The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies. ENPADASI_WP4 ONS 2024-07-03 editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label 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 label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label 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 OBI_0000281 has curation status has curation status definition definition textual definition A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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. 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 definition definition textual 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 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 alternative label alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative label alternative term alternative term alternative_term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 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 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source definition_source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note 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 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 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 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 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 term replaced by term replaced by term_mapping_to_UMLS term_mapping_to_NCIT NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term Super-property collecting all annotation properties assigning classes in ONS to specific subset (i.e. Metadata search). For each subset, there will be an annotation property. To assign a class to a subset, set the annotation property value to "TRUE" in subset of ONS Annotation properties assigning a class to the ONS-subset of metadata search classes. Set value to "TRUE" to assign a class. in minimal requirement ONS subset A metadata relation between a class and its taxonomic rank (eg species, family) has_rank The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source An account of the content of the resource. dcterms:description http://www.ebi.ac.uk/efo/MESH_definition_citation is an annotation property that is drawn from MESH http://www.ebi.ac.uk/efo/MSH_definition_citation is an annotation property that is drawn from MSH A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source. An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 FULL_SYN Synonym with Source Data has exact synonym has exact synonym has_exact_synonym An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym has synonym label label label label is part of a core relation that holds between a part and its whole part of part of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent 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 has part realized in realized in realizes realizes preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. preceded by concretizes has measurement unit label A (currently) primitive relation that relates an information artifact to an entity. Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E mentions A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q is quality measurement of relates a process to a time-measurement-datum that represents the duration of the process is duration of inverse of the relation of is quality measurement of is quality measured as provides_service_consumer_with The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. provides_service_consumer_with is_supported_by_data The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI Philly 2011 workshop is_supported_by_data has_specified_input has_specified_input The inverse property of is_specified_input_of has_specified_input is_specified_input_of A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. is_specified_input_of has_specified_output has_specified_output The inverse property of is_specified_output_of 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. is_specified_output_of is_proxy_for A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be. is_proxy_for achieves_planned_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. PPPB branch derived achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain is grain of A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 is grain of 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 objective_achieved_by is member of organization Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. Person:Alan Ruttenberg Person:Helen Parkinson is member of organization has organization member Relating an organization to a legal person or organization. has organization member specifies value of A relation between a value specification and an entity which the specification is about. specifies value of has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification has performer A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. OBI has performer process is result of is a relationship between a process and a preceding occurrent that directly caused the later one to occur process is result of inheres in 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. characteristic of bearer of Inverse of characteristic_of has characteristic has characteristic participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in has participant a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant 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 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 a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence function of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence quality of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence role of a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence has function a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence has quality has role 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 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 derives from 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 derives into is location of a relation between two independent continuants, the location and the target, in which the target is entirely within the location location of located in a relation between two independent continuants, the target and the location, in which the target is entirely within the location located in w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has component process immediately preceded by x overlaps y if and only if there exists some z such that x has part z and z part of y overlaps x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. in taxon w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has component x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x surrounded by x adjacent to y if and only if x and y share a boundary. adjacent to 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. 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. has output A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. has active substance has active ingredient q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. characteristic of part of A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) ecologically related to A mereological relationship or a topological relationship mereotopologically related to is member of is a mereological relation between a item and a collection. SIO member of has member is a mereological relation between a collection and an item. SIO has member p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. causally upstream of or within An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. biotically interacts with A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. causal relation between processes depends on causal relation between entities s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. determined by causally influenced by A relation that holds between an attribute or a qualifier and another attribute. has modifier participates in a biotic-biotic interaction with A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. causal relation between material entity and a process is related to has measurement value has specified numeric value A relation between a value specification and a number that quantifies it. OBI has specified numeric value has specified value A relation between a value specification and a literal. OBI has specified value beta12orEarlier Operation A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Function A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Computational method Computational operation Computational procedure Computational subroutine Function (programming) Lambda abstraction Mathematical function Mathematical operation Computational tool Process sumo:Function Operation beta12orEarlier Query and retrieval Search or query a data resource and retrieve entries and / or annotation. Search or query a data resource and retrieve entries and / or annotation. Database retrieval Query Query and retrieval beta12orEarlier Literature search Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics. Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics. Literature search beta12orEarlier Database search Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. Search Database search beta12orEarlier true Proteomics Protein and peptide identification, especially in the study of whole proteomes of organisms. true Protein and peptide identification, especially in the study of whole proteomes of organisms. Metaproteomics Peptide identification Protein and peptide identification Proteomics beta12orEarlier true Genomics Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. true Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. Personal genomics Genomics 1.1 true Metabolomics The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. true The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. Metabolomics 1.1 true Metagenomics The study of genetic material recovered from environmental samples, and associated environmental data. Community genomics Ecogenomics Environmental genomics Environmental omics The study of genetic material recovered from environmental samples, and associated environmental data. Biome sequencing Environmental sequencing Shotgun metagenomics Metagenomics 1.3 true Transcriptomics The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. true The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. Comparative transcriptomics Metatranscriptomics Transcriptome Transcriptomics Examples of interventions are putting health warnings on cigarette packets, providing free stop smoking services and banning smoking in public places. A planned process that has the aim of influencing an outcome. intervention Oral consumption behaviour that involves swallowing a liquid material. 2024-05-03T01:01:39Z drinking Oral consumption behaviour that involves chewing and swallowing some solid components 2024-05-03T00:57:04Z eating spatial region An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) process process disposition disposition A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable realizable entity quality specifically dependent continuant A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) characteristic material property specifically dependent continuant specifically dependent continuant https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role fiat object part ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. object aggregate site object function material entity An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity material entity immaterial entity b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) relational quality history A biological role that may be assigned to a dietary chemical component based on evidence that supports a role defined at the levels of molecular interaction, cellular process or physiological role. human dietary role Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals. aldose A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. polynucleotide Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. carbohydrate Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acid An aldohexose used as a source of energy and metabolic intermediate. glucose 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. lipid Any six-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldohexose) or a ketone group at position 2 (ketohexose). hexose Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity A role played by the molecular entity or part thereof within a biological context. biological role A cyclic compound having as ring members atoms of carbon and at least of one other element. organic heterocyclic compound Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). hydroxides A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule An oxoacid containing a single carboxy group. monocarboxylic acid Any fatty acid with one double or triple bond in the fatty acid chain and singly bonded carbon atoms in the rest of the chain. MUFAs have positive effects on the cardiovascular system, and in diabetes treatment. monounsaturated fatty acid oxygen molecular entity Any fatty acid containing more than one double bond. Acids in this group are reported to have cardioprotective effects; and levels are lowered in chronic fatigue syndrome. polyunsaturated fatty acid Any fatty acid containing no carbon to carbon multiple bonds. Known to produce adverse biological effects when ingested to excess. saturated fatty acid Any fatty acid containing at least one C=C or C#C bond. unsaturated fatty acid An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. amide A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. primary amide A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. heteroorganic entity A p-block molecular entity containing any pnictogen. pnictogen molecular entity Any p-block molecular entity containing a chalcogen. chalcogen molecular entity A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. carboxylic acid A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. main group molecular entity carbon group molecular entity Any molecule that consists of a series of atoms joined together to form a ring. cyclic compound hydrogen molecular entity A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character. aromatic compound organic aromatic compound An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity A main group molecular entity that contains one or more atoms of a p-block element. p-block molecular entity A macromolecule formed by a living organism. biomacromolecule information biomacromolecule A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid Any organic molecule that consists of atoms connected in the form of a ring. organic cyclic compound A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). heteroarene A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. macromolecule A hexose with a (potential) aldehyde group at one end. aldohexose Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compound Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. fatty acid Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group. monosaccharide carbon oxoacid A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. protein Any molecular entity consisting of more than one atom. polyatomic entity Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compound Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. organic oxo compound An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound An organochalcogen compound containing at least one carbon-oxygen bond. organooxygen compound A molecular entity consisting of two or more chemical elements. heteroatomic molecular entity An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. carboxamide A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. organic amino compound Any molecular entity that contains carbon. organic molecular entity A role is particular behaviour which a material entity may exhibit. role nitrogen molecular entity physiological role A cyclic compound having as ring members atoms of at least two different elements. heterocyclic compound Any compound that has a nucleobase as a part. nucleobase-containing molecular entity Any organic molecular entity that is acidic and contains carbon in covalent linkage. organic acid Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. organic molecule A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. food component Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. carbohydrates and carbohydrate derivatives A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cultured cell A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. experimentally modified cell in vitro A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation. clinical measurement Morphological measurement involving the entire body of an organism. whole body morphological measurement The heaviness or degree to which an entire organism's body is drawn to the earth by gravity. body weight body weight Measurement of the structure or forms of the entire body or parts of the body of an organism. body weights and measures body morphological measurement calculated body morphological measurement A quantification of a parameter of the chemical composition of blood. blood chemistry measurement Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in blood. blood protein measurement total blood protein measurement blood protein measurement A measurement of the blood, it's contents, cells or other factors contained within the blood. hematological measurement blood measurement The level of steroids found in a specific volume of blood. blood steroid level Any value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipid, any of a structurally diverse group of organic compounds found in blood that are insoluble in water but soluble innonpolar solvents that, among other biological functions, serve as a source of fuel and are an important constituent of cell structure. lipid measurement blood lipid measurement Measurement of the entire amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, without taking into account any association with other molecules such as lipoproteins, in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. total cholesterol measurement blood total cholesterol level Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in high-density lipoprotein (HDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. HDL is the smallest of the major lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The HDL class of lipoproteins, specifically the subtypes of HDL2 and HDL3, have densities between 1.063 and 1.210 g/ml. blood HDL-C high density lipoprotein cholesterol measurement blood high density lipoprotein cholesterol level Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in low-density lipoprotein (LDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. LDL constitute a class of relatively large, heterogeneous lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The LDL class of lipoproteins has a density between 1.019 and 1.063 g/ml. In some animal species, such as canine and rodents, this may overlap with the HDL1 class and be designated LDL/HDL1. low density lipoprotein cholesterol measurement blood low density lipoprotein cholesterol level A measurement relating body weight to height in an organism; typically calculated as the weight of an individual divided by the height of that individual squared. For quadrupeds, the square of body height is often replaced by the square of body length. true body mass index body mass index (BMI) The amount of lipoproteins, any of a group of conjugated proteins that have at least one lipid component, in a specific volume of blood. blood lipoprotein level The quantification of any morphological or physiological parameter related to intake or ingestion, especially of food or drink, or a value resulting from such a quantification. consumption measurement Amount of drink, that is, a liquid that is brought into the mouth and swallowed to quench thirst, for nourishment, etc., consumed per unit time. drink intake rate The quantification of any parameter related to the process whereby drink, any liquid that is brought into the mouth and swallowed to quench thirst, for nourishment, etc., is taken in for utilization by the body. beverage consumption measurement drink intake measurement The quantification of any parameter related to the process whereby food (i.e. material, usually of plant or animal origin, that contains essential nutrients such as carbohydrates, fats, proteins, vitamins, and/or minerals and that is ingested and assimilated by an organism to produce energy, stimulate growth, and maintain life) is taken in for utilization by the body. food intake measurement calculated body weight measurement The amount of ethanol, a colorless volatile flammable liquid CH3CH2OH that is the intoxicating agent in liquors, consumed per unit time. ethanol drink intake rate The amount of sterol, any of a group of steroids with a long (8 to 10 carbons) aliphatic side-chain at position 17 and at least one alcoholic group, in a specified sample of blood. blood sterol level The amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, in a specified sample of blood. Cholesterol in the blood is generally associated with various lipoproteins. blood cholesterol level A value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipoprotein, any of a class of complex molecules found in blood that consist of a protein membrane surrounding a core of lipids. blood lipoprotein measurement Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in lipoprotein molecules in a specified volume of blood. Lipoprotein particles are complexes that consist of protein surrounding a core of lipids. blood lipoprotein cholesterol level http://purl.obolibrary.org/obo/IAO_0000015 Pier 'representational entity' This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc information representation A physiological assay of the human body that uses such tools as body mass index, basal metabolic rate, bioelectrical impedance, and dual energy x-ray absorptiometry, along with measurements of skinfold thickness and arm muscle circumference, to assess the structure, form, and composition of the body for purposes of comparison. PERSON: Nicole Vasilevsky http://www.answers.com/topic/anthropometric-analysis true anthropometric analysis Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products. https://en.wikipedia.org/wiki/Food food product A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. mammalian meat food product This class includes food products which are derived from or produced by a plant. plant food product cheese starter culture food product A seafood product is a vertebrate or invertibrate organism from an aquatic environment. animal seafood product A food product which is derived from or produced by an animal that has a vertibrae. vertebrate animal food product A food product made from an avian egg. avian egg food product Suidae is a family of artiodactyl mammals which are commonly called pigs, hogs or boars. In addition to numerous fossil species, 17 extant species are currently recognized (or 18 counting domestic pigs and wild boars separately), classified into between four and eight genera. The family includes the domestic pig, Sus scrofa domesticus or Sus domesticus, in addition to numerous species of wild pig, such as babirusas and warthogs. All suids, or swine, are native to the Old World, ranging from Asia to Europe and Africa. https://en.wikipedia.org/wiki/Suidae swine food product bovine meat food product A food product consisting of an edible fungi or mushroom or yeast. fungus food product invertebrate animal food product Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. prepared food product This food product type includes food products which are derived from a large, diverse group of photosynthetic organisms. algal food product animal lipid food product A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). fish food product A food product that is derived from some avian. avian food product A dairy food product has mammilian milk or a milk component as an ingredient. dairy product milk product dairy food product milk or milk based food product A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. egg food product animal based refined or partially-refined food product A salad food product with a prominent animal meat ingredient. animal based salad food product animal fat or oil refined food product animal product based flavoring or seasoning animal soup food product A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component. food product component food flavoring or seasoning product human milk based food product refined or partially-refined food product amphibian or reptile food product salad food product soup food product A food product consisting of food material derived primarily from a single organism. food product by organism Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience food foodstuff nourishment sustenance food material requires discussion A process involving the physical transformation of a food source or food product into some derived organic material or food product food transformation process Food material which has been categorized by a characteristic such as granularity or temperature. food material by characteristic Game or quarry is any animal hunted for sport or for food. The type and range of animals hunted for food varies in different parts of the world. In some countries, game is classified, including legal classification with respect to licences required, as either "small game" or "large game" https://en.wikipedia.org/wiki/Game_(hunting) game animal food product A food product consisting of food material derived from ingredients sourced from multiple organisms. multi-component food product A lipid food product is a food product made primarily of plant or animal fat or oil fats and oils oils and fats lipid food product animal meat food product A whole animal. animal A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet). https://en.wikipedia.org/wiki/Vegetarian_cuisine vegetarian food vegetarian food product A plan specification for making a food product, which may have ingredient, device, action and objective specifications. food recipe A food product that is derived from some animal. animal food product Material which is produced by an animal. animal substance Milk which is produced by animal lactation. animal milk Raw animal milk. animal milk (raw) animal-derived food Breast milk is the milk produced by the breasts (or mammary glands) of a human female. https://en.wikipedia.org/wiki/Breast_milk human milk (raw) A food product that has not been cooked. food (raw) processed food product mammalian milk product Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. https://en.wikipedia.org/wiki/Mammal mammal A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. vertebrate animal This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups. organism by alternate grouping amphibian Anatomical or other part(s) or substances derived from plant or animal or fungal organisms. organism material A material that derives from some animal. animal material Food substance or component consisting predominantly of mixed glycerol esters of fatty acids and, in far lesser amounts, of fatty acids, sterols and pigments. A fat is a solid at room temperature, an oil is a liquid at room temperature (20 degrees C.). Excludes essential oils. fat or oil A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed. extract, concentrate or isolate of plant or animal A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*. food (liquid) The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. Index all methods for which information is available, even if a corresponding descriptor has already been used in *H. TREATMENT APPLIED*. Preservation descriptors refer to the finished food as a whole with these exceptions: (1) if the components of a multi-component food, such as cream pie, are preservation by different methods, index all methods; (2) if chemical preservatives are declared on the label, always index them even if it is known that the preservative was introduced through or is only present in a component or ingredient of the food; and (3) if the preservation method for an ingredient is declared on the label (such as brie cheese made from pasteurized milk) index it. Also use *INGREDIENT preservation by THERMAL PROCESSING* or *INGREDIENT preservation by IRRADIATION* when ingredients have been pasteurized, ultrapasteurized, sterilized or irradiated. food preservation process OBSOLETE. The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0022414 reproductive physiological process obsolete reproduction true A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. organ system process system process A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular function molecular_function Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. enzyme activity catalytic activity Catalysis of the reaction: ATP + D-fructose-6-phosphate = ADP + D-fructose 1,6-bisphosphate. 