Cross reference for SMART Protocols Ontology: workflow Module classes, properties and dataproperties back to ToC

This section provides details for each class and property defined by SMART Protocols Ontology: workflow Module.

Classes

tRNA threonylcarbamoyladenosinec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_86026

A threonylcarbamoyladenosine that is incorporated into a tRNA molecule.
has super-classes
ribonucleic acid c

10% ethanolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#TenPercentEthanol

An aqueous dilution of ethanol containing 10% ethanol by volume.
has super-classes
ethanol solution c

70% Ethanolc back to ToC or Class ToC

IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C62218

An aqueous dilution of ethanol containing 70% ethanol by volume.
has super-classes
ethanol solution c

75% ethanolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SeventyFivePercentEthanol

An aqueous dilution of ethanol containing 75% ethanol by volume.
has super-classes
ethanol solution c

A/Jc back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0001327

A/J is a mouse strain as described in Jackson Laboratory
Source
http://jaxmice.jax.org/strain/000646.html
has super-classes
Mus musculus c

actionc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_89

an action is “the process of doing something or being active” Reference: Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
has super-classes
occurrent c
participates in op some procedure c
has sub-classes
command action c, data action c, equipment setup action c, experiment action c

addc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_9

to add is an experiment action “to join or unite a component to another so as to increase the number, quantity in the container. The end container is the same for all components” Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of combination c

Advantage 2 PCR bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Advantage2PCRBuffer

Advantage 2 PCR buffer is a buffer optimized for amplifying genomic DNA, and in particular with products less than 1-2 kb.
Source
file:///Users/olgaxgiraldop/Downloads/PT3281-1_PR9Z3414%20(1).pdf
has super-classes
PCR buffer c

agarose gel electrophoresis protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AgaroseGelElectrophoresisProtocol

Agarose Gel Electrophoresis Protocol is a subclass of laboratory protocol. Agarose Gel Electrophoresis Protocol is a step by step description of a procedure used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.
has super-classes
electrophoresis protocol c

agarose in gel statec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AgaroseInGelState

AgaroseInGelState Is a gel resulting from the polymerization of agarose after heating agarose suspended in some buffer solution.
Source
Adapted from OBI
has super-classes
gel state c

agarose in liquid statec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AgaroseInLiquidState

The agarose will be in a liquid state acording to its gelling temperature and concentration.
has super-classes
liquid state c

alcoholc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_30879

A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
has super-classes
chemical compound reagent c
has sub-classes
primary alcohol c, secondary alcohol c

aldohexosec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33917

A hexose with a (potential) aldehyde group at one end.
has super-classes
aldose c
has sub-classes
glucose c

aldosec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_15693

Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals.
has super-classes
monosaccharide c
has sub-classes
aldohexose c

alert messagec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_121

An alert message is information, such as a warning or a caution that can be ignored by an automatic agent. The goal is to remind or alert the user.
has super-classes
textual entity c
has sub-classes
caution c, critical step c, hint c, pause point c, storage condition c, timing c, troubleshooting c
is in range of
has alert message op

alkali metal salt reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AlkaliMetalSaltReagent

Alkali metal salt reagent are any of the following chemical elements of the periodic table —namely, lithium (Li), sodium (Na) and potassium (K). Sodium and potassium are the sixth and seventh most abundant of the elements; constituting, respectively, 2.6 and 2.4 percent of Earth’s crust. Other alkali metals are considerably more rares, the lithium, for example, constitutes 0.007 percent of Earth’s crust.
Source
https://global.britannica.com/science/alkali-metal
has super-classes
chemical compound reagent c
has sub-classes
potassium salt reagent c, sodium salt reagent c

alkanesulfonate reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AlkanesulfonateReagent

alkanesulfonates are used for the separation of small or pollar cations.
has super-classes
chemical compound reagent c
has sub-classes
CHAPS c

alkyl sulfate reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AlkylSulfateReagent

Alkyl sulfate reagent is a reagent commonly used as an anionic surfactant in liquid soaps, detergents to clean wool, surface cleaners, as active ingredients in laundry detergents, shampoos and conditioners.
Source
https://en.wikipedia.org/wiki/Organosulfate
Example
A sodium dodecyl sulfate.
has super-classes
chemical compound reagent c
has sub-classes
sodium dodecyl sulfate c

alpha-aminoacyl-tRNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_2651

Any ribonucleic acid that is transfer RNA in which one or more of the free OH groups carries an alpha-aminoacyl group.
has super-classes
ribonucleic acid c

ammonium acetatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_62947

has super-classes
ammonium salt c
participates in op some precipitation reaction c

ammonium saltc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_47704

has super-classes
chemical compound reagent c
has sub-classes
ammonium acetate c

ammonium sulfatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_62946

An inorganic sulfate salt obtained by reaction of sulfuric acid with two equivalents of ammonia. A high-melting (decomposes above 280degreeC) white solid which is very soluble in water (70.6 g/100 g water at 0degreeC; 103.8 g/100 g water at 100degreeC), it is widely used as a fertilizer for alkaline soils.
has super-classes
inorganic sulfate salt c
participates in op some precipitation reaction c

amplified DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000809

DNA that has been produced in an enzymatic amplification process
Source
Alan Ruttenberg
Example
Amplied DNA created by PCR
has super-classes
processed DNA c

AmpliTaq DNA Polymerasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AmpliTaqDNAPolymerase

AmpliTaq DNA Polymerase is a 94 kDa, thermostable, recombinant DNA polymerase obtained by expression of a modified form of the Thermus aquaticus (Taq) DNA polymerase gene in E. coli.
Source
https://www.thermofisher.com/order/catalog/product/N8080155
has super-classes
taq polymerase c

AmpliTaq Goldc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AmpliTaqGold

AmpliTaq Gold is a thermostable DNA polymerase designed to make advanced polymerase Chain Reaction techniques. The key component in AmpliTaq Gold is AmpliTaq® DNA Polymerase (Deoxynucleoside triphosphate: DNA Deoxynucleotidyltransferase, E.C.2.7.7.7).
Source
http://mvz.berkeley.edu/egl/inserts/AmpliTaq%20Gold_041554.pdf
has super-classes
taq polymerase c

AMV reverse transcriptasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AMVReverseTranscriptase

AMV reverse transcriptase is an enzyme from the avian myeloblastosis virus like HIV has two subunits, a 63kDa subunit and a 95kDa subunit.
Source
http://link.springer.com/article/10.1007%2Fs10529-012-0904-9
has super-classes
reverse transcriptase c

analyzed data setc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AnalyzedDataSet

Is the result of data analysis process. This data can be organized into charts, graphs and tables to better visualize the information.
Source
Adapted from: www.unit5.org/villhauer/Glossary/Glossary.htm
has super-classes
data set c
has sub-classes
processed reads c
is disjoint with
raw data set c

ancient DNAc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AncientDNA

DNA recovered from ancient biological material (e.g., archaeological and historical skeletal material, mummified tissues, preserved plant remains, ice and permafrost cores).
Source
NCI Thesaurus
has super-classes
deoxyribonucleic acid c

animal cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000548

has super-classes
cell c

animal euthanization procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AnimalEuthanizationProcedure

A procedure in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject may later be refined with more specific list of organisms.
Source
OBI
has super-classes
laboratory procedure c
has protocol op some animal euthanization protocol c
is preceded by op some infection procedure c
has sub-classes
asphyxiation c, cervical dislocation c, decapitation c, electrocution c, intentional overdosing c

animal euthanization protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AnimalEuthanizationProtocol

A animal euthanization protocol is a protocol used in a parasitology experiments and defines instructions on how end the life of animals.
has super-classes
experimental protocol c

animal tissuec back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/CSP/4000-0119

tissue and cells derived from animals for use in research.
has super-classes
tissue c
has sub-classes
brain c, heart c, kidney c, liver c, lung c, spleen c

Apex Taq DNA Polymerasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ApexTaqDNAPolymerase

Apex Taq DNA Polymerase is a thermostable enzyme. The enzyme is isolated from Thermus aquaticus and has a molecular weight of approximately 94 kDa.
Source
https://corebio.ucsd.edu/4DCGI/Catalog/ProductDetail.html?prod_id=7924
has super-classes
taq polymerase c

aromatic ether reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#AromaticEtherReagent

Any ether in which the oxygen is attached to at least one aryl substituent.
Source
CHEBI
has super-classes
chemical compound reagent c
has sub-classes
Nonidet P-40 c, nonyl phenoxypolyethoxylethanol c

asphyxiationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302897

asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms.
Example
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
has super-classes
animal euthanization procedure c

aspiratec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_19

To aspirate is an experiment action “to draw in or remove by suction” Reference: Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
has super-classes
mode of separation c

assign namec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_41

To assign name is an experiment action to designate a new name to an entity
has super-classes
label c

bacterial cellc back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/285297004

has super-classes
cell c

bagc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Bag

A bag is a supply. A bag is a simple tool in the form of a non-rigid container.
Example
Laboratory bags: autoclavable biohazard bags, specimen/document zipper bags
has super-classes
equipment and supplies c

BALB/cc back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0000602

has super-classes
Mus musculus c

bead beaterc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BeadBeater

Disruption caused by collision with agitated beads in liquid suspension.
has super-classes
sample mill c

bile acid reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BileAcidReagent

Any member of a group of steroid carboxylic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
has super-classes
hydroxy-5beta-cholanic acid c
has sub-classes
chenodeoxycholic acid c, cholic acid c, deoxycholic acid c, lithocholic acid c

bile acid salt reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BileAcidSaltReagent

A salt of a bile acid.
Source
CHEBI
has super-classes
cholanoid c
has sub-classes
sodium deoxycholate c

blenderc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Blender

blender is an instrument that ensure a homogenized blending of the diluted sample.
has super-classes
sample mill c

boilc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_51

To boil is an experiment action “o bubble up in agitation through the action of heat causing the lowest portions of the liquid to pass into the gaseous form and escape; to reach the boiling point, to turn from the liquid into the gaseous state” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of property transformation c

brainc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000955

The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
has super-classes
animal tissue c

breakc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_47

To break is an experiment action “to separate into two or more pieces” regardless of precision of the separation Reference: based on Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
has super-classes
mode of category transform c
participates in op some cell disruption c

bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#buffer

A buffer is a solution that can resist pH change upon the addition of an acidic or basic components. It is able to neutralize small amounts of added acid or base, thus maintaining the pH of the solution relatively stable. This is important for processes and/or reactions which require specific and stable pH ranges.
Source
http://chemwiki.ucdavis.edu/Physical_Chemistry/Acids_and_Bases/Buffers
Example
The following could function as buffers when together in solution: i) Acetic acid (weak organic acid w/ formula CH3COOH) and a salt containing its conjugate base, the acetate anion (CH3COO-), such as sodium acetate (CH3COONa). ii) Pyridine (weak base w/ formula C5H5N) and a salt containing its conjugate acid, the pyridinium cation (C5H5NH+), such as Pyridinium Chloride. iii) Ammonia (weak base w/ formula NH3) and a salt containing its conjugate acid, the ammonium cation, such as Ammonium Hydroxide (NH4OH).
has super-classes
solution c
has sub-classes
PCR buffer c, lysis buffer c, phosphate buffered saline c

buffer ALc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BufferAL

Buffer AL is a lysis buffer used during DNA isolation using QIAamp and DNeasy kits.
Source
file:///Users/olgaxgiraldop/Downloads/HB12500021076579%20PS%20DNY%20Buffer%20AL%200513%20WW.pdf
Example
DNA purification
has super-classes
lysis buffer c

buffer AP1c back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BufferAP1

Buffer AP1 is a lysis buffer used during isolation of DNA from plant tissue with the DNeasy Plant Mini Kit.
Source
http://www.calpoly.edu/~bio/ubl/protocols_files/qiaplant.pdf
Example
DNA purification
has super-classes
lysis buffer c

buffer ATLc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BufferATL

Buffer ATL is a tissue lysis buffer for use in purification of nucleic acids.
Source
https://www.qiagen.com/es/shop/lab-essentials-and-accessories/buffer-atl/
has super-classes
lysis buffer c

buffer B1c back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BufferB1

Buffer B1 (Bacterial Lysis Buffer 1) consists of 50 mM Tris•Cl pH 8.0; 50 mM EDTA pH 8.0; 0.5% Tween 20; 0.5% Triton-X100. Buffer B1 is used in combination with lysozyme or lysostaphin and proteinase K for the efficient lysis of bacteria prior to DNA purification using QIAGEN Genomic-tips.
Source
https://www.qiagen.com/es/resources/faq?id=569abfa9-c05c-4a20-ae6b-793630da3d55&lang=en
has super-classes
lysis buffer c

buffer B2c back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BufferB2

Buffer B2 (Bacterial Lysis Buffer 2) consists of 3 M guanidine hydrochloride, 20% Tween 20. Buffer B2 is used in combination with Buffer B1, lysozyme or lysostaphin and Proteinase K for efficient lysis of bacteria prior to DNA purification using QIAGEN Genomic-tips.
Source
https://www.qiagen.com/es/resources/faq?id=92b08ae8-b395-4961-b71b-b1e784c7c8ea&lang=en
has super-classes
lysis buffer c

buffer C1c back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BufferC1

cell lysis buffer
cell lysis buffer
has super-classes
lysis buffer c

buffer Y1c back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BufferY1

yeast lysis buffer
has super-classes
lysis buffer c

C57BLc back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0005181

An inbred strain of mouse created in 1921 by C. C. Little at the Bussey Institute for Research in Applied Biology.
has super-classes
Mus musculus c
has sub-classes
C57BL/6 c

