To boil is an experiment action “o bubble up in agitation through the action of heat causing the lowest portions of the liquid to pass into the gaseous form and escape; to reach the boiling point, to turn from the liquid into the gaseous state”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Boil
Stop
"A set of instructions for performing a specific task"
[http://dictionary.oed.com/cgi/entry/50189128?single=1&query_type=word&queryword=procedure&first=1&max_to_show=10]
Procedure
Connect
To connect is an experiment action “to join, fasten, or link together … by the connecting medium or instrumentality”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
A plan of experiment actions is an ordered collection of experiment actions or operating procedures according to which the experiment is to be done.
Reference: based on The Oxford English Dictionary. Oxford University Press, 2 Ed., 1989
Plan of actions
Heat
To heat is an experiment action “to raise the temperature of”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
DC: title of protocol
PATO:0001502
http://www.ebi.ac.uk/ontology-lookup/?termId=PATO%3A0001502
A monadic quality of continuant inhering in a bearer by virtue of its being intricate and compounded.
PATO: Complexity
Atomic
map to [simple - PATO:0001503]
http://www.ebi.ac.uk/ontology-lookup/?termId=PATO%3A0001503
A complexity quality in a bearer by virtue of its having few parts; not complex, complicated or compound.
To streak is an experiment action to spread a microbial sample in a line across the surface of solid culture medium to isolate individual cells
Streak
To pour is an experiment action “to cause or allow (a substance, esp. a liquid) to flow out of a vessel or receptacle; to emit in a stream”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Pour
Continue
DC: author of protocol
Yes-command
a command that is used when the value of a boolean expression is true
"Corresponds roughly to the class of ordinary objects. Examples include normal physical objects, geographical regions, and locations of Processes, the complement of Objects in the Physical class." [SUMO]
Object
Centrifuge
To centrifuge is an experiment action “to subject to centrifugal motion; to separate by means of a centrifuge”.
Reference: Based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
a mode of property transformation is an experimental action with a goal of property transformation
Mode of property transformation
TO: Temporal entity
A data action is an action of estimation or evaluation of data
Data action
Weigh
To weigh is an experiment action to “To be equivalent to in weight”
Reference: http://www.biology-online.org/dictionary/Weigh
To record is an experiment action to represent symbolically a value of a measurement or an observation in order to preserve information for later use
Record
A preparation procedure is a procedure with a goal of preparation for the execution of a protocol.
Preparation procedure
Command action
a command action is an action with a goal to control the flow of the process of executing of the experiment, e.g. stop, check, continues.
Re-suspend
To re-suspend is an experiment action to suspend material that have been previously suspended, being made homologies, uniformly distributed
Start location is a location at the beginning of an experiment action
Start location
Mix
To mix is an experiment action “to put together or combine (two or more substances or things) so that the constituents or particles of each are interspersed or diffused more or less evenly among those of the rest”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
PATO: Complex
PATO:0001504
http://www.ebi.ac.uk/ontology-lookup/?termId=PATO%3A0001504
A complexity quality inhering in a bearer by virtue of its being intricate and compounded.
an action is “the process of doing something or being active”
Reference: Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
Action
Move
To move is an experiment action to change a spatial location of an entity from a start location to an end location
To measure is an experiment action “to determine the extent, quantity, amount or degree of something”
Reference: Based on Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
Measure
Assessment
Assessment is a goal to achieve a state where data are estimated or evaluated.
Shake
To shake is an experiment action to move regularly in the defined restricted space
Equipment setup action
An equipment setup action is an action to put equipment into a required state for the experiment action to be executed
Break
To break is an experiment action “to separate into two or more pieces” regardless of precision of the separation
Reference: based on Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
Filter
To filter is an experiment action “to pass (a liquid) through a filter, or some porous medium, for the purpose of removing solid particles or impurities”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Pyrophoric
Ignates in air.
Reference: Nature Protocols
"the class of things that happen and have temporal parts or stages" [SUMO]
Process
To de-lid is an experiment action to remove a lid from a base and move it to a lid location
De-lid
Condition
A condition is a statement to be checked.
DC term for description of protocol
DC term for description of protocol is Dublin Core metadata for the description of a protocol.
DC: submission date of protocol
Transformation is a goal to achieve a state where properties, spatial location, category or time have been changed.
Transformation
Preparation for experiment action
Preparation for experiment action is a goal to achieve a state where experiment equipment is put into a state required for the experiment action to be executed.
To incubate is an experiment action to maintain optimal environmental conditions in order to promote growth or chemical reaction
to cause to develop in an incubator or culture medium
Incubate
To aspirate is an experiment action “to draw in or remove by suction”
Reference: Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
Aspirate
Add
to add is an experiment action “to join or unite a component to another so as to increase the number, quantity in the container. The end container is the same for all components”
Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
PATO: Volume
http://www.ebi.ac.uk/ontology-lookup/?termId=PATO%3A0000918
A 3-D extent quality of the amount of 3-dimensional space an object occupies.
a mode of category transformation is an experimental action with a goal of category transformation
Mode of category transform
A mode of time transformation is an experimental action with a goal of time transformation
Mode of time transformation
an equipment role is a role played by an object used in an experiment as a tool, a device, or material.
Equipment role
A goal of experiment action is the state that a plan of actions is intended to achieve.
Reference: Based on WordNet: http://www.cogsci.princeton.edu/cgi-bin/webwn2.0?stage=1&word=goal+
Goal of experiment action
handle in well-ventilated charcoal-filtered hood
Reference: Nature Protocols
Volatile
refrence: Nature Protocols
Critical step
Separation
Separation is a goal to achieve a state of being separated or parted.
Reference: OED
Preservation of information is a goal to achieve a state where the information has been recorded for future use.
Preservation of information
No-command
a command that is used when the value of a boolean expression is false
Expression
"representing (a meaning, thought, state of things) in words or symbols" [http://dictionary.oed.com/cgi/entry/50080633?single=1&query_type=word&queryword=Expression&first=1&max_to_show=10]
A false value is a value of a statement that does not correspond to reality.
False value
Ignite
To ignite is an experiment action “to subject to the action of fire”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
avoid contact with skin, eyes or mucous membranes; keep away from sources of ignition.
Reference: Nature Protocols
Highly flammable
"Instances of Abstract can be said to exist in the same sense as mathematical objects such as sets and relations, but they cannot exist at a particular place and time without some physical encoding or embodiment." [SUMO]
Abstract entity
A true value is a value of a statement that corresponds to reality.
True value
IF-condition is a condition to be check before a command action be selected.
IF-condition
Mode of separation
A mode of separation is a way of separation, an experiment action with a goal of separation
Base
"The lowest or supporting part." [http://dictionary.oed.com/cgi/entry/50017991?query_type=word&queryword=Base&first=1&max_to_show=10&sort_type=alpha&result_place=1&search_id=6ner-5uBQpF-1182&hilite=50017991]
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.
Proposition
"entities that express a complete thought or a set of such thoughts." [SUMO]
"that which contains, esp. a receptacle designed to contain or store certain articles" [http://dictionary.oed.com/cgi/entry/50048348?single=1&query_type=word&queryword=Container&first=1&max_to_show=10]
Container
To Divide is an experiment action “to separate (a thing) into parts, or (a number or collective body) into smaller groups; to split up, cleave; to break or cut asunder”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Divide
Inoculate
To inoculate is an experiment action “to join or unite by insertion”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Check
Waist location
Waist location is a location of palcing of waist.
DC: subject of protocol
Pierce
To penetrate; to pass or break through or into something, esp. as or in the manner of a sharp-pointed object
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Go
Caution
A caution is a message given to a user of a protocol about potentially dangerous properties of materials used in the experiment.
A protocol method is the description of a technique and technical considerations for a procedure, ‘sterile technique’. A protocol method is usually already familiar to a typical user of a protocol; the method is stored in the knowledge base.
Protocol method
Command
a role played by "an expression, that defines an operation, or results in the performance of an operation" [http://dictionary.oed.com/cgi/entry/50044797?query_type=word&queryword=Command+&first=1&max_to_show=10&sort_type=alpha&result_place=2&search_id=6ner-RBKHA3-1348&hilite=50044797]
Discard
To discard is an experiment action to move something to a waste location
TO: Instant
Thaw
to thaw is an experiment action to change a substance from a frozen state to a liquid state
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Wait
To wait is an experiment action to allow a time interval to pass without experiment actions
Store
Location
a location is a role played by an object that is used for placing entities.
avoid contact with skin, eyes or mucous membranes; keep away from sources of ignition. When handling , wear gloves.
Reference: Nature Protocols
Neurotoxic
lid location is a location of palcing of a lid
Lid location
Equipment
Experiment equipment is the set of tools, devices, materials, computer systems assembled for performing the experiment. Reference: following Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
a container that is used by the end of an experiment action
End container
Boolean expression
A Boolean expression is an expression that results in a Boolean value, that is, true value or false value.
Reference: Wikipedia
A mode of transformation is an experimental action with a goal of transformation
Mode of transformation
A mode of transformation of a spatial location is an experimental action with a goal of transformation of a spatial location
Mode of transformation of spatial location
to dissolve is an experiment action “to change or cause to change from a solid to a dispersed form by immersion in a fluid of suitable properties”
Reference: biology online dictionary http://www.biology-online.org/dictionary/Dissolve -
Dissolve
Cover
To cover is an experiment action to put or lay a top over a base, with the effect of enclosing
Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Swirl
To swirl is an experiment action to shake fluid in constant circular or semicircular motion
An operating procedure is an ordered collection of experiment actions with defined goals.
Operating procedure
A storage-condition is a condition to be checked before a command action ‘store’ can be executed.
Storage-condition
TO: Interval
Calibrate
To calibrate is an experiment action “to determine the correct position, value, capacity, etc., of; to set an instrument so that readings taken from it are absolute rather than relative”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
A protocol is a procedure to execute an experiment to achieve experiment goals, which includes a plan of experiment actions or operating procedures, preparation procedures, instructions to users and metadata about the protocol.
Protocol
To join is an experiment action “to put (things) together, so that they become physically united or continuous; to fasten, attach, connect, unite (one thing to another); also, to connect by means of something intervening or attached to each”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Join
a container that is used at the beginning of an experiment action
Start container
An experimental action is a process of manipulation in the domain of the experiment in order to achieve a particular sub goal, which is a part of the goal of the experiment.
Reference: EXPO
Experiment action
Role
a role is played by a role holder in a particular context
To sterilise is an experiment action to make something free from micro-organisms
Sterilise
Quality
"Qualities which we cannot or choose not to reify into subclasses of Object." [SUMO]
To place is an experiment action “to put in a particular place, spot, or position” (into the end location), it is a part of a move action
Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Place
Post-condition
A post-condition is a condition to be checked after an operating procedure was executed.
Take
To take is an experiment action “to lay hold of, grasp”, it is a part of a move action
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Combination is a goal to achieve a state where two or more entities are combined.
Combination
Re-name
To re-name is an experiment action to designate a new name instead of the old name to an entity
Calculate
To calculate is an experiment action to estimate or determine a value of an entity by arithmetical or mathematical reckoning
Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Seal
To Seal is an experiment action to close or fasten tightly a base and a top by any substance or devise used as sealant
Reference: based on Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993.
End location
end location is a location at the end of an experiment action
To label is an experiment action to designate a name to an entity
Label
Assign name
To assign name is an experiment action to designate a new name to an entity
Rotate
To rotate is an experiment action “to cause (a thing) to turn round or revolve on a centre or axis”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
A pre-condition is a condition to be checked before an operating procedure can be executed.
Pre-condition
To vortex is an experiment action of a spiral rotatory movement of matter with the increasing gravity round a centre or axis
Reference: based on THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
Vortex
Remove
To remove is an experiment action “to move or shift from or out of the place occupied; to lift or push aside; to lift up and take away; to take off”
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
avoid inhalation, ingestion or contact with skin, eyes or mucous membranes
Reference: Nature Protocols
Toxic
Wash
To wash is an experiment action “to cleanse, remove” the unwanted material” from (something) by affusion of or immersion in” fluid
Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED.
"A piece or part placed upon or fitted to anything, and forming its upper part or covering." [http://dictionary.oed.com/cgi/entry/50254453?query_type=word&queryword=Top&first=1&max_to_show=10&sort_type=alpha&result_place=1&search_id=6ner-jycL9g-1160&hilite=50254453]
Top
A warning is a message given to a user of a protocol that a certain action can cause unexpected results and errors.
Warning
A mode of combination is a way of combining, an experimental action with a goal of combination
Mode of combination
keep away from sources of ignition.
Reference: Nature Protocols
Flammable
ro: located in
ro: participates in
ro: has quality
ro: location of
is part of
has part of
ro: has role
ro: has participant
has proposition