VIBSO Workgroup
_WIP - NOT READY FOR PRODUCTION_ The Vibration Spectroscopy Ontology (VIBSO) is used to represent information regarding the excution and analysis of vibrational spectroscopy assays.
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
alternative term
definition source
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
is denotator type
Relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
Alan Ruttenberg
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand assertion to
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
Use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
has ID digit count
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
Person:Alan Ruttenberg
has ID range allocated
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID range allocated to
has ID policy for
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
has ID prefix
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
Add as annotation triples in the granting ontology
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
may be identical to
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
David Osumi-Sutherland
VFB
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
scheduled for obsoletion on or after
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
GO ontology
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
logical characteristic of object property
'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
A synonym type for describing abbreviations or initalisms
A synonym type for describing ambiguous synonyms
A synonym type for describing dubious synonyms
EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
A synonym type for describing layperson or colloquial synonyms
CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
A synonym type for describing pluralization synonyms
CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
A synonym type for describing UK spelling variants
A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
A synonym type for names that have been used as primary labels in the past.
The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
A synonym type for the legal entity name
CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
A synonym type for describing Latin term synonyms.
NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
has related synonym
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
has measurement unit label
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
is quality measurement of
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
is quality measured as
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is_specified_input_of
has_specified_output
The inverse property of is_specified_output_of
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
has organization member
Relating an organization to a legal person or organization.
See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
A relation between a value specification and an entity which the specification is about.
A relation between an information content entity and a value specification that specifies its value.
has performer
A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process.
OBI
The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system).
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
characteristic of part of
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
Genetic information generically depend on molecules of DNA.
The novel *War and Peace* generically depends on this copy of the novel.
The pattern shared by chess boards generically depends on any chess board.
The score of a symphony g-depends on a copy of the score.
This pdf file generically depends on this server.
A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
Molecules of DNA are carriers of genetic information.
This copy of *War and Peace* is carrier of the novel written by Tolstoy.
This hard drive is carrier of these data items.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
is carrier of
the relationship between a fraction and the number above the line
AGB
relationship between a planned process and the plan specification that it carries out; it is defined as equivalent to the composed relationship (realizes o concretizes)
the relationship between a fraction and the number below the line (or divisor)
has measurement value
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
continuant
An 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.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A 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.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object part
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
material entity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
The simultaneous measurement of spectra and images. A radiation source illuminates the sample and a series of spatially resolved spectra are collected.
The collection of spatially resolved Raman spectra of a sample during optical microscopy.
Equivalence asserted manually in VIBSO based on the textual definition of this class.
Any technique where a microscope is used to view a small object (or specimen) by producing a magnified image.
Equivalence asserted manually in VIBSO based on the definitions of both classes.
Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.
Microscopy where visible light coming from the specimen is collected and guided through a pinhole before it is detected. The pinhole allows only light from the focal point to pass to the detector, reducing background interference.
The study of the interaction of a sample with radiation or particles for measurement or detection.
Any type of chemical imaging spectroscopy where an optical microscope is used to image the sample and locate a small area for spectral analysis.
Spectroscopy which probes the vibrational degrees of freedom of a molecule.
Spectroscopy where a metal-molecule-metal sandwich is formed and electrons tunnel from metal to metal through the molecules. Any additional molecules adsorbed onto the inner layer of the sandwhich can affect the tunneling via the excitation of vibrational states.
inelastic electron tunnelling spectrometry
inelastic electron tunnelling spectroscopy
Spectroscopy where the sample absorbs radiation from the infrared region (0.78 to 1000 micrometres).
Spectroscopy using radiation in the infrared region (0.78–1000 μm) where an evanescent wave is generated using an optical fibre.
Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm) with sufficient energy to cause photodissociation by the absorption of two or more photons.
infra-red multiphoton dissociation spectrometry
infrared multiphoton dissociation spectrometry
infrared multiphoton dissociation spectroscopy
Spectroscopy where the sample absorbs resonant radiation from the infrared region (0.78–1000 μm) with sufficient energy to cause photodissociation by the absorption of two or more photons.
resonance-enhanced infrared multiphoton dissociation spectrometry
resonance-enhanced infrared multiphoton dissociation spectroscopy
resonant infra-red multiphoton dissociation spectrometry
resonant infra-red multiphoton dissociation spectroscopy
resonant infrared multiphoton dissociation spectrometry
resonant infrared multiphoton dissociation spectroscopy
Spectroscopy where the sample absorbs radiation in the mid infrared region (3–8 μm).
Spectroscopy where the sample absorbs a single pulse of radiation from the infrared region (0.78–1000 μm) and the spectrum obtained is subject to a Fourier transform.
Fourier transform infra-red absorption spectroscopy
Fourier transform infra-red spectrometry
Fourier transform infrared (FT-IR) spectroscopy
Fourier-transform infra-red absorption spectrometry
Fourier-transform infrared (FTIR) absorption spectroscopy
Spectroscopy where the sample absorbs radiation from a finely focused beam (<10 μm diameter) of infrared light (0.78–1000 μm).
Spectroscopy where the sample absorbs radiation from the near infrared region (0.8–2 μm).
Spectroscopy where the sample absorbs a single pulse of radiation from the near infrared region (0.8–2 μm) and the spectrum obtained is subject to a Fourier transform.
Fourier transform near infra-red absorbance spectrometry
Fourier transform near infra-red absorption spectrometry
Fourier transform near infra-red spectrometry
Fourier transform near infra-red spectroscopy
Fourier transform near infrared absorbance spectrometry
Fourier transform near infrared absorbance spectroscopy
Fourier transform near infrared absorption spectrometry
Fourier transform near infrared absorption spectroscopy
Spectroscopy where the difference in infrared radiation (0.78–1000 μm) bsorption of a sample cell against a reference cell is measured.
Spectroscopy where the rough metal surface of a sample absorbs radiation in the infrared region (0.78–1000 μm).
surface enhanced infra-red absorption spectrometry
surface enhanced infra-red absorption spectroscopy
surface enhanced infrared absorption spectrometry
surface enhanced infrared absorption spectroscopy
Spectroscopy where transient species such as radicals, ions or reactive intermediates are studied using pulses from an infrared laser. The infrared absorbance of the sample before and after an excitation laser pulse is measured.