6-phosphofructokinase reduction 6-phosphofructokinase activity Catalysis of the reaction: beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate. fructose-bisphosphate aldolase activity Catalysis of the reaction: D-glucose 6-phosphate = D-fructose 6-phosphate. glucose-6-phosphate isomerase activity Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+. glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate. lactate dehydrogenase activity Catalysis of the hydrolysis of any O-glycosyl bond. O-glucosyl hydrolase activity hydrolase activity, hydrolyzing O-glycosyl compounds Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides. beta-galactosidase activity Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H+. phosphoglycerate kinase activity Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate. PGM phosphoglycerate mutase activity Catalysis of the reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O. 2-phospho-D-glycerate-hydrolase activity phosphopyruvate hydratase activity Catalysis of the reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate. triose-phosphate isomerase activity The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. carbohydrate metabolism carbohydrate metabolic process The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. monosaccharide metabolism monosaccharide metabolic process The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. cellular glucose metabolic process glucose metabolism glucose metabolic process The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose. glucose breakdown glucose catabolism glucose degradation glucose catabolic process The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage. organic acid metabolism organic acid metabolic process The chemical reactions and pathways involving lactate, the anion of lactic acid. 2-hydroxypropanoate metabolic process 2-hydroxypropanoate metabolism alpha-hydroxypropionate metabolic process alpha-hydroxypropionate metabolism lactate metabolism lactate metabolic process The chemical reactions and pathways involving pyruvate, 2-oxopropanoate. pyruvate metabolism pyruvate metabolic process The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances. generation of precursor metabolites and energy The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules. glycolytic process The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP). fermentation Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase-containing compound metabolic process The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. purine nucleotide metabolism purine nucleotide metabolic process OBSOLETE. The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate. obsolete nucleoside diphosphate phosphorylation true The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. purine nucleotide breakdown purine nucleotide catabolism purine nucleotide degradation purine nucleotide catabolic process OBSOLETE. The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. GO:0008152 obsolete cellular aromatic compound metabolic process true The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid. NAD (reduced) metabolic process NAD (reduced) metabolism NADH metabolism reduced NAD metabolic process reduced NAD metabolism reduced nicotinamide adenine dinucleotide metabolic process reduced nicotinamide adenine dinucleotide metabolism NADH metabolic process A metabolic process that generates a pool of NADH by the reduction of NAD+. NAD (reduced) regeneration reduced NAD regeneration reduced nicotinamide adenine dinucleotide regeneration NADH regeneration The chemical reactions and pathways involving any phosphorylated nucleoside. nucleoside phosphate metabolism nucleoside phosphate metabolic process OBSOLETE. The process of introducing a phosphate group into ADP, adenosine diphosphate, to produce ATP. ADP phosphorylation obsolete ATP generation from ADP true The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus. phosphorus metabolism phosphorus metabolic process The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. phosphate metabolism phosphate-containing compound metabolic process OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GO:0008152 obsolete nitrogen compound metabolic process true The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. digestion The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. behavioral response to stimulus behaviour behavioural response to stimulus behavior Behavior associated with the intake of food. behavioral response to food behavioural response to food feeding behaviour feeding behavior biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. biological process physiological process biological_process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. metabolism metabolic process Catalysis of the transfer of a phosphate group, usually from ATP, to a phosphofructose substrate molecule. phosphofructokinase activity The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. breakdown catabolism degradation catabolic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. anabolism biosynthesis synthesis biosynthetic process The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates). nucleotide metabolism nucleotide metabolic process The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar. nucleoside diphosphate metabolism nucleoside diphosphate metabolic process The chemical reactions and pathways resulting in the breakdown of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar. nucleoside diphosphate breakdown nucleoside diphosphate catabolism nucleoside diphosphate degradation nucleoside diphosphate catabolic process The chemical reactions and pathways involving purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar. purine nucleoside diphosphate metabolism purine nucleoside diphosphate metabolic process The chemical reactions and pathways resulting in the breakdown of purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar. purine nucleoside diphosphate breakdown purine nucleoside diphosphate catabolism purine nucleoside diphosphate degradation purine nucleoside diphosphate catabolic process The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar. nucleoside triphosphate metabolism nucleoside triphosphate metabolic process The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar. purine nucleoside triphosphate metabolism purine nucleoside triphosphate metabolic process The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. purine ribonucleotide metabolism purine ribonucleotide metabolic process The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. purine ribonucleotide breakdown purine ribonucleotide catabolism purine ribonucleotide degradation purine ribonucleotide catabolic process The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates). nucleotide breakdown nucleotide catabolism nucleotide degradation nucleotide catabolic process The chemical reactions and pathways involving purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar. purine ribonucleoside diphosphate metabolism purine ribonucleoside diphosphate metabolic process The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar. purine ribonucleoside diphosphate breakdown purine ribonucleoside diphosphate catabolism purine ribonucleoside diphosphate degradation purine ribonucleoside diphosphate catabolic process The chemical reactions and pathways involving a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar. ribonucleoside diphosphate metabolism ribonucleoside diphosphate metabolic process The chemical reactions and pathways resulting in the breakdown of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar. ribonucleoside diphosphate breakdown ribonucleoside diphosphate catabolism ribonucleoside diphosphate degradation ribonucleoside diphosphate catabolic process The chemical reactions and pathways involving a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar. ribonucleoside triphosphate metabolism ribonucleoside triphosphate metabolic process The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar. purine ribonucleoside triphosphate metabolism purine ribonucleoside triphosphate metabolic process The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. ribonucleotide metabolism ribonucleotide metabolic process The chemical reactions and pathways resulting in the breakdown of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. ribonucleotide breakdown ribonucleotide catabolism ribonucleotide degradation ribonucleotide catabolic process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. cell physiology cellular physiological process cellular process Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative. galactosidase activity The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released. chemoorganotrophy energy derivation by oxidation of organic compounds The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. carbohydrate breakdown carbohydrate catabolism carbohydrate degradation catabolic carbohydrate metabolic process catabolic carbohydrate metabolism carbohydrate catabolic process The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage. organic acid anabolism organic acid biosynthesis organic acid formation organic acid synthesis organic acid biosynthetic process Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. phosphokinase activity kinase activity The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. phosphorylation Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. redox activity oxidoreductase activity Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. oxidoreductase activity, acting on CH-OH group of donors Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. transferase activity Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor). phosphotransferase activity, alcohol group as acceptor Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a carboxyl group (acceptor). phosphotransferase activity, carboxyl group as acceptor Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. hydrolase activity Catalysis of the hydrolysis of any glycosyl bond. glycosidase activity hydrolase activity, acting on glycosyl bonds Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. lyase activity Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. carbon-carbon lyase activity Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone. aldehyde-lyase activity Catalysis of the breakage of a carbon-oxygen bond. carbon-oxygen lyase activity Catalysis of the cleavage of a carbon-oxygen bond by elimination of water. hydro-lyase activity Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. isomerase activity Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor are the same molecule, and no oxidized product appears. intramolecular isomerase activity intramolecular oxidoreductase activity Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor, which is an aldose or a ketose, are the same molecule, and no oxidized product appears. intramolecular isomerase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity, interconverting aldoses and ketoses Catalysis of the transfer of a functional group from one position to another within a single molecule. mutase activity intramolecular transferase activity Catalysis of the transfer of a phosphate group from one position to another within a single molecule. intramolecular transferase activity, phosphotransferases phosphomutase activity phosphotransferase activity, with regeneration of donors, apparently catalyzing intramolecular transfers intramolecular phosphotransferase activity Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. oxidoreductase activity, acting on the aldehyde or oxo group of donors Catalysis of the transfer of a phosphate group, usually from ATP, to a carbohydrate substrate molecule. carbohydrate kinase activity The chemical reactions and pathways resulting in the formation of lactate from other compounds, including pyruvate. lactate anabolism from pyruvate lactate formation from pyruvate lactate synthesis from pyruvate pyruvate fermentation to lactate lactate biosynthetic process from pyruvate The chemical reactions and pathways resulting in the formation of lactate, the anion of lactic acid. lactate anabolism lactate biosynthesis lactate formation lactate synthesis lactate biosynthetic process The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule. hexose metabolism hexose metabolic process The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule. hexose breakdown hexose catabolism hexose degradation hexose catabolic process The chemical reactions and pathways involving a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base. pyridine nucleotide metabolism pyridine nucleotide metabolic process The chemical reactions and pathways resulting in the breakdown of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base. pyridine nucleotide breakdown pyridine nucleotide catabolism pyridine nucleotide degradation pyridine nucleotide catabolic process The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound. organophosphate metabolism organophosphate metabolic process The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, and possibly ethanol, yielding energy in the form of adenosine triphosphate (ATP). glucose fermentation to lactate lactate fermentation glucose catabolic process to lactate Fermentation that includes the anaerobic conversion of glucose to pyruvate via the glycolytic pathway. glycolytic fermentation The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, via canonical glycolysis, yielding energy in the form of adenosine triphosphate (ATP). glucose fermentation to lactate via pyruvate homofermentation homofermentative lactate fermentation homofermentative pathway homolactate fermentation homolactic fermentation glucose catabolic process to lactate via pyruvate The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid. NAD (oxidized) metabolic process NAD (oxidized) metabolism NAD metabolism nicotinamide adenine dinucleotide metabolic process nicotinamide adenine dinucleotide metabolism oxidized NAD metabolic process oxidized NAD metabolism oxidized nicotinamide adenine dinucleotide metabolic process oxidized nicotinamide adenine dinucleotide metabolism NAD metabolic process The chemical reactions and pathways resulting in the breakdown of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; catabolism may be of either the oxidized form, NAD, or the reduced form, NADH. NAD (oxidized) catabolic process NAD (oxidized) catabolism NAD (reduced) catabolic process NAD (reduced) catabolism NAD breakdown NAD catabolism NAD degradation NADH catabolic process NADH catabolism nicotinamide adenine dinucleotide catabolic process nicotinamide adenine dinucleotide catabolism oxidized NAD catabolic process oxidized NAD catabolism oxidized nicotinamide adenine dinucleotide catabolic process oxidized nicotinamide adenine dinucleotide catabolism reduced NAD catabolic process reduced NAD catabolism reduced nicotinamide adenine dinucleotide catabolic process reduced nicotinamide adenine dinucleotide catabolism NAD catabolic process The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar. ribose phosphate metabolism ribose phosphate metabolic process The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). carboxylic acid metabolism carboxylic acid metabolic process A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. digestive system process The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. blood cell biosynthesis blood cell formation haemopoiesis hematopoiesis hemopoiesis Any biological process, occurring at the level of a multicellular organism, pertinent to its function. organismal physiological process multicellular organismal process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. developmental process The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-). monocarboxylate metabolic process monocarboxylic acid metabolism monocarboxylic acid metabolic process OBSOLETE. The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. GO:0008152 cellular nitrogen compound metabolism obsolete cellular nitrogen compound metabolic process true The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid breakdown nucleobase, nucleoside, nucleotide and nucleic acid catabolism nucleobase, nucleoside, nucleotide and nucleic acid degradation nucleobase-containing compound catabolic process The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue. eating behaviour eating behavior The specific behavior of an organism relating to the intake of liquids, especially water. drinking behaviour drinking behavior The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). keto acid metabolic process keto acid metabolism ketoacid metabolic process ketoacid metabolism oxo acid metabolic process oxo acid metabolism oxoacid metabolism oxoacid metabolic process Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H + H+. D-glyceraldehyde 3-phosphate:NAD(P)+ oxidoreductase (phosphorylating) glyceraldehyde-3-phosphate dehydrogenase (NAD(P)) (phosphorylating) triosephosphate dehydrogenase (NAD(P)) glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism cellular metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. primary metabolism primary metabolic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular anabolism cellular biosynthesis cellular formation cellular synthesis cellular biosynthetic process The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. small molecule metabolism small molecule metabolic process The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule. small molecule catabolism small molecule catabolic process The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. small molecule biosynthesis small molecule biosynthetic process The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate. ADP metabolism ADP metabolic process The chemical reactions and pathways resulting in the breakdown of ADP, adenosine 5'-diphosphate. ADP breakdown ADP catabolism ADP degradation ADP catabolic process The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator. ATP metabolism ATP metabolic process The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. monosaccharide breakdown monosaccharide catabolism monosaccharide degradation monosaccharide catabolic process The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. carboxylic acid anabolism carboxylic acid biosynthesis carboxylic acid formation carboxylic acid synthesis carboxylic acid biosynthetic process The chemical reactions and pathways resulting in the breakdown of organophosphates, any phosphate-containing organic compound. organophosphate breakdown organophosphate catabolism organophosphate degradation organophosphate catabolic process OBSOLETE. The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). GO:0008152 obsolete heterocycle metabolic process true The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide. nicotinamide nucleotide metabolism nicotinamide nucleotide metabolic process OBSOLETE. The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside. obsolete nucleotide phosphorylation true The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. cell development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. development of an anatomical structure anatomical structure development A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. cellular developmental process A process in which nutrients are taken up from the contents of the intestine. intestinal absorption The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide. nucleobase, nucleoside and nucleotide metabolism nucleobase-containing small molecule metabolic process The chemical reactions and pathways resulting in the breakdown of a monosaccharide into pyruvate, occurring through a fructose-6-phosphate intermediate, with the concomitant production of ATP and NADH. glycolysis through fructose-6-phosphate glycolytic process through fructose-6-phosphate The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, occurring through a glucose-6-phosphate intermediate, with the concomitant production of a small amount of ATP. glycolytic process through glucose-6-phosphate The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP. canonical glycolysis The chemical reactions and pathways resulting in the breakdown of glucose, with the production of pyruvate. glucose catabolism to pyruvate glucose catabolic process to pyruvate The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism organic substance metabolic process The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group. monocarboxylic acid anabolism monocarboxylic acid biosynthesis monocarboxylic acid formation monocarboxylic acid synthesis monocarboxylic acid biosynthetic process The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof. purine and derivative metabolic process purine-containing compound metabolism purine-containing compound metabolic process The chemical reactions and pathways resulting in the breakdown of a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof. purine and derivative catabolic process purine-containing compound breakdown purine-containing compound catabolism purine-containing compound degradation purine-containing compound catabolic process The chemical reactions and pathways involving a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof. pyridine and derivative metabolic process pyridine-containing compound metabolism pyridine-containing compound metabolic process The chemical reactions and pathways resulting in the breakdown of a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof. pyridine and derivative catabolic process pyridine-containing compound breakdown pyridine-containing compound catabolism pyridine-containing compound degradation pyridine-containing compound catabolic process The chemical reactions and pathways involving carbohydrate derivative. carbohydrate derivative metabolism carbohydrate derivative metabolic process The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative. carbohydrate derivative breakdown carbohydrate derivative catabolism carbohydrate derivative degradation carbohydrate derivative catabolic process The chemical reactions and pathways resulting in the breakdown of a nucleoside phosphate. nucleoside phosphate breakdown nucleoside phosphate catabolism nucleoside phosphate degradation nucleoside phosphate catabolic process The chemical reactions and pathways involving organic cyclic compound. organic cyclic compound metabolism organic cyclic compound metabolic process The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. organic cyclic compound breakdown organic cyclic compound catabolism organic cyclic compound degradation organic cyclic compound catabolic process The chemical reactions and pathways involving organonitrogen compound. organonitrogen compound metabolism organonitrogen compound metabolic process The chemical reactions and pathways resulting in the breakdown of organonitrogen compound. organonitrogen compound breakdown organonitrogen compound catabolism organonitrogen compound degradation organonitrogen compound catabolic process The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. organic molecular entity catabolic process organic substance breakdown organic substance catabolism organic substance degradation organic substance catabolic process The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. organic molecular entity anabolism organic molecular entity biosynthesis organic molecular entity biosynthetic process organic molecular entity formation organic molecular entity synthesis organic substance anabolism organic substance biosynthesis organic substance formation organic substance synthesis organic substance biosynthetic process The chemical reactions and pathways involving organic hydroxy compound. organic hydroxy compound metabolism organic hydroxy compound metabolic process The chemical reactions and pathways resulting in the formation of organic hydroxy compound. organic hydroxy compound anabolism organic hydroxy compound biosynthesis organic hydroxy compound formation organic hydroxy compound synthesis organic hydroxy compound biosynthetic process A phenotypic abnormality. Organ abnormality Phenotypic abnormality Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels. Body fails to respond to insulin Insulin resistance Laboratory abnormality Metabolism abnormality Abnormality of metabolism/homeostasis Impaired ability to absorb one or more nutrients from the intestine. Intestinal malabsorption Malabsorption Malabsorption An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine. Abnormality of the intestine Enteropathy Abnormal intestine morphology Any deviation from the normal concentration of a lipid in the blood circulation. Abnormal circulating lipid concentration An inability to digest lactose. Lactose intolerance Milk intolerance Lactose intolerance Abnormality of glucose homeostasis. Abnormal glucose homeostasis An abnormality of the gastrointestinal tract. Abnormality of the GI tract Abnormality of the gastrointestinal tract Abnormality of the gastrointestinal tract An anomaly in the processes involved in the maintenance of an internal equilibrium. Abnormal homeostasis Abnormal structure of the gastrointestinal tract. Abnormal shape of the digestive system Morphological abnormality of the GI tract Morphological abnormality of the gastrointestinal tract Morphological anomaly of the digestive system Abnormal gastrointestinal tract morphology Abnormality of the digestive system A functional anomaly of the digestive system. Abnormality of digestive system physiology A structural anomaly of the digestive system. Abnormality of digestive system morphology Abnormal digestive system morphology An abnormal level of an analyte measured in the blood. Abnormal circulating metabolite concentration Any deviation of the concentration of an orrganic compound from the normal range. An organic compound is defined as any compound that contains a carbon atom. Abnormal circulating organic compound concentration conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. a directive information entity that specifies what should happen if the trigger condition is fulfilled OBI branch derived OBI_0000349 conditional specification measurement unit label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. measurement unit label objective specification 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. OBI Plan and Planned Process/Roles Branch OBI_0000217 true objective specification A directive information entity that describes an action the bearer will take. OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label datum label journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. A report that is published in a journal. a report that is published in a journal person:Alan Ruttenberg person:Chris Stoeckert OBI_0000159 group:OBI journal article data item 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. data item symbol An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. based on Oxford English Dictionary symbol information content entity A generically dependent continuant that is about some thing. OBI_0000142 Pier: 'data, information or knowledge'. OR 'representation information information content entity information entity A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. directive information entity directive information entity graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. OBI_0000240 group:OBI graph rule A rule is an executable which guides, defines, restricts actions. a rule is an executable which guides, defines, restricts actions OBI_0500021 PRS rule algorithm 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. OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification report Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record) 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification PERSON: Alan Ruttenberg PERSON: Melanie Courtot PERSON:Chris Stoeckert GROUP: OBI OBI_0000099 report data set 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. OBI_0000042 group:OBI data set data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term data about an ontology part plan specification A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. OBI Plan and Planned Process branch OBI_0000344 plan specification plan specification measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. OBI_0000305 group:OBI measurement datum version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. version number conclusion textual entity A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. conclusion textual entity textual entity A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. textual entity citation A textual entity intended to identify a particular publication. citation figure An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. figure diagram A figure that expresses one or more propositions diagram document A collection of information content entities intended to be understood together as a whole document publication A journal article or book A document that has been accepted by a publisher A document that is the output of a publishing process. PERSON: Lawrence Hunter true publication publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation document part An information content entity that is part of a document. document part supplementary material to a document A part of a document that is segregated from the rest of the document due to its size supplementary material to a document A scalar measurement datum that is the result of measuring a temporal interval time measurement datum email address email address author role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. author role A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing data item extraction from journal article A planned process in which a document is created or added to by including the specified input in it. wikipedia http://en.wikipedia.org/wiki/Documenting documenting A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity assigning a centrally registered identifier A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. Original proposal from Bjoern, discussions at IAO calls centrally registered identifier A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry ethical approval textual entity A textual entity that documents the ethical approval of some study design. ethical approval textual entity identifier An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. identifier An identifier referring to an individual entity that is ascribed personhood by the user of the identifier. http://en.wikipedia.org/wiki/Personal_name personal name An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. code set A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification). document act input document A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred. A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject. The term definition is adapted from NCIt definition of 'consent form' (C16468) with modification. Compared to the NCIt definition, the ICO definition does not restrict the form to a clinical trial. AK, FM, YH, YL, MH, EE NCIt C16468 NCIt C16468 C0009797 C16468 informed consent form An informed consent form that has been signed by at least one participant. an informed consent form that has been signed by at least one participant. YH true signed informed consent form signed informed consent form A person who is the contact for questions about research. true contact person for questions about research arterial disorder endocrine pancreas disorder Scomberomorus plurilineatus Momordiceae Sicyoeae Benincaseae Cucurbiteae Ondatra Solenocera membranacea Ondatra zibethicus Aequipecten Aequipecten opercularis Fragaria chiloensis Fragaria virginiana Digitaria exilis Isacia Isacia conceptionis Oxynotus centrina Vimba Benincasa Benincasa hispida Viruses Asteroideae Anthemideae Calenduleae Heliantheae Eupatorieae Cardueae Eledone cirrhosa Euphausia pacifica Vitis rotundifolia Vitis labrusca Hoplobatrachus tigerinus Castanea crenata Zizania palustris Mycteroperca Odontesthes Atherinopsinae Lactuca sativa var. capitata Doryteuthis Doryteuthis pealeii Doryteuthis pleii Cyperus esculentus Hiatelloidea Arcticoidea Cardioidea Microstomus kitt Pectinida Pectinoidea Mytiloidea Arcoidea Mactroidea Solenoidea Malus baccata Malus mandshurica Opuntia Beryx decadactylus Lepidopus Lepidopus caudatus Chaceon Coregonus peled Genypterus chilensis Eriphiidae Theobroma grandiflorum Chaerophyllum bulbosum Pachyrhizus Pachyrhizus erosus Haliotis asinina Ambloplites Ambloplites rupestris Illex coindetii Todaropsis Todaropsis eblanae Hoplobatrachus Eleocharis dulcis Diospyros digyna Eragrostis tef Jasus frontalis Jasus paulensis Jasus tristani Eriogonoideae Polygonoideae Fagopyreae Rumiceae Pseudolais micronemus Moolgarda Moolgarda engeli Penaeoidea Reinhardtius Reinhardtius hippoglossoides Columbina Columbina passerina Mustelus mustelus Mustelus asterias Munididae Hordeum vulgare subsp. vulgare Polyprionidae Polyprion Polyprion americanus Flacourtia Lycium barbarum Lycium chinense Chroicocephalus Sileneae Cichorium endivia Pseudopodospermum hispanicum Prunus spinosa Pharidae Arundinarieae Pseudupeneus Pseudupeneus prayensis Attalea Urophycis brasiliensis Hyphaene Hyphaene thebaica Palaemonoidea Pandaloidea Crangonoidea Palinuroidea Galatheoidea Vigna subterranea Mercenaria campechiensis Myliobatidae Mobulinae Thecostraca Sarsostraca Eubrachyura