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

This section provides details for each class and property defined by SMART Protocols Ontology: Document 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

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

advantage of the Protocolc back to ToC or Class ToC

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

Advantage of the protocol is a subclass of textual entity. It should be made clear in which situations the Protocol has been successfully employed.
Source
http://www.nature.com/nprot/info/gta.html
has super-classes
textual entity c
is in domain of
advantage of op
is in range of
has advantage op
is disjoint with
primer sequence 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

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
part of op some methods section c
has sub-classes
caution c, critical step c, hint c, pause point c, storage condition c, timing c, troubleshooting c
is in domain of
alert message of op
is in range of
has alert message op
is disjoint with
name c, application of the protocol c, catalog number c, limitation of the protocol c, primer sequence c, provenance of the protocol c, purpose of the protocol c, title of the protocol c

alkali metal salt reagentc back to ToC or Class ToC

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

alkali metal salts usually are very water soluble. Some alkali metal salt are: potasium salt, sodium salt.
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

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

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

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

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 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

antibodyc back to ToC or Class ToC

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

a blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood. The antibodies also can be considered reagents used to detect some analyte in a experimental protocol.
has super-classes
material entity c
derives from op some organism c
has_role op some reagent role c
has sub-classes
monoclonal antibody reagent c, polyclonal antibody reagent 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

application of the protocolc back to ToC or Class ToC

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

Application of the protocol is a subclass of textual entity. Applications of the protocol list the full diversity of the applications of the method and support if is possible to extend the range of applications of the protocol.
Example
The protocol works in northern blot assays using cactus, agave, banana, tomato, Arabidopsis and tobacco. Allwood, J.W., et al., Inter-laboratory reproducibility of fast gas chromatography-electron impact-time of flight mass spectrometry (GC-EI-TOF/MS) based plant metabolomics. Metabolomics, 2009. 5(4): p. 479-496.
has super-classes
textual entity c
is in domain of
application of op
is in range of
has application op
has members
application 1 ni
is disjoint with
name c, catalog number c, limitation of the protocol c, primer sequence c, provenance of the protocol c, purpose of the protocol c, title of the protocol c, alert message 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

artificial chromosomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001133

A construct that is generated by inserting exogenous DNA into a plasmid containing features of a eukaryotic chromosome or prokaryotic episome that support replication and preservation in a host cell. Artificial chromosomes are used to clone large DNA fragments between 100,000 bases and 3,000,000 bases in size.
Example
An artificial mouse chromosome.
has super-classes
construct c
has sub-classes
BAC c

authorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGI.owl#Author

a human being that bears an author role.
has super-classes
material entity c
has name op some author name c
has author identification op some author identifier c
is in domain of
author of op, has author identification op, has first name op, has last name op
is in range of
author identification of op, has author op
has members
author1 ni, author2 ni, author3 ni, author4 ni, author5 ni, author6 ni, author7 ni

author identifierc back to ToC or Class ToC

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

Author identifier is a unique number to all authors as a form of authority control. Example of usage: orcid ID
Example
orcid ID
has super-classes
identifier c
is in domain of
author identification of op
is in range of
has author identification op

author listc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000321

part of a document that enumerates the authors of the document
Example
Lawrence Hunter and Kevin Brettonel Cohen
has super-classes
document part c
has part op some author name c
has members
author list 1 ni
is disjoint with
equipment and supplies list c, reagent list c, recipe list c, software list c, specimen list c

author namec back to ToC or Class ToC

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

Author name is a textual entity. Author name is the name of a person or institution. If is applicable, the author name should include the first name and last name.
Example
Olga Giraldo
has super-classes
name c
part of op some author list c
has members
Anthony J. Freemont ni, Crispin J. Miller ni, John A. Radford ni, Kim M. Linton ni, Sian Dibben ni, Stuart D. Pepper ni, Yvonne Hey ni

BACc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0000286

An artificial chromosome vector that contains portions of the bacterial fertility plasmid (F-plasmid). Used for transforming and cloning in bacteria, usually E. coli.
has super-classes
artificial chromosome 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

BALB/c is an albino, laboratory-bred strain of the house mouse from which a number of common substrains are derived. BALB/c mice are distributed globally, and are among the most widely used inbred strains used in animal experimentation.
Source
https://en.wikipedia.org/wiki/BALB/c
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

bibliographic referencec back to ToC or Class ToC

IRI: http://purl.org/spar/biro/BibliographicReference

An expression of a bibliographic record in a specific format, that references a particular textual or data publication (or a work in preparation for publication). Each bibliographic reference is a list of items containing entities that describe aspects of the referenced work - for example authors, title, journal, publication year - selected from the bibliographic record. Note that because different journal styles may require omission of elements of the bibliographic record in references included in a paper's reference list (e.g. the title, the identifier, the names of the eighth and subsequent authors), and because errors can be introduced when an author creates a bibliographic reference, the bibliographic reference to a published work may not be a complete or fully accurate expression of the information contained within the authoritative bibliographic record for that work.
has super-classes
information content entity 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

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

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, TAE buffer c, Tris buffer c, lysis buffer c, phosphate buffered saline c, protein precipitation buffer 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 AP2c back to ToC or Class ToC

IRI: http://purl.org/net/SMARTprotocol#BufferAP2

has super-classes
protein precipitation buffer c

buffer ATLc back to ToC or Class ToC

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

Buffer ATL is a 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
has super-classes
lysis buffer c

buffer namec back to ToC or Class ToC

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

Buffer name is a textual entity. Buffer name is the name of the buffer produced by or used in a reaction involving changes in atoms or molecules. If is applicable, the name of the buffer should be including the follow information: buffer concentration, and final volume.
Example
1X Queen’s lysis buffer (1L), AB lysis buffer (500ml).
has super-classes
name c
is disjoint with
equipment or supplies name c, primer name c, software name 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

