SMART Protocols Ontology: Document Module
type: Ontology
contributor: http://www.alexandergarcia.name/
creator: http://oxgiraldo.wordpress.com/
created: 2013-07-01
version info: 2.0
preferred namespace prefix: sp
license: http://creativecommons.org/licenses/by-nc-sa/2.0/
description: SMART Protocols Ontology: Document Module is an ontology designed to represent metadata used to report a laboratory protocol.
contributor: http://delicias.dia.fi.upm.es/members/DGarijo/#me
contributor: http://www.dia.fi.upm.es/index.php

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

is manufactured by
type: ObjectProperty
domain: material entity
range: manufacturer
example of usage: 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)
definition: 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.
alternative term: has_manufacturer
imported from: OBI

has alert message
type: ObjectProperty
range: alert message
example of usage: "DNA Extraction Protocol" hasAlertMessage "Critical Step"
definition: hasAlertMessage is a relation that binds a chemical substance or protocol to an alert message such as caution, critical step, timing, etc.

has author
type: ObjectProperty
example of usage: "Laboratory protocol" hasAuthor "John Smith"
definition: hasAuthor is a relation that binds a document such as laboratory protocol to an author of protocol.

has catalog number
type: ObjectProperty
domain: material entity
range: catalog number
example of usage: "Nalgene Cryogenic Tube" hasCatalogNumber "5000-0012"
definition: hasCatalogNumber binds a thing to a numeral or string of numerals that is used for identification.

has name
type: ObjectProperty
domain: material entity
range: name
example of usage: "Buffer" hasName "1X Queen’s lysis buffer (1L)"
definition: 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
type: ObjectProperty
domain: primer
range: primer sequence
example of usage: The primer CII-fw hasSequence 5′-GAATGATGTACCACCTTTG-3′
definition: hasSequence binds a oligonucleotide or nucleic acid to a sequence.

has title
type: ObjectProperty
range: title of the protocol
example of usage: "Laboratory protocol" hasTitle "An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection"
definition: hasTitle is a relation that binds a document such as laboratory protocol to a title of protocol.

has version
type: ObjectProperty
domain: information content entity
range: version
example of usage: "LightCycler 480 Software" hasVersion "Version 1.5"
definition: 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
type: ObjectProperty
inverse of: part of
type: TransitiveProperty
imported from: OBI

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

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

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

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

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

version
type: Class
subclass of: textual entity
disjoint with: name
disjoint with: application of the protocol
disjoint with: catalog number
disjoint with: limitation of the protocol
disjoint with: primer sequence
disjoint with: provenance of the protocol
disjoint with: purpose of the protocol
disjoint with: title of the protocol
disjoint with: alert message
definition: A form or variant of a type or original; one of a sequence of copies of a program, each incorporating new modifications.
alternative term: VERS Versioned
imported from: NCI thesaurus

concentration
type: Class
subclass of: quality
definition: 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.
imported from: NCI thesaurus

name
type: Class
subclass of: textual entity
disjoint with: application of the protocol
disjoint with: catalog number
disjoint with: limitation of the protocol
disjoint with: primer sequence
disjoint with: provenance of the protocol
disjoint with: purpose of the protocol
disjoint with: title of the protocol
disjoint with: alert message
definition: The words or language units by which a thing is known.
imported from: NCI thesaurus

solution
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has alert message
  some values from: hint
subclass of: Restriction
  on property: has alert message
  some values from: storage condition
subclass of: Restriction
  on property: has alert message
  some values from: caution
subclass of: Restriction
  on property: has part
  some values from: initial concentration
subclass of: Restriction
  on property: has part
  some values from: final concentration
subclass of: Restriction
  on property: part of
  some values from: solution list
subclass of: Restriction
  on property: has name
  all values from: solution name
disjoint with: equipment and supplies
disjoint with: material sample
disjoint with: organism
disjoint with: manufacturer
definition: A homogeneous mixture of two or more substances; frequently (but not necessarily) a liquid solution.
imported from: NCI thesaurus

freezer
type: Class
subclass of: equipment and supplies
definition: A refrigerated cabinet or room for preserving materials at or below 32F (0C).
imported from: NCI thesaurus

initial concentration
type: Class
subclass of: concentration
subclass of: Restriction
  on property: part of
  some values from: solution
subclass of: Restriction
  on property: part of
  some values from: buffer
disjoint with: final concentration
definition: The first measured concentration of a compound in a substance. In pharmacology, the initial concentration is given only for bolus IV models.
imported from: NCI thesaurus

document version
type: Class
subclass of: version
disjoint with: software version
definition: A representation of a particular edition or snapshot of a document as it exists at a particular point in time.
imported from: NCI thesaurus

equipment and supplies
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is manufactured by
  some values from: manufacturer
subclass of: Restriction
  on property: has catalog number
  some values from: catalog number
subclass of: Restriction
  on property: has name
  all values from: equipment or supplies name
subclass of: Restriction
  on property: part of
  all values from: equipment and supplies list
disjoint with: reagent
disjoint with: buffer
disjoint with: material sample
disjoint with: organism
disjoint with: manufacturer
disjoint with: primer
definition: Expendable and nonexpendable equipment, supplies, apparatus, and instruments that are used in diagnostic, surgical, therapeutic, scientific, and experimental procedures.
alternative term: 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
imported from: Medical Subject Headings (MeSH)

reagent
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is manufactured by
  some values from: manufacturer
subclass of: Restriction
  on property: has catalog number
  some values from: catalog number
subclass of: Restriction
  on property: part of
  all values from: reagent list
disjoint with: material sample
disjoint with: organism
disjoint with: manufacturer
definition: A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
imported from: ChEBI

buffer
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has alert message
  some values from: hint
subclass of: Restriction
  on property: has alert message
  some values from: storage condition
subclass of: Restriction
  on property: has alert message
  some values from: caution
subclass of: Restriction
  on property: has part
  some values from: initial concentration
subclass of: Restriction
  on property: has part
  some values from: final concentration
subclass of: Restriction
  on property: part of
  some values from: buffer list
subclass of: Restriction
  on property: has name
  all values from: buffer name
disjoint with: material sample
disjoint with: organism
disjoint with: manufacturer
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.
alternative term: buffer compound
imported from: ChEBI

software
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has name
  all values from: software name
subclass of: Restriction
  on property: has version
  all values from: software version
subclass of: Restriction
  on property: part of
  all values from: software list
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
definition source: GROUP: OBI

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.
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
definition source: OBI_0000142
imported from: OBI

data set
type: Class
subclass of: information content entity
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).
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.
definition source: group:OBI OBI_0000042
imported from: OBI

plan specification
type: Class
subclass of: information content entity
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
definition: 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.
definition source: OBI Plan and Planned Process branch OBI_0000344
imported from: OBI

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

author identification
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: part of
  some values from: author list
disjoint with: application of the protocol
example of usage: orcid ID, O.Giraldo
definition: A textual entity intended to identify a particular author
imported from: IAO

document
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: document part
subclass of: Restriction
  on property: has part
  some values from: purpose of the protocol
example of usage: A journal article, patent application, laboratory notebook, or a book
definition: A collection of information content entities intended to be understood together as a whole
imported from: OBI

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: part of
  some values from: document
example of usage: An abstract, introduction, method or results section.
definition: an information content entity that is part of a document
imported from: OBI

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author identification
example of usage: Lawrence Hunter and Kevin Brettonel Cohen
definition: part of a document that enumerates the authors of the document
imported from: IAO

incubator
type: Class
subclass of: equipment and supplies
example of usage: 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
definition: a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
definition source: http://www.medterms.com/script/main/art.asp
imported from: OBI

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

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

lyophilizer
type: Class
subclass of: equipment and supplies
definition: A device that is used to freeze dry material.
definition source: http://en.wikipedia.org/wiki/Freeze_drying
imported from: OBI

microcentrifuge
type: Class
subclass of: centrifuge
definition: 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.
definition source: http://en.wikipedia.org/wiki/Laboratory_centrifuge
imported from: OBI

micropipette
type: Class
subclass of: equipment and supplies
definition: A microinjection device that is used to measure very small volumes of liquids.
definition source: http://www.answers.com/topic/micropipette
imported from: OBI

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

centrifuge
type: Class
subclass of: equipment and supplies
definition: A device with a rapidly rotating container that applies centrifugal force to its contents
definition source: http://en.wikipedia.org/wiki/Centrifuge
imported from: OBI

thermal cycler
type: Class
subclass of: equipment and supplies
example of usage: Piko(tm) 96-well Thermal Cycler
definition: An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
alternative term: DNA_amplifier PCR_machine Polymerase_Chain_Reaction_ machine thermocycler
definition source: MO
imported from: OBI

temperature control bath
type: Class
subclass of: equipment and supplies
example of usage: 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.
definition: 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.
definition source: OBI Instrument branch
imported from: OBI

water bath
type: Class
subclass of: temperature control bath
example of usage: A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
definition: 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).
imported from: OBI

advantage of the Protocol
type: Class
subclass of: textual entity
disjoint with: primer sequence
definition: Advantage of the protocol is a subclass of textual entity. It should be made clear in which situations the Protocol has been successfully employed.
definition source: http://www.nature.com/nprot/info/gta.html

application of the protocol
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: part of
  all values from: introduction section
disjoint with: catalog number
disjoint with: limitation of the protocol
disjoint with: primer sequence
disjoint with: provenance of the protocol
disjoint with: purpose of the protocol
disjoint with: title of the protocol
disjoint with: alert message
example of usage: banana.com
example of usage: 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.
definition: 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.

bag
type: Class
subclass of: equipment and supplies
example of usage: Laboratory bags: autoclavable biohazard bags, specimen/document zipper bags
definition: A bag is a supply. A bag is a simple tool in the form of a non-rigid container.

buffer list
type: Class
subclass of: data set
subclass of: Restriction
  on property: part of
  some values from: materials section
disjoint with: equipment and supplies list
disjoint with: primer list
disjoint with: software list
definition: 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
type: Class
subclass of: name
disjoint with: equipment or supplies name
disjoint with: primer name
disjoint with: software name
example of usage: 1X Queen’s lysis buffer (1L), AB lysis buffer (500ml).
definition: 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
type: Class
subclass of: textual entity
disjoint with: limitation of the protocol
disjoint with: primer sequence
disjoint with: provenance of the protocol
disjoint with: purpose of the protocol
disjoint with: title of the protocol
disjoint with: alert message
example of usage: 5000-0012
definition: Catalog number is a subclass of textual entity. Catalog number is a numeral or string of numerals that is used for identification.

centrifuge tube
type: Class
subclass of: equipment and supplies
example of usage: Weigh 300-400 mg of ground, lyophilized tissue, into a 15 ml polypropylene centrifuge tube.
definition: 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.
alternative term: centrifuge tips
definition source: http://en.wikipedia.org/wiki/Laboratory_centrifuge#Centrifuge_tubes

critical step
type: Class
subclass of: alert message
example of usage: 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)
definition: 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.

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

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 descriptionof a procedure about the use of enzymes to increase the number of molecules from a material entity.

equipment and supplies list
type: Class
subclass of: data set
subclass of: Restriction
  on property: part of
  some values from: materials section
disjoint with: primer list
disjoint with: reagent list
disjoint with: software list
disjoint with: solution list
definition: 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
type: Class
subclass of: name
disjoint with: primer name
disjoint with: reagent name
disjoint with: software name
disjoint with: solution name
example of usage: Nalgene Cryogenic Tube, sterile, 1.2 ml. S1000 Thermal Cycler with 96-Deep Well Reaction Module.
definition: Equipment or supply name is a textual entity. Equipment or supply name is the name of equipment or supply.

experimental protocol
type: Class
subclass of: document
subclass of: Restriction
  on property: has alert message
  some values from: critical step
subclass of: Restriction
  on property: has alert message
  some values from: hint
subclass of: Restriction
  on property: has alert message
  some values from: pause point
subclass of: Restriction
  on property: has alert message
  some values from: timing
subclass of: Restriction
  on property: has alert message
  some values from: troubleshooting
subclass of: Restriction
  on property: has part
  some values from: document part
subclass of: Restriction
  on property: has part
  some values from: advantage of the Protocol
subclass of: Restriction
  on property: has part
  some values from: application of the protocol
subclass of: Restriction
  on property: has part
  some values from: limitation of the protocol
subclass of: Restriction
  on property: has part
  some values from: provenance of the protocol
subclass of: Restriction
  on property: has title
  all values from: title of the protocol
subclass of: Restriction
  on property: has version
  all values from: document version
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
example of usage: Protein extraction buffer, DNA extraction buffer (CTAB extraction buffer), RNA extraction 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.

final concentration
type: Class
subclass of: concentration
subclass of: Restriction
  on property: part of
  some values from: solution
subclass of: Restriction
  on property: part of
  some values from: buffer
definition: The final measured concentration of a compound in a substance.
alternative term: Last concentration
definition source: Adopted from NCI thesaurus

flammable
type: Class
subclass of: caution
example of usage: Keep away from sources of ignition. Reference: Nature Protocols
definition: Easily ignited.
alternative term: Inflammable
definition source: http://wordnetweb.princeton.edu/perl/webwn

grinding machine
type: Class
subclass of: equipment and supplies
example of usage: Put the number of seed indicated by the kit protocol in the grinding machine and grind the seed to a powder.
definition: Grinding machine is a equipment. Grinding machine is a machine used to grind grains and leaves.
alternative term: Grinding device

hint
type: Class
subclass of: alert message
example of usage: HINT: Mix well by vortex before to use. HINT: ADD NaOH to WATER to avoid splashing.
definition: A hint is a message given to a user of a protocol that will help to perform the experiment.

introduction section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: application of the protocol
subclass of: Restriction
  on property: has part
  some values from: limitation of the protocol
subclass of: Restriction
  on property: has part
  some values from: provenance of the protocol
subclass of: Restriction
  on property: has part
  some values from: purpose of the protocol
definition: 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
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is manufactured by
  some values from: manufacturer
subclass of: Restriction
  on property: has catalog number
  some values from: catalog number
subclass of: Restriction
  on property: has name
  all values from: kit name
subclass of: Restriction
  on property: part of
  all values from: kit list
disjoint with: manufacturer
example of usage: Universal Linker Kit, laboratory kit that allows customization of protein microarrays.
definition: A set of chemical substances, articles or equipment needed for a specific purpose.

kit list
type: Class
subclass of: data set
subclass of: Restriction
  on property: part of
  some values from: materials section
comment: 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
type: Class
subclass of: name
example of usage: Spectrum Plant Total RNA Kit, sufficient for 50 purifications.
definition: Kit name is a textual entity. Kit name is the name of a kit.

limitation of the protocol
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: part of
  all values from: introduction section
disjoint with: primer sequence
disjoint with: provenance of the protocol
disjoint with: purpose of the protocol
disjoint with: title of the protocol
disjoint with: alert message
example of usage: 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
definition: 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.
definition source: http://www.nature.com/nprot/info/gta.html

manufacturer
type: Class
subclass of: material entity
disjoint with: primer
example of usage: Bio-Rad, Nalgene, Thermoscientific, Eppendorf, Falcon.
definition: 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
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: sample from organism
subclass of: Restriction
  on property: has part
  some values from: buffer list
subclass of: Restriction
  on property: has part
  some values from: equipment and supplies list
subclass of: Restriction
  on property: has part
  some values from: kit list
subclass of: Restriction
  on property: has part
  some values from: primer list
subclass of: Restriction
  on property: has part
  some values from: reagent list
subclass of: Restriction
  on property: has part
  some values from: software list
subclass of: Restriction
  on property: has part
  some values from: solution list
definition: 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
type: Class
subclass of: document part
definition: Methods section is part of a document. This is the section where the protocol is presented.

microcentrifuge tube
type: Class
subclass of: equipment and supplies
example of usage: Pour off supernatant into 1.5 ml microfuge tube.
definition: Microcentrifuge tube is a supply. Microcentrifuge tubes are plastic tubes with capacities from 250 ul to 2.0 ml.
alternative term: Microcentrifuge tips microfuge tube
definition source: http://en.wikipedia.org/wiki/Laboratory_centrifuge#Centrifuge_tubes

neurotoxic
type: Class
subclass of: caution
example of usage: avoid contact with skin, eyes or mucous membranes; keep away from sources of ignition. When handling , wear gloves. Reference: Nature Protocols
definition: Poisonous to nerves or nerve cells.
definition source: http://wordnetweb.princeton.edu/perl/webwn

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.

pause point
type: Class
subclass of: alert message
example of usage: PAUSE POINT: Can be left overnight at 48 C or frozen for up to a month at -20 C.
definition: Pause point is the point were the protocol naturally breaks into separate stages.

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

portable ice chest
type: Class
subclass of: equipment and supplies
example of usage: Place bags in a portable ice chest or other container with ice to keep samples cool.
definition: 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.
alternative term: cooler cool box chilly bin esky
definition source: http://en.wikipedia.org/wiki/Cooler

primer
type: Class
subclass of: material entity
subclass of: Restriction
  on property: is manufactured by
  some values from: manufacturer
subclass of: Restriction
  on property: part of
  some values from: primer list
subclass of: Restriction
  on property: has name
  all values from: primer name
subclass of: Restriction
  on property: has sequence
  all values from: primer sequence
example of usage: Oligos used in PCR.
definition: A primer is a short strand of nucleic acid that serves as a starting point for DNA or RNA synthesis.
definition source: http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29

primer list
type: Class
subclass of: data set
subclass of: Restriction
  on property: part of
  some values from: materials section
disjoint with: software list
definition: 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
type: Class
subclass of: name
disjoint with: software name
example of usage: CII-fw, CII-rv.
definition: Primer name is a textual entity. Primer name is the name of a primer.

primer sequence
type: Class
subclass of: textual entity
disjoint with: provenance of the protocol
disjoint with: purpose of the protocol
disjoint with: title of the protocol
disjoint with: alert message
example of usage: 5′-GAATGATGTACCACCTTTG-3′
definition: 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
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

provenance of the protocol
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: part of
  all values from: introduction section
disjoint with: purpose of the protocol
disjoint with: title of the protocol
disjoint with: alert message
example of usage: 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
definition: 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.

purpose of the protocol
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: part of
  all values from: introduction section
disjoint with: title of the protocol
disjoint with: alert message
example of usage: 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.
definition: 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
type: Class
subclass of: caution
example of usage: 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.
definition: A chemical substance that will ignite spontaneously in air at or below a temperature of 130 F (54.4 C).
definition source: http://www.utexas.edu/safety/ehs/msds/glossary/

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

reagent list
type: Class
subclass of: data set
subclass of: Restriction
  on property: part of
  some values from: materials section
disjoint with: software list
definition: 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
type: Class
subclass of: name
disjoint with: software name
example of usage: Taq DNA Polymerase from Thermus aquaticus with 10X reaction buffer without MgCl2.
definition: Reagent name is a textual entity. Reagent name is the name of a reagent.

software list
type: Class
subclass of: data set
subclass of: Restriction
  on property: part of
  some values from: materials section
disjoint with: solution list
definition: Software list is a data set of the names of softwares that are part of materials section of a protocol.

software name
type: Class
subclass of: name
disjoint with: solution name
example of usage: LightCycler 480 Software.
definition: Software name is a textual entity. Software name is the name of a software.

software version
type: Class
subclass of: version
example of usage: Version 1.5
definition: Software version is a textual entity. A software version number is a software attribute that represents the version of software.

solution list
type: Class
subclass of: data set
subclass of: Restriction
  on property: part of
  some values from: materials section
definition: Solution list is a data set of the names or identifiers of solutions that are part of materials section of a protocol.

solution name
type: Class
subclass of: name
example of usage: 3M NaOH (1L)
definition: 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
type: Class
subclass of: alert message
example of usage: Store the buffer in foil covered dark coloured bottle at room temperature. Light sensitive. Can be used up to 2 months.
definition: 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.

timing
type: Class
subclass of: alert message
example of usage: Steps 1-3, 30 min.; Steps 6-7, 2 h
definition: Timing is a message used to indicate the approximate time that a step, or set of steps, could take.

title of the protocol
type: Class
subclass of: textual entity
disjoint with: alert message
definition: Title of protocol is a subclass of textual entity. Title of protocol is the name of a protocol.

toxic
type: Class
subclass of: caution
example of usage: Avoid inhalation, ingestion or contact with skin, eyes or mucous membranes. Reference: Nature Protocols
definition: Of or relating to or caused by a toxin or poison 'suffering from exposure to toxic substances'
definition source: http://wordnetweb.princeton.edu/perl/webwn

troubleshooting
type: Class
subclass of: alert message
example of usage: 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.
definition: 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.

volatile
type: Class
subclass of: caution
example of usage: handle in well-ventilated charcoal-filtered hood. Reference: Nature Protocols
definition: The property of a substance of changing readily from a solid or liquid to a vapor.

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

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

entity
type: Class

continuant
type: Class
subclass of: entity
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

alert message
type: Class
subclass of: textual entity
definition: 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.
imported from: EXACT

caution
type: Class
subclass of: alert message
definition: A caution is a message given to a user of a protocol about potentially dangerous properties of materials used in the experiment.
imported from: EXACT

CIMMYT
type: NamedIndividual
type: Restriction
  on property: has part
  some values from: author list

DNAExtractionProtocol01
type: NamedIndividual
type: DNA extraction protocol
has author: CIMMYT
has title: GenomicDNAIsolation
has part: IntroductionSection01
has part: MaterialsSection01
has part: MethodsSection01

GenomicDNAIsolation
type: NamedIndividual
type: title of the protocol

IntroductionSection01
type: NamedIndividual
type: introduction section
has part: Plant DNA Extraction Of High Quality
has part: PNAS 81:8014-8019
part of: DNAExtractionProtocol01

MaterialsSection01
type: NamedIndividual
type: materials section
part of: DNAExtractionProtocol01

Plant DNA Extraction Of High Quality
type: NamedIndividual
type: purpose of the protocol
part of: IntroductionSection01

PNAS 81:8014-8019
type: NamedIndividual
type: provenance of the protocol
part of: IntroductionSection01