SMART Protocols Ontology: Document Module
SMART Protocols Ontology: Document Module is an ontology designed to represent metadata used to report a laboratory protocol.
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
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.
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)
has alert message
"DNA Extraction Protocol" hasAlertMessage "Critical Step"
hasAlertMessage is a relation that binds a chemical substance or protocol to an alert message such as caution, critical step, timing, etc.
has author
"Laboratory protocol" hasAuthor "John Smith"
hasAuthor is a relation that binds a document such as laboratory protocol to an author of protocol.
has catalog number
"Nalgene Cryogenic Tube" hasCatalogNumber "5000-0012"
hasCatalogNumber binds a thing to a numeral or string of numerals that is used for identification.
has name
"Buffer" hasName "1X Queen’s lysis buffer (1L)"
hasName binds to a person, animal, place or thing to a word or set of words by which someone or something is known, addressed, or referred to.
has sequence
The primer CII-fw hasSequence 5′-GAATGATGTACCACCTTTG-3′
hasSequence binds a oligonucleotide or nucleic acid to a sequence.
has title
"Laboratory protocol" hasTitle "An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection"
hasTitle is a relation that binds a document such as laboratory protocol to a title of protocol.
has version
"LightCycler 480 Software" hasVersion "Version 1.5"
hasVersion binds a document, software, or other type of information content entity to a version (one of a sequence of copies of a program, document or software).
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.
version
A form or variant of a type or original; one of a sequence of copies of a program, each incorporating new modifications.
VERS Versioned
concentration
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.
name
The words or language units by which a thing is known.
solution
A homogeneous mixture of two or more substances; frequently (but not necessarily) a liquid solution.
freezer
A refrigerated cabinet or room for preserving materials at or below 32F (0C).
initial concentration
The first measured concentration of a compound in a substance. In pharmacology, the initial concentration is given only for bolus IV models.
document version
A representation of a particular edition or snapshot of a document as it exists at a particular point in time.
equipment and supplies
Device Apparatus and Instruments Device, Medical Devices, Medical Instruments and Apparatus Inventory Medical Device Supplies and Equipment MED DEVICE EQUIPMENT SUPPLIES MED DEVICES APPARATUS INSTRUM DEVICES MED DEVICE MED Devices Equipment Inventories Medical Devices Supplies
Expendable and nonexpendable equipment, supplies, apparatus, and instruments that are used in diagnostic, surgical, therapeutic, scientific, and experimental procedures.
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.
buffer compound
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
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).
plan specification
OBI Plan and Planned Process branch OBI_0000344
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
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
author identification
A textual entity intended to identify a particular author
IAO
orcid ID, O.Giraldo
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
document part
An abstract, introduction, method or results section.
an information content entity that is part of a document
author list
Lawrence Hunter and Kevin Brettonel Cohen
part of a document that enumerates the authors of the document
incubator
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
a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
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
lyophilizer
A device that is used to freeze dry material.
microcentrifuge
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.
micropipette
A microinjection device that is used to measure very small volumes of liquids.
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
centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
thermal cycler
An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
DNA_amplifier PCR_machine Polymerase_Chain_Reaction_ machine thermocycler
Piko(tm) 96-well Thermal Cycler
temperature control bath
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.
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.
water bath
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).
A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
advantage of the Protocol
Advantage of the protocol is a subclass of textual entity. It should be made clear in which situations the Protocol has been successfully employed.
application of the protocol
Applications 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.
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.
bag
A bag is a supply. A bag is a simple tool in the form of a non-rigid container.
Laboratory bags: autoclavable biohazard bags, specimen/document zipper bags
buffer list
Buffer list is a data set of the names or identifiers of the buffers that are part of materials section of a protocol.
buffer name
1X Queen’s lysis buffer (1L), AB lysis buffer (500ml).
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.
catalog number
Catalog number is a subclass of textual entity. Catalog number is a numeral or string of numerals that is used for identification.
centrifuge tube
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.
Weigh 300-400 mg of ground, lyophilized tissue, into a 15 ml polypropylene centrifuge tube.
centrifuge tips
critical step
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.
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)
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
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 descriptionof a procedure about the use of enzymes to increase the number of molecules from a material entity.
equipment and supplies list
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.
equipment or supplies name
Equipment or supply name is a textual entity. Equipment or supply name is the name of equipment or supply.
Nalgene Cryogenic Tube, sterile, 1.2 ml. S1000 Thermal Cycler with 96-Deep Well Reaction Module.
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.
final concentration
Adopted from NCI thesaurus
Last concentration
The final measured concentration of a compound in a substance.
flammable
Easily ignited.
Inflammable
Keep away from sources of ignition. Reference: Nature Protocols
grinding machine
Grinding device
Grinding machine is a equipment. Grinding machine is a machine used to grind grains and leaves.
Put the number of seed indicated by the kit protocol in the grinding machine and grind the seed to a powder.
hint
A hint is a message given to a user of a protocol that will help to perform the experiment.
HINT: Mix well by vortex before to use. HINT: ADD NaOH to WATER to avoid splashing.
introduction section
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.
kit
A set of chemical substances, articles or equipment needed for a specific purpose.
Universal Linker Kit, laboratory kit that allows customization of protein microarrays.
kit list
Kit list is a data set of the names or identifiers of the kits that are part of materials section of a protocol.
kit name
Kit name is a textual entity. Kit name is the name of a kit.
Spectrum Plant Total RNA Kit, sufficient for 50 purifications.
limitation of the protocol
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
Limitations 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.
manufacturer
Bio-Rad, Nalgene, Thermoscientific, Eppendorf, Falcon.
Manufacturer is a subclass of material entity. Manufacturer is a person, enterprise, or entity that produces equipments, reagents, primers or other laboratory supplies.
materials section
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.
methods section
Methods section is part of a document. This is the section where the protocol is presented.
microcentrifuge tube
Microcentrifuge tips microfuge tube
Microcentrifuge tube is a supply. Microcentrifuge tubes are plastic tubes with capacities from 250 ul to 2.0 ml.
Pour off supernatant into 1.5 ml microfuge tube.
neurotoxic
Poisonous to nerves or nerve cells.
avoid contact with skin, eyes or mucous membranes; keep away from sources of ignition. When handling , wear gloves. Reference: Nature Protocols
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.
pause point
PAUSE POINT: Can be left overnight at 48 C or frozen for up to a month at -20 C.
Pause point is the point were the protocol naturally breaks into separate stages.
plant tissue
Plant tissue is a material entity. Plant tissue is the tissue derived from plants.
roots, leaves, flowers, stems.
portable ice chest
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.
Place bags in a portable ice chest or other container with ice to keep samples cool.
cooler cool box chilly bin esky
primer
A primer is a short strand of nucleic acid that serves as a starting point for DNA or RNA synthesis.
primer list
Primer list is a data set of the names or identifiers of the primers that are part of materials section of a protocol.
primer name
CII-fw, CII-rv.
Primer name is a textual entity. Primer name is the name of a primer.
primer sequence
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.
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
provenance of the protocol
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.
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
purpose of the protocol
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.
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.
pyrophoric
A chemical substance that will ignite spontaneously in air at or below a temperature of 130 F (54.4 C).
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.
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
reagent list
Reagent list is a data set of the names or identifiers of the reagents that are part of materials section of a protocol.
reagent name
Reagent name is a textual entity. Reagent name is the name of a reagent.
Taq DNA Polymerase from Thermus aquaticus with 10X reaction buffer without MgCl2.
software list
Software list is a data set of the names of softwares that are part of materials section of a protocol.
software name
LightCycler 480 Software.
Software name is a textual entity. Software name is the name of a software.
software version
Software version is a textual entity. A software version number is a software attribute that represents the version of software.
Version 1.5
solution list
Solution list is a data set of the names or identifiers of solutions that are part of materials section of a protocol.
solution name
3M NaOH (1L)
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 buffer should including the follow information: solution concentration, and final volume.
storage condition
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.
Store the buffer in foil covered dark coloured bottle at room temperature. Light sensitive. Can be used up to 2 months.
timing
Steps 1-3, 30 min.; Steps 6-7, 2 h
Timing is a message used to indicate the approximate time that a step, or set of steps, could take.
title of the protocol
Title of protocol is a subclass of textual entity. Title of protocol is the name of a protocol.
toxic
Avoid inhalation, ingestion or contact with skin, eyes or mucous membranes. Reference: Nature Protocols
Of or relating to or caused by a toxin or poison 'suffering from exposure to toxic substances'
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.
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.
volatile
The property of a substance of changing readily from a solid or liquid to a vapor.
handle in well-ventilated charcoal-filtered hood. Reference: Nature Protocols
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
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.
alert message
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.
caution
A caution is a message given to a user of a protocol about potentially dangerous properties of materials used in the experiment.