C57BL/6c back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0004472

C57BL/6 is a mouse strain as described in Jackson Laboratory strain index
has super-classes
C57BL c

calculatec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_60

To calculate is an experiment action to estimate or determine a value of an entity by arithmetical or mathematical reckoning Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
data action c

calibratec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_23

To calibrate is an experiment action “to determine the correct position, value, capacity, etc., of; to set an instrument so that readings taken from it are absolute rather than relative” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
equipment setup action c

carbohydratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_16646

Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
has super-classes
chemical compound reagent c
has sub-classes
monosaccharide c, oligosaccharide c

carbon dioxidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_16526

A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food.
has super-classes
one-carbon compound c
participates in op some animal euthanization procedure c

cautionc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_122

A caution is a message given to a user of a protocol about potentially dangerous properties of materials used in the experiment.
has super-classes
alert message c
has sub-classes
flammable c, neurotoxic c, pyrophoric c, toxic c, volatile c

cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000000

A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
has super-classes
sample from organism c
has sub-classes
animal cell c, bacterial cell c, fungal cell c, plant cell c

cell disruptionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#CellDisruption

Breaking the cells open, is the first basic step in a DNA extraction. This is commonly achieved by chemical and physical methods-blending, grinding or sonicating the sample.
has super-classes
protocol instruction c
part of op some nucleic acid extraction protocol c
precedes op some denaturation reaction c
has members
cell disruption 1 ni

centrifugec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400106

A device with a rapidly rotating container that applies centrifugal force to its contents
Source
http://en.wikipedia.org/wiki/Centrifuge
has super-classes
equipment and supplies c
has sub-classes
microcentrifuge c

centrifugec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_53

To centrifuge is an experiment action “to subject to centrifugal motion; to separate by means of a centrifuge”. Reference: Based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of separation c
participates in op some precipitation reaction c

centrifuge tubec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#CentrifugeTube

Centrifuge tube is a supply. centrifuge tubes are tapered tubes of various sizes made of glass or plastic. They may vary in capacity from tens of millilitres.
Source
http://en.wikipedia.org/wiki/Laboratory_centrifuge#Centrifuge_tubes
Example
Weigh 300-400 mg of ground, lyophilized tissue, into a 15 ml polypropylene centrifuge tube.
has super-classes
equipment and supplies c

cervical dislocationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302896

cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion
Example
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3
has super-classes
animal euthanization procedure c

cetyltrimethylammonium bromidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_3567

The organic bromide salt that is the bromide salt of cetyltrimethylammonium; one of the components of the topical antiseptic cetrimide.
Example
cetyltrimethylammonium bromide acts a cationic detergent and is suitable for use in DNA precipitation. CTAB has been used for the isolation of plant high molecular weight DNA as well as plant DNA for use in PCR analysis. It has been utilized to precipitate nucleic acids.
has super-classes
quaternary ammonium salt reagent c
participates in op some cell disruption c

CHAPSc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_1418

A nondenaturing zwitterionic detergent for solubilizing membrane proteins and breaking protein-protein interactions. Combines the useful properties of both the sulfobetaine-type and the bile salt detergents. Commonly used for protein solubilization in isoelectric focusing and two-dimensional electrophoresis especially for non-denaturing (without urea) isoelectric focusing. CHAPS have been shown to give excellent resolution of some subcellular preparations and plant proteins. (source: http://agscientific.com/blog/index.php/2012/10/01/chaps14-faqs-protocols-you-must-have/)
an alkanesulfonate that has formula C32H58N2O7S.
Example
Concentrations between 1-4% (v/v) are typically used in an isoelectric focusing gel. A commonly used isoelectric focusing sample solution consists of 8 M urea, 4% CHAPS, 50-100 mM dithiothreitol (DTT) and 40 mM Tris. Its small micellar molecular weight (6150) and high CMC (6-10 mM) allow it to be removed from samples by dialysis. It can be used as a non-toxic stabilizing agent for growth factors.
has super-classes
alkanesulfonate reagent c
participates in op some cell disruption c

checkc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_93

has super-classes
command action c

chemical compound reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ChemicalCompoundReagent

chemical compound reagent is a reagent that is added to a system in order to bring about a chemical reaction or are added to see if a reaction occurs.
has super-classes
reagent c
has sub-classes
alcohol c, alkali metal salt reagent c, alkanesulfonate reagent c, alkyl sulfate reagent c, ammonium salt c, aromatic ether reagent c, carbohydrate c, chloride salt reagent c, copolymer macromolecule reagent c, disaccharide derivative reagent c, glycol reagent c, one-carbon compound c, organic aromatic compound c, phenacyl bromide reagent c, poly ethylene glycol reagent c, quaternary ammonium salt reagent c, saponin reagent c, sarcosine reagent c, steroid reagent c, sulfate salt reagent c, vinyl polymer macromolecule reagent c

chenodeoxycholic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_16755

A dihydroxy-5beta-cholanic acid that is (5beta)-cholan-24-oic acid substituted by hydroxy groups at positions 3 and 7 respectively.
Example
chenodeoxycholic acid acts as an anionic detergents that often completely disrupt cell membranes and fully denature proteins.
has super-classes
bile acid reagent c
participates in op some cell disruption c
participates in op some denaturation reaction c

chloride salt reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ChlorideSaltReagent

Chloride salts such as sodium chloride are often very soluble in water. It is an essential electrolyte located in all body fluids responsible for maintaining acid/base balance, transmitting nerve impulses and regulating fluid in and out of cells.
Source
https://en.wikipedia.org/wiki/Chloride
has super-classes
chemical compound reagent c
has sub-classes
inorganic chloride c

chloroformc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_35255

A one-carbon compound that is methane in which three of the hydrogens are replaced by chlorines.
has super-classes
one-carbon compound c
participates in op some denaturation reaction c

Chloroform:Isoamyl alcoholc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ChloroformIsoamylAlcoholMixture

mixture suitable for nucleic acid purification in plants.
has super-classes
solution c

cholanic acidsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_36278

has super-classes
steroid acid reagent c
has sub-classes
hydroxy-5beta-cholanic acid c

cholanoidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_36078

has super-classes
steroid reagent c
has sub-classes
bile acid salt reagent c

cholic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_16359

A bile acid that is 5beta-cholan-24-oic acid bearing three alpha-hydroxy substituents at position 3, 7 and 12.
Example
Non-denaturing ionic detergent used for extraction of membrane proteins.
has super-classes
bile acid reagent c
participates in op some cell disruption c

chopc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Chop

cut (something) into pieces with repeated sharp blows using a sharp instrument.
has super-classes
mode of category transform c
participates in op some cell disruption c

coffee millc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#CoffeMill

Coffee mill is an instrument used (during the first stage of nucleic acids purification), to crush leaf tissue to make leaf powder.
has super-classes
sample mill c

command actionc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_90

a command action is an action with a goal to control the flow of the process of executing of the experiment, e.g. stop, check, continues.
has super-classes
action c
has sub-classes
check c, continue c, go c, stop c, store c

complementary DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/REO_0000045

a DNA moelcule representing sequence reverse transcribed from a messenger RNA template, in a reaction catalyzed by the enzyme reverse transcriptase and the enzyme DNA polymerase.
has super-classes
deoxyribonucleic acid c

connetc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_28

To connect is an experiment action “to join, fasten, or link together … by the connecting medium or instrumentality” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of combination c
has sub-classes
join c

continuantc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/snap#Continuant

Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
has super-classes
entity c
has sub-classes
dependent continuant c, independent continuant c
is in domain of
participates in op
is in range of
has experimental input op, has output op
is disjoint with
occurrent c

continuec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_91

has super-classes
command action c

copolymer macromolecule reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#CopolymerMacromoleculeReagent

A macromolecule derived from two or more species of monomer.
Source
CHEBI
has super-classes
chemical compound reagent c
has sub-classes
pluronic c

coverc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_32

To cover is an experiment action to put or lay a top over a base, with the effect of enclosing Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of combination c
has sub-classes
seal c

critical stepc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#CriticalStep

A critical step is a message given to a user to perform a protocol instruction in a very precise manner e.g., where the time and temperature of a step is crucial or the use of RNase free solutions is required.
Example
Remove the combs and flush out the wells using a syringe. This is a CRITICAL STEP, especially for polymorphic bands that are close to each other. Otherwise, unpolymerized acrylamide solution will be polymerized at the bottom of the wells and will affect the migration of the fragments. (Laboratory Protocols CIMMYT, 2005) CRITICAL STEP: The supernatant in each step should be carefully transferred without disturbing the other layers. (Sudha, 2012)
has super-classes
alert message c

CTAB bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#CTABBuffer

CTAB buffer is a buffer used during the extraction/isolation of highly polymerized DNA from plant material. The main chemical compound, CTAB, simultaneously solubilizes the plant cell wall and lipid membranes of internal organelles and denatures proteins (enzymes).
Source
PERSON:Olga Giraldo
Example
DNA purification
has super-classes
lysis buffer c

cultivarc back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Cultivar

a plant variety obtained in agriculture in horticulture.
has super-classes
strain or line c

cytoplasmic extraction bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#CytoplasmicExtractionBuffer

The cytoplasmic extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. This buffer causes selective membrane permeabilization, releasing soluble cytoplasmic contents.
Source
https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/protein-biology-application-notes/subcellular-protein-fractionation.html
has super-classes
lysis buffer c
part of op only subcellular protein fractionation kit for tissues c

data actionc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_111

A data action is an action of estimation or evaluation of data
has super-classes
action c
has sub-classes
calculate c, label c, measure c, record c

data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000100

A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
Source
group:OBI OBI_0000042
Example
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has super-classes
information content entity c
participates in op some laboratory procedure c
participates in op some laboratory subprocedure c
participates in op some experimental protocol execution c
has sub-classes
analyzed data set c, equipment and supplies list c, raw data set c, reagent list c, recipe list c, software list c, specimen list c, three dimensional image c

de-lidc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_26

To de-lid is an experiment action to remove a lid from a base and move it to a lid location
has super-classes
remove c

decapitationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302899

decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..)
Example
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
has super-classes
animal euthanization procedure c

decyl beta-D-maltopyranosidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_67097

A glycoside resulting from attachment of a decyl group to the reducing-end anomeric centre of a beta-maltose molecule.
Example
decyl beta-D-maltopyranoside acts as a non-ionic detergent used for solubilizing proteins while maintaining native subunit structure, enzymatic activity, or other structural functions.
has super-classes
disaccharide derivative reagent c
participates in op some denaturation reaction c

denaturation reactionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#DenaturationReaction

Denaturation reaction is a set of instructions in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state, by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), radiation or heat.
Source
https://en.wikipedia.org/wiki/Denaturation_(biochemistry)
Example
protocols for extracting DNA use detergents or surfactants for denaturating membrane lipids; or adding protease for denaturing proteins; or RNase for denaturing RNA.
has super-classes
protocol instruction c
is preceded by op some cell disruption c
part of op some nucleic acid extraction protocol c
precedes op some precipitation reaction c
has members
denaturation reaction 1 ni

deoxycholic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_28834

A dihydroxy-5beta-cholanic acid that has formula C24H40O4.
has super-classes
bile acid reagent c

deoxyribonucleic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_16991

High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
has super-classes
nucleic acid c
has sub-classes
ancient DNA c, complementary DNA c, double-stranded DNA c, processed DNA c, single-stranded DNA c
is disjoint with
ribonucleic acid c

deoxyribonucleoside triphosphate reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/REO_0000421

a nucleoside triphosphate reagent containing three phosphate groups bound to a 2'-deoxyribo- sugar ring
has super-classes
nucleoside triphosphate reagent c
participates in op some reverse transcription c
participates in op some PCR amplification c

dependent continuantc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/snap#DependentContinuant

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.
is equivalent to
generically dependent continuant c or specifically dependent continuant c
has super-classes
continuant c
has sub-classes
generically dependent continuant c, specifically dependent continuant c

digitoninc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_27729

A spirostanyl glycoside that has formula C56H92O29.
Example
digitonin acts as a nonionic detergent used to solubilize receptors and permeabilize cellular and nuclear membranes.
has super-classes
saponin reagent c
participates in op some cell disruption c

disaccharide derivative reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#DisaccharideDerivativeReagent

A carbohydrate derivative that is formally obtained from a disaccharide.
Source
CHEBI
has super-classes
chemical compound reagent c
has sub-classes
decyl beta-D-maltopyranoside c

disaccharide reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#DisaccharideReagent

A compound in which two monosaccharides are joined by a glycosidic bond.
Source
CHEBI
has super-classes
oligosaccharide c
has sub-classes
sucrose c

discardc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_27

To discard is an experiment action to move something to a waste location
has super-classes
remove c

dissolvec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_44

to dissolve is an experiment action “to change or cause to change from a solid to a dispersed form by immersion in a fluid of suitable properties” Reference: biology online dictionary http://www.biology-online.org/dictionary/Dissolve -
has super-classes
mode of combination c

dithiothreitolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Dithiothreitol