Heterotremata Thoracotremata Abelmoschus moschatus Hyperoartia Teleostomi Euteleostomi Cyrenoidea Cyrenidae Rosoideae incertae sedis Apium graveolens Dulce Group Aloe ferox Myliobatiformes Amblyraja Dipturus Leucoraja Rostroraja Arhynchobatidae Bathyraja Rhinopristiformes Batoidea Dalatiidae Oxynotidae Somniosidae Etmopteridae Centrophoridae Vanilla pompona Palaemon Echinorhiniformes Squalomorphii Muraenesox bagio Nettastomatidae Fragariinae Dicroglossinae Galeoidea Galeomorphii Selachii Cinnamomum aromaticum Cinnamomum burmanni Chroicocephalus ridibundus Archosargus Archosargus probatocephalus Etelinae Lutjaninae Eugenia Eugenia uniflora Psidium Psidium guajava Rhombosolea leporina Rhombosolea plebeia Ensis ensis Brassica rapa Broccoletto Group Lateolabracidae Eupulmonata Ecdysozoa Lophotrochozoa Bembrops anatirostris Bembrops gobioides Hyporthodus Arca imbricata Pelophylax Rana <subgenus> Aquarana Pleoticus robustus Rhinobatos rhinobatos Echinochloa esculenta Prunus americana Prunus angustifolia Pseudomonadota Eugenia brasiliensis Lampridacea Neoteleostei Eurypterygia Ctenosquamata Acanthomorphata Euacanthomorphacea Glebocarcinus Glebocarcinus amphioetus Atherininae Belonoidei Bacillota Husinae Acipenserinae Acipenserini Leuconostoc Illicium verum Pleuroncodes planipes Azadirachta Azadirachta indica Ammodytes dubius Menticirrhus saxatilis Esox masquinongy Micrococcaceae Physalis peruviana Paralichthys woolmani Trachurus trecae Dimocarpus Dimocarpus longan Cinnamomum verum Gymnachirus melas Mullus auratus Belone Belone belone Cololabis Cololabis saira Scomberesox Scomberesox saurus Strongylura exilis Strongylura marina Paspaleae Paspalinae Anthephorinae Cenchrinae Boivinellinae Panicinae Crocodylia Alligatoridae Asimina Asimina triloba Ruditapes philippinarum Longirostres Syngnathiformes Streptococcaceae Nematalosa come Streptococcus Cynoscion Cynoscion nebulosus Allium chinense Atripliceae Anserineae Chenopodioideae Salsoloideae Salsoleae Hypophthalmichthys molitrix Illicium Juniperus Lepomis Lepomis macrochirus Streptophytina Crescentiina Tabebuia alliance cellular organisms Oreochromini Piper Pomatoschistus Pomatoschistus minutus Kali <eudicots> Archelosauria Toxicofera Episquamata Unidentata Bifurcata Prunus virginiana Acanthocybium Acanthocybium solandri Annona Annona muricata Arbutus Auxis Auxis thazard Eleutherozoa Borago Borago officinalis Dipnotetrapodomorpha Xiphopenaeus Xiphopenaeus kroyeri Penaeus Carcharodon Carcharodon carcharias Carya Chrysophyllum Cichorium Cichorium intybus Cinnamomum Stramonita Stramonita haemastoma Corylus Corylus cornuta Coryphaena Lophioidei Alepocephalidae Alepocephalus Alepocephalus bairdii Diospyros Diospyros virginiana Panopea abrupta Enterococcus Congrinae Ribes uva-crispa Lactococcus Istiophorus Istiophorus platypterus Maccullochella Maccullochella peelii Macquaria ambigua Sillaginodes Sillaginodes punctatus Katsuwonus Lepidocybium Lepidocybium flavobrunneum Spirinchus Scomber Scomber japonicus Scomber scombrus Scomberomorus Scomberomorus cavalla Sphyraena Rheum officinale Rheum palmatum Trichiurus Trichiurus lepturus Vaccinium Vaccinium macrocarpon Hypomesus Bacillales Neptunia Cocos Cocos nucifera Pinus subgen. Pinus Penaeus chinensis Prunus cerasus Brama dussumieri Carissa carandas Paralichthys lethostigma Harpadontinae Saurida Synodontinae Saurida undosquamis Monacanthidae Boreoeutheria Acrogymnospermae Mesangiospermae Petrosaviidae Pentapetalae Notacanthus chemnitzii Notacanthiformes Eriphia smithii Pyracantha Cycadidae Ginkgoidae Cupressales Pinales Cantareus apertus Borassus Attalea speciosa Hoplunnis macrura Berberidoideae Selar Decapterus macarellus Decapterus russelli Selar crumenophthalmus Glycine subgen. Soja Papaveroideae Ranunculoideae Caltheae Ammodytes marinus Diospyros sintenisii Callinectes danae Paspalum Bambusoideae Oryzoideae Pooideae Panicoideae PACMAD clade Chloridoideae Bambuseae Oryzeae Poeae Triticeae Paniceae Andropogoneae Cynodonteae Eragrostideae Saccharomycotina Cyclostomata Glebionis Micropterus dolomieu Ninnigobius Trichodontidae Arctoscopus Arctoscopus japonicus Holostei Elopocephalai Osteoglossocephalai Osteoglossocephala Hiodontiformes Euteleosteomorpha Clupeoidei Alepocephali Alepocephaliformes Knerioidei Siluroidei Stomiati Aulopa Aulopoidei Paracanthopterygii Zeiogadaria Zeariae Gadariae Macrouroidei Gadoidei Berycimorphaceae Percomorphaceae Ophidiaria Gobiaria Gobiiformes Syngnathiaria Pelagiaria Mulloidea Anabantaria Scombriformes Anabantiformes Carangaria Carangaria incertae sedis Istiophoriformes Carangiformes Ovalentaria Cichlomorphae Cichliformes Atherinomorphae Mugilomorphae Eupercaria Eupercaria incertae sedis Uranoscopiformes Labriformes Spariformes Moloidei Terapontoidei Pempheriformes Centrarchiformes Bembropidae Serranoidei Triglioidei Anoplopomatales Cottales Panulirus cygnus Panulirus homarus Panulirus ornatus Panulirus penicillatus Panulirus regius Panulirus versicolor Euphausia frigida Epinephelini Xanthosoma Litchi Litchi chinensis Nephelium Nephelium lappaceum Salsola Kali turgidum Candida/Lodderomyces clade Epinephelus morio Boraginales Dendrocalamus Lepidorhombus Lepidorhombus whiffiagonis Cyttidae Centrarchoidei Cirrhitioidei Percichthyoidei Hexagrammales Serripes groenlandicus Genypterus Genypterus blacodes Galloanserae Vimba vimba Aspalathus linearis Eriphia Eriphia sebana Plantaginaceae Apeibeae Phyllostachys Vigna radiata Lactobacillus Ziziphus mauritiana Mobula mobular Chelydroidea Americhelydia Durocryptodira Phyllanthoideae Vanilloideae Percophinae Ferulinae Tordyliinae Limonia acidissima Passiflora incarnata Zizania Cantareus Cephalopholis fulva Hyporthodus acanthistius Epinephelus analogus Epinephelus areolatus Epinephelus fasciatus Epinephelus itajara Epinephelus striatus Mycteroperca phenax Mycteroperca venenosa Acanthopagrus australis Chrysophylloideae Sapotoideae Penaeus esculentus Penaeus penicillatus Penaeus latisulcatus Penaeus plebejus Beta vulgaris Epinephelus malabaricus Dialium guineense Maranta Molva Molva molva Phycidae Raniceps Raniceps raninus Centrolophidae Pampus Arripidae Arripis Arripis georgianus Girella Mimoseae Alismatales Cicereae Crotalarieae Dalbergieae Hedysareae Indigofereae Phaseoleae Psoraleeae Trifolieae Fabeae Dipterygeae Arundinariinae Bambusinae Hordeinae Oryzinae Rottboelliinae Sorghinae Tripsacinae Triticinae Zizaniinae Andropogonodae Arundinarodae Bambusodae Panicodae Poodae Triticodae Poeae Chloroplast Group 1 (Aveneae type) Corynebacteriaceae Solen Decapterus macrosoma Periophthalmus barbarus Juglandaceae Juglans Juglans nigra Schisandraceae Piperales Piperaceae Rauvolfioideae Carisseae Bifidobacterium Schinus terebinthifolia Phractolaemus Phractolaemus ansorgii Rubioideae Ixoroideae Gardenieae Morindeae Arecoideae Calamoideae Coryphoideae Cocoseae Attaleinae Elaeidinae Calameae Metroxylinae Borasseae Phoeniceae Hyphaeninae Lataniinae Myrtoideae Syzygieae Myrteae Malpighia Pimenta group Eugenia group Dalatias Dalatias licha Squatina californica Citrus hystrix Hyperoglyphe Citrus limonia Citrus medica Penaeus californiensis Paralichthyidae Bacteroidales Prevotellaceae Corynebacterium Amygdaloideae Rosoideae Anacardium Anacardium occidentale Tilia cordata Argyrosomus Argyrosomus regius Parophrys Parophrys vetulus Aurantioideae Vanilleae Leucoraja ocellata Arca zebra Caranx crysos Caranx caballus Carangoides ruber Carangoides bartholomaei Decapterus punctatus Elagatis Elagatis bipinnulata Trachinotus Trachinotus goodei Trachinotus carolinus Oligoplites Oligoplites saurus Lepidopodinae Trichiurinae Semecarpus Dacryodes Paspalum scrobiculatum Amorphophallus paeoniifolius Lithodes Lithodes aequispinus Lithodes maja Paralithodes brevipes Ribes rubrum Cynoscion regalis Actinomycetes Selenicereus undatus Syzygium FCB group Terrabacteria group Brassica oleracea var. medullosa Alectis Alectis alexandrina Alectis ciliaris Carangoides Trachurus lathami Psettodoidei Epinephelus caninus Epinephelus marginatus Epinephelus aeneus Mammea Betoideae Chenopodiaceae Eruca vesicaria Vaccinium myrtillus Vaccinium parvifolium Vaccinium reticulatum Ophidioidei Ophidiinae Allocyttus Allocyttus niger Cyclopterinae Ficus benjamina Ficus sycomorus Osmerinae Thaleichthys Salangidae Hypomesinae Hoplunnis Raja asterias Raja miraletus Dipturus oxyrinchus Raja undulata Abelmoschus Abelmoschus manihot Hibiscus sabdariffa Hippoglossina oblonga Peprilus Peprilus triacanthus Urophycis Urophycis chuss Urophycis tenuis Sicyos edulis Ammodytes americanus Centropristis Centropristis striata Diplectrum Paralabrax callaensis Stereolepis Stereolepis gigas Esox niger Engraulis encrasicolus Plantago ovata Arctogadus Arctogadus glacialis Molva dypterygia Pollachius pollachius Coccolobeae Cactoideae Opuntioideae Hylocereeae Ruditapes Polyodontinae Polyodontini Acipenseroidei Actinopteri Elopocephala Clupeocephala Otophysi Cypriniphysae Characiphysae Chanoidei Anotophysi Otomorpha Scombrinae Scombrini Scomberomorini Sardini Thunnini Lactobacillales Carnobacteriaceae Daucus sect. Daucus Boraginoideae Boragininae Boragineae Aframomum Trachurus picturatus Rubus flagellaris Vaccinium ovalifolium Vaccinium uliginosum Crateva Bromelioideae Empetrum nigrum Eruca Lophius budegassa Somniosus Somniosus microcephalus Lepidium Trachurus murphyi Annonoideae Annoneae Pyracantha coccinea Ardenna Hippophae rhamnoides Artocarpus altilis Brosimum Brosimum alicastrum Sphyrna mokarran Sphyrna zygaena Eopsetta Eopsetta jordani Glyptocephalus zachirus Hippoglossus stenolepis Isopsetta Isopsetta isolepis Lepidopsetta Lepidopsetta bilineata Limanda aspera Lyopsetta Lyopsetta exilis Platichthys stellatus Psettichthys Psettichthys melanostictus Psettodes erumei Atheresthes evermanni Achiridae Trinectes Trinectes maculatus Xystreurys Xystreurys liolepis Sardinella aurita Sardinella maderensis Sprattus Sprattus sprattus Cassia clade Amherstieae Myomorpha Neptunia oleracea Gardenieae - Pavetteae clade Gardenieae complex Procambarus acutus Pancrustacea Mandibulata Selar boops Hippocastanoideae Sapindoideae Hippocastaneae Plantago indica Paullinieae Melicocceae Detarioideae Dialioideae Melanitta Cyperus subgen. Cyperus Scyllarus Scyllarus arctus Palinurus elephas Palinurus delagoae Palinurus gilchristi Mobula birostris Chaceon quinquedens Mammea americana Valeriana Valeriana officinalis Ebenaceae Alpinia officinarum Bacteria Bacteroidia Todarodes sagittatus Actinomycetota Hucho taimen Pomoxis annularis Lutjaniformes Labrus viridis Lachnolaimus Lachnolaimus maximus Tautoga Tautoga onitis Crateva religiosa Epinephelus tauvina Apostichopus californicus C4 Cyperus C4 Cyperus incertae sedis Sisymbrium officinale Rhodospirillales Bembropoidei Pachyrhizus ahipa Pachyrhizus tuberosus Solanum muricatum Pinguipedidae Pentanemus Pentanemus quinquarius Anatinae Homininae Sepiolinae Trichodon <bony fishes> Trichodon trichodon Maranta arundinacea Panicum sect. Dichotomiflora Eleutheronema Eleutheronema tetradactylum Castanea Fagus Canarium pimela Flacourtia indica Mora <bony fishes> Ranzania <bony fishes> Ophidion <bony fishes> Centrophorus Centrophorus granulosus Leucoraja circularis Myzopsetta Coccinia Girella tricuspidata Gentianaceae Malvoideae Grewioideae Byttnerioideae Tilioideae Sterculioideae Helicteroideae Bombacoideae Gentiana Bramidae Brama Brama japonica Larimichthys Larimichthys crocea Parapercis Parachanna Ranzania laevis Todarodes angolensis Nototodarus sloanii Decapodiformes Octopodiformes Averrhoa Archaea Boraginaceae Lottioidea Vetigastropoda Haliotoidea Littorinimorpha Stromboidea Heterobranchia Euthyneura <gastropods> Helicina <clade> Nepetoideae Mentheae Ocimeae Plantagineae Auxis rochei Arbutoideae Ericoideae Vaccinioideae Empetreae Vaccinieae Multicrustacea Engraulis ringens Carassius carassius Mentha Lutjanus malabaricus Scomberomorus commerson Salvia Verbenaceae Carduoideae Cichorioideae Cichorieae Coreopsideae Syzygium aqueum Syzygium malaccense Verbena Monimiaceae Chrysophyllum cainito Annonaceae Myristicaceae NPAAA clade ADA clade genistoids sensu lato core genistoids dalbergioids sensu lato Pterocarpus clade 50 kb inversion clade Diodon Diodon hystrix Masturus Masturus lanceolatus Hologalegina IRL clade indigoferoid/millettioid clade Epigonidae Raja radula Raja brachyura Raja microocellata Leucoraja naevus Leucoraja fullonica Diplectrum formosum Odontophoridae Alosa aestivalis Harengula Harengula jaguana Brevoortia Brevoortia patronus Brevoortia tyrannus Opisthonema Opisthonema oglinum Etrumeus Etrumeus teres Anchoa Anchoa mitchilli Micropterus punctulatus Lottia gigantea Ophiodon Ophiodon elongatus Aplodinotus Aplodinotus grunniens Punica Punica granatum Trapa Trapa natans Solanum quitoense Berberis Jeotgalicoccus Pseudobatos Parapenaeus Salvia incertae sedis Anoplopoma Anoplopoma fimbria Citrus x tangelo Chrysobalanaceae Chrysobalanus Chrysobalanus icaco Macrobrachium carcinus Viteae Grossulariaceae Lepetellida Eriobotrya Prunus serotina Pyrus communis Rubus Lutjanus sebae Sorbus Magnoliidae Proteales Chionoecetes bairdi Squalius Pouteria campechiana Pouteria sapota Synsepalum Phyllanthaceae Mangifera Rutaceae Mackinlayoideae Phyllantheae Sapindaceae Viburnum edule Saliceae Flacourtieae Simaroubaceae Atherina hepsetus Menidiinae Menidia Menidia menidia Engraulis mordax Bignoniaceae Hypomesus olidus Thaleichthys pacificus Clinocardium Dinocardium Dinocardium robustum Serripes Odacidae Odax Odax pullus Apioideae apioid superclade Pyramidoptereae Scandiceae Apieae Sinodielsia clade Daucinae Scandicinae Psettodes belcheri Bagre Bagre marinus Pseudocyttus Pseudocyttus maculatus Lepas anserifera Averrhoa bilimbi Cyttus traversi Allocyttus verrucosus Valerianella eriocarpa Dacryodes edulis Lycium Physalis Scomberomorus queenslandicus Scomberomorus munroi Scomberomorus semifasciatus Macruronus novaezelandiae Mora moro Engraulis anchoita Rubiaceae Crocoideae Croceae Catostomoidei Acheilognathidae Ensis siliqua Solen marginatus Pleuroncodes Gentianinae Pseudoclavibacter Clidoderma Clidoderma asperrimum Trachichthyiformes Aloe Esox reichertii Alkekengi Ninnigobius canestrinii Berberis vulgaris Blighia Blighia sapida Atractoscion Atractoscion nobilis Elaeagnaceae Opisthonema libertate Psidium guineense Syzygium cumini Syzygium samarangense Spirinchus thaleichthys Caprimulgimorphae Apodinae Cicca acida Scardinius graecus Nymphaeales Chionoecetes tanneri Iridaceae Squatina squatina Lutjanus sanguineus Diplotaxis tenuifolia Loganiaceae Strychnos Whippomorpha Ancodonta Enteroctopus Enteroctopus dofleini Ipomoeeae Rosa suffulta Plantago Eleusine coracana subsp. africana Origanum majorana Spiralia Cochlearia officinalis Lepomis gibbosus Erilepis Erilepis zonifer Arripis trutta Epigonus Citrus Osphronemidae Osphronemus Osphronemus goramy Percophidae Bembrops Theaceae Trachurus symmetricus Trachurus declivis Trachurus novaezelandiae Rumex subgen. Acetosa Lutjanus johnii Paralithodes platypus Penaeus japonicus Limosilactobacillus Barbinae Cyprininae Labeoninae Labeonini Gobionidae Gobioninae Leuciscidae Leuciscinae Phoxininae Tincidae Xenocyprididae Xenocypridinae Sebastidae Scorpaeninae Sebastinae Anthiinae Epinephelinae Serraninae Cheilodactylus variegatus Cornu <genus> Cornu <subgenus> Raja montagui eucaryotes eukaryotes Eukaryota Bovinae Lacticaseibacillus Balaena Balaena mysticetus Lactiplantibacillus Levilactobacillus Lentilactobacillus Sardina Sardina pilchardus Gobio Gobio gobio Micropterus Micropterus salmoides Tinca Tinca tinca Trisopterus Coryphaenidae Gempylidae Istiophoridae Sphyraenidae Trichiuridae Silene subgen. Behenantha Silene sect. Behenantha Limanda limanda Coregonus Triglidae Eretmochelys Eretmochelys imbricata Chelonioidea Chlamys islandica Alosa alosa Myida Adapedonta Cardiida Autobranchia Imparidentia Camarodonta Micropogonias furnieri Menticirrhus Menticirrhus americanus Menticirrhus littoralis Clinocardiinae Laevicardiinae Lymnocardiinae Alphaproteobacteria Conifers II Conifers I Betaproteobacteria Cyclopsettidae Squaliformes Clupei Sander Sander canadensis Sander lucioperca Sander vitreus Malus pumila Menthinae Salviinae Ociminae Faxonius limosus Sardinops Sardinops sagax Testudinata Lasioideae Aroideae Arctiinae <eudicots> Xanthosoma sagittifolium Aliger Macrostrombus Coilia Coilia mystus Alcidae Cepphus Cepphus grylle Fratercula Fratercula arctica Fratercula corniculata Centropomus Centropomus undecimalis Metanephrops armatus Fagus sylvatica Averrhoa carambola Semecarpus anacardium Lepadoidea Thoracicalcarea Penaeus stylirostris Lutjanus peru Sicyonia brevirostris Ursus maritimus Neoheterodontei Metapenaeus joyneri Paullinia Paullinia pinnata Pseudopodospermum Atelecyclidae Gonorynchiformes Chanidae Chanos Chanos chanos Lates niloticus Scomber australasicus Osmerus eperlanus Micropogonias Micropogonias undulatus Mytilus galloprovincialis Crassostrea gigas CUG-Ser1 clade Acanthochitonina Aliger gigas Atopostipes Caladieae Thomsonieae Palaemon vulgaris Mentha pulegium Patinopecten caurinus Emblica officinalis Dioscorea cayenensis Mentha spicata Eruca vesicaria subsp. sativa Vitis vinifera Zanthoxyloideae Berberideae Mangifera indica Ginkgoopsida Plantago major Erimacrus Erimacrus isenbeckii Grapsoidea Cancroidea Metacarcinus magister Canarium album Valerianella dentata Capparaceae Annona squamosa Annona glabra Annona reticulata Modiolinae Mytilinae Seriola lalandi Gentianeae Ranoidea <superfamily> Aluterus Meuschenia Sphoeroides spengleri Atherina presbyter Carcharhinus perezii Carcharhinus signatus Squatina dumeril Physalis philadelphica Parachanna obscura Procellariiformes Procellariidae Fulmarus Fulmarus glacialis Strigiformes Strigidae Bubo Rajidae Carcharhiniformes Triakis semifasciata Lamniformes Carcharias Carcharias taurus Squalidae Acropomatiformes Bos grunniens Dama dama Moreae Ficeae Artocarpeae Dorstenieae Balaenidae Panicum sumatrense Faxonius Epinephelus chlorostigma Cicca Emblica Annona senegalensis Crangon franciscorum Clupea pallasii Cyprinoidei Pinnipedia Moridae Macrouridae Phractolaeminae Kneriidae Opuntia polyacantha Pachygrapsus crassipes Apostichopus Labrus Haemulidae Lutjanidae Monodactylidae Mullidae Pomatomidae Sciaenidae Serranidae Paralabrax Sillaginidae Terapontidae Channidae Polynemidae Ficus thonningii Pleuronectoidei Hippoglossoides Hippoglossoides elassodon Soleidae Psettodidae Umbridae Plecoglossidae Mallotus <bony fishes> Mallotus villosus Oncorhynchus clarkii Hexagrammidae Anoplopomatidae Siluridae Pangasianodon Pangasianodon gigas Schilbidae Pimelodidae Ariidae Tetraodontiformes Balistoidea Tetraodontoidei Molidae Tetraodontidae Diodontidae Osteoglossomorpha Hiodontidae Pangasianodon hypophthalmus Zeiformes Oreosomatidae Zeidae Saxidomus Argopecten Argopecten irradians Littorinidae Littorina Littorina littorea Osphroneminae Anisotremus Laurasiatheria Euarchontoglires Glires Simiiformes Hominoidea Centrolophus Centrolophus niger Seriolella Seriolella caerulea Seriolella brama Seriolella punctata Dorosomatinae Nematalosa Palinurus mauritanicus Pseudocrenilabrinae Cichlasomatinae Cichlasomatini New World cichlids African cichlids Embryophyta Lutjanus argentiventris Bifidobacteriaceae Allocyttus folletti Ophidion scrippsae Paralichthys californicus Polydactylus Cynoscion parvipinnis Genyonemus Genyonemus lineatus Menticirrhus undulatus Allothunnus Allothunnus fallai Ponticola kessleri Scomberomorus niphonius Rubus sorbifolius Carya illinoinensis Eriobotrya japonica Metapenaeus Dioscorea esculenta Chondrostei Teleostei Clupeiformes Tetradontoidea Ostariophysi Elopomorpha Tetrapoda Amniota Theria <mammals> Paliureae Sauria Acanthistius Cyclopsetta Cyclopsetta chittendeni Cycadopsida Cycadales Ginkgoales Ginkgoaceae Viridiplantae Ginkgo Ginkgo biloba Capsicum baccatum Alkekengi officinarum Lepidium sativum Papaver rhoeas Phaseolus acutifolius Pinidae Opisthokonta Pinaceae Metazoa Bilateria Protostomia Pinus Taraxacum kok-saghyz Syzygium jambos Pinus pinea Hyperoglyphe antarctica Rastrelliger brachysoma Sarda australis Monodactylus Monodactylus argenteus Parupeneus Argyrosomus hololepidotus Larimichthys polyactis Atractoscion aequidens Polyprion oxygeneios Chelidonichthys kumu Scorpaena cardinalis Etmopterus Centrophorus squamosus Mustelus lenticulatus Squalus megalops Saccostrea Deuterostomia Chelidonichthys Sciuromorpha Carnivora Balaenoptera bonaerensis Cupressaceae Brachyplatystoma Cricetidae Muroidea Xerinae Marmotini Channa Cycadaceae Cycas Lactobacillaceae Magnoliopsida Magnoliales Spondias purpurea Citrus australis Aloe vera Mentha x piperita Atriplex hortensis Gossypium herbaceum Laurales Lauraceae Persea Persea americana Ranunculaceae Caltha Caltha palustris Sepiolidae Sepiola Megapitaria maculata Megapitaria Oegopsida Mopaliidae Katharina Katharina tunicata Papaveraceae Papaver Papaver somniferum Senna obtusifolia Alosa Alosa sapidissima Alosa pseudoharengus Kathetostoma Kathetostoma giganteum Cannabaceae Coryphaena hippurus Morone Morone saxatilis Hippoglossoides platessoides Glyptocephalus Glyptocephalus cynoglossus Cannabis Sebastes Cannabis sativa Molva macrophthalma Rupicapra Rupicapra rupicapra Moraceae Coregonus nasus Coregonus oxyrinchus Cervinae Artocarpus Eumetopias Eumetopias jubatus Artocarpus heterophyllus Alligatorinae Prunus avium x P. cerasus x P. canescens Ficus <eudicots> Engraulis australis Ficus carica Parapristipoma Parapristipoma octolineatum Plectorhinchus Pseudocaranx Pseudocaranx dentex Brama brama Dentex angolensis Epigonus telescopus Morus <eudicots> Morus alba Urticaceae Urtica Urtica dioica Fagales Fagaceae Betulaceae Caryophyllales Aizoaceae Streptophyta Suina Atriplex Pecora Beta Stenotomus Stenotomus chrysops Chenopodium Chenopodium album Salsola soda Spinacia Spinacia oleracea Caryophyllaceae Silene Basellaceae Allium fistulosum Basella Basella alba BOP clade Cactaceae Vitaceae Vitis Vitis aestivalis Plectorhinchus pictus Metanephrops rubellus Metanephrops thomsoni Rhamnaceae Haliotis tuberculata Polygonaceae Fagopyrum Fagopyrum esculentum Rumex Coregonus albula Coregonus artedi Thymallus Thymallus thymallus Rheum Rheum rhabarbarum Trachurus Trachurus trachurus Boops Boops boops Actinidiaceae Actinidia Actinidia chinensis Senna tora Malvaceae Gossypium Gossypium hirsutum Theobroma Lecythidaceae Apiineae Bertholletia Bertholletia excelsa Malpighiales Caricaceae Carica Carica papaya Cucurbitaceae Sardinella zunasi Dussumieriidae Coilinae Engraulinae Citrullus Citrullus lanatus Cucumis Pangasius larnaudii Pangasius sanitwongsei Pseudolais Cucumis melo Prunus armeniaca Sorbus aucuparia Cucurbita Cormus Cormus domestica Cydonia Cydonia oblonga Cucurbita moschata Cucurbita pepo Luffa Gymnachirus Luffa aegyptiaca Momordica Momordica charantia Trichosanthes Passifloraceae Passiflora Passiflora quadrangularis Salicaceae Saccostrea cucullata Brassicales Micromesistius australis Brassicaceae Mullus Mullus barbatus Brassica Ardenna grisea Illex cf. oxygonius DBC-2006 Brassica juncea Brassica nigra Brassica rapa Brassica oleracea Brassica oleracea var. alboglabra Brassica oleracea var. capitata Palinurus charlestoni Ovibos Ovibos moschatus Melanitta fusca Patagioenas Patagioenas fasciata Sinapis Sinapis alba Scomberomorus koreanus Pseudocaranx chilensis Sisymbrium Diplotaxis <eudicots> Citrus maxima Sapotaceae Manilkara Manilkara zapota Synsepalum dulcificum Rosales Rosaceae Fragaria Fragaria x ananassa Diospyros texana Malus Malus domestica Psidium cattleyanum Prunus Prunus dulcis Prunus persica Ostrea edulis Rosa Crassostrea rhizophorae Citrus x paradisi Pyrus Mustelus schmitti Pyrus pyrifolia Haplorrhini Lepas anatifera Nephropoidea Ostrea Lepas Caniformia Artemiidae Ribes Lepadidae Chionista Chionista fluctifraga Fabaceae Caesalpinioideae mimosoid clade Zea mays subsp. mays Papilionoideae Menippe adina Arachis Arachis hypogaea Cajanus Cajanus cajan Canavalia Canavalia ensiformis Canavalia gladiata Cicer Cicer arietinum Cyamopsis Cyamopsis tetragonoloba Eragrostis Rastrelliger faughni Scomberomorus sinensis Glycine Glycine max Abramis Abramis brama Lathyrus Lamna ditropis Lathyrus odoratus Lathyrus sativus Alligator sinensis Amblyraja radiata Phyllostachys edulis Coccinia grandis Strombus alatus Macrostrombus costatus Strombus pugilis Dendrocalamus asper Poales Phaseolus Phaseolus lunatus Phaseolus vulgaris Gentiana lutea Phaseolus coccineus Pisum Pisum sativum Psophocarpus Psophocarpus tetragonolobus Perna Trifolium Vicia Vicia faba Vicia sativa Arvicolinae Phoca groenlandica Phoca largha Sphoeroides Vigna Vigna angularis Vigna mungo Vigna unguiculata Melissa Ocimum Origanum Vigna aconitifolia Erignathus Gymnocephalus Cyrtosperma Paullinia cupana Lythraceae Cyrtosperma merkusii Erignathus barbatus Myrtaceae Melissa officinalis Ocimum basilicum Origanum vulgare Cancer borealis Sebastes fasciatus Sebastes viviparus Muricoidea Muricidae Rumex arcticus Combretaceae Grapsidae Lutjanus gibbus Lutjanus quinquelineatus Brachyplatystoma vaillantii Chionoecetes angulatus Pandalus dispar Pandalus montagui Simmondsiaceae Simmondsia Simmondsia chinensis Terminalia Terminalia catappa Linaceae Linum Linum usitatissimum Anacardiaceae Burseraceae Monodon Monodon monoceros Tropaeolaceae Tropaeolum Tropaeolum majus Modiolus Modiolus modiolus Carissa macrocarpa Oxalidaceae Apiales Vitales Apiaceae Daucus Daucus carota Apium Apium graveolens Lutjanus Lutjanus analis Araliaceae Lutjanus vivanus Lutjanus griseus Lutjanus buccanella Lutjanus campechanus Etelis Etelis oculatus Panax Piper cubeba Panax ginseng Dioscoreales Gentianales Arecales Allioideae Apocynaceae Mammalia Salix Solanales Solanaceae Capsicum Capsicum annuum Solanum lycopersicum Barbus Barbus barbus Scandix Scandix pecten-veneris Saxidomus gigantea Clinocardium nuttallii Solanum Solanum nigrum Solanum tuberosum Anchoa hepsetus Convolvulaceae Ipomoea Ipomoea batatas Chionoecetes Chionoecetes opilio Rumex acetosa Lamiaceae Lamiales Seriola dumerili Citrus limetta Calendula Calendula officinalis Citrus australasica Neopterygii Batrachia Sardinops melanostictus Livistoneae Livistoneae incertae sedis Protacanthopterygii Osmeriformes Ranunculales Berberidaceae Mugiliformes Cornales Sapindales Malvales Myrtales Ericales Saxifragales Dipsacales Caprifoliaceae Sambucus Sambucus nigra Viburnum Silene vulgaris Rostroraja alba Dipturus batis Adoxaceae Asterales Asteraceae Moronidae Arctium Arctium lappa Carthamus Cornaceae Carthamus tinctorius Helianthus Helianthus annuus Helianthus tuberosus Acipenser naccarii Crescentieae Bidens Bidens pilosa Phoenix dactylifera Lactuca Lactuca sativa Solanoideae Capsiceae Lycieae Physaleae Solaneae Schilbe Anarhichas denticulatus Eutrigla Eutrigla gurnardus Viticoideae Cynara Mugil liza Cynara cardunculus Phoxinus Malpighiaceae Byrsonima Byrsonima crassifolia Atheresthes Atheresthes stomias Cornus Cornus mas Engraulis Engraulis japonicus Glycymeris glycymeris Carissa spinarum Aquifoliaceae Ilex Ilex aquifolium Aulopus filamentosus Engraulidae Centella Acetobacteraceae Fratercula cirrhata Aesculus Acetobacter Ericaceae Harpadon nehereus Morinda Morinda citrifolia Parastromateus Parastromateus niger Dinosauria Saurischia Theropoda Coelurosauria Canarium <eudicots> Canarium ovatum Meliaceae Quassia Quassia amara Schinus Schinus molle Spondias Spondias dulcis Nymphaeaceae Penaeus notialis Euryale <flowering plants> Euryale ferox Nuphar Nelumbonaceae Nelumbo Nelumbo nucifera Parapercis colias Pseudocaranx wrighti Aldrichetta Aldrichetta forsteri Bidyanus Bidyanus bidyanus Lotella Lotella rhacina Paratrachichthys Percophis Percophis brasiliensis Pseudophycis Pseudophycis bachus Rhombosolea Camellia Camellia sinensis Liliopsida Pleoticus Pleoticus muelleri Penaeus brevirostris Parapenaeus longirostris Saurida tumbil Sphyraena jello Araceae Panax quinquefolius Arca Malva verticillata Panax japonicus Poaceae Avena Avena sativa Coix Coix lacryma-jobi Eleusine Eleusine coracana Hordeum Hordeum vulgare Coccoloba Coccoloba uvifera Dikarya Gobius Origanum onites Oryza Oryza sativa Tetragonia <eudicots> Tetragonia tetragonoides Oryza glaberrima Panicum Panicum miliaceum Pampus cinereus Lutjanus purpureus Cenchrus americanus Secale Secale cereale Abelmoschus esculentus Hippoglossina Setaria <monocots> Lutjanus guttatus Setaria italica Sorghum Sorghum bicolor Echinochloa Pelophylax lessonae Triticum Triticum aestivum Triticum turgidum subsp. durum Triticum monococcum Triticum turgidum Zea Zea mays Macquaria Cenchrus Solanum dulcamara Pediomelum Pediomelum esculentum Acanthistius brasilianus Bassanago Lycengraulis Lycengraulis grossidens Parona Parona signata Seriolella porosa Empetrum Corbicula Corbicula fluminea Cyperaceae Cyperus Bromeliaceae Ananas Claytonia Claytonia perfoliata Atherinopsidae Ananas comosus Zingiberales Marantaceae Morone chrysops Morone americana Leukoma Leukoma staminea Eleocharis Musaceae Ensete Ensete ventricosum Musa Musa acuminata Zingiberaceae Hedychium Aerodramus Aerodramus fuciphagus Zingiber Perdicinae Meleagridinae Lactuca sativa var. crispa Amaryllidaceae Dioscoreaceae Dioscorea Allium Allium cepa Allium ampeloprasum Allium sativum Alosa mediocris Hedysarum Melilotus Melilotus officinalis Arecaceae Phoenix Phoenix reclinata Serenoa Serenoa repens Vaccinium angustifolium Allium canadense Neogobius Neogobius melanostomus Proterorhinus Typhaceae Proterorhinus marmoratus Typha Typha latifolia Macrourus berglax commelinids Orchidaceae Fungi Lutjanus lutjanus Hibiscus Ammodytes hexapterus Bassanago bulbiceps Oreochromis aureus Aluterus monoceros Coregonus pidschian Borassus aethiopum Levisticum Levisticum officinale Caryocar brasiliense Centella asiatica Euphausia crystallorophias Euphausia vallentini Meganyctiphanes Meganyctiphanes norvegica Thunnus atlanticus Thunnus tonggol Mugil cephalus Mugil curema Hippophae Sphoeroides maculatus Orthopristis Orthopristis chrysoptera Eriphia verrucosa Crocodylus acutus Zoarces Zoarces viviparus Capreolus pygargus Rutilus Rutilus rutilus Ascomycota ascomycetes sac fungi Ascomycota Saccharomycetes Saccharomycetales Saccharomycetaceae Tordylieae Tordylium apulum Anisotremus virginicus Plectorhinchus macrolepis Polydactylus macrochir Brachydeuterus Brachydeuterus auritus Rhombosoleidae Metanephrops andamanicus Metanephrops arafurensis Metanephrops australiensis Metanephrops binghami Metanephrops boschmai Metanephrops challengeri Metanephrops formosanus Metanephrops japonicus Metanephrops neptunus Metanephrops sagamiensis Metanephrops sibogae Metanephrops sinensis Metanephrops velutinus Kluyveromyces Crangon crangon Alepocephalus australis Salvia hispanica Triticum turgidum subsp. dicoccum Solanum subgen. Lycopersicon Saccharomyces Annona cherimola Saccharomyces cerevisiae baker's yeast brewer's yeast lager beer yeast yeast Saccharomyces cerevisiae Cetengraulis Gobiinae Taraxacum Oxudercinae Cynoscion striatus Thyrsites Thyrsites atun Artemesia Artemesia longinaris Sonchus Sonchus asper Sonchus oleraceus Taraxacum officinale Anabantoidei Channoidei Ameiurus Mimachlamys Mimachlamys varia Eriphia gonagra Coregoninae Salmoninae Thymallinae Barbarea Barbarea verna Barbarea vulgaris Trichosanthes cucumerina Pagellus Pagellus erythrinus Alcaligenaceae Euthynnus lineatus Hyperoplus Hyperoplus lanceolatus Myristica Myristica fragrans Piper guineense Vanilla Vanilla planifolia Juglans regia Xanthosoma brasiliense Rana dalmatina Brassica rapa subsp. rapa Todarodes filippovae Asphodelaceae Seriphus Seriphus