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

catalog numberc back to ToC or Class ToC

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

Catalog number is a subclass of textual entity. Catalog number is a numeral or string of numerals that is used for identification.
Example of usage: 5000-0012
Example
5000-0012
has super-classes
symbol c
is in domain of
catalog number of op
is in range of
has catalog number op
is disjoint with
name c, application of the protocol c, limitation of the protocol c, primer sequence c, provenance of the protocol c, purpose of the protocol c, title of the protocol c, alert message 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

cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0000031

A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
has super-classes
material entity c
derives from op some organism c
has_role op some reagent role c
has sub-classes
immortal cell line c, mortal cell line c, stem cell line c, stem cell-differentiated cell line c

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

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

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

CHAPSc back to ToC or Class ToC

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

an alkanesulfonate that has formula C32H58N2O7S.
has super-classes
alkanesulfonate reagent 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

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.
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

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

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

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

concentrationc back to ToC or Class ToC

IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C41185

The quantity of a substance per unit volume or weight; a measure of the amount of substance present in a unit amount of mixture, particularly, the amount of solute dissolved in a solvent. The amounts can be expressed as moles, masses, volumes, or parts.
has super-classes
quality c
has sub-classes
final concentration c, initial concentration c
is in range of
has concentration op

constructc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0000285

A reagent that is a virus or DNA molecule capable of autonomous replication, used as a vehicle to transfer foreign genetic material into a host cell. A construct may contain an insert of DNA from an external source, and may be used for cloning or for expression purposes.
Example
Cells are transfected with constructs expressing a gene of interest to study the gene function.
has super-classes
material entity c
has sub-classes
artificial chromosome 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

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

cover datec back to ToC or Class ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/prism:coverDate

Date on the cover of a magazine issue, suitable for storing in a database field with a 'date' data type.
The cover date on a magazine indicates the last date the printed issue should be displayed for sale, NOT the publication date as commonly believed. Not applicable to non-print platforms.
has super-classes
textual entity 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 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
has sub-classes
equipment and supplies list c, reagent list c, recipe list c, software list c, specimen list 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

denaturation reactionc back to ToC or Class ToC

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

The biological activity of a biopolymer is closely linked to its native structure which is retained only if critical factors such as temperature, pH, solvent and solute are kept within narrow limits. Any alteration of the native structure causing a loss of biological activity is called denaturation.
Source
http://www.sigmaaldrich.com/life-science/metabolomics/bioultra-reagents/denaturation.html#sthash.5rKMTmls.dpuf
has super-classes
protocol instruction c

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

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

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

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

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 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 washing nucleic acids c
has instruction op some precipitation reaction 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
A journal article, patent application, laboratory notebook, or a book
has super-classes
information content entity c
has part op some document part c
has sub-classes
experimental protocol c, license c

document partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000314

an information content entity that is part of a document
Example
An abstract, introduction, method or results section.
has super-classes
information content entity c
part of op some document c
has sub-classes
author list c, introduction section c, materials section c, methods section c, reference list c, results section 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

dsRNA oligonucleotidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001207

An RNA interference oligonucleotide comprised of complementary strands of RNA that form double-stranded duplexes, and can be processed through the RNAi pathway into short interfering RNA (siRNA) molecules used to silence target gene expression.
has super-classes
RNA interference oligonucleotide 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

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

entityc back to ToC or Class ToC

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

has sub-classes
continuant 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

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, gel documentation system 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
has members
equipment or supplies 1 ni, equipment or supplies 2 ni, equipment or supplies 3 ni, equipment or supplies 4 ni, equipment or supplies 5 ni
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
has members
equipment list 1 ni
is disjoint with
reagent list c, software list c, author list c, reagent list c, recipe list c, software list c, specimen list 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
has members
Forceps ni, Homogenizer blades ni, Scalpel ni, Scalpel holder ni, Tissue storage container ni
is disjoint with
buffer name c, primer name c, reagent name c, software name c, solution name 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

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

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 experimental input op some equipment and supplies list c
has instruction op some protocol instruction c
published in op some publication c
has limitation op some limitation of the protocol c
has identifier op some protocol identifier c
has part op some keyword c
has version op some version number c
has advantage op some advantage of the Protocol c
has part op some author list c
has part op some cover date c
has alert message op some alert message c
has experimental input op some software list c
has experimental input op some recipe list c
has provenance op some provenance of the protocol c
has title op some title of the protocol c
has experimental input op some reagent list c
has outcome op some outcome of the protocol c
has part op some reference list c
has application op some application of the protocol c
located in op some repository name c
has purpose op some purpose of the protocol c
has experimental input op some specimen list 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
accepted by op, has advantage op, has application op, has author op, has experimental input op, has instruction op, has license op, has limitation op, has outcome op, has provenance op, has purpose op, has subject op, has title op, located in op, modified by op, published in op, validated by op
is in range of
advantage of op, application of op, author of op, instruction of op, license of op, limitation of op, outcome of op, provenance of op, purpose of op

final concentrationc back to ToC or Class ToC

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

The final measured concentration of a compound in a substance.
Source
Adopted from NCI thesaurus
has super-classes
concentration c
is in range of
has final concentration op
is disjoint with
initial concentration 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. Reference: Nature Protocols
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

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

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 documentation systemc back to ToC or Class ToC

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

Gel documentation system is equipment widely used in molecular biology laboratories for the imaging and documentation of nucleic acid and protein suspended within polyacrylamide or agarose gels. These gels are typically stained with ethidium bromide or other fluorophores such as SYBR Green. Generally, a gel doc includes an ultraviolet (UV) light transilluminator, a hood or a darkroom to shield external light sources and protect the user from UV exposure, and a CCD or CMOS camera for image capturing.
Source
https://en.wikipedia.org/wiki/Gel_doc
has super-classes
equipment and supplies 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

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
sample mill 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

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

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

homogenized tissuec back to ToC or Class ToC

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

homogenized tissue is a tissue that is brought to a state such that all fractions of the tissue are equal in composition.
has super-classes
tissue 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, 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 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

identifierc back to ToC or Class ToC

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

label, number or something else which identifies an entity, but which may not be persistent (stable) or unique (a material entity may have multiple identifiers).
has super-classes
symbol c
has sub-classes
author identifier c, protocol identifier c, specimen identifier c
is in domain of
identifier of op
is in range of
has identifier op

immortal cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0009828

A cell line that is expected to be capable of indefinite propagation in an vitro culture.
has super-classes
cell line 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 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, 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
bibliographic reference c, data set c, document c, document part c, measurement value c, publication c, repository c, textual entity c
is in range of
accepted by op, experimental input of op

initial concentrationc back to ToC or Class ToC

IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C85644

The first measured concentration of a compound in a substance. In pharmacology, the initial concentration is given only for bolus IV models.
has super-classes
concentration c
is in range of
has initial concentration op
is disjoint with
final concentration 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

introduction sectionc back to ToC or Class ToC

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

Introduction section is part of a document. In the context of a protocol, this section show to reader about essential components of the protocol. So, the scientific community could make a decision as to the suitability of the protocol to their experimental problem.This section must include: applications of the protocol, comparison with other protocols, development of the protocol, limitations and purpose.
has super-classes
document part c

keywordc back to ToC or Class ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/prism:keyword

An element used to tag keywords that are likely to be used in search queries.
Note that this differs from a subject or elements such as dc:subject, prism:person, prism:event, or prism:organization that are the subject of the article. Best practice is to use values from a keyword controlled vocabulary for this element
has super-classes
textual entity 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.
Example
Universal Linker Kit, laboratory kit that allows customization of protein microarrays.
has super-classes
material entity c
has name op some kit name c
has sub-classes
subcellular protein fractionation kit for tissues c
is disjoint with
reagent c

kit namec back to ToC or Class ToC

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

Kit name is a textual entity. Kit name is the name of a kit.
Example
Spectrum Plant Total RNA Kit, sufficient for 50 purifications.
has super-classes
name 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

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

licensec back to ToC or Class ToC

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

A document that provides access to documented permission to do something, either from a government or under a law or regulation.
Source
adapted of Biomedical Resource Ontology
has super-classes
document c
is in domain of
license of op
is in range of
has license op

limitation of the protocolc back to ToC or Class ToC

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

Limitation of the protocol is a subclass of textual entity where the possible limitations of the protocol should be discussed. It should be made clear in which situations the Protocol would be unreliable or otherwise unsuccessful.
Source
http://www.nature.com/nprot/info/gta.html
Example
A major problem faced both in this and other safflower transformation studies is the hyperhydration of transgenic shoots which result in the loss of a large proportion of transgenic shoots. Belide Srinivas., 2011
has super-classes
textual entity c
is in domain of
limitation of op
is in range of
has limitation op
is disjoint with
name c, application of the protocol c, catalog number c, primer sequence c, provenance of the protocol c, purpose of the protocol c, title of the protocol c, alert message 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

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

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

has super-classes
lyophilized tissue c

lyophilized leafc back to ToC or Class ToC

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

has super-classes
lyophilized tissue c

lyophilized rootc back to ToC or Class ToC

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

has super-classes
lyophilized tissue c

lyophilized seedc back to ToC or Class ToC

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

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

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
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

manufacturerc back to ToC or Class ToC

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

Manufacturer is a subclass of material entity. Manufacturer is a person, enterprise, or entity that produces equipments, reagents, primers or other laboratory supplies.
Example
Bio-Rad, Nalgene, Thermoscientific, Eppendorf, Falcon.
has super-classes
material entity c
has name op some manufacturer name c
has members
manufacturer1 ni, manufacturer2 ni
is disjoint with
solution c, reagent c

manufacturer namec back to ToC or Class ToC

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

Manufacturer name is a subclass of textual entity. Manufacturer name is the name of a person, enterprise, or entity that produces equipments, reagents, primers or other laboratory supplies.
has super-classes
name c
has members
Sigma-Aldrich ni, invitrogen ni

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
has sub-classes
antibody c, author c, cell line c, construct c, equipment and supplies c, kit c, manufacturer c, material sample c, organism c, reagent c, software c
is in domain of
experimental input of op, has catalog number op, has concentration op, has name op
is in range of
catalog number of op, name of 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

materials sectionc back to ToC or Class ToC

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

Materials section is part of a document. In the context of a protocol, this section should list the sample, buffers, reagents, consumables, equipments, kits, software etc., necessary for carrying out your technique.
has super-classes
document part c

measurement valuec back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_000070

A measurement value is a quantitative description that reflects the magnitude of some attribute.
has super-classes
information content entity c
has sub-classes
quantity 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

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

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

methods sectionc back to ToC or Class ToC

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

Methods section is part of a document. This is the section where the protocol is presented.
has super-classes
document part c
has part op some alert message 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

miRNA oligonucleotidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001208

An RNA interference oligonucleotide that includes gene-specific targeting sequences intended to silence expression of a target gene through the RNAi pathway, and also contains flanking miRNA sequence elements that allow for processing by cellular microRNA processing machinery into active miRNA molecules.
has super-classes
RNA interference oligonucleotide 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

monoclonal antibody reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0000229

Antibody reagent that recognizes a single epitope.
Example
An mouse anti-human Mad4 antibody.
has super-classes
antibody 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

mortal cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0009829

A cell line is able to support only a limited number of passages in vitro.
A mortal cell line is not capable of supporting indefinite propagation in vitro, being limited by entry of its cells into senescence.
has super-classes
cell line 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

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

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
author name c, buffer name c, equipment or supplies name c, kit name c, manufacturer name c, primer name c, publication name c, reagent name c, recipe name c, repository name c, software name c, solution name c, specimen name c
is in domain of
name of op
is in range of
has name op
is disjoint with
application of the protocol c, catalog number c, limitation of the protocol c, primer sequence c, provenance of the protocol c, purpose of the protocol c, title of the protocol c, alert message c

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. Reference: Nature Protocols
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

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

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 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 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, RNA 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

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

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

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

outcome of the protocolc back to ToC or Class ToC

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

protocol outcome is a textual entity that is an outcome or expected result by a protocol execution.
has super-classes
textual entity c
is in domain of
outcome of op
is in range of
has outcome op

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 used in molecular biology to amplify a single copy or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. It is a way to amplify a focused segment of DNA, useful for such purposes as the diagnosis and monitoring of genetic diseases, identification of criminals (in the field of forensics), and studying the function of a targeted segment of DNA.
Source
http://learn.genetics.utah.edu/content/labs/pcr/
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
has sub-classes
Advantage 2 PCR buffer c, GeneAmp PCR Buffer c, NH4 buffer c, Taq polymerase buffer c, TaqMan buffer 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

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

physical disruption equipment and suppliesc back to ToC or Class ToC

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

Equipment used for cell disruption methods. Some examples: mortar and pestle; handheld device (for example, Dounce and Potter-Elvehjem homogenizers), motorized devices (for example, blenders).
has super-classes
equipment and supplies c
has sub-classes
lyophilizer c, sample mill c, sonicator 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
http://bit.do/thermofisher-PluronicF68
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

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
has sub-classes
Triton X-100 c, polysorbate c, tergitol c

polyclonal antibody reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0000230

Antibody reagent that recognizes multiple epitopes.
Example
A rabbit anti-human SHH antibody.
has super-classes
antibody 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

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

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

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

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

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

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

powdered leafc back to ToC or Class ToC

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

has super-classes
powdered tissue c

powdered rootc back to ToC or Class ToC

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

has super-classes
powdered tissue c

powdered seedc back to ToC or Class ToC

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

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

precipitation reactionc back to ToC or Class ToC

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

precipitation reaction, is the third basic step in a DNA extraction. This is commonly achieved by ice-cold ethanol, or isopropanol, or phenol-chloroform, or by using minicolumn.
has super-classes
protocol instruction c

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 in domain of
has annealing temperature op, has annealing time op, has primer length op, has sequence op
is disjoint with
equipment and supplies c, information biomacromolecule c, material sample c, organism c

primer namec back to ToC or Class ToC

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

Primer name is a textual entity. Primer name is the name of a primer.
Example
CII-fw, CII-rv.
has super-classes
name c
is disjoint with
buffer name c, equipment or supplies name c, software name c

primer sequencec back to ToC or Class ToC

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

Primer sequence is a textual entity. Primer sequence is a serie ordered of bases coded as letters (A,C,G,T) without spaces, that identify to a particular primer.
Example
5′-GAATGATGTACCACCTTTG-3′
has super-classes
textual entity c
is in range of
has sequence op
is disjoint with
name c, advantage of the Protocol c, application of the protocol c, catalog number c, limitation of the protocol c, provenance of the protocol c, purpose of the protocol c, title of the protocol c, alert message 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.
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 RNAc back to ToC or Class ToC

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

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

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 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

protein precipitation bufferc back to ToC or Class ToC

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

has super-classes
buffer c
has sub-classes
buffer AP2 c

protocol identifierc back to ToC or Class ToC

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

Any number that identifies a specific experimental protocol
has super-classes
identifier c
has members
protocol Id1 ni

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 domain of
instruction of op
is in range of
has instruction op

provenance of the protocolc back to ToC or Class ToC

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

Provenance of the protocol is a subclass of textual entity. Provenance of the protocol include references to key papers where the protocol has been used previously. Indicate if your protocol is the result of modify a previous one or if it is the result of reuse steps of several (more than 1) protocols.
Example
The extraction procedure precisely followed that of Lisec et al. (2006), which was developed from the protocol of Fiehn et al. (2000a). Allwood J. W., 2009
has super-classes
textual entity c
is in domain of
provenance of op
is in range of
has provenance op
has members
provenance 1 ni
is disjoint with
name c, application of the protocol c, catalog number c, limitation of the protocol c, primer sequence c, purpose of the protocol c, title of the protocol c, alert message c

publicationc back to ToC or Class ToC

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

publication is a magazine, or other publication, in which a resource was/will be published.
has super-classes
information content entity c
has name op some publication name c

publication namec back to ToC or Class ToC

IRI: http://prismstandard.org/namespaces/basic/2.0/prism:publicationName

Title of the magazine, or other publication, in which a resource was/will be published.
has super-classes
name c

purpose of the protocolc back to ToC or Class ToC

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

The purpose of a protocol is a subclass of textual entity. Its role, is to enable readers to make a decision as to the suitability of the protocol to their experimental problem.
Example
Development of a method to isolate small RNAs from different plant species (...) that no need of first total RNA extraction and is not based on the commercially available TRIzol; Reagent or columns. Rosas-Cardenas, F.d.F., et al., A simple and efficient method for isolating small RNAs from different plant species. Plant Methods, 2011. 7(4): p. 7.
has super-classes
textual entity c
is in domain of
purpose of op
is in range of
has purpose op
is disjoint with
name c, application of the protocol c, catalog number c, limitation of the protocol c, primer sequence c, provenance of the protocol c, title of the protocol c, alert message c

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
concentration c

quantityc back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_000052

A quantity is an informational entity that gives the magnitude of a property.
has super-classes
measurement value 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