Dithiothreitol (DTT) is the common name for a small-molecule redox reagent also known as Cleland's reagent. DTT's formula is C4H10O2S2. Its name derives from the four-carbon sugar, threose. DTT has an epimeric ('sister') compound, dithioerythritol (DTE).
Source
https://en.wikipedia.org/wiki/Dithiothreitol
Example
DTT is used as a reducing or "deprotecting" agent for thiolated DNA. DTT is frequently used to reduce the disulfide bonds of proteins. DTT can also be used as an oxidizing agent.
has super-classes
glycol reagent c
participates in op some denaturation reaction c

dividec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_7

To Divide is an experiment action “to separate (a thing) into parts, or (a number or collective body) into smaller groups; to split up, cleave; to break or cut asunder” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of category transform c

DNA extractc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001051

The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
Source
Group: UPenn group
has super-classes
processed DNA c

DNA extraction procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#DNAExtractionProcedure

A DNA extraction procedure is a subclass of nucleic acid extraction procedure where the desired output material is DNA.
has super-classes
nucleic acid extraction procedure c
has protocol op some DNA extraction protocol c

DNA extraction protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#DNAExtractionProtocol

DNA extraction protocol is a subclass of nucleic acid extraction protocol. DNA extraction protocol, is a step by step description of a procedure in which is recovered a fraction of DNA from a material entity.
has super-classes
nucleic acid extraction protocol c
has instruction op some cell disruption c
has instruction op some denaturation reaction c
has instruction op some precipitation reaction c
has instruction op some washing nucleic acids c
is disjoint with
RNA extraction protocol c

DNA oligonucleotidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001203

A DNA reagent consisting of a short, linear DNA polymer, typically with 100 or fewer bases.
Example
A primer.
has super-classes
DNA reagent c
has sub-classes
primer c

DNA pelletc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#DNAPellet

A material entity which results from the aggregation of DNA produced by the application of centrifugal force to a liquid containing DNA in suspension.
Source
Adapted from OBI
has super-classes
processed DNA c

DNA reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001201

A reagent that is a polymer comprised of DNA nucleotides.
Source
PERSON: Matthew Brush
Example
A primer.
has super-classes
nucleic acid reagent c
has sub-classes
DNA oligonucleotide c

DNA separated by molecular sizec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#DNASeparatedByMolecularSize

DNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix.
has super-classes
processed DNA c

documentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000310

A collection of information content entities intended to be understood together as a whole.
Example
an experimental protocol
has super-classes
information content entity c
has sub-classes
experimental protocol c

double-stranded DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_4705

has super-classes
deoxyribonucleic acid c

double-stranded RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_67208

A ribonucleic acid with two complementary strands, similar to the DNA found in all cells.
has super-classes
ribonucleic acid c

dounce homogenizerc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#DounceHomogenizer

Shearing caused by a round glass pestle that is manually driven into a glass tube
has super-classes
homogenizer c

drillc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Drill

a tool or machine with a rotating cutting tip or reciprocating hammer or chisel, used for making holes.
has super-classes
sample mill c

ecotypec back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Ecotype

a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
has super-classes
strain or line c

electrocutionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302895

electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process.
Example
PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376.
has super-classes
animal euthanization procedure c

electrophoresis procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ElectrophoresisProcedure

Electrophoresis procedure is a subclass of laboratory procedure. Electrophoresis procedure is 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.
Example
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.
has super-classes
laboratory procedure c
is preceded by op some polymerase chain reaction procedure c
is preceded by op some nucleic acid extraction procedure c
has protocol op some electrophoresis protocol c

electrophoresis protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ElectrophoresisProtocol

Electrophoresis protocol is a subclass of laboratory protocol. Electrophoresis protocol is a step by step description of an electrophoresis procedure in which are recovered fragments of biomolecules separated by charge.
has super-classes
experimental protocol c
has sub-classes
agarose gel electrophoresis protocol c

endopeptidase Kc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#EndopeptidaseK

An enzyme that catalyzes the hydrolysis of keratin, and of other proteins with subtilisin-like specificity. It hydrolyses peptide amides. Endopeptidase K is from the mold Tritirachium album Limber.
Source
National Drug File-Reference Terminology
Example
Proteinase K is commonly used in molecular biology to digest protein and remove contamination from preparations of nucleic acid.
has super-classes
enzyme reagent c
participates in op some denaturation reaction c

entityc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1#Entity

is equivalent to
continuant c or occurrent c
has sub-classes
continuant c, occurrent c

enzimatic amplification protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#EnzimaticAmplificationProtocol

Enzimatic amplification protocol is a subclass of laboratory protocol. Enzimatic amplification protocol, is a step by step description of a procedure about the use of enzymes to increase the number of molecules from a material entity.
has super-classes
experimental protocol c
has sub-classes
polimerase chain reaction protocol c, reverse transcription PCR protocol c

enzymatic amplification procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#EnzymaticAmplificationProcedure

Enzymatic amplification procedure is a subclass of laboratory procedure that uses enzymes to increase the number of molecules of a biomaterial.
Example
polymerase chain reaction (PCR), reverse transcribed polymerase chain reaction (RT-PCR).
has super-classes
laboratory procedure c
has sub-classes
polymerase chain reaction procedure c, reverse transcription PCR procedure c

enzyme reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#EnzymeReagent

Enzymes are biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified.
Source
MESH
has super-classes
reagent c
has sub-classes
endopeptidase K c, reverse transcriptase c, taq polymerase c

equipment and suppliesc back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/MSH/D004864

Expendable and nonexpendable equipment, supplies, apparatus, and instruments that are used in diagnostic, surgical, therapeutic, scientific, and experimental procedures.
has super-classes
material entity c
has name op some equipment or supplies name c
has sub-classes
bag c, centrifuge c, centrifuge tube c, incubator c, microcentrifuge tube c, micropipette c, physical disruption equipment and supplies c, portable ice chest c, temperature control bath c, thermal cycler c
is disjoint with
reagent c, material sample c, organism c, primer c

equipment and supplies listc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#EquipmentAndSuppliesList

Equipment and supplies list is a data set of the names or identifiers of the equipments and supplies that are part of materials section of a protocol.
has super-classes
data set c
has part op some equipment or supplies name c

equipment or supplies namec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#EquipmentOrSuppliesName

Equipment or supply name is a textual entity. Equipment or supply name is the name of equipment or supply.
Example
Nalgene Cryogenic Tube, sterile, 1.2 ml. S1000 Thermal Cycler with 96-Deep Well Reaction Module.
has super-classes
name c
part of op some equipment and supplies list c

equipment setup actionc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_112

An equipment setup action is an action to put equipment into a required state for the experiment action to be executed
has super-classes
action c
has sub-classes
calibrate c

ethanolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_16236

A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group.
has super-classes
primary alcohol c
participates in op some precipitation reaction c

ethanol solutionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#EthanolSolution

A homogeneous mixture of ethanol and water.
Source
http://cameochemicals.noaa.gov/chemical/19240
Example
70% ethanol
has super-classes
solution c
has sub-classes
10% ethanol c, 70% Ethanol c, 75% ethanol c

experimentc back to ToC or Class ToC

IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C42790

A coordinated set of actions and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing
has super-classes
occurrent c
has sub-classes
parasitology experiment c

experiment actionc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_1

An experimental action is a process of manipulation in the domain of the experiment in order to achieve a particular sub goal, which is a part of the goal of the experiment. Reference: EXPO
has super-classes
action c
has sub-classes
mode of combination c, mode of separation c, mode of transformation c

experimental protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ExperimentalProtocol

An experimental protocol is a sequence of tasks and operations executed to perform experimental research. The protocols often include equipment, reagents, critical steps, troubleshooting, tips and all the information that facilitates reusability.
has super-classes
document c
has instruction op some protocol instruction c
has sub-classes
animal euthanization protocol c, electrophoresis protocol c, enzimatic amplification protocol c, housing condition protocol c, infection protocol c, nucleic acid extraction protocol c, protein extraction protocol c, specimen preparation protocol c
is in domain of
has instruction op, has outcome op
is in range of
has protocol op, is documented in op

experimental protocol executionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ExperimentalProtocolExecution

has super-classes
planned process c
is documented in op some experimental protocol c
has procedure op some laboratory procedure c
has experimental input op some data set c
has output op some data set c
is in domain of
has procedure op, is documented in op

filterc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_25

To filter is an experiment action “to pass (a liquid) through a filter, or some porous medium, for the purpose of removing solid particles or impurities” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
remove c

flammablec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Flammable

Easily ignited.
Source
http://wordnetweb.princeton.edu/perl/webwn?s=flammable
Example
Keep away from sources of ignition.
has super-classes
caution c

flowerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PO_0009046

A determinate reproductive shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part.
has super-classes
plant tissue c

forward primerc back to ToC or Class ToC

IRI: http://purl.org/obo/owl/SO#SO_0000121

A single stranded oligo used for polymerase chain reaction.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
primer c
participates in op some PCR amplification c

freezer millingc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#FreezerMilling

Freezer milling is a type of cryogenic milling that uses a solenoid to mill samples. The solenoid moves the grinding media back and forth inside the vial, grinding the sample down to analytical fineness.
has super-classes
sample mill c

french pressure cell pressc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#FrenchPressureCellPress

French pressure cell press is a sample mill. The shearing is caused by high pressure when sample is forced through a small hole.
has super-classes
sample mill c

fungal cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000521

has super-classes
cell c
has sub-classes
yeast cell c

gel statec back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/npo#NPO_1509

Physical state which is characteristic of a gel.
has super-classes
physical state c
has sub-classes
agarose in gel state c
is disjoint with
liquid state c

gene-specific primerc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#GeneSpecificPrimer

A gene-specific primer is a short strand of nucleic acid that hybridizes only to sequences exactly complementary to the primer sequence.
Source
PERSON: Olga Giraldo
has super-classes
primer c
participates in op some reverse transcription c

GeneAmp PCR Bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#GeneAmpPCRBuffer

GeneAmp PCR Buffer is optimized for use with the enzyme AmpliTaq DNA Polymerase.
has super-classes
PCR buffer c

generically dependent continuantc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant

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.
has super-classes
dependent continuant c
has sub-classes
information content entity c
is disjoint with
specifically dependent continuant c

geno grinderc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#GenoGrinder

Geno grinder is a plant and animal tissue homogenizer used for high-throughput applications involving sample preparation for DNA, RNA, and protein extractions, pesticide residue analysis, and more.
has super-classes
homogenizer c

glucosec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_17234

An aldohexose used as a source of energy and metabolic intermediate.
has super-classes
aldohexose c

glycol reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#GlycolReagent

A diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent.
Source
CHEBI
has super-classes
chemical compound reagent c
has sub-classes
dithiothreitol c

goc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_94

has super-classes
command action c

grindc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Grind

Grind is a experimetnal action. Grind is to reduce (something) to small particles or powder by crushing it.
has super-classes
mode of category transform c
participates in op some cell disruption c

grinding machinec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#GrindingMachine

Grinding machine is a equipment. Grinding machine is a machine used to grind grains and leaves.
Example
Put the number of seed indicated by the kit protocol in the grinding machine and grind the seed to a powder.
has super-classes
sample mill c

ground tissuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PO_0025059

Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015).
has super-classes
plant tissue c

guanidinium thiocyanate-phenolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#GuanidiniumThiocyanatePhenol

guanidinium thiocyanate-phenol is a mixture used in RNA/DNA/protein extraction.
has super-classes
solution c

heartc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000948

A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
has super-classes
animal tissue c

heatc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_50

To heat is an experiment action “to raise the temperature of” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of property transformation c

hintc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Hint

A hint is a message given to a user of a protocol that will help to perform the experiment.
Example
HINT: Mix well by vortex before to use. HINT: ADD NaOH to WATER to avoid splashing.
has super-classes
alert message c

homogenizec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Homogenize

Homogenize is a experimental action. Homogenize is to make uniform or similar.
has super-classes
mode of category transform c
participates in op some cell disruption c

homogenizerc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Homogenizer

A homogenizer is a equipment of laboratory used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. Many different models have been developed using various physical technologies for disruption.
Source
https://en.wikipedia.org/wiki/Homogenizer
has super-classes
sample mill c
has sub-classes
dounce homogenizer c, geno grinder c, polytron homogenizer c, potter-elvehjem homogenizer c

Hot Start Taq DNA Polymerasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#HotStartTaqDNAPolymerase

Hot Start Taq DNA Polymerase is a mixture of Taq DNA Polymerase and an aptamer-based inhibitor.
Source
https://www.neb.com/products/m0495-hot-start-taq-dna-polymerase
has super-classes
taq polymerase c

housing condition procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#HousingConditionProcedure

The term “housing conditions” includes the physiological, chemical, and social environment as well as handling procedures and environmental enrichment. Scientists strive to standardize these conditions so that it is only the factor of interest which is changed in order to obtain both reliable and repeatable results from the minimum number of animals.
Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378295/
has super-classes
laboratory procedure c
has protocol op some housing condition protocol c

housing condition protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#HousingConditionProtocol

