handle in well-ventilated charcoal-filtered hood Reference: Nature Protocols Volatile Preparation procedure An equipment setup action is an action to put equipment into a required state for the experiment action to be executed Equipment setup action 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. Atomic Streak 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 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. Centrifuge 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. Precision A mode of combination is a way of combining, an experimental action with a goal of combination Mode of combination DC: submission date of protocol Mode of transformation A mode of transformation is an experimental action with a goal of transformation TO: Interval Action an action is “the process of doing something or being active” Reference: Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993. Location role Post-condition Truth IF-condition Component Sterilise To sterilise is an experiment action to make something free from micro-organisms Stop Start location TO: Instant Lid location Equipment role Boolean expression To label is an experiment action to designate a name to an entity Label Waist location To ignite is an experiment action “to subject to the action of fire” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED. Ignite De-lid To de-lid is an experiment action to remove a lid from a base and move it to a lid location Biomaterial entity role 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. Cover Procedure Continue 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 Command role Pre-condition Old name DC: subject of protocol Yes-command False Data action A data action is an action of estimation or evaluation of data 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. Wash 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. Aspirate To aspirate is an experiment action “to draw in or remove by suction” Reference: Collins Softback English Dictionary, HarperCollins Publishers, Glasgow, 1993. To move is an experiment action to change a spatial location of an entity from a start location to an end location Move Protocol To heat is an experiment action “to raise the temperature of” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED. Heat OBI: biomaterial entity Neurotoxic avoid contact with skin, eyes or mucous membranes; keep away from sources of ignition. When handling , wear gloves. Reference: Nature Protocols 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. 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 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. Remove End location 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. DC: author of protocol 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. Add 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. PATO: Complex 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. Calculate Preservation of information 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. 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. DC: title of protocol Abstract entity Record 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 Plan of actions 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 Warning Combination 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. refrence: Nature Protocols Critical step Role Highly flammable avoid contact with skin, eyes or mucous membranes; keep away from sources of ignition. Reference: Nature Protocols Leading organization 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. Caution Top Container Operating procedure Re-suspend To re-suspend is an experiment action to suspend material that have been previously suspended, being made homologies, uniformly distributed Approximate precision Go Process Object 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. Expression Method Check Mode of property transformation a mode of property transformation is an experimental action with a goal of property transformation Proposition 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 Preparation for experiment action Transformation Quality 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 Mode of time transformation A mode of time transformation is an experimental action with a goal of time transformation Name Location Experiment action 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 Store Separation 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. Mode of category transform a mode of category transformation is an experimental action with a goal of category transformation To shake is an experiment action to move regularly in the defined restricted space Shake Condition 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 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 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 Vortex 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. Ignates in air. Reference: Nature Protocols Pyrophoric 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. New name Wait To wait is an experiment action to allow a time interval to pass without experiment actions To discard is an experiment action to move something to a waste location Discard Inoculate To inoculate is an experiment action “to join or unite by insertion” Reference: THE OXFORD ENGLISH DICTIONARY (1989) OXFORD UNIVERSITY PRESS, 2 ED. End container Equipment Goal of experiment action 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 Start container Instruction TO: Temporal entity DC annotation of protocol A mode of separation is a way of separation, an experiment action with a goal of separation Mode of separation Place 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. To re-name is an experiment action to designate a new name instead of the old name to an entity Re-name To swirl is an experiment action to shake fluid in constant circular or semicircular motion Swirl avoid inhalation, ingestion or contact with skin, eyes or mucous membranes Reference: Nature Protocols Toxic Storage-condition To assign name is an experiment action to designate a new name to an entity Assign name keep away from sources of ignition. Reference: Nature Protocols Flammable No-command Base 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. To weigh is an experiment action to “To be equivalent to in weight” Reference: http://www.biology-online.org/dictionary/Weigh Weigh has Organization has Action has Yes-command has Object has Command has Equipment has Method has No-command has Component has New name has Volume has Name has Complexity has Plan has Base has Location has Old name has Interval has Goal has Container has Author is Part of has Lid location has Boolean expression has Submission date has Instruction has Precision has End location has Subject has Part of has Top has Condition has Title has Start location seal join between ypd agar plate base and ypd agar plate lid