politus Vaccinium oxycoccos Elaeis Elaeis guineensis Cetengraulis edentulus Etrumeus whiteheadi Scorpaenichthys Scorpaenichthys marmoratus Tordylium Ferula Ferula assa-foetida Trachyspermum Trachyspermum ammi Chondrostoma Chondrostoma nasus Psettodes bennettii Pelotretis Pelotretis flavilatus Peltorhamphus Peltorhamphus novaezeelandiae Scophthalmidae Scophthalmus Scophthalmus maximus Glycymerididae Glycymeris Canarium schweinfurthii Echinacea <eudicots> Echinacea pallida Echinacea purpurea Dialium Dipteryx Dipteryx odorata Senna Vitex Vitex agnus-castus Alburnus Alburnus alburnus Apsilinae Apsilus Chaerophyllum Meuschenia scaber Hiodon Hiodon alosoides Alloteuthis media Lophius vomerinus Notacanthidae Notacanthus Clupeidae Alosinae Sepiida Teuthida Myopsida Sepiina Squatiniformes Squatinidae Squatina Sciuridae Alloteuthis Huso Diospyros lotus Pistacia Pistacia vera Metacarcinus Dioscorea cayenensis subsp. rotundata Dioscorea trifida Stevia Stevia rebaudiana Melicoccus Melicoccus bijugatus Cardiidae Cerastoderma Cerastoderma edule Chaceon granulatus Bathyraja spinicauda Clusiaceae Hypericum Zoarcinae Bubo virginianus Scolopax Scolopax minor Luffa acutangula Nematalosa nasus Kocuria Hedysarum alpinum Trifolium pratense Homarinus Homarinus capensis Gymnocephalus cernua Fragaria vesca Rubus chamaemorus Isurus oxyrinchus Pinopsida Tracheophyta Spermatophyta Cycas rumphii Juniperus communis Decapterus Decapterus maruadsi Garcinia Garcinia mangostana Scardinius Phoxinus phoxinus Rhodeus Rhodeus sericeus Genipa Genipa americana Ensis directus Parupeneus cyclostomus Crangon septemspinosa Tamarindus Tamarindus indica Phyllanthus <eudicots> Triticum spelta Zizania latifolia Crocus Typha angustifolia Nemapteryx nenga Nemapteryx Valerianella Valerianella locusta Arcticidae Arctica Arctica islandica Coregonus lavaretus Stenodus Stenodus leucichthys Rubus parviflorus Rubus spectabilis Sardinops neopilchardus Sardinops ocellatus Scyllaridae Metanephrops Metanephrops mozambicus Panulirus longipes Leiostomus Leiostomus xanthurus Coregonus clupeaformis Odontesthes regia Rexea Rexea solandri Portuninae Girellidae Castanea mollissima Fagus grandifolia Eumetazoa Plecoglossus Plecoglossus altivelis Anguilla dieffenbachii Boswellia serrata Hiatellidae Panopea Acipenser sturio Apsilus dentatus Hapalochlaena Hapalochlaena maculosa Cucumis metuliferus Acipenser nudiventris Huso huso Hucho hucho Lepus arcticus Ostrea lurida Scalpellomorpha Hypericaceae Macrourinae Coelorinchus aspercephalus Coelorinchus kaiyomaru Macrourus carinatus Hypsophrys Chenopodium quinoa Aframomum melegueta Ponticola Peumus Peumus boldus Aveninae Zeus Zeus faber Myzopsetta proboscidea Pleuronectes quadrituberculatus Percinae Luciopercinae Anabantidae Anabas Anabas testudineus Channa striata Oncorhynchus gilae Sicyos Procambarus alleni Sicyoniidae Sicyonia Penaeus canaliculatus Penaeus duorarum Penaeus semisulcatus Penaeus setiferus Mollusca Gastropoda Haliotidae Palaemon serratus Haliotis Haliotis corrugata Haliotis rufescens Haliotis cracherodii Haliotis fulgens Haliotis kamtschatkana Haliotis sorenseni Tilia Haliotis walallensis Neogastropoda Oncorhynchus chrysogaster Etmopterus spinax Scophthalmus rhombus Stylommatophora Helicidae Helix Cornu aspersum Lepidium campestre Helix pomatia Bivalvia Pteriomorphia Mytilida Mytilidae Mytilus Mytilus californianus Mytilus edulis Mytilus trossulus Arcoida Arcidae Hypericum perforatum Barbatia Ostreida Ostreidae Crassostrea Crassostrea virginica Pectinidae Chlamys Patinopecten Anarhichas minor Placopecten Placopecten magellanicus Pecten Pecten maximus Venerida Mactridae Spisula Spisula solidissima Solenidae Ensis Veneridae Macrocallista Macrocallista nimbosa Mercenaria Mercenaria mercenaria Heteroconchia Myoidea Digitaria <monocots> Myidae Mya Mya arenaria Cephalopoda Coleoidea Sepiidae Sepia Sepia officinalis Sphyrna tudes Loliginidae Loligo Paratrachichthys trailli Loligo vulgaris Ommastrephidae Illex Illex argentinus Illex illecebrosus Nototodarus Nototodarus gouldi Todarodes Todarodes pacificus Octopoda Ficus pumila Eledone Eledone moschata Octopus Tragelaphus angasii Octopus vulgaris Incirrata Octopodidae Polyplacophora Neoloricata Chitonida Arthropoda Crustacea Branchiopoda Anostraca Artemia Durio Durio zibethinus Bixaceae Bixa Bixa orellana Barbatia cancellaria Paralichthys dentatus Cirripedia Thoracica Malacostraca Eucarida Decapoda Dendrobranchiata Penaeidae Penaeus monodon Penaeus vannamei Ameiurus catus Ameiurus natalis Ictalurus furcatus Pleocyemata Caridea Palaemonidae Macrobrachium Salix pulchra Vanilla x tahitensis Pandalidae Pandalus Pandalus borealis Nephropidae Homarus Homarus americanus Homarus gammarus Benthophilinae Neogobiini Ponticolini Astacidea Astacidae Astacus Astacus astacus Astacoidea Cambaridae Procambarus Procambarus clarkii Achelata Palinuridae Palinurus Panulirus Panulirus japonicus Panulirus argus Anomura Lithodidae Paralithodes Paralithodes camtschaticus Paguroidea Brachyura Cancridae Cancer Cancer pagurus Cancer irroratus Portunidae Callinectes Callinectes sapidus Portunoidea Geryonidae Callipepla californica Xanthoidea Menippe Menippe mercenaria Crescentia alata Majoidea Majidae Euphausiacea Euphausiidae Euphausia Euphausia superba Nephrops Nephrops norvegicus Bacteroidota/Chlorobiota group Scyliorhinus stellaris Crocodylus siamensis Aulopiformes Dicroglossidae Macrourus Casimiroa Casimiroa edulis Pseudobatos percellens Adansonia Adansonia digitata Pachira Atherinidae Ethmidium Ethmidium maculatum Vaccinium corymbosum Tragelaphus buxtoni Pusa Caenogastropoda Patellogastropoda Lottiidae Littorinoidea Strombidae Strombus Lutjanus colorado Leuciscus idus Schilbe mystus Lota Lota lota Aspalathus Mugil trichodon Harengula clupeola Harengula humeralis Scorpaena grandicornis Sepiola atlantica Thymallus arcticus Allieae Calophyllaceae Montiaceae Asphodeloideae Rastrelliger Rastrelliger kanagurta Uranoscopidae Cucurbitales eudicotyledons Oxalidales asterids rosids Camelina Sisymbrium altissimum Penaeus brasiliensis Penaeus kerathurus Penaeus merguiensis Cetengraulis mysticetus Hedychium coronarium Malpighia glabra saccharomyceta saccharomyceta Fabales Eumalacostraca Sebastes alutus Sebastes diploproa Sebastes entomelas Sebastes flavidus Sebastes goodei Sebastes levis Sebastes melanops Sebastes miniatus Sebastes mystinus Sebastes ovalis Sebastes paucispinis Sebastes pinniger Sebastes ruberrimus Sebastes rufus Sebastes saxicola Sebastes serranoides Scorpaena Ziziphus Potentilleae Amygdaleae Maleae Conodon Conodon nobilis Trinectes inscriptus Mobula hypostoma Caryocaraceae Caryocar Senna alexandrina Cambarinae Pachygrapsus Pachygrapsus transversus Lottia Asparagales Euheterodonta Zeus capensis Carduinae Centaureinae Veneroidea Scorzonerinae Lactucinae Hyoseridinae Crepidinae Cichoriinae Cilus Cilus gilberti Rosa gallica Rosa canina Amorphophallus Allium schoenoprasum Oncorhynchus tshawytscha Caranx latus Pomatomus Pomatomus saltatrix Rubus caesius Rubus occidentalis Rubus odoratus Rubus phoenicolasius Rubus ulmifolius Rubus ursinus Eragrostidinae Eleusininae Pomatoschistus minutus complex Pylodictis Pylodictis olivaris Pagrus auratus Zizania aquatica Echinodermata Dallia Dallia pectoralis Lactuca serriola Beloniformes Echinozoa Echinoidea Hypsophrys nematopus Sciaenops Sciaenops ocellatus Euechinoidea Echinus Echinus esculentus Debaryomycetaceae Echinacea <sea urchins> Echinidea Echinidae Aspidochirotacea Aspidochirotida Genypterus maculatus Stichopodidae Cheilodactylidae Cheilodactylus Nemadactylus Nemadactylus douglasii Nemadactylus macropterus Citrus japonica Limonia <eudicots> Holothuroidea Chordata Nuphar lutea Vertebrata <vertebrates> Petromyzontiformes Petromyzontidae Petromyzon Petromyzon marinus Gobius cobitis Gnathostomata <vertebrates> Chondrichthyes Elasmobranchii Raja Raja clavata Leucoraja erinacea Squalus Squalus acanthias Odontaspididae Carcharhinidae Carcharhinus Carcharhinus obscurus Carcharhinus plumbeus Carcharhinus porosus Mustelus Mustelus canis Mustelus antarcticus Passiflora edulis Sphyrna Sphyrna lewini Sphyrna tiburo Scyliorhinidae Scyliorhinus Scyliorhinus canicula Echinorhinidae Echinorhinus Triakidae Triakis Lamninae Isurus Isurus paucus Lamna Lamna nasus Alopiidae Ribes nigrum Argopecten gibbus Trigonella Trigonella foenum-graecum Euphyllophyta Rajiformes Rhinobatidae Rhinobatos Holocephali Chimaeriformes Callorhinchidae Callorhinchus Callorhinchus milii Chimaeridae Chimaera Chimaera monstrosa Galeorhinus Actinopterygii Acipenseriformes Acipenseridae Acipenser Acipenser gueldenstaedtii Acipenser stellatus Acipenser transmontanus Acipenser ruthenus Acipenser medirostris Polyodontidae Polyodon Polyodon spathula Amiiformes Amiidae Amia Amia calva Anguilliformes Anguillidae Anguilla Anguilla anguilla Anguilla japonica Anguilla rostrata Anguilla australis Congridae Conger Muraenesocidae Muraenesox Muraenesox cinereus Clupeinae Clupea Clupea harengus Cypriniformes Cyprinidae Carassius Ctenopharyngodon Ctenopharyngodon idella Cyprinus Cyprinus carpio Fulmarus glacialoides Hypophthalmichthys Macrobrachium rosenbergii Catostomidae Catostomus Merluccius bilinearis Catostomus commersonii Verbena officinalis Siluriformes Ictaluridae Ictalurus Ictalurus punctatus Pangasiidae Pangasius Pangasius pangasius Salmoniformes Esociformes Esocidae Esox Esox lucius Osmeridae Osmerus Osmerus mordax Salmonidae Oncorhynchus Oncorhynchus gorbuscha Oncorhynchus keta Oncorhynchus kisutch Oncorhynchus masou Oncorhynchus mykiss Oncorhynchus nerka Boswellia Salmo Salmo salar Salmo trutta Salvelinus Spondias mombin Salvelinus alpinus Capsicum chinense Salvelinus fontinalis Salvelinus malma Salvelinus namaycush Hucho Gadiformes Gadidae Gadus Gadus morhua Gadus ogac Melanogrammus Melanogrammus aeglefinus Merlangius Merlangius merlangus Pollachius Pollachius virens Merlucciidae Merluccius Merluccius merluccius Cynoscion arenarius Lophiiformes Lophiidae Lophius Gadus macrocephalus Trisopterus esmarkii Lophius americanus Lophius piscatorius Atheriniformes Portunus Portunus pelagicus Burkholderiales Cottidae Cottioidei Cyclopteridae Cyclopterus Cyclopterus lumpus Scorpaenoidei Scorpaenidae Perciformes Percoidei Cichlidae Oreochromis mossambicus Oreochromis niloticus Aulopidae Aulopus Lampridae Lampris Lampris guttatus Lampriformes Oreochromis Synodontidae Synodus Synodus saurus Carangidae Caranx Seriola Percichthyidae Lateolabrax Micromesistius Micromesistius poutassou Brosme Brosme brosme Lateolabrax japonicus Lotidae Percidae Perca Perca flavescens Perca fluviatilis Sparidae Pagrus Pagrus pagrus Sparus Sparus aurata Acanthopagrus Centrarchidae Pomoxis Pomoxis nigromaculatus Centropomidae Enterococcaceae Lates Lates calcarifer Mugilidae Mugil Zoarcales Zoarcidae Iguaninae Anarhichadidae Anarhichas Anarhichas lupus Gobioidei Gobiidae Scombridae Euthynnus Katsuwonus pelamis Euthynnus affinis Euthynnus alletteratus Sarda Sarda orientalis Sarda chiliensis Sarda sarda Thunnus Thunnus alalunga Thunnus albacares Thunnus thynnus Thunnus maccoyii Thunnus obesus Tilia platyphyllos Xiphiidae Xiphias Xiphias gladius Cola Labridae Pleuronectiformes Crocus sativus Paralichthys Paralichthys olivaceus Pleuronectidae Limanda Myzopsetta ferruginea Platichthys Platichthys flesus Pleuronectes Pleuronectes platessa Pseudopleuronectes Pseudopleuronectes americanus Conger conger Hippoglossus Hippoglossus hippoglossus Beryciformes Leuciscus Squalius cephalus Sarcopterygii Amphibia Austrobaileyales Aesculus turbinata Coelorinchus Anura Selenicereus Arctostaphylos Prevotella Trachurus japonicus Boehmeria Boehmeria nivea Crescentia Ranidae Rana <genus> Aquarana catesbeiana Arbutus unedo Arctostaphylos uva-ursi Pelophylax ridibundus Rana temporaria Neobatrachia Sauropsida Testudines Ammodytidae Ammodytes Ammodytes tobianus Menippe nodifrons Cryptodira Labeo Labeo rohita Cheloniidae Caretta Caretta caretta Chelonia Solenoceridae Solenocera Chelonia mydas Chelydridae Chelydra Chelydra serpentina Carissa Archosauria Crocodylidae Alligator Alligator mississippiensis Crocodylus Bifidobacteriales Micrococcales Mycobacteriales Crocodylus niloticus Crocodylus porosus Microbacteriaceae Crocodylus novaeguineae Lepidosauria Squamata Iguania Iguanidae Iguana Iguana iguana Morus nigra Pouteria Gobius auratus Gobius niger Gobius paganellus Knipowitschia Knipowitschia panizzae Zosterisessor Zosterisessor ophiocephalus Artemia salina Citrus reticulata Galeorhinus galeus Coregonus macrophthalmus Coregonus wartmanni Periophthalmus Echinorhinus brucus Etmopterus baxteri Oxynotus Mobula Cactineae Anguilla nebulosa Vigna umbellata Harengula thrissina Mullus surmuletus Sarpa Sarpa salpa Atherina Atherina boyeri Aves Palaeognathae Casuariiformes Helicoidea Dromaiidae Dromaius Dromaius novaehollandiae Rheiformes Rheidae Rhea pennata Rhea Rhea americana Struthioniformes Struthionidae Struthio Struthio camelus Peprilus paru Prunus salicina Cancer productus Chenopodium pallidicaule Neognathae Anseriformes Anatidae Anas Anas platyrhynchos Cairina Cairina moschata Berycidae Beryx Beryx splendens Mediterranean clade Glebionidinae Cyttus Cyttus australis Panarthropoda Apodiformes Apodidae Microstomus Microstomus achne Microstomus pacificus Charadriiformes Laridae Larus Larus marinus Larus fuscus Musa x paradisiaca Scolopacidae Columbiformes Columbidae Bubalus bubalis Craniata <chordates> Ipomoea aquatica Galliformes Merluccius albidus Merluccius australis Merluccius capensis Merluccius gayi Merluccius hubbsi Merluccius paradoxus Merluccius polli Merluccius productus Merluccius senegalensis Phasianidae Buglossidium Buglossidium luteum Microchirus Microchirus variegatus Callipepla Colinus Colinus virginianus Oligella Gallus Gallus gallus Camelina sativa Phasianinae Verbeneae Coturnix Coturnix coturnix Staphylococcaceae Meleagris ocellata Meleagris Meleagris gallopavo Bacilli Heliantheae alliance Juglans cinerea Artiodactyla Cephalopholis Gunneridae rosids incertae sedis fabids malvids campanulids Aquifoliales lamiids Macruronus Macruronus magellanicus Silybum Silybum marianum Lycoteuthidae Lycoteuthis Lycoteuthis lorigera Metroxylon Metroxylon sagu Silurus aristotelis Squalus blainville Eutheria Corchorus Corchorus olitorius Cola acuminata Epinephelus Mola Mola mola Psettodes Stromateidae Etrumeus micropus Harpadon Alpinia <monocots> Zingiber officinale Pachira insignis Primates Perna perna Ophidiiformes Ophidiidae Belonidae Strongylura Dentex Dentex dentex Silurus Silurus glanis Catarrhini Jasus Jasus edwardsii Hominidae Homo Homo sapiens Homo sapiens Homo sapiens Homo sapiens Ursidae Ursus Ursus americanus Ursus arctos Malva Trachichthyidae Hoplostethus Hoplostethus atlanticus Sardinella Sardinella fimbriata Sardinella longiceps Otariidae Odobenidae Odobenus Odobenus rosmarus Phocidae Latridae Latridopsis Latridopsis ciliaris Phoca Pusa hispida Cetacea Odontoceti Monodontidae Delphinapterus Delphinapterus leucas Bacteroidota Mysticeti Balaenopteridae Balaenoptera Balaenoptera acutorostrata Panpulmonata Cochlearia Perissodactyla Equidae Equus Equus zebra Equus asinus Equus caballus Camelineae Cardamineae Crangonidae Crangon Lepidieae Brassiceae Sisymbrieae Cochlearieae Suidae Sus Sus scrofa Ostreoidea Hippopotamidae Hippopotamus Hippopotamus amphibius Tylopoda Camelidae Camelus Camelus bactrianus Camelus dromedarius Lama Lama glama Ruminantia Cervidae Alces Alces alces Capreolus Capreolus capreolus Cervus Cervus elaphus Cyperoideae Eleocharideae Cypereae Cervus nippon Dama Rangifer Rangifer tarandus Odocoileus Odocoileus hemionus Odocoileus virginianus Odocoileinae Dentex canariensis Dentex gibbosus Dentex macrophthalmus Dentex maroccanus Bovidae Bison Bison bison Bison bonasus Bos Glebionis coronaria Bos taurus Bubalus Capra Capra hircus Strychnos spinosa Scomberomorus concolor Scomberomorus guttatus Scomberomorus maculatus Scomberomorus regalis Scomberomorus sierra Ovis Ovis aries musimon Ovis aries Tragelaphus Tragelaphus strepsiceros Tragelaphus imberbis Jasus lalandii Caprinae Syncerus Syncerus caffer Nematalosa vlaminghi Lagomorpha Leporidae Lepus Lepus europaeus Rodentia Marmota Marmota monax Mammea africana Calophylleae Garcinieae Hypericeae species The collection of subjects that have a common set of parameters defined in the protocol (could be experimental parameters, treatment parameters, or sponsor-defined attributes). Subject Trial Set Subject Trial Set Records pertaining to site specific approvals from an Institutional Review Board (IRB)/Independent Ethics Committee (IEC) or other governing body regarding human subjects in a biomedical or behavioral research. true IRB-IEC Doc Subcat IRB-IEC Documents Subcategory IRB/IEC Trial Approval Institutional Review Board Independent Ethics Committee Documents Institutional Review Board Independent Ethics Committee Human Subject in Research Approval Documentation Institutional Review Board Independent Ethics Committee Human Subject in Research Approval Documentation A 2-oxo monocarboxylic acid anion that is the conjugate base of pyruvic acid, which is an important metabolic product for energy-producing biochemical pathways. Pyruvate is the final product of glycolysis and, when hypoxic conditions arise, can be metabolized anaerobically to form lactate. This chemical is a precursor of both acetyl-coenzyme A and oxaloacetate, which are involved in the citric acid cycle. Additionally, oxaloacetate is a substrate in the gluconeogenesis pathway. 2-Oxopropanoate Propanoic Acid, 2-Oxo-, Ion(1-) Pyruvate Pyruvate The amount of an individual's total body mass that is fat, expressed as a percent. true BODYFATP Body Fat Percentage Body Fat Percentage The process by which information about the health status of an individual is obtained after a study has officially closed; an activity that continues something that has already begun or that repeats something that has already been done. true Active Follow-up CLSFUP Clinical Signs Follow-up Follow Up Follow-Up Follow-up Followed Followup follow up follow-up follow_up Follow-Up A nutritional supplement composed of a fermented milk drink prepared by inoculating cow, goat, or sheep milk with kefir grains, with potential immunomodulating and probiotic activities. Upon oral administration of kefir, the kefir grains may stimulate the proliferation of beneficial bacteria in the gastrointestinal (GI) tract. This modulates the GI flora ecosystem, improves the functions of the intestinal barrier and protects against harmful viruses and bacteria. In addition, this prebiotic modulates the immune system and may inhibit inflammation. Kefir Kephir Kefir A facility established for research, often designed to promote interactions between faculty, scholars, students, and industry. true Research Center Research Institute Research Center An organic or inorganic substance, element, isotope, food or other materials derived from microorganism, plant, or animal sources. They can be used for the prevention, diagnosis, treatment or research of disease states, for industrial purposes, or for the promotion or maintenance of organism viability or health. Drug, Food, Chemical or Biomedical Material Drug, Food, Chemical or Biomedical Material Substances that are grouped or classified by chemical composition. Drug or Chemical by Structure Drug or Chemical by Structure Substances introduced into the body by dietary means. Food Component Food Component The distinguishing qualities or prominent aspects of an individual person. Personal Personal Attribute Subject Characteristics Personal Attribute Organic acids that have oxygen atoms in the acidic groups. (NCI) Organic Oxoacids Organic Oxoacids Processed or unprocessed substances obtained from animal, plant, microorganism and mining source that provide nutrients for living organisms to maintain biological processes or functions. FOOD OR FOOD PRODUCT Food Food Product Food or Food Product Food or Food Substance FoodProduct Food or Food Product Groups with a focus on clinical or health related studies. Study Related Group Study Related Group An organizational header for concepts representing mostly abstract entities. Conceptual Entity Conceptual Entity One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing. Descriptor Designation Designator ID Identifier id identifier Identifier The selection and obtaining of small representative quantities of biological material for the purpose of analysis; also, in biomedical statistics, sampling is the selection and implementation of statistical observations in order to estimate properties of an underlying population; also, in environmental science, the collection of representative specimens analyzed to characterize site conditions. true Sampling Sampling The street name and building number where a person or organization is located. Address Line STREET Street Street Address Street Address The act of abiding by a stated treatment plan or protocol. Adherence Adherence A group used as a standard of comparison in a control experiment. Control Control Group control group Control Group LACTOSE, UNSPECIFIED FORM Lactose lactose Lactose A class of hydrocarbons with an empirical formula of Cm(H20)n (where m and n may be equal) and includes monomers, polymers and derivatives of aldoses, ketoses, saccharides, and alditols. Carbohydrate Carbohydrates carbohydrate Carbohydrate An organic oxoacid that contains a carboxy moiety (-COOH) as a functional group. Carboxylic Acids Carboxylic Acids An active process; excludes processes and mechanisms which fulfill biological functions. Activity General activity Activity Natural or synthetic substances that are used in various industries or in laboratories for a broad range of applications. This group includes, but is not limited to, pharmaceutical excipients, research/diagnostic agents, agricultural agents, and other non-edible products that may have human health implication. Industrial Additive Industrial Aid Industrial Aid A characteristic of a treatment regimen employed as a comparator against which the study treatment is evaluated. Control Type TCNTRL Control Type A method of selecting a sample from a population in such a way that every sample that could be selected has an equal chance of being selected. true Probabilty Sampling Random Sampling Random Sampling true Simple Random Sampling Simple Random Sampling true Convenience Sampling Volunteer Sample Convenience Sampling Bioactive Food Component Bioactive Food Component A collection of web pages and other files. true Internet Website Web Site Website website www-website Web Site Dietary Carbohydrate Dietary Carbohydrate Disaccharide Disaccharide The name applied to a scientific investigation. true Study Name clinical study name clinical_study_name Study Name true Stratified Random Sampling Stratified Random Sampling Judgement Sampling Judgment Sampling Judgment Sampling true Multi-Stage Sampling Multistage Sampling Multi-Stage Sampling Molecule that contains atoms of the element carbon, usually combined with itself and with atoms of one or more other element such as hydrogen, oxygen, nitrogen, sulfur, phosphorus, chlorine, or fluorine. Excludes carbides, carbonates and carbon oxides. Organic Chemical Organic Chemical LACTIC ACID, UNSPECIFIED FORM Lactate Lactic Acid lactic acid Lactic Acid A single serving of a beverage; any liquid suitable for drinking. true Drink Drink Probiotic Probiotic Supplement Probiotic supplements (pills, liquid, powder; or other probiotics) probiotic Probiotic The textual representation of the study objective. true Study Objective Description StudyObjective.description Study Objective Description The non-unique initials or abbreviated name used for identification of the study. true Study Acronym Study Protocol Version Acronym StudyProtocolVersion.acronym Trial Acronym Study Protocol Version Acronym A sequence of letters, numbers, or other characters that uniquely identifies a clinical trial within a clinical trial registry. true Clinical Trial Registry Identifier REGID Registry Identifier Clinical Trial Registry Identifier A planned process that gathers and measures information on variables of interest, in an established systematic fashion that enables one to answer stated research questions, test hypotheses, and evaluate outcomes. Data collection results in a collection of data. WEB: http://en.wikipedia.org/wiki/Data_collection data collection A data sampling design that uses randomization for sample selection randomization sampling design A data item that is more specifically a rectangular array of numbers, symbols, or expressions, arranged in rows and columns. WEB: https://en.wikipedia.org/wiki/Matrix_(mathematics) data matrix A data collection process that results in a collection of data from the literature. data collection from literature A data item that is produced as the output of a data transformation. transformed data item A document editing process in which one or more fields in a form are filled with related information, such as when answering a questionnare. Penn Group form filling A patient questionnaire which has been filled out by a patient. Person: Jie Zheng, Chris Stoeckert Penn Group filled patient questionnaire A questionnaire that comprises a set of demographic and medical questions about a patient which will be filled by the patient or their legally authorized representative. A questionnaire that comprises a set of questions about a patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by the human subject. Person: Jie Zheng, Chris Stoeckert Penn Group patient questionnaire A time measurement datum which is the end date of a smoking behavior. Penn Group smoking end date A protocol that is a set of step-by-step instructions compiled by an organization for carrying out routine operations. https://en.wikipedia.org/wiki/Standard_operating_procedure standard operating procedure A textual entity describing a study aim or a sample collection. sample collection or study aim description A proper name that designates a study. study proper name An objective specification that specifies the total number of individuals who are planned to participate in study. true number of total human study participant objective planned process planned process A process that realizes a plan which is the concretization of a plan specification. A processual entity that realizes a plan which is the concretization of a plan specification. branch derived planned process regulator role a regulatory role involved with making and/or enforcing relevant legislation and governmental orders OBI regulator role biological feature identification objective Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. biological feature identification objective regulatory role a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. OBI, CDISC regulatory role material supplier role a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. material supplier role processed material Is a material entity that is created or changed during material processing. processed material chromatography device chromatography device A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. Frank Gibson chromatography instrument http://en.wikipedia.org/wiki/Chromatography http://en.wikipedia.org/wiki/Chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography device chromatography device mass spectrometer A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). OBI branch derived investigation evaluant role 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 OBI evaluant role assay A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. OBI branch derived assay sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. OBI branch derived sample preparation for assay diagnosis textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. diagnosis textual entity culture medium a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. OBI culture medium reagent role 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 role patient role a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider OBI, CDISC patient role material processing A planned process which results in physical changes in a specified input material OBI branch derived material processing protocol testing objective Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. protocol testing objective study subject role A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. OBI participant under investigation role responsible party role responsible party role he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study Person: Jennifer Fostel responsible party OBI responsible party role principal investigator role a responsible party role played by a person responsible for the overall conduct of a study true principal investigator role specimen role a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation OBI specimen role intervention design An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. OBI branch derived intervention design baseline participant role a reference participant role which is realized by making the reference to qualities at the start of the study or intervention baseline participant role filter paper filter paper A device manufacture with the intent to provide a porous unsized paper used for filtering. a device manufacture with the intent to provide a porous unsized paper used for filtering. Frank Gibson sep:00107 sep:00107 filter paper filter paper crossover population role a role realized when a participant serves as reference to itself crossover population role study group role a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol study group role population a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area adapted from Oxford English Dictionnary population biological replicate role a reference participant role realized by equivalent treatment of participants OBI biological replicate role investigation agent role A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. OBI investigation agent role methodology testing objective Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. methodology testing objective reference subject role a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference OBI reference subject role organization An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. GROUP: OBI organization technical replicate role technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay technical replicate role cohort role a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study. WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students. WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site). WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation. cohort role plan A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. branch derived plan protocol A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) true protocol protocol adding a material entity into a target is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. branch derived adding a material entity into a target analyte role A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. OBI analyte role material to be added role A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target). OBI material to be added role interpreting data A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion Bjoern Peters drawing a conclusion based on data planning a process of creating or modifying a plan specification Bjoern Peters Plans and Planned Processes Branch planning mass analyzer mass analyzer The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. Frank Gibson PERSON: Daniel Schober http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer mass analyzer mass analyzer ion source ion source The ion source of a Voyager-DE??? STR Biospectrometry Workstation An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source ion source ion source ion detector ion detector The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Detector ion detector ion detector contain function A contain function is a function to constrain a material entities location in space contain function heat function A heat function is a function that increases the internal kinetic energy of a material heat 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. material separation 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 filter function ionization function An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. http://en.wikipedia.org/wiki/Ionization ionization function cool function A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. cool function environment control function An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. environment control function measuring glucose concentration in blood serum measuring glucose concentration in blood serum assay An assay that determines the concentration of glucose molecules in a blood serum sample Person:Bjoern Peters OBI measuring glucose concentration in blood serum measuring glucose concentration in blood serum assay extract an extract is a material entity which results from an extraction process GROUP: OBI Biomatrial Branch extract adding material objective is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity adding material objective analyte measurement objective an assay objective to determine the presence or concentration of an analyte in the evaluant PPPB branch analyte measurement objective assay objective an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch assay objective analyte assay analyte assay example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. 