Housing condition protocol is a protocol that defines instructions about the environmental conditions and handling of experimental organims.
has super-classes
experimental protocol c

hydroxy-5beta-cholanic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_24663

has super-classes
cholanic acids c
has sub-classes
bile acid reagent c

ignitec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_37

To ignite is an experiment action “to subject to the action of fire” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of property transformation c

incubatec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_49

To incubate is an experiment action to maintain optimal environmental conditions in order to promote growth or chemical reaction to cause to develop in an incubator or culture medium
has super-classes
mode of property transformation c

incubatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000136

a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
Source
http://www.medterms.com/script/main/art.asp?articlekey=18426
Example
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
has super-classes
equipment and supplies c

independent continuantc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant

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.
has super-classes
continuant c
has sub-classes
material entity c

infection procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#InfectionProcedure

The state of being infected such as from the introduction of a foreign agent such as serum, vaccine, antigenic substance or organism
Source
EFO
has super-classes
laboratory procedure c
is preceded by op some housing condition procedure c
has protocol op some infection protocol c

infection protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#InfectionProtocol

Infection protocol is a protocol used in parasitology experiments and defines instructions on how carry out the infection of a organism that acts as host.
has super-classes
experimental protocol c

information biomacromoleculec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33695

has super-classes
sample from organism c
has sub-classes
nucleic acid c, protein c
is disjoint with
solution c, reagent c, organism c, primer c

information content entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000030

an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
Source
OBI_0000142
Example
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has super-classes
generically dependent continuant c
has sub-classes
data set c, document c, textual entity c

injectionc back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/59108006

injection is a introduction procedure where a substance is introduced into a organism, usually by means of a hypodermic syringe, as a liquid into the veins or muscles of the body.
has super-classes
Introduction procedure c
has sub-classes
intraperitoneal injection c

inoculatec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_31

To inoculate is an experiment action “to join or unite by insertion” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of combination c

inorganic chloridec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_36093

has super-classes
chloride salt reagent c
has sub-classes
lithium chloride c, sodium chloride c

inorganic sulfate saltc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_24840

has super-classes
sulfate salt reagent c
has sub-classes
ammonium sulfate c

Instructionc back to ToC or Class ToC

IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C42688

A message describing how something is to be done.
has super-classes
textual entity c
has sub-classes
protocol instruction c

intentional overdosingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0302898

intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death
Example
In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment. J Neurooncol. 1994;22(3):209-20. PMID: 7760097
has super-classes
animal euthanization procedure c

intraperitoneal injectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0000376

Injection of a substance into the body cavity.
Example
Injection of a substance into the peritoneal cavity.
has super-classes
injection c
participates in op some infection procedure c

Introduction procedurec back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/107733003

Introduction of object AND/OR substance into or onto body, including injection, implantation, infusion, perfusion, transfusion, irrigation, instillation, insertion, placement, replacement, packing, intubation, catheterization, cannulation Introduction of object AND/OR substance into or onto body, including injection, implantation, infusion, perfusion, transfusion, irrigation, instillation, insertion, placement, replacement, packing, intubation, catheterization, cannulation.
has super-classes
laboratory procedure c
has sub-classes
injection c

joinc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_34

To join is an experiment action “to put (things) together, so that they become physically united or continuous; to fasten, attach, connect, unite (one thing to another); also, to connect by means of something intervening or attached to each” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
connet c

kidneyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002113

A paired organ of the urinary tract which has the production of urine as its primary function.
has super-classes
animal tissue c

kitc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Kit

A set of chemical substances, articles or equipment needed for a specific purpose.
A set of chemical substances, articles or equipment needed for a specific purpose. Example of usage: Universal Linker Kit, laboratory kit that allows customization of protein microarrays.
Example
Universal Linker Kit, laboratory kit that allows customization of protein microarrays.
has super-classes
material entity c
has sub-classes
subcellular protein fractionation kit for tissues c

KlenTaq DNA Polymerasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#KlenTaqDNAPolymerase

KlenTaq DNA Polymerase is missing the N-terminal portion of the gene, encoding Thermus aquaticus (Taq) DNA polymerase, leaving a highly active and even more thermal stable DNA polymerase activity. The missing N-terminal portion is homologous to the 5’→3’ exonuclease region of E. coli. DNA polymerase I.
Source
http://www.klentaq.com/products/klentaq
has super-classes
taq polymerase c

labelc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_61

To label is an experiment action to designate a name to an entity
has super-classes
data action c
has sub-classes
assign name c, re-name c

laboratory procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#LaboratoryProcedure

A laboratory procedure is the conversion of an input into an output.
has super-classes
procedure c
has output op some data set c
has experimental input op some data set c
has subprocedure op some laboratory subprocedure c
has alert message op some alert message c
has description op some procedure description c
has sub-classes
Introduction procedure c, animal euthanization procedure c, electrophoresis procedure c, enzymatic amplification procedure c, housing condition procedure c, infection procedure c, nucleic acid extraction procedure c, protein extraction procedure c, specimen preparation procedure c
is in domain of
has protocol op, has subprocedure op
is in range of
has procedure op

laboratory subprocedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#LaboratorySubprocedure

A Sub procedure is a serie of statements that are executed. A sub procedure acts as a module of a procedure.
has super-classes
procedure c
has alert message op some alert message c
has description op some subprocedure description c
has output op some data set c
has experimental input op some data set c
is in domain of
has alert message op, has description op
is in range of
has subprocedure op

leafc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PO_0025034

A phyllome (PO:0006001) that is not associated with a reproductive structure.
has super-classes
plant tissue c

liquid statec back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/npo#NPO_1504

Physical state which is characteristic of a liquid.
has super-classes
physical state c
has sub-classes
agarose in liquid state c
is disjoint with
gel state c

lithium chloridec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_48607

A metal chloride salt with a Li(+) counterion.
has super-classes
inorganic chloride c
participates in op some precipitation reaction c

lithocholic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_16325

A monohydroxy-5beta-cholanic acid with a alpha-hydroxy substituent at position 3. It is a bile acid obtained from chenodeoxycholic acid by bacterial action.
has super-classes
bile acid reagent c
participates in op some denaturation reaction c

liverc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002107

An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
has super-classes
animal tissue c

lungc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002048

Respiration organ that develops as an oupocketing of the esophagus.
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
has super-classes
animal tissue c

lyophilized ground tissuec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#LyophilizedGroundTissue

lyophilized ground tissue is a ground tissue dried by freezing in a high vacuum.
has super-classes
lyophilized tissue c

lyophilized leafc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#LyophilizedLeaf

lyophilized leaf is a leaf tissue dried by freezing in a high vacuum.
has super-classes
lyophilized tissue c

lyophilized rootc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#LyophilizedRoot

lyophilized root is a root tissue dried by freezing in a high vacuum.
has super-classes
lyophilized tissue c

lyophilized seedc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#LyophilizedSeed

lyophilized seed is a seed tissue dried by freezing in a high vacuum.
has super-classes
lyophilized tissue c

lyophilized tissuec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#LyophilizedTissue

lyophilized tissue is a tissue dried by freezing in a high vacuum.
Example
lyophilized leaf, lyophilized root, lyophilized seed
has super-classes
tissue c
has sub-classes
lyophilized ground tissue c, lyophilized leaf c, lyophilized root c, lyophilized seed c

lyophilizerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001087

A device that is used to freeze dry material.
Source
http://en.wikipedia.org/wiki/Freeze_drying
has super-classes
physical disruption equipment and supplies c
participates in op some cell disruption c

lysis bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#LysisBuffer

A lysis buffer is a buffer solution used for the purpose of lysing cells for use in molecular biology experiments that analyze the compounds of the cells (e.g. western blot). Most lysis buffers contain salts (e.g. Tris-HCl or EDTA) to regulate the acidity and osmolarity of the lysate, while detergents (such as Triton X-100 or SDS) are added to break up membrane structures. In studies like DNA fingerprinting the lysis buffer is used for DNA isolation. Dish soap can be used in a pinch to break down the cell and nuclear membranes, allowing the DNA to be released.
Source
https://en.wikipedia.org/wiki/Lysis_buffer
has super-classes
buffer c
participates in op some cell disruption c
has sub-classes
CTAB buffer c, MPDB buffer c, buffer AL c, buffer AP1 c, buffer ATL c, buffer B1 c, buffer B2 c, buffer C1 c, buffer Y1 c, cytoplasmic extraction buffer c, membrane extraction buffer c, nuclear extraction buffer c, nuclear extraction buffer plus MNase c, pellet extraction buffer c, stain extraction buffer c

M-MLV reverse transcriptasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#M-MLVReverseTranscriptase

M-MLV reverse transcriptaseis an enzyme from the Moloney murine leukemia virus is a single 75 kDa monomer.
Source
http://link.springer.com/article/10.1007%2Fs10529-012-0904-9
has super-classes
reverse transcriptase c

material entityc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/snap#MaterialEntity

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.
has super-classes
independent continuant c
participates in op some experimental protocol execution c
participates in op some laboratory procedure c
participates in op some laboratory subprocedure c
has sub-classes
equipment and supplies c, kit c, material sample c, organism c, reagent c, software c
is in domain of
has name op
is in range of
has outcome op

material samplec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000747

A material entity that has the material sample role
Example
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has super-classes
material entity c
has name op some specimen name c
has sub-classes
sample from organism c
is disjoint with
solution c, equipment and supplies c, reagent c, primer c

measurec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_59

To measure is an experiment action “to determine the extent, quantity, amount or degree of something” Reference: Based on Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
has super-classes
data action c

mechanical millingc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#MechanicalMilling

mechanical milling is a plant and animal tissue homogenizer used for applications involving sample preparation for DNA, RNA, and protein extractions.
has super-classes
sample mill c

membrane extraction bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#MembraneExtractionBuffer

The membrane extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues.Membrane extraction buffer is a buffer used for membrane protein solubilization.
Source
https://www.embl.de/pepcore/pepcore_services/protein_purification/extraction_clarification/solubilisation_membrane_proteins/
Example
Protein purification
has super-classes
lysis buffer c
part of op only subcellular protein fractionation kit for tissues c

mercaptoethanolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_41218

Mercaptoethanol is an alkanethiol that has formula C2H6OS.
Example
2-Mercaptoethanol is used for reducing some proteins. 2-Mercaptoethanol is used in some RNA isolation procedures to eliminate ribonuclease released during cell lysis.
has super-classes
primary alcohol c
participates in op some denaturation reaction c

messenger RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33699

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.
has super-classes
ribonucleic acid c
participates in op some reverse transcription c

methanolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_17790

The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.
has super-classes
primary alcohol c
participates in op some precipitation reaction c

microcentrifugec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001100

A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint.
Source
http://en.wikipedia.org/wiki/Laboratory_centrifuge
has super-classes
centrifuge c

microcentrifuge tubec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#MicrocentrifugeTube

Microcentrifuge tube is a supply. Microcentrifuge tubes are plastic tubes with capacities from 250 ul to 2.0 ml.
Source
http://en.wikipedia.org/wiki/Laboratory_centrifuge#Centrifuge_tubes
Example
Pour off supernatant into 1.5 ml microfuge tube.
has super-classes
equipment and supplies c

micropestlec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Micropestle

micropestle is a very small pestle used for tissue homogenization. Some micropestles have an end which fits 1.5mL microcentrifuge tube; others micropestles have an end which fits 2ml microcentrifuge tube.
has super-classes
sample mill c

micropipettec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001128

A microinjection device that is used to measure very small volumes of liquids.
Source
http://www.answers.com/topic/micropipette
has super-classes
equipment and supplies c

mixc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_45

To mix is an experiment action “to put together or combine (two or more substances or things) so that the constituents or particles of each are interspersed or diffused more or less evenly among those of the rest” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of combination c
has sub-classes
rotate c, vortex c

mixer millc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#MixerMill

Mixer mill is a machine used for grinding dry, brittle samples.
has super-classes
sample mill c

mode of category transformc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_46

a mode of category transformation is an experimental action with a goal of category transformation
has super-classes
mode of transformation c
has sub-classes
break c, chop c, divide c, grind c, homogenize c, pierce c

mode of combinationc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_3

A mode of combination is a way of combining, an experimental action with a goal of combination
has super-classes
experiment action c
has sub-classes
add c, connet c, cover c, dissolve c, inoculate c, mix c, pour c

mode of property transformationc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_12

a mode of property transformation is an experimental action with a goal of property transformation
has super-classes
mode of transformation c
has sub-classes
boil c, heat c, ignite c, incubate c, thaw c

mode of separationc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_2

A mode of separation is a way of separation, an experiment action with a goal of separation
has super-classes
experiment action c
has sub-classes
aspirate c, centrifuge c, precipitate c, re-suspend c, remove c, shake c, sterilise c, streak c, wash c, weigh c

mode of time transformationc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_35

A mode of time transformation is an experimental action with a goal of time transformation
has super-classes
mode of transformation c
has sub-classes
wait c

mode of transformationc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_4

A mode of transformation is an experimental action with a goal of transformation
has super-classes
experiment action c
has sub-classes
mode of category transform c, mode of property transformation c, mode of time transformation c, mode of transformation of spacial location c

mode of transformation of spacial locationc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_36

A mode of transformation of a spatial location is an experimental action with a goal of transformation of a spatial location
has super-classes
mode of transformation c
has sub-classes
move c, place c, take c

monosaccharidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_35381

Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group.
has super-classes
carbohydrate c
has sub-classes
aldose c

mortar and pestlec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#MortarAndPestle

