SMART Protocols Ontology: Protocol Module
type: Ontology
created: 2013-07-01
contributor: http://delicias.dia.fi.upm.es/members/DGarijo/#me
creator: http://oxgiraldo.wordpress.com/
contributor: http://www.alexandergarcia.name/
contributor: http://www.dia.fi.upm.es/index.php
license: http://creativecommons.org/licenses/by-nc-sa/2.0/
preferred namespace uri: http://purl.org/net/SMARTprotocol#
version info: 2.0
preferred namespace prefix: sp
description: SMART Protocols is an ontology designed to describe the minimum information to report a laboratory protocol.
comment: SMART protocol as a workflow extending the P-PLAN ontology to guide the execution of laboratory processes.

example of usage
type: AnnotationProperty
definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not

definition
type: AnnotationProperty
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.

alternative term
type: AnnotationProperty
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)

definition source
type: AnnotationProperty
definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007

imported from
type: AnnotationProperty
definition: For external terms/classes, the ontology from which the term was imported

precedes
type: ObjectProperty
type: TransitiveProperty
imported from: BFO

is preceded by
type: ObjectProperty
type: TransitiveProperty
alternative term: preceded by
imported from: BFO
inverse of: precedes
domain: Class
  union of: laboratory procedure
  union of: p-plan:Step
range: Class
  union of: laboratory procedure
  union of: p-plan:Step

has protocol
type: ObjectProperty
definition: hasProtocol is a relation that binds a laboratory procedure to a laboratory protocol.
domain: laboratory procedure

p-plan:hasInputVar
type: ObjectProperty
imported from: The P-PLAN Ontology
definition: p-plan:hasInputVar binds a p-plan:Step to the p-plan:Variable that takes as input for the planned execution.
domain: p-plan:Step
range: p-plan:Variable

p-plan:hasOutputVar
type: ObjectProperty
imported from: The P-PLAN Ontology
definition: p-plan:hasOutputVar binds a p-plan:Step to the p-plan:Variable that takes as Output for the planned execution.
domain: p-plan:Step
range: p-plan:Variable

p-plan:isStepOfPlan
type: ObjectProperty
imported from: The P-PLAN Ontology
definition: p-plan:isStepOfPlan links a p-plan:Step to the p-plan:Plan which it corresponds to.
range: p-plan:Plan
domain: p-plan:Step

has part
type: ObjectProperty
type: TransitiveProperty
imported from: OBO Relation Ontology
inverse of: part of

part of
type: ObjectProperty
type: TransitiveProperty
imported from: OBO Relation Ontology
definition: 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.

cultivar
type: Class
subclass of: strain or line
imported from: Microarray and Gene Expression Data Ontology (MGEDO)
definition: a plant variety obtained in agriculture in horticulture.

ecotype
type: Class
subclass of: strain or line
imported from: Microarray and Gene Expression Data Ontology (MGEDO)
definition: a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler

strain or line
type: Class
subclass of: organism
imported from: Microarray and Gene Expression Data Ontology (MGEDO)
definition: 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.

tissue
type: Class
subclass of: sample from organism
subclass of: p-plan:Variable
definition source: CDISC
imported from: NCI thesaurus
definition: An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function.

laboratory procedure
type: Class
subclass of: occurrent
imported from: NCI thesaurus
definition: Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting.
alternative term: Test LBTEST Laboratory Test Tests Lab Test Lab Tests

solution
type: Class
subclass of: material entity
disjoint with: information biomacromolecule
disjoint with: material sample
disjoint with: organism
imported from: NCI thesaurus
definition: A homogeneous mixture of two or more substances; frequently (but not necessarily) a liquid solution.

liquid state
type: Class
subclass of: physical state
disjoint with: gel state
imported from: NanoParticle Ontology
definition: Physical state which is characteristic of a liquid.

gel state
type: Class
subclass of: physical state
imported from: NanoParticle Ontology
definition: Physical state which is characteristic of a gel.

physical state
type: Class
subclass of: quality
imported from: NanoParticle Ontology
alternative term: state of matter
definition: A quality, which is the physical condition of a material entity, based on its chemical composition and structure.100428NPODennis Thomas

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
disjoint with: ribonucleic acid
imported from: ChEBI
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.

information biomacromolecule
type: Class
subclass of: material entity
disjoint with: reagent
disjoint with: buffer
disjoint with: organism
disjoint with: primer
imported from: ChEBI

nucleic acid
type: Class
subclass of: information biomacromolecule
disjoint with: protein
imported from: ChEBI
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.

ribonucleic acid
type: Class
subclass of: nucleic acid
imported from: ChEBI
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.

reagent
type: Class
subclass of: material entity
disjoint with: material sample
disjoint with: organism
imported from: ChEBI
definition: A substance used in a chemical reaction to detect, measure, examine, or produce other substances.

buffer
type: Class
subclass of: material entity
disjoint with: material sample
disjoint with: organism
disjoint with: primer
definition: Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base.
imported from: ChEBI
alternative term: buffer compound buffer compounds

protein
type: Class
subclass of: information biomacromolecule
imported from: ChEBI
definition: A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.

information content entity
type: Class
subclass of: generically dependent continuant
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
imported from: OBI
definition source: OBI_0000142
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity

data set
type: Class
subclass of: information content entity
definition: 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.
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
imported from: OBI
definition source: group:OBI OBI_0000042

textual entity
type: Class
subclass of: information content entity
imported from: OBI
definition: 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 of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
alternative term: text

sample from organism
type: Class
subclass of: material sample
subclass of: Restriction
  on property: part of
  some values from: organism
imported from: OBI
definition: a material obtained from an organism in order to be a representative of the whole

material sample
type: Class
subclass of: material entity
disjoint with: primer
imported from: OBI
definition: A material entity that has the material sample role
example of usage: 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.
alternative term: sample population

amplified DNA
type: Class
subclass of: processed DNA
subclass of: p-plan:Variable
definition source: Alan Ruttenberg
example of usage: Amplied DNA created by PCR
definition: DNA that has been produced in an enzymatic amplification process
imported from: OBI

RNA extract
type: Class
subclass of: processed RNA
subclass of: p-plan:Variable
definition source: Group: UPenn Group
imported from: OBI
definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.

DNA extract
type: Class
subclass of: processed DNA
subclass of: p-plan:Variable
definition source: Group: UPenn group
imported from: OBI
definition: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.

organism
type: Class
subclass of: material entity
disjoint with: primer
imported from: OBI
definition source: http://en.wikipedia.org/wiki/Organism
definition: 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.
example of usage: fungus, animal, virus, plant

agarose gel electrophoresis protocol
type: Class
subclass of: electrophoresis protocol
definition: 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.

agarose in gel state
type: Class
subclass of: gel state
subclass of: p-plan:Variable
definition source: Adapted from OBI
definition: AgaroseInGelState Is a gel resulting from the polymerization of agarose after heating agarose suspended in some buffer solution.

agarose in liquid state
type: Class
subclass of: liquid state
subclass of: p-plan:Variable
definition: The agarose will be in a liquid state acording to its gelling temperature and concentration.

analyzed data set
type: Class
subclass of: data set
subclass of: p-plan:Variable
disjoint with: raw data set
definition source: Adapted from: www.unit5.org/villhauer/Glossary/Glossary.htm
definition: Is the result of data analysis process. This data can be organized into charts, graphs and tables to better visualize the information.

analyzing sample data
type: Class
subclass of: basic step of electrophoresis
subclass of: Restriction
  on property: p-plan:isStepOfPlan
  some values from: electrophoresis protocol
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: analyzed data set
subclass of: Restriction
  on property: p-plan:hasInputVar
  some values from: raw data set
subclass of: Restriction
  on property: is preceded by
  some values from: loading and running the gel
definition: Analyzing sample data is the third basic step in a electrophoresis procedure. This step include the data collection and analysis of sample data.

basic step of DNA extraction
type: Class
subclass of: p-plan:Step
disjoint with: basic step of electrophoresis
disjoint with: basic step of PCR
definition: Basic steps of DNA extraction are the steps commonly used in any DNA extraction protocol.

basic step of electrophoresis
type: Class
subclass of: p-plan:Step
disjoint with: basic step of PCR
definition: Basic steps of electrophoresis are the steps commonly used in any electrophoresis protocol.

basic step of PCR
type: Class
subclass of: p-plan:Step
definition: Basic steps of PCR are the steps commonly used in any PCR protocol.

casting the gel
type: Class
subclass of: basic step of electrophoresis
subclass of: Restriction
  on property: p-plan:hasInputVar
  some values from: agarose in liquid state
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: agarose in gel state
subclass of: Restriction
  on property: p-plan:isStepOfPlan
  some values from: agarose gel electrophoresis protocol
definition: This is the first basic step in a electrophoresis procedure. This step include:1) the preparation of the gel matrix, 2) its solidification and 3) place it into electrophoresis apparatus.

cell disruption
type: Class
subclass of: basic step of DNA extraction
subclass of: Restriction
  on property: p-plan:hasInputVar
  some values from: plant tissue
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: powdered tissue
subclass of: Restriction
  on property: p-plan:isStepOfPlan
  some values from: DNA extraction protocol
definition: 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.
alternative term: Cell lysis

choosing PCR reaction condition
type: Class
subclass of: basic step of PCR
subclass of: Restriction
  on property: p-plan:isStepOfPlan
  some values from: polimerase chain reaction protocol
subclass of: Restriction
  on property: is preceded by
  some values from: setting up the PCR reaction
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: PCR program
definition: Choosing the Reaction Conditions is the third basic step in a PCR reaction. The reaction conditions of a PCR amplification are composed of the total number of cycles to be run and the temperature and duration of each step in those cycles. The decision as to how many cycles to run is based upon the amount of DNA target material. In general, 25 to 35 cycles is the standard for a PCR reaction.

choosing target substrate and PCR primer
type: Class
subclass of: basic step of PCR
subclass of: Restriction
  on property: p-plan:isStepOfPlan
  some values from: polimerase chain reaction protocol
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: DNA extract
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: primer
definition: This is the first step in a PCR. The choice of the target DNA is dictated by the specific experiment. The choosing of PCR primers is fundamental to avoid amplification of the wrong thing.

digested RNA
type: Class
subclass of: digested contaminant

DNA extraction procedure
type: Class
subclass of: nucleic acid extraction procedure
definition: A DNA extraction procedure is a subclass of nucleic acid extraction procedure where the desired output material is DNA.
alternative term: DNA isolation procedure

DNA extraction protocol
type: Class
subclass of: nucleic acid extraction protocol
disjoint with: RNA extraction protocol
definition: 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.
alternative term: DNA isolation protocol

DNA pellet
type: Class
subclass of: processed DNA
subclass of: p-plan:Variable
definition: A material entity which results from the aggregation of DNA produced by the application of centrifugal force to a liquid containing DNA in suspension.
definition source: Adapted from OBI

DNA purification
type: Class
subclass of: basic step of DNA extraction
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: DNA extract
subclass of: Restriction
  on property: is preceded by
  some values from: digestion reaction
subclass of: Restriction
  on property: p-plan:isStepOfPlan
  some values from: DNA extraction protocol
subclass of: Restriction
  on property: p-plan:hasInputVar
  some values from: digested contaminant
definition: DNA purification, 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.

DNA separated by molecular size
type: Class
subclass of: processed DNA
subclass of: p-plan:Variable
definition: DNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix.

digested contaminant
type: Class
subclass of: p-plan:Variable
definition: Digested contaminants are all those organelles and biomolecules that result degradated during the digestion reaction in a DNA extraction procedure.

digested lipid membrane
type: Class
subclass of: digested contaminant

digested protein
type: Class
subclass of: digested contaminant

digestion reaction
type: Class
subclass of: basic step of DNA extraction
subclass of: Restriction
  on property: is preceded by
  some values from: cell disruption
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: digested contaminant
subclass of: Restriction
  on property: p-plan:hasInputVar
  some values from: powdered tissue
subclass of: Restriction
  on property: p-plan:isStepOfPlan
  some values from: DNA extraction protocol
definition: it is the DNA extraction stage where are removed membrane lipids, proteins and RNA.

electrophoresis procedure
type: Class
subclass of: laboratory procedure
subclass of: Restriction
  on property: is preceded by
  some values from: polimerase chain reaction procedure
subclass of: Restriction
  on property: is preceded by
  some values from: nucleic acid extraction procedure
disjoint with: plant tissue harvest procedure
definition: Electrophoresis procedure is a subclass of laboratory procedure. Electrophoresis procedure is a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge.
example of usage: Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.

electrophoresis protocol
type: Class
subclass of: experimental protocol
definition: 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.

enzimatic amplification protocol
type: Class
subclass of: experimental protocol
definition: 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.

enzymatic amplification procedure
type: Class
subclass of: laboratory procedure
disjoint with: plant tissue harvest procedure
definition: Enzymatic amplification procedure is a subclass of laboratory procedure that uses enzymes to increase the number of molecules of a biomaterial.
example of usage: polymerase chain reaction (PCR), reverse transcribed polymerase chain reaction (RT-PCR)

experimental protocol
type: Class
subclass of: p-plan:Plan
definition: 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.

extraction buffer
type: Class
subclass of: buffer
definition: Extraction buffer is a subclass of buffer. An extraction buffer with correct pH, gets rid of the cell components, but retains the organelles.
example of usage: Protein extraction buffer, DNA extraction buffer (CTAB extraction buffer), RNA extraction buffer.

loading and running the gel
type: Class
subclass of: basic step of electrophoresis
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: RNA separated by molecular size
subclass of: Restriction
  on property: p-plan:isStepOfPlan
  some values from: electrophoresis protocol
subclass of: Restriction
  on property: p-plan:hasInputVar
  some values from: RNA extract
subclass of: Restriction
  on property: is preceded by
  some values from: casting the gel
subclass of: Restriction
  on property: p-plan:hasInputVar
  some values from: amplified DNA
subclass of: Restriction
  on property: p-plan:hasInputVar
  some values from: DNA extract
subclass of: Restriction
  on property: p-plan:hasOutputVar
  some values from: DNA separated by molecular size
definition: Loading and running the gel is the second basic step in a Electrophoresis procedure. This stage has as input: loading of the samples; and as output: DNA fragments separated acording to their molecular weight.

nucleic acid extraction procedure
type: Class
subclass of: laboratory procedure
subclass of: Restriction
  on property: is preceded by
  some values from: plant tissue harvest procedure
example of usage: DNA extraction procedure, RNA extraction procedure
definition: Nucleic acid extraction procedure is a subclass of laboratory procedure used to recover the nucleic acid fraction of an input material entity.
alternative term: Nucleic acid isolation procedure

nucleic acid extraction protocol
type: Class
subclass of: experimental protocol
disjoint with: protein extraction protocol
definition: 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.

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

plant tissue
type: Class
subclass of: tissue
subclass of: p-plan:Variable
definition: Plant tissue is a material entity. Plant tissue is the tissue derived from plants.
example of usage: roots, leaves, flowers, stems.

plant tissue harvest procedure
type: Class
subclass of: laboratory procedure
definition: Plant tissue harvest procedure is a subclass of laboratory procedure that may to have one or several protocols associated.

polimerase chain reaction procedure
type: Class
subclass of: enzymatic amplification procedure
subclass of: Restriction
  on property: is preceded by
  some values from: DNA extraction procedure
definition: PCR is a subclass of enzymatic amplification procedure. PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
alternative term: PCR procedure PCR process
definition source: adapted from wikipedia

polimerase chain reaction protocol
type: Class
subclass of: enzimatic amplification protocol
definition: PCR protocol is a step by step description of the procedure to amplify a particular DNA sequence.

powdered tissue
type: Class
subclass of: tissue
subclass of: p-plan:Variable
example of usage: Grind the seed to a powder. Transfer the powdered seed to a container and weigh the specified amount.
definition: Powdered tissue is a material entity. Powdered tissue is a tissue that has been pulverirized.

primer
type: Class
subclass of: p-plan:Variable
subclass of: material entity
example of usage: Oligos used in PCR.
definition source: http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29
definition: A primer is a short strand of nucleic acid that serves as a starting point for DNA or RNA synthesis.

processed DNA
type: Class
subclass of: deoxyribonucleic acid
definition: Is a DNA that suffers changes during a laboratory procedure.

processed RNA
type: Class
subclass of: ribonucleic acid
definition: Is a RNA that suffers changes during a laboratory procedure.

protein extraction protocol
type: Class
subclass of: experimental protocol
definition: Protein extraction protocol is a subclass of laboratory protocol. Protein extraction is an extraction where the desired output material is protein.
alternative term: Protein isolation protocol

RNA extraction procedure
type: Class
subclass of: nucleic acid extraction procedure
definition: A RNA extraction procedure is a subclass of nucleic acid extraction procedure where the desired output material is RNA
alternative term: RNA isolation procedure

RNA extraction protocol
type: Class
subclass of: nucleic acid extraction protocol
definition: 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.
alternative term: RNA isolation protocol

RNA separated by molecular size
type: Class
subclass of: processed RNA
definition: RNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix.

raw data set
type: Class
subclass of: data set
subclass of: p-plan:Variable
definition source: wordnetweb.princeton.edu/perl/webwn
imported from: OBI
example of usage: Preliminary results about a DNA extraction, PCR, sequensing, etc.
definition: Raw data set is an unanalyzed data set; data not yet subjected to analysis.

setting up the PCR reaction
type: Class
subclass of: basic step of PCR
subclass of: Restriction
  on property: p-plan:isStepOfPlan
  some values from: polimerase chain reaction protocol
subclass of: Restriction
  on property: is preceded by
  some values from: choosing target substrate and PCR primer
definition: Setting Up the PCR Reaction is the second basic step in this type of procedure. Here are defined the quantities and/or concentrations of each one of the components reaction (Water, 10x Reaction Buffer, MgCl2, dNTPs, Forward Primer, Reverse Primer, Target DNA and Polymerase enzyme).

stained DNA
type: Class
subclass of: processed DNA
subclass of: p-plan:Variable
definition source: http://en.wikipedia.org/wiki/Gel_electrophoresis
definition: 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.

p-plan:Plan
type: Class
subclass of: entity
definition: A p-plan:Plan is a specific type of prov:Plan. It is composed of smaller steps (p-plan:Step) that use and produce Variables (p-plan:Variable).

p-plan:Step
type: Class
subclass of: entity
imported from: P-PLAN Ontology
definition: A p-plan:Step represents the plan for a specific activity. A p-plan:Step can be a p-plan:Plan.

p-plan:Variable
type: Class
subclass of: entity
imported from: P-PLAN Ontology
definition: A p-plan:Variable represents a description of the input or output of the planned Activity (p-plan:Step).

forward primer
type: Class
subclass of: primer
imported from: SNP Ontology
definition: A single stranded oligo used for polymerase chain reaction.
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
alternative term: forward DNA primer DNA forward primer forward primer oligonucleotide forward primer oligo forward primer polynucleotide forward primer forward primer sequence

reverse primer
type: Class
subclass of: primer
imported from: SNP Ontology
definition: A single stranded oligo used for polymerase chain reaction.
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
alternative term: reverse primer oligonucleotide reverse primer sequence reverse primer oligo DNA reverse primer reverse primer reverse DNA primer

entity
type: Class
equivalent class: Class
  union of: continuant
  union of: occurrent

continuant
type: Class
subclass of: entity
disjoint with: occurrent
comment: 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.
comment: Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building
comment: Synonyms: endurant

dependent continuant
type: Class
equivalent class: Class
  union of: generically dependent continuant
  union of: specifically dependent continuant
subclass of: continuant
disjoint with: independent continuant
comment: 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.

generically dependent continuant
type: Class
subclass of: dependent continuant
disjoint with: specifically dependent continuant
comment: 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.
comment: Examples: a certain PDF file that exists in different and in several hard drives

independent continuant
type: Class
subclass of: continuant
comment: 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.
comment: Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
comment: Synonyms: substantial entity

material entity
type: Class
subclass of: independent continuant
comment: 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.
comment: Examples: collection of random bacteria, a chair, dorsal surface of the body

quality
type: Class
subclass of: specifically dependent continuant
comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
comment: Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee

specifically dependent continuant
type: Class
subclass of: dependent continuant
comment: 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.
comment: Examples: 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.
comment: Synonyms: property, trope, mode

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