2013-09-23: simplify equivalent axiom Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement. logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration')) PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg Alan Ruttenberg Bjoern Peters Helen Parkinson OBI Planned process branch PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch Philippe Rocca-Serra analyte assay analyte assay target of material addition role A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity. OBI target of material addition role normalized data set A data set that is produced as the output of a normalization data transformation. normalized data set measure function Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. measure function material transformation objective an objective specifiction that creates an specific output object from input materials. GROUP: OBI PlanAndPlannedProcess Branch material transformation objective manufacturing A planned process with the objective to produce a processed material which will have a function for future use. GROUP: OBI PlanAndPlannedProcess Branch manufacturing manufacturing objective is the objective to manufacture a material of a certain function (device) GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective study design execution a planned process that carries out a study design branch derived study design execution clinical chemistry assay An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. url:https://en.wikipedia.org/wiki/Clinical_chemistry clinical chemistry assay manufacturer role Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. OBI manufacturer role scattered molecular aggregate a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 scattered molecular aggregate hematology hematology assay Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. Godsland IF, Johnston DG. Metabolism. 2008 Sep;57(9):1190-7. PMID: 18702943 An assay that studies blood and blood producing organs using a variety of techniques and instruments hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments Philippe Rocca-Serra blood analysis, haematology OBI branch derived hematology hematology assay material separation objective is an objective to transform a material entity into spatially separated components. PPPB branch material separation objective urine specimen a portion of urine collected from an organism true urine specimen material combination is a material processing with the objective to combine two or more material entities as input into a single material entity as output. bp material combination device setting Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device PERSON: Frank Gibson device setting blood specimen a material entity derived from a portion of blood collected from an organism Bjoern Peters blood specimen specimen collection process A planned process with the objective of collecting a specimen. specimen collection process sample from organism a material obtained from an organism in order to be a representative of the whole sample from organism portioning objective A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective separation into different composition objective A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). separation into different composition objective specimen collection objective A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters specimen collection objective material combination objective is an objective to obtain an output material that contains several input materials. bp material combination objective glucose tolerance test PMID: 19527607 Using the 100-g Oral Glucose Tolerance Test to Predict Fetal and Maternal Outcomes in Women with Gestational Diabetes Mellitus. Lin CH, Wen SF, Wu YH, Huang MJ. Chang Gung Med J. 2009 May-Jun;32(3):283-9. An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. 30-10-2013:[author: PRS] removing "realizes some (concretizes some 'time series design')" axiom as it causes 'gtt' to be classified under study design execution instead of assay Philippe Rocca-Serra NuGO OBI plan branch glucose tolerance test host role host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role material sample role A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. material sample role material sample A material entity that has the material sample role material sample independent variable specification a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables study design independent variable dependent variable specification dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables study design dependent variable material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters material maintenance objective informed consent process A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate. http://clinicaltrials.gov/ct2/info/glossary#informed informed consent process to be treated with active ingredient role A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient PERSON: Helen Parkinson to be treated with active ingredient role to be treated with placebo role A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo to be treated with placebo role research organization An organization formed with a goal to have its members conduct investigations research organization measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device material maintenance A planned process with the objective to maintain some or all of the characteristics of an input material over time. material maintenance study intervention A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study. GROUP: OBI study intervention material separation device flow cytometer A device with a separation function realized in a planed process material separation device service consumer role a role which inheres in a person who uses a service OBI service consumer role service provider role is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person service provider role compound treatment design an intervention design in which the treatment is the administration of a compound MO_555 compound_treatment_design compound treatment design processed specimen A specimen that has been intentionally physically modified. Bjoern Peters processed specimen container A device that can be used to restrict the location of material entities over time container device A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. OBI development call 2012-12-17. device dose specification a directive information entity that describes the dose that will be administered to a target dose specification sequence data A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. GROUP: OBI sequence data dose A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. dose administration of material to specimen The directed combination of a material entity with a specimen. Bjoern Peters administration of material to specimen questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster true questionnaire nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. UPenn Group nucleic acid extract environmental control device An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. OBI environmental control device nucleic acid sequencer An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell nucleic acid sequencer protein sequencer An device that is used to determine the order of amino acids in protein sequences. PERSON: Erik Segerdell protein sequencer service A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. OBI workshop San Diego 2011 service quality control testing design A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. MO_981 quality_control_testing_design quality control testing design dose response design A study design that examines the relationship between the size of the administered dose and the extent of the response. MO_485 dose_response_design dose response design specimen from organism A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). MO_954 organism_part specimen from organism material maintenance service A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. PERSON: Matthew Brush material maintenance service material service A service which has a material entity as specified input and/or specified output. PERSON: Carlo Torniai material service material analysis service A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. PERSON: Matthew Brush material analysis service material storage service A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. PERSON: Matthew Brush material storage service investigation description A textual entity that describes an investigation. NIAID GSCID-BRC metadata working group project description true investigation description specimen identifier A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Person: Chris Stoeckert, Jie Zheng specimen ID NIAID GSCID-BRC metadata working group Specimen ID NIAID GSCID-BRC specimen identifier 1 PubMed ID A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/ Person: Chris Stoeckert, Jie Zheng PMID PubMed Identifier Website: http://en.wikipedia.org/wiki/Wikipedia:PMID Publication Citation NIAID GSCID-BRC PubMed ID investigation title A textual entity that denotes an investigation. NIAID GSCID-BRC metadata working group project title true investigation title Bioinformatics Resource Center An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them. Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers Bioinformatics Resource Center country name A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography. NIAID GSCID-BRC metadata working group Website: http://en.wikipedia.org/wiki/Country Specimen Collection Location - Country true country name investigation identifier A CRID symbol used to identify an investigation. Person: Chris Stoeckert, Jie Zhneg NIAID GSCID-BRC metadata working group project ID NIAID GSCID-BRC investigation identifier grant identifier A CRID symbol used to identify a grant. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group grant ID NIAID GSCID-BRC grant identifier analytical chromatography An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. IEDB analytical chromatography grant A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role. OBI grant contact representative role A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. contact representative role selection criterion A directive information entity which defines and states a principle of standard by which selection process may take place. OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ selection criterion specimen collector role An Investigation agent role borne by a person or organization which is realized in a specimen collection process. An Investigation agent role borne by a person or organization which is realized in a specimen collection process. Person: Jie Zheng, Chris Stoeckert Penn Group NIAID GSCID-BRC specimen collector role drawing a conclusion A planned process in which new information is inferred from existing information. drawing a conclusion organization of specimen provider principal investigator An organization that is the affiliation of the principal investigator providing the specimens for the investigation NIAID GSCID-BRC metadata working group Sample Provider PI's Institution organization of specimen provider principal investigator organization of Bioinformatics Resource Center contact person An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's Institution organization of Bioinformatics Resource Center contact person specimen-based scope of investigation specification A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. NIAID GSCID-BRC metadata working group Sample Scope specimen-based scope of investigation specification specimen repository organization An organization that provides a service to store and distribute specimens NIAID GSCID-BRC metadata working group Specimen Repository specimen repository organization email address of Bioinformatics Resource Center contact person An email address of the person who is contact representative of a Bioinformatics Resource Center NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's email email address of Bioinformatics Resource Center contact person email address of specimen collector An email address of the person collecting the specimen NIAID GSCID-BRC metadata working group Specimen Collector's email email address of specimen collector sequencing facility organization An organization that provides sequence determination service NIAID GSCID-BRC metadata working group Sequencing Facility sequencing facility organization organization of specimen collector An organization that is the affiliation of the person collecting the specimen NIAID GSCID-BRC metadata working group Specimen Collector's Institution organization of specimen collector email address of sequencing facility contact person An email address of the contact representative at the sequencing facility NIAID GSCID-BRC metadata working group Sequencing Facility Contact's email email address of sequencing facility contact person investigation assay specification A plan specification which indicates the assay type used to obtain data. NIAID GSCID-BRC metadata working group Project Method investigation assay specification organization of sequencing facility contact person An organization that is the affiliation of the contact representative at the sequencing facility NIAID GSCID-BRC metadata working group Sequencing Facility Contact's Institution organization of sequencing facility contact person comment on investigation A textual entity that is about any of the aspects of an investigation worth noting NIAID GSCID-BRC metadata working group Comments comment on investigation specimen identifier assigned by specimen repository A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID NIAID GSCID-BRC specimen identifier assigned by specimen repository specimen identifier assigned by sequencing facility A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample ID - Sequencing Facility NIAID GSCID-BRC specimen identifier assigned by sequencing facility sample preparation for sequencing assay A sample preparation for assay that preparation of nucleic acids for a sequencing assay NIAID GSCID-BRC metadata working group Nucleic Acid Preparation Method sample preparation for sequencing assay email address of specimen provider principal investigator An email address of the principal investigator providing the specimens for the investigation NIAID GSCID-BRC metadata working group Sample Provider PI's email email address of specimen provider principal investigator sequencing service A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. Adpated from 'DNA sequencing service' sequencing service testable hypothesis An information content entity that expresses an assertion that is intended to be tested. Group:2013 Philly Workshop group testable hypothesis conclusion based on data An information content entity that is inferred from data. Group:2013 Philly Workshop group true conclusion based on data cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. cell freezing medium selection A planned process with the objective to create a group of entities by applying a predefined criteria to a larger group of entities. OBI selection scalar value specification A value specification that consists of two parts: a numeral and a unit label scalar value specification comparing prediction to measurement A planned process in which predicted values for some thing are compared to measured values for that thing. comparing prediction to measurement value specification An information content entity that specifies a value within a classification scheme or on a quantitative scale. value specification predicted value an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. predicted value grant agency An organization that provides funding support for projects such as investigations. NIAID GSCID-BRC metadata working group true grant agency collection of specimens A material entity that has two or more specimens as its parts. OBIB, OBI collection of specimens specimen set collection process Collection of both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy. A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. Chris Stoeckert, Jie Zheng OBIB, OBI specimen set collection process specimens collected in one encounter A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. OBIB, OBI specimens collected in one encounter human specimen set A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time. Duke Biobank, OBIB, OBI human specimen set specimens collected longitudinally A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity. Bjoern Peters, OBI specimens collected longitudinally physical store physical store a freezer. a humidity controlled box. A container with an environmental control function. A container with an environmental control function. For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ Chris Stoeckert Duke Biobank, OBIB Duke Biobank, OBIB Biobank physical store physical store digital object identifier The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/ OBI developers DOI https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/ digital object identifier high performance liquid chromotography assay On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. ImmPort HPLC PMID:9491555 http://www.ncbi.nlm.nih.gov/pubmed/9491555 high performance liquid chromotography assay molecular analysis facility organization An organization that provides molecular analysis service. NCI BBRB, OBIB molecular analysis facility organization measurand role A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. https://en.wiktionary.org/wiki/measurand measurand role bile specimen A specimen that is derived from bile. Chris Stoeckert, Penn Medicine Biobank bile specimen feces specimen A specimen that is derived from feces. Chris Stoeckert, Penn Medicine Biobank true feces specimen digestive system fluid or secretion specimen A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert, Penn Medicine Biobank digestive system fluid or secretion specimen milk specimen A specimen that is derived from milk. Chris Stoeckert, Penn Medicine Biobank milk specimen saliva specimen A specimen that is derived from saliva. Chris Stoeckert, Penn Medicine Biobank true saliva specimen sputum specimen A specimen that is derived from sputum. Chris Stoeckert, Penn Medicine Biobank sputum specimen sweat specimen A specimen that is derived from sweat. Chris Stoeckert, Penn Medicine Biobank sweat specimen reactant role A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction. reactant role blood plasma specimen a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. WEB: http://en.wikipedia.org/wiki/Blood_plasma true blood plasma specimen blood serum specimen A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. WEB: http://en.wikipedia.org/wiki/Blood_plasma true blood serum specimen organism A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. WEB: http://en.wikipedia.org/wiki/Organism organism specimen A material entity that has the specimen role. GROUP: OBI Biomaterial Branch specimen cultured cell population A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. PERSON:Matthew Brush cultured cell population glucose in solution A scattered aggregate of glucose molecules in a liquid glucose in solution data transformation A planned process that produces output data from input data. Branch editors data transformation data transformation objective An objective specification to transformation input data into output data PERSON: James Malone data transformation objective data normalization objective A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. PERSON: Elisabetta Manduchi PERSON: Helen Parkinson PERSON: James Malone data normalization objective normalization data transformation A normalization data transformation is a data transformation that has objective normalization. PERSON: James Malone normalization data transformation scaling objective is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum scaling objective sequential design Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does MUSC sequential design observation design observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. OBI branch derived observation design pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. GROUP: CEBS pool of specimens validated information an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means. OBI validated information curated information An information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts. OBI curated information randomized group participant role a role that borne by an organism and realized by some group randomization process randomized group participant role extraction A material separation in which a desired component of an input material is separated from the remainder extraction filtration filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device OBI-Branch: adapted from wikipedia and wordnet filtration centrifugation centrifugation PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation Philippe Rocca-Serra adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm centrifugation storage A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment. OBI-Branch storage group randomization A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] true group randomization document editing is a planned process with specified input original document and specified output edited document adapted from wikipedia document editing validation a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results adapted from wordnet (wkipedia) validation digital curation Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally. wikipedia digital curation DNA sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. MO DNA sequencer centrifuge centrifuge A device with a rapidly rotating container that applies centrifugal force to its contents Melanie Courtot Person: Jennifer Fostel Trish Whetzel http://en.wikipedia.org/wiki/Centrifuge http://en.wikipedia.org/wiki/Centrifuge centrifuge centrifuge study design A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. true study design clinical study design Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] Clinical Research Glossary Version 4.0 CDICS glossary group clinical study design repeated measure design a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design cross over design a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) cross over design n-to-1 design N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) n-to-1 design matched pairs design A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. http://www.holah.karoo.net/experimentaldesigns.htm matched pairs design parallel group design A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment http://www.holah.karoo.net/experimentaldesigns.htm parallel group design randomized complete block design A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. http://www.tufts.edu/~gdallal/ranblock.htm randomized complete block design balanced incomplete block design balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html balanced incomplete block design loop design A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design MO_912 loop design reference design A reference experiment design type is where all samples are compared to a common reference. MO_699 reference design latin square design Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and latin square design graeco latin square design Greco-Latin square design is a study design which relates to Latin square design Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and graeco latin square design hyper graeco latin square design PRS to do Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and hyper graeco latin square design factorial design factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) factorial design 2x2 factorial design a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors PMID: 17561240 2x2 factorial design fractional factorial design A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control fractional factorial design dye swap design An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip MO_858 dye swap design replicate design A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. MO_885 replicate design self vs self design A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. MO_490 self vs self design time series design Groups of assays that are related as part of a time series. MO_887 time series design stopping rule a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen PRS stopping rule compliance rule a compliance rule is a rule which ensures a compliance process occurs PRS compliance rule standard compliance rule a standard compliance rule is a compliance rule which defines conformity to a representation standard PRS PRS standard compliance rule ethical standard compliance rule an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur PRS PRS ethical standard compliance rule eligibility criterion an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group eligibility criterion inclusion criterion an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group true inclusion criterion exclusion rule an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group true exclusion criterion human subject enrollment A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. IEDB human subject enrollment collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism administering substance in vivo A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. IEDB administering substance in vivo material component separation a material processing in which components of an input material become segregated in space IEDB material component separation group assignment group assignment is a process which has an organism as specified input and during which a role is assigned OBI Plan group assignment maintaining cell culture A planned process with the objective to keep cells alive in a defined environment outside of an organism. OBI branch derived maintaining cell culture 'establishing cell culture' a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). PERSON:Matthew Brush establishing cell culture sequencing assay sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template An assay the uses chemical or biochemical means to infer the sequence of a biomaterial the use of a chemical or biochemical means to infer the sequence of a biomaterial has_output should be sequence of input; we don't have sequence well defined yet PlanAndPlannedProcess Branch OBI branch derived OBI branch derived sequencing assay sequencing assay dialysis the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition PERSON:Kevin Clancy OBI branch derived dialysis nucleic acid extraction a material separation to recover the nucleic acid fraction of an input material OBI branch derived nucleic acid extraction disposition to cause an allergic reaction The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease. IEDB disposition to cause an allergic reaction allergic reaction an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen) IEDB allergic reaction occurrence of allergy The process of an allergic disease occurring in an organism. IEDB occurrence of allergy infectious disease is a disease caused by an infectious agent IEDB infectious disease allergy is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect IEDB allergy cancer A disease characterized by abnormal and uncontrolled cell division IEDB cancer autoimmune disease Is a disease characterized by an immune response of an organism against parts of itself IEDB autoimmune disease blood harvesting blood harvesting A material separation where blood is taken from an organism. IEDB IEDB blood harvesting pathologic process abnormal, harmful processes caused by or associated with a disease IEDB pathologic process allergen A material entity bearing the disposition to cause an allergic reaction IEDB allergen bodily fluid specimen A specimen that is derived from some bodily fluid Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 bodily fluid specimen glucose assay An analyte assay that measures the abundance of glucose PennTURBO team glucose assay A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf clinical finding A series of statements representing health-relevant qualities of a patient and of a patient's family. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf clinical history A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf laboratory finding phenotype A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf phenotype disease A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf disease A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf clinical laboratory test A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf physical examination disease course The totality of all processes through which a given disease instance is realized. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf disease course The representation of a conclusion of a diagnostic process. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf diagnosis A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process http://code.google.com/p/ogms/issues/detail?id=35 treatment A hypothesis about some future part of a disease course. http://code.google.com/p/ogms/issues/detail?id=35 prognosis A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 health care process A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. health care process assay A data item that is about a patient and is the specified output of a health care process assay or diagnostic process clinical data item A microbiome located in a human body https://www.ncbi.nlm.nih.gov/pubmed/3418802/ human microbiome A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520061/ microbiome a human microbiome that is located in a human gastrointestinal system microbiome in human gastrointestinal system A microbiome located in a human gut. human gut microbiome The observable manifestation of the genotype of a microbial cell or group of cells in an environment. microbial phenotype A population growth range phenotype related to how growth of a microbial population is affected by the temperature of the environment. temperature effects on population growth phenotype A population growth phenotype relating to how the rate and/or extent of growth of a microbial population is affected by the pH of the environment. pH effects on population growth phenotype A population growth range phenotype related to how growth of a microbial population is affected by the concentration of solutes (water activity) in the environment. solute and water activity effects on population growth phenotype A microbial phenotype where the phenotype is observed at the level of a microbial population. population phenotype A microbial phenotype that is altered in some way relative to a designated control. altered microbial phenotype A population growth phenotype where the rate and/or extent of growth of a microbial population at a specified pH is altered relative to a designated control. altered effects of pH on population growth A population growth phenotype where the rate and/or extent of growth of a microbial population is altered relative to a designated control. altered population growth A microbial phenotype relating to the growth of a microbial population, i.e. an increase in the size of the population resulting from reproduction of individual microbes in the population. population growth phenotype A population growth phenotype related to how non-nutrient environmental factors affect growth of a microbial population. effect of non-nutrient environmental factors on population growth phenotype A microbial phenotype that affects a biological process. biological process phenotype A biological process phenotype where the rate, frequency, timing, or extent of a biological process is altered relative to a designated control. altered biological process A population growth phenotype relating to the vegetative growth of a microbial population in conditions of high osmolarity, which refers to osmotic conditions where the osmolarity of the environment is higher than the osmolarity that allows for optimal population growth. Population growth may refer to growth rate, growth yield, or both. population growth in high osmolarity phenotype A population growth phenotype where the growth of a microbial population in conditions of high osmolarity is altered relative to a designated control. altered population growth in high osmolarity A population growth range phenotype where the rate and/or extent of growth of a microbial population in a specified environmental condition is altered relative to a designated control. altered population growth range A microbial population phenotype where the phenotype of a microbial population is altered in some way relative to a designated control. altered population phenotype A population growth phenotype where the rate and/or extent of growth of a microbial population at a temperature that is towards the upper end of the organism's temperature growth range is altered relative to a designated control. altered population growth at high temperature A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law. Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008. legal person role Partecipants' identification number Aphanumeric string (1 to 8 digits) which univocally identify a partecipant/subject. ENPADASI_WP4 participants' identification number Month of anthropometry assessment Month of anthropometry assessment counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 months/y= 1332; 1332 + 5 (May=05)= 1337) ENPADASI_WP4 month of anthropometry assessment true For past smokers: time in years since quitting smoking ENPADASI_WP4 Time since quitting smoking Month of physical activity assessment by questionnaire counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 months/y= 1332; 1332 + 5 (May=05)= 1337) ENPADASI_WP4 Month of physical activity assessment by questionnaire Categories of physical activity level 1=low; 2= Medium; 3= High ENPADASI_WP4 categories of physical activity level Total physical activity in MET-hours/day (without sedentary or sleeping time) derived from questionnaire data ENPADASI_WP4 total physical activity by questionnaire Physical activity from recreational or leisure-time activities in MET-hours/day derived from questionnaire data ENPADASI_WP4 physical activity from recreational or leisure-time activities by questionnaire time spent in light physical activity in minutes/day derived from questionnaire data ENPADASI_WP4 light physical activity by questionnaire Time spent in moderate physical activity in minutes/day derived from questionnaire data ENPADASI_WP4 moderate physical activity by questionnaire Time spent in vigorous physical activity in minutes/day derived from questionnaire data ENPADASI_WP4 vigorous physical activity by questionnaire Time spent sedentary (PC use, TV watching) in minutes/day derived from questionnaire data ENPADASI_WP4 sedentary time by questionnaire Number of physical activity bouts of moderate or vigorous physical activity of at least 10 minutes per day ENPADASI_WP4 number of bouts by questionnaire Month of physical activity assessment by accelerometer counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 months/y= 1332; 1332 + 5 (May=05)= 1337) ENPADASI_WP4 Month of physical activity assessment by accelerometer Time spent in light physical activity in minutes/day derived from accelerometer data ENPADASI_WP4 light physical activity by accelerometer Time spent in moderate physical activity in minutes/day derived from accelerometer data ENPADASI_WP4 moderate physical activity by accelerometer Time spent in vigorous physical activity in minutes/day derived from accelerometer data ENPADASI_WP4 vigorous physical activity by accelerometer Time spent sedentary in minutes/day derived from accelerometer data ENPADASI_WP4 sedentary time by accelerometer Number of bouts of moderate or vigorous physical activity per day ENPADASI_WP4 number of bouts by accelerometer Average minutes per bout of moderate or vigorous physical activity per day ENPADASI_WP4 average duration of bouts Dietary assessment used for uploaded dietary variables 1=24-hour recall; 2=FFQ; 3=Food record; 4=other ENPADASI_WP4 ENPADASI_WP4 obsolete: Dietary assessment method true Month of dietary assessment counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 months/y= 1332; 1332 + 5 (May=05)= 1337) ENPADASI_WP4 month of dietary assessment Carbohydrate intake per unit time ENPADASI_WP4 calculated carbohydrate intake Fiber intake per unit time ENPADASI_WP4 calculated fiber intake Total fat intake per unit time ENPADASI_WP4 calculated total fat intake Saturated fatty acid intake per unit time ENPADASI_WP4 calculated saturated fatty acid intake Monounsaturated fatty acid intake per unit time ENPADASI_WP4 calculated monounsaturated fatty acid intake Polyunsaturated fatty acid intake per unit time ENPADASI_WP4 calculated polyunsaturated fatty acid intake Protein intake in per unit time ENPADASI_WP4 calculated protein intake Month of blood draw counted from 1900; e.g. May 2011=1337 (2011-1900=111; 111x12 = 1332; 1332 + 5 = 1337) ENPADASI_WP4 month of blood draw Fasting status before blood draw (measured in hours of fasting before blood draw) 1=less than 9 hours; 2=9 hours or more ENPADASI_WP4 true fasting status The process of collecting information on the diet/eating habits of a subject using a questionnaire. ENPADASI_WP4 Dietary assessment Anthropometric and habits information of the subject. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology. ENPADASI_WP4 ENPADASI_WP4 subject informations true A study short name is a short alphanumeric string used to abbreviate a study proper name (OMIABIS_0000037) ENPADASI_WP4 short study name Name of the consortium which the study refers to ENPADASI_WP4 true consortium The name of the method used for randomization (OBCS_0000089), if any randomization was adopted. ENPADASI_WP4 true randomization method Indicate whether blinded experiment were conducted or not ENPADASI_WP4 blinding If blinded experiment were conducted, indicate the method used for blinding ENPADASI_WP4 blinding method Indicated whether the study is terminated or not ENPADASI_WP4 true study terminated Indicate whethet the compliance was assessed or not ENPADASI_WP4 compliance assessment The ration between the circumference of the waist to that of the hips ENPADASI_WP4 waist:hip ratio A (short) alphanumeric string which identify the event/tretment ENPADASI_WP4 event identifier name An alphanumeric string which identify and describe the event/tretment ENPADASI_WP4 treatment descriptive name A long description of the sampling method used ENPADASI_WP4 Sampling method description Long text describing the assay used. ENPADASI_WP4 assay description Platform used for the assay ENPADASI_WP4 Assay platform The unique sampling event identifier for the sample collection producing the sample ENPADASI_WP4 sampling identifier This field is usually 0 for the overall intervention but may be several time points for challenges, e.g. at 0 and 12 weeks. ENPADASI_WP4 absolute start times This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology of the terms pertinent to physical activity assessment assay ENPADASI_WP4 Physical activity assessment This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology pertinent to blood analystics assay ENPADASI_WP4 blood analytics START TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology. ENPADASI_WP4 obsolete: Start tab true SUBJECT TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology. ENPADASI_WP4 Subject tab true EVENTS TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology. ENPADASI_WP4 Event tab true SAMPLING TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology. ENPADASI_WP4 Sampling tab true PHYSIOLOGY ASSAY TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology. ENPADASI_WP4 obsolete: physiology assay tab true INFORMATIONS TAB. This class should not be used as an ontology term, it is included as a superclass for the purpose to give a better organization to the ontology. ENPADASI_WP4 Information tab true The process of collecting various chemical-biological data (e.g. blood analytics) ENPADASI_WP4 Chemical-biological assay The process of collecting data from a sample using 'omic' technologies ENPADASI_WP4 Omics technology assay Type of omic assay performed (i.e. targeted metabolomics, untargeted metabolomics) ENPADASI_WP4 true Type of omics Assay type (i.e. Clinical chemistry assay: Standard kit #34567 from 'vendor' assayed on a Cobas Mira analyzer) ENPADASI_WP4 Assay type A short text identifying the question ENPADASI_WP4 short question name Type of question or question variable code ENPADASI_WP4 question type Type of physiology assay performed ENPADASI_WP4 obsolete: Physiology assay type true An assay which purpose is to collect all the general information (e.g. anthropometric measurement) available on the subjects of nutritional studies ENPADASI_WP4 Subject Information collection The subject (Human) participating in a nutritional study. ENPADASI_WP4 true subject of a nutritional study An experimental comparison study in which participants are allocated to treatment/intervention or control/placebo groups using a random mechanism (see randomisation). Best for study the effect of an intervention. ENPADASI_WP4 Randomised Controlled Trial http://www.cebm.net/study-designs/ A controlled trial where each study participant has both therapies, e.g, is randomised to treatment A first, at the crossover point they then start treatment B. Only relevant if the outcome is reversible with time, e.g, symptoms. ENPADASI_WP4 Crossover Design http://www.cebm.net/study-designs/ Data are obtained from groups who have been exposed, or not exposed, to the new technology or factor of interest (eg from databases). No allocation of exposure is made by the researcher. Best for study the effect of predictive risk factors on an outcome. ENPADASI_WP4 true Cohort Study http://www.cebm.net/study-designs/ Patients with a certain outcome or disease and an appropriate group of controls without the outcome or disease are selected (usually with careful consideration of appropriate choice of controls, matching, etc) and then information is obtained on whether the subjects have been exposed to the factor under investigation. ENPADASI_WP4 true Case-Control Study http://www.cebm.net/study-designs/ A study that examines the relationship between diseases (or other health-related characteristics) and other variables of interest as they exist in a defined population at one particular time (ie exposure and outcomes are both measured at the same time). Best for quantifying the prevalence of a disease or risk factor, and for quantifying the accuracy of a diagnostic test. ENPADASI_WP4 true Cross-Sectional Survey http://www.cebm.net/study-designs/ Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental con-taminants. Concept of food component can be viewer both as a role and as a material entity. This class, for convenience, represents the material entity "food component", including all those material entity having the role of "Food Component" ENPADASI_WP4 food component entity Component added to food to improve or preserve it ENPADASI_WP4 additive Unwanted food component that makes the food no longer suitable for use ENPADASI_WP4 contaminant A food bioactive is a food component other than those needed to meet basic human nutritional needs (nutrients). Food bioactives modulates one or more metabolic processes, possibly resulting in the promotion of better health. The daily required intake for food bioactives is not established yet, and there is no demonstration that malnutrition occurs when the right amount is not provided ENPADASI_WP4 food bioactive A nutrient is a food component used by the body for normal physiologic functions that guarantee survival and growth. It must be supplied in adequate and defined amounts from foods consumed within a diet. Malnutrition occurs when the right amount of nutrient is not provided ENPADASI_WP4 nutrient An ingredient is a material entity used as part for the preparatio of food. Recipes specify which ingredients are used to prepare a specific food ENPADASI_WP4 Ingredient The food is a complex matrix that is consumed by a person through the process of eating or drinking. Food are bearer of the nutrients, bioactives and sometimes other food components. Food consumption, through the meal consumption, follows a certain dietary pattern, which define the diet. Nutrients and bioactives contained in food can be exploited by the human organism thanks to the process of digestion, absorption, metabolization, or through the intervention of the gut microflora ENPADASI_WP4 true MSH:D005502 food A descriptive diet which is the regular course of eating and drinking adopted by an organism. ENPADASI_WP4 https://github.com/FoodOntology/joint-food-ontology-wg https://github.com/enpadasi/Ontology-for-Nutritional-Studies MSH:D004032 individual regular diet A diet administered during an intervention study. It usually comprises the adoption of a certain nutritional intervention, intended as the prescription of consuming or not consuming certain food, and follows a precise study design. Intervention studies usually compare at least two subgroups of a population, one control group receiving a null nutritional intervention, and one or more test groups receiving the intervention ENPADASI_WP4 https://github.com/FoodOntology/joint-food-ontology-wg study intervention diet A diet prescribed by a physician/ nutritionist to meet specific nutritional needs of a person. ENPADASI_WP4 https://github.com/FoodOntology/joint-food-ontology-wg clinical treatment protocol diet therapy dietetic diet medically proscribed diet clinically prescribed diet A descriptive diet consumed by a population in a certain geographical area, or in a certain cultural setting, or following certain common eating behaviour. ENPADASI_WP4 https://github.com/FoodOntology/joint-food-ontology-wg usual diet population regular diet Cook role is the role of the person responsible for food prepraration ENPADASI_WP4 cook role A meal is an eating/drinking occasion which usually occurs at certain time during the day. ENPADASI_WP4 meal The consumption of liquids. Not for drinking alcohol or alcohol consumption ( = ALCOHOL DRINKING); differentiate from DRINKING BEHAVIOR. ENPADASI_WP4 MSH:D004326 obsolete: drinking true The consumption of edible substances. The act of eating: do not confuse with FOOD (the substance eaten) or EATING BEHAVIOR (the manner of eating). ENPADASI_WP4 MSH:D004435 obsolete: eating true A class which groups the data item collected as results from the subject information collection assay ENPADASI_WP4 subject information collection data A class which groups the data item collected as results from the dietary assessment assay ENPADASI_WP4 dietary assessment data A class which groups the data item collected as results from the chemical biological assay ENPADASI_WP4 chemical biological data A class which groups the data item collected as results from the analysis performed with an omics platform ENPADASI_WP4 omics data A class which groups the data item collected as results from the physical activity assay ENPADASI_WP4 physical activity assessment data The process in which food is made. ENPADASI_WP4 food preparation A descriptive diet pertaining to an individual organism. ENPADASI_WP4 eating pattern obsolete: individual dietary pattern https://www.sciencedirect.com/topics/medicine-and-dentistry/dietary-pattern true An objective measurement to assess the exposure (including food intake), effect, or succeptibility of the human organism (or an animal etc.) ENPADASI_WP4 https://www.ncbi.nlm.nih.gov/pubmed/28974991 true biomarker An exposure biomarker reflects the level of extrinsic variables that humans are exposed to, such as diets or food compounds, including nutrients and non-nutrients. ENPADASI_WP4 Intake Biomarker https://www.ncbi.nlm.nih.gov/pubmed/28974991 exposure biomarker An effect biomarker reflects the funciontal response of the human body to an exposure. ENPADASI_WP4 https://www.ncbi.nlm.nih.gov/pubmed/28974991 effect biomarker Measurable indicator including genetic or acquired host factors and intrinsic factors, influencing the response of an individual to a (dietary) exposure. ENPADASI_WP4 https://www.ncbi.nlm.nih.gov/pubmed/28974991 susceptibility biomarker A raw food is an uncooked, unprocessed food that is consumed in its natural state ENPADASI_WP4 raw food A processed food is the result of the process of home or industrial food preparation ENPADASI_WP4 processed food Digestion is the breakdown of large food molecules into small water-soluble food molecules. The breakdown is both mechanical and chemical (enzymatic digestion). During digestion, food components are released from the food matrix and may become bioaccessible. ENPADASI_WP4 Should break the definition down into separate terms, e.g. bioaccessable should be defined separately. food digestion Process mainly occurring in the small intestine and allowing the passage of the biaoccessible food components from the gastro-intestinal lumen into the blood vessels. Absorption occurs through either diffusion or active transport. The degree and rate at which a substance is absorbed and is made available at the site of physiological activity is called bioavailability ENPADASI_WP4 food component absorption Sum of the chemical changes occurring to nutrients and food component within the body. Changes can be anabolic (constructive) or catabolic (destructive). Anabolism converts simpler compounds into organized substances that the body can use. Catabolism converts more organized substances into simpler compounds. In the oxidative or energetic catabolism, this is coupled with the production of ATP ENPADASI_WP4 food component metabolization true MSH:D016036 Seroepidemiologic Studies Finite list of foods and beverages with response categories to indicate usual frequency of consumption over the time period queried. The time period can vary (from 1 week to 1 year and over). To assess the total diet, the number of foods and beverages queried typically ranges from 80 to 120. Usual portion size can be asked separately for each food and beverage. Alternatively, portion size can be combined with frequency information by asking respondents to translate usual consumption amount to number of specified units (e.g., spoon, cup, glass, etc). Some questionnaires include portion size images in an attempt to enhance reporting accuracy. In addition to foods and beverages, FFQs often ask about the frequency of intake and dosages of dietary supplements. ENPADASI_WP4 true Food Frequency Questionnaire A structured interview intended to capture detailed information about all foods and beverages (and possibly, dietary supplements) consumed by the respondent in the past 24 hours, most commonly, from midnight to midnight the previous day. A key feature of the 24HR is that, when appropriate, the respondent is asked for more detailed information than first reported. For example, a respondent reporting chicken for dinner or a sandwich for lunch would be asked about the preparation method and type of bread. This open-ended response structure is designed to prompt respondents to provide a comprehensive and detailed report of all foods and beverages consumed. A 24h can also be filled at home by the responder, and be checked during an interview to further improve it with additional details ENPADASI_WP4 true 24-hour dietary recall A food diary is a record of eaten foods on a meal-by-meal, daily, or weekly basis. It is directly filled by the investigated subject, and it can include nutritional or other dietary information, organize and track foods by food group, and allows monitoring what, when, and how often the filling subject eats. ENPADASI_WP4 true Food Diary Nutritional researcher role is the role of a researcher with specific training and expertise in the nutritional science field ENPADASI_WP4 Nutritional researcher role ENPADASI_WP4 Literature database query any type of assay that can be performed in the context of a nutritional study Francesco Vitali https://github.com/FoodOntology/joint-food-ontology-wg nutritional research assay an assay that is aimed at discovering new potential metabolites as food consumption biomarkers, or to measure/validate known food consumption biomarkers in a biological sample (e.g. urine, blood, serum, feces). Francesco Vitali https://github.com/FoodOntology/joint-food-ontology-wg food biomarker analysis assay An assay that is aimed at measuring the quantity (or presence) of food intake biomarkers in a biological sample (e.g. urine, blood, serum, feces) in order to evaluate the consumption of defined foods Francesco Vitali https://github.com/FoodOntology/joint-food-ontology-wg Food biomarker validation assay An assay that is aimed at measuring the quantity (or presence) of food related metabolites in a biological sample (e.g. urine, blood, serum, feces) in order to identify/discover new food intake biomarkers Francesco Vitali https://github.com/FoodOntology/joint-food-ontology-wg food biomarker discovery assay A data item which is a quantitative estimate of nutrient intake to be used as a reference value for planning and assessing diets for healthy people. Damion Dooley Francesco Vitali DRI dietary reference intake A dietary reference intake which is an average of daily nutrient intake values to be used as a reference for planning and assessing diets for healthy people. Damion Dooley Francesco Vitali https://www.nap.edu/catalog/10490/dietary-reference-intakes-for-energy-carbohydrate-fiber-fat-fatty-acids-cholesterol-protein-and-amino-acids average daily nutrient intake level daily dietary intake level average daily nutrient intake level An average daily nutrient intake level which is sufficient to meet the nutrient requirement of nearly all (97 to 98 percent) healthy individuals in a group. Damion Dooley Francesco Vitali https://www.nap.edu/catalog/10490/dietary-reference-intakes-for-energy-carbohydrate-fiber-fat-fatty-acids-cholesterol-protein-and-amino-acids RDA recommended dietary allowance An average daily nutrient intake level which is recommended based on observed or experimentally determined approximations or estimates of nutrient intake by a group (or groups) of apparently healthy people that are assumed to be adequate with respect to deficiency or disease criteria. Damion Dooley Francesco Vitali https://www.nap.edu/catalog/10490/dietary-reference-intakes-for-energy-carbohydrate-fiber-fat-fatty-acids-cholesterol-protein-and-amino-acids AI Adequate intake is used when an RDA cannot be determined. adequate intake An average daily nutrient intake level which is the highest level that is likely to pose no risk of adverse health effects to almost all individuals in the general population. Damion Dooley Francesco Vitali https://www.nap.edu/catalog/10490/dietary-reference-intakes-for-energy-carbohydrate-fiber-fat-fatty-acids-cholesterol-protein-and-amino-acids UL As intake increases above the UL, the potential risk of adverse effects may increase. tolerable upper intake level If a specified group is at the EAR threshold of a nutrient intake, then half of the individuals in the specified group are not having their nutritional needs met. An average daily nutrient intake level which is estimated to meet the requirement of half the healthy individuals in a particular life stage and gender group. Damion Dooley Francesco Vitali https://www.nap.edu/catalog/10490/dietary-reference-intakes-for-energy-carbohydrate-fiber-fat-fatty-acids-cholesterol-protein-and-amino-acids EAR estimated average requirement An average daily nutrient intake level which is predicted to maintain energy balance in healthy, normal weight individuals of a defined age, gender, weight, height, and level of physical activity consistent with good health. Damion Dooley Francesco Vitali https://www.nap.edu/catalog/10490/dietary-reference-intakes-for-energy-carbohydrate-fiber-fat-fatty-acids-cholesterol-protein-and-amino-acids EER In children and pregnant and lactating women, the EER includes the needs associated with growth or secretion of milk at rates consistent with good health. • Relative body weight (i.e. loss, stable, gain) is the preferred indicator of energy adequacy estimated energy requirement A dietary reference intake data item which is a range of intake for a particular energy source (protein, fat, or carbohydrate), expressed as a percentage of total energy (kcal), that is associated with reduced risk of chronic disease while providing adequate intakes of essential nutrients. Damion Dooley Francesco Vitali https://www.nap.edu/catalog/10490/dietary-reference-intakes-for-energy-carbohydrate-fiber-fat-fatty-acids-cholesterol-protein-and-amino-acids AMDR Relative body weight (i.e. loss, stable, gain) is the preferred indicator of energy adequacy acceptable macronutrient distribution range unselected, autochthonous microbial consortia that initiates the fermentation natural starter culture microorganisms selected for specific technological and sensory properties that are inoculated directly into food materials used to initiate the fermentation process and in order to bring about desired and predictable changes in the finished product commercial starter cultures microorganisms naturally present in the raw food or processing environment autochthonous food microbiota the role of a material entity that is the vehicle for introduction of one or more microorganisms (representing starter culture) into a suitable substrate to initiate the fermentation process microbial inoculum a complex matrix composed of a polysaccharide (kefiran) in association with bacteria and yeasts formed during kefir fermentation kefir grains the addition of a small amount of a previously fermented batch to the raw food, with the aim of initiating a new fermentation process bakslopping the food choice management process refers to the complex decision-making process an organism carry out to realize choices about which food to be consumed, and to the choices regarding quantity and mode of consumption of foods. https://orcid.org/0000-0001-9125-4337 https://orcid.org/0000-0002-0892-7164 food choice management process wine consumption is part of the Mediterranean diet; as opposed to the "mismanagement of food choice" an healthy management food choice of red wine consumption in the context of mediterranean diet dietary pattern, would be that of limit consumption to a maximum of 2 glasses per day during meals (https://www.health.harvard.edu/blog/a-practical-guide-to-the-mediterranean-diet-2019032116194) a food choice management process resulting in healthy food choice https://orcid.org/0000-0001-9125-4337 https://orcid.org/0000-0002-0892-7164 healthy management of food choice Wine consumption is part of the Mediterranean diet, which can be regarded as a healthy dietary pattern. A mismanagement of red wine, which might be related to alcohol addiction, leads to unhealthy food choice about the number of red wine servings consumed per day (> 2). This produces a specific dietary pattern and diet, with unfavourable health consequences, even though all the other requirements to adhere to a Mediterranean diet are met a food choice management process resulting in unhealthy food choice https://orcid.org/0000-0002-0892-7164 mismanagement of food choice a determinant of diet is any factor that drive the food choices of an organism evaluate if it is more convenient to use the determinant of diet as superclass of a series of factor, or else to define the various factor as separate classes (i.e. palatabiliyt) with a "determinant of diet" role. Could be convenient in case of determinants imported from other ontologies, to avoid changing the original superclass assertion https://orcid.org/0000-0001-9125-4337 https://orcid.org/0000-0002-0892-7164 determinant of diet food choice refers to any decision an organism makes regarding food and diet. It both refers to the selection of specific foods to be consumed by an organism, from a variety of available options, and to the choices regarding quantity and mode of consumption of foods. Food choice are direct consequence of the food management process, and depends on a variety of determinants of diet https://orcid.org/0000-0001-9125-4337 https://orcid.org/0000-0002-0892-7164 food selection food choice https://www.eufic.org/en/food-safety/category/food-choice https://www.sciencedirect.com/topics/food-science/food-choice "Food choices" [ONS:0000132] are driven by the "food choice management process" [ONS:0000128], which in turn is influenced by a multitude of factors defined as "determinant of diet" [ONS:0000131]. Among these, there is the appeal to eat very tasty foods because of the positive effect they exert on the dopamine reward circuitry. In this way, foods rich in highly palatable ingredients such as simple sugars and fats might be preferred to healthier nutrient-dense alternatives. the palatability of a food refers to its capacity of triggering a reward (i.e. hedonic reward, or pleasure, via a stimulation of the dopamine reward pathway) upon consumption. This property can be related to various aspects of food, usually related to fats and sugars content. https://orcid.org/0000-0001-9125-4337 https://orcid.org/0000-0002-0892-7164 palatability https://en.wikipedia.org/wiki/Palatability microbial culture responsible for the beginning of the fermentation process https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://en.wikipedia.org/wiki/Fermentation_starter starter culture for food fermentation microbial cultures that do not take part to the fermentation process but contribute to the development of flavours, aroma and organoleptic properties during maturation/ripening through other metabolic pathways https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 non starter culture for food fermentation This is a high-level term with the purpose of organization of more granular children term. Should not be used in annotation, favoring more specific sub-classes https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 technological processes during dairy food fermentation This is a high-level term with the purpose of organization of more granular children term. Should not be used in annotation, favoring more specific sub-classes https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 biological process during dairy food fermentation This is a high-level term with the purpose of organization of more granular children term. Should not be used in annotation, favoring more specific sub-classes https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 microbiota in finished or semi-finished fermented products and in the entire food-chain a process in the cheese-making consisting of the storage of cheese in controlled temperature and condition, for defined amount of time. The process is associated to microbial activities such as proteases and lipases which change the morphology and physical texture of the cheese as well as develop taste and flavor of the final product https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 fermented food ripening the set of reactions leading to the conversion of fats (triglycerides) into free fatty acids, monoacylglycerol, diacylglycerol, and glycerol during the fermentation process https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 lipolysis during food fermentation the set of reactions leading to the hydrolysis of milk proteins into peptides during the food fermentation process https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 proteolysis during food fermentation the set of reactions leading to the conversion of glucose into pyruvic acid, which is substrate for the fermentation processes https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 glucose metabolism during food fermentation Water-soluble exopolisaccharide produced by Lactobacillus kefiranofaciens during kefir fermentation. It is present in kefir grains https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 kefiran consortium of living microorganisms present in kefir, characterized by bacteria and yeast components (has part) https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 kefir microbiota The set of reactions leading to the conversion of carbohydrates into organic acids, ethanol and CO2 by the enzymatic activity of kefir microbiota https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 kefir fermentation vital biomass containing microorganisms added to start the fermentation process https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 inoculum for fermentation complex matrix composed of an exopolysaccharide in association with bacteria and yeast cells added to milk for kefir production https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 kefir grain as inoculum the procedure in which a small amount of the finished or intermediate fermentation product is used to inoculate a new batch with the aim of starting a new fermentation process https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 backslopping kefir recipe includes and defines the set of ingredients and procedures that should be employed to obtain kefir https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 kefir recipe consortium of living microrganisms present in whey, characterized by bacteria and yeast components (has part) https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 whey microbiota mixture of milk originating from different animal species or from different milking times https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://www.parmigianoreggiano.com/product-art-of-making/ mixed milk the process of destabilization of casein micelles, which flocculate and aggregate to form a gel enclosing the soluble milk components. It is caused by acidification, by enzymatic activities or by the combination of the two processes https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 milk coagulation the set of reactions leading to the conversion of carbohydrates into organic acids by the enzymatic activity of starter microbes in the production of Parmigiano Reggiano. It can also be extended to the proteolitic and lipolytic reactions characterizing maturation and ripening steps. https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://www.parmigianoreggiano.com/product-art-of-making/ parmigiano reggiano fermentation Parmigiano Reggiano recipe includes and defines the set of ingredients and procedures that must be employed to obtain Parmigiano Reggiano cheese https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://www.parmigianoreggiano.com/consortium-specifications-and-legislation/ parmigiano reggiano recipe the result of moulding and final pressing of Parmigiano Reggiano mass retrieved from cauldron https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://www.parmigianoreggiano.com/product-art-of-making/ shaped parmigiano reggiano the set of reactions leading to the conversion of carbohydrates into organic acids, ethanol and CO2 by the enzymatic activity in the absence of oxygen https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://en.wikipedia.org/wiki/Fermentation_in_food_processing fermentation ons foods or beverages produced through controlled microbial growth, and the conversion of food components through enzymatic action https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 fermented food microbial culture responsible for the beginning of the fermentation process https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://en.wikipedia.org/wiki/Fermentation_starter starter culture a chemical and/or physical factor that exerts selection pressure and brings about natural selection within microbiota components https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 agent for physico-chemical selection of microbiota the process in which the cheese is placed in a mould giving rise to it its final shape, and immersed in a saturated solution of water and salt https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 cheese shaping and salting a heating process in which the curd is cooked at defined temperature for a defined amount of time. As a result the curd sink to the bottom of the cauldron forming a single mass https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 curd cooking the microbial consortium associated to curd https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 curd microbiota a hard, cooked, brittle cheese with a long ripening time (minimum of 12 months), produced using raw semiskim high-quality cow milk, natural fermented whey, calf rennet and sodium chloride, designed as PDO https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://en.wikipedia.org/wiki/Parmigiano_Reggiano https://www.parmigianoreggiano.com/product-art-of-making/ parmigiano reggiano a heating process were curd is cooked at 55 °C for 12 minutes, after which the cheesy granules sink to the bottom of the cauldron forming a single mass https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://www.parmigianoreggiano.com/product-art-of-making/ parmigiano reggiano curd cooking the process in which the shaped cheese is stored in controlled temperature condition and for defined amount of time to give rise to the ripened cheese https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 cheese maturation the process during which the parmigiano reggiano cheese wheels are stored at 18-20 °C for a minimum of 12 months giving rise to the ripened parmigiano reggiano https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://www.parmigianoreggiano.com/product-art-of-making/ parmigiano reggiano maturation the microbial consortium associated to parmigiano reggiano cheese https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 parmigiano reggiano microbiota the process in which the cheese, wrapped in typical linen cloth, is placed in a mould that gives it its final shape and immersed in a saturated solution of water and salt. https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://www.parmigianoreggiano.com/product-art-of-making/ parmigiano reggiano shaping and salting the result of moulding and final pressing in cheese-making https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 shaped cheese mixture obtained by combining milk from morning milking with milk from previous evening milking and used as initial ingredient in Parmigiano Reggiano making https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://www.parmigianoreggiano.com/product-art-of-making/ starting milk mixture consortium of living microrganisms present in milk before processing, characterized by bacteria and yeast components (has part) https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 starting milk mixture microbiota the role of a material entity, generally a chemical compound, such as the material entity is not suitable for consumption by a defined group of individuals. This role has a causal relation (is determined by) with another material entity such that it exerts a strong causal influence on the role, and its removal cause the termination of the existence of the role https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 suitable for consumption the role of a material entity, generally a chemical compound, such as the material entity is unfit for consumption by a defined group of individuals. This role has a causal relation (is determined by) with another material entity such that it exerts a strong causal influence on the role, and its removal cause the termination of the existence of the role https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 unfit for consumption the ratio between the vapor pressure of the food, when in a completely undisturbed balance with the surrounding air media, and the vapor pressure of distilled water under identical conditions https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 https://en.wikipedia.org/wiki/Water_activity water activity in food whey from the previous day manufacture containing the consortium of living microorganisms, added to start the fermentation process https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 whey as inoculum the procedure in which a small amount of the finished or intermediate kefir is used to inoculate a new batch with the aim of starting a new fermentation process https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 backslopping in kefir fermentation the procedure in which a small amount of whey product of the parmigiano reggiano milk coagulation is used to inoculate a new batch with the aim of starting a new fermentation process https://github.com/FrancescoVit https://orcid.org/0000-0001-9446-7979 https://orcid.org/0000-0002-7114-7726 backslopping in parmigiano reggiano fermentation 2024-01-10T22:08:29Z nutritional study A collection of food types or items which have organoleptic, nutritional, availability, safety, meal time, or socially relevant characteristics with respect to a consuming individual or population. https://github.com/FoodOntology/joint-food-ontology-wg https://en.wikipedia.org/wiki/Diet_(nutrition) http://id.nlm.nih.gov/mesh/D004032 OLD definition: In nutrition, diet is the sum of food consumed by a person or other organism diet A feline biologically and anatomically follows a carnivorous diet; Homo sapiens biologically and anatomically follow an omnivorous diet A diet that is defined by the biological, anatomical, and evolutionistic digestive capabilities of a given organism. https://github.com/FoodOntology/joint-food-ontology-wg diet by digestive capability A diet that is defined by characteristics of ingested food. https://github.com/FoodOntology/joint-food-ontology-wg diet by type of food A diet which involves food produced under certain agricultural conditions. https://github.com/FoodOntology/joint-food-ontology-wg diet by agricultural treatment A diet defined by the nutritional presence or absence of types of food bioactive compounds. https://github.com/FoodOntology/joint-food-ontology-wg diet by nutritional composition An eating pattern that excludes a given diet. https://github.com/FoodOntology/joint-food-ontology-wg restrictive diet A diet which is prescribed to meet some dietary pattern objective for an individual organism or group. https://github.com/FoodOntology/joint-food-ontology-wg prescribed diet A diet which represents food types or items consumed in the regular course of eating and drinking by an individual or population over some duration of time. https://github.com/FoodOntology/joint-food-ontology-wg The food entities in a descriptive diet may be characterized by kind of diet as well as other (food survey or log) parameters such as quantity, time, frequency or duration of aggregate consumption, meal type and/or setting. descriptive diet An eating pattern pertaining to a single organism (an instance of organism). This can be used descriptively or prescriptively. https://github.com/FoodOntology/joint-food-ontology-wg obsolete: individual dietary pattern true Pregnant women should not drink more than 2 glasses of wine a day. A prescribed diet which pertains to a population or sub-population of organism. https://github.com/FoodOntology/joint-food-ontology-wg Was labeled "population dietary pattern", but semantics are now reserved for proscriptive use. For descriptive use see "population regular diet". recommended diet A food consumption process in which the timing of food and/or liquid ingestion is limited. https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody https://pubmed.ncbi.nlm.nih.gov/30897855 fasting process https://pubmed.ncbi.nlm.nih.gov/30897855 Intermittent fasting is a broad term that encompasses a variety of programs that manipulate the timing of eating occasions by utilizing short-term fasts with the intention of modulating body composition and/or overall health. https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody https://pubmed.ncbi.nlm.nih.gov/26374764/ intermittent fasting https://pubmed.ncbi.nlm.nih.gov/26374764/ involving fasting periods that are longer than a normal overnight fast of 8–12 hours. A form of time restricted eating, typically 16 h fasting and 8 h eating. A type of intermittent fasting process which allows ad libitum energy intake within controlled time frames, generally a 3-12 hour range each day. https://github.com/FoodOntology/joint-food-ontology-wg https://pubmed.ncbi.nlm.nih.gov/24739093/ TRE time-restricted feeding time-restricted feeding https://pubmed.ncbi.nlm.nih.gov/24739093/ The fasting protocol indicated fasting for 16 hrs per 24 hrs for a duration of 3 months. A protocol that specifies the timing of food consumption. https://github.com/FoodOntology/joint-food-ontology-wg fasting schedule fasting protocol The process of ingesting food during a single eating and/or drinking session. This does not include the digestion process. https://github.com/FoodOntology/joint-food-ontology-wg episodic food intake process A diet of a carnivore, which focuses almost exclusively on the consumption of animal food sources. https://github.com/FoodOntology/joint-food-ontology-wg carnivorous diet A diet of an omivore, which includes both plant and animal food sources. https://github.com/FoodOntology/joint-food-ontology-wg omnivorous diet A diet of a herbivore, which focuses almost exclusively on the consumption of plants, fungi and/or lichen. https://github.com/FoodOntology/joint-food-ontology-wg herbivorous diet A diet defined by the food source organisms it allows or excludes. https://github.com/FoodOntology/joint-food-ontology-wg diet by food organism A diet which focuses almost exclusively on the consumption of plants, fungi and/or lichen. https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-VEGETARIAN vegetarian diet A diet that excludes all animal products (including fish and seafood). https://github.com/FoodOntology/joint-food-ontology-wg https://en.wikipedia.org/wiki/Veganism https://www.gs1.org/voc/DietTypeCode-VEGAN vegan diet A diet that includes vegetarian and milk-derived food. https://github.com/FoodOntology/joint-food-ontology-wg lacto-vegetarian diet A diet that includes vegetarian and avian egg derived food. https://github.com/FoodOntology/joint-food-ontology-wg ovo-vegetarian diet A diet that includes vegetarian, avian egg, and milk derived food. https://github.com/FoodOntology/joint-food-ontology-wg lacto-ovo vegetarian diet primarily a plant-based diet but includes meat, dairy, eggs, poultry and fish on occasion or in small quantities https://github.com/FoodOntology/joint-food-ontology-wg flexitarian diet semi-vegetarian diet A diet which includes vegetarian food as well as fish and seafood. https://github.com/FoodOntology/joint-food-ontology-wg pescetarian diet A diet that excludes food containing beef food products. https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-WITHOUT_BEEF non-beef diet A diet that excludes food containing swine food products. https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-WITHOUT_PORK non-pork diet A diet consisting entirely of breast milk. https://github.com/FoodOntology/joint-food-ontology-wg infant breast milk diet A diet involving formula milk. https://github.com/FoodOntology/joint-food-ontology-wg formula milk diet infant formula milk diet A diet defined by the texture of prepared food. https://github.com/FoodOntology/joint-food-ontology-wg diet by food texture A soft textured diet was the most often prescribed followed by pureed texture and then minced texture. A diet containing carefully selected foods of an appropriate consistency which can be more easily chewed and managed by a person with dysphagia. https://github.com/FoodOntology/joint-food-ontology-wg https://www.wlmht.nhs.uk/wp-content/uploads/2015/06/High-risk-foods-info-sheet-2pp-A4.pdf texture modified diet https://www.wlmht.nhs.uk/wp-content/uploads/2015/06/High-risk-foods-info-sheet-2pp-A4.pdf A full liquid diet is made up only of fluids and foods that are normally liquid and foods that turn to liquid when they are at room temperature. A full liquid diet excludes solid foods. https://github.com/FoodOntology/joint-food-ontology-wg https://medlineplus.gov/ency/patientinstructions/000206.htm liquid diet https://medlineplus.gov/ency/patientinstructions/000206.htm A diet consisting of food produced from organic agriculture (food that is grown without the use of synthetic fertilizers, sewage sludge, irradiation, genetic engineering, pesticides, or drugs.) https://github.com/FoodOntology/joint-food-ontology-wg http://www.fao.org/organicag/oa-faq/oa-faq1/en/ https://extension.arizona.edu/sites/extension.arizona.edu/files/pubs/az1603.pdf https://www.gs1.org/voc/DietTypeCode-ORGANIC biological agriculture diet organic agriculture diet http://www.fao.org/organicag/oa-faq/oa-faq1/en/ https://extension.arizona.edu/sites/extension.arizona.edu/files/pubs/az1603.pdf A diet consisting of food that may have been reared with the use of pesticides, herbicides or chemical fertilizers. https://github.com/FoodOntology/joint-food-ontology-wg https://extension.arizona.edu/sites/extension.arizona.edu/files/pubs/az1603.pdf non-organic agriculture diet https://extension.arizona.edu/sites/extension.arizona.edu/files/pubs/az1603.pdf A ketogenic diet is a high-fat, low-carbohydrate, adequate-protein diet that mimics a fasting state, resulting in the substitution of ketone bodies as a source of energy. The ketogenic diet can be used to reduce recurrent epileptic seizures in individuals with intractable epilepsy. Intractable epilepsy is defined as epilepsy that failed to respond to three or more antiepileptic drugs. A high-fat, adequate-protein, low-carbohydrate diet. It is primarily used in medicine to treat difficult-to-control epilepsy in children https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody PMID:27759811 PMID:28701250 https://www.healthdirect.gov.au/ketogenic-diet PMID:23419562 Modified Atkins diet ketogenic diet PMID:27759811 PMID:28701250 https://www.healthdirect.gov.au/ketogenic-diet PMID:23419562 Dietary Approaches to Stop Hypertension (DASH) trial, which demonstrated that consuming a diet rich in fruits, vegetables, and low-fat dairy products and reduced in saturated fat and cholesterol https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody PMID: 29141784 DASH diet PMID: 29141784 https://medlineplus.gov/dasheatingplan.html A moderate-fat, restricted-calorie, Mediterranean diet is rich in vegetables and low in red meat, with poultry and fish replacing beef and lamb. https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody PMID:18635428 MeDi mediterranean diet PMID:18635428 A diet which provides > 60% of total dietary energy from carbohydrates. It consists predominantly of high glycemic carbohydrates have detrimental metabolic effects https://github.com/FoodOntology/joint-food-ontology-wg high-carbohydrate diet Low-carbohydrate diets restrict carbohydrate consumption relative to the average diet. Foods high in carbohydrates (e.g., sugar, bread, pasta) are limited, and replaced with foods containing a higher percentage of fat and protein (e.g., meat, poultry, fish, shellfish, eggs, cheese, nuts, and seeds), as well as low carbohydrate foods (e.g. spinach, kale, chard, collards, and other fibrous vegetables). https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody https://en.wikipedia.org/wiki/Low-carbohydrate_diet PMID:18635428 Low carbohydrate diet low-carbohydrate, high-protien, high fat diet https://en.wikipedia.org/wiki/Low-carbohydrate_diet PMID:18635428 A diet involving the a larger proportion of fat than normal. high fat diet A restricted-energy diet with less than 30% of energy from fat. https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody PMID:23651522 low fat diet PMID:23651522 A diet which minimises or eliminates the consumption of gluten. https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-FREE_FROM_GLUTEN gluten free diet A diet that an individual organism has chosen as an objective. https://github.com/FoodOntology/joint-food-ontology-wg self-prescribed diet A diet prescribed to a group in a research study. https://github.com/FoodOntology/joint-food-ontology-wg research prescribed diet A dietairy pattern adhered to by a study control group. (possibly a placebo). https://github.com/FoodOntology/joint-food-ontology-wg null nutritional diet study null nutritional diet A diet designed to reduce the symptoms of Coeliac disease which is caused by a reaction to gliadin (a gluten protein found in wheat) and similar proteins found in other crops. https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-COELIAC celiac diet coeliac diet A diet involving the avoidance of Fermentable Oligo-Di-Monosaccharides and Polyols. https://github.com/FoodOntology/joint-food-ontology-wg https://en.wikipedia.org/wiki/FODMAP FODMAP diet https://en.wikipedia.org/wiki/FODMAP A diet designed to reduce the presence of fat in an organism. https://github.com/FoodOntology/joint-food-ontology-wg weight loss diet A diet which has an athletic performance objective https://github.com/FoodOntology/joint-food-ontology-wg performance diet A cultural or religious eating pattern. https://github.com/FoodOntology/joint-food-ontology-wg ethnographic diet A diet consisting of halal approved food. https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-HALAL halal diet A diet consisting of kosher approved food. https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-KOSHER kosher diet An ingested food data set which is subjectively recorded or recalled by an individual consuming the food. https://github.com/FoodOntology/joint-food-ontology-wg diet record self-reported diet https://doi.org/10.1093/ajcn/63.4.491 A descriptive diet which is observed by a researcher to have been consumed by a subject organism or population of organisms. https://github.com/FoodOntology/joint-food-ontology-wg objectively-reported diet A descriptive diet which contains a list of foods that an individual organism has ingested over some period of time. https://github.com/FoodOntology/joint-food-ontology-wg ingested food data set A population regular diet which is a long-term average daily intake of nutrients and/or foods calculated according to a National Cancer Institute statistical model. https://github.com/FoodOntology/joint-food-ontology-wg https://epi.grants.cancer.gov/diet/usualintakes/ NCI usual diet https://epi.grants.cancer.gov/diet/usualintakes/ An ingested food data set of food consumption events detailing food ingested and the time of ingestion. https://github.com/FoodOntology/joint-food-ontology-wg This may include the mass or quantity of a food item, and other details such as its preparation process.' ingested food log A descriptive diet containing food types or items pertinent to an average day or a given day which are ingested by an individual or organism population. The collection may indicate quantities or counts of food material. https://github.com/FoodOntology/joint-food-ontology-wg daily food intake A descriptive diet containing nutrient classes and their average daily intake quantity for an individual or organism population. https://github.com/FoodOntology/joint-food-ontology-wg daily average nutritional intake The whole of the processes by which food components released by food digestion are able to reach bloodstream https://orcid.org/0000-0001-9125-4337 https://github.com/FoodOntology/joint-food-ontology-wg food component absorption process https://askthescientists.com/nutrient-absorption/ A set of restrictions on food type ingestion and/or timing of food ingestion. https://github.com/FoodOntology/joint-food-ontology-wg dietary protocol dietary regimen The process an organism has which achieves a dietary pattern and involves food availability, physiological or psychological motivation, selection, episodic consumption, and digestion. https://github.com/FoodOntology/joint-food-ontology-wg organism food management process A data item recording data about a dietary pattern dietary pattern data item the diet resulting from the lifestyle adaptation following the industrial revolution. It is often associated with western countries, but is increasingly becoming adopted also in other geographic areas. It is known to be rich in red and processed meats, sweets, fried foods, and refined grains while being poor in fruits, vegetables, legumes, fish, poultry, and whole grains. In terms of micronutrients, this diet is usually rich in salt, yet poor in other minerals and vitamins, whereas in terms of fats, it is high in saturated and trans-fatty acids, and low in mono- and polyunsaturated fatty acids. Its fibre and complex carbohydrates contents are also very low due to the high consumption of refined sugars instead of whole-grain foods. "Western diet" synonym of this concept has a wider use in the literature, nevertheless it imply a misleading association to specific geographic location, even though it has a broader distribution. Another possible synonym, taking into consideration that this lifestyle is considered the result of the Industrial Revolution, is "industrialized diet" https://orcid.org/0000-0001-9125-4337 https://orcid.org/0000-0002-0892-7164 industrialized diet urban diet western diet globalized diet the diet characteristic of the lifestyle in isolated/rural areas, commonly in developing countries. It is mainly composed of naturally available food products, including fresh animal protein and vegetables while excluding industrially processed foods. Nevertheless, it is common to use traditional food processing methods to improve nutrient availability, digestibility or to increase conservation time to avoid scarcity. These methods include soaking, fermentation, cooking, pounding, and sprouting. https://orcid.org/0000-0001-9125-4337 https://orcid.org/0000-0002-0892-7164 local agrarian diet traditional diet rural diet The temporal aspect of a dietary pattern that details meal frequency or fasting as a daily or episodic activity. https://github.com/FoodOntology/joint-food-ontology-wg This should be placed under BCIO "consumption behaviour pattern" BCIO:050210 timing of food intake A dietary pattern that define the quantity, variety or combination of different food in a diet by digestive capabilities. https://github.com/FoodOntology/joint-food-ontology-wg obsolete: dietary pattern by digestive capability true A dietary pattern that define the quantity, variety or combination of different food in a diet by type of food https://github.com/FoodOntology/joint-food-ontology-wg obsolete: dietary pattern by type of food true A dietary pattern that define the quantity, variety or combination of different food in a diet by agriculture treatment https://github.com/FoodOntology/joint-food-ontology-wg obsolete: dietary pattern by agriculture treatment true A dietary pattern that define the quantity, variety or combination of different food in a diet by nutritional composition https://github.com/FoodOntology/joint-food-ontology-wg obsolete: dietary pattern by nutritional composition true A dietary pattern that define the quantity, variety or combination of different food in a proscribed diet https://github.com/FoodOntology/joint-food-ontology-wg obsolete: proscribed dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a prescribed diet https://github.com/FoodOntology/joint-food-ontology-wg obsolete: prescribed dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in descriptive diet https://github.com/FoodOntology/joint-food-ontology-wg obsolete: descriptive dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a diet by food organism https://github.com/FoodOntology/joint-food-ontology-wg obsolete: dietary pattern by food organism true A dietary pattern that define the quantity, variety or combination of different food in a vegetarian diet https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-VEGETARIAN obsolete: vegetarian dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a vegan diet https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-VEGAN obsolete: vegan dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a lacto-vegetarian diet https://github.com/FoodOntology/joint-food-ontology-wg obsolete: lacto-vegetarian dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a ovo-vegetarian diet https://github.com/FoodOntology/joint-food-ontology-wg obsolete: ovo-vegetarian dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a lacto-ovo vegetarian diet https://github.com/FoodOntology/joint-food-ontology-wg obsolete: lacto-ovo vegetarian dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a semi-vegetarian diet https://github.com/FoodOntology/joint-food-ontology-wg flexitarian diet obsolete: semi-vegetarian dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a pescetarian diet https://github.com/FoodOntology/joint-food-ontology-wg obsolete: pescetarian dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a ketogenic diet https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody obsolete: ketogenic diet dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a DASH diet https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody obsolete: DASH diet dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a Mediterranean diet https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody obsolete: meditteranean diet dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a high-carbohydrate diet https://github.com/FoodOntology/joint-food-ontology-wg obsolete: high-carbohydrate diet dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a low-carbohydrate, high-protien, high fat diet https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody https://en.wikipedia.org/wiki/Low-carbohydrate_diet PMID:18635428 obsolete: low-carbohydrate, high-protien, high fat diet dietary pattern https://en.wikipedia.org/wiki/Low-carbohydrate_diet PMID:18635428 true A dietary pattern that define the quantity, variety or combination of different food in a high fat diet obsolete: high fat diet dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a low fat diet https://github.com/FoodOntology/joint-food-ontology-wg Leigh Carmody obsolete: low fat diet dietary pattern true A dietary pattern that define the quantity, variety or combination of different food in a gluten free diet https://github.com/FoodOntology/joint-food-ontology-wg https://www.gs1.org/voc/DietTypeCode-FREE_FROM_GLUTEN obsolete: gluten free dietary pattern true a dietary pattern that define the quantity, variety or combination of different food in a globalized diet https://orcid.org/0000-0001-9125-4337 https://orcid.org/0000-0002-0892-7164 obsolete: globalized diet dietary pattern true a dietary pattern that define the quantity, variety or combination of different food in a rural diet https://orcid.org/0000-0001-9125-4337 https://orcid.org/0000-0002-0892-7164 obsolete: rural diet dietary pattern true A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality A time quality inhering in a bearer by virtue of how long the bearer has existed. age A composite chromatic quality composed of hue, saturation and intensity parts. colour relative color color A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. composed of compositionality content structure, composition composition A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. concentration concentration of An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. true biological sex A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced hardness A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. morphology qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. deviation (from_normal) A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. size length A 1-D extent quality which is equal to the distance between two points. length mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass 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. relational structural quality structure A physical quality of the thermal energy of a system. temperature A quality in which events occur in sequence. time An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. behavioural quality behavioral quality A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development. maturity An age which is relatively high. old An age which is relatively low. young A color that lacks any hues as parts. black A color hue with low wavelength of that portion of the visible spectrum lying between green and indigo, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 490 nanometers. blue A color consisting of green and blue hue. cyan A color hue with medium-low wavelength of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers. green A color consisting of red and blue hues. magenta A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers. red An achromatic color of maximum brightness; the color of objects that reflect nearly all light of all visible wavelengths. white A color hue with medium wavelength of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers. yellow A color quality inhering in a bearer by virtue of the bearer's having color. colored A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. female A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. male A hardness quality of being rigid and resistant to pressure. hard A hardness quality of giving little resistance to pressure. soft A maturity quality inhering in a bearer by virtue of the bearer's having arrived at the onset of puberty (the age at which sex glands become functional) but not yet fully mature. pubescent A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. abnormal A size quality which is relatively high. increased size A size quality which is relatively low. decreased size A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. volume A color between white and black colors. grey A color that falls about midway between red and blue in hue. purple A color consisting of dark orange, red, of very low intensity. brown A color hue with high-medium wavelength that of that portion of the visible spectrum lying between red and yellow, evoked in the human observer by radiant energy with wavelengths of approximately 585 to 620 nanometers. orange Red color having medium to high brightness and low to moderate saturation. pink A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow. viscosity A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity. viscous A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. relational physical quality physical quality A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. pressure A concentration quality inhering in a bearer by virtue of the bearer's exhibiting concentration. concentrated A concentration which is higher relative to the normal or average. high concentration increased concentration A concentration which is lower relative to the normal or average. low concentration decreased concentration A maturity quality inhering in a bearer by virtue of the bearer's indirect development, undergoing metamorphosis. larval A maturity quality inhering in a bearer by virtue of the bearer's being at the age immediately before puberty. prepubescent A maturity quality inhering in a insect by virtue of the bearer's being in the chrysalis (cocoon) or post larval stage. pupal A maturity quality inhering in a bearer by virtue of the bearer's being in an inactive stage in the development of some insects, between the larval and the pupal stages. prepupal A maturity quality inhering in a bearer by virtue of the bearer's being between the onset of puberty and maturity. adolescent A maturity quality inhering in a bearer by virtue the bearer's being not fully grown or developed. juvenile A quality which inheres in an process. quality of a process quality of occurrent quality of process relational quality of occurrent process quality quality of a single physical entity A physical object quality which inheres in a single-bearer. obsolete: quality of a single physical entity true quality of related physical entities A physical entity quality which exists in relation towards some other entity. quality of related physical entities A quality which inheres in a continuant. monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant physical object quality A color consisting of blue hue and high brightness. light blue A color consisting of blue hue and low brightness. dark blue A color consisting of brown hue and low brightness. dark brown A color consisting of brown hue and high brightness. light brown A color consisting of cyan hue and high brightness. light cyan A color consisting of cyan hue and low brightness. dark cyan A color consisting of green hue and low brightness. dark green A color consisting of green hue and high brightness. light green A color consisting of grey color and low brightness. dark grey A color consisting of grey color and high brightness. light grey A color consisting of magenta color and high brightness. light magenta A color consisting of magenta with low brightness. dark magenta A color consisting of orange hue and high brightness. light orange A color consisting of orange color and low brightness. dark orange Pink color having high brightness and moderate saturation. light deep pink Pink color having medium brightness and moderate saturation. deep pink A color consisting of purple color and low brightness. dark purple A color consisting of purple color and high brightness. light purple A color consisting of red hue and low brightness. dark red A color consisting of red hue and high brightness. light red A color consisting of yellow hue and low brightness. dark yellow A color consisting of yellow hue and high brightness. light yellow A color consisting of blue hue and high saturation. saturated blue A color consisting of blue hue and low saturation. pale blue desaturated blue A color consisting of brown hue and high saturation. saturated brown A color consisting of brown hue and low saturation. pale brown desaturated brown A color consisting of cyan colour and high saturation. saturated cyan A color consisting of cyan colour and low saturation. pale cyan desaturated cyan A color consisting of green hue and high saturation. saturated green A color consisting of green hue and low saturation. pale green desaturated green A color consisting of magenta color and high saturation. saturated magenta A color consisting of magenta color and low saturation. pale magenta desaturated magenta A color consisting of orange hue and high saturation. saturated orange A color consisting of orange hue and low saturation. pale orange desaturated orange Pink color having medium brightness and low saturation. dark pale pink A color consisting of purple color and high saturation. saturated purple A color consisting of purple color and low saturation. pale purple desaturated purple A color consisting of red hue and high saturation. saturated red A color consisting of red hue and low saturation. pale red desaturated red A color consisting of yellow hue and high saturation. saturated yellow A color consisting of yellow hue and low saturation. pale yellow desaturated yellow A color consisting of red and brown hue. red brown A color consisting of red and brown hue and low brightness. dark red brown A color consisting of red and brown hue and high brightness. light red brown An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. optical quality A color consisting of red and orange hue with a slight amount of gray. vermilion A temperature which is relatively high. high temperature hot increased temperature A temperature which is relatively low. cold low temperature decreased temperature A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. period duration A temperature which is increased by a low degree. mild increased temperature A temperature which is increased by a medium degree. moderate increased temperature A temperature which is increased by a high degree. severe increased temperature mixed sex A biological sex quality inhering in a population of multiple sexes. mixed sex A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. hermaphroditic intersex hermaphrodite A color hue with very low wavelength of that portion of the visible spectrum lying between reddish blue or bluish purple, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 380 nanometers. violet A color hue consisting of red hue and yellow hue and high brightness. rosy A color consisting of purple and brown hue. maroon A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. immature A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking. flexibility A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. bendy flexible A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. stiff inflexible A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. solidity quality of a solid A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. liquidity quality of a liquid A viscosity which relatively high. high viscosity increased viscosity A viscosity which relatively low. low viscosity decreased viscosity A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development. mature A color consisting of violet hue and high saturation. saturated violet A color consisting of violet hue and low saturation. pale violet desaturated violet A color consisting of violet hue and high brightness. light violet A color consisting of violet hue and low brightness. dark violet A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. 1-D size 1-D extent A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. 3D size 3-D extent A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. liquid liquid configuration A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of solids. solid solid configuration A flexibility which is relatively high. high flexibility increased flexibility A flexibility which is relatively low. low flexibility decreased flexibility A composition quality inhering in an bearer by virtue of the quantities or relative ratios of water of the inhering entity. water composition A composition quality inhering in an bearer by virtue of the reduction in amount of water the bearer contains. dehydrated decreased water composition A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex. pseudohermaphrodite A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of male and external sexual characteristics of female. male pseudohermaphrodite A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of female and external sexual characteristics of male. female pseudohermaphrodite A quality of a liquid inhering in a bearer by virtue of the bearer's ability to mix with (dissolve in) another liquid. miscibility An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. phenotypic sex A color consisting of yellow and green hues. yellow green A color consisting of brown and green hues. olive green brown green A purple color which has low saturation and low brightness. lilac A color consisting of yellow and orange hue. yellow orange A moderate yellow-orange to orange color. ochre A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. frozen A quality that inheres in an entire organism or part of an organism. organismal quality A quality that inheres in an entire population or part of a population. population quality Pink color having high brightness and low saturation. pale pink physical quality of a process A solid configuration inhering in a material entity by virtue of its constituent atoms, molecules, or ions being arranged in an orderly repeating pattern extending in all three spatial dimensions. crystal configuration A hardness quality of being rigid and resistant to pressure and fibrous. scirrhous A physical quality inhering in a bearer by virtue of the bearer's disposition to being fit to be eaten. edibleness edibility A physical quality inhering in a bearer by virtue of the bearer being suitable for use as food. edible A physical quality inhering in a bearer by virtue of the bearer not being suitable for use as food. inedible A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. relational molecular quality molecular quality A quality inhering in a bearer by virtue of its constitution. quality of a substance A maturity quality inhering to a bearer by virtue of the bearer's being at the point or short after birth. neonatal A quality that has a value that is increased compared to normal or average. increased quality A quality that has a value that is decreased compared to normal or average. decreased quality A quality of an object that has a value that is decreased compared to normal or average. decreased object quality A quality of an object that has a value that is increased compared to normal or average. increased object quality A medium brown color with a metallic sheen, resembles the actual alloy bronze. bronze Female quality of having complete, unaltered reproductive organs intact female Male quality of having complete, unaltered reproductive organs. intact male Male quality of being incapable to reproduce because of functional loss of the testicles from surgical removal or chemical means. castrated male A colour that is very pale yellowish brown. beige A color consisting of yellow and brown hue. yellow brown A color consisting of yellow and brown hue and low brightness. dark yellow brown A color consisting of yellow and brown hue and high brightness. light yellow brown A hardness quality of giving significant resistance to pressure. firm Female quality of being incapable to reproduce because of functional loss of the ovaries and/or uterus from surgical removal. spayed female A biological sex quality inhering in an individual or a population who are otherwise male of a non-hermaphroditic species who has ambiguous or atypical congenital development of the reproductive system. male with differences of sexual differentiation male with disorder of sexual development male, DSD male with DSD A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have two stamens. diandrous A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have only one stamen. monandrous A sequential hermaphroditic quality whereby organisms start out as female and change to male at a later life stage. protogyny protogynous A sequential hermaphroditic quality whereby organisms start out as male and change to female at a later life stage. protandry protandrous A protogynous quality whereby organisms start out as female and change to hermaphrodite at a later life stage. protogynous hermaphrodite protogynous hermaphroditic protogynous hermaphroditism A protandrous quality whereby organisms start out as male and change to hermaphrodite at a later life stage. protandrous hermaphrodite protandrous hermaphroditic protandrous hermaphroditism A biological sex quality inhering in an individual or a population who are otherwise female of a non-hermaphroditic species who has ambiguous or atypical congenital development of the reproductive system. female with differences of sexual differentiation female with disorder of sexual development female, DSD female with DSD A quality of an object that has a value that is normal or average. normal object quality A flexibility which is relatively normal or average. normal flexibility A temperature which is relatively normal or average normal temperature A viscosity which is relatively normal or average normal viscosity A hermaphroditic quality that inheres in a population or organism where an organism changes is a different sexes during different life stages. sequential hermaphroditic sequential hermaphrodite A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength. quality of interaction of a substance with electromagnetic radiation collection of organisms A material entity that minimally consists of a protein. protein-containing material entity region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. region stratification is a planned process which executes a stratification rule using as input a population and assign it member to mutually exclusive subpopulation based on the values defined by the stratification rule PRS+AGB adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013 population stratification prior to sampling a stratification rule/criteria is a criteria used to determine population strata so that a stratification process implementing the rule can result in any member of the total population being assigned to one and only one stratum STATO adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013 stratification rule a stratum population is a population resulting from a population stratification prior to sampling process which aims to produce homogenous subpopulations from an heterogeneous population by applying one or more stratification criteria STATO stratum population statistical sampling is a planned process which aims at assembling a population of observation units (samples) in as an unbiaised manner as possible in order to obtain or infer information about the actual population these samples have been drawn. STATO statistical sampling Simple random sampling is a statistical sampling process which creates a sample of a size n entirely by chance. In such process, each unit has the same probability of being selected. Depending on the size of the population being sampled, the sampling process may be done with or without replacement https://en.wikipedia.org/wiki/Simple_random_sample simple random sampling Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. biological structure connected biological structure anatomical structure Anatomical structure that performs a specific function or group of functions [WP]. organ A multicellular structure that is a part of an organ. cardinal organ part organ part Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. bowel intestine The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). regio oralis mouth A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. excreted substance portion of excreted substance waste substance excreta A fluid that is composed of blood plasma and erythrocytes. true portion of blood vertebrate blood blood Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. haemolymphatic fluid A portion of organism substance that is produced by exocrine glands. bodily secretion exocrine gland fluid/secretion secreted substance secretion of exocrine gland Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. body fluid or substance body substance organism substance portion of body substance portion of organism substance organism substance Anatomical entity that has mass. material anatomical entity Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. body system connected anatomical system organ system anatomical system Anatomical structure that is an individual member of a species and consists of more than one cell. multi-cellular organism multicellular organism Anatomical group whose component anatomical structures lie in close proximity to each other. anatomical cluster Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. portion of tissue tissue portion tissue An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. stomach Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. digestive system Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. fat fat tissue fatty tissue adipose tissue Excretion that is the output of a kidney. urine Secretion produced by a sweat gland. sweat A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. large bowel colon A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. salivary gland secretion saliva An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. mammal milk mammary gland milk milk Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. bile Portion of semisolid bodily waste discharged through the anus[MW,modified]. faeces fecal material fecal matter piece of shit portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool feces Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. portion of connective tissue textus connectivus connective tissue Gonochoristic organism that can produce female gametes. female organism A proximal-distal subdivision of the digestive tract. subdivision of digestive tract The part of the digestive system that excludes the hepatobiliary system. alimentary part of gastrointestinal system Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. body fluid bodily fluid A portion of organism substance that secreted_by a respiratory system. respiratory system fluid/secretion A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards. mammary gland fluid/secretion digestive system fluid or secretion digestive system secreted substance A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. adults adult organism Matter ejected from the lungs, bronchi, and trachea, through the mouth. sputum An anatomical structure that has more than one cell as a part. multicellular structure multicellular anatomical structure An organ of the digestive tract that is capable of retaining and storing food. food storage organ Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. irregular connective tissue Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) dense irregular connective tissue Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets. dense connective tissue A substance that is consumed by the organism for food. ingested food subdivision of tube Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. digestive organ digestive system organ digestive system element Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. disconnected anatomical group unit length unit mass unit time unit temperature unit substance unit base unit concentration unit volume unit frequency unit pressure unit volumetric flow rate unit rate unit gram based unit minute based unit hour based unit day based unit week based unit year based unit A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. vaccine a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response. vaccination true start date quantity measurement value question sentence true dimensional quantity number time measurement study group time instant biological quality geometric entity point endpoint terminal point country start time end time ethnicity true control group cardiovascular disease diabetes mellitus digestive system disease disease duration hypertension metabolic disease temporal measurement endocrine system disease measurement risk factor energy intake true physical activity vascular disease anthropometric measurement drinking behavior true smoking behavior body weights and measures true alcohol drinking true body weight true body height true waist circumference bone measurement hip circumference true sample collection protocol smoking behaviour measurement increased risk cigarettes per day measurement glucose metabolism disease pancreas disease Temporal Instant Time extent; duration of a time interval separate from its particular start position Temporal Duration example to be eventually removed example to be eventually removed metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion 4.5 lactic acid concentration in kefir 4.8 lactose concentration in starting milk mixture 0.01 lactose concentration in parmigiano reggiano 55 temperature of parmigiano reggiano curd cooking 10 duration of parmigiano reggiano curd cooking 0.93 water activity of parmigiano reggiano 12 duration of parmigiano reggiano maturation axiom holds for all times ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times meter A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. m meter second A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. s sec second centimeter A length unit which is equal to one hundredth of a meter or 10^[-2] m. cm centimeter millimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. mm millimeter micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. um micrometer nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nm nanometer angstrom A length unit which is equal to 10 [-10] m. angstrom milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. mg milligram microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. ug microgram nanogram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. ng nanogram picogram A mass unit which is equal to 10^[-12] g. pg picogram degree Celsius A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. C degree C degree Celsius month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. umol micromole nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nmol nanomole picomole A substance unit equal to 10^[-12] mol. pmol picomole molar A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). M molar millimolar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. mM millimolar micromolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. uM micromolar nanomolar A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. nM nanomolar picomolar A unit of molarity which is equal to 10^[-12] M. pM picomolar cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cc cubic centimeter milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. ml milliliter liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. L liter cubic decimeter A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. cubic decimeter microliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. ul microliter nanoliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nl nanoliter picoliter A volume unit which is equal to 10^[-12] L. pl picoliter hertz A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. hertz mass percentage A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. % w/w percent weight pr weight mass percentage mass volume percentage A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. % w/v percent vol per vol mass volume percentage volume percentage A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. % v/v percent vol per vol volume percentage gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. g per L g/L gram per liter milligram per milliliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. mg per ml mg/ml milligram per milliliter pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. ml per L ml/l milliliter per liter gram per deciliter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. g/dl gram per deciliter colony forming unit per volume A concentration unit which a measure of viable bacterial numbers in a given volume. colony forming unit per volume microliters per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. microliters per minute count per nanomolar second A rate unit which is equal to one over one nanomolar second. count per nanomolar second count per molar second A rate unit which is equal to one over one molar second. count per molar second count per nanomolar A rate unit which is equal to one over one nanomolar. count per nanomolar count per molar A rate unit which is equal to one over one molar. count per molar microgram per liter A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. ng/ml ug/L microgram per liter geographical location kilogram gram minute hour day week year