A mortar and pestle is a device used to crushing and grinding tissue into a fine powder.
Source
https://en.wikipedia.org/wiki/Mortar_and_pestle
has super-classes
sample mill c

movec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_8

To move is an experiment action to change a spatial location of an entity from a start location to an end location
has super-classes
mode of transformation of spacial location c

MPDB bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#MPDBBuffer

MPDB buffer is a lysis buffer used during isolation of DNA
Example
DNA purification
has super-classes
lysis buffer c

Musc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10088

Mus (commonly mice) is a small mammal belonging to the order of rodents.
has super-classes
organism c
has sub-classes
Mus musculus c

Mus musculusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10090

has super-classes
Mus c
has sub-classes
A/J c, BALB/c c, C57BL c

N-phenacylthiazolium bromidec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#N-PhenacylthiazoliumBromide

N-phenacylthiazolium bromide is a compound that breaks cross-links in Advanced glycation end products.
Source
https://en.wikipedia.org/wiki/Phenacyl
Example
N-phenacylthiazolium bromide (PTB) is used during DNA extraction. This chemical compound has demonstrated to cleave Maillard products, thus freeing up DNA for PCR amplification.
has super-classes
phenacyl bromide reagent c
participates in op some denaturation reaction c

namec back to ToC or Class ToC

IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C42614

The words or language units by which a thing is known.
has super-classes
textual entity c
has sub-classes
equipment or supplies name c, reagent name c, recipe name c, software name c, specimen name c
is in range of
has name op

Nannomonasc back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/NCBITAXON/47569

has super-classes
Trypanosoma c
has sub-classes
Trypanosoma congolense c

neurotoxicc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Neurotoxic

Poisonous to nerves or nerve cells.
Source
http://wordnetweb.princeton.edu/perl/webwn?s=neurotoxic
Example
avoid contact with skin, eyes or mucous membranes; keep away from sources of ignition. When handling , wear gloves.
has super-classes
caution c

NH4 bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#NH4Buffer

NH4 Buffer is an ready-to-use buffer for PCR using Taq DNA Polymerases (both recombinant and native).
Source
PERSON:Olga Giraldo
has super-classes
PCR buffer c

Nonidet P-40c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_78708

A poly(ether) macromolecule that is polyethylene glycol in which one of the terminal hydroxy groups has been converted to the corresponding p-octylphenyl ether. A nonionic, non-denaturing detergent, it is used for solubilising membrane proteins during isolation of membrane-protein complexes.
Example
Nonidet P-40 acts as a non-ionic detergent used for solubilizing proteins while maintaining native subunit structure, enzymatic activity, or other structural functions.
has super-classes
aromatic ether reagent c
participates in op some denaturation reaction c

nonyl phenoxypolyethoxylethanolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_63016

Poly(ether) macoromolecule comprising a branched nonyl group bonded to one of the ring positions in 2-[phenoxypoly(ethoxy)]ethanol. A commericially available detergent, it is used to help crystallise proteins and extract the cytoplasmic contents of cellular culture.
Example
Tergitol type NP-40 acts as a non-ionic detergent used for solubilizing proteins while maintaining native subunit structure, enzymatic activity, or other structural functions.
has super-classes
aromatic ether reagent c
participates in op some denaturation reaction c

nuclear extraction bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#NuclearExtractionBuffer

The nuclear extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues.
has super-classes
lysis buffer c
part of op only subcellular protein fractionation kit for tissues c

nuclear extraction buffer plus MNasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#NEBPlusMNase

The nuclear extraction buffer plus MNase is part of the Subcellular Protein Fractionation Kit for Tissues. Nuclear extraction buffer with micrococcal nuclease releases chromatin-bound nuclear proteins.
Source
https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/protein-biology-application-notes/subcellular-protein-fractionation.html
has super-classes
lysis buffer c
part of op only subcellular protein fractionation kit for tissues c

nucleic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33696

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.
has super-classes
information biomacromolecule c
has sub-classes
deoxyribonucleic acid c, ribonucleic acid c
is disjoint with
protein c

nucleic acid extraction procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#NucleicAcidExtractionProcedure

Nucleic acid extraction procedure is a subclass of laboratory procedure used to recover the nucleic acid fraction of an input material entity.
Example
DNA extraction procedure, RNA extraction procedure.
has super-classes
laboratory procedure c
has sub-classes
DNA extraction procedure c, RNA extraction procedure c

nucleic acid extraction protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#NucleicAcidExtractionProtocol

Nucleic acid extraction protocol is a subclass of laboratory protocol. A nucleic acid extraction protocol is a step by step description of a procedure used to recover the nucleic acid fraction of an input material entity.
has super-classes
experimental protocol c
has instruction op some denaturation reaction c
has instruction op some cell disruption c
has instruction op some washing nucleic acids c
has instruction op some precipitation reaction c
has sub-classes
DNA extraction protocol c, RNA extraction protocol c
is disjoint with
protein extraction protocol c

nucleic acid reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0000630

Reagent that is a polymer comprised of nucleotides, each of which consists of three components: a nitrogenous heterocyclic base, which is either a purine or a pyrimidine; a pentose sugar; and a phosphate group.
Source
http://en.wikipedia.org/wiki/Nucleic_acid
Example
A primer
has super-classes
reagent c
has sub-classes
DNA reagent c

nucleoside triphosphate reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/REO_0000458

A nucleoside triphosphate reagent is a reagent that is a nucleoside containing three phosphate groups bound to its sugar ring.
has super-classes
reagent c
has sub-classes
deoxyribonucleoside triphosphate reagent c

occurrentc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/span#Occurrent

Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
has super-classes
entity c
has sub-classes
action c, experiment c, planned process c, procedure c
is in domain of
has experimental input op, has output op
is in range of
participates in op
is disjoint with
continuant c

oligo (dT) primerc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#OligodTprimer

oligo (dT) primer is a short sequence of deoxy-thymine nucleotides. Oligo (dT) is tagged as a complementary primer which binds to the poly-A tail providing a free 3'-OH end that can be extended by reverse transcriptase to create the complementary DNA strand.
Source
https://en.wikipedia.org/wiki/CDNA_library
has super-classes
primer c
participates in op some reverse transcription c

oligosaccharidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_50699

A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues.
has super-classes
carbohydrate c
has sub-classes
disaccharide reagent c

one-carbon compoundc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_64708

An organic molecular entity containing a single carbon atom (C1).
has super-classes
chemical compound reagent c
has sub-classes
carbon dioxide c, chloroform c

organic aromatic compoundc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33659

has super-classes
chemical compound reagent c
has sub-classes
phenols c

organic sodium saltc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_38700

has super-classes
sodium salt reagent c
has sub-classes
sodium acetate c, sodium citrate c

organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100026

A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
Source
http://en.wikipedia.org/wiki/Organism
Example
fungus, animal, virus, plant
has super-classes
material entity c
has name op some specimen name c
has sub-classes
Mus c, Trypanosoma c, strain or line c
is disjoint with
solution c, equipment and supplies c, information biomacromolecule c, reagent c, primer c

parasitology experimentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ParasitologyExperiment

Parasitology experiment is an experiment. In this type of experiments are tested (under controlled conditions), parasites, their hosts, and the relationship between them.
has super-classes
experiment c
has sub-classes
Trypanosoma experiment c

pause pointc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PausePoint

Pause point is the point were the protocol naturally breaks into separate stages.
Example
PAUSE POINT: Can be left overnight at 48 C or frozen for up to a month at -20 C.
has super-classes
alert message c

PCR amplificationc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PCRAmplification

PCR amplification is a set of instructions describing the concentration and quantity of the PCR components (target DNA, thermostable DNA polymerase, primers, deoxynucleotide triphosphates (dNTPs), reaction buffer and magnesium); as well as, the cycling conditions.
has super-classes
protocol instruction c

PCR bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PCRBuffer

PCR buffer is a solution that provide a suitable chemical environment for optimum activity and stability of the DNA polymerase
Source
https://en.wikipedia.org/wiki/Polymerase_chain_reaction
Example
Taqman buffer, PCR Buffer with (or without) MgCl2
has super-classes
buffer c
participates in op some PCR amplification c
has sub-classes
Advantage 2 PCR buffer c, GeneAmp PCR Buffer c, NH4 buffer c, Taq polymerase buffer c, TaqMan buffer c

PCR programc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PCRProgram

PCR program is a textual entity that consists in define a series of 20-40 repeated temperature changes, called cycles, with each cycle commonly consisting of 2-3 discrete temperature steps, usually three (denaturation, annealing and extention).
Example
1) 95 C, forever 2) 95 C, 5:00 3) 95 C, 0:30 4) 45-65 C, 0:30 5) 72 C, 1:00 6) Go to step 3, 34 times 7) 72 C, 5:00 8) 10 C, forever
has super-classes
textual entity c

pellet extraction bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PelletExtractionBuffer

The pellet extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. Pellet extraction buffer is used to isolate cytoskeletal proteins.
has super-classes
lysis buffer c
part of op only subcellular protein fractionation kit for tissues c

phenacyl bromide reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PhenacylBromideReagent

Phenacyl bromide reagent is a reagent that has formula C8H7BrO.
Source
CHEBI
has super-classes
chemical compound reagent c
has sub-classes
N-phenacylthiazolium bromide c

phenolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_15882

An organic hydroxy compound that consists of benzene bearing a single hydroxy substituent. The parent of the class of phenols.
has super-classes
phenols c
participates in op some denaturation reaction c

Phenol:Chloroform:Isoamyl alcoholc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PhenolChloroformIsoamylAlcohol

A mixture consisting of equal parts of equilibrated phenol and chloroform:isoamyl alcohol (24:1) is frequently used to remove proteins from preparations of nucleic acids. The chloroform denatures proteins and facilitates the separation of the aqueous and organic phases, and the isoamyl alcohol reduces foaming during extraction.
Source
http://cshprotocols.cshlp.org/content/2006/1/pdb.rec8282.full?text_only=true
has super-classes
solution c

phenolsc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33853

Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring.
has super-classes
organic aromatic compound c
has sub-classes
phenol c

phosphate buffered salinec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PhosphateBufferedSaline

Phosphate buffered saline (PBS) is a non toxic solution used in many biological laboratories. Unlike water, PBS prevents cells rupturing or shrivelling up due to osmosis. PBS can be used for the extraction of spermatozoa and cells from swabs and PBS does not affect subsequent DNA profiling.
Source
http://www.maths.lancs.ac.uk/~lucy/publications/Martin-Pirie-Ford-Callaghan-McTurk-Lucy-Scrimger-2006.pdf
Example
PBS has many uses because it is isotonic and non-toxic to cells. It can be used to dilute substances. It is used to rinse containers containing cells. PBS can be used as a diluent in methods to dry biomolecules, as water molecules within it will be structured around the substance (protein, for example) to be ‘dried’ and immobilized to a solid surface. The thin film of water that binds to the substance prevents denaturation or other conformational changes. Carbonate buffers may be used for the same purpose but with less effectiveness. PBS can be used to take a reference spectrum when measuring the protein adsorption in ellipsometry (http://protocolsonline.com/recipes/phosphate-buffered-saline-pbs/)
has super-classes
buffer c
participates in op some intraperitoneal injection c

physical disruption equipment and suppliesc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PhysicalDisruptionEquipmentAndSupplies

physical disruption equipment and supplies are instruments used during a physical cell disruption.
has super-classes
equipment and supplies c
has sub-classes
lyophilizer c, sample mill c, sonicator c

physical statec back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/npo#NPO_888

A quality, which is the physical condition of a material entity, based on its chemical composition and structure.100428NPODennis Thomas
has super-classes
quality c
has sub-classes
gel state c, liquid state c

piercec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_48

To penetrate; to pass or break through or into something, esp. as or in the manner of a sharp-pointed object Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of category transform c

placec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_40

To place is an experiment action “to put in a particular place, spot, or position” (into the end location), it is a part of a move action Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of transformation of spacial location c

planned processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000011

A processual entity that realizes a plan which is the concretization of a plan specification.
has super-classes
occurrent c
has sub-classes
experimental protocol execution c

plant cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PO_0009002

A cell which is a plant structure (PO:0009011).
Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall.
has super-classes
cell c

plant tissuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PO_0009007

A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.
Example
roots, leaves, flowers, stems.
has super-classes
tissue c
has sub-classes
flower c, ground tissue c, leaf c, root c, seed c, stem c

pluronicc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53514

A triblock copolymer composed of a central hydrophobic chain of poly(propylene oxide) flanked by two hydrophilic chains of poly(ethylene oxide).
Example
Pluronic acts as a non-ionic detergent, protects cells from hydrodynamic damage.
has super-classes
copolymer macromolecule reagent c
has sub-classes
pluronic F-68 c, pluronic P-123 c

pluronic F-68c back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PluronicF68

Pluronic F68 is used in cell culture as a stabilizer of cell membranes protecting from membrane shearing and additionally acts as an anti-foaming agent.
Source
https://www.thermofisher.com/jp/ja/home/life-science/cell-culture/mammalian-cell-culture/media-supplements/pluronic-f68.html
has super-classes
pluronic c

pluronic P-123c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53515

A triblock copolymer composed of a central hydrophobic chain of poly(propylene oxide) (70 units) flanked by two hydrophilic chains of poly(ethylene oxide) (20 units each). A polymer with the formula HO[CH2CH2O]2O[CH2CH(CH3)O]70[CH2CH2O]2OH.
has super-classes
pluronic c

polimerase chain reaction protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PolimeraseChainReactionProtocol

PCR protocol is a step by step description of the procedure to amplify a particular DNA sequence.
has super-classes
enzimatic amplification protocol c
is preceded by op some DNA extraction protocol c

poly ethylene glycol reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PolyEthyleneGlycolReagent

example of usage source: chrome-extension://padcapdkhelngdelppbbjmkmkfceoikg/content/pdf/viewer/viewer.html?file=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC333871%2Fpdf%2Fnar00242-0172.pdf
poly ethylene glycol is a polymer composed of repeating ethyleneoxy units.
Source
CHEBI
Example
precipitation of DNA
has super-classes
chemical compound reagent c
participates in op some precipitation reaction c
has sub-classes
Triton X-100 c, polysorbate c, tergitol c

polymerase chain reaction procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PolimeraseChainReactionProcedure

PCR is a subclass of enzymatic amplification procedure. PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
Source
adapted from wikipedia
has super-classes
enzymatic amplification procedure c
is preceded by op some DNA extraction procedure c
has protocol op some polimerase chain reaction protocol c

polysorbatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53422

A polymer composed of PEG-ylated sorbitan [2-(1,2-dihydroxyethyl)tetrahydrofuran-3,4-diol] normally containing a total of 20 oxyethylene groups, with one or more of the terminal hydroxy groups esterified with a fatty acyl group. They are used as emulsifiers and dispersing agents in some pharmaceuticals products and as defoamers and emulsifiers in some foods.
has super-classes
poly ethylene glycol reagent c
has sub-classes
polysorbate 20 c, polysorbate 40 c, polysorbate 60 c, polysorbate 80 c

polysorbate 20c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53424

A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by a dodecanoyl group.
example of usage source: http://www.sigmaaldrich.com/catalog/product/sial/p1379?lang=en&region=CO&gclid=CjwKEAjw-vewBRDH1-b52Lig1hkSJACTPfVFKmIFgDeASxRzyjDXAt8-HmEYpgjOYCfQWDgPWdodbhoCRV3w_wcB
Example
TWEEN 20 acts as a non-ionic detergent. TWEEN 20 has been used in pre-extraction of membranes to remove peripheral proteins (used at 2% for extraction of membrane-bound proteins). TWEEN 20 has been used as a blocking agent for membrane based immunoassays at a typical concentration of 0.05%. TWEEN 20 can be used for lysing mammalian cells at a concentration of 0.005 to 0.5%.
has super-classes
polysorbate c
participates in op some cell disruption c

polysorbate 40c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53423

A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by a palmitoyl group.
Example
Tween 40 acts as a non-ionic detergent used for cell lysis, nuclei isolation and cell fractionation.
has super-classes
polysorbate c
participates in op some cell disruption c

polysorbate 60c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53425

A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by a stearate group.
example of usage source: http://www.sigmaaldrich.com/catalog/product/sigma/p1629?lang=en&region=CO
Example
Polyethylene glycol sorbitan monostearate, or TWEEN 60, has been used in a study to assess encapsulation of functional lipophilic components in surfactant-based colloidal delivery systems. It has also been used in a study to investigate doxorubicin loaded magneto-niosomes for targeted drug delivery.
has super-classes
polysorbate c

polysorbate 80c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53426

A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by an oleoyl group.
Example
Non-ionic detergent used for selective protein extraction and isolation of nuclei from mammalian cell lines.
has super-classes
polysorbate c
participates in op some cell disruption c

polytron homogenizerc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PolytronHomogenizer

Polytron homogenizer is a instrument used for pulverizing plant and animal tissue, grain and seed, soil extraction, DNA/RNA extraction.
has super-classes
homogenizer c

polyvinylpyrrolidonec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Polyvinylpyrrolidone

A vinyl polymer composed of repeating -CH2-CR- units where R is a 2-oxopyrrolidin-1-yl group.
Source
CHEBI
Example
PVP (polyvinylpyrrolidone) is added to remove phenolic compounds from plant DNA extracts. PVP precipitates polyphenolics.
has super-classes
vinyl polymer macromolecule reagent c
participates in op some precipitation reaction c

portable ice chestc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PortableIceChest

A portable ice chest is a supply. A cooler, cool box, portable ice chest, chilly bin (in New Zealand), or esky (Australia) most commonly is an insulated box used to keep the things cool.
Source
http://en.wikipedia.org/wiki/Cooler
Example
Place bags in a portable ice chest or other container with ice to keep samples cool.
has super-classes
equipment and supplies c

potassium acetatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_32029

A potassium salt that has formula C2H3O2.K.
Example
In molecular biology, potassium acetate is used to precipitate dodecyl sulfate (DS) and DS-bound proteins, allowing the removal of proteins from DNA. It is also used as a salt for the ethanol precipitation of DNA.
has super-classes
potassium salt reagent c
participates in op some precipitation reaction c

potassium chloridec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_32588

potassium chloride (KCl) is a inorganic chloride composed of potassium and chloride.
Source
https://en.wikipedia.org/wiki/Potassium_chloride
has super-classes
potassium salt reagent c
participates in op some precipitation reaction c

potassium salt reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PotassiumSaltReagent

Any alkali metal salt having potassium(1+) as the cation.
Source
CHEBI
has super-classes
alkali metal salt reagent c
has sub-classes
potassium acetate c, potassium chloride c

potter-elvehjem homogenizerc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PotterElvehjemHomogenizer

Shearing is caused by a PTFE- coated pestle that is manually or mechanically driven into a conical vessel
has super-classes
homogenizer c

pourc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_11

To pour is an experiment action “to cause or allow (a substance, esp. a liquid) to flow out of a vessel or receptacle; to emit in a stream” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of combination c

powdered leafc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PowderedLeaf

Powdered leaf is a material entity. Powdered leaf is a leaf tissue that has been pulverirized.
has super-classes
powdered tissue c

powdered rootc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PowderedRoot

Powdered root is a material entity. Powdered root is a root tissue that has been pulverirized.
has super-classes
powdered tissue c

powdered seedc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PowderedSeed

Powdered seed is a material entity. Powdered seed is a seed tissue that has been pulverirized.
has super-classes
powdered tissue c

powdered tissuec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PowderedTissue

Powdered tissue is a material entity. Powdered tissue is a tissue that has been pulverirized.
Example
Grind the seed to a powder. Transfer the powdered seed to a container and weigh the specified amount.
has super-classes
tissue c
has sub-classes
powdered leaf c, powdered root c, powdered seed c

precipitatec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Precipitate

A solid or solid phase separated from a solution.
has super-classes
mode of separation c
participates in op some precipitation reaction c

precipitation reactionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#PrecipitationReaction

Precipitation reactions can be used for removing denatured proteins, cells, salts and nucleic acids. Precipitation may occur when an antisolvent (a solvent in which the product is insoluble) is added, drastically reducing the solubility of the desired product. Thereafter, the precipitate may easily be separated by filtration, decanting, or centrifugation. An important application of an antisolvent is in ethanol precipitation of DNA.
has super-classes
protocol instruction c
part of op some nucleic acid extraction protocol c
is preceded by op some denaturation reaction c
precedes op some washing nucleic acids c
has members
precipitation reaction 1 ni

primary alcoholc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_15734

has super-classes
alcohol c
has sub-classes
ethanol c, mercaptoethanol c, methanol c

primerc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Primer

A primer is a short strand of nucleic acid that serves as a starting point for DNA or RNA synthesis.
Source
http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29
Example
Oligos used in PCR.
has super-classes
DNA oligonucleotide c
has sub-classes
forward primer c, gene-specific primer c, oligo (dT) primer c, random primer c, reverse primer c
is disjoint with
equipment and supplies c, information biomacromolecule c, material sample c, organism c

procedurec back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_000999

A procedure is a process that attempts to achieve one or more objectives by following an established set of actions.
has super-classes
occurrent c
has output op some data set c
has alert message op some alert message c
has experimental input op some data set c
has sub-classes
laboratory procedure c, laboratory subprocedure c

procedure descriptionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ProcedureDescription

A procedure description is a short statement that describe the goal to achieve with the execution of a series of steps.
has super-classes
textual entity c

processed DNAc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ProcessedDNA

Is a DNA that suffers changes during a laboratory procedure.
Is a DNA that suffers changes during a laboratory procedure.
has super-classes
deoxyribonucleic acid c
has sub-classes
DNA extract c, DNA pellet c, DNA separated by molecular size c, amplified DNA c, stained DNA c

processed readsc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ProcessedReads

Reads that have suffered some processing.
Source
NGS ontology
has super-classes
analyzed data set c

processed RNAc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ProcessedRNA

Is a RNA that suffers changes during a laboratory procedure.
Is a RNA that suffers changes during a laboratory procedure.
has super-classes
ribonucleic acid c
has sub-classes
RNA separated by molecular size c

propan-2-olc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_17824

A secondary alcohol that is propane in which one of the hydrogens attached to the central carbon is substituted by a hydroxy group.
has super-classes
secondary alcohol c
participates in op some precipitation reaction c

proteinc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_36080

A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
has super-classes
information biomacromolecule c
is disjoint with
nucleic acid c

protein extraction procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ProteinExtractionProcedure

Protein purification is a series of processes intended to isolate one or a few proteins from a complex mixture, usually cells, tissues or whole organisms. Protein purification is vital for the characterization of the function, structure and interactions of the protein of interest. The purification process may separate the protein and non-protein parts of the mixture, and finally separate the desired protein from all other proteins. Separation of one protein from all others is typically the most laborious aspect of protein purification. Separation steps usually exploit differences in protein size, physico-chemical properties, binding affinity and biological activity. The pure result may be termed protein isolate.
Source
https://en.wikipedia.org/wiki/Protein_purification
has super-classes
laboratory procedure c

protein extraction protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ProteinExtractionProtocol

Protein extraction protocol is a subclass of laboratory protocol. Protein extraction is an extraction where the desired output material is protein.
has super-classes
experimental protocol c
is disjoint with
nucleic acid extraction protocol c

protocol instructionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ProtocolInstruction

A protocol instruction should have sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the procedure.
Source
EFO
has super-classes
Instruction c
has sub-classes
PCR amplification c, cell disruption c, denaturation reaction c, precipitation reaction c, reverse transcription c, washing nucleic acids c
is in range of
has instruction op

pyrophoricc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Pyrophoric

A chemical substance that will ignite spontaneously in air at or below a temperature of 130 F (54.4 C).
Source
http://www.utexas.edu/safety/ehs/msds/glossary/?page=p
Example
Iron sulfide and many reactive metals including uranium, when powdered or thinly sliced. Pyrophoric materials are often water-reactive as well and will ignite when they contact water or humid air. They can be handled safely in atmospheres of argon or (with a few exceptions) nitrogen. Most pyrophoric fires should be extinguished with a Class D fire extinguisher for burning metals.
has super-classes
caution c

qualityc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/snap#Quality

Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
has super-classes
specifically dependent continuant c
has sub-classes
physical state c

quaternary ammonium salt reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#QuaternaryAmmoniumSaltReagent

Derivatives of ammonium compounds, (NH4(+))Y(-), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually hydrocarbyl) groups.
Source
CHEBI
has super-classes
chemical compound reagent c
has sub-classes
cetyltrimethylammonium bromide c

random primerc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#RandomPrimer

Random primers are used for synthesizing large pools of cDNA. They are also ideal for non-polyadenylated RNA, such as bacterial RNA, because they anneal throughout the target molecule. Degraded transcripts such as FFPE samples and secondary structure within the RNA do not pose as big a problem with random primers as they do with gene-specific primers and oligo(dT) primers.
Source
https://www.thermofisher.com/es/en/home/life-science/pcr/reverse-transcription/rna-priming-strategies.html
has super-classes
primer c
participates in op some reverse transcription c

raw data setc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#RawDataSet

Raw data set is an unanalyzed data set; data not yet subjected to analysis.
Source
wordnetweb.princeton.edu/perl/webwn
Example
Preliminary results about a DNA extraction, PCR, sequensing, etc.
has super-classes
data set c
has sub-classes
raw reads c
is disjoint with
analyzed data set c

raw readsc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#RawReads

Raw output of a Sequencing Process.
Source
NGS ontology
has super-classes
raw data set c

re-namec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_42

To re-name is an experiment action to designate a new name instead of the old name to an entity
has super-classes
label c

re-suspendc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_57

To re-suspend is an experiment action to suspend material that have been previously suspended, being made homologies, uniformly distributed
has super-classes
mode of separation c

reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33893

A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
has super-classes
material entity c
has name op some reagent name c
has sub-classes
chemical compound reagent c, enzyme reagent c, nucleic acid reagent c, nucleoside triphosphate reagent c, solution c
is disjoint with
equipment and supplies c, information biomacromolecule c, material sample c, organism c

reagent listc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ReagentList

Reagent list is a data set of the names or identifiers of the reagents (purchased ready-to-use), that are part of materials section of a protocol.
has super-classes
data set c
has part op some reagent name c

reagent namec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ReagentName

Reagent name is a textual entity. Reagent name is the name of a reagent.
Example
Taq DNA Polymerase from Thermus aquaticus with 10X reaction buffer without MgCl2.
has super-classes
name c
part of op some reagent list c

recipec back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_001042

A recipe is a set of instructions that describe how to prepare or make something.
has super-classes
textual entity c
has name op some recipe name c

recipe listc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#RecipeList

recipe list is a data set of the names or identifiers of the recipes, that are part of materials section of a protocol.
has super-classes
data set c
has part op some recipe name c

recipe namec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#RecipeName

Recipe name is a textual entity. Recipe name is the name of a solution, buffer, media, etc that is prepared in the laboratory.
has super-classes
name c
part of op some recipe list c

recordc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_56

To record is an experiment action to represent symbolically a value of a measurement or an observation in order to preserve information for later use
has super-classes
data action c

removec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_55

To remove is an experiment action “to move or shift from or out of the place occupied; to lift or push aside; to lift up and take away; to take off” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of separation c
has sub-classes
de-lid c, discard c, filter c

reverse primerc back to ToC or Class ToC

IRI: http://purl.org/obo/owl/SO#SO_0000132

A single stranded oligo used for polymerase chain reaction.
has super-classes
primer c
participates in op some PCR amplification c

reverse transcriptasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ReverseTranscriptase

A Reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription.
Source
https://en.wikipedia.org/wiki/Reverse_transcriptase
Example
HIV-1 reverse transcriptase M-MLV reverse transcriptase AMV reverse transcriptase
has super-classes
enzyme reagent c
participates in op some reverse transcription c
has sub-classes
AMV reverse transcriptase c, M-MLV reverse transcriptase c, SuperScript reverse transcriptase c

reverse transcriptionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ReverseTranscription

In this step, total RNA or messenger RNA (mRNA) is first transcribed into complementary DNA (cDNA) by reverse transcriptase.
has super-classes
protocol instruction c

reverse transcription PCR procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ReverseTranscriptionPCRProcedure

Reverse transcription PCR is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
Source
EFO
has super-classes
enzymatic amplification procedure c
has protocol op some reverse transcription PCR protocol c

reverse transcription PCR protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ReverseTranscriptionPCRProtocol

reverse transcription PCR protocol is a step by step description of the procedure to reverse-transcribe and amplify RNA to cDNA.
has super-classes
enzimatic amplification protocol c

ribonucleic acidc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33697

High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
has super-classes
nucleic acid c
has sub-classes
tRNA threonylcarbamoyladenosine c, alpha-aminoacyl-tRNA c, double-stranded RNA c, messenger RNA c, processed RNA c, ribosomal RNA c, small nuclear RNA c, total RNA c, transfer RNA c
is disjoint with
deoxyribonucleic acid c

ribosomal RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_18111

RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis.
has super-classes
ribonucleic acid c

RNA extraction procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#RNAExtractionProcedure

A RNA extraction procedure is a subclass of nucleic acid extraction procedure where the desired output material is RNA
has super-classes
nucleic acid extraction procedure c
has protocol op some RNA extraction protocol c

RNA extraction protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#RNAExtractionProtocol

RNA extraction protocol is a subclass of nucleic acid extraction protocol. RNA extraction protocol, is a step by step description of a procedure in which is recovered a fraction of RNA from a material entity.
has super-classes
nucleic acid extraction protocol c
has instruction op some cell disruption c
has instruction op some washing nucleic acids c
has instruction op some precipitation reaction c
has instruction op some denaturation reaction c
has members
RNA extraction 1 ni
is disjoint with
DNA extraction protocol c

RNA pelletc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#RNAPellet

A material entity which results from the aggregation of RNA produced by the application of centrifugal force to a liquid containing RNA in suspension.
has super-classes
RNA separated by molecular size c

RNA separated by molecular sizec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#RNASeparatedByMolecularSize

RNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix.
has super-classes
processed RNA c
has sub-classes
RNA pellet c

rootc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PO_0025025

A collective plant organ structure (PO:0025007) that produces root apical meristems (PO:0020147) and the plant structures that arise from them.
has super-classes
plant tissue c

rotatec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_30

To rotate is an experiment action “to cause (a thing) to turn round or revolve on a centre or axis” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mix c

sample from organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000671

a material obtained from an organism in order to be a representative of the whole
has super-classes
material sample c
part of op some organism c
has sub-classes
cell c, information biomacromolecule c, tissue c

sample millc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SampleMill

sample mills cover a broad range of sample preparation equipment and supplies. The range includes homogenizers, blenders and mills for the preparation of high-fat, high-moisture, dry, frozen and fibrous samples.
has super-classes
physical disruption equipment and supplies c
participates in op some cell disruption c
has sub-classes
bead beater c, blender c, coffee mill c, drill c, freezer milling c, french pressure cell press c, grinding machine c, homogenizer c, mechanical milling c, micropestle c, mixer mill c, mortar and pestle c, waring blender polytron c

saponin reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SaponinReagent

Saponin is a compound containing one or more hydrophilic glycoside moieties combined with a lipophilic triterpenoid or steroid derivative. Found in particular abundance in plant species.
example usage source: http://www.sigmaaldrich.com/catalog/product/sigma/s4521?lang=en&region=CO
Source
CHEBI
Example
surfactant that enhances penetration of proteins and other macromolecules through cell membranes; it also has been used as an adjuvant for vaccines.
has super-classes
chemical compound reagent c
participates in op some cell disruption c
has sub-classes
digitonin c

sarcosine reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SarcosineReagent

A N-alkylglycine that is the N-methyl derivative of glycine. It is an intermediate in the metabolic pathway of glycine.
Source
CHEBI
has super-classes
chemical compound reagent c
has sub-classes
Sodium lauroyl sarcosinate c

sealc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_33

To Seal is an experiment action to close or fasten tightly a base and a top by any substance or devise used as sealant Reference: based on Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
has super-classes
cover c

secondary alcoholc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_35681

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.
has super-classes
alcohol c
has sub-classes
propan-2-ol c

seedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PO_0009010

A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).
A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms).
has super-classes
plant tissue c

shakec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_20

To shake is an experiment action to move regularly in the defined restricted space
has super-classes
mode of separation c
has sub-classes
swirl c

single-stranded DNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_9160

has super-classes
deoxyribonucleic acid c

small nuclear RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_74035

A class of small RNA molecules which are comprised of approximately 150 nucleotides and which are found within the nucleus of eukaryotic cells.
has super-classes
ribonucleic acid c

sodium acetatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_32954

An organic sodium salt that has formula C2H3NaO2.
has super-classes
organic sodium salt c
participates in op some precipitation reaction c

sodium chloridec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_26710

An inorganic chloride salt having sodium(1+) as the counterion.
has super-classes
inorganic chloride c
participates in op some precipitation reaction c

sodium citratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53258

The trisodium salt of citric acid.
has super-classes
organic sodium salt c

sodium deoxycholatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_9177

A bile acid salt that has formula C24H39NaO4.
example of usage source: http://www.sigmaaldrich.com/catalog/product/sial/d6750?lang=en&region=CO
Example
Sodium deoxycholate acts as a anionic detergent; useful for extraction of membrane receptors and other plasma membrane proteins and for nuclei isolation.
has super-classes
bile acid salt reagent c
participates in op some cell disruption c

sodium dodecyl sulfatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_8984

An alkyl sulfate that has formula C12H25NaO4S.
Example
Sodium dodecyl sulfate acts as a anionic detergent that often completely disrupt cell membranes and fully denature proteins.
has super-classes
alkyl sulfate reagent c
participates in op some cell disruption c
participates in op some denaturation reaction c

Sodium lauroyl sarcosinatec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SodiumLauroylSarcosinate

Sodium lauroyl sarcosinate also known as sarkosyl, is an ionic surfactant derived from sarcosine. In molecular biology experiments, sarkosyl is used to inhibit the initiation of DNA transcription.
Source
https://en.wikipedia.org/wiki/Sodium_lauroyl_sarcosinate
Example
Sarkosyl is effective in solubilizing functionally active membrane proteins, the major use of Sarkosyl has been to isolate DNA and RNA. The principal reason for this is that Sarkosyl is highly efficient in dissociating nucleosomes and ribosomes.
has super-classes
sarcosine reagent c
participates in op some cell disruption c
participates in op some denaturation reaction c

sodium salt reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SodiumSaltReagent

Any alkali metal salt having sodium(1+) as the cation.
Source
CHEBI
has super-classes
alkali metal salt reagent c
has sub-classes
organic sodium salt c

softwarec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0000071

Software is a general term primarily used for digitally stored data such as computer programs and other kinds of information read and written by computers.
Source
http://en.wikipedia.org/wiki/Computer_software
Example
Microsoft Word is commonly used word processing software.
has super-classes
material entity c
has name op some software name c

software listc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SoftwareList

has super-classes
data set c
has part op some recipe name c

software namec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SoftwareName

Software name is a textual entity. Software name is the name of a software.
Example
LightCycler 480 Software.
has super-classes
name c
part of op some software list c

solutionc back to ToC or Class ToC

IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C70830

A homogeneous mixture of two or more substances; frequently (but not necessarily) a liquid solution.
has super-classes
reagent c
has sub-classes
Chloroform:Isoamyl alcohol c, Phenol:Chloroform:Isoamyl alcohol c, buffer c, ethanol solution c, guanidinium thiocyanate-phenol c
is disjoint with
information biomacromolecule c, material sample c, organism c

sonicatorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400114

A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions.
Example
Sonicator 3000
has super-classes
physical disruption equipment and supplies c
participates in op some cell disruption c

specifically dependent continuantc back to ToC or Class ToC

IRI: http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant

Definition: A continuant [snap: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.
has super-classes
dependent continuant c
has sub-classes
quality c
is disjoint with
generically dependent continuant c

specimen listc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SpecimenList

specimen list is a data set of the names or identifiers of the specimens that are part of materials section of a protocol.
has super-classes
data set c
has part op some specimen name c

specimen namec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SpecimenName

Specimen name is a textual entity. Specimen name is the name of the organism, strain, line, ecotype, cultivar, etc. used in a protocol.
has super-classes
name c
part of op some specimen list c

specimen preparation procedurec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SpecimenPreparationProcedure

Any method used to modify an existing sample/specimen
has super-classes
laboratory procedure c
is preceded by op some animal euthanization procedure c
has protocol op some specimen preparation protocol c

specimen preparation protocolc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SpecimenPreparationProtocol

A specimen preparation protocol is a protocol used in a biological experiment and defines instructions on how a specimen or sample should be treated in a given experimental scenario.
has super-classes
experimental protocol c

spleenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002106

the organ that functions to filter blood and to store red corpuscles and platelets
has super-classes
animal tissue c

stain extraction bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#StainExtractionBuffer

Stain extraction buffer is a buffer used to digest and extract DNA.
Example
DNA purification
has super-classes
lysis buffer c

stained DNAc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#StainedDNA

Stained DNA is a material entity. After the electrophoresis is complete, the molecules in the gel can be stained to make them visible. DNA may be visualized using ethidium bromide which, when intercalated into DNA, fluoresce under ultraviolet light. EtBr is a known mutagen, and safer alternatives are available, such as GelRed, which binds to the minor groove. SYBER Green I is another dsDNA stain. It is 25 times more sensitive, and possibly safer than EtBr, though there is no data addressing its mutagenicity or toxicity in humans. SYBER 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. If the molecules to be separated contain radioactivity, for example in DNA sequencing gel, an autoradiogram can be recorded of the gel. If the molecules to be separated not contain radioactivity in a DNA sequencing gel, it may be visualized using silver nitrate.
Stained DNA is a material entity. After the electrophoresis is complete, the molecules in the gel can be stained to make them visible. DNA may be visualized using ethidium bromide which, when intercalated into DNA, fluoresce under ultraviolet light. EtBr is a known mutagen, and safer alternatives are available, such as GelRed, which binds to the minor groove. SYBER Green I is another dsDNA stain. It is 25 times more sensitive, and possibly safer than EtBr, though there is no data addressing its mutagenicity or toxicity in humans. SYBER 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. If the molecules to be separated contain radioactivity, for example in DNA sequencing gel, an autoradiogram can be recorded of the gel. If the molecules to be separated not contain radioactivity in a DNA sequencing gel, it may be visualized using silver nitrate. Definition source: http://en.wikipedia.org/wiki/Gel_electrophoresis
Source
http://en.wikipedia.org/wiki/Gel_electrophoresis
has super-classes
processed DNA c

stemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PO_0009047

A shoot axis (PO:0025029) that is the primary axis of a plant.
Often bears leaves and buds. It is usually above ground, more or less negatively geotropic, and exogenous in origin.
has super-classes
plant tissue c

sterilisec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_22

To sterilise is an experiment action to make something free from micro-organisms
has super-classes
mode of separation c

steroid acid reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SteroidAcidReagent

Any steroid substituted by at least one carboxy group.Annotations
has super-classes
steroid reagent c
has sub-classes
cholanic acids c

steroid reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SteroidReagent

Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from triterpenoids.
has super-classes
chemical compound reagent c
has sub-classes
cholanoid c, steroid acid reagent c

stopc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_92

has super-classes
command action c

storage conditionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#StorageCondition

Storage condition is a message given to a user of a protocol about the shelf life (maximum storage time) and temperature of storage of a buffer, reagent or solution.
Example
Store the buffer in foil covered dark coloured bottle at room temperature. Light sensitive. Can be used up to 2 months.
has super-classes
alert message c

storec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_114

has super-classes
command action c

strain or linec back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#StrainOrLine

A strain or line is an animal or plant offspring that has a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings. This class is extended to include F1 offspring and established breeding lines. For microbes, these are isolates derived from nature or in the laboratory.
has super-classes
organism c
has sub-classes
cultivar c, ecotype c

streakc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_52

To streak is an experiment action to spread a microbial sample in a line across the surface of solid culture medium to isolate individual cells
has super-classes
mode of separation c

subcellular protein fractionation kit for tissuesc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SubcellularProteinFractionationKitforTissues

subcellular protein fractionation kit for tissues includes five cellular components to obtain proteins.
Source
https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/protein-biology-application-notes/subcellular-protein-fractionation.html
has super-classes
kit c
participates in op some cell disruption c

subprocedure descriptionc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SubprocedureDescription

A textual entity that describes the execution of a protocol insrtuction or step.
has super-classes
textual entity c
is in range of
has description op

sucrosec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_17992

Sucrose is a disaccharide formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose.
has super-classes
disaccharide reagent c
participates in op some cell disruption c

sulfate salt reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SulfateSaltReagent

has super-classes
chemical compound reagent c
has sub-classes
inorganic sulfate salt c

SuperScript reverse transcriptasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#SuperScriptReverseTranscriptase

SuperScript reverse transcriptase (RT) is a family of enzymes widely used for cDNA synthesis.
has super-classes
reverse transcriptase c

swirlc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_21

To swirl is an experiment action to shake fluid in constant circular or semicircular motion
has super-classes
shake c

takec back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_39

To take is an experiment action “to lay hold of, grasp”, it is a part of a move action Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of transformation of spacial location c

taq polymerasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#TaqPolymerase

Taq polymerase is a heat stable DNA-direct DNA polymerase from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of Polymerase Chain Reaction.
has super-classes
enzyme reagent c
participates in op some PCR amplification c
has sub-classes
AmpliTaq DNA Polymerase c, AmpliTaq Gold c, Apex Taq DNA Polymerase c, Hot Start Taq DNA Polymerase c, KlenTaq DNA Polymerase c, Titanium Taq DNA Polymerase c

Taq polymerase bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#TaqPolymeraseBuffer

Taq polymerase buffer is a buffer formulated to provide efficient activation of the enzyme Taq DNA polymerase, resulting in PCR amplification.
Source
PERSON:Olga Giraldo
has super-classes
PCR buffer c

TaqMan bufferc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#TaqManBuffer

TaqMan buffer is PCR buffer with ROX added for florescence.
Source
http://cancer.ucsf.edu/_docs/cores/genome/protocols/TaqManBuffer.pdf
has super-classes
PCR buffer c

temperature control bathc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400120

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.
Source
OBI Instrument branch
Example
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.
has super-classes
equipment and supplies c
has sub-classes
water bath c

tergitolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_53774

A polymer consisting of nonylbenzene with a poly(ethylene glycol) moiety attached at position 4.
has super-classes
poly ethylene glycol reagent c

textual entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000300

A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
Example
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has super-classes
information content entity c
has sub-classes
Instruction c, PCR program c, alert message c, name c, procedure description c, recipe c, subprocedure description c

thawc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_38

to thaw is an experiment action to change a substance from a frozen state to a liquid state Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of property transformation c

thermal cyclerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400116

An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
Source
MO
Example
Piko(tm) 96-well Thermal Cycler
has super-classes
equipment and supplies c
participates in op some PCR amplification c

three dimensional imagec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#ThreeDimensionalImage

images which show length, width and depth of the object; can be generated or simulated by assembling multiple tomographic images with the aid of a computer
has super-classes
data set c

timingc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Timing

Timing is a message used to indicate the approximate time that a step, or set of steps, could take.
Example
Steps 1-3, 30 min.; Steps 6-7, 2 h
has super-classes
alert message c

tissuec back to ToC or Class ToC

IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12801

An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function.
Source
CDISC
has super-classes
sample from organism c
has sub-classes
animal tissue c, lyophilized tissue c, plant tissue c, powdered tissue c

Titanium Taq DNA Polymerasec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#TitaniumTaqDNAPolymerase

Titanium Taq is a mixture consisting of a 5’ exonuclease-deficient Taq polymerase, and TaqStart Antibody, a monoclonal antibody which inhibits Taq at ambient temperatures. TaqStart Antibody provides automatic hot start PCR.
Source
http://www.clontech.com/RO/Products/cDNA_Synthesis_and_Library_Construction/cDNA_and_Genomic_DNA/RACE-Ready_cDNA/ibcGetAttachment.jsp?cItemId=31113&fileId=5994516&sitex=10020:22372:US
has super-classes
taq polymerase c

total RNAc back to ToC or Class ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0004964

A RNA extract that is the output of an extraction process in which total RNA from either whole cells or from specific cellular compartment(s)/organelle(s) are isolated from a specimenA RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
has super-classes
ribonucleic acid c
participates in op some reverse transcription c

toxicc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Toxic

Of or relating to or caused by a toxin or poison 'suffering from exposure to toxic substances'
Source
http://wordnetweb.princeton.edu/perl/webwn?s=toxic
Example
Avoid inhalation, ingestion or contact with skin, eyes or mucous membranes.
has super-classes
caution c

transfer RNAc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_17843

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.
has super-classes
ribonucleic acid c

Triton X-100c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_9750

Triton X-100 is a A poly ethylene glycol terminated with a 4-(2,4,4-trimethylpentan-3-yl) phenyl group at one end.
Example
Triton X-100 acts as a nonionic surfactant used for solubilizing proteins while maintaining native subunit structure, enzymatic activity, or other structural functions.
has super-classes
poly ethylene glycol reagent c
participates in op some cell disruption c

troubleshootingc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Troubleshooting

A troubleshooting is a message given to a user of a protocol where common problems, possible causes, and solutions/methods of correction should be listed.
Example
Problem: Low detection level for tested a miRNA (CT value>35) (Step 9 - 10) Possible reason: low abundant amiRNA, or low efficiency of low of polyA tailing and reverse transcription, or amplification condition is too stringent, or amiRNA is not correctly expressed or processed. Possible solutions: increase amount of cDNA template in PCR; use new polyA tailing and reverse transcription reagent, (...) or using low stringent PCR program; check PCR product sequence.
has super-classes
alert message c

Trypanosomac back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/NCBITAXON/5690

Trypanosoma is a genus of kinetoplastids (class Kinetoplastida), a monophyletic group of unicellular parasitic flagellate protozoa.
Source
https://en.wikipedia.org/wiki/Trypanosoma
has super-classes
organism c
has sub-classes
Nannomonas c, Trypanozoon c

Trypanosoma bruceic back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/NCBITAXON/5691

has super-classes
Trypanozoon c

Trypanosoma brucei bruceic back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_5702

has super-classes
Trypanozoon c

Trypanosoma congolensec back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/NCBITAXON/5692

has super-classes
Nannomonas c
participates in op some Trypanosoma experiment c

Trypanosoma experimentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#TrypanosomaExperiment

Trypanosoma experiment is a parasitology experiment. In this type of experiments physiological, metabolic, immunologic, biochemical, nutritional, and chemotherapeutic aspects of trypanosoma and host-parasite relationships are tested (under controlled conditions).
has super-classes
parasitology experiment c
has part op some animal euthanization procedure c
has part op some specimen preparation procedure c
has part op some infection procedure c
has part op some housing condition procedure c

Trypanozoonc back to ToC or Class ToC

IRI: http://purl.bioontology.org/ontology/NCBITAXON/39700

has super-classes
Trypanosoma c
has sub-classes
Trypanosoma brucei c, Trypanosoma brucei brucei c

vinyl polymer macromolecule reagentc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#VinylPolymerMacromoleculeReagent

A macromolecule composed of repeating -CHR-CH2- units.
Source
CHEBI
has super-classes
chemical compound reagent c
has sub-classes
polyvinylpyrrolidone c

volatilec back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#Volatile

The property of a substance of changing readily from a solid or liquid to a vapor.
Example
handle in well-ventilated charcoal-filtered hood. Reference: Nature Protocols
has super-classes
caution c

vortexc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_29

To vortex is an experiment action of a spiral rotatory movement of matter with the increasing gravity round a centre or axis Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mix c

waitc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_13

To wait is an experiment action to allow a time interval to pass without experiment actions
has super-classes
mode of time transformation c

waring blender polytronc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#WaringBlenderPolytron

Instrument used in mechanical lysis. Rotating blades grind and disperse cells and tissues
Source
https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/traditional-methods-cell-lysis.html
has super-classes
sample mill c

washc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_54

To wash is an experiment action “to cleanse, remove” the unwanted material” from (something) by affusion of or immersion in” fluid Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
has super-classes
mode of separation c
participates in op some washing nucleic acids c

washing nucleic acidsc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#WashingNucleicAcids

This step is to wash any residual salt away from the pelleted DNA/RNA.
Source
http://bitesizebio.com/253/the-basics-how-ethanol-precipitation-of-dna-and-rna-works/
has super-classes
protocol instruction c
is preceded by op some precipitation reaction c
part of op some nucleic acid extraction protocol c
has members
washing nucleic acids 1 ni

water bathc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400155

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).
Example
A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
has super-classes
temperature control bath c

weighc back to ToC or Class ToC

IRI: http://www.owl-ontologies.com/Ontology1184060740.owl#Class_24

To weigh is an experiment action to “To be equivalent to in weight” Reference: http://www.biology-online.org/dictionary/Weigh
has super-classes
mode of separation c

yeast cellc back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#YeastCell

A general term denoting true fungi of the family Saccharomycetaceae that are widely distributed in substrates that contain sugars (such as fruits), and in soil, animal excreta, the vegetative parts of plants, etc. Because of their ability to ferment carbohydrates, some yeasts are important to the brewing and baking industries.
Source
Yeast cell. (n.d.) Farlex Partner Medical Dictionary. (2012). Retrieved July 11 2016 from http://medical-dictionary.thefreedictionary.com/Yeast+cell
has super-classes
fungal cell c

Object Properties

derives fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001000

a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
Example
this cell derives from this parent cell (cell division); this nucleus derives from this parent nucleus (nuclear division)

has alert messageop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasAlertMessage

hasAlertMessage is a relation that binds a chemical substance or protocol to an alert message such as caution, critical step, timing, etc.
has domain
laboratory subprocedure c
has range
alert message c

has descriptionop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasDescription

hasDescription is a relation that binds a subprocedure to a subprocedure description.

has experimental inputop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasExperimentalInput

hasExperimentalInput is a relation that binds a experimental protocol to a material entity participating in a protocol.
has domain
occurrent c
has range
continuant c

has instructionop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasInstruction

hasInstruction is a relation that binds a experimental protocol to a protocol instruction.
has domain
experimental protocol c
has range
protocol instruction c

has nameop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasName

hasName binds to a person, animal, place or thing to a word or set of words by which someone or something is known, addressed, or referred to
has domain
material entity c
has range
name c

has outcomeop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasOutcome

hasOutcome is a relation that binds a document such as experimental protocol to an outcome of the protocol.
has domain
experimental protocol c
has range
material entity c

has outputop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasOutput

hasOutput is a relation that binds a experimental protocol execution to a material entity (such as organism) or a data set (such as sequence reads).
has domain
occurrent c
has range
continuant c

has partop back to ToC or Object Property ToC

IRI: http://www.obofoundry.org/ro/ro.owl#has_part

has characteristics: transitive

is inverse of
part of op

has procedureop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasProcedure

has procedure is a relation that binds a experimental protocol execution and a laboratory procedure.

has protocolop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasProtocol

hasProtocol is a relation that binds a laboratory procedure to a experimental protocol.
has domain
laboratory procedure c
has range
experimental protocol c

has subprocedureop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#hasSubprocedure

has subprocedure is a relation that binds a laboratory procedure and a laboratory subprocedure.

is documented inop back to ToC or Object Property ToC

IRI: http://purl.org/net/SMARTprotocol#isDocumentedIn

is documented in is a relation that binds a planned process such as a experimental protocol execution to a document such as an experimental protocol

is preceded byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000062

has characteristics: transitive

is inverse of
precedes op

part ofop back to ToC or Object Property ToC

IRI: http://www.obofoundry.org/ro/ro.owl#part_of

Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.

has characteristics: transitive

is inverse of
has part op

participates inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000056

participates in is a relation that binds a material entity name and a laboratory procedure or laboratory subprocedure
has domain
continuant c
has range
occurrent c

precedesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000061

x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.

has characteristics: transitive

is inverse of
is preceded by op

Named Individuals

cell disruption 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#cellDisruption1

belongs to
cell disruption c
has facts
precedes op denaturation reaction 1

denaturation reaction 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#denaturationReaction01

belongs to
denaturation reaction c
has facts
is preceded by op cell disruption 1
precedes op precipitation reaction 1

precipitation reaction 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#precipitationReaction01

belongs to
precipitation reaction c
has facts
is preceded by op denaturation reaction 1
precedes op washing nucleic acids 1

RNA extraction 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#RNAextraction01

belongs to
RNA extraction protocol c
has facts
has instruction op cell disruption 1
has instruction op denaturation reaction 1
has instruction op precipitation reaction 1
has instruction op washing nucleic acids 1

washing nucleic acids 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#washingNucleicAcid01

belongs to
washing nucleic acids c
has facts
is preceded by op precipitation reaction 1

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals