protection in a low infection environment, good multi-purpose glove for general use and activities that do not require highest degree of tactile precision, but does not fit as well as latex.
IAO_0000111: editor preferred term: vinyl glove
subclass of: M4L:glove

M4L:glove
type: Class
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Rubber_glove
subclass of: M4L:laboratory_supply
IAO_0000115: definition: The most common material used for making gloves, is the latex, a form of rubber. Its primary purpose is protection of the hands while performing tasks involving chemicals.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000111: editor preferred term: glove

M4L:in_vitro_nucleic_acid_amplification
type: Class
IAO_0000119: definition source: http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-N/nucleic_acid_ampl_assay.html
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000111: editor preferred term: in vitro nucleic acid amplification
IAO_0000115: definition: An assay that uses purified enzymes to isolate and then replicate specific nucleic acids to levels where they can be detected. Examples are PCR, TAS, NASBA, etc.
subclass of: assay

assay
type: Class
IAO_0000119: Definition Source: OBI branch derived
IAO_0000117: Definition Editor: PlanAndPlannedProcess Branch
IAO_0000112: Example Of Usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
IAO_0000111: Editor Preferred Term: assay
subclass of: planned_process
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000118: alternative term: ~#en scientific observation ~#en measuring
IAO_0000115: Definition: A planned process with the objective to produce information about some evaluant

M4L:1.0mm_thick_comb_with_20_wells
type: Class
subclass of: M4L:comb

M4L:comb
type: Class
subclass of: M4L:horizontal_electrophoresis_instrument

GO:transferase_activity
type: Class
IAO_0000111: editor preferred term: transferase activity
IAO_0000412: imported from: Gene Ontology, Version 1.931
IAO_0000115: Definition: Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).
subclass of: catalytic_activity

catalytic_activity
type: Class
IAO_0000115: 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.
IAO_0000111: Editor Preferred Term: catalytic activity
subclass of: M4L:extension_activity
IAO_0000412: Imported From: oboContent:GO

SNOMED:scissors
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Peterson, C., M. Maraia, and C. Deschamp, Scissors. 2007, Fiskars Brands, Inc. (Madison, WI, US) United States. p. 7.
IAO_0000111: editor preferred term: scissors
IAO_0000115: definition: scissors, are a tool used for cutting.
subclass of: M4L:laboratory_supply

M4L:laboratory_supply
type: Class
subclass of: MaterialEntity
IAO_0000111: editor preferred term: laboratory supply
IAO_0000112: example of usage: lab coats, globes, beads, bags, batteries, PCR plates and tubes, centrifuge tubes, filter paper, magnetig stir bar, parafilm, micropipettes and tips, respirators, slides, spatulas, thermometer, weighing dish, wipes, etc.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: refers to a variety of supplies used for scientific experiments and other work in science, especially in chemistry and biology laboratories.
IAO_0000119: definition source: http://www.labdepotinc.com/c-70-laboratory-supplies.php

quality_of_a_single_physical_entity
type: Class
IAO_0000111: Editor Preferred Term: quality of a single physical entity
IAO_0000115: Definition: A physical object quality which inheres in a single-bearer.
IAO_0000412: Imported From: oboContent:PATO
subclass of: Quality

M4L:taq_DNA_polymerase
type: Class
IAO_0000111: editor preferred term: taq DNA polymerase
subclass of: M4L:thermostable_DNA_polymerase
IAO_0000115: definition: Taq DNA Polymerase is a thermostable DNA Polymerase isolated from an E. coli strain that carries the Taq DNA polymerase gene. Taq DNA Polymerase is the most common polymerase used for PCR* reactions.
IAO_0000118: alternative term: taq polymerase DNA Polymerase, Taq polymerase, taq polymerase, taq DNA polymerase, taq1 polymerase, thermus aquaticus taq1 Polymerase thermus aquaticus Polymerase aquaticus polymerase, thermus
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: GenScript. http://taqpolymerase.net/

M4L:thermostable_DNA_polymerase
type: Class
IAO_0000111: editor preferred term: thermostable DNA polymerase
IAO_0000115: definition: Thermostable DNA polymerases revolutionized and popularized PCR because of their ability to withstand the high denaturation temperatures. The use of thermostable DNA polymerases also allowed higher annealing temperatures, which improved the stringency of primer annealing.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Promega, Protocols & Applications Guide. http://www.promega.com/paguide/chap1.htm
subclass of: NCI:DNA-directed_DNA_polymerase

CHEBI:sulfoxide
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:organosulfur_compound
IAO_0000111: editor preferred term: sulfoxide
IAO_0000115: Definition: Compounds having the structure R2S=O (R =/= H).

CHEBI:organosulfur_compound
type: Class
IAO_0000115: Definition: An organosulfur compound is a compound containing at least one carbon-sulfur bond.
IAO_0000111: editor preferred term: organosulfur compound
subclass of: CHEBI:sulfur_molecular_entity
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

M4L:P-20_micropipette
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: P-20 model
IAO_0000115: definition: P-20 model, refer to the maximum volume in microliters. P20 is a micropipette designed for dispensing volumes between 2µl and 20µl.
IAO_0000111: editor preferred term: P-20_micropipette
subclass of: M4L:adjustable_micropipette
IAO_0000119: definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F123600

M4L:adjustable_micropipette
type: Class
subclass of: M4L:laboratory_supply
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Micropipette
IAO_0000111: editor preferred term: adjustable micropipette
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: micropipette
IAO_0000115: definition: A micropipette is one instrument used in science laboratories. Micropipettes are used to accurately measure and dispense small volumes of liquid. The capacity of a micropipette can range from less than 1µl to 1000µl (1ml).

M4L:tris-EDTA_buffer
type: Class
IAO_0000115: definition: TE buffer is a commonly used buffer solution in molecular biology, especially in procedures involving DNA or RNA. "TE" is derived from its components: Tris, a common pH buffer, and EDTA, a molecule chelating cations like Mg2+. The purpose of TE buffer is to protect DNA or RNA from degradation.
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: CHEBI:buffer
IAO_0000118: alternative term: TE buffer
IAO_0000119: definition source: http://en.wikipedia.org/wiki/TE_buffer
IAO_0000111: Editor preferred term: tris EDTA buffer

CHEBI:buffer
type: Class
subclass of: CHEBI:reagent
IAO_0000115: Definition: Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base.
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68

M4L:P-2 micropipette
type: Class
subclass of: M4L:adjustable_micropipette
IAO_0000119: definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F144801
IAO_0000118: alternative term: P-2 model
IAO_0000111: editor preferred term: P-2 micropipette
IAO_0000115: definition: P-2 model, refer to the maximum volume in microliters. P2 is a micropipette designed for dispensing volumes between 0.2µl and 2µl.
IAO_0000117: definition editor: Olga-Ximena Giraldo

GO:transferase_activity,_transferring_phosphorus-containing_groups
type: Class
IAO_0000115: Definition: Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
subclass of: GO:transferase_activity
IAO_0000111: editor preferred term: transferase activity, transferring phosphorus-containing groups
IAO_0000412: imported from: Gene Ontology, Version 1.931
comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.

CHEBI:formamide
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:monocarboxylic_acid_amide
IAO_0000111: editor preferred term: formamide
IAO_0000118: alternative term: Ameisensaeureamid Formamid formimidic acid carbamaldehyde Methanamid Methanamide CH3NO
IAO_0000115: Definition: A member of the formamides that has formula CH3NO.

CHEBI:monocarboxylic_acid_amide
type: Class
subclass of: CHEBI:carboxamide
IAO_0000111: editor preferred term: monocarboxylic acid amide
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

M4L:AMV_reverse_transcriptase
type: Class
IAO_0000115: definition: The AMV reverse transcriptase (AMV RT), is isolated from Avian Myeloblastosis Virus as the beta holoenzyme of molecular weight 157,000 daltons, using a modification of the method described by Houts et al. (1979). AMV RT is qualified for cDNA synthesis and also for dideoxy sequencing of DNA and RNA. Using AMV Reverse Transcriptase, the reverse transcription step can be carried out at elevated temperatures up to 70 °C. High temperature increases the specificity of priming and helps to increase the efficiency by reducing RNA secondary structures.
subclass of: reverse_transcriptase
IAO_0000111: editor preferred term: AMV reverse transcriptase
IAO_0000119: definition source: Finnzymes, Tools for Molecular Biology. http://www.finnzymes.fi/rt-pcr/amv_reverse_transcriptase.html
IAO_0000118: alternative term: AMV RT
IAO_0000117: definition editor: Olga-Ximena Giraldo

reverse_transcriptase
type: Class
IAO_0000119: Definition Source: group:OBI
IAO_0000111: Editor Preferred Term: reverse transcriptase
IAO_0000117: Definition Editor: person:Melanie Courtot
IAO_0000115: Definition: enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity).
IAO_0000114: Has Curation Status: obo:IAO_0000125
subclass of: MSH:RNA-directed_DNA_polymerase

MSH:endoribonuclease
type: Class
IAO_0000115: Definition: A family of enzymes that catalyze the endonucleolytic cleavage of RNA.
IAO_0000111: editor preferred term: endoribonuclease
subclass of: M4L:ribonuclease
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17

M4L:ribonuclease
type: Class
subclass of: M4L:nuclease
IAO_0000115: definition: ribonuclease (RNase), is an enzyme which degrades RNA by cleaving the phosphodiester bond. It is ubiquitous in living organisms and is exceptionally stable. The prevention of RNase activity is the primary problem in handling RNA.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Eurofins MWG Operon's Glossary of Biotechnical Terms. http://www.operon.com/products/custom_oligos/glossary.aspx
IAO_0000118: alternative term: RNase
IAO_0000111: preferred term: ribonuclease

CHEBI:propan-2-ol
type: Class
subclass of: CHEBI:secondary_alcohol
IAO_0000115: Definitions: A secondary alcohol that has formula C3H8O.
IAO_0000118: alternative term: 2-hydroxypropane Isopropylalkohol sec-propanol IPA 1-methylethanol i-Propylalkohol 1-methylethyl alcohol i-propanol isopropyl alcohol 2-Propanol Isopropanol C3H8O CC(C)O
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68

CHEBI:secondary_alcohol
type: Class
IAO_0000118: alternative term: R-CHOH-R' CH2OR2
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
IAO_0000115: Definitions: A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it.
subclass of: CHEBI:alcohol

CHEBI:triol
type: Class
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
IAO_0000115: Definitions: A chemical compound containing three hydroxyl groups.
subclass of: CHEBI:polyol

CHEBI:polyol
type: Class
subclass of: CHEBI:alcohol
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
IAO_0000115: Definitions: A compound that contains three or more hydroxyl groups.

BIRNLex:polyacrylamide_gel_electrophoresis_instrument
type: Class
IAO_0000412: imported from: BIRNLex, Version 1.3.1
IAO_0000111: editor preferred term: polyacrylamide gel electrophoresis instrument
subclass of: BIRNLex:gel_electrophoresis_instrument

BIRNLex:gel_electrophoresis_instrument
type: Class
subclass of: BIRNLex:electrophoresis_instrument
IAO_0000111: editor preferred term: gel electrophoresis instrument
IAO_0000115: definition: gel electrophoresis instrument is used to separate macromolecules, either nucleic acids or proteins, on the basis of size, electric charge, and other physical properties. Gel electrophoresis instrument allows researchers to maintain a uniform electric field across a gel such as agarose or acrylamide gel.
IAO_0000119: definition source: Globalspec, the engineering search engine. http://www.globalspec.com/learnmore/labware_scientific_instruments/separation_techniques/gel_electrophoresis_equipment
IAO_0000412: imported from: BIRNLex, Version 1.3.1
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: gel_electrophoresis_equipment

M4L:masking_tape
type: Class
subclass of: M4L:laboratory_supply
IAO_0000119: definition source: http://www.tesa.co.uk/AdhesiveTapeRange/MaskingTape/general_purpose
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: General purpose masking tapes comprise of a paper backing or carrier and a natural rubber adhesive. The adhesive have a limited temperature resistance and should not be left longer than 24 hours or 3 days before removal otherwise they may leave adhesive residues.
IAO_0000111: editor preferred term: masking tape

M4L:TBE_buffer
type: Class
subclass of: M4L:electrophoresis_buffer
IAO_0000115: definition: TBE buffer is commonly used in all DNA electrophoresis applications (both for acrylamide and for agarose gels), including sequencing. In general, TBE buffer offers better resolution of 0.1 to 3 kb fragments; TBE is better suited for high-voltage (>150V) electrophoresis because of its higher buffering capacity and lower conductivity than TAE.
IAO_0000111: editor preferred term: TBE buffer
IAO_0000119: definition source: http://www.interchim.com/interchim/bio/produits_uptima/product_line/electrobuffer_tae_tbe.htm#tbe_buffer
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: Tris-Borate-EDTA buffer

M4L:electrophoresis_buffer
type: Class
IAO_0000111: editor preferred term: electrophoresis buffer
subclass of: CHEBI:buffer
IAO_0000115: definition: the buffer system in electrophoresis controls the pH of the gel, preventing damage to sample molecules and, in certain cases, controlling the ionization state of the molecules. A second, though no less significant function derives from the fact that the vast majority of current flowing through the electrophoresis gel is carried by the buffer ions.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: National diagnostics. http://nationaldiagnostics.com/article_info.php/articles_id/8

material_component_separation
type: Class
subclass of: material_processing
IAO_0000119: Definition Source: IEDB
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000112: Example Of Usage: Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
IAO_0000117: Definition Editor: Bjoern Peters
IAO_0000115: Definition: a material processing in which components of an input material become segregated in space
IAO_0000111: Editor Preferred Term: material component separation

material_processing
type: Class
IAO_0000112: Example Of Usage: A cell lysis, production of a cloning vector, creating a buffer.
IAO_0000111: Editor Preferred Term: material processing
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000118: alternative term: ~#en material transformation
IAO_0000115: Definition: A planned process which results in physical changes in a specified input material
IAO_0000117: Definition Editor: PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Bjoern Peters PERSON: Philippe Rocca Serra
subclass of: planned_process
IAO_0000119: Definition Source: OBI branch derived

M4L:0.1uM_reverse_primer
type: Class
IAO_0000115: definition: The recommended primer concentration for PCR is between 0.1μM and 1μM of each primer. The use of higher concentrations of primers can have the following effects: 1. If the primers are capable of forming dimers, raising their concentration only results in the creation of primer-dimers and does not improve the amplification of the desired PCR product. Primer-derived oligomers will possibly contaminate the reaction. 2. If the primers do not form primer-dimers, it is likely that raising the primer concentration will lead to non-specific primer binding and the creation of spurious, undesirable PCR products. Raising the primer concentration does not therefore cause an increase in the effective concentration of the primers. Low primer concentration generally ensures cleaner product and lower background.
IAO_0000111: editor preferred term: 0.1uM reverse primer
subclass of: CHEBI:reagent
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: 0.1uM_downstream_primer 0.1uM_antisense_primer
IAO_0000119: definition source: PCR Troubleshooting: Primer Concentration. http://www.caister.com/molecular-biology-blog/2008/10/pcr-troubleshooting-primer.html

CHEBI:reagent
type: Class
subclass of: processed_material
IAO_0000115: Definition: A test substance that is added to a system in order to bring about a reaction or to see whether a reaction occurs.
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
IAO_0000118: alternative term: reactif reactivo

M4L:distilled_water
type: Class
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Distilled_water
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000111: editor preferred term: distilled water
IAO_0000115: definition: Distilled water is water that has many of its impurities removed through distillation. Distillation involves boiling the water and then condensing the steam into a clean container.
subclass of: CHEBI:water

CHEBI:water
type: Class
IAO_0000118: alternative term: aqua hydrogen hydroxide Wasser water [OH2] oxidane dihydrogen oxide dihydridooxygen HOH eau agua acqua H2O BOUND WATER [H]O[H]
IAO_0000115: Definition: An inorganic hydroxy compound that has formula H2O.
IAO_0000111: editor preferred term: water
subclass of: CHEBI:inorganic_hydroxy_compound

SEP:scanner
type: Class
IAO_0000115: Definition: A scanner is an image acquistion device that generates a digital representation of an image for data input to a computer.
IAO_0000111: editor preferred term: scanner
IAO_0000412: imported from: Sample processing and separation techniques, Version 1.070708
subclass of: SEP:image_acquisition_device

SEP:image_acquisition_device
type: Class
IAO_0000412: imported from: Sample processing and separation techniques, Version 1.070708
IAO_0000111: editor preferred term: image acquisition device
subclass of: SNOMED:laboratory_equipment
IAO_0000115: Definition: An image acquisition device is a device which captures a digitiesed image of an object.

SNOMED:nitrogen
type: Class
IAO_0000111: editor preferred term: nitrogen
subclass of: CHEBI:elemental_nitrogen
IAO_0000115: definition: nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: N - Nitrogen N2 - Nitrogen Nitrogen (substance) Nitrogen, NOS
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Nitrogen

CHEBI:elemental_nitrogen
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:nitrogen_molecular_entity
IAO_0000111: editor preferred term: elemental_nitrogen

M4L:0.1uM_forward_primer
type: Class
IAO_0000111: editor preferred term: 0.1uM forward primer
IAO_0000119: definition source: PCR Troubleshooting: Primer Concentration. http://www.caister.com/molecular-biology-blog/2008/10/pcr-troubleshooting-primer.html
IAO_0000115: definition: The recommended primer concentration for PCR is between 0.1μM and 1μM of each primer. The use of higher concentrations of primers can have the following effects: 1. If the primers are capable of forming dimers, raising their concentration only results in the creation of primer-dimers and does not improve the amplification of the desired PCR product. Primer-derived oligomers will possibly contaminate the reaction. 2. If the primers do not form primer-dimers, it is likely that raising the primer concentration will lead to non-specific primer binding and the creation of spurious, undesirable PCR products. Raising the primer concentration does not therefore cause an increase in the effective concentration of the primers. Low primer concentration generally ensures cleaner product and lower background.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: 0.1uM upstream primer 0.1uM sense primer
subclass of: CHEBI:reagent

water bath
type: Class
IAO_0000119: Definition Source: PERSON: Daniel Schober
IAO_0000117: Definition Editor: Daniel Schober
IAO_0000115: Definition: A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure).
IAO_0000114: Has Curation Status: obo:IAO_0000120
IAO_0000112: Example Of Usage: A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
IAO_0000111: Editor Preferred Term: water bath
subclass of: temperature control bath

temperature control bath
type: Class
subclass of: SNOMED:laboratory_equipment
IAO_0000111: Editor Preferred Term: temperature control bath
IAO_0000112: Example Of Usage: VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C.
IAO_0000114: Has Curation Status: obo:IAO_0000120
IAO_0000115: Definition: A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well.
IAO_0000117: Definition Editor: Alan Ruttenburg Frank Gibson Daniel Schober
IAO_0000119: Definition Source: OBI Instrument branch

GO:DNA_polymerase_activity
type: Class
subclass of: GO:nucleotidyltransferase_activity
IAO_0000118: alternative term: deoxynucleate polymerase activity deoxyribonucleate nucleotidyltransferase activity deoxyribonucleic acid polymerase activity deoxyribonucleic polymerase activity DNA nucleotidyltransferase activity
IAO_0000115: Definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and primer.
IAO_0000111: editor preferred term: DNA polymerase activity
IAO_0000412: imported from: Gene Ontology, Version 1.931

M4L:betaine_role
type: Class
subclass of: M4L:PCR_additive_role
IAO_0000115: definition: betaine is an agent that has been used successfully for increasing yield and specificity of PCR products. Betaine, an isostabilizing agent, equalizes the contribution of GC- and AT- base pairing to the stability of the DNA duplex.
IAO_0000111: editor preferred term: betaine role
IAO_0000119: definition source: Frackman, S., et al., Betaine and DMSO: Enhancing Agents for PCR. 1998, Promega Corporation. p. 4.
IAO_0000117: definition editor: Olga-XImena Giraldo

M4L:PCR_additive_role
type: Class
IAO_0000118: alternative term: PCR enhance role
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: *http://www.invitrogen.com/Content/benchtopics/Benchtopics_Amplification_Volume1_Number_3.pdf *http://www.pcrlinks.com/glossary/P.htm
subclass of: Role
IAO_0000111: editor preferred term: PCR additive role
IAO_0000115: definition: PCR additives, including formamide, DMSO, glycerol, betaine, and PCRx Enhancer Solution can enhance amplification. Their proposed mechanism is to lower the melting temperature, thereby aiding primer annealing and helping the DNA polymerase extend through regions of secondary structure.