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 catalog number op some catalog number c
has alert message op some caution c
has name op some reagent name c
has part op some measurement value c
is manufactured by op some manufacturer name c
has alert message op some storage condition c
part of op some recipe c
has sub-classes
chemical compound reagent c, enzyme reagent c, nucleic acid reagent c, nucleoside triphosphate reagent c, solution c
is in domain of
has final concentration op, has initial concentration op
has members
reagent1 ni, reagent2 ni, reagent3 ni, reagent4 ni
is disjoint with
equipment and supplies c, software c, material sample c, organism c, kit c, manufacturer 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
has members
reagent list 1 ni
is disjoint with
equipment and supplies list c, software list c, author list c, equipment and supplies list c, recipe list c, software list c, specimen list 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
has members
Chloroform ni, Ethyl alcohol ni, Isopropyl alcohol ni, t r i zol ni
is disjoint with
equipment or supplies name c, software name c

reagent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000086

a role played by a material entity used to produce a chemical reaction to detect, measure, or produce other substances
has super-classes
role 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 alert message op some hint c
has part op some reagent c
has alert message op some alert message c
part of op some recipe list c
has alert message op some storage condition c
has name op some recipe name c
has alert message op some caution c
has part op some measurement value c
has concentration op some final concentration 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
is disjoint with
author list c, equipment and supplies list c, reagent list c, software list c, specimen list 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

reference listc back to ToC or Class ToC

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

Reference lists contain a complete list of all the sources (books, journal articles, websites, etc.) that you have cited directly in a document. That means that if there are in-text citations for a source there is a reference list entry, and vice versa.
has super-classes
document part c
has part op some bibliographic reference c

repositoryc back to ToC or Class ToC

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

a central location in which experimental protocols are stored and managed.
has super-classes
information content entity c
has name op some repository name c
is in range of
located in op

repository namec back to ToC or Class ToC

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

Title of the repository in which a resource was/will be stored and managed.
has super-classes
name c

results sectionc back to ToC or Class ToC

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

Results section is part of a document. In the context of a protocol, this section should show the output of a protocol.
has super-classes
document part 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.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
has super-classes
primer 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
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 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

reviewer rolec back to ToC or Class ToC

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

a person who formally assesses or examines a document, for example, a protocol.
has super-classes
role 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 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 precipitation reaction c
has instruction op some denaturation reaction c
has instruction op some cell disruption c
has instruction op some washing nucleic acids c
has members
RNA extraction 1 ni
is disjoint with
DNA extraction protocol c

RNA interference oligonucleotidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001206

An RNA interference reagent used to silence expression of a target gene in cells, through the RNA interference pathway.
has super-classes
RNA oligonucleotide c
has sub-classes
dsRNA oligonucleotide c, miRNA oligonucleotide c, siRNA oligonucleotide c

RNA oligonucleotidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001205

An RNA reagent consisting of a short, linear RNA polymer, typically with 100 or fewer bases.
has super-classes
RNA reagent c
has sub-classes
RNA interference oligonucleotide c

RNA reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001202

A reagent that is a polymer comprised of RNA nucleotides.
has super-classes
nucleic acid reagent c
has sub-classes
RNA oligonucleotide 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

rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000023

A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
has super-classes
specifically dependent continuant c
has sub-classes
reagent role c, reviewer role c, validator role 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

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 specimen list c
derives from 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
has sub-classes
bead beater c, blender c, coffee mill c, drill c, freezer milling c, french pressure cell press c, geno grinder 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
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

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

single-stranded DNAc back to ToC or Class ToC

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

has super-classes
deoxyribonucleic acid c

siRNA oligonucleotidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001209

An RNA interference oligonucleotide capable of silencing expression of a target gene through the RNAi pathway. siRNAs are synthesized as single-stranded molecules, typically 19-25 nucleotides in length, and paired with complementary sequences to form duplexes that serve as substrates for cellular RNAi processing machinery.
has super-classes
RNA interference oligonucleotide 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

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

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

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

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

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
is disjoint with
reagent c

software listc back to ToC or Class ToC

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

Software list is a data set of the names of softwares that are part of materials section of a protocol.
has super-classes
data set c
has part op some software name c
is disjoint with
equipment and supplies list c, reagent list c, author list c, equipment and supplies list c, reagent list c, recipe list c, specimen list 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
is disjoint with
buffer name c, equipment or supplies name c, primer name c, reagent name c, solution name 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 name op some solution name c
has alert message op some storage condition c
has alert message op some caution c
has part op some measurement value c
has concentration op some final concentration c
has sub-classes
Chloroform:Isoamyl alcohol c, Phenol:Chloroform:Isoamyl alcohol c, buffer c, ethanol solution c, guanidinium thiocyanate-phenol c, wash solution c
is disjoint with
information biomacromolecule c, material sample c, organism c, manufacturer c

solution namec back to ToC or Class ToC

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

Solution name is a textual entity. Solution name is the name of a liquid preparation that contains at least 2 chemical substances, one playing the role of solvent and the other one playing the role of solute. If is applicable, the name of the solution should including the follow information: solution concentration, and final volume.
Example
3M NaOH (1L)
has super-classes
name c
is disjoint with
equipment or supplies name c, software name 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

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.
Example
the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
has super-classes
dependent continuant c
has sub-classes
quality c, role c
is disjoint with
generically dependent continuant c

specimen identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001616

A symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
has super-classes
identifier 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
is disjoint with
author list c, equipment and supplies list c, reagent list c, recipe list c, software list 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
has members
tumor tissue ni

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.
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

stem cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0002003

A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.
has super-classes
cell line c

stem cell-differentiated cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ERO_0001400

A cell line that results from in vitro differentiation of stem cells into a more lineage-restricted cell type.
Example
Mouse embryonic fibroblasts
has super-classes
cell line 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

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

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

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

subjectc back to ToC or Class ToC

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

a particular branch of scientific knowledge; ecology, zoology, cell biology, etc.
has super-classes
textual entity c
is in range of
has subject 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

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

symbolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000028

An information content entity that is a mark or character used as a conventional representation of another entity.
has super-classes
textual entity c
has sub-classes
catalog number c, identifier c, version number c

TAE bufferc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHMO_0001750

An acetate buffer solution prepared from Tris, acetic acid, and EDTA.
has super-classes
buffer 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
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 solution 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

TE bufferc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHMO_0002069

A buffer solution where the pH is maintained by Tris [tris(hydroxymethyl)aminomethane] and EDTA (ethylenediaminetetraacetic acid). TE buffer is used to protect DNA or RNA from degradation.
has super-classes
Tris 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
advantage of the Protocol c, alert message c, application of the protocol c, cover date c, instruction c, keyword c, limitation of the protocol c, name c, outcome of the protocol c, primer sequence c, provenance of the protocol c, purpose of the protocol c, subject c, recipe c, symbol c, title of the protocol c
is in range of
published in op

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

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, homogenized 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

title of the protocolc back to ToC or Class ToC

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

Title of protocol is a subclass of textual entity. Title of protocol is the name of a protocol.
has super-classes
textual entity c
is in range of
has title op
has members
title1 ni
is disjoint with
name c, application of the protocol c, catalog number c, limitation of the protocol c, primer sequence c, provenance of the protocol c, purpose of the protocol c, alert message 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

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. Reference: Nature Protocols
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

Tris bufferc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHMO_0001754

A buffer where the pH is maintained by a Tris--HTris equilibrium. Tris = tris(hydroxymethyl)aminomethane.
has super-classes
buffer c
has sub-classes
TE buffer c, Tris-HCl buffer c

Tris-HCl bufferc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHMO_0001755

A buffer solution in which the pH is maintained by Tris [tris(hydroxymethyl)aminomethane] and HCl solution.
has super-classes
Tris buffer 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

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

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

validator rolec back to ToC or Class ToC

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

validator is a person who formally assesses or examines that the protocol can be understood and carried out correctly by users.
has super-classes
role c

version numberc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000129

A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
has super-classes
symbol c
is in range of
has current version op, has version op

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

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

wash solutionc back to ToC or Class ToC

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

has super-classes
solution 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

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

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.
has super-classes
fungal cell c

Object Properties

accepted byop back to ToC or Object Property ToC

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

The property acceptedBy indicates the person or authoritative body who, after theprocess of validation of a protocol, accepts the modifications made to this document before to its massive implementation.

advantage ofop back to ToC or Object Property ToC

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

advantageOf is a relation that binds an advantage of the protocol to an experimental protocol.
has domain
advantage of the Protocol c
has range
experimental protocol c
is inverse of
has advantage op

alert message ofop back to ToC or Object Property ToC

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

alertMessageOf is a relation that binds an alert message to a material entity or protocol intruction.
has domain
alert message c
is inverse of
has alert message op

application ofop back to ToC or Object Property ToC

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

applicationOF is a relation that binds an application of the protocol to a document such as experimental protocol.
has domain
application of the protocol c
has range
experimental protocol c
is inverse of
has application op

author identification ofop back to ToC or Object Property ToC

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

authorIdentificationOf is a relation that binds an author identifier to an author.
has domain
author identifier c
has range
author c
is inverse of
has author identification op

author ofop back to ToC or Object Property ToC

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

authorOf is a relation that binds an author to a document such as experimental protocol.
has domain
author c
has range
experimental protocol c
is inverse of
has author op

catalog number ofop back to ToC or Object Property ToC

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

catalogNumberOf is a relation that binds a catalog number to a material entity.
has domain
catalog number c
has range
material entity c
is inverse of
has catalog number op

derives fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001000

derives from is 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).

experimental input ofop back to ToC or Object Property ToC

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

experimentalInputOf is a relation that binds a material entity participating in a protocol to a experimental protocol or protocol instruction.
has domain
material entity c
has range
information content entity c
is inverse of
has experimental input op

has advantageop back to ToC or Object Property ToC

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

hasAdvantage is a relation that binds an experimental protocol to an advantage of the protocol.
has domain
experimental protocol c
has range
advantage of the Protocol c
is inverse of
advantage of op

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. Example of usage: "DNA Extraction Protocol" hasAlertMessage "Critical Step"
has range
alert message c
is inverse of
alert message of op

has annealing temperatureop back to ToC or Object Property ToC

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

The property hasAnnealingTemperature indicates the temperature allowing annealing of the primers to the single-stranded DNA template during a PCR. The temperature should be from 42-65°C.
has domain
primer c

has annealing timeop back to ToC or Object Property ToC

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

The property hasAnnealingTime indicates the time allowing annealing of the primers to the single-stranded DNA template during a PCR. Typical annealing times are 15-30 seconds.
has domain
primer c

has applicationop back to ToC or Object Property ToC

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

hasApplication is a relation that binds a document such as experimental protocol to a application of the protocol.
has domain
experimental protocol c
has range
application of the protocol c
is inverse of
application of op

has authorop back to ToC or Object Property ToC

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

hasAuthor is a relation that binds a document such as experimental protocol to an author
Example
"Laboratory protocol" hasAuthor "John Smith"
has domain
experimental protocol c
has range
author c
is inverse of
author of op

has author identificationop back to ToC or Object Property ToC

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

hasAuthorIdentification is a relation that binds an author to an author identifier.
has domain
author c
has range
author identifier c
is inverse of
author identification of op

has catalog numberop back to ToC or Object Property ToC

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

hasCatalogNumber is a relation that binds a material entity to a catalog number used for identification.
Example
"Nalgene Cryogenic Tube" hasCatalogNumber "5000-0012"
has domain
material entity c
has range
catalog number c
is inverse of
catalog number of op

has concentrationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BCGO_0000183

The property has concentration relates a molecular entity, compound, substance, reagent or solute present in a unit amount of mixture.
has sub-properties
has final concentration op, has initial concentration op
has domain
material entity c
has range
concentration c

has current versionop back to ToC or Object Property ToC

IRI: http://purl.org/pav/hasCurrentVersion

has range
version number c

has developmental stageop back to ToC or Object Property ToC

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

hasDevelopmentalStage is a relation that binds a specimen to an developmental stage.

has experimental inputop back to ToC or Object Property ToC

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

hasExperimentalInput is a relation that binds a experimental protocol to a material entity participating in a protocol.
has domain
experimental protocol c
is inverse of
experimental input of op

has final concentrationop back to ToC or Object Property ToC

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

The property hasFinalConcentration relates the final measured concentration of a molecular entity, compound, substance, reagent or solute and the class final concentration.
has super-properties
has concentration op
has domain
reagent c
has range
final concentration c

has first nameop back to ToC or Object Property ToC

IRI: http://purl.org/net/OCRe/OCRe.owl#OCRE900225

First name of a person
has super-properties
has name op
has domain
author c

has growth conditionsop back to ToC or Object Property ToC

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

hasGrowthConditions is a relation that binds a specimen entry to an growth conditions entry

has identifierop back to ToC or Object Property ToC

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

hasIdentifier is a relation that binds a document such as an experimental protocol or material entity to a identifier
has range
identifier c
is inverse of
identifier of op

has initial concentrationop back to ToC or Object Property ToC

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

The property hasInitialConcentration relates the first measured concentration of a molecular entity, compound, substance, reagent or solute and the class initial concentration.
has super-properties
has concentration op
has domain
reagent c
has range
initial concentration 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
is inverse of
instruction of op

has last nameop back to ToC or Object Property ToC

IRI: http://purl.org/net/OCRe/OCRe.owl#OCRE900226

Last name of a person
has super-properties
has name op
has domain
author c

has licenseop back to ToC or Object Property ToC

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

hasLicense is a relation that binds a protocol to a license
has domain
experimental protocol c
has range
license c
is inverse of
license of op

has limitationop back to ToC or Object Property ToC

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

hasLimitation is a relation that binds a document such as experimental protocol to a limitation of protocol.
has domain
experimental protocol c
has range
limitation of the protocol c
is inverse of
limitation of op

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
Example
"Buffer" hasName "1X Queen’s lysis buffer (1L)"
has sub-properties
has first name op, has last name op
has domain
material entity c
has range
name c
is inverse of
name of op

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
outcome of the protocol c
is inverse of
outcome of op

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 primer lengthop back to ToC or Object Property ToC

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

The property primerLength indicates the length of PCR primers. This length is long enough for adequate specificity and short enough for primers to bind easily to the template at the annealing temperature. The typical length of PCR primers is 18-30bp.
has domain
primer c

has provenanceop back to ToC or Object Property ToC

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

hasProvenance is a relation that binds an experimental protocol to the provenance of the protocol.
has domain
experimental protocol c
has range
provenance of the protocol c
is inverse of
provenance of op

has purposeop back to ToC or Object Property ToC

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

hasPurpose is a relation that binds a document such as experimental protocol to an purpose of the protocol.
has domain
experimental protocol c
has range
purpose of the protocol c
is inverse of
purpose of op

has quantityop back to ToC or Object Property ToC

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

The property hasQuantity indicates how much there is of something that you can measure; the total amount or number.

has sequenceop back to ToC or Object Property ToC

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

hasSequence is a relation that binds a oligonucleotide or nucleic acid to a sequence.
Example
The primer CII-fw hasSequence 5′-GAATGATGTACCACCTTTG-3′
has domain
primer c
has range
primer sequence c

has specimen treatmentop back to ToC or Object Property ToC

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

hasSpecimenTreatment is a relation that binds a specimen to a specimen treatment protocol

has subjectop back to ToC or Object Property ToC

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

The property hasSubject indicates the topic or topics of a resource.
has domain
experimental protocol c
has range
subject c

has techniqueop back to ToC or Object Property ToC

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

has titleop back to ToC or Object Property ToC

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

hasTitle is a relation that binds a document such as laboratory protocol to a title of protocol.
Example
"Laboratory protocol" hasTitle "An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection"
has domain
experimental protocol c
has range
title of the protocol c
is inverse of
title of op

has versionop back to ToC or Object Property ToC

IRI: http://purl.org/pav/hasVersion

has range
version number c

has_roleop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000316

A relation between a continuant C and a role R. The reciprocal relation of role_of.

identifier ofop back to ToC or Object Property ToC

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

identifierOf is a relation that binds an identifier to a experimental protocol or material entity.
has domain
identifier c
is inverse of
has identifier op

instruction ofop back to ToC or Object Property ToC

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

instructionOf is a relation that binds a protocol instruction to an experimental protocol.
has domain
protocol instruction c
has range
experimental protocol c
is inverse of
has instruction op

is manufactured byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000304

c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
Example
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)

license ofop back to ToC or Object Property ToC

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

licenseOf is a relation that binds a license to a protocol.
has domain
license c
has range
experimental protocol c
is inverse of
has license op

limitation ofop back to ToC or Object Property ToC

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

limitationOf is a relation that binds a limitation of protocol to a document such as experimental protocol.
has domain
limitation of the protocol c
has range
experimental protocol c
is inverse of
has limitation op

located inop back to ToC or Object Property ToC

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

the property publishedIn is the retationship that binds a Protocol to a RepositoryName
has domain
experimental protocol c
has range
repository c

modified byop back to ToC or Object Property ToC

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

The property modifiedBy indicates the person or authoritative body who changed an item, for example, a protocol.
has domain
experimental protocol c

name ofop back to ToC or Object Property ToC

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

nameOf binds a name to a person, animal, place or thing.
has domain
name c
has range
material entity c
is inverse of
has name op

outcome ofop back to ToC or Object Property ToC

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

outcomeOf is a relation that binds an outcome of the protocol to a document such as experimental protocol.
has domain
outcome of the protocol c
has range
experimental protocol c
is inverse of
has outcome 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

provenance ofop back to ToC or Object Property ToC

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

provenanceOf is a relation that binds the provenance of a protocol to an experimental protocol.
has domain
provenance of the protocol c
has range
experimental protocol c
is inverse of
has provenance op

published inop back to ToC or Object Property ToC

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

the property publishedIn is the retationship that binds a protocol to a publication name or repository name.
has domain
experimental protocol c
has range
textual entity c

purpose ofop back to ToC or Object Property ToC

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

purposeOf is a relation that binds the purpose of a protocol to a document such as experimental protocol.
has domain
purpose of the protocol c
has range
experimental protocol c
is inverse of
has purpose op

title ofop back to ToC or Object Property ToC

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

has characteristics: transitive

is inverse of
has title op

validated byop back to ToC or Object Property ToC

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

The property validatedBy indicates the person who formally assesses or examines that the protocol can be understood and carried out correctly by users.
has domain
experimental protocol c

Named Individuals

Anthony J. Freemontni back to ToC or Named Individual ToC

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

belongs to
author name c
has facts
part of op author list 1

application 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#application1

belongs to
application of the protocol c

author list 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#authorList1

belongs to
author list c
has facts
has part op Anthony J. Freemont
has part op Crispin J. Miller
has part op John A. Radford
has part op Kim M. Linton
has part op Sian Dibben
has part op Stuart D. Pepper
has part op Yvonne Hey

author1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#author1

belongs to
author c
has facts
has name op Anthony J. Freemont

author2ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#author2

belongs to
author c
has facts
has name op Crispin J. Miller

author3ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#author3

belongs to
author c
has facts
has name op John A. Radford

author4ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#author4

belongs to
author c
has facts
has name op Kim M. Linton

author5ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#author5

belongs to
author c
has facts
has name op Sian Dibben

author6ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#author6

belongs to
author c
has facts
has name op Stuart D. Pepper

author7ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#author7

belongs to
author c
has facts
has name op Yvonne Hey

Chloroformni back to ToC or Named Individual ToC

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

belongs to
reagent name c
has facts
is manufactured by op Sigma-Aldrich
part of op reagent list 1

Crispin J. Millerni back to ToC or Named Individual ToC

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

belongs to
author name c
has facts
part of op author list 1

equipment list 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#equipmentList1

belongs to
equipment and supplies list c
has facts
has part op Forceps
has part op Homogenizer blades
has part op Scalpel
has part op Scalpel holder
has part op Tissue storage container

equipment or supplies 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#equipmentorsupplies1

belongs to
equipment and supplies c
has facts
has name op Homogenizer blades

equipment or supplies 2ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#equipmentorsupplies2

belongs to
equipment and supplies c
has facts
has name op Scalpel holder

equipment or supplies 3ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#equipmentorsupplies3

belongs to
equipment and supplies c
has facts
has name op Tissue storage container

equipment or supplies 4ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#equipmentorsupplies4

belongs to
equipment and supplies c
has facts
has name op Forceps

equipment or supplies 5ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#equipmentorsupplies5

belongs to
equipment and supplies c
has facts
has name op Scalpel

Ethyl alcoholni back to ToC or Named Individual ToC

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

belongs to
reagent name c
has facts
is manufactured by op Sigma-Aldrich
part of op reagent list 1

Forcepsni back to ToC or Named Individual ToC

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

belongs to
equipment or supplies name c
has facts
part of op equipment list 1

Homogenizer bladesni back to ToC or Named Individual ToC

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

belongs to
equipment or supplies name c
has facts
part of op equipment list 1

invitrogenni back to ToC or Named Individual ToC

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

belongs to
manufacturer name c

Isopropyl alcoholni back to ToC or Named Individual ToC

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

belongs to
reagent name c
has facts
is manufactured by op Sigma-Aldrich
part of op reagent list 1

John A. Radfordni back to ToC or Named Individual ToC

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

belongs to
author name c
has facts
part of op author list 1

Kim M. Lintonni back to ToC or Named Individual ToC

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

belongs to
author name c
has facts
part of op author list 1

manufacturer1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#manufacturer1

belongs to
manufacturer c
has facts
has name op Sigma-Aldrich

manufacturer2ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#manufacturer2

belongs to
manufacturer c
has facts
has name op invitrogen

protocol Id1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#Id1

belongs to
protocol identifier c

provenance 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#provenance1

belongs to
provenance of the protocol c

reagent list 1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#reagentList1

belongs to
reagent list c
has facts
has part op Ethyl alcohol
has part op Isopropyl alcohol
has part op t r i zol
has part op Chloroform

reagent1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#reagent1

belongs to
reagent c
has facts
has name op Ethyl alcohol

reagent2ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#reagent2

belongs to
reagent c
has facts
has name op Isopropyl alcohol

reagent3ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#reagent3

belongs to
reagent c
has facts
has name op Chloroform

reagent4ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#reagent4

belongs to
reagent c
has facts
has name op t r i zol

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 identifier op protocol Id1
has application op application 1
has author op author list 1
has experimental input op equipment list 1
has experimental input op reagent list 1
has title op title1
has experimental input op tumor tissue

Scalpelni back to ToC or Named Individual ToC

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

belongs to
equipment or supplies name c
has facts
part of op equipment list 1

Scalpel holderni back to ToC or Named Individual ToC

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

belongs to
equipment or supplies name c
has facts
part of op equipment list 1

Sian Dibbenni back to ToC or Named Individual ToC

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

belongs to
author name c
has facts
part of op author list 1

Sigma-Aldrichni back to ToC or Named Individual ToC

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

belongs to
manufacturer name c

Stuart D. Pepperni back to ToC or Named Individual ToC

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

belongs to
author name c
has facts
part of op author list 1

t r i zolni back to ToC or Named Individual ToC

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

belongs to
reagent name c
has facts
is manufactured by op invitrogen
part of op reagent list 1

Tissue storage containerni back to ToC or Named Individual ToC

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

belongs to
equipment or supplies name c
has facts
part of op equipment list 1

title1ni back to ToC or Named Individual ToC

IRI: http://purl.org/net/SMARTprotocol#title1

belongs to
title of the protocol c

tumor tissueni back to ToC or Named Individual ToC

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

belongs to
specimen name c

Yvonne Heyni back to ToC or Named Individual ToC

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

belongs to
author name c
has facts
part of op author list 1

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals