Domain ontology for thin-film solar cells and related tandem solar cells. Contains relevant terms and concepts from BFO, IAO, UO, PATO, OBI, CHMO. Ontology for thin-film solar cells (TFSCO) The Ontology for thin-film solar cells strives to build a collection of experimental parameter from the sytnhesis- and measurement processes of thin-film solar cells. 2022-08-01T00:00:00 tfsco release, latest changes: 2025-08-25 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source 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 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from 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. Chris Mungall expand assertion to An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object 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:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label 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 elucidation 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 #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg 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 Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. Chris Mungall Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?x owl:disjointWith [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . } never in taxon A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. non-overlapping with shares no parts with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; owl:disjointWith [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . } mutually spatially disjoint with https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. taxonomic class assertion S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] ambiguous for taxon S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. https://orcid.org/0000-0002-6601-2165 This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost dubious for taxon S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S https://orcid.org/0000-0002-6601-2165 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon defined by inverse An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. annotation property cardinality A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a class A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property logical macro assertion on an annotation property An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. dispositional interpretation 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. shares no connection with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) has no connections with inherited annotation property Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) curator guidance link brain always_present_in_taxon 'Vertebrata' forelimb always_present_in_taxon Euarchontoglires S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. never lost in always present in taxon This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. temporal logical macro assertion on a class measurement property has unit has start time value has end time value Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. start, days post fertilization Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. end, days post fertilization Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. start, years post birth Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 end, years post birth Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. start, months post birth Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 end, months post birth Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. month of gestation A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process has developmental stage marker Count of number of days intervening between the start of the stage and the time of coitum. For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) start, days post coitum Count of number of days intervening between the end of the stage and the time of coitum. end, days post coitum start, weeks post birth end, weeks post birth If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p is asymmetric relational form of process class http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p is symmetric relational form of process class http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process is relational form of process class http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y Chris Mungall is indirect form of logical macro assertion on an axiom If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom 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 annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. is relational form of a class A shortcut relationship that holds between two entities based on their identity criteria logical macro assertion involving identity A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. in approximate one to one relationship with x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" is approximately equivalent to 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is opposite of x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). is indistinguishable from evidential logical macro assertion on an axiom A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. axiom has evidence A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. axiom contradicted by evidence In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion is representative IRI for equivalence set OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. cjm nominally disjoint with Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" cjm 2018-03-13T23:59:29Z is directional form of cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of part-of is homeomorphic for independent continuants. R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. cjm 2018-10-21T19:46:34Z R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. is homeomorphic for pg 2020-09-22T11:05:29Z valid_for_go_annotation_extension pg 2020-09-22T11:05:18Z valid_for_go_gp2term pg 2020-09-22T11:04:12Z valid_for_go_ontology pg 2020-09-22T11:05:45Z valid_for_gocam eco subset A summary of the resource. Abstract An entity responsible for making contributions to the resource. Contributor Date of creation of the resource. Recommended practice is to describe the date, date/time, or period of time as recommended for the property Date, of which this is a subproperty. Date Created An entity responsible for making the resource. Recommended practice is to identify the creator with a URI. If this is not possible or feasible, a literal value that identifies the creator may be provided. Creator A person or organization owning or managing rights over the resource. Recommended practice is to refer to the rights holder with a URI. If this is not possible or feasible, a literal value that identifies the rights holder may be provided. Rights Holder A name given to the resource. Title The preferred namespace prefix to use when using terms from this vocabulary in an XML document. Preferred Namespace Prefix Issue Tracker subset_property has_narrow_synonym in_subset has documentation is defined by is defined by This is an experimental annotation The property that identifies the version IRI of an ontology. versionIRI 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/ 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 http://www.obofoundry.org/ro/#OBO_REL: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. 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/ 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 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 realized in 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 realizes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process has 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. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about 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. Alan Ruttenberg is quality measurement of relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of 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 Person:Alan Ruttenberg is quality measured as A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. Person:Alan Ruttenberg Person:Bjoern Peters is quality specification of inverse of the relation of is quality specification of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg Person:Bjoern Peters quality is specified as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum has_specified_input has_specified_input see is_input_of example_of_usage 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. 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 PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of 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. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output 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. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective 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. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective objective_achieved_by 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. OBI OBI objective_achieved_by inheres in this fragility is a characteristic of this vase 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. 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 characteristics of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of 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 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 http://www.obofoundry.org/ro/#OBO_REL:has_participant 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). 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 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 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. 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 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. 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 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. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces has output An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c Chris Mungall has intermediate product has intermediate a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel produced by provides input for true transferring device A transferring device is a device that is designed to transfer material. [Allotrope] transferring device nozzle A nozzle is a transferring device consisting of jet port with an opening for regulating and/or directing the flow of fluid. [Allotrope] nozzle Additive is a role of material that is added to a mixture in order to achieve a supportive purpose. [Allotrope] additive role The planned process of finding the number of elements in a finite set of objects. Mathias Brochhausen http://en.wikipedia.org/wiki/Counting The planned process of finding the number of elements in a finite set of objects. counting molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity chemical entity UniProt A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 atom chebi_ontology atome atomo atoms atomus element elements CHEBI:33250 atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements ChEBI A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. chebi_ontology Chemische Substanz CHEBI:59999 chemical substance Chemische Substanz ChEBI A pure substance is a chemical substance composed of multiple molecules, which are all of the same kind. chebi_ontology Reine Substanz CHEBI:60003 pure substance Reine Substanz ChEBI A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. chebi_ontology Mischung CHEBI:60004 mixture Mischung ChEBI A mixture that is homogeneous, made up of at least two scattered molecular aggregates, one playing the role of solute and the other playing the role of solvent. PMID:18289311 Wikipedia:Solution chebi_ontology chemical solution CHEBI:75958 solution PMID:18289311 Europe PMC chemical solution ChEBI Any technique where a microscope is used to view a small object (or specimen) by producing a magnified image. FIX:0000005 CHMO:0000067 microscopy Any technique where a microscope is used to view a small object (or specimen) by producing a magnified image. https://orcid.org/0000-0002-0640-0422 Any method for determining structure where the change in direction or intensity of reflected radiation or particles is detected. CHMO:0000208 reflection method Any method for determining structure where the change in direction or intensity of reflected radiation or particles is detected. https://orcid.org/0000-0002-0640-0422 Any method for determining structure by directing a beam of particles or X-rays onto an extremely flat surface and measuring the intensity of the reflected radiation as a function of angle. reflectivity CHMO:0000209 reflectometry Any method for determining structure by directing a beam of particles or X-rays onto an extremely flat surface and measuring the intensity of the reflected radiation as a function of angle. https://orcid.org/0000-0002-0640-0422 A method for determining structure by directing a beam of X-rays at an extremely flat surface and measuring the intensity of the reflected X-rays as a function of angle. X-ray reflectometry is used to determine the structure of thin-films. X-ray reflectivity XRR CHMO:0000219 X-ray reflectometry A method for determining structure by directing a beam of X-rays at an extremely flat surface and measuring the intensity of the reflected X-rays as a function of angle. X-ray reflectometry is used to determine the structure of thin-films. https://orcid.org/0000-0002-0640-0422 The study of the interaction of a sample with radiation or particles for measurement or detection. spectrometry CHMO:0000228 spectroscopy The study of the interaction of a sample with radiation or particles for measurement or detection. https://doi.org/10.1351/goldbook.S05848 An information content entity that is output by an assay. experimental data CHMO:0000793 assay output An information content entity that is output by an assay. https://orcid.org/0000-0001-5985-7429 https://orcid.org/0000-0002-0640-0422 A plot of a measured quantity against some experimental parameter. spectra spectrum plot CHMO:0000800 spectrum A plot of a measured quantity against some experimental parameter. https://orcid.org/0000-0001-5985-7429 A method used to synthesise a sample. CHMO:0001301 synthesis method A method used to synthesise a sample. https://orcid.org/0000-0002-0640-0422 The process of the settling of particles (atoms or molecules) from a solution, suspension or vapour onto a pre-existing surface, resulting in the growth of a new phase. deposition CHMO:0001310 sample deposition The process of the settling of particles (atoms or molecules) from a solution, suspension or vapour onto a pre-existing surface, resulting in the growth of a new phase. https://orcid.org/0000-0002-0640-0422 deposition A thin-film deposition technique based on the sequential reaction of gaseous precursors at a surface to produce a monolayer ALD atomic-layer deposition CHMO:0001311 atomic layer deposition A thin-film deposition technique based on the sequential reaction of gaseous precursors at a surface to produce a monolayer https://orcid.org/0000-0002-0640-0422 The process of the settling of particles (atoms or molecules) from a solution or suspension onto a pre-existing surface, resulting in the growth of a new phase. chemische Lösungsabscheidung CBD CSD chemical bath deposition chemical deposition chemical-bath deposition chemical-solution deposition CHMO:0001312 Chemical solution deposition The process of the settling of particles (atoms or molecules) from a solution or suspension onto a pre-existing surface, resulting in the growth of a new phase. https://orcid.org/0000-0002-0640-0422 The process of the settling of (nm sized) particles from a colloidal suspension onto a pre-existing surface, resulting in ceramic materials. The desired solid particles (e.g. metal alkoxides) are suspended in a liquid, forming the 'sol', which is deposited on a substrate by spinning, dipping or coating, or transferred to a mould. The particles in the sol are polymerised by partial evaporation of the solvent, or addition of an initiator, forming the 'gel', which is then heated at high temperature to give the final solid product. colloid process colloidal processing sol-gel method sol-gel process sol-gel processing solgel method solgel process solgel processing sol–gel processing CHMO:0001313 sol–gel method The process of the settling of (nm sized) particles from a colloidal suspension onto a pre-existing surface, resulting in ceramic materials. The desired solid particles (e.g. metal alkoxides) are suspended in a liquid, forming the 'sol', which is deposited on a substrate by spinning, dipping or coating, or transferred to a mould. The particles in the sol are polymerised by partial evaporation of the solvent, or addition of an initiator, forming the 'gel', which is then heated at high temperature to give the final solid product. https://orcid.org/0000-0002-0640-0422 A synthesis method where the substrate is exposed to one or more volatile precursors, which react or decompose on the surface to produce a deposit. CVD CVD (chemical vapour deposition) synthesis chemical vapor deposition chemical-vapor deposition chemical-vapour deposition CHMO:0001314 chemical vapour deposition A synthesis method where the substrate is exposed to one or more volatile precursors, which react or decompose on the surface to produce a deposit. https://orcid.org/0000-0002-0640-0422 A synthesis method where the substrate is exposed to volatile precursors (one of which is an organometallic compound) which react or decompose on the surface to produce a deposit. MOCVD OMCVD metal-organic chemical vapor deposition metal-organic chemical vapour deposition metalorganic CVD metalorganic chemical vapor deposition metalorganic chemical vapour deposition organometallic chemical vapor deposition organometallic chemical vapour deposition CHMO:0001324 metal–organic chemical vapour deposition A synthesis method where the substrate is exposed to volatile precursors (one of which is an organometallic compound) which react or decompose on the surface to produce a deposit. https://orcid.org/0000-0002-0640-0422 A synthesis method where the substrate is exposed to one or more volatile precursors, in the presence of a plasma (a partially ionised gas, containing free electrons), which react or decompose on the surface to produce a deposit. The plasma enhances the rate of reaction on the substrate surface. PACVD PECVD plasma assisted CVD plasma assisted chemical vapor deposition plasma assisted chemical vapour deposition plasma enhanced CVD plasma-assisted CVD plasma-assisted chemical vapor deposition plasma-enhanced CVD plasma-enhanced chemical vapor deposition plasma-enhanced chemical vapour deposition CHMO:0001325 plasma-assisted chemical vapour deposition A synthesis method where the substrate is exposed to one or more volatile precursors, in the presence of a plasma (a partially ionised gas, containing free electrons), which react or decompose on the surface to produce a deposit. The plasma enhances the rate of reaction on the substrate surface. https://doi.org/10.1039/b816034a A synthesis method which consists of depositing a monocrystalline film (from a molecular beam) on a monocrystalline substrate under high vacuum (<10^{-8} Pa). Molecular beam epitaxy is very slow, with a deposition rate of <1000 nm per hour. MBE molecular-beam epitaxy CHMO:0001341 molecular beam epitaxy A synthesis method which consists of depositing a monocrystalline film (from a molecular beam) on a monocrystalline substrate under high vacuum (<10^{-8} Pa). Molecular beam epitaxy is very slow, with a deposition rate of <1000 nm per hour. https://orcid.org/0000-0002-0640-0422 A synthesis method where a flow of precursors is projected onto a surface, resulting in a deposit. JD CHMO:0001349 Jet deposition A synthesis method where a flow of precursors is projected onto a surface, resulting in a deposit. https://orcid.org/0000-0002-0640-0422 A synthesis method where an aerosol containing precursors is projected onto a surface, resulting in a deposit. AJD aerosol JD CHMO:0001350 aerosol jet deposition A synthesis method where an aerosol containing precursors is projected onto a surface, resulting in a deposit. https://orcid.org/0000-0002-0640-0422 A synthesis method where a flow of carrier gas containing vaporised precursors is projected onto a surface, resulting in a deposit. GJD JVD PJD VJD gas-jet deposition jet vapor deposition jet vapour deposition jet-vapor deposition jet-vapour deposition physical JD physical jet deposition physical-jet deposition vapor jet deposition vapor-jet deposition vapour jet deposition vapour-jet deposition CHMO:0001351 gas jet deposition A synthesis method where a flow of carrier gas containing vaporised precursors is projected onto a surface, resulting in a deposit. https://doi.org/10.1088/0256-307X/17/11/018 A synthesis method where a plasma (a partially ionised gas containing free electrons) containing precursors is projected onto a surface, resulting in a deposit. plasma JD CHMO:0001353 plasma jet deposition A synthesis method where a plasma (a partially ionised gas containing free electrons) containing precursors is projected onto a surface, resulting in a deposit. https://orcid.org/0000-0002-0640-0422 A synthesis technique where vaporized molecules or atoms condense on a surface, forming a thin layer. The process is purely physical; no chemical reaction occurs at the surface. PVD physical vapor deposition CHMO:0001356 physical vapour deposition A synthesis technique where vaporized molecules or atoms condense on a surface, forming a thin layer. The process is purely physical; no chemical reaction occurs at the surface. https://orcid.org/0000-0002-0640-0422 A synthesis method where an electron beam is used to decompose gaseous molecules leading to deposition of a solid on a nearby substrate. EB deposition EBD EBID electron beam deposition electron beam-induced deposition electron-beam deposition CHMO:0001358 electron-beam-induced deposition A synthesis method where an electron beam is used to decompose gaseous molecules leading to deposition of a solid on a nearby substrate. https://orcid.org/0000-0002-0640-0422 A synthesis technique where a high-power pulsed laser beam is focused (inside a vacuum chamber) onto a target of the desired composition. Material is then vaporized from the target ('ablation') and deposited as a thin-film on a substrate facing the target. PLA deposition PLD laser ablation growth pulsed laser ablation deposition pulsed-laser ablation deposition pulsed-laser deposition CHMO:0001363 pulsed laser deposition A synthesis technique where a high-power pulsed laser beam is focused (inside a vacuum chamber) onto a target of the desired composition. Material is then vaporized from the target ('ablation') and deposited as a thin-film on a substrate facing the target. https://orcid.org/0000-0002-0640-0422 A synthesis technique where a solid target is bombarded with electrons or energetic ions (e.g. Ar+) causing atoms to be ejected ('sputtering'). The ejected atoms then deposit, as a thin-film, on a substrate. sputter coating sputtering CHMO:0001364 sputter deposition A synthesis technique where a solid target is bombarded with electrons or energetic ions (e.g. Ar+) causing atoms to be ejected ('sputtering'). The ejected atoms then deposit, as a thin-film, on a substrate. https://orcid.org/0000-0002-0640-0422 The application of a thin cover to sample by immersing it in a tank containing coating material, allowing it to remain there for a certain 'dwell time', removing the piece from the tank ('withdrawal'), and allowing it to drain. dip-coating CHMO:0001471 Dip coating The application of a thin cover to sample by immersing it in a tank containing coating material, allowing it to remain there for a certain 'dwell time', removing the piece from the tank ('withdrawal'), and allowing it to drain. https://orcid.org/0000-0002-0640-0422 A coating method for applying a thin (<1 μm thickness) cover to flat substrates where an excess amount of coating solution (in a volatile solvent) is placed on the substrate, which is then rotated at high speed (8000 rpm) for approximately 30 s in order to spread the solution by centripetal force. The solvent then evaporates, leaving a thin-film. Rotationsbeschichtung spin casting spin-casting spin-coating CHMO:0001472 spin coating A coating method for applying a thin (<1 μm thickness) cover to flat substrates where an excess amount of coating solution (in a volatile solvent) is placed on the substrate, which is then rotated at high speed (8000 rpm) for approximately 30 s in order to spread the solution by centripetal force. The solvent then evaporates, leaving a thin-film. https://orcid.org/0000-0002-0640-0422 The chemical degradation of a sample caused by spraying it, as a liquid mixture, onto a heated substrate. Sprühpyrolyse CHMO:0001516 Spray pyrolysis The chemical degradation of a sample caused by spraying it, as a liquid mixture, onto a heated substrate. https://orcid.org/0000-0002-0640-0422 The process of chemically removing a thin layer from a sample surface, usually to leave behind a pattern. CHMO:0001558 etching The process of chemically removing a thin layer from a sample surface, usually to leave behind a pattern. https://orcid.org/0000-0002-0640-0422 The process of removing a thin layer of a sample surface by sputtering or dissolving using reactive ions or a vapour-phase etchant CHMO:0001559 dry etching The process of removing a thin layer of a sample surface by sputtering or dissolving using reactive ions or a vapour-phase etchant https://orcid.org/0000-0002-0640-0422 The process of removing a thin layer of a sample surface using short pulses of a plasma (a partially ionised gas containing free electrons and radicals). RIE reactive ion etching reactive-ion etching CHMO:0001560 plasma etching The process of removing a thin layer of a sample surface using short pulses of a plasma (a partially ionised gas containing free electrons and radicals). https://orcid.org/0000-0002-0640-0422 The process of removing a thin layer of a sample surface by bombarding it with energetic ions. ion etching ion milling CHMO:0001568 sputter etching The process of removing a thin layer of a sample surface by bombarding it with energetic ions. https://doi.org/10.1351/goldbook.S05895 The combining of components, particles or layers into a more homogeneous state. The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps or by revolving or shaking the container. The process μst not permit segregation of particles of different size or properties. Homogeneity may be considered to have been achieved in a practical sense when the sampling error of the processed portion is negligible compared to the total error of the measurement system. CHMO:0001685 mixing The combining of components, particles or layers into a more homogeneous state. The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps or by revolving or shaking the container. The process μst not permit segregation of particles of different size or properties. Homogeneity may be considered to have been achieved in a practical sense when the sampling error of the processed portion is negligible compared to the total error of the measurement system. https://doi.org/10.1351/goldbook.M03945 A method for the synthesis of solid particles from an aerosol. The desired solid particles are suspended in a liquid, which is heated to 275–330 °C under pressure and passed through an orifice so that an aerosol forms. The particles in the aerosol are polymerised by partial evaporation of the solvent. https://orcid.org/0000-0001-5985-7429 2009-06-18T10:08:38Z aerosol process aerosol processing CHMO:0001988 aerosol method A method for the synthesis of solid particles from an aerosol. The desired solid particles are suspended in a liquid, which is heated to 275–330 °C under pressure and passed through an orifice so that an aerosol forms. The particles in the aerosol are polymerised by partial evaporation of the solvent. ISBN:0815515804 The application of a thin cover to a sample by depositing consecutive drops of a solution on its surface, and allowing the solvent to evaporate. Tropfbeschichtung https://orcid.org/0000-0001-5985-7429 2009-07-14T09:53:36Z drop-coating CHMO:0002163 drop coating The application of a thin cover to a sample by depositing consecutive drops of a solution on its surface, and allowing the solvent to evaporate. https://orcid.org/0000-0002-0640-0422 The application of a thin cover to sample by converting the coating solution to an aerosol then allowing the droplets to settle on the sample surface under the influence of gravity or using an electrostatic field. Sprühbeschichtung https://orcid.org/0000-0001-5985-7429 2009-10-13T02:46:08Z spray-coating CHMO:0002530 Spray coating The application of a thin cover to sample by converting the coating solution to an aerosol then allowing the droplets to settle on the sample surface under the influence of gravity or using an electrostatic field. https://doi.org/10.1039/b917294g A sample preparation step involving the increase in temperature of a sample. CHMO:0002770 ought to be in OBI. Will put here pro tem. sample heating A sample preparation step involving the increase in temperature of a sample. https://orcid.org/0000-0001-5985-7429 A mixing step where a soluble component is mixed with a liquid component. CHMO:0002773 dissolving A mixing step where a soluble component is mixed with a liquid component. https://orcid.org/0000-0001-5985-7429 Mixing involving the agitation of a solution through circular motion. CHMO:0002774 stirring Mixing involving the agitation of a solution through circular motion. https://orcid.org/0000-0001-5985-7429 Material processing in which a sample is cooled by immersion in a fluid. CHMO:0002917 sample quenching Material processing in which a sample is cooled by immersion in a fluid. https://www.britannica.com/technology/quenching-materials-processing a datum label that specifies units that are associated with a variable (if any) in a human-readable format. http://purl.obolibrary.org/obo/EUPATH_0001008 unit label 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: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg 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 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n 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. datum label 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: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item 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 PERSON: Jonathan Rees based on Oxford English Dictionary symbol 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. PERSON: Chris Stoeckert OBI_0000142 information content entity 1 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity 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 OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set 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:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image 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. 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. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 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 plan specification 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? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum 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 A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum a measurement datum that contains the result of some measurement process and additional information about the point in time at which the measurement datum has been collected time stamped measurement datum pmid:20604925 - time-lapse live cell microscopy A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series time sampled measurement data set planned process A process that realizes a plan which is the concretization of a plan specification. planned process 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. PERSON: Alan Ruttenberg processed material 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") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 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. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush reagent PERSON:Matthew Brush Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent role 1 material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing imaging assay An assay that produces a picture of an entity. An imaging assay is an assay to produce a picture of an entity. PlanAndPlannedProcess Branch OBI branch derived CHMO:0000048 imaging assay OBI:0000185 imaging assay An imaging assay is an assay to produce a picture of an entity. obi:pppb planning 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'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning light emission function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. Bill Bug Daniel Schober Frank Gibson Melanie Courtot light emission function material separation function A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. Bill Bug Daniel Schober Frank Gibson Melanie Courtot material separation function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot excitation function filter function A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through Frank Gibson filter function assay objective 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) PPPB branch PPPB branch assay objective material transformation objective 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. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective material maintenance A process with that achieves the objective to maintain some or all of the characteristics of an input material over time. a process with that achieves the objective to maintain some or all of the characteristics of an input material over time OBI:0000838 material maintenance A process with that achieves the objective to maintain some or all of the characteristics of an input material over time. obi:bp material separation device flow cytometer A device with a separation function realized in a planed process material separation device device 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. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) A device which has a function to emit light. Person:Helen Parkinson OBI light emission device X-ray source A device that is used to generate X-rays. PERSON: Erik Segerdell x-ray generator http://en.wikipedia.org/wiki/X-ray_generator X-ray source selection criterion rats should be aged between 6 and 8 weeks and weight between 180-250grams A directive information entity which defines and states a principle of standard by which selection process may take place. Person: Philippe Rocca-Serra selection rule OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ selection criterion selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) Person: Philippe Rocca-Serra selection process OBI selection ultraviolet light source A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system. Person: Jie Zheng UV light source Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB ultraviolet light source visible light source A light source that provides visible light for use in a distant area using a delivery system. Person: Jie Zheng Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB visible light source solar light source A light source that light is produced from solar energy. Person: Chris Stoeckert Person: Jie Zheng Person: Chris Stoeckert Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB solar light source data transformation A planned process that produces output data from input data. data processing data transformation data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability. Philippe Rocca-Serra OBI-Branch OBI:0302893 storage storage A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability. obi:prs band pass filter 530/30 BP filter, 585/42 BP filter A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others. Person:John Quinn http://en.wikipedia.org/wiki/Band_pass_filter band pass filter laser A laser is the most common way to irradiate a cell in a flow cytometer. A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer. Daniel Schober light amplification by the stimulated emission of radiation John Quinn http://en.wikipedia.org/wiki/Laser laser light source A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 light source long pass filter 750 LP filter A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm. John Quinn http://en.wikipedia.org/wiki/high-pass_filter long pass filter optical filter 720 LP filter, 580/30 BP filter An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. John Quinn http://en.wikipedia.org/wiki/Optical_filter optical filter short pass filter 620 SP filter A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm. John Quinn http://en.wikipedia.org/wiki/Low-pass_filter short pass filter acquisition Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. the planned process of gaining possession of a continuant 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria Relates to the creation of a class 'selection rule' Bjoern Peters IEDB This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition acquisition material acquisition Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI. An acquisition in which possession of a material entity is gained. The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation This excludes processes that create or change materials, such as material transformations. Bjoern Peters, Alan Ruttenberg, Helen Parkinson material procurement IEDB material acquisition information acquisition Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC An acquisition in which possession of information is gained. This excludes processes that create or change information, such as assays and data transformations. Bjoern Peters data collection OBI branch derived information acquisition A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position. quality velocity PATO:0000008 speed A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position. Wikipedia:http://en.wikipedia.org/wiki/Velocity composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATO:0002015 composed of compositionality content structure, composition quality PATO:0000025 For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATOC:GVG concentration of A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. concentration quality PATO:0000033 concentration of A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. Wikipedia:http://en.wikipedia.org/wiki/concentration A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. quality PATO:0000044 frequency A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. Wikipedia:http://en.wikipedia.org/wiki/frequency morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. morphology A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0001647 relational shape quality quality PATO:0000052 Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. shape A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATOC:GVG size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. quality PATO:0000117 size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. WordNet:WordNet A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. quality PATO:0000119 height A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. PATOC:GVG length A 1-D extent quality which is equal to the distance between two points. https://github.com/pato-ontology/pato/issues/337 quality PATO:0000122 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. length A 1-D extent quality which is equal to the distance between two points. PATOC:GVG mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass A physical quality inhering in a bearer that has mass near a gravitational body. Important usage note: Note that this ontology has a class for a similar concept, mass (PATO:0000125). Mass and weight are not equivalent. For most use cases, the class mass is strongly preferred over weight. quality PATO:0000128 For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. weight A physical quality inhering in a bearer that has mass near a gravitational body. Important usage note: Note that this ontology has a class for a similar concept, mass (PATO:0000125). Mass and weight are not equivalent. For most use cases, the class mass is strongly preferred over weight. Wikipedia:http://en.wikipedia.org/wiki/Weight https://en.wikipedia.org/wiki/Mass#Weight_vs._mass 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. PATO:0000137 angular placement quality amount of rotation angle angular magnitude plane angle PATO:0000133 orientation 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. PATOC:JE A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATO:0001032 PATO:0001631 location placement relational spatial quality quality PATO:0000140 position A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATOC:GVG structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0001452 conformation relational structural quality quality PATO:0000141 structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATOC:GVG conformation VT:1000738 temperature A physical quality of the thermal energy of a system. quality PATO:0000146 temperature A physical quality of the thermal energy of a system. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. quality PATO:0000161 rate A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. PATOC:melissa time A quality in which events occur in sequence. quality PATO:0000165 time A quality in which events occur in sequence. PATOC:GVG A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width. https://github.com/pato-ontology/pato/issues/337 quality PATO:0000915 Thickness often refers to the smallest 1-D extent compared to the other two orthogonal dimensions, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion. thickness A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width. WordNet:WordNet volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. quality PATO:0000918 volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. PATOC:GVG A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite. https://github.com/pato-ontology/pato/issues/337 quality breadth PATO:0000921 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. width A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite. PATOC:GVG physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. physical quality A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality density PATO:0001019 mass density A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. WordNet:WordNet A physical quality inhering in a bearer by virtue of the bearer's capacity to do work. quality PATO:0001021 energy A physical quality inhering in a bearer by virtue of the bearer's capacity to do work. Wikipedia:http://en.wikipedia.org/wiki/Energy A physical quality inhering in a bearer by virtue of the bearer's rate of doing work. quality PATO:0001024 power A physical quality inhering in a bearer by virtue of the bearer's rate of doing work. Wikipedia:http://en.wikipedia.org/wiki/Power pressure A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. quality PATO:0001025 pressure A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. PATOC:GVG A physical quality which is equal to the energy transferred by a force to a moving object. W quality PATO:0001026 work A physical quality which is equal to the energy transferred by a force to a moving object. Wikipedia:http://en.wikipedia.org/wiki/Work A physical quality inhering in a bearer by virtue of the rate of change of the bearer's velocity in either speed or direction. quality PATO:0001028 acceleration A physical quality inhering in a bearer by virtue of the rate of change of the bearer's velocity in either speed or direction. Wikipedia:http://en.wikipedia.org/wiki/Acceleration A physical quality inhering in a bearer by virtue of ratio of the bearer's output to the bearer's input. quality PATO:0001029 efficiency A physical quality inhering in a bearer by virtue of ratio of the bearer's output to the bearer's input. WordNet:WordNet A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. force amplitude quality PATO:0001035 force A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. thesaurus.maths:thesaurus.maths A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in an process. PATOC:GVG physical object quality A quality which inheres in a continuant. physical object quality A physical quality which is equal to the distance between repeating units of a wave pattern. quality PATO:0001242 wavelength A physical quality which is equal to the distance between repeating units of a wave pattern. PATOC:GVG A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATO:0000081 period quality time PATO:0001309 duration A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATOC:mellybelly A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. quality PATO:0001323 area A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. Wikipedia:http://en.wikipedia.org/wiki/Area A length quality which is equal to the length of any straight line segment that passes through the center of a circle and whose endpoints are on the circular boundary. quality PATO:0001334 diameter A length quality which is equal to the length of any straight line segment that passes through the center of a circle and whose endpoints are on the circular boundary. Wikipedia:http://en.wikipedia.org/wiki/Diameter A physical quality inhering in a bearer by virtue of the rate of change of the bearer's angular velocity. quality PATO:0001350 angular acceleration A physical quality inhering in a bearer by virtue of the rate of change of the bearer's angular velocity. Wikipedia:http://en.wikipedia.org/wiki/Angular_acceleration A physical quality inhering in a bearer by virtue of the rate of the bearer's angular movement about an axis; the angle rotated in a given time. quality PATO:0001413 angular velocity A physical quality inhering in a bearer by virtue of the rate of the bearer's angular movement about an axis; the angle rotated in a given time. Wikipedia:http://en.wikipedia.org/wiki/Angular_velocity A quality that is equal to the potential energy per unit charge associated with a static (time-invariant) electric field, also called the electrostatic potential. quality PATO:0001464 electric potential A quality that is equal to the potential energy per unit charge associated with a static (time-invariant) electric field, also called the electrostatic potential. Wikipedia:http://en.wikipedia.org/wiki/Electric_potential quality of a gas A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. gaseous quality PATO:0001547 quality of a gas A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. Chemistry:http://chemistry.about.com/od/chemistryglossary/a/gasdefinition.htm PATOC:GVG flow rate A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. quality PATO:0001574 flow rate A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. WordNet:WordNet A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium. quality PATO:0001585 Examples could be heat or electricity or sound. conductivity A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium. PATOC:GVG A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension. quality PATO:0001595 depth A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension. WordNet:WordNet A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. 1-D size quality PATO:0001708 1-D extent A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. 2-D size quality PATO:0001709 2-D extent A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. PATOC:GVG 3-D extent A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. 3D size quality PATO:0001710 3-D extent A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. PATOC:GVG An 1-D extent quality inhering in two-dimensional bearer by virtue of being equal to the distance around it. quality PATO:0001711 perimeter An 1-D extent quality inhering in two-dimensional bearer by virtue of being equal to the distance around it. Wikipedia:http://en.wikipedia.org/wiki/Perimeter A conductivity quality inhering in a bearer by virtue of the bearer's disposition to spontaneous transfer of thermal energy from a region of higher temperature to a region of lower temperature. thermal conduction quality PATO:0001756 heat conductivity A conductivity quality inhering in a bearer by virtue of the bearer's disposition to spontaneous transfer of thermal energy from a region of higher temperature to a region of lower temperature. Wikipedia:http://en.wikipedia.org/wiki/Heat_conduction A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity. quality PATO:0001757 electrical conductivity A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity. Wikipedia:http://en.wikipedia.org/wiki/Electrical_conduction movement quality A physical quality inhering in a bearer by virtue of the bearer's participation in movement. quality PATO:0001906 movement quality A physical quality inhering in a bearer by virtue of the bearer's participation in movement. PATOC:GVG 2009-06-05T09:16:46Z quality PATO:0002062 physical quality of a process A composition quality inhering in a bearer by virtue of the bearer's being composed of more than one identifiable entities. 2009-10-06T04:29:17Z quality PATO:0002122 mixed A composition quality inhering in a bearer by virtue of the bearer's being composed of more than one identifiable entities. PATOC:GVG molecular quality A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. 2010-03-10T03:18:15Z PATO:0002061 relational molecular quality quality PATO:0002182 molecular quality A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. PATOC:GVG quality of a substance A quality inhering in a bearer by virtue of its constitution. 2010-03-15T04:35:27Z quality PATO:0002198 quality of a substance A quality inhering in a bearer by virtue of its constitution. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's rate of change of the position. 2010-07-28T02:52:48Z quality PATO:0002242 velocity A physical quality inhering in a bearer by virtue of the bearer's rate of change of the position. url:http://en.wikipedia.org/wiki/Velocity fluid flow rate A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. 2010-07-28T03:00:20Z volume flow rate volumetric flow rate quality PATO:0002243 fluid flow rate A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. url:http://en.wikipedia.org/wiki/Volumetric_flow_rate A flow rate quality inhering in a substance by virtue of the mass of substance which passes through a given surface per unit time. 2010-07-28T03:02:03Z quality PATO:0002244 mass flow rate A flow rate quality inhering in a substance by virtue of the mass of substance which passes through a given surface per unit time. url:http://en.wikipedia.org/wiki/Mass_flow_rate An orientation inhering in a bearer by virtue of the bearer's placement at an angle. 2011-11-23T12:06:09Z quality PATO:0002326 angle An orientation inhering in a bearer by virtue of the bearer's placement at an angle. PATOC:GVG A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter. 2012-11-15T05:17:15Z quality PATO:0002390 radius A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter. PATO:DS A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content. quality PATO:0015009 humidity A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content. https://github.com/pato-ontology/pato/issues/90 The number of repeated events per unit time, occurring in a repeating series. (e.g. the number of heart beats occurring over 1 minute) quality PATO:0050000 rate of occurence The number of repeated events per unit time, occurring in a repeating series. (e.g. the number of heart beats occurring over 1 minute) https://orcid.org/0000-0002-9943-9018 length unit A unit which is a standard measure of the distance between two points. "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] length unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] mass unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] time unit time derived unit "A unit which is a standard measure of the flow of electric charge." [Wikipedia:Wikipedia] electric current unit temperature unit "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia] temperature unit temperature derived unit "A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST] base unit An indication of the type of unit of measure being used to express an area. http://purl.obolibrary.org/obo/NCIT_C48037 area unit A unit of the rate of change of linear or angular velocity with respect to time. A unit of the rate of change of linear or angular velocity with respect to time. acceleration unit "A unit which is a standard measure of the rate of change of angular velocity." [Wikipedia:Wikipedia] angular acceleration unit concentration unit "A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG] concentration unit "A unit which is a standard measure of the rate of movement. Speed is measured in the same physical units of measurement as velocity, but does not contain the element of direction that velocity has. Speed is thus the magnitude component of velocity." [Wikipedia:Wikipedia] speed/velocity unit volume unit "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] volume unit frequency unit "A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST] frequency unit pressure unit "A unit which is a standard measure of the force applied to a given area." [NIST:NIST] pressure unit "A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST] energy unit "A unit which is a standard measure power or the rate of doing work." [NIST:NIST] power unit "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia] angle unit "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] density unit "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] dimensionless unit "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia] electric potential difference unit "A unit which is a standard measure of the quantity of unbalanced electricity in a body (either positive or negative) and construed as an excess or deficiency of electrons." [WordNet:WordNet] electric charge volumetric flow rate unit "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia] volumetric flow rate unit rate unit "A unit which represents a standard measurement occurrence of a process per unit time." [UOC:GVG] rate unit A cell is a sample, which is an electronic device that converts the energy of light directly into electrical energy by using the photovoltaic effect. Device PV Cell Photovoltaic cell Photovoltaische Zelle Solarzelle Zelle solar cell A Non photo-absorber Layer that is the base material on which processing is conducted. A surface onto which a coating might be deposited. Carrier A non photo-absorber layer that ensure contacting to the external electrical circuit situated at the back of a solar cell. Back contact A composition of at least two materials in which the concentrations are comparable. Mixture of raw materials A non photo-absorber layer that is placed in between a back contact and an electron transport layer to avoid electrodes from arcing. Mehrdad Mehdizadeh. 2009. Microwave/RF Applicators and Probes for Material Heating, Sensing, and Plasma Generation. ScienceDirect. Buffer layer a non photo-absorber layer that connects to the external electrical circuit situated at the front of a solar cell. Front contact a flat fiat object part, constitutet as a film of molecules on or in a object Schicht layer A layer whose role is absorbing light and generating charge pairs. Photo absorber layer A layer whose role is not absorbing light and generating charge pairs. Non photo-absorber layer A layer between a substrate and a perovskite in nip-device or between perovskite and a back contact in pin-device Electron transport layer Hole transport layer a non photo-absorber layer that decreases the reflectivity of an object Antireflective coating a layer that converts high-energy photons into low-energy photons and vice versa SISER (Scottish Institute for Solar Energy Research). (21.04.2023). Up and Down-conversion for Solar cells. Retrieved from: https://www.siser.ac.uk/research/next-generation/up-and-down-conversion. Conversion layer describes the distance between individual cells in a module Cell spacing Back reflection Dielectric mirror Down conversion a layer role that describes the purpose of some layer to divide it from other layers Encapsulation Light management Upconversion the role of a thin-film Layer role A planned process to expose an entity to some light. illumination process Perovskit a photo absorber layer based on the component perovskite perovskite layer Doped raw material A liquid that dissolves or that is capable of dissolving; the component of a solution that is present in greater amount. http://purl.obolibrary.org/obo/NCIT_C45790 solvent Mixture of solvents 1 a solar cell that is made from non-carbon based molecules Anorganische Solarzelle Inorganic cell a solalr cell that contains at least one organic semiconductor in the cell active region Organische Solarzelle Brabec, C.J., Gowrisanker, S., Halls, J.J.M.,Laird, D., Jia, S., and Williams, S.P. (2010)Polymer–fullerene bulk-heterojunctionsolar cells.Adv. Mater.,22, 3839–3856.2Sariciftci, N.S., Smilowitz, L., Heeger, Organic cell a solar cell that contains both organic and inorganic materials Hybrid-Solarzelle Inorganic material is used as the acceptor and electron transporter. Organic material is used as light absorber, donor and transports holes. Hybrid cell Inorganic p-n homojunction is the gap in energy between the bound state and the free state, between the valence band and conduction band. Therefore it is the minimum amount of energy required for an electron to break free of its bound state. PVeducation. Retreived from: https://www.pveducation.org/pvcdrom/pn-junctions/band-gap. Date of retrieval: 27.04.2023 Bandgap Direct bandgap Indirect bandgap Innermaterial process passive transport of molecules from places with higher concentration to places with lower concentration Spektrum. (2000). Diffusion. Retrieved from: https://www.spektrum.de/lexikon/neurowissenschaft/diffusion/2845 Diffusion Charge transport Charge hopping An area where multiple conductors or semiconductors make physical contact. Junction a junction that occurs between similar materials Homo-junction a junction between different kinds of material Hetero-junction Schottky-junction Photon energy Electric energy Elektrische Stromstärke "Electric Current" is the flow (movement) of electric charge. The amount of electric current through some surface, for example, a section through a copper conductor, is defined as the amount of electric charge flowing through that surface over time. Current is a scalar-valued quantity. Electric current is one of the base quantities in the International System of Quantities, ISQ, on which the International System of Units, SI, is based. https://qudt.org/vocab/quantitykind/ElectricCurrent 24.10.2022 10:24 current Elektrische Stromdichte is a measure of the density of flow of electric charge; it is the electric current per unit area of cross section. https://qudt.org/vocab/quantitykind/ElectricCurrentDensity current density a material processing which deposits thin layers onto an material entity layer deposition a process to remove impurities from an object cleaning is a material processing, with the objective of removing impurities and contaminants from some material entity Reinigen cleaning Schlitzdüsenbeschichtung a coating technique, where the solution (ink) is delievered through a precise coating head (slot die) slot die coating a spectroscopy assay, that measures the number of electrons collected per per photon incident on the solar cell EQE Measurement external quantum efficiency measurement iv measurement is a scanning process to determine a electric devices characteristics and performance Current-Voltage measurement University of Warwick Department of Physics.Retrieved from: https://warwick.ac.uk/fac/sci/physics/current/postgraduate/regs/mpagswarwick/ex5/techniques/electronic/iv/ (31.03.2023, 12:54) iv measurement Hole transportation Electron transportation Energy conversion Multi-junction solar cell Tandem Solarzelle a cell, that consists of multiple cells that are capable of absorbing different frequencies of light tandem cell electromagnetic radiation that can be witnessed by the human eye Licht light According to the quantum theory of radiation, the elementary quantities of radiant energy. They are regarded as discrete quantities having a momentum equal to hv/c, where h is the Planck constant, v is the frequency of the radiation, and c is the speed of light in a vacuum. Photons are never at rest, have no electric charges and no magnetic moments, but they have spin moments. The energy of a photon (the unit quantum of energy) is equal to hv. Nasa Scientific and Technical Information Program Office. NASA Thesaurus. January 2012. Photon Is a innermaterial process in which a bound electron is pushed to a higher energy level without removing it from the atomic shell Elektronenanregung Electron excitation thermal annealing the total area of an object total area the area of a photovoltaic device which is active in the conversion of light to current active area a solution handling , in which some solution is controlled dropwise released http://purl.obolibrary.org/obo/CHMO_0001544 dispensing roughness Luftfeuchtigkeit Relative Humidity is the ratio of the partial pressure of water vapor in an air-water mixture to the saturated vapor pressure of water at a precise temperature. The relative humidity of air depends not only on temperature but also on the pressure of the system of interest. https://qudt.org/vocab/quantitykind/RelativeHumidity 24.10.2022 10:44 relative humidity the gaseous material entity that surrounds a process/object Atmosphäre atmosphere Minimal cell bending radius Maximal semi transparent wavelength Minimal semi transparent wavelength The stack sequence of some solar cell solar cell stack sequence the architecture of some solar cell solar cell architecture a solar cell boolean quality that describes the ability of some bearer to be turned, twisted or bend without breaking http://purl.obolibrary.org/obo/PATO_0001543 Is flexible a solar cell boolean quality that describes if an object is partially transparent http://purl.obolibrary.org/obo/NCIT_C96284 Is semitransparent A transmittance is a physical object quantity that quantifies the ratio of the transmitted radiant power (P_λ) to that incident on the sample (P0_λ): T = P_λ/ P0_λ. Transmission http://purl.allotrope.org/ontologies/result#AFR_0002261 Durchlässigkeit transmittance average visible transmittance 1 Modul a object consisting of multiple cells solar module Pipetting solution aspirating is the process of solution handling that is to draw an amount of a liquid by suction http://purl.allotrope.org/ontologies/process#AFP_0001824 Solution aspiration Anlassen Glühen Thermische Behandlung A heat treatment that alters the microstructure of a material causing changes in its properties such as strength and hardness annealing is the electric potential at zero current Md. Shahiduzzaman, Md. Hossain, Mohammad Ismail. (2022). Organometal halide perovskite photovoltaics. In Md. Akhtaruzzaman Comprehensive Guide on Organic and Inorganic Solar Cells Voc open circuit voltage PL measurement PLI photoluminescence (PL) imaging photovoltaic device efficiency Mechanical etching is an etching process, that uses a laser to remove a thin layer of a sample surface Laser etching the solvent cleaning is a cleaning process, that utilizes some solvent to remove impurities and contaminants from some material entity Lösungsmittelreinigung solvent cleaning the ultraviolet cleaning is a cleaning process, that utilizes some ultraviolet radiation to remove impurities and contaminants from some material entity UV-Reinigung uv cleaning ultraviolet cleaning the plasma cleaning is a cleaning process, that utilizes some energetic plasma to remove impurities and contaminants from some material entity Plasmareinigung plasma cleaning Solution synthesis is a synthesis process, where some solvents, solutions and/or solutes are mixed together in specified ratios to produce a new solution. solution manufacturing a solution manufacturing process, in which substances are mixed, blended or agitated in a container by short rapid motions Schütteln shaking A quantitative assessment of the homogeneity or uniformity of a mixture. Alternatively, purity refers to the degree of being free of contaminants or heterogeneous components. http://purl.obolibrary.org/obo/NCIT_C62352 purity solvent annealing anti solvent quenching is a sample quenching method, that uses some anti solvent to affect the crystallization of some layer anti solvent quenching a solution manufacturing process, in which substrate are mixed, blended or agitated via ultrasound ultrasonic the soap cleaning is a cleaning process, that utilizes some lipophilic solution to remove impurities and contaminants from some material entity Seifenreinigung soap cleaning a cleaning process, that uses ultrasound to remove impurities the ultrasonic bath is a cleaning process, that utilizes ultrasound to stimulate some fluid to remove impurities and contaminants from some material entity Ultraschallbad utrasonic bath 1 A substance that is added to a system or compound to improve its characteristics. http://purl.obolibrary.org/obo/NCIT_C63495 Doping material Additive is a wet chemical deposition in which a layer is deposited by dipping the substrate into a solution, that contains the chemical of interest. CBD Chemical Solution deposition Chemische Badabscheidung Chemical bath deposition the temperrature of a substrate for example in a measurement process device temperature Zeit Time is a basic component of the measuring system used to sequence events, to compare the durations of events and the intervals between them, and to quantify the motions of objects. https://qudt.org/vocab/quantitykind/Time 24.10.2022 10:42 time range process time temperature quality of a process Partial pressure is the component of total pressure associated with a specific gas species partial pressure perovscite boolean quality Is single crystal Is zero dimensional Is two dimensional Is 2D/3D mixture Is three dimensional Is 3D with 2D capping layer Has ABC3 structure Has perovscite inspired structure A ratio is a relational quality that is the proportion of the magnitude of two qualities of the same kind. http://purl.allotrope.org/ontologies/quality#AFQ_0000005 Ratio the mixing ratio of mixed objects Mixing ratio gas quenching is a sample quenching method, that uses some gas to affect the crystallization of some layer gas quenching A solute is a substance that becomes dissolved in a solvent. http://semanticscience.org/resource/SIO_010418 solute A solid substance in the form of tiny loose particles; a solid that has been pulverized. http://purl.obolibrary.org/obo/NCIT_C45302 Powder precursor ink precursor solution Encapsulation layer doped precursor solution is a molecular quality, that describes the ratio between the amounts of moles in two chemicals involved in a chemical process. Molar Ratio A chemical formula is a symbol representing the chemical structure of an chemical substance. Chemical formula the total pressure is the sum of partial pressures for all gas species contributing in a particular location where the pressure is measured total pressure The time since last planned process is the time range from the end time point of the last planned process until now. time since last process Zertifiziert certified a planned process to determine the deviation of another entity calibration a physical object quality that describes the property of a object or substance of resisting or opposing the flow of an electrical current. Widerstand http://purl.obolibrary.org/obo/NCIT_C68787 resistance shunt resistance series resistance current density maximum power point voltage maximum power point The fill factor is a measure of quality of a solar cell. It can be calculated by dividing the power at the maximum power point (MPP) divided by the open circuit voltage (Voc) and the short circuit current (Isc). Füllfaktor fill factor short circuit current density Solution dispense Logistical processing is a material processing where a material entity is oved around in space. logistical processing Mask area is a orientation quality, that describes the direction from which light falls onto an object either by moving the illuminated object of the light source. illumination direction Scan speed Delay time is a quality, that describes the power transfered per area unit Intensität Tipler, Paul A.. Mosca, Gene. 2019. Physik für Studierende der Naturwissenschaften und Technik. Springer Spektrum. intensity is a physical quality, that indicates the intensity of some light light intensity Pumping Syringe pumping integrated current density Ink jetting Stability measurement Load condition a process quality that specifies the ultraviolet filter used in some process ultraviolett filter used Cycling time a material process moving a solution around solution handling a data tranformation output, that interprets a measurement output to calculate a devices deviation calibration data a data transformation process, which interprets the raw experimental data of an jv measurement jv analysis shaking rate the hotplate temperature is a temperature, that describes the temperature of some hotplate hotplate temperature is a setting datum, which indicates the settings for the rotation acceleration rotation acceleration setting datum An iv curve is a tabular data which consists of two columns voltage and current. It is the result of an iv measurement. The voltage is set by the voltage setting datums and the current is measured. i-v curve current-voltage curve plate spacing is a setting datum, which indicates the settings for the rotation speed rotation speed setting datum is a setting datum, that specifies the duration of some occurent duration setting datum the gathering of data or some images with a sensing device http://purl.obolibrary.org/obo/NCIT_C17999 scan a physical vapour deposition in which the evaporation process is supported by heat thermal physical vapour deposition Laser energy the logged assay output of an external quantum efficiency measurement eqe curve external quantum efficiency curve Elektrische Leistung Electric Power is the rate at which electrical energy is transferred by an electric circuit. https://qudt.org/vocab/quantitykind/ElectricPower electric power 1 Volumetric Flow Rate is the volume of fluid which passes through a given surface per unit time https://qudt.org/vocab/quantitykind/VolumeFlowRate volumetric flow rate final temperature heating rate a data item that describes the returned data from an data transformation data transformation output the photovoltaic device efficiency datum is a scalar datum, that quantifies the efficiency of some photovoltaic device photovoltaic device efficiency datum Aspiration speed Dispense speed Aspiration acceleration is the acceleration, with which an liquid of gas gets sucked into an object. aspiration acceleration Dispense acceleration is the acceleration, which which an liquid or gas gets pushed out of an object. dispense acceleration scalar datums are data items, that are represented by a numerical part and a unit part scalar datum a conversion layer that converts two or more low-energy photons into one high-energy photons SISER (Scottish Institute for Solar Energy Research). (21.04.2023). Up and Down-conversion for Solar cells. Retrieved from: https://www.siser.ac.uk/research/next-generation/up-and-down-conversion. Up conversion layer a conversion layer that converts one high-energy photons into two or more low-energy photons SISER (Scottish Institute for Solar Energy Research). (21.04.2023). Up and Down-conversion for Solar cells. Retrieved from: https://www.siser.ac.uk/research/next-generation/up-and-down-conversion. Down conversion layer Kupfer-Indium-Gallium-Diselenid copper indium gallium selenide solar cell is a photo absorber layer based on the components copper, indium, gallium and selenide CIGS a speed quality that describes the inheriting speed of a bearer traveling in circular motion around some point Rotation speed Außendruck Ambient pressure A unit for measurement of electrical charge http://www.ebi.ac.uk/efo/EFO_0000388 current unit solar cell morphology a algorithm that specifies the transformation of some data into another data format data processing algorithm data transforming algorithm Analytisches Modell Analytical model a setting datum, that specifies the positioning of the light source in relation to the sample illumination direction setting datum wavelength step size is a setting datum, which indicates the settings for the light intensity light intensity setting datum pvd source is a setting datum, which specifies the settiing of some time range time range setting datum Emulsion A chemical composition is a list of symbols of some chemical entity which lists the chemical elements. Chemical composition the cycling time setting datum is a setting datum, that specifies some cycling time cycling time setting datum is a setting datum, which indicates the settings for the wavelength wavelength setting datum is a setting datum, which indicates the settings for the load balance load balance setting datum a device that can transforms light into electricity via the photovoltaic effect photovoltaic device Sublayer a functional layer is a layer that is capable of fullfilling some function Functional layer solar cell boolean quality is a rate, that indicates the quantity of measurements per time unit scan rate a scan rate, that indicates the voltage increase or decrease scan rate voltage vacuum quenching is a sample quenching method, that affects the crystallization of some layer by reducing the pressure around the substrate vacuum quenching Rotation acceleration the fill factor datum is a scalar datum, that quantifies some fill factor fill factor datum are layer deposition processes, which use precursors in liquid state Wet chemical deposition Vapor deposition generally refers to the deposition of a material on to a substrate by use of the gaseous phase of the depositing material. ScienceDirect. Retrieved from: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwiin6aHuIb-AhW5cvEDHReDA9IQFnoECA8QAQ&url=https%3A%2F%2Fwww.sciencedirect.com%2Ftopics%2Fengineering%2Fvapour-deposition&usg=AOvVaw093gJPkrnyIbgFp85mVr1R Date: 31.03.2023 Gasphasenabscheidung vapour phase deposition Tintenstrahldruck a wet chemical deposition method, which deposits a liquid precursor (ink) onto a substrate by jetting it through a print head. ink jet printing Tiefdruck a wet chemical deposition which prints an ink onto a substrate via a image carrier. The image carrier (often a cylinder) comes in direct contact with the substrate. Rotogravure Gravure printing a wet chemical deposition which deposits an ink onto a substrate via a image carrier. The image carrier (often a cylinder) does not come into direct contact with the substrate. Offsetdruck Offset printing a wet chemical deposition which deposits an ink onto a substrate via a image carrier. The image carrier (usually a mesh) does come into direct contact with the substrate. Siebdruck Screen printing a wet chemical deposition method, which deposits a vapourized precursor onto a substrate by jetting it through a print head. Aerosol Jet Druck Aerosol jet printing Aerosol printing is a setting datum, which indicates the settings for the scan rate scan rate setting datum a wet chemical deposition in which a layer is deposited onto a substrate by dropping liquid drops, that contain the dissolved chemical of interest Drop casting Doctor blading Rakelbeschichtung doctor blade coating a small amount of solution is placed on a substrate and spread evenly using a doctor blade. The substrate is then dried to form a thin-film. Blade coating EPD Elektrophoretische Abscheidung a substrate is immersed in a solution containing a salt of the material to be deposited and an electric current is passed through the solution, which causes the material to be deposited on the substrate as a thin-film. Electrophoretic deposition Sol-Gel-Prozess a solution containing precursor materials is formed, which is then deposited onto a substrate and dried to form a thin-film. This process can be used to deposit a wide range of materials, including ceramics, metals and polymers. Sol-gel deposition the open circuit voltage datum is a scalar datum, that quantifies some open circuit voltage open circuit voltage datum the voltage maximum power point datum is a scalar datum, that quantifies some votlage maximum power point voltage maximum power point datum the current density maximum power point datum is a scalar datum, that quantifies the current density at the maximum power point current density maximum power point datum Nahraumsublimation Close space sublimation the short circuit current datum is a scalar datum, that quantifies some short circuit current short circuit current datum A unit for measurement of magnitude of the electrical current per cross-sectional area. http://purl.obolibrary.org/obo/NCIT_C68745 current density unit the total area datum is a scalar datum. that quantifies the total area of some entity total area datum the effective area datum is a scalar datum, that quantifies the area that actively participates in the conversion of light into electric energy effective area datum is a setting datum, which indicates the settings for the process temperature process temperature setting datum is a duration setting datum, which indicates the settings for the process time process time setting datum is a setting datum, which indicates the settings for the annealing temperature hotplate temperature setting datum is a setting datum, which indicates the voltage settings for the scan rate scan rate voltage setting datum Scan rate voltage unit is a unit label which is a standard measure of the rate of change of voltage in a scan. scan rate voltage unit the duration over which the sensor collects incoming light integration time settling time compliance scan direction An assay which collects information measured during an material process. The material this information is about can be inferred from the material processing it contains. process logging starting voltage stopping voltage voltage step size an illuminated iv measurement is a iv measurement with a dedicated light source illuminated iv measurement A reference cell is a solar cell which is used as a reference for other solar cells in a variety of measurements. reference solar cell a wavelength setting datum that specifies some size configuration of wavelength steps wavelength step size setting datum Power density unit is a unit label which is a standard measure of power per area. power density unit is a setting datum, which indicates the settings for the scan direction scan direction setting datum is a setting datum, which indicates the settings for the starting voltage starting voltage setting datum is a setting datum, which indicates the settings for the stopping voltage stopping voltage setting datum is a setting datum, which indicates the settings for the voltage step size voltage step size setting datum is a setting datum, which indicates the settings for the time settling time setting datum a setting datum that specifies some integration time integration time setting datum compliance setting datum pvd process logging The area measurement datum is a scalar measurement datum, that quantifies the result of area measurement area measurement datum The active area measurement datum is a scalar measurement datum, that quantifies the result of some active area measurement active area measurement datum The current measurement datum is a scalar measurement datum, that quantifies the result of some current measurement current measurement datum the shunt resistance datum is a scalar datum, that quantifies some shunt resistance shunt resistance datum the series resistance datum is a scalar datum, that quantifies some series resistance series resistance datum Resistance area unit is a unit label which is a standard measure for by area normalized resistance, i.e. resitance unit times area unit. resistance area unit The temperature measurement datum is a scalar measurement datum, that quantifies the result of some temperature measurement temperature measurement datum The power measurement datum is a scalar measurement datum, that quantifies the result of some power measurement power measurement datum is a setting datum, which indicates the power setting power setting datum a setting datum, that describes the set status of the shutter shutter status setting datum gas mixture a setting datum, that specifies the gas flow per time unit gas flow rate setting datum shutter status thin-film depostion rate the temperature setting datum is a setting datum, that specifies the thermal energy of some material entity temperature setting datum is a setting datum, which indicates the settings for the device temperature device temperature setting datum thermal pvd source is a flow rate, that describes how much gas passes through a given surface per time unit gas flow rate tabular data is a data set, that is organised in rows and columns tabular data A process log is a steadily updated information object containing data of events in time during a process execution. process log the process log of some pvd process pvd process log The pressure measurement datum is a scalar measurement datum, that quantifies the result of some pressure measurement pressure measurement datum The thin-film deposition rate measurement datum is a scalar measurement datum, that quantifies the result of some thin-film deposition rate measurement thin-film deposition rate measurement datum The total pressure measurement datum is a scalar measurement datum, that quantifies the result of some total pressure measurement total pressure measurement datum The partial pressure measurment datum is a pressure measurement datum, that quantifies the result of some partial pressure measurement partial pressure measurement datum A substrate is a processed material which is used in synthesis and deposition of thin-film layers. sample substrate light bias is a setting datum, which indicates the settings for the bias light light bias setting datum chopper frequency the chopper frequency setting datum is a setting datum, which specifies some chopper frequency chopper frequency setting datum voltage bias is a setting datum, which indicates the settings for the voltage bias voltage bias setting datum is a scan rate, that indicates the step size of wavelength increase or decrease scan rate wavelength is a setting datum, which indicates the wavelength settings for the scan rate scan rate wavelength setting datum time quality of a process a data tranformation process, which interprets the raw experimental data of an eqe measurement eqe analysis the eqe bandgap datum is a scalar datum. that quantifies some eqe bandgap eqe bandgap datum the integrated jsc datum is a scalar datum, that quantifies some integrated jsc integrated jsc datum the integrated j0rad datum is a scalar datum, that quantifies some integradted j0rad integrated j0rad datum the radiative open-circuit voltage datum is a scalar datum, that quantifies some radiative open-circuit voltage voc rad datum radiative open-circuit voltage datum the urbach energy datum is a scalar datum, that quantifies some urbach energy urbach energy datum the urbach energy fit standard deviation datum is a scalar datum, that quantifies some urbach energy fit standard deviation urbach energy fit standard deviation datum the external quantum efficiency datum is a scalar datum, that quantifies some external quantum efficiency external quantum efficiency datum eqe bandgap integrated jsc integrated short-circuit current density integrated j0rad integrated radiative recombination saturation-current density voc rad urbach energy urbach energy fit standard deviation is a physical quality, that is the ratio of the number of charge carriers collected by the photovoltaic device to the number of photons of a given wavelength or energy onto the device. Lee, Sanghyun. Price, Kent J.. (February 22nd, 2017). Optolelectronics. Advanced Device Structures. Spectral Repsonses in Quantum Efficiency of Emerging Kesterite Thin-FIlm Solar Cells. IntechOpen. external quantum efficiency The electric potential measurement datum is a scalar measurement datum, that quantifies the result of some electric potential measurement electric potential measurement datum A biased illumination process is a secondary illumination process of some measurement techniques such as EQE. biased illumination process electrical potential quality of a process anti solvent dropping time the anti solvent dropping time setting datum is a setting datum, that specifies the dropping duration of some anti solvent anti solvent dropping time setting datum chemical substance role product role anti solvent role The dropping time is a time quality of a process which specifies the point in time where a dropping event happens, e.g. the dropping of an precursor in a spin coating process. dropping time the dropping time setting datum is a setting datum, that specifies the dropping duration of some fluid dropping time setting datum a setting datum that specifies some volume configuration volume setting datum a volume setting datum that specifies some volume configuration of some anti solvent anti solvent volume setting datum a volume setting datum that specifies some volume configuration of some precursor solution precursor solution volume setting datum The volume measurement datum is a scalar measurement datum, that quantifies the result of some volumetric measurement volume measurement datum perovskite solar cell The characteristic shape or pattern of some entity architecture A stack sequence is a property of a sample or a functional layer which gives the order of all deposited layers in that sample or functional layer. stack sequence the number of averages is a process quality, that describes the number of values that match the average value in a dataset number of averages camera a current, that is able to fullfill some excitation function excitation current an excitation source is a source that fullfills some excitation function excitation source a wavelength, that fullfills some excitation function excitation wavelength image pixel length the position of filter describes thespatially relation between a filter and another continuant position of filter the current setting datum is a setting datum, that specifies the set value of the current current setting datum the excitation current setting datum is a current setting datum, that specifies some excitation current excitation current setting datum a wavelength setting datum that specifies some excitation wavelength excitation wavelength setting datum gas quenching with round nozzle the delay time between the start of the rotation and the quenching quenching starting delay time The round nozzle distance to substrate is a nozzle distance to substrate, that describes the distance between some round nozzle and some substrate. round nozzle distance to substrate The nozzle distance to substrate is a distance to substrate, that describes the distance between some nozzle and some substrate nozzle distance to substrate nozzle shape is a angle, at which some nozzle is capable of depositing nozzle spray angle the velocity setting datum is a setting datum, that specifies the value of some velocity datum velocity setting datum the round nozzle distance to substrate setting datum is a nozzle distance to substrate setting datum, that specifies the distance of some nozzle to some substrate round nozzle distance to substrate setting datum the angle setting datum is a setting datum, that specifies some angle angle setting datum a setting datum, that specifies the duration of the delay of some occurent delay setting datum is a delay setting datum, that specifies the amount of time some subprocess is being delayed the start of some occurent starting delay time setting datum is a velocity, that describes the velocity at the tip of some nozzle of some material entity exiting thorugh that nozzle velocity at nozzle tip is a velocity setting datum, that specifies the velocity setting at some nozzle tip velocity at nozzle tip setting datum is a scan which determines the maximum power output of some device under changing conditions maximum power point tracking The mppt time series is a time sampled measurement data set which contains values of current, voltage and power of some device over a defined time period maximum power point tracking time series a data tranformation process, which interprets the raw experimental data of an maximum power point tracking maximum power point tracking analysis describes the time span after which a solar cell drops to 80% of its original efficiency time until 80 percent efficiency describes the time span after which a solar cell drops to 90% of its original efficiency time until 90 percent efficiency the time until 80 percent efficiency datum is a scalar datum, that quantifies the time until a solar cell drops to 80 percent of its initial efficiency time until 80 percent efficiency datum the time until 90 percent efficiency datum is a scalar datum, that quantifies the time until a solar cell drops to 90 percent of its initial efficiency time until 90 percent efficiency datum is a area that describes the 2-d extent of some pixel pixel area is a scalar datum that quantifies some power power datum sample uv/vis spectroscopy reflection uv/vis measurement transmittance uv/vis measurement a spectrum, that displays the amount of absorption of ultraviolet and visible light as a function of wavelength as a plot ultraviolet–visible spectrophotometry curve uv-vis curve is a setting datum, that specifies some electric potential electric potential setting datum a uv-vis curve, that displays the reflection of ultraviolet and visible light as a function of wavelength as a plot reflection ultraviolet–visible spectrophotometry curve reflection uv-vis curve a uv-vis curve, that displays the transmittance of ultraviolet and visible light as a function of wavelength as a plot transmittance ultraviolet–visible spectrophotometry curve transmittance uv-vis curve The transmittance measurement datum is a scalar measurement datum, that quantifies the result of some transmittance measurement transmittance measurement datum The reflectance measurement datum is a scalar measurement datum, that quantifies the result of some reflectance measurement reflectance measurement datum a physical object quality that describes the fraction of incident radiation reflected by a surface or discontinuity Retrieved from: https://goldbook.iupac.org/terms/view/R05235. Retreived on: 14.11.2023, 15:48. reflectance wavenlength quality of a process the wavelength at the beginning of some process starting wavelength the wavelength at the end of some process stopping wavelength a wavelength setting datum that specifies some starting wavelength configuration starting wavelength setting datum a wavelength setting datum that specifies some stopping wavelength configuration stopping wavelength setting datum plasma power An instrument used to apply uniform thin-films to flat substrates by centrifugal force. http://purl.obolibrary.org/obo/ERO_0000850 spin coater a power setting datum, that concretizes the power of some plasma plasma power setting datum plasma a setting datum, that concretizes the set amount of some entity mass setting datum The pressure of the gas coming out of an air knife. air knife pressure nozzle pressure The air knife distance to thin-film is a nozzle distance to thin flm, that describes the distance between some air knife and some thin-film air knife distance to thin-film the air knife impingement angle is an impingement angle, that describes the angle at which a stream from a air knife collides with another object air knife impingement angle The speed of an air knife in an air knife gas quenching, i.e. the speed which with the air knife moves over the thin-film. The speed can be relative, i.e. not the air knife is moving but the sample beneath it. air knife speed a speed setting datum that specifies some air knife speed air knife speed setting datum a setting datum, that describes the set pressure of an air knife air knife pressure setting datum the air knife distance to thin-film setting datum is a nozzle distance to substrate setting datum, that specifies the distance between some air knife and some entity air knife distance to thin-film setting datum the air knife impingement angle setting datum is a transferring device impingement setting datum, that specifies the impingement angle of some air knife air knife impingement angle setting datum An air knife is a material entity which is used in air knife gas quenching. It includes the whole instrument, including a pump for the gas flow. air knife is a object that distributes the coating fluid across the desired coating width befor coating onto the substrate Wikipedia. Retrieved from: https://en.wikipedia.org/wiki/Slot-die_coating. Retrieved on: 05.12.2023 slot die head the air knife gas quenching is a gas quenching technique, that involves an air knife to redirect an airflow onto some substrate air knife gas quenching The speed of the slot die head in slot die coating, i.e. the speed which with the slot die head moves over the thin-film. The speed can be relative, i.e. not the slot die head is moving but the sample beneath it. slot die head speed The distance of the slot die head to the thin-film in slot die coating. slot die head distance to thin-film The width of a shim used in a slot die head, reducing the width of the slot die head width for slot die coating. slot die shim width The thickness of a shim used in a slot die head. slot die shim thickness a shim that is used to alter the width of the slot die heads channel slot die shim The width of the slot die head, where the ink can exit the slot die head. slot die head width The flow rate of the ink used in slot die coating. slot die coating flow rate the pressure setting datum is a setting datum, that specifies the applied force on a surface per unit area of some entity pressure setting datum 1-D extent setting datum a setting datum, that specifies the speed of some slot die head slot die head speed setting datum a setting datum that specifies some speed configuration speed setting datum the slot die head distance to thin-film setting datum is a 1-d extent setting datum, that specifies the distance between some slot-die-head and some thin-film slot die head distance to thin-film setting datum the slot die shim width setting datum is a 1-d extent setting datum, that specifies the width of some slot die shim slot die shim width setting datum the slot die shim thickness setting datum is a 1-d extent setting datum, that specifies the thickness of some slot die shim slot die shim thickness setting datum the slot die head width setting datum is a 1-d extent setting datum, that specifies the width of some slot die head slot die head width setting datum a setting datum, that describes the flow rate that is set for a slot die coating process slot die coating flow rate setting datum a processed material, that consists of multiple layers ranging from fractions of nanometer to several micrometers in thickness Wikimedia Foundation. (2023, September 29). Thin film. Wikipedia. https://en.wikipedia.org/wiki/Thin_film thin-film stack illuminated jv analysis a carrier made from glass (usually silicates) glass carrier a front contact layer that consists of Indium Tin Oxide (ITO) ITO a front contact layer that consists of fluorine-doped tin oxide (FTO) FTO a buffer layer consisting of lithium flouride LiF buffer layer a buffer layer consisting of polyimide PI buffer layer silver back contact 2PacZ hole transport layer triple halide perovskite layer C60 electron transport layer thermal pvd process logging The current density measurement datum is a scalar measurement datum, that quantifies the result of some current density measurement current density measurement datum The external quantum efficiency measurement datum is a scalar measurement datum that quantifies the result of some external quantum efficiency measurement external quantum efficiency measurement datum 1 thin-film solar cell an object through which a chemical gets distributed onto a surface print head A print nozzle is a transferring object consisting of jet port with an opening for regulating and/or directing the flow of fluid or ink. http://purl.allotrope.org/ontologies/equipment#AFE_0002222 print nozzle print head width print nozzle width An ink cartridge or inkjet cartridge is a object/component of an inkjet printer that contains the ink that is deposited onto a substrate during printing. Wikimedia Foundation. (2023, October 31). Ink cartridge. Wikipedia. https://en.wikipedia.org/wiki/Ink_cartridge. Retrieved on: 22.11.2023 cartridge cartridge pressure print head temperature the cartridge temperature is a temperature, that describes the temperature of some cartridge cartridge temperature is a nozzle distance that describes the distance between a printing nozzle and some material entity print nozzle distance substrate height print speed resolution is a process quality that describes the smallest change in a quality being measured by a sensor (measurement instrument, detector) that causes a perceptible change in the corresponding indication. http://purl.allotrope.org/ontologies/result#AFR_0001619 resolution printing resolution x printing direction The print head distance to substrate is a distance to substrate, that describe the distance between some print head and some substrate. print head distance to substrate print head angle print nozzle drop volume printing resolution y a profile is a datasets which defines the set values of an instrument or part of an instrument at specific time points. profile a print nozzle voltage profile is a profile which determines the voltage set of a nozzle in a printing process print nozzle voltage profile a print head path is a profile which describes how a print head is moving in a printing process. print head path a setting datum that specifies some time configuration time setting datum print nozzle voltage a setting datum, which describes the voltage to which a nozzle is set. print nozzle voltage setting datum the print head position is the position of a print head relative to the geometry of the printer. print head position a setting datum, that describes the position to which an entity is set. position setting datum a setting datum, that describes the position to which an print head is set. print head position setting datum anti solvent dropping flow rate The anti solvent dropping height is a dnozzle distance to substrate, that describes the height out of which some anti solvent is dropped onto some entity. anti solvent dropping height the anti solvent dropping height setting datum is a nozzle distance to substrate setting datum, that specifies the dropping height of some anti solvent anti solvent dropping height setting datum the anti solvent dropping flow rate setting datum is a setting datum, that specifies the flow rate of some anti solvent anti solvent dropping flow rate setting datum the print nozzle width setting datum is a 1-d extent setting datum, that specifies the width of some print nozzle print nozzle width setting datum a volume setting datum that specifies some drop volume configuration of some print nozzle print nozzle drop volume setting datum a setting datum, that describes the set pressure of an cartridge cartridge pressure setting datum the print head distance to substrate setting datum is a distance to substrate setting datum, that specifies the distance between some print head and some substrate print head distance to substrate setting datum a setting datum that specifies some print speed print speed setting datum a setting datum that specifies the temperature of some print head print head temperature setting datum a setting datum, that describes the set angle of an print head print head angle setting datum the print head width setting datum is a 1-d extent setting datum, that specifies the width of some print head print head width setting datum the cartridge temperature setting datum is a temperature setting datum, that specifies the thermal energy of some cartridge cartridge temperature setting datum the print nozzle distance setting datum is a 1-d extent setting datum, that specifies the distance between some nozzle and some entity print nozzle distance setting datum air knife shim width the air knife shim width setting datum is a 1-d extent setting datum, that specifies the set width of some air knife shim air knife shim width setting datum the contact angle is an angle, at which some liquid surface and some solid surface collide contact angle hotplate infrared light source radiation quenching is a sample quenching method, that uses heat to affect the crystallization of some layer thermal quenching radiation quenching is a sample quenching method, that uses some radiation to affect the crystallization of some layer radiation quenching pipet pipette substrate length substrate width a deposited wet film has a wet film thickness the wet film thickness is a thickness, that describes the spatial dimension of some wet film wet film thickness pipette volume pipette tip opening diameter substrate area The distance to substrate is a length, that describes the distance between some continuant and some substrate distance to substrate tip diameter round nozzle tip diameter output velocity the substrate speed is the speed at which some substrate moves (e.g.the speed of the substrate in a roll to roll coater) substrate speed the air velocity describes the velocity of some air after being accelerated by some entity (e.g. some air knife) gas velocity the gas velocity setting datum is a velocity setting datum, that specifies the set velocity value of some gas stream gas velocity setting datum the flow rate setting datum is a setting datum, that specifies the set flow rate value flow rate setting datum the volumetric flow rate setting datum is a flow rate setting datum, that specifies the set flow rate value of some liquid volumetric flow rate setting datum the distance to substrate setting datum is a 1-d extent setting datum, that specifies the distance between some substrate and some entity distance to substrate setting datum The hotplate distance to substrate is a distance to substrate, that describes the distance between a hotplate and some substrate hotplate distance to substrate pipette tip opening diameter setting datum The angle measurement datum is a scalar measurement datum, quantifies the result of some angle measurement angle measurement datum the contact angle measurement datum is a angle measurement datum, that quantifies the result of some contact angle measurement contact angle measurement datum the hotplate distance to substrate setting datum is a distance to susbtrate setting datum, that specifies the distance between some hotplate and some entity hotplate distance to substrate setting datum transferring device impingement angle the transferring device impingement angle setting datum is a angle setting datum, that specifies the impingement angle of some transferring device transferring device impingement angle setting datum the nozzle speed is a speed quality, that specifies the rate of movement of some nozzle round nozzle speed the nozzle speed setting datum is a speed setting datum, that specifies the amount of rate of movement of some nozzle nozzle speed setting datum the nozzle impingement angle is an impingement angle, that describes the angle at which a stream from a nozzle collides with another object round nozzle impingement angle the round nozzle impingement angle setting datum is a transferring device impingement angle setting datum, that specifies the impingement angle of some round nozzle round nozzle impingement angle setting datum the air knife impingement angle measurement datum is a angle measurement datum, that quantifies the result of some air knife impingement angle measurement air knife impingement angle measurement datum the nozzle impingement angle measurement datum is a angle measurement datum, that quantifies the result of some round nozzle impingement angle measurement round nozzle impingement angle measurement datum the count measurement datum that specifies the output of some counting count measurement datum the number of averages setting datum is a setting datum that is the specification of the amount of averages number of averages setting datum count is a process quality, that describes the result of some counting process count The layer morphology describes the morphology of some layer layer morphology The layer thickness describes the thickness of some layer. layer thickness the layer transmittance describes the energy loss of some radiatant power that passes through some layer layer transmittance sheet resistance describes the resistance of some entity with a negligible dimension (often thickness) sheet resistance describes the time span after which a solar cell drops to 95% of its original efficiency time until 95 percent efficiency the time until 95 percent efficiency datum is a scalar datum, that quantifies the time until a solar cell drops to 95 percent of its initial efficiency time until 95 percent efficiency datum the conductivity measurement datum is a scalar measurement datum, that quantifies the output of some conductivity measurement conductivity measurement datum the blade distance to substrate is a distance to substrate quality, that describes the distance between some blade and some substrate blade distance to substrate the blade distance to substrate setting datum is a distance to substrate setting datum, that specifies the distance between some blade and some substrate blade distance to substrate setting datum the blade speed is a speed, that describes the relative rate of movement of some blade relative to some material entity blade traverse speed the blade speed setting datum is a speed setting datum, that specifies the relative rate of movement between some blade and some material entity blade traverse speed setting datum the blade angle is an angle. that describes the angle between some blade and some material entity blade angle the blade angle setting datum is a angle setting datum, that specifies the angle between some blade and some material entity blade angle setting datum the blade pressure is a pressure, that describes the force per area applied by some blade blade pressure the blade pressure setting datum is a pressure setting datum, that specifies the force per area applied by some blade blade pressure setting datum a doctor blade is a device, that is being used to remove excess ink by traversing over some surface during wet chemical deposition doctor blade doctor blade width the doctor blade edge shape describes the geometry of the part of the blade, that gets in contact with the removed excess ink during blade coating doctor blade edge shape The solution temperature is a temperature, that is the physical quality of the thermal energy of some solution solution temperature The precursor solution temperature is a solution temperature, that is the physical quality of the thermal energy of some precursor solution precursor solution temperature The solution temperature setting datum is a temperature setting datum, that specifies the temperature settings of some solution solution temperature setting datum The precursor solution temperature setting datum is a solution temperature setting datum, that specifies the temperature settings for some precursor solution precursor solution temperature setting datum the precursor solution volume is volume, that is the amount of 3 dimensional space some precursor solution occupies precursor solution volume fluid based quenching heat based quenching round nozzle round nozzle tip diameter setting datum the nozzle distance to substrate setting datum is a distance to substrate setting datum, that specifies the distance between some nozzle and some entity nozzle distance to substrate setting datum nozzle speed round nozzle speed setting datum reynolds number the reynolds number datum is a scalar datum, that quantifies some reynolds number reynolds number datum raditation source distance to substrate the radiation source distance to substrate setting datum is a distance to substrate setting datum, that specifies the distance between some radiation source and some substrate raditation source distance to substrate setting datum drying is a heat based quenching, that involves no additional heat source device Trocknen drying transferring device pressure round nozzle pressure pipette pressure transferring device pressure setting datum pipette pressure setting datum nozzle pressure setting datum round nozzle pressure setting datum a setting datum that specifies the temperature of some substrate substrate temperature setting datum the temperrature of a device for example in a measurement process substrate temperature the efficiency of a solar cell with respect to its active area photovoltaic device efficiency active area the efficiency of a solar cell with respect to its total area photovoltaic device efficiency total area a photovaltaic device which consists of multiple distinct stacked solarcells stacked tandem cell Chlorobenzene Ethanol IPA Water 1-Butanol 2-Methoxy Ethanol Chloroform Dichlorobenzene n-Butylalcohol n-Butyl Alcohol 2-Butanol 1-Butanol Ethanol Acetonitil Acetonitrile Acetyl Aceton Anhydrous 1-Butanol Anisole a-Terpineol Butanol DCB Distilled Water DMF Ethanol Ethanol Amine Ethyl Alcohol Ethyl Cellulose HCl Isopropyl Alcohol Lauric Acid Methanol NaOH Aqueous Solution n-Butanol n-Butyl Alcohol Nitric Acid Octane OP P25 Polyethylene Glycol TAA Terpineol Tetralin TiO2-np Trifluor Ethanol TritonX-100 Mechanical Scrubbing HCL Aceton cleaning DI Water cleaning Isopropanol cleaning Mucasol cleaning Scrubbing Lead iodide pin nip true TODO: Add homeomorphy axiom person