IR laser transient absorption spectroscopy
infrared laser transient absorption spectroscopy
infrared transient absorption spectroscopy
Spectroscopy where the reflection or scattering of infrared radiation (0.78–1000 μm) by a sample is detected.
Spectroscopy where the diffuse reflection of infrared radiation by a sample is measured.
diffuse reflectance infrared spectroscopy
Spectroscopy where the diffuse reflection of a single pulse of infrared radiation by a sample is measured, and the spectrum obtained is subject to a Fourier transform.
diffuse reflectance infra-red Fourier transform spectrometry
diffuse reflectance infrared Fourier transform spectrometry
diffuse reflectance infrared Fourier transform spectroscopy
diffuse reflectance infrared spectroscopy by Fourier transform
Spectroscopy where the reflection or scattering of near infrared radiation (0.8-2 micrometres) by a sample is detected.
Spectroscopy where the absorption and reflection of low incident angle infrared light by the surface molecules of a highly reflective or polished sample is measured.
infrared reflection absorption spectrometry
infrared reflection absorption spectroscopy
reflection absorption infra-red spectrometry
reflection absorption infrared spectrometry
reflection absorption infrared spectroscopy
reflection-absorption infrared spectroscopy
reflection–absorption infrared spectroscopy
Spectroscopy where infrared light is introduced into a prism at an angle exceeding the critical angle for internal reflection. This produces an evanescent wave at the reflecting surface (a surface which is transparent to infrared such as thallium bromide) on which the sample is supported, and the distortion of the evanescent wave by the sample is measured.
attenuated total reflectance infra-red spectroscopy
attenuated total reflectance spectrometry
multiple internal reflection spectrometry
multiple internal reflection spectroscopy
attenuated total reflectance infrared spectroscopy
Spectroscopy where the sample is heated and the infrared radiation (0.78–1000 μm) emitted during cooling is detected.
Spectroscopy where the sample is heated in a flame and the infrared radiation (0.78–1000 μm) emitted during cooling is detected.
Spectroscopy where the sample is heated in a flame and the infrared radiation (0.78–1000 μm) emitted during cooling is detected. The spectrum obtained is subject to a Fourier transform.
Fourier transform flame infra-red emission spectrometry
Fourier transform flame infrared emission spectroscopy
IR emission spectroscopy where the spectrum is obtained by a single pulse of (UV) radiation, and is subject to a Fourier transform.
Fourier transform infra-red emission spectrometry
Fourier transform infra-red emission spectroscopy
Fourier transform infrared emission spectrometry
Fourier transform infrared emission spectroscopy
Spectroscopy where the sample is heated and the mid infrared radiation (0.78–1000 μm) emitted during cooling is detected.
Spectroscopy where the sample is heated and the infrared radiation (0.78–1000 μm) emitted during cooling is detected with a two-dimensional focal plane array infrared camera.
planar array infra-red emission spectrometry
planar array infrared emission spectrometry
planar array infrared emission spectroscopy
Spectroscopy where the sample is heated using ultraviolet excitation (single photon) and the infrared radiation (0.78–1000 μm) emitted during cooling is detected.
single photon infra-red emission spectrometry
single photon infra-red emission spectroscopy
single-photon infra-red emission spectrometry
single-photon infrared emission spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range by a sample is detected.
Spectroscopy where vibrational optical activity is measured by means of a small difference in the intensity of Raman scattering from chiral molecules of right- and left-circularly polarised incident light.
Spectroscopy where the Raman scattering of monochromatic light from three lasers (known as pump, probe and Stokes/anti-Stokes) by a sample is detected. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. An anti-Stokes frequency stimulation beam is used and a Stokes frequency beam is observed. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
coherent Stokes Raman scattering spectrometry
coherent Stokes Raman scattering spectroscopy
Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. An anti-Stokes frequency stimulation beam is used and a Stokes frequency beam is observed and the difference between the pump and the Stokes beams coincides with the frequency of an electronic transition within the molecule. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
coherent Stokes resonance Raman spectroscopy
Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. A Stokes frequency stimulation beam is used and an anti-Stokes frequency beam is observed. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
coherent anti-Stokes Raman scattering spectrometry
coherent anti-Stokes Raman scattering spectroscopy
Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. A Stokes frequency stimulation beam is used and an anti-Stokes frequency beam is observed and the difference between the pump and the anti-Stokes beams coincides with the frequency of an electronic transition within the molecule. multiphoton excitation is used to produce a signal in which the emitted waves are coherent.
coherent anti-Stokes resonance Raman spectroscopy
Spectroscopy where the Raman scattering of monochromatic light is detected. An aperture is used to discriminate between Raman signal coming from the focused laser spot and Raman signal coming from the out-of-focus region of the sample.
The collection of spatially resolved Raman spectra of a sample during optical microscopy. An aperture is used to discriminate between Raman signal coming from the laser spot and that coming from the out-of-focus region of the sample.
Spectroscopy where the Raman scattering of light (produced by a single laser pulse) by a sample is detected and the spectrum is subject to a Fourier transform.
Spectroscopy where the Raman scattering of light by a (liquid) sample is detected. During scattering, photons from the incident laser (with frequency ω) are scattered by sample into photons of the second harmonic (photons with frequency 2ω).
Spectroscopy where the polarisation of light which has been subjected to Raman scattering by a sample is determined.
Raman spectroscopy where the energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition in the sample.
Spectroscopy where the Raman scattering of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range, by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample, and the laser is combined with a Kerr gate fluorescence rejection system.
Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a sample adsorbed onto a metal (Au, Ag or Cu) surface is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample.
surface enhanced resonance Raman scattering spectrometry
surface enhanced resonance Raman scattering spectroscopy
surface enhanced resonance Raman spectrometry
surface-enhanced resonance Raman spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from an ultraviolet laser, by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample.
ultra-violet resonance Raman spectroscopy
ultraviolet resonance Raman spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from a deep ultraviolet (<300 nm) laser, by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light coincides with an electronic transition within the sample.
deep ultra-violet resonance Raman spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from a laser, by a sample is detected. Scattered light is collected from regions laterally offset from the excitation laser spot.
spatially offset Raman scattering spectrometry
spatially offset Raman scattering spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from two lasers ('pump' and 'probe') by a sample is detected.
stimulated Raman scattering spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from a femtosecond laser pulse, by a sample is detected. The laser pulse is generated by the mixing of two lasers ('pump' and 'probe').
emtosecond broadband stimulated Raman scattering spectrometry
femosecond stimulated Raman scattering spectrometry
femosecond stimulated Raman scattering spectroscopy
femosecond stimulated Raman spectrometry
femtosecond broadband stimulated Raman scattering spectroscopy
femtosecond broadband stimulated Raman spectrometry
femtosecond broadband stimulated Raman spectroscopy
femosecond stimulated Raman spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a sample adsorbed onto a metal (Au, Ag or Cu) surface is detected.
surface-enhanced Raman scattering (SERS) spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from a visible laser (500–650 nm), by metal surfaces, where scattering is enhanced by the optical near-field of a metal-coated scanning probe microscopy tip, is detected.
tip-enhanced Raman scattering spectrometry
tip-enhanced Raman scattering spectroscopy
Spectroscopy where the Raman scattering of visible laser light, by metal surfaces, where scattering is enhanced by the optical near field of a scanning tunnelling tip, under ultra-high vacuum is detected.
ultra-high vacuum tip-enhanced Raman spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from an ultraviolet laser, by a sample is detected.
Spectroscopy where infrared light is introduced into a prism at an angle exceeding the critical angle for internal reflection. This produces an evanescent wave at the reflecting surface (a surface which is transparent to infrared such as thallium bromide) on which the sample is supported. The distortion of the evanescent wave by the sample is measured producing a spectrum which is then subject to a Fourier transform.
Fourier transform attenuated total reflectance infra-red
Fourier transform attenuated total reflectance infra-red spectroscopy
Fourier transform attenuated total reflectance infrared
Fourier transform attenuated total reflectance infrared spectroscopy
Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy
Fourier transform infrared attenuated total reflectance spectroscopy
Fourier transform infrared attenuated total reflection (FTIR-ATR) spectroscopy
attenuated total reflectance Fourier transform infra-red spectroscopy
attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy
attenuated total reflectance Fourier transform infrared spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a single molecule sample adsorbed onto a metal (Au, Ag or Cu) surface is detected.
single molecule surface enhanced Raman scattering
single molecule surface enhanced Raman scattering spectroscopy
single molecule surface-enhanced Raman scattering
single molecule surface-enhanced Raman scattering spectroscopy
single molecule surface-enhanced Raman spectroscopy
An information content entity that is output by an assay.
A plot of a measured quantity against some experimental parameter.
A plot of intensity vs. Raman shift (cm-1) obtained by measuring the Raman scattering of monochromatic light from a sample.
The FTIR analysis of volatile compounds released during the measurement of the mass of a sample as a function of temperature.
thermogravimetry coupled to Fourier transform infrared spectroscopy
thermogravimetry-Fourier transform infrared spectroscopy
Spectroscopy where the Raman scattering of near-infrared radiation (radiation in the range 0.8–2 μm) is detected.
Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, at a metal (Au, Ag or Cu) electrochemcial interface is detected.
electrochemical surface enhanced Raman scattering
electrochemical surface-enhanced Raman scattering
electrochemical surface-enhanced Raman spectroscopy
Spectroscopy where vibrational optical activity from a sample absorbed onto a metal (Au, Ag or Cu) surface is measured by means of a small difference in the intensity of Raman scattering from chiral molecules of right- and left-circularly polarised incident light.
surface enhanced chiral Raman spectroscopy
surface-enhanced chiral Raman spectroscopy
A piece of apparatus which is used to generate an image of the surface of a specimen, whether by focusing reflected light onto where it can be collected or by scanning a given area of the surface.
Spectroscopy where the differential absorption and reflection of low incident angle p- and s-polarized infrared light by the surface molecules of a highly reflective or polished sample is measured. The ultra-thin layers on metal surfaces interact with the p-polarized component of light, but not with the s-polarized component.
polarization modulation infrared reflection adsorption spectroscopy
polarization modulation-infrared reflection-adsorption spectroscopy
polarization modulation infrared reflection–adsorption spectroscopy
A technique for measuring the time-resolved concentration of monomers during polymerisation reactions. The polymerisation is initiated by a single pulse of laser radiation and the monomer concentration is monitored by measuring absorbance in the near-infrared (0.8–2 μm) region.
single pulse-pulsed laser polymerization-near-infrared
single pulse–pulsed laser polymerization–near-infrared technique
A piece of apparatus used to measure a spectrum.
A piece of apparatus that consists of a laser, a beam splitter, an interferometer and a detector and is used to measure Raman spectra.
Any method where a sample mixture is first separated by column chromatography where the mobile phase is a gas, then the absorption of radiation from the infrared region by the sample is measured.
gas chromatography infrared spectrometry
gas chromatography infrared spectroscopy
gas chromatography-infrared spectrometry
gas chromatography-infrared spectroscopy
Any method where a sample mixture is first chemically degraded by heating then separated by column chromatography where the mobile phase is a gas, then the absorption of radiation from the infrared region by the sample is measured.
pyrolysis gas chromatography infrared spectrometry
pyrolysis gas chromatography infrared spectroscopy
pyrolysis-gas chromatography-infrared spectrometry
pyrolysis-gas chromatography-infrared spectroscopy
pyrolysis gas chromatography-infrared spectroscopy
Spectroscopy where the sample is first chemically degraded by heating then its absorption of radiation from the infrared region (0.78–1000 μm) is measured.
A method for generating surface-specific vibrational spectra by mixing two light beams at a surface and detecting the output beam, which has frequency equal to the sum of the two input frequencies.
sum frequency generation (SFG) spectroscopy
sum frequency generation (SFG) vibrational spectroscopy
vibrational sum-frequency generation (VSFG) spectroscopy
vibrational sum-frequency generation spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, usually from a laser, by a sample is detected. The light is collected from the non-illuminated side of the sample.
transmission Raman scattering spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, usually from a laser, by a sample (e.g. a biological cell) constrained using optical tweezers is detected.
Fourier transform infrared spectroscopy where the sample is initially transferred from a matrix to a liquid phase using a supercritical fluid.
supercritical fluid extraction-Fourier transform infrared absorption spectroscopy
supercritical fluid extraction-Fourier transform infrared spectroscopy
Spectroscopy where the absorption and reflection of low-incident-angle infrared light by the surface molecules of a highly reflective or polished sample is measured. The sample absorbs a single pulse of radiation and the spectrum obtained is subject to a Fourier transform.
Fourier transform infrared reflection absorption spectrometry
Fourier transform infrared reflection absorption spectroscopy
reflection absorption Fourier transform infra-red spectrometry
reflection absorption Fourier transform infrared spectrometry
reflection absorption Fourier transform infrared spectroscopy
reflection-absorption Fourier transform infrared spectroscopy
reflection–absorption Fourier transform infrared spectroscopy
A piece of apparatus, consisting of a laser beam (<10 μm diameter), a monochromator and a detector coupled to an optical microscope, which is used to measure Raman spectra.
A type of chemical imaging spectroscopy where an optical microscope is used to image the sample and locate a small area for spectral analysis that probes the vibrational degrees of freedom of a molecule.
Spectroscopy where the sample absorbs a single pulse of radiation from the infrared region (0.78–1000 μm), produced in a synchrotron, and the spectrum obtained is subject to a Fourier transform.
synchrotron Fourier transform infra-red absorption spectroscopy
synchrotron Fourier transform infra-red spectrometry
synchrotron Fourier transform infrared (FT-IR) spectroscopy
synchrotron Fourier transform infrared (S-FTIR)
synchrotron Fourier transform infrared spectrometry
synchrotron Fourier transform infrared spectroscopy
Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm). Spectra are collected at a rate of approx. 0.05 s per spectrum.
rapid scan infrared absorption spectroscopy
rapid-scan infrared absorption spectroscopy
Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm). Spectra are collected at a rate of approx. 0.001 s per spectrum.
ultra rapid scan infrared absorption spectroscopy
ultra-rapid-scan infrared absorption spectroscopy
Spectroscopy where the Raman scattering of monochromatic light from two lasers ('pump' and 'probe') by a sample is detected. In stimulated Raman gain spectroscopy the probe laser has a lower frequency than the pump laser.
Spectroscopy where the Raman scattering of monochromatic light from two lasers ('pump' and 'probe') by a sample is detected. In stimulated Raman gain spectroscopy the pump laser has a lower frequency than the probe laser.
Spectroscopy where the Raman scattering of monochromatic light by a sample is detected. Two lasers ('pump and 'probe') are mixed and focused on the sample cell. When the frequency difference between the lasers corresponds to a Raman transition, an acoustic signal (a sound wave produced by an increase in pressure) is generated and detected by a sensitive microphone.
Spectroscopy where the Raman scattering of monochromatic light, from two lasers ('pump' and 'probe') by a sample is detected. The molecules in the sample are ionised using an ultraviolet laser in order to improve the signal-to-noise ratio of the spectrum.
ionization-detected stimulated Raman spectroscopy
ionisation-detected stimulated Raman spectroscopy
Spectroscopy where the Raman scattering of monochromatic light, from a two-colour laser, by a sample is detected.
higher order Raman spectral excitation studies
higher-order Raman spectral excitation spectroscopy
higher-order Raman spectral excitation studies
Spectroscopy where the Raman scattering of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range by a sample is detected. The energy of the incoming laser is adjusted such that it or the scattered light does not coincide with an electronic transition in the sample.
A type of Raman spectroscopy where the spectral signal is enhanced by pre-concentration of the sample. Drops of the sample in solution are deposited onto a surface and dry in a 'coffee-ring' pattern. Spectra are then obtained from this ring of excess of material, after evaporation has completed.
drop coating deposition Raman (DCDR) spectroscopy
drop-coating deposition Raman spectroscopy
drop-coating-deposition Raman spectroscopy
drop coating deposition Raman spectroscopy
Spectroscopy where the sample absorbs a single pulse of polarised radiation from the infrared region (0.78–1000 μm) and the spectrum obtained is subject to a Fourier transform.
polarised Fourier transform infra-red absorption spectroscopy
polarised Fourier transform infra-red spectrometry
polarised Fourier transform infrared (FT-IR) spectroscopy
polarised Fourier transform infrared spectrometry
polarised Fourier transform infrared spectroscopy
polarized Fourier transform infra-red absorption spectroscopy
polarized Fourier transform infra-red spectrometry
polarized Fourier transform infrared (FT-IR) spectroscopy
polarized Fourier transform infrared spectrometry
polarized Fourier transform infrared spectroscopy
Spectroscopy where the sample is first chemically degraded by heating then its absorption of radiation from the infrared region (0.78–1000 μm) is measured and the spectrum obtained is subject to a Fourier transform.
pyrolysis Fourier transform infrared spectroscopy
Spectroscopy where the sample absorbs a single pulse of polarised radiation from the infrared region (0.78–1000 μm) and the spectrum obtained, recorded as a function of time, is subject to a Fourier transform.
time-resolved polarised Fourier transform infra-red absorption spectroscopy
time-resolved polarised Fourier transform infra-red spectrometry
time-resolved polarised Fourier transform infrared (FT-IR) spectroscopy
time-resolved polarised Fourier transform infrared spectrometry
time-resolved polarised Fourier transform infrared spectroscopy
time-resolved polarized Fourier transform infra-red absorption spectroscopy
time-resolved polarized Fourier transform infra-red spectrometry
time-resolved polarized Fourier transform infrared (FT-IR) spectroscopy
time-resolved polarized Fourier transform infrared spectrometry
time-resolved polarized Fourier transform infrared spectroscopy
Spectroscopy where the sample absorbs a single pulse of radiation from the infrared region (0.78–1000 μm) and the spectrum obtained is subject to a fast Fourier transform.
fast Fourier transform infrared spectroscopy
Spectroscopy where the transmission of infrared radiation (0.78–1000 μm) through a sample is detected.
Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 μm). The infrared beam is passed through a diffraction grating which separates (or disperses) the wavelength of the light and directs each wavelength individually through a slit to a detector.
Spectroscopy where the Raman scattering of monochromatic light, from a visible laser, by a sample adsorbed onto a metal (Au, Ag or Cu) surface is detected. The energy of the incoming laser is adjusted such that it or the scattered light does not coincide with an electronic transition within the sample.
surface-enhanced non-resonance Raman spectroscopy
Any method that measures the amount of light that a substance scatters at certain wavelengths, incident angles, and polarization angles.
A method for generating surface-specific vibrational spectra by mixing two light beams (visible and IR) at a surface and detecting the output beam, which has frequency equal to the sum of the two input frequencies.
infrared-visible sum-frequency generation (SFG) spectroscopy
infrared-visible sum-frequency generation spectroscopy
infrared–visible sum-frequency generation spectroscopy
The measurement of the temperature difference between the sample and a reference material during the measurement of the mass of the sample as a function of temperature.
differential thermal analysis and thermal gravimetry analysis
differential thermalgravimetric analysis
thermogravimetric and differential thermal analyses
thermogravimetry coupled to differential thermal analysis
thermogravimetry-differential thermal analysis
A method for generating surface-specific electronic spectra by mixing two light beams at a surface and detecting the output beam, which has frequency equal to the sum of the two input frequencies.
electronic sum frequency generation spectroscopy
electronic sum-frequency generation (ESFG) spectroscopy
electronic sum-frequency generation spectroscopy
Spectroscopy where the sample absorbs radiation from the infrared region (0.78–1000 \μm) over two frequency axes. Cross peaks in the spectrum encode the couplings and orientation between vibrations.
two-dimensional infrared (2D-IR) spectroscopy
A piece of apparatus that is used to measure a physical quantity.
Diffuse reflectance infrared Fourier transform spectroscopy of a sample that is carried out in the environment where the sample might be used.
For example, the sample might be a catalyst, so during those catalytic processes.
in situ diffuse reflectance infrared Fourier transform spectroscopy
Experimental method output expressing the contribution of one constituent to the composition of a mixture.
based heavily on https://doi.org/10.1351/goldbook.C01222
Experimental method output expressing a concentration in terms of the mass of a constituent divided by the volume of the mixture.
based heavily on https://doi.org/10.1351/goldbook.M03713
Experimental method output expressing a concentration in terms of the amount of a constituent divided by the volume of the mixture.
based heavily on https://doi.org/10.1351/goldbook.A00295
Experimental method output expressing a concentration in terms of the volume of a constituent divided by the volume of the mixture.
Experimental method output expressing a concentration in terms of the number of entities of a constituent divided by the volume of the mixture.
based heavily on https://doi.org/10.1351/goldbook.N04260
A directive information entity which specifies a device and its settings for use within a plan specification.
device specification
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
information carrier
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
A quality of an information bearer that imparts the information content
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
model number
A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
Person: Alan Ruttenberg
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
10 feet. 3 ml.
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
person:Allyson Lister
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
person:Chris Stoeckert
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Clint Dowland
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
A settings datum is a datum that denotes some configuration of an instrument.
2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
setting datum
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
PERSON:Chris Stoeckert
PERSON:James Malone
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
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.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
text
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
publication
journal article, newspaper story, book, etc.
A document that is the output of a publishing process.
PERSON: Jie Zheng
published document
Revisit the term in Octorber 2020. Improve the defintion.
A scalar measurement datum that is the result of measurement of length quality
length measurement datum
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
A scalar measurement datum that is the result of measurement of mass quality
mass measurement datum
A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
Person: Jie Zheng
VEuPathDB
publishing process
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
centrally registered identifier
PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
Justin Whorton
centrally registered identifier registry
identifier
An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
Mathias Brochhausen
proper name
Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
dubbing process
naming
identifier creating process
An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
code map
code system
codeset
coding system
controlled vocabulary
Code sets might include non-entities/things (e.g. missing thumbs).
Does not imply absence vs. presence of any taxonomy.
Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
The information content entities do not denote each other.
code set
ontology module
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
base ontology module
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
editors ontology module
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
main release ontology module
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
bridge ontology module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
import ontology module
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
import file
subset ontology module
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
ontology slim
subset ontology
curation subset ontology module
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
analysis ontology module
An ontology module that is intended for usage in analysis or discovery applications.
analysis subset ontology module
single layer ontology module
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
ribbon subset
single layer subset ontology module
exclusion subset ontology module
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
antislim
external import ontology module
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
external import
species subset ontology module
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
taxon subset
reasoned ontology module
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
generated ontology module
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
template generated ontology module
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
taxonomic bridge ontology module
ontology module subsetted by expressivity
obo basic subset ontology module
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports
ontology module subsetted by OWL profile
EL++ ontology module
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
OBI branch derived
Could add specific objective specification
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
measuring
scientific observation
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
study
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
An assay that produces a picture of an entity.
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
GROUP: Role Branch
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
planning
magnify function
A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
excitation function
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
image acquisition function
An image acquisition function is a function to acquire an image of a material
An image creation device is a device which captures a digitized image of an object
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
A planned process with the objective to produce a processed material which will have a function for future use.
A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
center value
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
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.
A material entity that has the material sample role
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
A person or organization that has a manufacturer role.
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
A planned process that captures an image of an object.
investigation assay specification
Some examples of Project Method are Sequence, Array, Mass Spectrometry
A plan specification which indicates the assay type used to obtain data.
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Person: Chris Stoeckert, Jie Zheng
Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy.
An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye.
animal
fungus
plant
virus
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.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
PERSON: James Malone
center calculation objective
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
center calculation data transformation
A center calculation data transformation is a data transformation that has objective of center calculation.
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
The number of entities of this type that are part of the whole organism.
This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
A 1-D extent quality which is equal to the distance between two points.
Length often refers to the longer or longest dimension of an object, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism.
A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A physical quality of the thermal energy of a system.
A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite.
Width often refers to the dimension that is greater than the extent in only one of the other two orthogonal dimensions, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
A physical quality which is equal to the distance between repeating units of a wave pattern.
The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
extra or missing physical or functional parts
A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension.
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed laterally.
An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis.
A quality of an entity that can be represented numerically, including anything that can be counted, measured, or given a numerical value.
a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
Alejandra Gonzalez-Beltran
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
statistic
signal to noise ratio is a measurement datum comparing the amount of meaningful, useful or interesting data (the signal) to the amount of irrelevant or false data (the noise). Depending on the field and domain of application, different variables will be used to determinate a 'signal to noise ratio'. In statistics, the definition of signal to noise ratio is the ratio of the mean of a measurement to its standard deviation. It thus corresponds to the inverse of the coefficient of variation
adapted from Wikipedia: http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition last accessed: 2013-10-18
S/N
SNR
signal to noise ratio
A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
review formal definition as both numerator and denominator should be of the same type, not just some data item
adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7
"A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia]
"A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG]
"A unit which is a standard measure of the mass of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia]
"A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution." [UOC:GVG]
"A concentration unit which is a standard measure of the number of moles of a given substance per kilogram of solvent." [UOC:GVG]
"A unit of concentration which highlights the chemical nature of salts." [Wikipedia:Wikipedia]
"A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution." [Webmd:Webmd]
"A concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline]
"A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG]
"A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST]
"A concentration unit which a measure of viable bacterial numbers in a given volume." [Wikipedia:Wikipedia]
"A concentration unit which a measure of plaque forming units in a given volume." [UOC:GVG]
"A concentration unit which is a standard measure of the amount of a substance in a given container." [UOC:GVG]
"A unit which is equal to one microgram per disk, where a disk is some physical surface/container upon which the substance is deposited." [UOC:MD]
"A unit which is equal to one nanomole per disk, where a disk is some physical surface/container upon which the substance is deposited." [UOC:MD]
"A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered to a recipient subject, expressed in terms of the size of the subject." [UO:PC]
"A unit of cell concentration which is equal to one cell in a volume of 1 microliter." [UO:GVG]
"A unit of cell concentration which is equal to 1 cell in a well or discrete container of arbitrary volume." [UO:PC]
"A concentration unit which is a standard measure of the amount of radioactivity in a given volume." [UO:GVG]
"A unit of radioactivity concentration which is equal to one curie in a volume of 1 liter." [UO:GVG]
"A unit of radioactivity concentration which is equal to one micro curie in a volume of 1 liter." [UO:GVG]
A concentration unit which denotes the minimum amount of a substance in a solution that still yields a positive reading, as determined by serial dilution.
titer
colony forming unit per milliliter based unit
plaque forming unit per milliliter based unit
A setting datum that specifies the needed settings of a spectrometer used in vibrational spectroscopy.
vibrational spectrometer configuration specification
The set of meassured configuration characteristics of a Raman spectrometer, like the operating temperature of a Raman spectrometer.
A device setting that represents the measured or set physical qualities which make up the configuration state of a Raman spectrometer at the time of a measurement (e.g. operating temperature, exitation wavelength, groove density, ...).
Raman spectrometer configuration
A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed.
This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
integration period setting
integration time
integration time setting
A setting datum that specifies the preamplifier gain in CCD sensors.
This class should better be defined in a more general device ontology.
preamplifier gain setting
A setting datum that specifies the horizontal shift speed in CCD sensors.
horizontal shift speed setting
A setting datum that specifies the vertical shift speed in CCD sensors.
vertical shift speed setting
A setting datum that specifies the operating temperature of a device.
device temperature setting
A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio.
This class might better be defined in a more general device ontology.
number of acquisitions
number of accumulations
A setting datum that specifies the binning read mode of a device with a CCD sensor.
CCD sensor binning read mode setting
A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter.
temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541)
groove frequency
groove density
A setting datum that specifies the number of grooves in a diffraction grating device.
grating
grating setting
groove density setting
A device that is an optical component with a periodic structure that diffracts light into several beams travelling in different directions (i.e. different diffraction angles)
diffraction grating
A physical quality of the light source that is used used to excite a system to a higher energy state.
This class is not needed, as PATO:wavelength is sufficient, if this quality of a Raman device is really needed.
deprecated_excitation wavelength
A setting datum that specifies the wavelength of an electromagnetic radiation source (e.g. a laser) which has the function to excite the energy state of a target material.
excitation wavelength setting
A setting datum that specifies the magnification factor of the objective collecting the scattered light.
magnification
magnification setting
objective magnification factor setting
A setting datum that specifies the upper boundary of the spectral window range utilized during the acquisition of spectroscopic data.
It needs to be determined, if this is also part of another kind of spectrum, such as a vibrational spectrum in general. We also need to decide, if we need to also model the terms window size and window center, from which this term is derived.
acquisition band maximum
spectral window range maximum
A setting datum that specifies the lower boundary of the spectral window range utilized during the acquisition of spectroscopic data.
acquisition band minimum
spectral window range minimum
200 mW
A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components.
excitation light power
light power on the sample
The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot.
incident light power datum
A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded.
See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402
ROI
imaging region of interest
region of interest
1 mm
A setting datum that specifies the width (length in the X direction) of the region of interest.
ROI horizontal length
ROI width
region of interest width = (point distance X) * (number of measurements X)
region of interest width
0.5 mm
A setting datum that specifies the height (length in the Y direction) of the region of interest.
ROI breadth
ROI lateral length
region of interest breadth = (point distance Y) * (number of measurements Y)
region of interest breadth
0.1 mm
A setting datum that specifies the depth (length in the Z direction) of the region of interest.
ROI depth
ROI vertical length
region of interest depth = (point distance Z) * (number of measurements Z)
region of interest depth
20 µm
A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy.
sampling pace in the X direction
sampling step in the X direction
voxel distance in the X direction
point distance X = (region of interest width) / (number of measurements X)
point distance X
10 µm
A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy.
sampling pace in the Y direction
sampling step in the Y direction
voxel distance in the Y direction
point distance Y = (region of interest breadth) / (number of measurements Y)
point distance Y
A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy.
axial mapping distance
sampling pace in the Z direction
sampling step in the Z direction
vertical mapping distance
voxel distance in the Z direction
point distance Z = (region of interest depth) / (number of measurements Z)
point distance Z
A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width.
number of points in the X direction
number of points per line
number of measurements X = (region of interest width) / (point distance X)
number of measurements X
A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth.
number of lines per layer
number of points in the Y direction
number of measurements = (region of interest breadth) / (point distance Y)
number of measurements Y
A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth.
number of layers per acquisition
number of points in the Z direction
number of measurements Z = (region of interest depth) / (point distance Z)
number of measurements Z
A measurement datum that is obtained from a calibrated and ready Raman spectrometer and prior to be submitted to any mathematical modification. The only corrections on the data shall be the one associated with the spectrometer. The data will assign pixels readouts with nm as per calibration of the spectrometer and a.u. as intensity readout but will not be corrected in relationship of the incident monochromatic beam.
raw Raman data
Raman raw data
The light was focused onto the embedded sample using a 100× objective with a numerical aperture of 0.9, resulting in a diffraction-limited in-plane laser spot size of <1 μm.
A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located.
possible equivalents in other terminologies: http://purl.obolibrary.org/obo/NCIT_C181921 & https://w3id.org/reproduceme#LensNA
numerical aperture
lens numerical aperture
A data item that is obtained by processing raw Raman data.
primary Raman data
A physical quality of a measurement device that expresses (realizes) the device's capacity to distinguish between two distinct but closely related measurements of the same physical quality or type, often quantified as the smallest detectable difference (resolution interval) between measured values.
This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far.
resolution
A data item that quantifies a resolution, by representing the minimum measurable difference between two measurements of the same physical quality or type, such that the measurements can be distinguished as different.
resolution interval
A ratio that quantifies the ability of a measurement device to distinguish between small differences in measurement values, expressed as the ratio between a typical measurement datum and the corresponding resolution interval.
resolution power
A resolution interval that quantifies the minimum distance between two points such that they can be considered two separate points in a given microscope under specific experimental parameters.
spatial resolution interval
A spatial resolution interval that quantifies the minimum angular separation between two points on a plane orthogonal to the light ray, expressed as an angle centered in the lens (Formula: δθ = 1.22 * λ / D).
$δθ = 1.22cdotλ/D$
lateral resolution interval as angle
A spatial resolution interval that quantifies the minimum linear separation between two points on a plane orthogonal to the light ray, expressed as the distance from the center of the optical spot (Formula: δr = 0.61 * λ / NA).
$δr = 0.61cdotλ/NA$ (Abbe formula, derived from the Rayleigh criterion with the Kirchhoff, Debye and paraxial approximation) $= 1.22 λcdot(f/sharp)$
lateral resolution interval as length
A spatial resolution interval that quantifies the minimum measurable separation between two points along the axis of propagation of the light ray, expressed as a linear distance (Formula: δz = 2 ⋅ n ⋅ λ / NA²).
$δz = 2cdot ncdotλ/NA²$
axial resolution interval as length
A resolution interval that quantifies the minimum separation between two narrow peaks in a spectrum such that they can be distinguished as two separate peaks.
spectral resolution interval
A spectral resolution interval that quantifies the minimum separation between two wavelengths such that they can be distinguished as different (Formula: δλ = λ / (n * N)).
$δλ = λ / (ncdot N) = RFcdot Δλcdot WS / n$
spectral resolution interval as wavelength
A spectral resolution interval that quantifies the minimum separation between two wavenumbers such that they can be distinguished as different (Formula: δν~ = δλ / λ²).
$δbarν$
spectral resolution interval as wavenumber
A spectral resolution interval that quantifies the minimum separation between two frequencies such that they can be distinguished as different (Formula: δν = c * δν~ = c * δλ / λ²).
$δν$
spectral resolution interval as frequency
A spectral resolution interval that quantifies the minimum separation between two energy levels such that they can be distinguished as different (Formula: δE = h * δν = h * c * δν~ = h * c * δλ / λ²).
$δE$
spectral resolution interval as energy
A resolution interval that quantifies the minimum difference in irradiated energy, often coded as gray level in a grayscale or look-up-table (LUT).
radiometric resolution interval
A resolution interval that quantifies the temporal separation between two measurements or frames, often expressed as the inverse of the frame rate. In techniques where temporal resolution is not directly derived from frame rate, it quantifies the minimum temporal interval between two resolvable events.
In techniques where the temporal resolution is not given directly from a temporal distance between subsequent measurements (e.g., pulsed time resolved pump-probe techniques), it can be used more properly as defined above
temporal resolution interval
A spatial resolution interval that quantifies the theoretical maximum spatial resolution achievable by an optical system, constrained by the diffraction of light.
The Abbe diffraction limit, is defined as λ/ (2 NA) in which λ is the wavelength of the illuminating light and NA is the numerical aperture.
diffraction limit
A setting datum that specifies the middle wavelength/wavenumber of a spectrum, equal to the average of the maximum and minimum of the spectral window range utilized during the acquisition of spectroscopic data. It corresponds to the optimal alignment or centering of the spectrometer to ensure that the most relevant spectral features are captured effectively within the defined acquisition range.
spectral window center
VIBSO Working Group
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
obsolete_core
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality.
This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore).
The assay A is planned to produce as a specified output the data item D which is a specific kind of information about the material entity M, which has the evaluant role R that gets realized in this planned observation process. This example instance is part of the ontology to demonstrate the OBI assay pattern. The type and number of relations between this instance and other example instances are based on the subclassOf and equivalentTo axioms asserted on OBI's assay.
The laser wavelength of _Raman_Spectrometer_1 which is a general attribute (aka quality/characteristic) of _Raman_Spectrometer_1. The quantity of this attribute is represented by the _Wavelength_Value_Specification_1.
_Laser_Wavelength_1
The Raman spectrometer that is used in _RamanAssay_1.
_Raman_Spectrometer_1
The Raman spectroscopy in which _Sample_1 is being assayed according to _Raman_Spectroscopy_Method_1 in order to achieve _Raman_Spectrum_Objective_1.
_Raman_Spectroscopy_1
The information that indicates the type of _Raman_Spectroscopy_1 by describing its method, specifying its inputs and outputs, as well as the necessary steps and actions that have to be taken in order to achieve _Raman_Spectrum_Objective_1. For the sake of keeping it simple, not all parts of this assay specification will be provided as assertions on this example.
_Raman_Spectroscopy_Method_1
The Raman spectrum (the data outputed by _RamanSpectrometer_1 NOT the plot) of _Sample_1 created by _RamanAssay_1. Currently classified as an IAO:'data item' as a more specific subclass thereof has yet to be minted in VIBSO (see alos: https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77)
_Raman_Spectrum_1
The information that specifies the intended outcome of _Raman_Spectroscopy_1 to be the creation of a Raman Spectrum.
_Raman_Spectrum_Objective_1
The material entity that is being evaluated in _RamanAssay_1.
_Sample_1
The information that determines the wavelength of the laser of _Raman_Spectrometer_1 which is used to excite the sample. This information gets encoded by the _Laser_Value_Specification_1.
_Wavelength_Setting_Info_1
The encoding of the value determined by _Wavelength_Setting_Info_1, which consists of the unit label and the literal value of the laser wavelength of _Raman_Spectrometer_1.
_Wavelength_Value_Specification_1
German National Library of Science and Technology Hannover
Technische Informationsbibliothek (TIB)
German National Metrology Institute
Physikalisch-Technische Bundesanstalt (PTB)
"A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST]
"A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France." [BIPM:BIPM, NIST:NIST]
"A length unit which is equal to one hundredth of a meter or 10^[-2] m." [NIST:NIST]
"A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST]
"A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST]
"A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST]
"A length unit which is equal to 10 [-10] m." [NIST:NIST]
"A length unit which is equal to 10^[-12] m." [NIST:NIST]
"A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST]
"A mass unit which is equal to one thousandth of a gram or 10^[-3] g." [UOC:GVG]
"A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG]
"A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG]
"A mass unit which is equal to 10^[-12] g." [UOC:GVG]
"A mass unit which is equal to 10^[-15] g." [NIST:NIST]
"A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L)." [UOC:GVG]
"A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M." [UOC:GVG]
"A unit of molarity which is equal to one millionth of a molar or 10^[-6] M." [UOC:GVG]
"A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M." [UOC:GVG]
"A unit of molarity which is equal to 10^[-12] M." [UOC:GVG]
"A unit of concentration which expresses a concentration of a solution of 1 mole per kilogram of solvent (mol/kg)." [UOC:GVG]
"A molality unit which is equal to one thousandth of a molal or 10^[-3] m." [UOC:GVG]
"A molality unit which is equal to one millionth of a molal or 10^[-6] m." [UOC:GVG]
"A molality unit which is equal to one thousandth of one millionth of a molal or 10^[-9] m." [UOC:GVG]
"A molality unit which is equal to 10^[-12] m." [UOC:GVG]
"A unit of molarity which is equal to 10^[-15] M." [UOC:GVG]
"A unit of concentration which is one gram equivalent of a solute per liter of solution. A gram equivalent weight or equivalent is a measure of the reactive capacity of a given molecule." [Wikipedia:Wikipedia]
"A concentration unit which denotes the number of moles of solute as a proportion of the total number of moles in a solution." [Wikipedia:Wikipedia]
"A molar mass unit which is equal to one kilogram of mass of one mole of chemical element or chemical compound." [NIST:NIST]
"A molar mass unit which is equal to one gram of mass of one mole of chemical element or chemical compound." [NIST:NIST]
"A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [Wikipedia:Wikipedia]
"A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [UOC:GVG]
"A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [UOC:GVG]
"A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one milliliter." [Webmd:Webmd]
"A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one liter." [UOC:GVG]
"A concentration unit which is a standard measure of the mass of a substance in a given volume (density)." [Wikipedia:Wikipedia]
"A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia]
"A unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline]
"A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter." [NIST:NIST]
"A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter." [NIST:NIST]
"A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution." [NIST:NIST]
"A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [NIST:NIST]
"A colony forming unit which a measure of viable bacterial numbers in one milliliter." [Wikipedia:Wikipedia]
"A concentration unit which a measure of plaque forming units in one milliliter." [UOC:GVG]
"An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia]
"A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia]
"A unit per milliliter unit which is equal to one thousandth of a unit of an agreed arbitrary amount per one milliliter." [UOC:GVG]
"A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC]
"A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per square meter of surface area of the recipient subject." [UO:PC]
"A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered over time to a recipient subject, expressed in terms of the size of the subject." [UO:PC]
"A dosage unit which is equal to 1 milligram per day of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC]
"A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]
"A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]
"A specific concentration unit which is equal to 1 micromole in a given volume of one thousandth of a cubic meter." [NIST:NIST]
"A specific concentration unit which is equal to 1 micromole of a given substance per kilogram of solvent." [UOB:LKSR]
"A mass unit which is equal to 1/12 the mass of 12C" [Wikipedia:Wikipedia]
"A length unit which is equal to 0.0254 metres." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.0254 millimetres." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.3048 metres, or 12 inches." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.9144 metres, or 3 feet." [Wikipedia:Wikpiedia]
"A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards." [Wikipedia:Wikpiedia]
"A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains." [Wikipedia:Wikpiedia]
"A length unit which is equal to 1,609.344 metres, or 8 furlongs." [Wikipedia:Wikpiedia]
"A length unit which is equal to 3 miles, or 4,828.032 metres" [Wikipedia:Wikpiedia]
"A maritime length unit is one used primarily at sea." [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 6.08 feet, or 1.853184 metres" [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 608 feet, 100 fathoms, or 185.3184 metres" [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 6,080 feet, 10 cables, or 1,853.184 metres" [Wikipedia:Wikpiedia]
"An imperial mass unit which is equivalent to 64.798,91 milligrams." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 1.771,845,195,3125 grams, or 1/256 of 1 pound." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 28.349,523,125 grams, or 1/16 of 1 pound." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 453.592,37 grams." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 6,350.293,18 grams, or 14 pounds." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 12.700,586,36 kilograms, or 28 pounds." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 50.802,345,44 kilograms, 112 pounds, or 8 stone." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 1,016.046,9088 kilograms, or 2,240 pounds." [Wikipedia:Wikipedia]
"A length unit which is equal to one thousand meters." [UOB:LKSR]