CHEBI:ammonium_compound
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:nitrogen_molecular_entity
IAO_0000118: alternative term: azanium compound
IAO_0000115: Definition: Compounds (NH4(+))Y(-) and derivatives, in which one or more of the hydrogens bonded to nitrogen have been replaced with univalent groups.
IAO_0000111: editor preferred term: ammonium compound

CHEBI:nitrogen_molecular_entity
type: Class
IAO_0000111: editor preferred term: nitrogen molecular entity
IAO_0000118: alternative term: nitrogen compound
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: PDPP:chemical_entity

incubator
type: Class
IAO_0000114: Has Curation Status: obo:IAO_0000124
IAO_0000112: Example Of Usage: Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells.
IAO_0000111: Editor Preferred Term: incubator
IAO_0000119: Definition Source: http://www.medterms.com/script/main/art.asp?articlekey=18426
subclass of: SNOMED:laboratory_equipment
IAO_0000117: Definition Editor: Frank Gibson
IAO_0000115: Definition: An incubator is an instrument in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled

SNOMED:laboratory_equipment
type: Class
IAO_0000111: editor preferred term: laboratory equipment
IAO_0000118: alternative term: laboratory instrument
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Laboratory_equipment
IAO_0000115: definition: laboratory equipment refers to machine, apparatus or device used by scientists working in a laboratory. Laboratory equipment is generally used to either perform an experiment or to take measurements and gather data.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000112: example of usage: laboratory equipment include: DNA sequencer, microscopes, electrophoresis instrument, incubator, temperature control bath, microarray instrument, freezer, refrigerator, thermocycler, etc.
subclass of: M4L:laboratory_supply

M4L:TAE_buffer
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: Tris-Acetate-EDTA buffer
IAO_0000119: definition source: http://www.interchim.com/interchim/bio/produits_uptima/product_line/electrobuffer_tae_tbe.htm#tae_buffer
IAO_0000115: definition: TAE buffer is commonly used in DNA electrophoresis on agarose gel.
subclass of: M4L:electrophoresis_buffer
IAO_0000111: editor preferred term: TAE buffer
IAO_0000112: example of usage: Better resolution of fragments greater than 4 kb.

thermal_cycler
type: Class
IAO_0000117: Definition Editor: Melanie Courtot Trish Whetzel
IAO_0000119: Definition Source: MO
subclass of: SNOMED:laboratory_equipment
IAO_0000118: alternative term: ~#en DNA_amplifier ~#en PCR_machine ~#en thermocycler ~#en Polymerase_Chain_Reaction_ machine
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000112: Example Of Usage: Piko(tm) 96-well Thermal Cycler
IAO_0000115: Definition: An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
IAO_0000111: Editor Preferred Term: thermal cycler

M4L:transcription-based_amplification_system
type: Class
IAO_0000115: definition: In a transcription-based amplification system (TAS) each cycle of the TAS is composed of two steps. The first is a cDNA synthesis step that produces one copy of a double-stranded DNA template for each copy of RNA or DNA target nucleic acid. During the course of this cDNA synthesis step, a sequence recognized by a DNA-dependent RNA polymerase is inserted into the cDNA copy of the target sequence to be amplified. The second step is the amplification of the target sequence by the transcription of the cDNA template into multiple copies of RNA.
IAO_0000111: editor preferred term: transcription-based amplification system
subclass of: enzymatic_amplification
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: TAS
IAO_0000119: definition source: Kwoh, D.Y., et al., Transcription-Based Amplification System and Detection of Amplified Human Immunodeficiency Virus Type-1 with a Bead-Based Sandwich Hybridization Format. Proceedings of the National Academy of Sciences of the United States of America, 1989. 86(4): p. 1173-1177.

enzymatic_amplification
type: Class
IAO_0000119: Definition Source: OBI branch derived
IAO_0000117: Definition Editor: PERSON:Kevin Clancy
IAO_0000115: Definition: the use of enzymes to increase the number of molecules of a biomaterial
subclass of: material_processing
IAO_0000114: Has Curation Status: obo:IAO_0000125
IAO_0000112: Example Of Usage: the use of a polymerase chain reaction to amplify a fragment of DNA
IAO_0000111: Editor Preferred Term: enzymatic amplification

M4L:nuclease
type: Class
IAO_0000119: definition source: http://www.biochem.northwestern.edu/holmgren/Glossary/Dedinitions/Def-N/nuclease.html
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: one of the several classes of enzymes that degrade nucleic acid. An enzyme that can degrade DNA or RNA by breaking phosphodiester bonds.
IAO_0000111: editor preferred term: nuclease
subclass of: GRO:enzyme

M4L:DNA_extraction_buffer
type: Class
subclass of: CHEBI:buffer
IAO_0000111: editor preferred term: DNA extraction buffer
IAO_0000118: alternative term: DNA isolation buffer
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: an extraction buffer with correct pH, gets rid of the cell components, but retains the organelles.
IAO_0000119: definition source: http://wiki.answers.com/Q/What_is_an_extraction_buffer

CHEBI:nucleotide
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000115: Definition: A nucleotide is a nucleoside phosphate. It is composed of a nucleobase, a sugar moiety and one to three phosphate groups.
subclass of: CHEBI:nucleoside_phosphate
IAO_0000111: editor preferred term: nucleotide

CHEBI:nucleoside_phosphate
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:organic_phosphate
IAO_0000111: editor preferred term: nucleoside_phosphate

CHEBI:boron_molecular_entity
type: Class
IAO_0000118: alternative term: boron compound
IAO_0000111: editor preferred term: boron molecular entity
subclass of: PDPP:chemical_entity
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

PDPP:chemical_entity
type: Class
comment: A material continuant that is described chiefly with respect to its chemical composition.
subclass of: MaterialEntity

BioTop:enzyme_role
type: Class
subclass of: Role
IAO_0000412: Imported from: BioTop, Version dev
comment: The role a peptide plays in accelerating a biochemical reaction

M4L:degenerate_primer_role
type: Class
IAO_0000111: editor preferred term: degenerate primer role
subclass of: primer_role
IAO_0000115: definition: Degenerate primers are useful for pulling out one part of a gene sequence when you only know the gene sequence in related organisms. The more distant those related organsims, the more difficult it can be to design primers.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: *http://hcgs.unh.edu/protocol/basic/pcrdegenpri.html *http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29#PCR_primer_design

primer_role
type: Class
subclass of: Role
IAO_0000114: Has Curation Status: obo:IAO_0000124
IAO_0000412: imported from: Ontology for Biomedical Investigations, Version 2009-11-06 Philly (aka version 1.0) Release Candidate
IAO_0000111: Editor Preferred Term: primer role
IAO_0000119: Definition Source: *(cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer *http://es.wikipedia.org/wiki/Cebador
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: Definition: primer role is inheres to nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation.

MSH:ribonuclease_H
type: Class
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000111: editor preferred term: ribonuclease_H
IAO_0000115: Definition: A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.
IAO_0000118: alternative term: Endoribonuclease H RNAase H RNase H Ribonuclease H, Calf Thymus
subclass of: MSH:endoribonuclease

graph
type: Class
IAO_0000117: Definition Editor: person:Allyson Lister person:Alan Ruttenberg PERSON: Lawrence Hunter
IAO_0000119: Definition Source: group:OBI OBI_0000240
IAO_0000111: Editor Preferred Term: graph
IAO_0000115: Definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
IAO_0000114: Has Curation Status: obo:IAO_0000125
subclass of: diagram

diagram
type: Class
IAO_0000111: Editor Preferred Term: diagram
IAO_0000112: Example Of Usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
IAO_0000117: Definition Editor: PERSON: Lawrence Hunter
IAO_0000114: Has Curation Status: obo:IAO_0000120
IAO_0000115: Definition: A figure that expresses one or more propositions
subclass of: figure

CHEBI:agarose
type: Class
IAO_0000118: alternative term: (C12H18O9)n (1->4)-3,6-anhydro-alpha-L-galactopyranosyl-(1->3)-beta-D-galactopyranan
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
IAO_0000115: definition: A polysaccharide that has formula (C12H18O9)n.
subclass of: CHEBI:polysaccharide

CHEBI:polysaccharide
type: Class
subclass of: CHEBI:biomacromolecule
IAO_0000118: alternative term: Glycane Glycan polisacarido Glykane Glykan
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
IAO_0000115: definition: A macromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.

PCR_product
type: Class
IAO_0000112: Example Of Usage: PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
IAO_0000111: Editor Preferred Term: PCR product
subclass of: amplified_DNA
IAO_0000116: Editor Note: We are using PCR and not the written out words, as this is the most common used.
IAO_0000117: Definition Editor: GROUP: OBI BIomaterial Branch
IAO_0000115: Definition: is double stranded DNA that is the specified output of a polymerase chain reaction
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000119: Definition Source: GROUP: OBI BIomaterial Branch

M4L:PCR_buffer
type: Class
subclass of: CHEBI:buffer
IAO_0000115: definition: PCR buffer is necessary to create optimal conditions for activity of Taq DNA polymerase. Buffers often contain Tris-Hcl, KCl, and sometimes MgCl2. PCR buffers are often available in 10X concentration and are sometimes Taq formulation-specific.
IAO_0000111: editor preferred term: PCR buffer
IAO_0000119: definition source: *http://www.eeescience.utoledo.edu/Faculty/Sigler/RESEARCH/Protocols/PCR/PCR.pdf * http://www.pcrlinks.com/glossary/B.htm
IAO_0000117: definition editor: Olga-Ximena Giraldo

SNOMED:refrigerator
type: Class
IAO_0000115: definition: A refrigerator is a cooling appliance comprising a thermally insulated compartment and a heat pump-chemical or mechanical means-to transfer heat from it to the external enviroment, cooling the contents to a temperature below ambient.
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Refrigerator
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: Refrigerator, device Refrigerator, device (physical object) Icebox fridge
IAO_0000111: editor preferred term: refrigerator
subclass of: SNOMED:laboratory_equipment

CHEBI:sulfur_molecular_entity
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: PDPP:chemical_entity
IAO_0000111: editor preferred term: sulfur molecular entity

separation_function
type: Class
IAO_0000117: Definition Editor: Frank Gibson Bill Bug Daniel Schober Melanie Courtot
disjoint with: molecular_function
disjoint with: mechanical_function
subclass of: Function
disjoint with: freeze_function
disjoint with: cool_function
disjoint with: heat_function
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000115: Definition: A separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
IAO_0000111: Editor Preferred Term: separation function
disjoint with: contain_function

molecular_function
type: Class
disjoint with: mechanical_function
disjoint with: cool_function
IAO_0000115: 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.
disjoint with: separation_function
disjoint with: heat_function
IAO_0000412: Imported From: oboContent:GO
disjoint with: contain_function
disjoint with: freeze_function
subclass of: Function
IAO_0000111: Editor Preferred Term: molecular_function

mechanical_function
type: Class
IAO_0000119: Definition Source: http://en.wikipedia.org/wiki/Mechanical_work
disjoint with: molecular_function
disjoint with: heat_function
IAO_0000115: Definition: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force.
IAO_0000117: Definition Editor: Bill Bug Frank Gibson Daniel Schober Melanie Courtot
IAO_0000114: Has Curation Status: obo:IAO_0000122
disjoint with: contain_function
subclass of: Function
disjoint with: cool_function
disjoint with: freeze_function
disjoint with: separation_function
IAO_0000111: Editor Preferred Term: mechanical function

freeze_function
type: Class
disjoint with: heat_function
IAO_0000111: Editor Preferred Term: freeze function
disjoint with: molecular_function
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000117: Definition Editor: Bill Bug Frank Gibson Daniel Schober Melanie Courtot
disjoint with: mechanical_function
disjoint with: cool_function
disjoint with: contain_function
disjoint with: separation_function
IAO_0000115: Definition: A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
subclass of: Function

cool_function
type: Class
IAO_0000117: Definition Editor: Frank Gibson Daniel Schober Melanie Courtot
disjoint with: contain_function
disjoint with: mechanical_function
IAO_0000114: Has Curation Status: obo:IAO_0000122
subclass of: Function
disjoint with: freeze_function
disjoint with: separation_function
disjoint with: molecular_function
IAO_0000111: Editor Preferred Term: cool function
IAO_0000115: Definition: A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
disjoint with: heat_function

heat_function
type: Class
disjoint with: molecular_function
disjoint with: mechanical_function
IAO_0000117: Definition Editor: Frank Gibson Bill Bug Daniel Schober Melanie Courtot
IAO_0000115: Definition: A heat function is a function that increases the internal kinetic energy of a material
IAO_0000114: Has Curation Status: ready for release
IAO_0000111: Editor Preferred Term: heat function
disjoint with: freeze_function
disjoint with: cool_function
disjoint with: contain_function
disjoint with: separation_function
subclass of: Function

contain_function
type: Class
IAO_0000115: Definition: A contain function is a function to bound or constrain some quantity of material in some space
IAO_0000111: Editor Preferred Term: contain function
disjoint with: heat_function
disjoint with: separation_function
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000117: Definition Editor: Bill Bug Frank Gibson Daniel Schober Melanie Courtot
disjoint with: cool_function
IAO_0000112: Example Of Usage: A syringe, a beaker
subclass of: Function
disjoint with: mechanical_function
disjoint with: freeze_function
disjoint with: molecular_function

M4L:microcentrifuge
type: Class
IAO_0000115: definition: microcentrifuge is a centrifuge used in laboratories to separate materials from small samples (specially of biological material).
IAO_0000111: editor preferred term: microcentrifuge
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: http://en.wiktionary.org/wiki/microcentrifuge
subclass of: centrifuge

centrifuge
type: Class
subclass of: SNOMED:laboratory_equipment
IAO_0000119: Definition Source: http://en.wikipedia.org/wiki/Centrifuge
IAO_0000112: Example Of Usage: Eppendorf Multipurpose Centrifuge
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000115: Definition: A centrifuge is an instrument, generally driven by a motor, that puts an object in rotation around a fixed axis, applying force perpendicular to the axis. The centrifuge works using the sedimentation principle, where the centripetal acceleration is used to separate substances of greater and lesser density.
IAO_0000117: Definition Editor: Melanie Courtot Trish Whetzel
IAO_0000111: editor preferred term: centrifuge

M4L:primer_list
type: Class
IAO_0000115: Definition: A primer list is a report of the names or identifiers of primers used in a studio or have been put together for the purpose of an analysis.
IAO_0000117: Definition editor: Olga-Ximena Giraldo
IAO_0000111: primer list
IAO_0000112: Example: primer list may be collected from the literature, data-bases or may be designed to be used in a particular studio (e.g, marker Assisted Selection).
subclass of: data_set

data_set
type: Class
subclass of: IAO_0000027

GO:RNA-directed_DNA_polymerase_activity
type: Class
IAO_0000115: Definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
IAO_0000118: alternative term: revertase activity RNA revertase activity RNA-dependent deoxyribonucleate nucleotidyltransferase activity RNA-dependent DNA polymerase activity RNA-directed DNA polymerase, group II intron encoded RNA-directed DNA polymerase, transposon encoded RNA-instructed DNA polymerase activity RT deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity DNA nucleotidyltransferase (RNA-directed) activity reverse transcriptase activity
subclass of: GO:DNA_polymerase_activity
IAO_0000111: editor preferred term: RNA-directed DNA polymerase activity
IAO_0000112: example of usage: enzyme reverse transcriptase is a RNA-directed DNA_polymerase activity.
IAO_0000412: imported from: Gene Ontology, Version 1.931

MSH:exodeoxyribonuclease
type: Class
IAO_0000115: Definition: A family of enzymes that catalyze the exonucleolytic cleavage of DNA.
IAO_0000111: editor preferred term: exodeoxyribonuclease
IAO_0000118: alternative term: DNA Exonuclease Exonuclease, DNA
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
subclass of: MSH:deoxyribonuclease

MSH:deoxyribonuclease
type: Class
IAO_0000111: editor preferred term: deoxyribonuclease
subclass of: M4L:nuclease
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition(1): a deoxyribonuclease (DNase, for short) is any enzyme that catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone. Deoxyribonucleases are thus one type of nuclease. A wide variety of deoxyribonucleases are known, which differ in their substrate specificities, chemical mechanisms, and biological functions. Definition(2): Enzymes which catalyze the hydrolases of ester bonds within DNA.
IAO_0000119: definition source: *http://en.wikipedia.org/wiki/Deoxyribonuclease *Medical Subject Headings, Version 2010_2009_08_17
IAO_0000118: alternative term: DNA Nucleases DNAase DNase DNase, Acid DNase, Alkaline Nucleases, DNA Acid DNase Alkaline DNase

M4L:extension_activity
type: Class
IAO_0000115: definition: phase of PCR cycle following annealing of primer during which the Taq polymerase synthesizes a strand of DNA. The optimum temperature depends on the enzyme used but is usually between 68 - 72 degree C.
IAO_0000119: definition source: http://www.wellscenter.iupui.edu/MMIA/htm/pcr.htm#4
IAO_0000118: alternative term: elongation activity
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: molecular_function
IAO_0000111: editor preferred term: extension activity

CHEBI:nucleoside_triphosphate
type: Class
IAO_0000111: editor preferred term: nucleoside triphosphate
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000118: alternative term: NTP C5H12O13P3R
subclass of: CHEBI:nucleoside_phosphate

CHEBI:biomacromolecule
type: Class
IAO_0000111: editor preferred term: biomacromolecule
IAO_0000119: definition source: Biology Online, Answers to all your Biology Questions. http://www.biology-online.org/dictionary/Macromolecule.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: biological macromolecule
IAO_0000115: definition: In biology, a macromolecule is a term used to a large complex molecule, such as nucleic acids, proteins, carbohydrates and lipids, which are made up of small monomers linked together and with relatively large molecular weight.
subclass of: PDPP:chemical_entity

primary_structure_of_DNA_macromolecule
type: Class
IAO_0000115: Definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
IAO_0000117: Definition Editor: BP et al
IAO_0000116: Editor Note: placeholder for SO
subclass of: primary_structure_of_sequence_macromolecule
IAO_0000111: Editor Preferred Term: primary structure of DNA macromolecule

primary_structure_of_sequence_macromolecule
type: Class
IAO_0000111: Editor Preferred Term: primary structure of sequence macromolecule
subclass of: quality_of_a_single_physical_entity
IAO_0000116: Editor Note: These are all placeholders and should be replaced by SO terms
IAO_0000115: Definition: A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds
IAO_0000117: Definition Editor: Person:Bjoern Peters

M4L:elisa_plate
type: Class
IAO_0000115: definition: This is an example of the type of plate used in ELISA assays. It uses 48 or 96 well microtiter plate format, and is made of inexpensive transparent plastic material. These types of plates are sometimes used in ELISPOT assays as well. They have the advantage of being much cheaper than other plates which are commonly used in ELISPOT assays.
subclass of: M4L:laboratory_supply
IAO_0000112: example of usage: This type of plate is used in Enzyme-linked immunosorbent assay (ELISA), also known as an enzyme immunoassay (EIA), is a biochemical technique used mainly in immunology to detect the presence of an antibody or an antigen in a sample. The ELISA has been used as a diagnostic tool in medicine and plant pathology, as well as a quality control check in various industries.
IAO_0000111: editor preferred term: elisa plate
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: http://www.membrane-solutions.com/elisa_plate_products.htm

M4L:P-200_micropipette
type: Class
IAO_0000111: editor preferred term: P-200 micropipette
IAO_0000118: alternative term: P-200 model
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: P-200 model, refer to the maximum volume in microliters. P200 is a micropipette designed for dispensing volumes between 50µl and 200µl.
subclass of: M4L:adjustable_micropipette
IAO_0000119: definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F123601

M4L:secondary_structure_of_sequence_macromolecule
type: Class
subclass of: quality_of_a_single_physical_entity
IAO_0000117: Definition editor: Olga-Ximena Giraldo
IAO_0000115: Definition: the conformational arrangement (α-helix, β-pleated sheet, etc.) of the backbone segments of a macromolecule such as nucleic acids, a polypeptide chain of a protein without regard to the conformation of the side chains or the relationship to other segments.
IAO_0000119: definition source: PAC, 1996, 68, 2193 (Basic terminology of stereochemistry (IUPAC Recomendations 1996)) on page 2218.
IAO_0000111: secondary structure of sequence macromolecule

MSH:xylene_cyanol
type: Class
subclass of: PDPP:chemical_entity
IAO_0000111: editor preferred term: xylene cyanol
IAO_0000115: definition: Xylene cyanol can be used as a colour marker to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: Acid Blue 147 xylene cyanole xylene cyanol FF xylene cyanole FF
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Xylene_cyanol
IAO_0000412: term imported from: Medical Subject Headings, Version 2010_2009_08_17

CHEBI:phenol
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000115: Definition: Compounds having one or more hydroxy groups attached to a benzene or other arene ring.
IAO_0000118: alternative term: arenols aryl alcohol
subclass of: CHEBI:organic_hydroxy_compound
IAO_0000111: editor preferred term: phenol

M4L:plant_structure_harvesting
type: Class
IAO_0000111: editor preferred term: plant structure harvesting
subclass of: material_component_separation
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: the process of removing a organ or anatomical part from a plant.
IAO_0000119: definition source: IEDB

PO:plant_structure
type: Class
comment: Accession: PO:0009011
subclass of: anatomical_entity
IAO_0000119: source: POC:curators
IAO_0000115: Definition: Any morphological or anatomical feature of a plant.
IAO_0000412: imported from: plant structure ontology

anatomical_entity
type: Class
subclass of: MaterialEntity
IAO_0000115: Definition: An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'
IAO_0000111: Editor Preferred Term: anatomical entity
IAO_0000117: Definition Editor: Bjoern Peters Philippe Rocca-Serra Tina Boussard
IAO_0000114: Has Curation Status: obo:IAO_0000121
IAO_0000112: Example Of Usage: Tissue, organ, system, sperm, blood or body location (arm).
IAO_0000116: Editor Note: 13-02-2009: Biomaterial branch: change of label and definition following discussions at the OBI winter meeting 2009. It was felt that 'macroscopic part of multicellular organism' introduce an impractical delineation. IMPORTANT NOTE: OBI 'anatomical entity' would essentially correspond to FMA 'material anatomical entity' rather than FMA 'physical anatomical entity'. OBI does not include 'immaterial anatomical entity' as it would clash with the parent class 'material entity' DOCUMENTATION NOTE: OBI anatomical entity granularity level excludes cell and biological molecules. 10/20/09: This class and all subclasses are currently problematic. They should all be imported from other OBO foundry ontologies. (FMA / CARO / UBERON). Currently two problems exist: There is no cross species anatomy that covers all the entities we need. Secondly: there is not good boundary between anatomical entities and smaller parts in FMA. Currently we will use anatomical entities as if they are valid across species. not super happy about liquids (blood, sperm), as they seem to be 'granular' somewhat, and not form a structure. Biom call - January 2009 - Issues: parasites are not macroscopic part or organism. fetus is_a macroscopic part (but this is up for discussion)
IAO_0000119: Definition Source: MO

MSH:deoxyribonuclease,_type_II_site-specific
type: Class
subclass of: MSH:DNA_restriction_enzyme
IAO_0000115: Definition: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers.
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000111: editor preferred term: deoxyribonuclease, type II site-specific
IAO_0000118: alternative term: Deoxyribonucleases, Type II, Site Specific DNA Restriction Enzymes, Type II DNase, Site Specific, Type II DNase, Site-Specific, Type II Restriction Endonucleases, Type II Site-Specific DNase, Type II Type II Restriction Enzymes Type II Site Specific Deoxyribonucleases Type II Site Specific DNase Type II Site-Specific Deoxyribonucleases Type II Site-Specific DNase DNASE SS II Site Specific DNase, Type II Deoxyribonucleases, Type II Site Specific

MSH:DNA_restriction_enzyme
type: Class
IAO_0000115: Definition: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another.
IAO_0000118: alternative term: DNA Restriction Enzyme Endonuclease, Restriction Enzymes, DNA Restriction Restriction Endonuclease Restriction Enzyme, DNA
IAO_0000111: editor preferred term: DNA restriction enzyme
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
subclass of: MSH:endodeoxyribonuclease

M4L:horizontal_electrophoresis_instrument
type: Class
subclass of: BIRNLex:agarose_gel_electrophoresis_instrument

BIRNLex:agarose_gel_electrophoresis_instrument
type: Class
IAO_0000111: editor preferred term: agarose gel electrophoresis instrument
subclass of: BIRNLex:gel_electrophoresis_instrument
IAO_0000115: definition: agarose gel electrophoresis instruments are typically used for separating larger nucleic acids or protein samples. These apparatuses come in horizontal or vertical forms.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Globalspec, the engineering search engine. http://www.globalspec.com/learnmore/labware_scientific_instruments/separation_techniques/gel_electrophoresis_equipment
IAO_0000412: imported from: BIRNLex, Version 1.3.1

CHEBI:dTTP
type: Class
IAO_0000118: alternative term: deoxy-TTP pppdT thymidine 5'-triphosphate thymidine 5'-(tetrahydrogen triphosphate) TTP deoxythymidine triphosphate deoxythymidine 5'-triphosphate C10H17N2O14P3 2'-deoxythymidine triphosphate dThd5'PPP 5'-TTP
subclass of: CHEBI:pyrimidine_2'-deoxyribonucleoside_5'-triphosphate
IAO_0000111: editor preferred term: dTTP
IAO_0000115: definition: A pyrimidine 2'-deoxyribonucleoside 5'-triphosphate that has formula C10H17N2O14P3.
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

CHEBI:pyrimidine_2'-deoxyribonucleoside_5'-triphosphate
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:pyrimidine_deoxyribonucleoside_triphosphate
IAO_0000111: editor preferred term: pyrimidine_2'-deoxyribonucleoside_5'-triphosphate

study_subject_role
type: Class
IAO_0000115: Definition: study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about.
IAO_0000117: Definition Editor: GROUP: Role Branch
IAO_0000111: Editor Preferred Term: study subject role
IAO_0000119: Definition Source: OBI
subclass of: Role
IAO_0000118: Alternative Term: Subject
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000112: Example Of Usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example people infected, then extract parasite which are then tested = observation study of the parasite 1 study in which we observe people and 1 study in which subject is parasite is one way to split this. the true definition will come from the study design specification.

CHEBI:glycerol
type: Class
IAO_0000118: alternative term: Gro glycyl alcohol propane-1,2,3-triol Glyzerin glycerine Oelsuess glycerolum 1,2,3-Trihydroxypropane 1,2,3-Propanetriol Glycerin C3H8O3 OCC(O)CO
subclass of: CHEBI:triol
IAO_0000115: Definition: An alditol compound having three carbons.
IAO_0000111: editor preferred term: glycerol
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

M4L:DMSO_role
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: dimethyl sulfoxide role (methanesulfinyl)methane role
IAO_0000119: definition source: Frackman, S., et al., Betaine and DMSO: Enhancing Agents for PCR. 1998, Promega Corporation. p. 4.
subclass of: M4L:PCR_additive_role
IAO_0000115: definition: DMSO is probably the most commonly used enhancing agent and is frequently included as part of a standard optimization of PCR amplifications. The DMSO role, is disrupting base pairing to facilitate strand separation.
IAO_0000111: editor preferred term: DMSO role

electrophoresis
type: Class
IAO_0000112: Example Of Usage: Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
IAO_0000114: Has Curation Status: obo:IAO_0000125
IAO_0000111: Editor Preferred Term: electrophoresis
subclass of: material_component_separation
IAO_0000119: Definition Source: OBI branch derived
IAO_0000115: Definition: a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
IAO_0000117: Definition Editor: PERSON:Kevin Clancy

CHEBI:dimethyl_sulfoxide
type: Class
IAO_0000115: Definition: A 2-carbon sulfoxide in which the sulfur atom has two methyl substituents.
IAO_0000111: editor preferred term: dimethyl sulfoxide
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:sulfoxide
IAO_0000118: alternative term: (methanesulfinyl)methane S(O)Me2 dimethyl sulfur oxide (CH3)2SO dimethyli sulfoxidum dimetil sulfoxido methylsulfinylmethane sulfinylbis(methane) DMSO C2H6OS

quality_of_related_physical_entities
type: Class
subclass of: Quality
IAO_0000115: Definition: A physical entity quality which exists in relation towards some other entity.
IAO_0000111: Editor Preferred Term: quality of related physical entities
IAO_0000412: Imported From: oboContent:PATO

GO:endoribonuclease_activity,_producing_5'-phosphomonoesters
type: Class
IAO_0000115: Definitions: Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
IAO_0000111: editor preferred term: endoribonuclease activity, producing 5'-phosphomonoesters
subclass of: GO:endoribonuclease_activity
IAO_0000412: imported from: Gene Ontology, Version 1.931

GO:endoribonuclease_activity
type: Class
IAO_0000118: alternative term: endonuclease G activity
IAO_0000115: Definition: Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
IAO_0000111: editor preferred term: endoribonuclease activity
subclass of: GO:ribonuclease_activity
IAO_0000412: imported from: Gene Ontology, Version 1.931

MSH:ligase_chain_reaction
type: Class
IAO_0000111: editor preferred term: ligase chain reaction
subclass of: enzymatic_amplification
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000115: Definition: A DNA amplification technique based upon the ligation of OLIGONUCLEOTIDE PROBES. The probes are designed to exactly match two adjacent sequences of a specific target DNA. The chain reaction is repeated in three steps in the presence of excess probe: (1) heat denaturation of double-stranded DNA, (2) annealing of probes to target DNA, and (3) joining of the probes by thermostable DNA ligase. After the reaction is repeated for 20-30 cycles the production of ligated probe is measured.

M4L:laboratory_notebook
type: Class
IAO_0000119: definition source: Kanare, H.M., Writing the Laboratory Notebook. 1985, Washington D.C: American Chemical Society.
IAO_0000118: lab notebook
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: Definition: A lab notebook is a primary record of research. Researchers use a lab notebook to document their hypotheses, experiments and initial analysis or interpretation of these experiments. The notebook serves as an organizational tool, a memory aid, and can also have a role in protecting any intellectual property that comes from the research.
IAO_0000111: laboratory notebook
subclass of: document

document
type: Class
subclass of: IAO_0000030
IAO_0000114: Has Curation Status: obo:IAO_0000120
IAO_0000115: Definition: A collection of information content entities intended to be understood together as a whole
IAO_0000117: Definition Editor: PERSON: Lawrence Hunter
IAO_0000111: Editor Preferred Term: document
IAO_0000112: Example Of Usage: A journal article, patent application, laboratory notebook, or a book.

diluted
type: Class
IAO_0000115: Definition: A concentration which relative low.
IAO_0000111: Editor Preferred Term: diluted
IAO_0000412: Imported From: oboContent:PATO
subclass of: quality_of_related_physical_entities

M4L:small-scale_extraction_of_high_quality_DNA
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: these methods provide a cheap, fast, and easy way to obtain small-to-medium amounts of very high quality DNA.
IAO_0000111: editor preferred term: small-scale extraction of high quality DNA
subclass of: assay
IAO_0000119: definition source: Laboratory Protocols: CIMMYT Applied Molecular Genetics Laboratory. 2005, CIMMYT: Mexico, D.F. p. 102.

M4L:automated_DNA_sequencer
type: Class
IAO_0000119: definition source: http://en.wikipedia.org/wiki/DNA_sequencing
subclass of: BIRNLex:polyacrylamide_gel_electrophoresis_instrument
IAO_0000118: alternative term: Automated DNA-sequencing instrument DNA sequencer
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: Automated DNA sequencer, can sequence up to 384 DNA samples in a single batch (run) in up to 24 runs a day. DNA sequencers carry out capillary electrophoresis for size separation, detection and recording of dye fluorescence, and data output as fluorescent peak trace chromatograms. Sequencing reactions by thermocycling, cleanup and re-suspension in a buffer solution before loading onto the sequencer are performed separately. A number of commercial and non-commercial software packages can trim low-quality DNA traces automatically. These programs score the quality of each peak and remove low-quality base peaks (generally located at the ends of the sequence). The accuracy of such algorithms is below visual examination by a human operator, but sufficient for automated processing of large sequence data sets.
IAO_0000111: editor preferred term: automated_DNA_sequencer
IAO_0000112: example of usage: PhastSystem, LI-COR sequencer 4200 y ABI 377 DNA Synthesizer.

OGI:polymer
type: Class
IAO_0000111: polymer
IAO_0000115: definition: A compound made from monomers linked by chemical bonds. They are produced by polymerization, and occur either naturally or synthetically.
IAO_0000117: definition editor:Olga-Ximena Giraldo
IAO_0000119: definition source: Biology Online, Answers to all your Biology Questions. http://www.biology-online.org/dictionary/Polymer
subclass of: CHEBI:information_biomacromolecule

CHEBI:information_biomacromolecule
type: Class
subclass of: CHEBI:biomacromolecule
IAO_0000115: definition: A naturally occurring substance of large molecular weight, responsible of genetic transmision.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: Alternative term: genetically encoded biomacromolecule information macromolecule genetically encoded biopolymer information biopolymer
IAO_0000111: editor preferred term: information_biomacromolecule
IAO_0000112: example of usage: DNA, RNA, protein.
IAO_0000119: definition source: http://www.biology-online.org/dictionary/Biomacromolecule

M4L:PCR_strip_tubes
type: Class
subclass of: M4L:PCR_tube
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Light Labs. http://www.lightlabsusa.com/PCR-Strip-Tubes/
IAO_0000111: editor preferred term: PCR strip tubes
IAO_0000115: definition: PCR Strip Tubes come in several different styles and colors, for example, 8-strip tubes with seperate caps, hinged attached caps, and in the snapstrip version. Also there are 12-strip tubes with seperate caps. All pcr strip tubes are RNase/DNase/Pyrogen free and made from thin-walled plastic.

M4L:PCR_tube
type: Class
subclass of: M4L:laboratory_supply
IAO_0000119: definition source: *Axygen. http://www.axygen.com/categories/pcr *http://bioteknik.tradeindia.com/Exporters_Suppliers/Exporter16966.261147/Micro-Centrifuge-Tubes-PCR-Tubes.html
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: PCR Tubes are specifically designed for use in thermal cyclers. The tube walls are ultra thin and consistent, to ensure a fast temperature exchange between heating system and sample, resulting in faster cycles. A wide variety of sizes, configurations, and colors are offered to help organize PCR processes.
IAO_0000111: editor preferred term: PCR tube

CHEBI:magnesium_dichloride
type: Class
IAO_0000111: editor preferred term: magnesium dichloride
IAO_0000115: definition: A magnesium halide that has formula Cl2Mg.
subclass of: CHEBI:magnesium_halide
IAO_0000118: alternative term: Magnesium chloride MgCl2 Magnesium chloride anhydrous Magnesiumchlorid Cl2Mg [Mg++].[Cl-].[Cl-]
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

CHEBI:magnesium_halide
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:magnesium_molecular_entity
IAO_0000111: editor preferred term: magnesium_halide

CHEBI:quaternary_ammonium_salt
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: quaternary ammonium salt
IAO_0000118: alternative term: quaternary ammonium compound
IAO_0000115: Definition: Derivatives of ammonium compounds, (NH4(+))Y(-), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually hydrocarbyl) groups.
subclass of: CHEBI:organoammonium_salt

CHEBI:organoammonium_salt
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:ammonium_compound
IAO_0000111: editor preferred term: organoammonium salt

BIRNLex:electrophoresis_instrument
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: SNOMED:laboratory_equipment
IAO_0000119: definition source: *Fisher scientific. http://www.fishersci.com/wps/portal/CMSTATIC?href=Scientific/lifeScience/ProductsServices/Electrophoresis/electrophoresis_index.jsp&store=Scientific&segment=lifeScience *BIO-RAD. http://www3.bio-rad.com
IAO_0000412: imported from: BIRNLex, Version 1.3.1
IAO_0000115: definition: electrophoresis instrument is used for protein and nucleic acid separation. These instruments use gel systems or blotters.
IAO_0000118: alternative term: electrophoresis equipment
IAO_0000111: editor preferred term: electrophoresis instrument
IAO_0000112: example of usage: types of electrophoresis instruments: protein electrophoresis, nucleic acid electrophoresis, precast gel systems, 2-D systems.

M4L:touchdown_polymerase_chain_reaction
type: Class
IAO_0000118: alternative term: touchdown PCR
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: *Quality Assurance/Quality Control Guidance for Laboratories Performing PCR Analyses on Environmental Samples *http://www.pcrlinks.com/glossary/T.htm
IAO_0000111: editor preferred term: touchdown polymerase chain reaction
IAO_0000115: definition: Touchdown PCR is another modification of conventional PCR that may result in a reduction of nonspecific amplification. It involves the use of an annealing temperature that is higher than the target optimum in early PCR cycles. The annealing temperature is decreased by 1°C every cycle or every second cycle until a specified or 'touchdown' annealing temperature is reached. The touchdown temperature is then used for the remaining number of cycles. This allows for the enrichment of the correct product over any non-specific product.
subclass of: MSH:polymerase_chain_reaction

MSH:polymerase_chain_reaction
type: Class
IAO_0000111: editor preferred term: polymerase chain reaction
IAO_0000115: Definition: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000118: alternative term: PCR
subclass of: enzymatic_amplification

GO:ribonuclease_activity
type: Class
IAO_0000412: imported from: Gene Ontology, Version 1.931
subclass of: GO:nuclease_activity
IAO_0000115: Definition: Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
IAO_0000111: editor preferred term: ribonuclease activity

M4L:heat_resistant_glove
type: Class
IAO_0000115: definition: Gloves are excellent for handling hot objects out of the autoclave or oven. This gloves are Soft, pliant, all-cotton terry cloth. They are also excellent for use where other heat protection is needed whether in the lab, school or industry. Heat resistant up to 232°C (450°F), they replace hazardous asbestos gloves. Gloves provide wrist and forearm protection and the bright orange color offers high visibility. Machine wash, tumble dry.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Ted Pella, Inc. http://www.tedpella.com/gloves_html/gloves.htm
subclass of: M4L:glove
IAO_0000111: editor preferred term: heat resistant glove

M4L:scientific_control_role
type: Class
IAO_0000412: imported from: NCI Thesaurus, Version 10.01
IAO_0000111: editor preferred term: scientific control role
IAO_0000118: alternative term: control role
IAO_0000115: definition: Methodology that tests integrity in experiments by isolating variables as dictated by the scientific method in order to make a conclusion about such variables. In a controlled experiment, two virtually identical experiments are conducted, but the factor being tested is varied in only one of them. This serves to isolate any causal phenomena.
subclass of: Role

M4L:1.0mm_thick_comb_with_10_wells
type: Class
subclass of: M4L:comb

M4L:genetic_linkage_map
type: Class
IAO_0000118: Alternative Term: genetic map linkage map
IAO_0000119: Definition source: http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-G/genetic_linkage_map.html
IAO_0000115: Definition: A genetic map, is a map of a species or experimental population that shows the position of its known genes or genetic markers relative to each other in terms of recombination frequency, rather than as specific physical distance along each chromosome. Linkage mapping is critical for identifying the location of genes that cause different types of biotic and abiotic stresses in plants.
IAO_0000117: Definition editor: Olga-Ximena Giraldo
IAO_0000111: genetic linkage map
subclass of: graph

M4L:denaturing_activity
type: Class
IAO_0000111: editor preferred term: denaturing activity
IAO_0000119: definition source: A Glossary of Terms commonly used in Molecular Biology
IAO_0000115: definition: with respect to nucleic acids, refers to the conversion from double-stranded to the single-stranded state, often achieved by heating or alkaline conditions.
subclass of: molecular_function
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: melting DNA

CHEBI:dATP
type: Class
IAO_0000118: alternative term: C10H16N5O12P3 2'-deoxyadenosine 5'-(tetrahydrogen triphosphate) 2'-deoxyadenosine 5'-triphosphate deoxyadenosine 5'-triphosphate deoxyadenosine triphosphate
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000115: Definition: A purine 2'-deoxyribonucleoside 5'-triphosphate that has formula C10H16N5O12P3.
IAO_0000111: editor preferred term: dATP
subclass of: CHEBI:purine_2'-deoxyribonucleoside_5'-triphosphate

CHEBI:purine_2'-deoxyribonucleoside_5'-triphosphate
type: Class
subclass of: CHEBI:purine_deoxyribonucleoside_triphosphate
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: purine_2'-deoxyribonucleoside_5'-triphosphate

M4L:SYBR Safe role
type: Class
IAO_0000111: editor preferred term: SYBR Safe role
IAO_0000115: definition: A dye used to make DNA or RNA bands visible for agarose gel electrophoresis is SYBR Safe. SYBR Safe is a variant of SYBR Green that has been shown to have low enough levels of mutagenicity and toxicity to be deemed nonhazardous waste under U.S. Federal regulations. It has similar sensitivity levels to EtBr, but, like SYBR Green, is significantly more expensive. DNA or RNA bands stained with SYBR® Safe can be detected using a standard UV transilluminator, a visible-light transilluminator, or a laser-based scanner.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Invitrogen. SYBR Safe DNA Gel Stain.
subclass of: M4L:nucleic_acid_stain_role

M4L:nucleic_acid_stain_role
type: Class
subclass of: Role
IAO_0000111: editor preferred term: nucleic acid stain role
IAO_0000115: definition: nucleic acid stain is an intercalating agent commonly used to visualize and quantify nucleic acids.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Olga-Ximena Giraldo

M4L:PCR_plate
type: Class
subclass of: M4L:laboratory_supply
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Favorgen, biotech corp. http://www.favorgen.com/products_for_res_plastics_non-skirted_PCR_plate.htm
IAO_0000111: editor preferred term: PCR plate
IAO_0000115: definition: PCR plates are constructed of thin-wall polypropylene. Thin wall design delivers uniform, accurate, and rapid thermal transfer to each sample, improving cycle times and product specificity.

GRO:enzyme
type: Class
subclass of: GRO:protein
IAO_0000115: Definition: A protein that has catalytic activity.

GRO:protein
type: Class
IAO_0000119: definition source: http://www.qimr.edu.au/qimr_glossary.html
subclass of: OGI:polymer
IAO_0000115: Definition: a macromolecule composed of one or several polypeptides. Each polypeptide consists of a chain of amino acids linked together by covalent (peptide) bonds.

M4L:exponential_template_duplication
type: Class
IAO_0000119: definition source: PCR Down Under. http://www.uq.edu.au/vdu/PDU_PCR.htm
IAO_0000115: definition: the process is then repeated by cycling through the temperatures over and over again (35 to 55 times). Each cycle results in a new DNA duplex, each strand acting as a potential template for one or other primer.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000111: editor preferred term: exponential template duplication
subclass of: M4L:PCR_cycle_role

M4L:PCR_cycle_role
type: Class
IAO_0000111: editor preferred term: PCR cycle role
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: PCR cycle role, is to produce a new DNA duplex, each strand acting as a potential template for one or other primer.
IAO_0000119: definition source: PCR glossary. http://www.pcrlinks.com/index.html
subclass of: Role

M4L:secondary_structure_of_RNA_macromolecule
type: Class
IAO_0000111: editor preferred term: secondary structure of RNA macromolecule
IAO_0000115: definition: the secondary structure of biological RNA's can often be uniquely decomposed into stems and loops. Frequently these elements, or combinations of them, can be further classified, for example, tetraloops, pseudoknots and stem-loops. There are many secondary structure elements of functional importance to biological RNA's; some famous examples are the Rho-independent terminator stem-loops and the tRNA cloverleaf.
IAO_0000119: definition source: Westhof , E. and P. Aufﬁnger, RNA Tertiary Structure, in Encyclopedia of Analytical Chemistry, R.A. Meyers, Editor. 2000, John Wiley & Sons Ltd: Chichester. p. 5222 – 5232.
IAO_0000118: RNA secondary structure
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: M4L:secondary_structure_of_sequence_macromolecule

M4L:temperature_role
type: Class
IAO_0000119: definition source: Wu, D.Y., et al., The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction. DNA Cell Biol, 1991. 10(3): p. 233-8.
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: Role
IAO_0000115: definition: the effect of temperature, is a important factor in the specificity of PCR, because, the amplification of DNA occurs by repeated cycles of three temperature dependent steps: denaturing, annealing, and extention.
IAO_0000111: editor preferred term: temperature role

M4L:LB_buffer
type: Class
subclass of: M4L:electrophoresis_buffer
IAO_0000119: definition source: http://en.wikipedia.org/wiki/LB_buffer
IAO_0000111: editor preferred term: LB buffer
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: Lithium Borate buffer
IAO_0000115: definition: Lithium Borate buffer is a buffer solution used in agarose electrophoresis, typically for the separation of nucleic acids such as DNA and RNA. It is made up of Lithium borate (lithium hydroxide monohydrate and boric acid).

M4L:polyacrylamide_gel_loading_buffer
type: Class
IAO_0000111: editor preferred term: polyacrylamide_gel_loading_buffer
IAO_0000115: definition: This solution is used for loading DNA samples onto denaturing polyacrylamide gels. In a 4% (19:1 crosslinking ratio) denaturing polyacrylamide gel, the bromophenol blue migrates at approximately 40 bases and the xylene cyanol migrates at approximately 170 bases. In a 6% (19:1 crosslinking ratio) denaturing polyacrylamide gel, the bromophenol blue migrates at approximately 25 bases and the xylene cyanol FF component at approximately 105 bases.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Promega, http://www.promega.com/enotes/faqspeak/0003/fq0019.htm
subclass of: CHEBI:buffer

MSH:bacteriophage_T7_RNA_polymerase
type: Class
IAO_0000412: term imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000118: alternative term: bacteriophage T7 induced RNA polymerase T7 RNA polymerase
IAO_0000119: definition source: BioLabs. http://www.neb.com/nebecomm/products/productM0251.asp
IAO_0000115: definition: T7 RNA Polymerase catalyzes the synthesis of RNA in the 5´→ 3´ direction in the presence of a DNA template containing a T7 phage promoter. T7 RNA Polymerase can be used to generate high specific activity labeled RNA probes, RNA for in vitro translation, biologically active mRNA, and/or preparative quantities of defined length RNA by the run off transcription method.
IAO_0000111: editor preferred term: bacteriophage T7 RNA polymerase
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: NCI:DNA-directed_RNA_polymerase

NCI:DNA-directed_RNA_polymerase
type: Class
IAO_0000412: imported from: NCI Thesaurus, Version 10.01
subclass of: GRO:RNA_polymerase
IAO_0000115: Definition: Enzymes that catalyze the template-directed stepwise addition of ribonucleotides to the 3' end of a growing RNA chain using a single-stranded DNA template. The reaction is important in the flow of information from DNA to proteins. Three different forms of the polymerase have been identified and characterized.
IAO_0000118: alternative term: DNA-dependent RNA polymerase
IAO_0000111: editor preferred term: DNA-directed RNA polymerase

CHEBI:alcohol
type: Class
subclass of: CHEBI:organic_hydroxy_compound
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
IAO_0000118: alternative term: CHOR3 HOR
IAO_0000115: Definitions: A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.

image
type: Class
IAO_0000111: Editor Preferred Term: image
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000117: Definition Editor: person:Allyson person:Chris Stoeckert person:Alan Ruttenberg
subclass of: figure
IAO_0000115: Definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
IAO_0000119: Definition Source: group:OBI OBI_0000030

figure
type: Class
IAO_0000111: Editor Preferred Term: figure
IAO_0000112: Example Of Usage: Any picture, diagram or table.
IAO_0000114: Has Curation Status: obo:IAO_0000120
subclass of: IAO_0000030
IAO_0000117: Definition Editor: PERSON: Lawrence Hunter
IAO_0000115: Definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.

supernatant_role
type: Class
IAO_0000112: Example Of Usage: Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia
IAO_0000114: Has Curation Status: obo:IAO_0000120
IAO_0000115: Definition: supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material.
IAO_0000117: Definition Editor: GROUP: Role branch
IAO_0000111: Editor Preferred Term: supernatant role
subclass of: Role
IAO_0000119: Definition Source: OBI

CHEBI:potassium_salt
type: Class
subclass of: PDPP:chemical_entity
IAO_0000111: editor preferred term: potassium salt
IAO_0000118: alternative term: Kaliumsalze Kaliumsalz
IAO_0000119: definition source: Food-dictionary.com. http://www.food-dictionary.com/definition/potassium-salt.html
IAO_0000117: definition editor:Olga-Ximena Giraldo
IAO_0000115: definition: a crystalline compound formed from the neutralisation of an acid solution containing potassium.

M4L:latex_glove
type: Class
subclass of: M4L:glove
IAO_0000111: editor preferred term: latex glove
IAO_0000115: definition: gloves of natural latex is a product most trusted material and first choice for healthcare settings worldwide. Latex is a material that offer a consistent fit, flexibility, and resilience ( fits the best). Also, reliable performance and barrier protection against infection and contamination, but cause an allergic reaction for some users.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Emerald, Professional Protection Products. http://www.emeraldlatexgloves.com/gloves-101.htm

MSH:reverse_transcriptase_polymerase_chain_reaction
type: Class
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000111: editor preferred term: reverse transcriptase polymerase chain reaction
subclass of: MSH:polymerase_chain_reaction
IAO_0000115: Definition: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
IAO_0000118: alternative term: RT-PCR RTPCR

M4L:annealing_activity
type: Class
IAO_0000119: definition source: *http://www.ppsk.usm.my/lecturers/mravi/PDF_FIles/Group_3_2002.pdf *http://www.pcrlinks.com/glossary/A.htm
IAO_0000118: alternative term: hibridation activity
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: molecular_function
IAO_0000115: definition: Annealing is a molecular function, where the forward and reverse primers anneal to separated DNA template strand.
IAO_0000111: editor preferred term: annealing activity

M4L:deionized_water
type: Class
IAO_0000119: definition source: http://www.image2output.com/user_resources/TextFiles/pdfs/Deionised_Water.pdf
IAO_0000118: alternative term: demineralized water DI water DIW de-ionized water
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: Deionized water, also known as demineralized water, is water that has had its mineral ions removed, such as cations from sodium, calcium, iron, copper and anions such as chloride and bromide.
subclass of: CHEBI:water
IAO_0000111: editor preferred term: deionized water

M4L:laboratory_power_supply
type: Class
subclass of: SNOMED:laboratory_equipment
IAO_0000111: editor preferred term: laboratory power supply
IAO_0000112: example of usage: Bio Rad: PowerPac Basic power supply
IAO_0000115: definition: Power supplies are used for electrophoresis and blotting applications and it function is provide consistent voltage and current for a chosen application.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: BIO RAD power supplies. http://www3.bio-rad.com/B2B/vanity/gexp/product.do?language=English?language=English&ccatoid=-35457&pcatoid=-35440&com.broadvision.session.new=Yes&root=%2fProduct+Family%2fGX%2fHome&country=US&BV_SessionID=@@@@2062474633.1279054646@@@@&BV_EngineID=ccccadekmddhkeecfngcfkmdhkkdfll.0

CHEBI:monocarboxylic_acid
type: Class
IAO_0000115: Definition: An oxoacid containing a single carboxy group.
IAO_0000111: editor preferred term: monocarboxylic_acid
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:carboxylic_acid

CHEBI:carboxylic_acid
type: Class
subclass of: CHEBI:organic_molecular_entity
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000115: Definition: A molecular entity that contains carbon.
IAO_0000111: editor preferred term: carboxylic acid

MSH:endodeoxyribonuclease
type: Class
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000111: editor preferred term: endodeoxyribonuclease
IAO_0000115: Definition: A group of enzymes catalyzing the endonucleolytic cleavage of DNA.
subclass of: MSH:deoxyribonuclease

GO:ribonuclease_H_activity
type: Class
IAO_0000412: imported from: Gene Ontology, Version 1.931
subclass of: GO:endoribonuclease_activity,_producing_5'-phosphomonoesters
comment: Note that the EC recommended name for this enzyme activity is 'calf thymus ribonuclease H', even though it is found in many species.
IAO_0000118: alternative term: endoribonuclease H (calf thymus) endoribonuclease0 H activity hybrid nuclease activity hybrid ribonuclease activity hybridase (ribonuclease H) hybridase activity ribonuclease H1 activity ribonuclease H2 activity ribonuclease H3 activity RNA*DNA hybrid ribonucleotidohydrolase activity RNase H activity RNase H1 activity RNase H2 activity RNase H3 activity calf thymus ribonuclease H activity endoribonuclease H
IAO_0000115: Definition: Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
IAO_0000111: editor preferred term: ribonuclease H activity

MSH:deoxyribonuclease_HindIII
type: Class
IAO_0000118: alternative term: B Pertussis Restriction Enzyme I BpeI Endonuclease DNA Restriction Enzyme HindIII Endonuclease BstFI Endonuclease EcoVIII Endonuclease HindIII HINDIII LlaCI, Endonuclease Deoxyribonuclease BstFI Deoxyribonuclease EcoVIII Endodeoxyribonuclease BpeI Endonuclease Asp52I Endonuclease BbrI Endonuclease BpeI Endonuclease Cfr32I Endonuclease ChuI Endonuclease Eco65I Endonuclease Eco98I Endonuclease Hin1076III Endonuclease Hin173I Endonuclease HinbIII Endonuclease HinfII Endonuclease HinJCII Endonuclease HsuI Endonuclease MkiI Endonuclease LlaCI
IAO_0000115: Definition: One of the Type II site-specific deoxyribonucleases. It recognizes and cleaves the sequence A/AGCTT at the slash. HindIII is from Haemophilus influenzae R(d). Numerous isoschizomers have been identified.
IAO_0000111: editor preferred term: deoxyribonuclease HindIII
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
subclass of: MSH:deoxyribonuclease,_type_II_site-specific

primary_structure_of_RNA_macromolecule
type: Class
IAO_0000117: Definition Editor: Person:Bjoern Peters
IAO_0000115: Definition: The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
IAO_0000118: alternative term: RNA primary structure
IAO_0000111: Editor Preferred Term: primary structure of RNA molecule
subclass of: primary_structure_of_sequence_macromolecule

MSH:Pfu_DNA_polymerase
type: Class
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
subclass of: M4L:thermostable_DNA_polymerase
IAO_0000118: alternative term: Pfu polymerase
IAO_0000111: editor preferred term: Pfu DNA polymerase

CHEBI:polyethylene_glycol
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000115: Definition: A polymer composed of repeating ethyleneoxy units.
IAO_0000118: alternative term: alpha-hydro-omega-hydroxypoly(oxyethylene) ethylene glycol homopolymer Macrogol alpha,omega-hydroxypoly(ethylene oxide) ethylene glycol polymer polyethylene glycol Polyaethylenglykol Glycols, polyethylene polyoxyethylene poly(ethyleneoxide) PEG PEO poly(oxyethylene) polyethylene oxide POE (C2H4O)n alpha-hydro-omega-hydroxypoly(oxy-1,2-ethanediyl) 1,2-ethanediol homopolymer Polyaethylenglykole
subclass of: CHEBI:hydroxypolyether

CHEBI:hydroxypolyether
type: Class
subclass of: CHEBI:hydroxyether
IAO_0000111: editor preferred term: hydroxypolyether
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

IAO_0000027
IAO_0000117: Definition Editor: PERSON: Jonathan Rees PERSON: Chris Stoeckert PERSON: Alan Ruttenberg
IAO_0000116: Editor Note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
IAO_0000115: Definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
IAO_0000111: Editor Preferred Term: data item
IAO_0000114: Has Curation Status: obo:IAO_0000125
IAO_0000112: Example Of Usage: Data items include counts of things, analyte concentrations, and statistical summaries.

CHEBI:sodium_acetate
type: Class
subclass of: CHEBI:organic_sodium_salt
IAO_0000115: Definition: An organic sodium salt that has formula C2H3NaO2.
IAO_0000118: alternative term: acetic acid, sodium salt C2H3NaO2 Natriumazetat sodium acetate anhydrous anhydrous sodium acetate
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68

CHEBI:organic_sodium_salt
type: Class
subclass of: CHEBI:sodium_salt
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68

M4L:chloroplast_deoxyribonucleic_acid
type: Class
subclass of: CHEBI:deoxyribonucleic_acid
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: chloroplast DNA cpDNA
IAO_0000119: definition source: http://www.encyclopedia.com/doc/107-chloroplastDNA.html
IAO_0000111: editor preferred term: chloroplast deoxyribonucleic acid
IAO_0000115: definition: chloroplast DNA (cpDNA) is a circular DNA, like that of mitochondria but several times larger, which is found in chloroplasts and other plastids and contains genes involved in the photosynthetic pathway. It is independent of a nuclear DNA and is maternally inherited. Between 40 and 80 DNA molecules occur in each organelle.

CHEBI:deoxyribonucleic_acid
type: Class
IAO_0000412: term imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:nucleic_acid
IAO_0000115: Definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
disjoint with: CHEBI:ribonucleic_acid
IAO_0000118: alternative term: desoxyribose nucleic acid DNA

M4L:reclosable_bag
type: Class
IAO_0000119: definition source: Withers, P.C., Reclosable plastic bags 2010, International Consolidated Bussiness Pty Ltd., Windsor (AU): Australia. p. 5.
IAO_0000115: definition: reclosable plastic bag, is a plastic bag which can be repeatedly opened and closed to receive or retrieve contents, and sometimes known as "zipper bags".
IAO_0000118: alternative term: zip lock bag zipper bag
IAO_0000111: editor preferred term: reclosable bag
subclass of: M4L:laboratory_supply

M4L:96_well_PCR_plate
type: Class
IAO_0000119: definition source: Favorgen, biotech corp. http://www.favorgen.com/products_for_res_plastics_non-skirted_PCR_plate.htm
IAO_0000117: definiton editor: Olga-Ximena Giraldo
IAO_0000115: definition: PCR plates that can contain up to 96 samples. PCR plates, can be easily cut with scissors into 16, 24, 32, or 48-well pieces. The plate can be used in all 0.2ml V-bottom thermal cyclers and Real-Time thermal cyclers. finally, each plate is guaranteed RNase and DNase free.
IAO_0000111: editor preferred term: 96 well PCR plate
subclass of: M4L:PCR_plate

CHEBI:organic_molecular_entity
type: Class
subclass of: PDPP:chemical_entity
IAO_0000118: alternative term: organic entity organic compound
IAO_0000111: editor preferred term: organic molecular entity
IAO_0000115: Definition: A molecular entity that contains carbon.
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

CHEBI:dUTP
type: Class
subclass of: CHEBI:pyrimidine_2'-deoxyribonucleoside_5'-triphosphate
IAO_0000118: alternative term: 2'-deoxyuridine 5'-(tetrahydrogen triphosphate) deoxyuridine triphosphate 2'-deoxyuridine 5'-triphosphate C9H15N2O14P3
IAO_0000115: Definition: A pyrimidine 2'-deoxyribonucleoside 5'-triphosphate that has formula C9H15N2O14P3.
IAO_0000111: editor preferred term: dUTP
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

CHEBI:ethanol
type: Class
IAO_0000115: Definitions: A member of the ethanols that has formula C2H6O.
subclass of: CHEBI:primary_alcohol
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
IAO_0000118: alternative term: 1-hydroxyethane alcool ethylique Aethylalkohol spiritus vini Alkohol C2H5OH Aethanol Dehydrated ethanol alcohol alcohol etilico hydroxyethane EtOH Ethyl alcohol Methylcarbinol C2H6O CCO

CHEBI:primary_alcohol
type: Class
subclass of: CHEBI:alcohol
IAO_0000115: Definitions: A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it.
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
IAO_0000118: Alternative term: 1-Alcohol CH3OR

CHEBI:oligonucleotide
type: Class
subclass of: CHEBI:nucleotide
IAO_0000111: editor preferred term: oligonucleotide
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

buffer_role
type: Class
IAO_0000119: Definition Source: OBI
IAO_0000111: Editor Preferred Term: buffer role
IAO_0000112: Example Of Usage: A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3?) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution
IAO_0000114: Has Curation Status: obo:IAO_0000125
IAO_0000115: Definition: is a role which inheres in some molecular entity realized during the process of buffering
IAO_0000117: Definition Editor: Person:Helen Parkinson Philippe Rocca-Serra
subclass of: Role

M4L:portable_ice_chest
type: Class
subclass of: M4L:laboratory_supply
IAO_0000111: editor preferred term: portable ice chest
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: in chemistry and biology laboratories, the portable ice chest, is used for cooling samples (e.g. plant material, biological macromolecules), reagents, etc., during short time.
IAO_0000118: alternative term: cooler
IAO_0000119: definition source: *Woods, E.A. and G. Worsham, Quick- Chill Ice Chest. 1989: United States of America. p. 5. *Lexic.us. http://www.lexic.us/definition-of/ice_chest#1

M4L:5M_potassium_acetate_solution
type: Class
IAO_0000119: definition source: Weising, K., DNA fingerprinting in plants: principles, methods, and applications. Second Edition ed. 2005, Boca Raton, FL: Taylor & Francis Group.
subclass of: CHEBI:reagent
IAO_0000111: editor preferred term: 5M potassium acetate solution
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: in a plant DNA isolation protocol, the 5M potassium acetate solution is used to precipitated proteins and polysaccharides, leaving the nucleic acids in solution.

M4L:25mM_magnesium_chloride
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: Magnesium is a required cofactor for thermostable DNA polymerases, and magnesium concentration is a crucial factor that can affect the success of the amplification.
IAO_0000119: definition source: *http://www.promega.com/paguide/chap1.htm *http://www.pcrlinks.com/glossary/M.htm
IAO_0000118: alternative term: 25mM MgCl2
subclass of: CHEBI:reagent
IAO_0000111: editor preferred term: 25mM magnesium chloride

CHEBI:boron_oxoacid
type: Class
subclass of: CHEBI:boron_molecular_entity
IAO_0000118: alternative term: oxoacid of boron
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: boron_oxoacid

M4L:mechanical_pulverization_of_plant_material
type: Class
IAO_0000119: definition source: Olga-Ximena Giraldo
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: sample_preparation_for_assay
IAO_0000115: definition: mechanical pulverization of plant material, is a type of material processing. The plant materials are subjected to previous freezing with liquid nitrogen or dehydration. The purpose of the mechanical pulverization, is obtain a superfine powder to facilitate disruption of the cell wall of the plant cells.
IAO_0000111: editor preferred term: mechanical pulverization of plant material

sample_preparation_for_assay
type: Class
IAO_0000111: Editor Preferred Term: sample preparation for assay
IAO_0000118: alternative term: ~#en study
IAO_0000117: Definition Editor: PlanAndPlannedProcess Branch
IAO_0000119: Definition Source: OBI branch derived
IAO_0000115: Definition: A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
IAO_0000114: Has Curation Status: obo:IAO_0000125
subclass of: material_processing

M4L:real-time_PCR_thermal_cycler
type: Class
subclass of: SNOMED:laboratory_equipment
IAO_0000119: definition source: Quality Assurance/Quality Control Guidance for Laboratories Performing PCR Analyses on Environmental Samples.
IAO_0000118: alterantive term: real-time PCR Instrument real-time PCR system real-time PCR cycler
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: real-time PCR detection systems is an upgrade that adds real-time PCR capabilities to a base thermal cycler. The detection systems incorporate optical modules that enable detection of target sequences labeled with fluorescent probes. Sample quantitation by real-time PCR increases reliability of gene expression analyses, improves viral load assessment, and accelerates throughput in screening applications.
IAO_0000112: example ofo usage: DNA Engine Opticon 2 Real-Time Cycler
IAO_0000111: editor preferred term: real-time PCR thermal cycler

survival_curve
type: Class
IAO_0000111: Editor Preferred Term: survival curve
IAO_0000115: Definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
IAO_0000117: Definition Editor: PERSON:Melanie Courtot PERSON:James Malone PERSON:Chris Stoeckert
IAO_0000119: Definition Source: WEB: http://www.graphpad.com/www/book/survive.htm
subclass of: graph

CHEBI:glycine_betaine
type: Class
IAO_0000118: alternative term: C[N+](C)(C)CC([O-])=O
IAO_0000111: editor preferred term: glycine betaine
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:amino-acid_betaine

CHEBI:amino-acid_betaine
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: PDPP:chemical_entity
IAO_0000111: editor preferred term: amino-acid betaine
IAO_0000115: Definition: Any amino acid-derived zwitterion - such as glycine betaine (N,N,N-trimethylammonioacetate) - in which the ammonium nitrogen carries three methyl substituents.
IAO_0000118: alternative term: betaine

M4L:harvest_of_plant_material
type: Class
IAO_0000115: definition: the harvest of plant material include the cutting of whole plant or only a anatomical structure of the plant. Harvesting includes an immediate post-harvest handling, for example, cooling of plant material, sorting, cleaning and packing.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Harvest
IAO_0000112: example of usage: the harvest of plant material is particularly important for plant breeding studies such as evaluation of phenotypic features, biochemical studies such as enzyme purification, for biomolecular studies such as nucleic acid extraction.
IAO_0000111: editor preferred term: harvest_of_plant_material
subclass of: sample_preparation_for_assay

M4L:laboratory_glassware
type: Class
subclass of: M4L:laboratory_supply
IAO_0000111: editor preferred term: laboratory glassware
IAO_0000112: example of usage: beakers, conical flask or erlenmeyer flask, graduated cylinder, volumetric flask, test tube, thermometer, glass microArray slides, micro filter holder assembly.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Laboratory_glassware
IAO_0000115: definition: Laboratory glassware refers to a variety of equipment or item, traditionally made of glass, used for scientific experiments and other work in science, especially in chemistry and biology laboratories. Some of the equipment or item is now made of plastic for cost, ruggedness, and convenience reasons, but glass is still used for some applications because it is relatively inert, transparent, more heat-resistant than some plastics up to a point, and relatively easy to customize. Between the functions of the laboratory glassware items include volumetric measuring, holding or storing chemicals or samples, mixing or preparing solutions or other mixtures, containing lab processes like chemical reactions, heating, cooling, distillation, separations including chromatography, synthesis, growing biological organisms, spectrophotometry, and containing a full or partial vacuum.

M4L:loading_dye_role
type: Class
IAO_0000119: definition source: tools.invitrogen.com/content/sfs/manuals/10816015.pdf
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: components necessary for easy loading and tracking of DNA samples in agarose or polyacrylamide gels.
subclass of: Role
IAO_0000111: editor preferred term: loading_dye_role

CHEBI:hydroxyether
type: Class
IAO_0000111: editor preferred term: hydroxyether
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:alcohol

M4L:transilluminator
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: A device or instrument that projects light, ultraviolet radiation, etc. Optimized for use with nucleic acid and protein stains such SYBR Green, SYBR Safe, ethidium bromide, etc.
IAO_0000119: definition source: http://en.wiktionary.org/wiki/transilluminator
IAO_0000111: editor preferred term: transilluminator
subclass of: SNOMED:laboratory_equipment

M4L:nested_polymerase_chain_reaction
type: Class
IAO_0000115: definition: Nested PCR is a conventional PCR with a second round of amplification using a different set of primers. This second set of primers is specific to a sequence found within the DNA of the initial conventional PCR amplicon. The use of a second amplification step with the "nested" primer set results in a reduced background from products amplified during the initial PCR due to the nested primers’ additional specificity to the region. The amount of amplicon produced is increased as a result of the second round of amplification and due to a reduction in any inhibitor concentrations.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: nested PCR nested amplification
IAO_0000119: definition source: *Quality Assurance/Quality Control Guidance for Laboratories Performing PCR Analyses on Environmental Samples *http://www.pcrlinks.com/glossary/N.htm
IAO_0000111: editor preferred term: nested polymerase chain reaction
subclass of: MSH:polymerase_chain_reaction

extraction
type: Class
IAO_0000111: Editor Preferred Term: extraction
IAO_0000112: Example Of Usage: nucleic acid extraction using phenol chloroform
subclass of: material_component_separation
IAO_0000115: Definition: A material separation in which a desired component of an input material is separated from the remainder
IAO_0000114: Has Curation Status: obo:IAO_0000124
IAO_0000117: Definition Editor: Philippe Rocca-Serra Person:Bjoern Peters

GRO:RNA_polymerase
type: Class
subclass of: GRO:polymerase
IAO_0000119: dfinition source: Gene Ontology, Version 1.946. GO:0003899 DNA-directed RNA polymerase activity GO:0003968 RNA-directed RNA polymerase activity
IAO_0000115: Definition: An enzyme that catalyses the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA or RNA template.
IAO_0000111: editor preferred term: RNA polymerase

GRO:DNA_polymerase
type: Class
IAO_0000111: editor preferred term: DNA polymerase
IAO_0000115: 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.
IAO_0000119: definition source: GO:0003887 DNA-directed DNA polymerase activity GO:0003964 RNA-directed DNA polymerase activity
subclass of: GRO:polymerase

GRO:polymerase
type: Class
subclass of: GRO:enzyme
IAO_0000111: editor preferred term: polymerase
IAO_0000115: Definition: Enzymes that catalyze the synthesis of nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides.
IAO_0000119: definition source: http://www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html#p

CHEBI:potassium_acetate
type: Class
IAO_0000118: alternative term: C2H3O2.K C2H3KO2 Kaliumazetat
IAO_0000115: Definition: A potassium salt that has formula C2H3O2.K.
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68
subclass of: CHEBI:potassium_salt

CHEBI:sodium_salt
type: Class
subclass of: PDPP:chemical_entity
IAO_0000115: definition: a crystalline compound formed from the neutralisation of an acid solution containing sodium.
IAO_0000111: editor preferred term: sodium salt
IAO_0000119: definition source: Food-dictionary. http://www.food-dictionary.com/definition/sodium-salt.html
IAO_0000118: alternative term: Natriumsalze Natriumsalz
IAO_0000117: definition editor: Olga-Ximena Giraldo

M4L:ABI_PRISM_377_DNA_sequencer
type: Class
IAO_0000119: definition source: GMI, Inc. http://www.gmi-inc.com/Applied-Biosystems-ABI-377-DNA-Synthesizer.html
IAO_0000115: definition: ABI PRISM 377 DNA Sequencer automatically analyzes DNA molecules labeled with multiple fluorescent dyes. After samples are loaded onto the system's vertical gel- they undergo electrophoresis- laser detection- and computer analysis. Electrophoretic separation can be viewed on-screen in real-time- and final data can be output in a variety of formats. The 377 system accepts gel plates in four different lengths for flexibility in sample analysis.
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: M4L:automated_DNA_sequencer
IAO_0000112: example of usage: The human genome was sequenced with this instrument.
IAO_0000111: editor preferred term: ABI PRISM 377 DNA sequencer

M4L:complementary_deoxyribonucleic_acid
type: Class
IAO_0000118: alternative term: complementary DNA cDNA
IAO_0000115: definition: complementary DNA (cDNA) is DNA synthesized from a mature mRNA template in a reaction catalyzed by the enzyme reverse transcriptase.
IAO_0000111: editor preferred term: complementary_deoxyribonucleic_acid
subclass of: CHEBI:deoxyribonucleic_acid
IAO_0000412: imported from: Ontology for Genetic Interval, Version 0.15

vortexer
type: Class
IAO_0000117: Definition Editor: Melanie Courtot Trish Whetzel
IAO_0000119: Definition Source: http://en.wikipedia.org/wiki/Vortex_mixer
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000111: Editor Preferred Term: vortexer
subclass of: SNOMED:laboratory_equipment
IAO_0000115: Definition: A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created.
IAO_0000118: alternative term: ~#en vortex_mixer
IAO_0000112: Example Of Usage: VWR Genie 2

M4L:reverse_primer_role
type: Class
IAO_0000111: editor preferred term: reverse primer role
subclass of: primer_role
IAO_0000115: definition: reverse primer is the primer located at the 3'-end of the target sequence. the reverse primer has to be the reverse complement of the given cDNA sequence.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: downstream primer role antisense primer role
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29

BIRNLex:reagent_role
type: Class
IAO_0000111: Preferred term: reagent role
IAO_0000115: Definitions: Role played by a molecule or compound used to produce a chemical reaction to detect, measure, or produce other substances.
subclass of: Role

frozen
type: Class
IAO_0000412: Imported From: oboContent:PATO
subclass of: quality_of_a_single_physical_entity
IAO_0000111: Editor Preferred Term: frozen
IAO_0000115: Definition: A quality inhering in a bearer by virtue of being kept below its freezing point. A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.

CHEBI:organonitrogen_compound
type: Class
IAO_0000111: editor preferred term: organonitrogen_compound
IAO_0000115: Definition: A compound containing at least one carbon-nitrogen bond.
IAO_0000118: alternative term: organonitrogen
subclass of: CHEBI:nitrogen_molecular_entity
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

M4L:mitochondrial_deoxyribonucleic_acid
type: Class
IAO_0000115: definition: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial genome is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins (MSH).
subclass of: CHEBI:deoxyribonucleic_acid
IAO_0000118: alternative term: Mitochondrial DNA mtDNA
IAO_0000119: definition source: NIFSTD, Version 1.8

CHEBI:dCTP
type: Class
IAO_0000118: alternative term: C9H16N3O13P3 2'-deoxycytidine 5'-(tetrahydrogen triphosphate) 2'-deoxycytidine 5'-triphosphate deoxycytidine 5'-triphosphate deoxycytidine triphosphate
subclass of: CHEBI:pyrimidine_2'-deoxyribonucleoside_5'-triphosphate
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: Chemical entities of biological interest, Version 1.69
IAO_0000115: Definition: A pyrimidine 2'-deoxyribonucleoside 5'-triphosphate that has formula C9H16N3O13P3.

M4L:3′→5′_exonuclease_(nonproofreading)_activity
type: Class
IAO_0000111: editor preferred term: 3′→5′ exonuclease (nonproofreading) activity
IAO_0000112: example of usage: Taq DNApolymerase. When a simple detection of an amplification product is the goal, Taq DNA polymerase is the most commonly used enzyme because yields tend to be higher with a nonproofreading DNA polymerase.
IAO_0000115: definition: Nonproofreading DNA polymerases can't remove a misincorporated nucleotide from a growing DNA chain. Amplification with nonproofreading DNA polymerases results in the template-independent addition of a single nucleotide to the 3′-end of the PCR product.
subclass of: GO:DNA-directed_DNA_polymerase_activity
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: nonproofreading DNA polymerase
IAO_0000119: definition source: Promega, Protocols & Applications Guide. http://www.promega.com/paguide/chap1.htm#title4

M4L:blue light transilluminator
type: Class
IAO_0000119: definition source: Invitrogen. http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Nucleic-Acid-Purification-and-Analysis/Nucleic-Acid-Gel-Electrophoresis/nucleic_acid_gel_electrophoresis/Transillumination.html?CID=fl-safeimager
subclass of: M4L:transilluminator
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: This type of transiluminator, use pure visible blue light as the excitation source and there is NO damaging and dangerous ultra-violet radiation to worry about. Blue light transilluminators can be used for viewing a wide range of fluorescent samples including SYBR Green, SYBR Safe, GelStar, GelGreen, SYPRO Ruby, ProQ Diamond, fluorescein and various GFPs.
IAO_0000111: editor preferred term: blue light transilluminator

M4L:blue_juice,_agarose_gel_loading_buffer
type: Class
subclass of: CHEBI:buffer
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: tools.invitrogen.com/content/sfs/manuals/10816015.pdf
IAO_0000111: editor preferred term: blue juice, agarose gel loading buffer
IAO_0000115: definition: Blue juice agarose gel loading buffer, is a liquid containing all of the components necessary for easy loading and tracking of DNA samples in agarose.

PO:leaf
type: Class
IAO_0000412: imported from: plant structure ontology
IAO_0000118: alternative term: foliage leaf
IAO_0000115: Definition: Commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud.
comment: Accession: PO:0009025
IAO_0000119: definition source: APWeb:Glossary
subclass of: PO:plant_structure

CHEBI:2'-deoxyribonucleoside_triphosphate
type: Class
subclass of: CHEBI:nucleoside_triphosphate
IAO_0000111: editor preferred term: 2'-deoxyribonucleoside_triphosphate
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000118: alternative term: C5H12O12P3R

IAO_0000030
IAO_0000119: Definition Source: OBI_0000142
IAO_0000115: Definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
IAO_0000114: Has Curation Status: obo:IAO_0000125
IAO_0000116: Editor Note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
IAO_0000117: Definition Editor: PERSON: Chris Stoeckert
IAO_0000112: Example Of Usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
IAO_0000111: Editor Preferred Term: information content entity

M4L:minus_20_degree_Celsius_freezer
type: Class
subclass of: PEO:freezer
IAO_0000111: editor preferred term: minus 20 degree Celsius freezer
IAO_0000115: definition: suitable for life science, clinical and industrial applications, these freezers maintain a uniform cabinet temperature of -20 degree C to -40 degree C, and are designed to provide rapid temperature recovery following door openings, many with frost-free operation.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Mandel. http://www.mandel.ca/products/General_Lab_Equipment/Freezers_Refrigerators/-20C_Freezers/index.html

PEO:freezer
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Olga-Ximena Giraldo
subclass of: SNOMED:laboratory_equipment
IAO_0000111: editor preferred term: freezer
IAO_0000115: definition: A freezer is a dry, cold-storage machine. In a laboratory, the freezer is used to store tissue of the plant material, nucleic acids, enzymes, reagents and other supplies that needs to be stored at temperatures below zero degrees Celsius.

M4L:nitrile_glove
type: Class
IAO_0000119: definition source: Emerald, Professional Protection Products. http://www.emeraldlatexgloves.com/gloves-101.htm
IAO_0000115: definition: Nitrile is a synthetic Polymer that exhibits rubber-like characteristics. Nitrile is a material, protein and allergy free, offer the same flexibility, tensile strength, and durability as latex. the quality is superior to latex gloves in providing protection but are more expensive to produce than latex.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000111: editor preferred term: nitrile glove
subclass of: M4L:glove

centrifugation
type: Class
IAO_0000114: Has Curation Status: obo:IAO_0000120
IAO_0000115: Definition: centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
IAO_0000111: Editor Preferred Term: centrifugation
IAO_0000112: Example Of Usage: PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
IAO_0000117: Definition Editor: Philippe Rocca-Serra
IAO_0000119: Definition Source: adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
subclass of: material_component_separation

M4L:test_tube
type: Class
IAO_0000111: editor preferred term: test tube
IAO_0000119: definition source: * NiniScience. http://catalog.miniscience.com/catalog/Glassware/Test_Tube.html * Thomas Scott (transl., 1996), Concise Encyclopedia: Biology. Walter de Gruyter. ISBN 3110106612, 9783110106619. 1287 pages.
IAO_0000118: alternative term: culture tube sample tube
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: A test tube, also known as a culture tube or sample tube, is a common piece of laboratory glassware consisting of a finger-like length of glass or clear plastic tubing, open at the top, usually with a rounded U-shaped bottom. Test tubes are available in a multitude of lengths and widths, typically from 10 to 20 mm wide and 50 to 200 mm long. The top often features a flared lip to aid pouring out the contents; some sources consider that the presence of a lip is what distinguishes a test tube from a culture tube. Some test tubes have a flat bottom; some are made so as to accept a ground glass stopper or a screw cap. They are often provided with a small ground glass or white glaze area near the top for labeling with a pencil.
subclass of: M4L:laboratory_glassware

BIRNLex:negative_control_role
type: Class
subclass of: M4L:scientific_control_role
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Experiment
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000112: example of usage: negative control samples would contain all of the reagents for the PCR assay but no DNA.
IAO_0000111: editor preferred term: negative control role
IAO_0000115: definition: a negative control is known to give a negative result. The negative control demonstrates the base-line result obtained when a test does not produce a measurable positive result; often the value of the negative control is treated as a "background" value to be subtracted from the test sample results.

LI-COR 4200 sequencer
type: Class
subclass of: M4L:automated_DNA_sequencer
IAO_0000111: editor preferred term: LI-COR 4200 sequencer
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Hilary G. Morrison and Mitchell L. Sogin. Random Genomics Using LI-COR's Model 4200 IR2 System. http://www.licor.com/bio/posters/App_491/App491.jsp
IAO_0000115: definition: LI-COR sequencers can routinely provide 800-1100 nucleotide, one-pass reads with accuracy levels better than 99% on single and double-stranded DNA templates. These instruments produce long nucleotide reads through the use of a focusing microscope mounted on a scanning laser to detect near-infrared fluorescence labeled products from DNA sequencing reactions.

M4L:gel_casting_tray
type: Class
subclass of: M4L:horizontal_electrophoresis_instrument

M4L:RNA_polymerase_promoter_activity
type: Class
subclass of: GO:RNA_polymerase_activity
IAO_0000115: Definition: A region (DNA) to which RNA polymerase binds, to begin transcription.
IAO_0000111: editor preferred term: RNA polymerase promoter activity
IAO_0000412: imported from: NIFSTD, Version 1.8

M4L:1.0mm_thick_comb_with_30_wells
type: Class
subclass of: M4L:comb

M4L:glycerol_role
type: Class
IAO_0000119: definition source: Navaneetham, D. and B.M. Conti-Fine, Augmented PCR amplification by thermally activated DNA polymerase -AmpliTaq Gold, in the presence of densifying agents. 1998.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: an alditol compound having three carbons. Glycerol is reported to improve the PCR process. The activity of DNA polymerase is influenced by densifying agents like glycerol. Glycerol concentrations between 12% and 18% have positive influence, in terms of PCR product intensity on agarose gel. Therefore, inclusion of glycerol in PCR mixture, increase the PCR product band intensity.
subclass of: M4L:PCR_additive_role
IAO_0000111: editor preferred term: glycerol role

M4L:shaker
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: A shaker is a device used in chemistry and biology laboratories to stir liquids. A typical shaker has a table board that oscillates horizontally, powered by an electric motor. The liquids to be stirred are held in beakers or Erlenmeyer flasks that are placed over the table; or, sometimes, in test tubes or vials that are nested into holes in the plate.
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Shaker_%28laboratory%29
IAO_0000111: editor preferred term: shaker
subclass of: SNOMED:laboratory_equipment

GO:hydrolase_activity,_acting_on_ester_bonds
type: Class
subclass of: GO:hydrolase_activity
IAO_0000118: alternative term: esterase activity
IAO_0000115: Definitions: Catalysis of the hydrolysis of any ester bond.
IAO_0000412: imported from: Gene Ontology, Version 1.931
IAO_0000111: editor preferred term: hydrolase activity, acting on ester bonds

GO:hydrolase_activity
type: Class
IAO_0000111: editor preferred term: hydrolase activity
IAO_0000115: Definitions: Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
subclass of: catalytic_activity
IAO_0000412: imported from: Gene Ontology, Version 1.931

CHEBI:oxoacid_derivative
type: Class
subclass of: CHEBI:heteroatomic_molecular_entity
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: oxoacid_derivative

CHEBI:heteroatomic_molecular_entity
type: Class
IAO_0000115: Definition: A molecular entity consisting of two or more chemical elements.
IAO_0000118: alternative term: chemical compound
subclass of: PDPP:chemical_entity
IAO_0000111: editor preferred term: heteroatomic molecular entity

M4L:individual_PCR_tube
type: Class
IAO_0000119: definition source: Camlab. http://www.camlab.co.uk/item.asp?itemid=20614&categoryid=208&key=&letter=&browsecategoryid=0
IAO_0000111: editor preferred term: individual PCR tube
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: individual PCR tubes are manufactured from polypropylene, these tubes feature dimensional uniformity and conical bottom. Offered in 0.2 and 0.5ml sizes and with choice of dome or flat cap style.
subclass of: M4L:PCR_tube

CHEBI:carboxamide
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:primary_amide
IAO_0000115: Definition: Amides of carboxylic acids, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
IAO_0000118: alternative term: primary carboxamide
IAO_0000111: editor preferred term: carboxamide

CHEBI:primary_amide
type: Class
IAO_0000115: Definition: A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
subclass of: CHEBI:amide
IAO_0000111: editor preferred term: primary amide
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

M4L:SYBR_Green_role
type: Class
IAO_0000119: definition source: Beltrán, J., et al., Quantitative analysis of transgenes in cassava plants using real-time PCR technology. In Vitro Cellular & Developmental Biology - Plant, 2008. 45(1): p. 48-56.
IAO_0000117: definitio editor: Olga-Ximena Giraldo
IAO_0000115: definition: SYBR green is used as a dye for the quantification of double stranded DNA in some methods of real time PCR. It is also used to visualise DNA in gel electrophoresis.
IAO_0000111: editor preferred term: SYBR Green role
subclass of: M4L:nucleic_acid_stain_role

planned_process
type: Class
IAO_0000115: Definition: A processual entity that realizes a plan which is the concretization of a plan specification.
IAO_0000111: Editor Preferred Term: planned process
IAO_0000116: Editor Note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
IAO_0000114: Has Curation Status: obo:IAO_0000122
subclass of: ProcessualEntity
IAO_0000117: Definition Editor: Bjoern Peters
IAO_0000412: Imported From: Ontology(http://purl.obolibrary.org/obo/obi.owl)
IAO_0000119: Definition Source: branch derived
IAO_0000112: Example Of Usage: Injecting mice with a vaccine in order to test its efficacy

dendrogram
type: Class
IAO_0000111: Editor Preferred Term: dendrogram
IAO_0000112: Example Of Usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
IAO_0000115: Definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000117: Definition Editor: PERSON:Melanie Courtot PERSON:James Malone PERSON:Chris Stoeckert
subclass of: graph
IAO_0000119: Definition Source: WEB: http://en.wikipedia.org/wiki/Dendrogram

CHEBI:phosphoric_acid_derivative
type: Class
subclass of: CHEBI:oxoacid_derivative
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: phosphoric acid derivative

M4L:micropipette_tip(200-1000ul)
type: Class
IAO_0000119: definition source: Edvotek. http://www.edvotek.com/636.html
subclass of: M4L:micropipette_tip
IAO_0000115: definition: these tips are blue color and are designed for dispensing volumes between 200µl and 1000µl. Tips are available in bags of 1000 pieces non-sterile and in rack 96 pieces sterile, pyrogen-free. Material: polypropylene. Autoclavable.
IAO_0000118: alternative term: blue tips
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000111: editor preferred term: micropipette tip(200-1000ul)

M4L:micropipette_tip
type: Class
subclass of: M4L:laboratory_supply
IAO_0000111: editor preferred term: micropipette_tip
IAO_0000119: definition source: Mandel. http://www.mandel.ca/products/liquid_handling/tips/Specialty_Tips/index.htm
IAO_0000115: definition: micropipette tips have a wide tip opening that helps prevent damage to fragile cell and genomic DNA during pipetting. May also be used with viscous solutions for greater accuracy. Polypropylene tips are autoclavable. RNase, DNase, DNA free, and non-pyrogenic.
IAO_0000117: definition editor: Olga-Ximena Giraldo

CHEBI:amide
type: Class
IAO_0000111: editor preferred term: amide
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000115: Definition: An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
subclass of: CHEBI:nitrogen_molecular_entity

MSH:exoribonuclease
type: Class
IAO_0000111: editor preferred term: exoribonuclease
subclass of: M4L:ribonuclease
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000115: Definition: A family of enzymes that catalyze the exonucleolytic cleavage of RNA.

M4L:ethidium_bromide_role
type: Class
subclass of: M4L:nucleic_acid_stain_role
IAO_0000111: editor preferred term: ethidium bromide role
IAO_0000115: definition: Ethidium bromide is commonly used to detect nucleic acids in molecular biology laboratories. In the case of DNA this is usually double-stranded DNA from PCRs, restriction digests, etc. Single-stranded RNA can also be detected, since it usually folds back onto itself and thus provides local base pairing for the dye to intercalate. Detection typically involves a gel containing nucleic acids placed on or under a UV lamp.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: ethobromide role EtBr role dromilac role homidium Bromide role
IAO_0000119: definition source: *Bensaude, O. Ethidium Bromide and Safety- Readers Suggest Alternative Solutions. Trends Genet. 4:89; 1988. *Lunn, G.; Sansone, E.B. Decontamination of Ethidium Bromide Spills. Appl. Ind. Hyg. 4: 234-237; 1989.

CHEBI:organic_phosphate
type: Class
IAO_0000111: editor preferred term: organic phosphate
subclass of: CHEBI:phosphoric_acid_derivative
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

CHEBI:ethylenediaminetetraacetic_acid
type: Class
IAO_0000115: Definition: An ethylenediamine derivative that has formula C10H16N2O8.
IAO_0000118: alternative term: edetic acid Acide ethylenediaminetetracetique acido edetico acidum edeticum acide edetique (ethane-1,2-diyldinitrilo)tetraacetic acid N,N'-1,2-Ethane diylbis-(N-(carboxymethyl)glycine) H4edta Edetic acid EDTA C10H16N2O8
subclass of: CHEBI:tetracarboxylic_acid

CHEBI:tetracarboxylic_acid
type: Class
subclass of: CHEBI:carboxylic_acid
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: tetracarboxylic_acid
IAO_0000115: Definition: An oxoacid containing four carboxy groups.
IAO_0000118: alternative term: C4H4O8R

M4L:forward_primer_role
type: Class
IAO_0000115: definition: Forward primer is the primer located at the 5'-end of the target sequence. The forward primer has the same sequence as the "sense" strand (that produces the mRNA).
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: upstream primer role sense primer role
IAO_0000119: definition source: http://www.scientific.org/tutorials/articles/riley/riley.html
IAO_0000111: editor preferred term: forward primer role
subclass of: primer_role

M4L:tertiary_structure_of_sequence_macromolecule
type: Class
IAO_0000111: editor preferred term: tertiary structure of sequence macromolecule
IAO_0000115: definition: In biochemistry and molecular biology, the tertiary structure of a protein, nucleic acid or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.
IAO_0000119: definition source: *PAC, 1996, 68, 2193 (Basic terminology of stereochemistry (IUPAC Recomendations 1996)) on page 2220. *White book, p. 80.
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: quality_of_a_single_physical_entity

M4L:template_quality_role
type: Class
IAO_0000111: editor preferred term: template quality role
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: QIAGEN, Sample & Assay Technologies. http://www.qiagen.com/faq/faqview.aspx?faqid=74&SearchText=&FaqCategoryId=0&MenuItemId=0&catalog=1&ProductLineId=1000222
IAO_0000115: definition: the quality of nucleic acid starting template affect PCR, in particular the sensitivity and efficiency of amplification. PCR sensitivity and efficiency can be reduced by the presence of impurities in nucleic acid preparations or in biological samples.
subclass of: nucleic_acid_template_role

nucleic_acid_template_role
type: Class
subclass of: Role
IAO_0000112: Example Of Usage: a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
IAO_0000111: Editor Preferred Term: nucleic acid template role
IAO_0000115: Definition: nucleic acid template role is inhering in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
IAO_0000114: Has Curation Status: obo:IAO_0000124

M4L:positive_control_role
type: Class
IAO_0000115: definition: a positive control is a procedure that is very similar to the actual experimental test but which is known from previous experience to give a positive result. The positive control confirms that the basic conditions of the experiment were able to produce a positive result, even if none of the actual experimental samples produce a positive result.
IAO_0000112: example of usage: in a PCR assay, the investigators could make several positive control samples containing various dilutions of the taq polymerase enzyme.
subclass of: M4L:scientific_control_role
IAO_0000111: editor preferred term: positive control role
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Experiment
IAO_0000117: definition editor: Olga-Ximena Giraldo

molecular_concentration
type: Class
IAO_0000119: Definition Source: Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
IAO_0000115: Definition: A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity.
IAO_0000112: Example Of Usage: the phosphate concentration should be 0.1M
IAO_0000116: Editor Note: This term represent a quality of molecular concentration. If there is need for some other sort of concentration - e.g. ratio of counts of cells, another term is needed. OBI uses a standard unit for representing concentration qualities but this still needs to be decided on. A relation needs to be defined that relates the quality instance to the representation of its quantitative value in the chosen units. See http://en.wikipedia.org/wiki/Concentration Measurements of concentration may be in any appropriate unit. Note that precise concentrations are virtually never known. Finally, note that there is no such thing as a concentration of 0. A concentration is a *relational* quality and so can't exist unless both entities it inheres in exist. However one map make concentration measurements that turn out not to be about concentrations qualities, if it happens that the scattered molecular aggregate doesn't actually exist.
IAO_0000111: Editor Preferred Term: molecular concentration
subclass of: quality_of_related_physical_entities
IAO_0000117: Definition Editor: PERSON: Alan Ruttenberg
IAO_0000114: Has Curation Status: obo:IAO_0000123

M4L:secondary_structure_of_DNA_macromolecule
type: Class
subclass of: M4L:secondary_structure_of_sequence_macromolecule
IAO_0000111: editor preferred term: secondary_structure_of_DNA_macromolecule
IAO_0000115: definition: the secondary structure of DNA macromolecule, refers to the basepairing interactions within a single molecule or set of interacting molecules.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: Alternative term: DNA secondary structure
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Biomolecular_structure#Secondary_structure

M4L:PCR_master_mix_role
type: Class
subclass of: Role
IAO_0000119: definition source: http://www.molecularstation.com/wiki/Pcr_master_mix
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: a PCR master mix, is a mix of all most of the ingredients or factors necessary for PCR to occur. The goal of a PCR master mix is to decrease time spent pipetting.
IAO_0000111: editor preferred term: PCR master mix role

NCI:quantitative_reverse_transcriptase_PCR
type: Class
subclass of: MSH:reverse_transcriptase_polymerase_chain_reaction
IAO_0000412: imported from: NCI Thesaurus, Version 10.01
IAO_0000115: Definition: Quantitative PCR: a method to measure very small amounts of RNA transcripts as cDNA targets. There are two strategies currently used, one is called Competitive RTPCR and the other is called Real-Time PCR.
IAO_0000118: alternative term: qRTPCR quantitative RTPCR
IAO_0000111: editor preferred term: quantitative reverse transcriptase PCR

M4L:70_percentage_ethanol
type: Class
subclass of: CHEBI:reagent
IAO_0000119: definition source: *Weising, K., DNA fingerprinting in plants: principles, methods, and applications. Second Edition ed. 2005, Boca Raton, FL: Taylor & Francis Group. *"There are many disinfectants available". www.umsl.edu/~microbes/pdf/disinfectants.pdf
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: 70% ethanol in plant DNA isolation protocols, is used to wash pellet DNA. Ethanol is effective against a wide variety of pathogens if soaked for sufficient time (20-30 min). 70% ethanol is considered most effective disinfectant.
IAO_0000111: editor preferred term: 70 percentage ethanol

M4L:plant_material_list
type: Class
IAO_0000119: http://ciencia.glosario.net/botanica/material-vegetal-8606.html
IAO_0000117: Olga-Ximena Giraldo
IAO_0000115: Definition: A list of plant material can be seeds, part of a plant or whole plants used as a subject of study.
IAO_0000111: plant material list
subclass of: data_set

CHEBI:cyanine_dye
type: Class
subclass of: CHEBI:organonitrogen_compound
IAO_0000115: Definition: Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole.
IAO_0000111: editor preferred term: cyanine_dye
IAO_0000118: alternative term: Zyaninfarbstoff Cyaninfarbstoff
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

M4L:micropipette_tip(2-200ul)
type: Class
IAO_0000115: definition: these tips are yellow color and are designed for dispensing volumes between 2µl and 200µl. Tips are available in bags of 1000 pieces non-sterile and in rack 96 pieces sterile, pyrogen-free. Material: polypropylene. Autoclavable.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: yellow tips
IAO_0000119: definition source: Edvotek. http://www.edvotek.com/636.html
subclass of: M4L:micropipette_tip
IAO_0000111: editor preferred term: micropipette tip(2-200ul)

M4L:micropipette_tip(0.5-10ul)
type: Class
IAO_0000111: editor preferred term: micropipette tip(0.5-10ul)
IAO_0000119: definition source: Edvotek. http://www.edvotek.com/636.html
IAO_0000115: definition: these tips are white color and are designed for dispensing volumes between 0.2µl and 10µl. Tips are available in bags of 1000 pieces non-sterile and in rack 96 pieces sterile, pyrogen-free. Material: polypropylene. Autoclavable.
subclass of: M4L:micropipette_tip
IAO_0000118: alternative term: white tips
IAO_0000117: definition editor: Olga-Ximena Giraldo

M4L:reverse_primer
type: Class
IAO_0000111: editor preferred term: reverse primer
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: downstream primer antisense primer
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29
IAO_0000115: definition: reverse primer is the primer located at the 3'-end of the target sequence. the reverse primer has to be the reverse complement of the given cDNA sequence.
subclass of: CHEBI:oligonucleotide

FMA:nuclear_deoxyribonucleic_acid
type: Class
IAO_0000111: editor preferred term: nuclear deoxyribonucleic acid
subclass of: CHEBI:deoxyribonucleic_acid
IAO_0000118: alternative term: nuclear DNA nDNA
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Nuclear_DNA
IAO_0000115: definition: Nuclear DNA (nDNA), is DNA contained within a nucleus of eukaryotic organisms.
IAO_0000117: definition editor: Olga-Ximena Giraldo

MSH:self-sustained_sequence_replication
type: Class
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17
IAO_0000118: alternative term: NUCLEIC ACID SEQ BASED AMPLIFICATION SELF SUSTAINED SEQ REPLICATION Analysis, NASBA NASBA Analysis Nucleic Acid Sequence Based Amplification Nucleic Acid Sequence-Based Amplification Replication, Self-Sustained Sequence Self Sustained Sequence Replication Sequence Replication, Self-Sustained NASBA
IAO_0000115: definition: An isothermal in-vitro nucleotide amplification process. The process involves the concomitant action of a RNA-DIRECTED DNA POLYMERASE, a ribonuclease (RIBONUCLEASES), and DNA-DIRECTED RNA POLYMERASES to synthesize large quantities of sequence-specific RNA and DNA molecules.
IAO_0000111: editor preferred term: self-sustained sequence replication
subclass of: enzymatic_amplification

CHEBI:boric_acid
type: Class
IAO_0000115: Definition: A boron oxoacid that has formula BH3O3.
IAO_0000118: alternative term: boron trihydroxide trihydroxidoboron B(OH)3 orthoboric acid H3BO3 BH3O3 [H]OB(O[H])O[H]
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: boric_acid
subclass of: CHEBI:boron_oxoacid

CHEBI:tris
type: Class
IAO_0000118: alternative term: aminotris(hydroxymethyl)methane Tris base Tris amino Tris buffer Trometamol tris(hydroxymethyl)aminomethane THAM Tris-base Tromethamine 2-amino-2-(hydroxymethyl)propane-1,3-diol 2-Amino-2-(hydroxymethyl)-1,3-propanediol C4H11NO3 NC(CO)(CO)CO 1,1,1-tris(hydroxymethyl)methanamine
IAO_0000115: Definitions: A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.
subclass of: CHEBI:triol
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68

GO:nuclease_activity
type: Class
IAO_0000111: editor preferred term: nuclease activity
IAO_0000412: imported from: Gene Ontology, Version 1.931
comment: Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis.
subclass of: GO:hydrolase_activity,_acting_on_ester_bonds
IAO_0000115: Definition: Catalysis of the hydrolysis of ester linkages within nucleic acids.

M4L:UV_transilluminator
type: Class
IAO_0000119: definition source: Ehr, T.G.J., Transilluminator. 1994, Fotodyne Incorporated: United States. p. 7.
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: M4L:transilluminator
IAO_0000111: editor preferred term: UV transilluminator
IAO_0000115: definition: One apparatus used to illuminate electrophoresis gels produces ultraviolet light in a closed box. A light source within the box transmits UV light through a horizontal window provided in the top of the box. A gel is positioned over the window for illumination by the UV light, which passes through the gel from the window below. Such an apparatus is referred to as a transilluminator.

M4L:temperature_extension_role
type: Class
IAO_0000111: editor preferred term: temperature extension role
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: M4L:temperature_role
IAO_0000115: definition: the optimum extension temperature depends on the enzyme used but is usually between 68-72 degree C. In this phase of PCR cycle, the taq polymerase synthesizes a strand of DNA.
IAO_0000119: definition source: *http://www.wellscenter.iupui.edu/MMIA/htm/pcr.htm#4 *http://www.pcrlinks.com/glossary/E.htm
IAO_0000118: alternative term: temperature elongation role

M4L:graduated_cylinder
type: Class
subclass of: M4L:laboratory_glassware
IAO_0000111: editor preferred term: graduated cylinder
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: measuring cylinder
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Graduated_cylinder
IAO_0000115: definition: A graduated cylinder, also known as a measuring cylinder, is a piece of laboratory equipment used to accurately measure the volume of an object. Water displacement can be used to find out the volume of an object. Graduated cylinders are generally more accurate and precise for this purpose than flasks and beakers. Often, the largest graduated cylinders are made of polypropylene for its excellent chemical resistance or polymethylpentene for its clarity, making them lighter to ship and less fragile than glass. Polypropylene cylinders have excellent chemical high resistance and do not shatter when dropped, although one problem with this type of cylinder is that it can not be heated. Polypropylene is easy to repeatedly autoclave (sterilize); however, autoclaving of some polypropylene graduated cylinders may affect their accuracy.

M4L:DNA_ladder_role
type: Class
IAO_0000115: definition: A DNA ladder is a solution of DNA molecules of different lengths used in agarose and polyacrylamide gel electrophoresis. It is applied to an agarose and polyacrylamide gel as a reference to estimate the size of unknown DNA molecules. In addition it can be used to approximate the mass of a band by comparison to a special mass ladder.
IAO_0000119: definition source: http://en.wikipedia.org/wiki/DNA_ladder
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000112: example of usage: a λ DNA-HindIII Digest: a common lambda DNA ladder that has band sizes (in base pairs) of 23,130; 9,416; 6,557; 4,361; 2,322; 2,027; 564; and 125 bp.
IAO_0000111: editor preferred term: DNA ladder role
subclass of: Role

M4L:erlenmeyer_flask
type: Class
subclass of: M4L:laboratory_glassware
IAO_0000118: alternative term: Conical flask E-Spot flask
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: An Erlenmeyer, commonly known as a conical or E-Spot, is a widely used type of laboratory flask which features a flat, conical body, and a cylindrical neck. It's named after the German chemist Emil Erlenmeyer, who created it in 1861. The Erlenmeyer is usually marked on the side (graduated) to indicate the approximate volume of contents, and has a spot of ground glass or enamel where it can be labeled with a pencil. It differs from the beaker in its tapered body and narrow neck. The opening usually has slight rounded lips so that the Erlenmeyer can be easily stoppered using a piece of cotton wool. Alternatively, the neck may be fitted with a female ground glass joint to accept a glass stopper. The conical shape allows the contents to be swirled or stirred during an experiment, either by hand or by a shaker; the narrow neck keeps the contents from spilling out. The smaller neck also slows evaporative loss better than a bigger neck. The flat bottom of the conical makes it unlikely to tip over and spill.
IAO_0000111: editor preferred term: erlenmeyer flask
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Conical_flask

M4L:forward_primer
type: Class
IAO_0000119: definition source: http://www.scientific.org/tutorials/articles/riley/riley.html
IAO_0000118: alternative term: upstream primer sense primer
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000111: editor preferred term: forward primer
IAO_0000115: definition: Forward primer is the primer located at the 5'-end of the target sequence. The forward primer has the same sequence as the "sense" strand (that produces the mRNA).
subclass of: CHEBI:oligonucleotide

M4L:primer_desing_role
type: Class
subclass of: primer_role
IAO_0000115: definition: When designing primers for PCR, sequencing or mutagenesis it is often necessary to make predictions about these primers, for example melting temperature (Tm) and propensity to form dimers with itself or other primers in the reaction. Some thoughts on designing primers. 1. primers should be 17-28 bases in length; 2. base composition should be 50-60% (G+C); 3. primers should end (3') in a G or C, or CG or GC: this prevents "breathing" of ends and increases efficiency of priming; 4. Tms between 55-80oC are preferred; 5. 3'-ends of primers should not be complementary (ie. base pair), as otherwise primer dimers will be synthesised preferentially to any other product; 6. primer self-complementarity (ability to form secondary structures such as hairpins) should be avoided; 7. runs of three or more Cs or Gs at the 3'-ends of primers may promote mispriming at G or C-rich sequences (because of stability of annealing), and should be avoided.
IAO_0000111: editor preferred term: primer_desing_role
IAO_0000119: definition source: adapted from Innis and Gelfand,1991
IAO_0000117: definition editor: Olga-Ximena Giraldo

publication
type: Class
IAO_0000112: Example Of Usage: A journal article or book
IAO_0000111: Editor Preferred Term: publication
subclass of: document
IAO_0000115: Definition: A document that has been accepted by a publisher
IAO_0000114: Has Curation Status: obo:IAO_0000120
IAO_0000117: Definition Editor: PERSON: Lawrence Hunter

M4L:phage_RNA_polymerase_promoter_activity
type: Class
IAO_0000412: imported from: NIFSTD, Version 1.8
IAO_0000111: editor preferred term: phage RNA polymerase promoter activity
IAO_0000115: Definition: A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
subclass of: M4L:RNA_polymerase_promoter_activity

M4L:real_time_polimerase_chain_reaction
type: Class
IAO_0000111: editor preferred term: real time polimerase chain reaction
IAO_0000117: definition editor: Olga-Ximena Giraldo
comment: term adapted from: NCI Thesaurus, Version 10.01 ID: Real_Time_PCR Full Id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Real_Time_PCR
IAO_0000119: definition source: *http://en.wikipedia.org/wiki/Real-Time_PCR *http://www.pcrlinks.com/glossary/R.htm
subclass of: MSH:polymerase_chain_reaction
IAO_0000118: alternative term: Real Time PCR quantitative (real-time) PCR Real-Time Quantitative PCR RTQ-PCR
IAO_0000115: definition: Real-Time PCR, also called quantitative (real-time) PCR or Real-Time Quantitative PCR (RTQ-PCR), is a method of simultaneous DNA quantification and amplification. DNA is specifically amplified by polymerase chain reaction. After each round of amplification, the DNA is quantified. Common methods of quantification include the use of fluorescent dyes that intercalate with double-strand DNA and modified DNA oligonucleotides (called probes) that fluoresce when hybridized with a complementary DNA.

photograph
type: Class
subclass of: image
IAO_0000119: Definition Source: WEB: http://en.wiktionary.org/wiki/photograph
IAO_0000117: Definition Editor: PERSON:Joanne Luciano PERSON:Melanie Courtot PERSON:Alan Ruttenberg
IAO_0000115: Definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
IAO_0000114: Has Curation Status: obo:IAO_0000122

CHEBI:bromophenol_blue
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: bromophenol blue
IAO_0000115: Definition: 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye.
IAO_0000118: alternative term: 3',3'',5',5''-tetrabromophenolsulfophthalein 4,4'-(1,1-dioxido-3H-2,1-benzoxathiole-3,3-diyl)bis(2,6-dibromophenol) bromophenol blue, sultone form 3',3'',5',5''-tetrabromophenolsulfonephthalein C19H10Br4O5S
subclass of: CHEBI:phenol

CHEBI:pyrimidine_deoxyribonucleoside_triphosphate
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: pyrimidine_deoxyribonucleoside_triphosphate
subclass of: CHEBI:2'-deoxyribonucleoside_triphosphate

gene_list
type: Class
IAO_0000111: Editor Preferred Term: gene list
IAO_0000114: Has Curation Status: obo:IAO_0000125
IAO_0000112: Example Of Usage: Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
IAO_0000117: Definition Editor: person:Chris Stoeckert
IAO_0000115: Definition: A gene list is a report of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
IAO_0000119: Definition Source: group:OBI
subclass of: data_set

M4L:tetramethylammonium_chloride
type: Class
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Tetramethylammonium_chloride
IAO_0000115: definition: etramethylammonium chloride is a quaternary ammonium salt with the chemical formula [(CH3)4N]Cl. It is a colourless solid that is soluble in water and polar organic solvents. Tetramethylammonium chloride has few applications, unlike quaternary ammonium salts that feature more longer alkyl substituents.
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: CHEBI:quaternary_ammonium_salt
IAO_0000111: editor preferred term: tetramethylammonium chloride

CHEBI:transfer_RNA
type: Class
subclass of: CHEBI:ribonucleic_acid
IAO_0000111: editor preferred term: transfer RNA
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000115: Definition: A single-stranded RNA molecule containing about 70-90 nucleotides, folded by intrastrand base pairing into a characteristic secondary ('cloverleaf') structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis.
IAO_0000118: alternative term: tRNA

CHEBI:inorganic_hydroxy_compound
type: Class
IAO_0000118: alternative term: inorganic hydroxides
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:hydroxides
IAO_0000111: editor preferred term: inorganic hydroxy compound

M4L:minus_86_degree_Celsius_freezer
type: Class
subclass of: PEO:freezer
IAO_0000115: definition: ultra low temperature freezer (-86 degree C to -120 degree C) offers an array of ultra low temperature freezers. Uses of ultra low temperature freezer include prolonged storage of temperature sensitive biological samples, red cell samples and blood plasma.
IAO_0000111: editor preferred term: minus 86 degree Celsius freezer
IAO_0000119: definition source: Deepee Cooling Products Pvt. Ltd. http://www.hospitals-management.com/products_services/medicalequipment_technology/deepee_cooling_products.html
IAO_0000117: definition editor: Olga-Ximena Giraldo

M4L:3M_sodium_acetate_solution
type: Class
IAO_0000111: editor preferred term: 3M sodium acetate solution
subclass of: CHEBI:reagent
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: routinely used in DNA and RNA precipitation.
IAO_0000119: definition source: Fermentas. http://www.fermentas.com/en/products/all/reagents/r118-sodium-acetate-solution

SEP:polyacrylamide_gel_electrohoresis
type: Class
subclass of: electrophoresis
IAO_0000412: imported from: Sample processing and separation techniques, Version 1.070708
IAO_0000111: editor preferred term: polyacrylamide_gel_electrohoresis
IAO_0000115: Definition: Polyacrylamide gel electrophoresis is a one dimensional gel electrophoresis protocol which use the application of voltage to separate a sample along a separation medium which is a gel matrix made of polyacrylamide.

M4L:P-100_micropipette
type: Class
subclass of: M4L:adjustable_micropipette
IAO_0000115: definition: P-100 model, refer to the maximum volume in microliters. P100 is a micropipette designed for dispensing volumes between 20µl and 100µl.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: P-100 model
IAO_0000119: definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F123615
IAO_0000111: editor preferred term: P-100 micropipette

RNA_extraction
type: Class
subclass of: nucleic acid extraction
IAO_0000111: Editor Preferred Term: RNA extraction
IAO_0000114: Has Curation Status: obo:IAO_0000125
IAO_0000115: Definition: A RNA extraction is a nucleic acid extraction where the desired output material is RNA
IAO_0000117: Definition Editor: PlanAndPlannedProcess Branch
IAO_0000119: Definition Source: OBI branch derived

nucleic acid extraction
type: Class
IAO_0000117: Definition Editor: PlanAndPlannedProcess Branch
IAO_0000115: Definition: a material separation to recover the nucleic acid fraction of an input material
IAO_0000119: Definition Source: OBI branch derived
IAO_0000111: Editor Preferred Term: nucleic acid extraction
IAO_0000114: Has Curation Status: obo:IAO_0000125
IAO_0000112: Example Of Usage: Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
subclass of: extraction

M4L:double-distilled_water
type: Class
IAO_0000111: editor preferred term: double-distilled water
subclass of: CHEBI:water
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: ddH2O Bidest. water DDW
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Purified_water#Double-distillation
IAO_0000115: definition: Double-distilled water is prepared by double distillation of water. Historically, it was the de facto standard for highly purified laboratory water for biochemistry and trace analysis until combination methods of purification became widespread.

M4L:tetramethylammonium_chloride_role
type: Class
subclass of: M4L:PCR_additive_role
IAO_0000119: definition source: Chevet, E., G. Lemaitre, and M.D. Katinka, Low concentrations of tetramethylammonium chloride increase yield and specificity of PCR. Nucleic Acids Res, 1995. 23(16): p. 3343-4.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: in low concentrations, it is used with polymerase chain reactions to increase yield and specificity. It has been shown to enhance yield 5-10 fold at 3M by stabilizing the AT base pairs.
IAO_0000111: editor preferred term: tetramethylammonium chloride role

NCI:DNA-directed_DNA_polymerase
type: Class
subclass of: GRO:DNA_polymerase
IAO_0000111: Editor Preferred Name: DNA-directed DNA Polymerase
IAO_0000119: definition source: (1) medical dictionary. http://www.mondofacto.com/facts/dictionary?DNA-directed+DNA+polymerase (2) IUBMB Enzyme Nomenclature
IAO_0000118: alternative term: DNA-Dependent DNA Polymerase
IAO_0000115: definition (1): During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair. Definition (2): Catalyses DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time. Cannot initiate a chain de novo. Requires a primer, which may be DNA or RNA. (IUBMB Enzyme Nomenclature)

CHEBI:nucleic_acid
type: Class
IAO_0000115: Definition: A macromolecule 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.
subclass of: OGI:polymer
IAO_0000118: alternative term: acido nucleico Nukleinsaeuren acide nucleique NA Nukleinsaeure
IAO_0000119: definition source: Chemical entities of biological interest, Version 1.68

CHEBI:magnesium_molecular_entity
type: Class
subclass of: PDPP:chemical_entity
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: magnesium_molecular_entity
IAO_0000118: alternative term: magnesium compound

PO:juvenile leaf
type: Class
IAO_0000119: definition source: GR:pj, MaizeGDB:lv
IAO_0000115: Definition: Distinct from adult leaves, being characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.
comment: Accession: PO:0006339 The first juvenile leaves are e.g. the embryonic leaves found in the grass kernel (caryopsis).
subclass of: PO:leaf
IAO_0000412: imported from: plant structure ontology

CHEBI:acetic_acid
type: Class
IAO_0000115: Definition: A simple carboxylic acid containing two carbons; the active ingredient in vinegar. Unlike longer-chain carboxylic acids (the fatty acids), acetic acid does not occur in natural triglycerides. Reported to suppress accumulation of body fat and liver lipids in mice.
IAO_0000118: alternative term: ethoic acid HOAc Essigsaeure CH3-COOH acide acetique Ethylic acid Methanecarboxylic acid Ethanoic acid C2H4O2
subclass of: CHEBI:monocarboxylic_acid
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: acetic_acid

histogram
type: Class
IAO_0000119: Definition Source: GROUP:OBI
IAO_0000117: Definition Editor: PERSON:Melanie Courtot PERSON:James Malone PERSON:Chris Stoeckert
IAO_0000114: Has Curation Status: obo:IAO_0000122
IAO_0000115: Definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
IAO_0000111: Editor Preferred Term: histogram
subclass of: graph

M4L:tertiary_structure_of_RNA_macromolecule
type: Class
IAO_0000111: editor preferred term: tertiary structure of RNA macromolecule
IAO_0000115: definition: is a level of organization of RNA, in which, the secondary structure elements are associated through numerous van der Waals contacts, specific hydrogen bonds via the formation of a small number of additional Watson-Crick pairs and/or unusual pairs involving hairpin loops or internal bulges. The parsing of energy levels between secondary and tertiary structures is reasonable in large RNAs, considering the relative energies and the clear identification of the secondary structure elements. In some cases, it is even possible to cut RNA molecules into modular domains which can re-associate only through tertiary contacts. RNA tertiary structure comprises those interactions involving (a) two helices, (b) two unpaired regions, or (c) one unpaired region and a double-stranded helix.
subclass of: M4L:tertiary_structure_of_sequence_macromolecule
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: RNA tertiary structure
IAO_0000119: definition source: Westhof , E. and P. Aufﬁnger, RNA Tertiary Structure, in Encyclopedia of Analytical Chemistry, R.A. Meyers, Editor. 2000, John Wiley & Sons Ltd: Chichester. p. 5222 – 5232.

CHEBI:purine_deoxyribonucleoside_triphosphate
type: Class
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
IAO_0000111: editor preferred term: purine deoxyribonucleoside triphosphate
subclass of: CHEBI:2'-deoxyribonucleoside_triphosphate

M4L:fine_powder_of_plant_material
type: Class
subclass of: processed_material
IAO_0000115: definition: fine powder of plant material is obtained by mechanical action of grind the tissue in a mortar and pestle. This takes a fair amount of effort but it is worth it because the finer the grind, the greater the DNA yields.
IAO_0000111: editor preferred term: fine powder of plant material
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Laboratory Protocols: CIMMYT Applied Molecular Genetics Laboratory. 2005, CIMMYT: Mexico, D.F. p. 102.

M4L:beaker
type: Class
IAO_0000115: definition: A beaker is a simple container for stirring, mixing and heating liquids commonly used in many laboratories. Beakers are generally cylindrical in shape, with a flat bottom and a lip for pouring. Beakers are available in a wide range of sizes, from one millilitre up to several litre.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Oxford English Dictionary 1989 edition
subclass of: M4L:laboratory_glassware
IAO_0000111: editor preferred term: beaker

NCI:whole_genome_amplification
type: Class
IAO_0000412: imported from: NCI Thesaurus, Version 10.01
IAO_0000118: alternative term: WGA Whole Genome PCR
subclass of: MSH:polymerase_chain_reaction
IAO_0000115: definition: A PCR technique designed to amplify a limited genomic DNA sample so as to generate a new sample that is indistinguishable from the original but with a higher DNA concentration.
IAO_0000111: editor preferred term: whole genome amplification

M4L:formamide_role
type: Class
IAO_0000119: definition source: Sarkar, G., S. Kapelner, and S.S. Sommer, Formamide Can Dramatically Improve the Specificity of Pcr. Nucleic Acids Research, 1990. 18(24): p. 7465-7465.
subclass of: M4L:PCR_additive_role
IAO_0000111: editor preferred term: formamide role
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: role of formamide in the PCR, is eliminate most of the nonspecific products and increase the efficiency of the amplification.

M4L:laboratory_balance_instrument
type: Class
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Weighing_scale
IAO_0000115: definition: laboratory balance instrument, is a measuring instrument for determining the weight or mass of an object.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000111: editor preferred term: laboratory balance instrument
subclass of: SNOMED:laboratory_equipment

M4L:384_well_PCR_plate
type: Class
subclass of: M4L:PCR_plate
IAO_0000111: editor preferred term: 384 well PCR plate
IAO_0000119: definition source: Axigen. http://www.axygen.com/categories/pcr
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: PCR plates that can contain up to 384 samples. 384 PCR plates are designed to fit virtually all thermal cyclers available. Also, each plate is guaranteed RNase and DNase free.

M4L:P-10_micropipette
type: Class
IAO_0000118: alternative term: P-10 model
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: P-10 model, refer to the maximum volume in microliters. P10 is a micropipette designed for dispensing volumes between 1µl and 10µl.
IAO_0000111: editor preferred term: P-10_micropipette
subclass of: M4L:adjustable_micropipette
IAO_0000119: definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F144802

SEP:agarose_gel_electrophoresis
type: Class
subclass of: electrophoresis
IAO_0000115: definition: Agarose gel electrophoresis is a one dimensional gel electrophoresis protocol which use the application of voltage to separate a sample along a separation medium which is a gel matrix made of agarose.
IAO_0000111: editor preferred term: agarose gel electrophoresis
IAO_0000412: imported from: Sample processing and separation techniques, Version 1.070708

CHEBI:lithium_hydroxide
type: Class
IAO_0000115: Definition: An alkali metal hydroxide that has formula HLiO.
IAO_0000118: alternative term: LiOH HLiO Lithiumhydroxid lithium hydrate lithium hydroxide anhydrous
IAO_0000111: editor preferred term: lithium hydroxide
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69
subclass of: CHEBI:alkali_metal_hydroxide

CHEBI:alkali_metal_hydroxide
type: Class
subclass of: CHEBI:metallic_base
IAO_0000118: alternative term: alkali metal base
IAO_0000111: editor preferred term: alkali metal hydroxide
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

M4L:T7_RNA_polymerase_promoter_activity
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: Definition: A region (DNA) to which the T7 RNA polymerase binds, to begin transcription. T7 RNA Polymerase is an RNA polymerase that catalyzes the formation of RNA in the 5'→ 3' direction. T7 polymerase is extremely promoter-specific and only transcribes bacteriophage T7 DNA or DNA cloned downstream of a T7 promoter.
subclass of: M4L:phage_RNA_polymerase_promoter_activity
IAO_0000119: definition source: *http://en.wikipedia.org/wiki/T7_RNA_polymerase * NIFSTD, Version 1.8
IAO_0000412: imported from: NIFSTD, Version 1.8
IAO_0000111: editor preferred term: T7 RNA polymerase promoter activity

M4L:P-1000_micropipette
type: Class
IAO_0000111: editor preferred term: P-1000 micropipette
IAO_0000115: definition: P-1000 model, refer to the maximum volume in microliters. P1000 is a micropipette designed for dispensing volumes between 200µl and 1000µl.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: P-1000 model
IAO_0000119: definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F123602
subclass of: M4L:adjustable_micropipette

M4L:mortar_and_pestle
type: Class
IAO_0000115: definition: A mortar and pestle is a tool used to crush, grind, and mix solid substances (trituration). The pestle is a heavy bat-shaped object, the end of which is used for crushing and grinding. The mortar is a bowl, typically made of hard wood, marble, clay, or stone. The substance to be ground is placed in the mortar and ground, crushed or mixed with the pestle.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Mortar_and_pestle
IAO_0000111: editor preferred term: mortar and pestle
subclass of: M4L:laboratory_supply

patent
type: Class
IAO_0000117: Definition Editor: PERSON: Lawrence Hunter
IAO_0000114: Has Curation Status: obo:IAO_0000120
IAO_0000115: Definition: A document that has been accepted by a patent authority
IAO_0000111: Editor Preferred Term: patent
IAO_0000112: Example Of Usage: US Patent 6,449,603
subclass of: document

M4L:frozen_leaf
type: Class
IAO_0000111: Editor preferred term: frozen leaf
subclass of: frozen
IAO_0000115: Definition: A quality inhering in a leaf (anatomical part of a plant) by virtue of being kept below its freezing point. A quality inhering in a leaf (anatomicla part of a plant) by virtue of the leaf is being kept below its freezing point.
IAO_0000119: definition source: adapted from: oboContent:PATO
IAO_0000117: definition editor: Olga-Ximena Giraldo

agarose_ gel
type: Class
subclass of: SEP:gel
IAO_0000119: Definition Source: GROUP: OBI Biomaterial Branch
IAO_0000117: Definition Editor: PERSON: Philippe Rocca-Serra
IAO_0000115: Definition: agarose gel is a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution.
IAO_0000114: Has Curation Status: obo:IAO_0000120
IAO_0000112: Example Of Usage: Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
IAO_0000111: Editor Preferred Term: agarose gel

PO:adult_leaf
type: Class
IAO_0000115: Definition: Adult leaves are characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.
IAO_0000119: definition source: GR:pj, MaizeGDB:lv
comment: Accession: PO:0006340 The adult leaves are placed above the juvenile (oldest) leaves. However in some plants the juvenile leaves may go on to establish as adult leaves.
IAO_0000412: imported from: plant structure ontology
subclass of: PO:leaf

PO:whole_plant
type: Class
IAO_0000115: Definition: The entire plant, including roots, shoots and leaves, at any stage of its life cycle.
IAO_0000119: definition source: TAIR:ki
IAO_0000412: imported from: plant structure ontology
subclass of: MaterialEntity
comment: Accession: PO:0000003 This term is so general that it should be avoided whenever possible.

M4L:tertiary_structure_of_DNA_macromolecule
type: Class
subclass of: M4L:tertiary_structure_of_sequence_macromolecule
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: DNA tertiary structure
IAO_0000119: http://en.wikipedia.org/wiki/Nucleic_acid_tertiary_structure#cite_note-1
IAO_0000115: definition: the tertiary structure of a DNA is its precise three-dimensional structure, as defined by the atomic coordinates.
IAO_0000111: editor preferred term: tertiary structure of DNA macromolecule

SEP:camera
type: Class
subclass of: SEP:image_acquisition_device
IAO_0000412: imported from: Sample processing and separation techniques, Version 1.070708
IAO_0000115: Definition: A camera is an image acquistion device which is used for taking photographs (usually consisting of a lightproof box with a lens at one end and light-sensitive film at the other).
IAO_0000111: editor preferred term: camera

M4L:PCR_grade_water
type: Class
IAO_0000111: editor preferred term: PCR grade water
subclass of: CHEBI:water
IAO_0000119: definition source: Mo Bio, Laboratories, Inc. http://www.mobio.com/pcr-water/pcr-water-certified-dna-free.html
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: Water certified by PCR to be free of all DNA, RNase, and DNase contamination.

CHEBI:dGTP
type: Class
subclass of: CHEBI:purine_2'-deoxyribonucleoside_5'-triphosphate
IAO_0000115: Definition: A purine 2'-deoxyribonucleoside 5'-triphosphate that has formula C10H16N5O13P3.
IAO_0000118: alternative term: deoxyguanosine triphosphate C10H16N5O13P3 2'-deoxyguanosine 5'-(tetrahydrogen triphosphate) 2'-deoxyguanosine 5'-triphosphate deoxyguanosine 5'-triphosphate
IAO_0000111: imported from: Chemical entities of biological interest, Version 1.69

NCI:RNA-directed_RNA_polymerase
type: Class
IAO_0000412: imported from: NCI Thesaurus, Version 10.01
subclass of: GRO:RNA_polymerase
IAO_0000115: Definition: An enzyme that catalyzes the template-directed addition of ribonucleotides to the 3' end of a growing RNA chain. The enzyme utilizes single-stranded RNA as a template.
IAO_0000111: editor preferred term: RNA-directed RNA polymerase
IAO_0000118: alternative term: RNA-dependent RNA polymerase

CHEBI:metallic_base
type: Class
subclass of: CHEBI:inorganic_hydroxy_compound
IAO_0000111: editor preferred term: metallic base
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

MSH:RNA-directed_DNA_polymerase
type: Class
IAO_0000111: editor preferred term: RNA-directed DNA polymerase
IAO_0000115: Definition: An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements.
IAO_0000118: alternative term: DNA polymerase, RNA-dependent reverse transcriptase revertase RNA dependent DNA polymerase RNA transcriptase RNA-dependent DNA polymerase DNA polymerase, RNA directed DNA polymerase, RNA-directed deoxynucleotide-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) RNA directed DNA polymerase
subclass of: GRO:DNA_polymerase
IAO_0000412: imported from: Medical Subject Headings, Version 2010_2009_08_17

M4L:dNTP_mix
type: Class
subclass of: CHEBI:reagent
IAO_0000111: editor preferred term: dNTP_mix
IAO_0000115: definition: An incorrect concentration of deoxynucleotidetriphosphates (dNTPs) can cause problems for the PCR procedure. The usual dNTP concentration is between 40μM and 200μM of EACH of the four dNTPs. Excessive dNTP concentrations can inhibit the PCR preventing the formation of product. However, concentrations up to 400 μM each dNTP have been reported to work adequately. Low primer, target, Taq, and dNTP concentrations are preferable as these generally ensure cleaner product and lower background. For longer PCR-fragments a higher deoxynucleotidetriphosphate concentration may be required. A large change in the dNTP concentration may require a corresponding change in the concentration of MgCl2. definition: Mix consists of a solution of all four nucleotides (dATP, dCTP, dGTP, dTTP). Usually, each nucleotide at a concentration of 2.5 mM. It is neutralized to pH 8.0 with NaOH, and supplied in purified water. dNTP Mix is suitable for use in polymerase chain reaction (PCR), sequencing, fill-in, nick translation, cDNA synthesis, and TdT-tailing reactions.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: PCR Troubleshooting: Inadequate dNTPs. http://www.highveld.com/pages/pcr-troubleshooting.html

M4L:polyethylene_glycol_role
type: Class
IAO_0000119: definition source: Markoff, A., et al., Optimization of single-strand conformation polymorphism analysis in the presence of polyethylene glycol. Clinical Chemistry, 1997. 43(1): p. 30-33.
IAO_0000115: definition: polyethylene glycol (PEG) helps improve the differential separation of conformers (a conformation of a molecule). Therefore in PCR, the PEG is used to precipitate the PCR reaction.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000118: alternative term: PEG role
IAO_0000111: editor preferred term: polyethylene glycol role
subclass of: M4L:PCR_additive_role

M4L:multiplex_polymerase_chain_reaction
type: Class
subclass of: MSH:polymerase_chain_reaction
IAO_0000111: editor preferred term: multiplex polymerase chain reaction
IAO_0000115: definition: Multiplex PCR is the term used when more than one pair of primers is used in a PCR. The goal of multiplex PCR is to amplify several segments of target DNA simultaneously and thereby to conserve template DNA, save time, and minimize expense. It is a PCR strategy that enables the amplification of multiple DNA targets in one run.
IAO_0000118: alternative term: Multiplex PCR
IAO_0000119: definition source: *http://viroligo.okstate.edu/enterdata/PCRs.htm *http://www.pcrlinks.com/glossary/M.htm
IAO_0000117: definition editor: Olga-Ximena Giraldo

M4L:aluminum_foil
type: Class
subclass of: M4L:laboratory_supply
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: European Aluminium Foil Association (EAFA). [cited 2010; Available from: http://www.alufoil.org/front_content.php.
IAO_0000118: alternative term: aluminium foil
IAO_0000115: definition: is aluminium prepared in thin metal leafs, with a thickness less than 0.2 mm (0.008 in), although much thinner gauges down to 0.006 mm are commonly used.
IAO_0000111: editor preferred term: aluminum foil

M4L:cryo-glove
type: Class
IAO_0000115: definition: Used in cryogenic atmosphere, ultra low temperature freezers, dry ice, steam autoclaves and ovens. Suitable for temperatures from -160°C (-250°F) to +148°C (300°F).
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: M4L:glove
IAO_0000119: definition source: Ted Pella, Inc. http://www.tedpella.com/gloves_html/gloves.htm
IAO_0000111: editor preferred term: cryo-glove

M4L:gel_based_electrophoresis
type: Class
subclass of: assay
IAO_0000115: definition: Gel electrophoresis is used in forensics, molecular biology, genetics, microbiology and biochemistry. The results can be analyzed quantitatively by visualizing the gel with a transilluminator and a gel imaging device. The image is recorded with a camera, and the intensity of the band or spot of interest is measured and compared against standard or markers loaded on the same gel. Depending on the type of analysis being performed, other techniques are often implemented in conjunction with the results of gel electrophoresis, providing a wide range of field-specific applications.
IAO_0000117: definition editor: Olga-Ximena Giralo
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Gel_electrophoresis#Applications
IAO_0000111: editor preferred term: gel-based electrophoresis

M4L:temperature_denaturating_role
type: Class
IAO_0000111: editor preferred term: temperature denaturating role
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: denaturation temperature, plays a role in the process of splitting the complementary double strands of DNA to form single strands.
subclass of: M4L:temperature_role
IAO_0000119: definition source: *Short Tandem Repeat DNA Internet DataBase *http://www.pcrlinks.com/glossary/D.htm

M4L:frozen_DNA
type: Class
IAO_0000111: editor preferred term: frozen DNA
subclass of: frozen
IAO_0000119: definition source: adapted from: oboContent:PATO
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: Definition: A quality inhering in a DNA by virtue of being kept below its freezing point. A quality inhering in a DNA by virtue of the DNA is being kept below its freezing point.

M4L:microcentrifuge_tube
type: Class
IAO_0000117: definition editor: Olga-Ximena Giraldo
subclass of: M4L:laboratory_supply
IAO_0000119: definition source: http://www.cramster.com/reference/wiki.aspx?wiki_name=Microcentrifuge_tube
IAO_0000111: editor preferred term: microcentrifuge_tube
IAO_0000115: definition: Microcentrifuge tubes or microfuge tubes are small, cylindrical plastic containers with conical bottoms, typically with an integral snap cap. They are used in molecular biology and biochemistry to store and centrifuge small amounts of liquid. Made of polypropylene, they can be used in very low temperature (-20 °C) or with organic solvents such as chloroform. They come in many different sizes, generally ranging from 250 μL to 2.0 mL. The most common size is 1.5 mL. Disinfection is possible (1 atm, 120 °C, 20 minutes), but due to their low cost and the difficulty in cleaning the plastic surface, they are usually discarded after each use.
IAO_0000112: example of usage: Eppendorf tube has become a genericized trademark for microfuge tubes or microcentrifuge tubes. Eppendorf is a major manufacturer of this item, but by no means the only one.
IAO_0000118: alternative term: microfuge tube

centrifuge_pellet_role
type: Class
IAO_0000111: Editor Preferred Term: centrifuge pellet role
IAO_0000119: Definition Source: OBI
IAO_0000117: Definition Editor: GROUP: Role branch
subclass of: Role
IAO_0000114: Has Curation Status: obo:IAO_0000125
IAO_0000115: Definition: pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.
IAO_0000118: Alternative Term: pellet role
IAO_0000112: Example Of Usage: Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet

laboratory_microwave_oven
type: Class
IAO_0000111: editor preferred term: laboratory microwave oven
subclass of: SNOMED:laboratory_equipment
IAO_0000118: alternative term: microwave oven
IAO_0000119: definition source: http://www.microwaveresearch.com/
IAO_0000115: definition: Laboratory microwave ovens, are used in sample preparation for biological, chemical and medical applications.
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000112: example of usage: laboratory microwave oven, is used to heat chemical substances in solution, or return to liquid state to the agarose gels.

SNOMED:liquid_nitrogen
type: Class
IAO_0000111: editor preferred term: liquid nitrogen
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: nitrogen gas condensed to a liquid with a boling point of about -196 degree Celsius. Very commonly the medium in which containers of genetic material are stored.
IAO_0000119: definition source: Zaid, A., et al., Glossary of biotechnology and genetic engineering. 1999.
IAO_0000118: alternative term: LN - Liquid nitrogen Liquid nitrogen (substance)
subclass of: SNOMED:nitrogen

CHEBI:SYBR_Green_I
type: Class
subclass of: CHEBI:cyanine_dye
IAO_0000118: alternative term: 2-{[3-(dimethylamino)propyl](propyl)amino}-4-[(E)-(3-methyl-1,3-benzothiazol-2(3H)-ylidene)methyl]-1-phenylquinolinium 2-{(E)-[2-{[3-(dimethylamino)propyl](propyl)amino}-1-phenylquinolin-4(1H)-ylidene]methyl}-3-methyl-1,3-benzothiazol-3-ium
IAO_0000115: Definition: SYBR Green I is a cationic unsymmetrical cyanine dye used as a nucleic acid stain in molecular biology. SYBR Green I binds to double-stranded DNA.
IAO_0000111: editor preferred term: SYBR Green I
IAO_0000412: imported from: Chemical entities of biological interest, Version 1.69

M4L:template_quantity_role
type: Class
IAO_0000119: definition source: QIAGEN, Sample & Assay Technologies. http://www.qiagen.com/faq/faqview.aspx?faqid=74&SearchText=&FaqCategoryId=0&MenuItemId=0&catalog=1&ProductLineId=1000222
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000115: definition: the quantity of nucleic acid starting template affect PCR, in particular the sensitivity and efficiency of amplification. PCR sensitivity and efficiency can be reduced by the presence of impurities in nucleic acid preparations or in biological samples.
IAO_0000111: editor preferred term: template quantity role
subclass of: nucleic_acid_template_role

ProcessualEntity
IAO_0000115: Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
IAO_0000112: Example of usage: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird

M4L:analytical_balance_instrument
type: Class
subclass of: M4L:laboratory_balance_instrument
IAO_0000111: editor preferred term: analytical balance instrument
IAO_0000119: definition source: http://en.wikipedia.org/wiki/Analytical_balance#Analytical_balance
IAO_0000115: definition: An analytical balance is used to measure mass to a very high degree of precision and accuracy. The measuring pan(s) of a high precision (0.1 mg or better) analytical balance are inside a transparent enclosure with doors so that dust does not collect and so any air currents in the room do not affect the balance's operation.
IAO_0000117: definition editor: Olga-Ximena Giraldo

DNA_extraction
type: Class
subclass of: nucleic acid extraction
IAO_0000111: Editor Preferred Term: DNA extraction
IAO_0000114: Has Curation Status: obo:IAO_0000123
IAO_0000115: Definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
IAO_0000117: Definition Editor: PlanAndPlannedProcess Branch
IAO_0000119: Definition Source: OBI branch derived

M4L:temperature_annealing_role
type: Class
subclass of: M4L:temperature_role
IAO_0000115: definition: annealing temperature is one of the most important parameters that need adjustment in the PCR reaction. Moreover, the flexibility of this parameter allows optimization of the reaction in the presence of variable amounts of other ingredients (especially template DNA and oligonucleotide primer length).
IAO_0000111: editor preferred term: temperature annealing role
IAO_0000117: definition editor: Olga-Ximena Giraldo
IAO_0000119: definition source: Wu, D.Y., et al., The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction. DNA Cell Biol, 1991. 10(3): p. 233-8.

Process
IAO_0000115: Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
IAO_0000112: Example of usage: the life of an organism, the process of sleeping, the process of cell-division

SpecificallyDependentContinuant
IAO_0000118: Synonyms: property trope mode
IAO_0000115: Definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
IAO_0000112: Example: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxyrenated and oxygenated blood, etc.

IndependentContinuant
IAO_0000115: Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
IAO_0000112: Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
IAO_0000118: Synonyms: substantial entity

ThreeDimensionalRegion
IAO_0000115: Definition: A spatial region [snap:SpatialRegion] with three dimensions.
IAO_0000112: Example of usage: a cube-shaped part of space, a sphere-shaped part of space

Continuant
IAO_0000118: synonyms: endurant
IAO_0000115: Definition: An 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.
IAO_0000112: Example: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building.

ObjectBoundary
IAO_0000112: Example of usage: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall.
comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
IAO_0000115: Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.
IAO_0000118: alternative term: substance boundary

FiatProcessPart
IAO_0000115: Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
IAO_0000112: Example of usage: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life

real time PCR thermal cycler
IAO_0000232: alterantive term: real-time PCR Instrument real-time PCR system

ABI PRISM 377 DNA Sequencer
IAO_0000111: editor preferred term: ABI PRISM 377 DNA Sequencer

OneDimensionalRegion
IAO_0000115: Definition: A spatial region [snap:SpatialRegion] with one dimension.
IAO_0000112: Example of usage: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space.

gel-electrophoresis instrument
IAO_0000111: editor preferred term:

Occurrent
IAO_0000115: Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
IAO_0000118: alternative term: perdurant
IAO_0000112: Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor

automated DNA sequencer
IAO_0000115: definition:

DependentContinuant
IAO_0000115: Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.

TwoDimensionalRegion
IAO_0000112: Example of usage: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space.

automated electrophoresis equipment
IAO_0000112: editor preferred term: automated electrophoresis equipment

Site
IAO_0000112: Example of usage: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria.
IAO_0000115: Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.
comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).

SpatialRegion
IAO_0000115: Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
IAO_0000112: Example of usage: the sum total of all space in the universe, parts of the sum total of all space in the universe

ObjectAggregate
IAO_0000118: alternative term: substance aggregate
IAO_0000115: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
IAO_0000112: Example of usage: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital

ZeroDimensionalRegion
IAO_0000115: Definition: A spatial region [snap:SpatialRegion] with no dimensions.
IAO_0000112: Example of usage: a point

ProcessAggregate
IAO_0000115: Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.
IAO_0000112: Example of usage: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together

whole genome amplification
IAO_0000112: editor preferred term:

ProcessBoundary
IAO_0000112: Example of usage: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery
IAO_0000115: Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.

Object
IAO_0000112: Example of usage: an organism, a heart, a chair, a lung, an apple
IAO_0000115: Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.
IAO_0000118: alternative term: substance

tris EDTA buffer
IAO_0000119: M4L:tris-EDTA_buffer

RealizableEntity
IAO_0000115: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
IAO_0000112: Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity

biomacromolecule
IAO_0000119: CHEBI:biomacromolecule

upstream primer role
IAO_0000232: alternative term: upstream primer role

Phage RNA Polymerase Promoter activity
IAO_0000112: editor preferred term:

ProcessualContext
IAO_0000112: Example of usage: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.
IAO_0000115: Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.

FiatObjectPart
IAO_0000118: alternative term: fiat substance part
IAO_0000115: Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.
IAO_0000112: Example of usage: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso.