SMART Protocols Ontology: Protocol Module
SMART Protocols is an ontology designed to describe the minimum information to report a laboratory protocol.
SMART protocol as a workflow extending the P-PLAN ontology to guide the execution of laboratory processes.
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
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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
For external terms/classes, the ontology from which the term was imported
precedes
BFO
is preceded by
has protocol
hasProtocol is a relation that binds a laboratory procedure to a laboratory protocol.
p-plan:hasInputVar binds a p-plan:Step to the p-plan:Variable that takes as input for the planned execution.
p-plan:hasOutputVar binds a p-plan:Step to the p-plan:Variable that takes as Output for the planned execution.
p-plan:isStepOfPlan links a p-plan:Step to the p-plan:Plan which it corresponds to.
has part
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.
cultivar
Microarray and Gene Expression Data Ontology (MGEDO)
a plant variety obtained in agriculture in horticulture.
ecotype
a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
strain or line
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
An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function.
laboratory procedure
Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting.
Test LBTEST Laboratory Test Tests Lab Test Lab Tests
solution
A homogeneous mixture of two or more substances; frequently (but not necessarily) a liquid solution.
liquid state
Physical state which is characteristic of a liquid.
gel state
Physical state which is characteristic of a gel.
physical state
A quality, which is the physical condition of a material entity, based on its chemical composition and structure.100428NPODennis Thomas
deoxyribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
information biomacromolecule
nucleic acid
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
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
reagent
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
buffer
Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base.
protein
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
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
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.
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
textual entity
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.
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
text
sample from organism
a material obtained from an organism in order to be a representative of the whole
material sample
A material entity that has the material sample role
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.
sample population
amplified DNA
Amplied DNA created by PCR
DNA that has been produced in an enzymatic amplification process
OBI
RNA extract
Group: UPenn Group
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
DNA extract
Group: UPenn group
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
organism
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.
fungus, animal, virus, plant
agarose gel electrophoresis protocol
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
AgaroseInGelState Is a gel resulting from the polymerization of agarose after heating agarose suspended in some buffer solution.
agarose in liquid state
The agarose will be in a liquid state acording to its gelling temperature and concentration.
analyzed data set
Adapted from: www.unit5.org/villhauer/Glossary/Glossary.htm
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
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
Basic steps of DNA extraction are the steps commonly used in any DNA extraction protocol.
basic step of electrophoresis
Basic steps of electrophoresis are the steps commonly used in any electrophoresis protocol.
basic step of PCR
Basic steps of PCR are the steps commonly used in any PCR protocol.
casting the gel
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
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.
Cell lysis
choosing PCR reaction condition
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
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
DNA extraction procedure
A DNA extraction procedure is a subclass of nucleic acid extraction procedure where the desired output material is DNA.
DNA isolation procedure
DNA extraction protocol
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.
DNA isolation protocol
DNA pellet
A material entity which results from the aggregation of DNA produced by the application of centrifugal force to a liquid containing DNA in suspension.
DNA purification
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
DNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix.
digested contaminant
Digested contaminants are all those organelles and biomolecules that result degradated during the digestion reaction in a DNA extraction procedure.
digested lipid membrane
digested protein
digestion reaction
it is the DNA extraction stage where are removed membrane lipids, proteins and RNA.
electrophoresis procedure
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.
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
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
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
Enzymatic amplification procedure is a subclass of laboratory procedure that uses enzymes to increase the number of molecules of a biomaterial.
polymerase chain reaction (PCR), reverse transcribed polymerase chain reaction (RT-PCR)
experimental protocol
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
Extraction buffer is a subclass of buffer. An extraction buffer with correct pH, gets rid of the cell components, but retains the organelles.
Protein extraction buffer, DNA extraction buffer (CTAB extraction buffer), RNA extraction buffer.
loading and running the gel
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
DNA extraction procedure, RNA extraction procedure
Nucleic acid extraction procedure is a subclass of laboratory procedure used to recover the nucleic acid fraction of an input material entity.
Nucleic acid isolation procedure
nucleic acid extraction protocol
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
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
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
Plant tissue is a material entity. Plant tissue is the tissue derived from plants.
roots, leaves, flowers, stems.
plant tissue harvest procedure
Plant tissue harvest procedure is a subclass of laboratory procedure that may to have one or several protocols associated.
polimerase chain reaction procedure
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.
PCR procedure PCR process
adapted from wikipedia
polimerase chain reaction protocol
PCR protocol is a step by step description of the procedure to amplify a particular DNA sequence.
powdered tissue
Grind the seed to a powder. Transfer the powdered seed to a container and weigh the specified amount.
Powdered tissue is a material entity. Powdered tissue is a tissue that has been pulverirized.
primer
A primer is a short strand of nucleic acid that serves as a starting point for DNA or RNA synthesis.
processed DNA
Is a DNA that suffers changes during a laboratory procedure.
processed RNA
Is a RNA that suffers changes during a laboratory procedure.
protein extraction protocol
Protein extraction protocol is a subclass of laboratory protocol. Protein extraction is an extraction where the desired output material is protein.
Protein isolation protocol
RNA extraction procedure
A RNA extraction procedure is a subclass of nucleic acid extraction procedure where the desired output material is RNA
RNA isolation procedure
RNA extraction protocol
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.
RNA isolation protocol
RNA separated by molecular size
RNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix.
raw data set
Preliminary results about a DNA extraction, PCR, sequensing, etc.
Raw data set is an unanalyzed data set; data not yet subjected to analysis.
setting up the PCR reaction
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
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.
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).
A p-plan:Step represents the plan for a specific activity. A p-plan:Step can be a p-plan:Plan.
A p-plan:Variable represents a description of the input or output of the planned Activity (p-plan:Step).
forward primer
A single stranded oligo used for polymerase chain reaction.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
forward DNA primer DNA forward primer forward primer oligonucleotide forward primer oligo forward primer polynucleotide forward primer forward primer sequence
reverse primer
reverse primer oligonucleotide reverse primer sequence reverse primer oligo DNA reverse primer reverse primer reverse DNA primer
entity
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.
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
dependent continuant
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
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.
Examples: a certain PDF file that exists in different and in several hard drives
independent continuant
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.
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
material entity
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.
Examples: collection of random bacteria, a chair, dorsal surface of the body
quality
Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
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
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.
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.
occurrent
Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
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