Metabolomics Standards Initiative Ontology (MSIO) OWL https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO http://creativecommons.org/licenses/by/3.0/ 1.0.1 Silvia Marin Vitaly Selivanov Marta Cascante Pedro Ramon de Atauri Carulla Teresa Fan an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies. Andrew Lane Hunter Moseley Philippe Rocca-Serra Alejandra Gonzalez-Beltran Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label 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 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 definition definition definition textual definition textual definition 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition definition textual 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.obfoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note 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 has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has axiom label ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Contributor Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Format 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 Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Title has_alternative_id database_cross_reference has_exact_synonym has_obo_format_version has_obo_namespace has_related_synonym in_subset label label is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See 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 this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes precedes An object property linking a consent code to a specific restriction which further constrains it, such as research should be restricted to a specific disease or geographical location. DUO:0000010 is restricted to has measurement unit label This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point has coordinate unit label relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum a chemical entity is said to be an isotopomer of another one if it has the same number of each isotopic atom but differs in their positions. isotopomer is a contraction of isotopic isomer CH2DCH=0 is isotopomer of CH3CD=0 IUPAC compendium of chemical terminology (2nd edition, 1997) is isotopomer of CH4 is isotopologue of CH3D which is isotopologue of CH2D2 a molecular entity which differs only in isotopic composition (i.e the number of isotopic substitution differs but the overall chemical structure is unchanged) is said to be an isotologue Philippe Rocca-Serra IUPAC compendium of chemical terminology (2nd edition, 1997) is isotopologue of A relation associating a product to its manufacturer. Alejandra Gonzalez-Beltran Philippe Rocca-Serra manufactured by is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of is_proxy_for position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity 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. A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the measurement of c2. (another definition) Alan Ruttenberg is_proxy_for achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective 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 objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by 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. 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. Person:Alan Ruttenberg Person:Helen Parkinson Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case is member of organization has organization member Relating an organization to a legal person or organization. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng 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 inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role has_role derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into move to BFO? Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation has measurement value has x coordinate value has y coordinate value has specified numeric value A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI has specified numeric value has specified value A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value For 1r/1i spectra and for Bruker, this term describe an array of integers (32bits). integer32 A reference number relevant to the sample under study. value-type:xsd:string NMR NMR:1000001 sample number A reference number relevant to the sample under study. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. For 1r/1i spectra and for Bruker, this term describe an array of longs (64bits). long64 The chemical phase of a pure sample, or the state of a mixed sample. NMR NMR:1000003 sample state information The chemical phase of a pure sample, or the state of a mixed sample. MSI:NMR Total mass of sample used. value-type:xsd:float NMR NMR:1000004 sample mass information Total mass of sample used. MSI:NMR value-type:xsd:float The allowed value-type for this CV term. Total volume of solution used. value-type:xsd:float NMR NMR:1000005 sample volume Total volume of solution used. MSI:NMR value-type:xsd:float The allowed value-type for this CV term. Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used. value-type:xsd:float NMR NMR:1000006 sample concentration Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used. MSI:NMR value-type:xsd:float The allowed value-type for this CV term. One of the problems that should be apparent after observing the spectrum and the FID is that it is not possible to determine if the frequency is positive or negative. The instrument uses a spectrometer frequency and all signal frequencies are measured relative to the spectrometer frequency. If a molecule produces two signals, one at 300,000,001 Hz and another at 299,999,999 Hz, and the spectrometer frequency is 300,000,000 Hz, the first signal is at +1 Hz and the second is at -1 Hz. Electronically the lower frequency signals are very easy frequency to detect, transmit, amplify and sample. The complication with this rotating frame of reference is that a single detector can not distinguish positive and negative frequencies. This problem is why quadrature detection is important. Quadrature detection uses two detector channels separated by 90 degrees. These are referred to as the real channel and the imaginary channel. Using these two channels, it is possible to distinguish positive and negative frequencies. This section shows how the quadrature signal is processed to obtain an NMR spectrum. The Fourier transform produces a complex number with a real and an imaginary component. The Re function extracts the real spectrum and the Im function extracts the imaginary spectrum from the complex number. quadrature detection contact role data file attribute NMR instrument type 1D spectrum coordinate system descriptor pre-acquisition solvent suppression peak processing Hexafluorobenzene CDCl3 Chloroform-d CHEBI:41981 D2O heavy water sample pH post buffer pH Philippe Rocca-Serra http://www.scs.illinois.edu/nmr/handouts/general_pdf/ugi034.pdf apodization Apodization is an umbrella term that is used to refer to signal processing covering the manipulation of the FID to either increase signal-to-noise (S/N) or resolution. it is usually possible to gain either S/N or resolution, but not both. Apodization is usually performed by applying a window function to the FID http://www.metabolomicssociety.org/databases PRS: rename 'reference' to 'identifier' metabolomics database identifier Metabolights identifier acetonitrile 1,4-Dioxane 1H spectrum reference compound DSS 2,2-Dimethyl-2-silapentane-5-sulfonate sodium acetate TMS tetramethylsilane 13C spectrum reference compound Instrument model name not including the vendor's name. NMR NMR:1000031 NMR instrument model Instrument model name not including the vendor's name. MSI:NMR Free text description of a single customization made to the instrument; for several modifications, use several entries. value-type:xsd:string NMR NMR:1000032 instrument customization Free text description of a single customization made to the instrument; for several modifications, use several entries. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Chloroform-d1 keyword tetramethylammonium bromide 15N spectrum reference compound ammonia (liquid) ammonium bromide 1,4-morpholine nitromethane pyridine sodium nitrate solvent filtering post-acquisition solvent suppression Nuclear magnetic resonance decoupling (NMR decoupling for short) is a special method used in nuclear magnetic resonance (NMR) spectroscopy where a sample to be analyzed is irradiated at a certain frequency or frequency range to eliminate fully or partially the effect of coupling between certain nuclei. NMR coupling refers to the effect of nuclei on each other in atoms within a couple of bonds distance of each other in molecules. This effect causes NMR signals in a spectrum to be split into multiple peaks which are up to several hertz frequency from each other. Decoupling fully or partially eliminates splitting of the signal between the nuclei irradiated and other nuclei such as the nuclei being analyzed in a certain spectrum. NMR spectroscopy and sometimes decoupling can help determine structures of chemical compounds. http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_decoupling decoupling method homonuclear decoupling heteronuclear decoupling State if the sample is in emulsion form. NMR NMR:1000047 emulsion State if the sample is in emulsion form. MSI:NMR State if the sample is in gaseous form. NMR NMR:1000048 gas State if the sample is in gaseous form. MSI:NMR State if the sample is in liquid form. NMR NMR:1000049 liquid State if the sample is in liquid form. MSI:NMR State if the sample is in solid form. NMR NMR:1000050 solid State if the sample is in solid form. MSI:NMR State if the sample is in solution form. NMR NMR:1000051 solution State if the sample is in solution form. MSI:NMR State if the sample is in suspension form. NMR NMR:1000052 suspension State if the sample is in suspension form. MSI:NMR Sample batch lot identifier. value-type:xsd:string NMR NMR:1000053 sample batch information Sample batch lot identifier. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. broad band decoupling off resonance decoupling band-selective decoupling narowband decoupling specific decoupling angle of sinusoid 31P spectrum reference compound H3PO4 phosphoric acid P4 phosphorus (CH3O)3PO trimethyl phosphate P(C6H5)3 triphenylphosphine O=P(C6H5)3 triphenylphosphine oxide co-dissolved internal reference synthetic reference signal residual solvent signal FID zero filling data extrapolation using linear prediction multiplying FID by window function FID fourier transformation The mathematical conversion of time-resolved FID raw data into frequency resolved NMR spectra (frequency-resolved NMR data) by means of fourier transformation of coordinate systems. phasing spectral phasing phase correction peak integration peak alignment peak shape fitting spectral referencing Pohl, L.; Eckle, M. (1969). "Sodium 3-(trimethylsilyl)tetradeuteriopropionate, a new water-soluble standard for 1H.N.M.R.". Angewandte Chemie, International Edition in English 8 (5): 381. doi:10.1002/anie.196903811 TMSP trimethylsilyl propanoic acid sodium trimethylsilyl-propionate used to be 'linear scaling algorithm' linear scaling used to be called 'scaling algorithm' scaling used to be postfixed with algorithm non-linear scaling total spectral area scaling Dieterle F, Ross A, Schlotterbeck G, Senn H: Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Anal Chem 2006, 78(13):4281-90. probabilistic quotient normalization glog scaling scaling by generalized logarithmic transformation pareto scaling autoscaling JRES spectrum 2D J-resolved spectrum http://www.biomedcentral.com/1471-2105/12/366#B2 MetaboLab software Metaboquant software rNMR software open source NMR software commercial NMR software Günther U, Ludwig C, Rüterjans H: NMRLAB - advanced NMR data processing in Matlab., J Magn Reson 2000, 145(2):201-208. NMRLab software Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995, 6(3):277-293. NMRPipe software van Beek JD: matNMR: a flexible toolbox for processing, analyzing and visualizing magnetic resonance data in Matlab. J Magn Reson 2007, 187:19-26. matNMR software concentration of chemical compound manual phase correction automatic phase correction DC offset correction http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-366 Gibbs multiplication skyline projection shifted sine apodization shifted sine window function SINC Sinc window multiplication sinc window multiplication of FID (1D) http://www.sciencedirect.com/science/article/pii/S0003267008000950 https://github.com/nmrML/nmrML/issues/36 combined sine-bell–exponential window function SEM window function TRAP trapezoid apodization Functional form ( 0:t1 linear increase from 0.0 to 1.0, t1:size-t2 1.0 -t2: linear decrease from 1.0 to 0.0 / Parameters ( * data Array of spectral data., * t1 Left ramp length., * t2 Right ramp length., * inv Set True for inverse apodization. trapezoid window function shifted gaussian window function baseline correction using spline function HSQC NMR spectrum heteronuclear single quantum coherence spectrum Zangger-Sterk pulse sequence http://nmr.chemistry.manchester.ac.uk/?q=node/256 pure shift 1D Zangger-Sterk pulse sequence http://nmr.chemistry.manchester.ac.uk/?q=node/264 oneshot pulse sequence http://nmr.chemistry.manchester.ac.uk/?q=node/265 pure shift oneshot pulse sequence http://nmr.chemistry.manchester.ac.uk/?q=node/285 PE Watergate pulse sequence perfect echo watergate pulse sequence NMR Star 3.1 file format NMR Star 2.1 file format three dimensional spectrum 3D spectrum four dimensional spectrum 4D spectrum NMR spectrum by dimensionality homonuclear chemical shift spectrum heteronuclear chemical shift spectrum Bruker instrument model. NMR NMR:1000122 Bruker instrument model Bruker instrument model. MSI:NMR homonuclear exchange spectroscopy spectrum heteronuclear exchange spectroscopy spectrum homonuclear J-resolved spectrum heteronuclear J-resolved spectrum calibration test spectrum NMR star software http://www.felixnmr.com/ Felix software PIPP software TALOS+ software http://www.cyana.org/wiki/index.php/Main_Page CYANA software http://nmr.cit.nih.gov/xplor-nih/ XPLOR-NIH software computed concentration request these in UO ? http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/XEASY XEASY software sparky software http://nmr-software.blogspot.de/2007/04/cara.html CARA software Wattos software MADNMR software Pronto software TRIAD NMR software library based computed concentration Lorenzian (-Integration) (Modeled Area) Estimated Concentration https://docs.google.com/spreadsheets/d/1egsLQWoQuCxAYPr9MIo-F0A5K9RCbJSC8yWZyYq_fiQ/edit?usp=sharing Lorenzian estimated concentration Measured Area (Integration) based Concentration measured area based concentration time-domain amplitude computed concentration group time delay compensation http://nmr-analysis.blogspot.fr/2008/02/why-arent-bruker-fids-time-corrected.html This is independent of the bruker acquisition parameter named "GRPDLY" (Group Delay), but this is a "shift" applied on the fid to calibrate its zero scaling by forward linear prediction back calculation of first points by linear-prediction scaling by mirror image linear prediction digital filtering Daniel Schober http://jjhelmus.github.io/nmrglue/current/jbnmr_examples/s11_strip_plots.html 3D strip plot generation A spectrum vizualization method for 3D nmr spectra, assisting assignments for large sequential molecules, i.e. Proteins. The first two axis in the plot represent the ppms along the two acquisition nuclei, and a third dimension captures the sequential molecule order for the third nucleus. Batman software JEOL instrument model tecmag instrument model Bao et al. (2013) A new automatic baseline correction method based on iterative method, J. Magn. Res. 218:35-43 Golotvin & Williams (2000), Improved baseline recognition and modeling of FT NMR spectra, J. Magn. Res. 146:122-125 automatic baseline recognition TSP Trimethylsilyl propionate pulse sequence from Wishart lab library TMIC lab pulse sequence probe gradient strength e.g. Linux or Windows, ... NMR acquisition computer operating system e.g. Bruker Biospin ICON-NMR NMR autosampler software Bruker Biospin ICON-NMR software http://www.bruker.com/products/mr/nmr/nmr-software/software/iconnmr/overview.html buffer pH e.g. heavy water (D2O) lock frequency field frequency lock quantitation standard concentration standard NMR acquisition software CIMR MI standard signal line width signal line width at five percent intensity NMR spectrum descriptor pulse width hard pulse width spectrum width sweep width number of data points in spectrum number of first dimension data points number of data points tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. x end value y-axis type bucket x center center of bin on x-axis NMR spectrum quantification method spectral quantitation algorithm The NMRProcFlow open source software provides a complete set of tools for processing (e.g. Bucketing) and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization. NMRProcFlow software http://www.nmrprocflow.org/ Bayesil is a web system that automatically identifies and quantifies metabolites using 1D 1H NMR spectra of ultra-filtered plasma, serum or cerebrospinal fluid. The NMR spectra must be collected in a standardized fashion for Bayesil to perform optimally. Bayesil first performs all spectral processing steps, including Fourier transformation, phasing, solvent filtering, chemical shift referencing, baseline correction and reference line shape convolution automatically. It then deconvolutes the resulting NMR spectrum using a reference spectral library, which here contains the signatures of more than 60 metabolites. This deconvolution process determines both the identity and quantity of the compounds in the biofluid mixture. Ravanbakhsh S, Liu P, Bjorndahl TC, Mandal R, Grant JR, Wilson M, Eisner R, Sinelnikov I, Hu X, Luchinat C, Greiner R, Wishart DS. (2015) Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics. PLoS ONE 10(5): e0124219. Bayesil software http://bayesil.ca/ nmrML-Assign is a web server for creating an nmrML file from a FID and a structure. The FID is first automatically processed with Bayesil. The resulting interactive spectrum allows assigning peaks to specific atoms in the structure and the assignments are saved in the nmrML format. For more information about nmrML please visit nmrML.org. nmrML-Assign works with 1H and 13C NMR spectra in Bruker or Agilent/Varian format. Uses JspectraView Software nmrML Assign http://nmrml.bayesil.ca/ d doublet feature t triplet feature q quatruplet feature a set of peaks that are highly correlated in a series of samples a feature request by Daniel Jacob inserted at IBP hackathon cluster of peaks across samples simulated spectrum pulse parameter JEOL FID format dd doublet of doublets feature ABX multiplet pattern AMX, ABX and ABC patterns, and various related spin systems are very common in Proton NMR of organic molecules.When two of the protons of an AMX pattern approach each other to form an ABX pattern, the characteristic changes in intensities of a strongly coupled system (leaning) are seen, and, as the size of J approaches the value of νAB more complicated changes arise, so that the pattern can no longer be analyzed correctly by first order methods. http://www.chem.wisc.edu/areas/reich/nmr/05-hmr-12-abx.htm s singlet feature qi quintet feature dt doublet of triplets td triplet of douplets tt triplet of triplets NMR spectrum by pulse sequence NMR spectrum by processing step 2D spectrum coordinate system descriptor y-axis value type the subclasses come from the Rubtsov specification power value type magnitude value type real value type imaginary value type complex value types spectral projection axis f1 axis f2 axis NMR Format converter BML-NMR identifier will be further specified via a concentration value creatinine 2D pulse sequence used to be labeled 'NMR spectrum simulation' data simulation DNP NMR dynamic nuclear polarization enhanced NMR system dynamic nuclear polarization NMR Chemical shift is the resonance frequency of a nucleus related to a chemical shift standard. in ppm along x-axis http://en.wikipedia.org/wiki/Chemical_shift chemical shift an information object that describes the strength of the NMR signal nmr signal intensity baseline correction using polynomial function first transient of the tnnoesy-presaturation pulse sequence Varian acquisition parameter file procpar acqus Bruker acquisition parameter file NMR NMR:1000231 peak feature global Varian autosampler Varian SMS 50 Varian probe 5mm HCN probe Varian liquid cold probe e.g as in HMDB reference compound NMR spectrum Mestrelab software ACD spectrus software Mat NMR 3 software NMRLab software Spinworks NMR software NMR software vendor Spinworks iNMR software NMR pipe cule NMR software Git: nmrML\tools\Parser_and_Converters\Matlab By Batman/ Tim Ebbels Group Matlab to nmrML converter Bruker processing parameter file procs Varian processing parameter file http://mmcd.nmrfam.wisc.edu/ PRS: rename 'identifyer' to 'identifier' Madison Metabolomics Consortium Database MMCD identifier http://bigg.ucsd.edu/ PRS: rename 'identifyer' to 'identifier' Bigg metabolomics database identifier Lorentz-to-Gauss apodization Functional form: gm(x_i) = exp(e - g*g) Where: e = pi*i*g1 g = 0.6*pi*g2*(g3*(size-1)-i) Parameters: * data Array of spectral data. * g1 Inverse exponential width. * g2 Gaussian broaden width. * g3 Location of gauss maximum. * inv Set True for inverse apodization. Lorentz Gaussian window function TRAF Transform of Reverse Added FIDs traf window function A Window function described by Daniel Traficante in their original paper. TRAFS trafs window function peak fitting peak assignment deconvolution A method of sorting multiple spectra by position of chemical shift peaks. This method is used in Batman and improves the fit for shifted/overlapped peaks. chemical shift sorting fid file Varian FID file Bruker FID file Jacob D. et al (2013) Analytical and Bioanalytical Chemistry, 405, 5049-5061 ERVA-based bucketing cluster of peaks Match NMR tube shaped tube Shigemi tube standard tube Bruker tube JEOL magnet http://www.jeolusa.com/PRODUCTS/Nuclear-Magnetic-Resonance/Magnets JEOL ECS magnet JEOL ECA magnet JEOL ECX magnet Varian NMR software VnmrJ software Wilmad tube 4mm Match tube 2.5mm Match tube 3mm Match tube 5mm Match tube 1mm Match tube 1.7mm Match tube 2mm Match tube 4.25mm Match tube 3mm standard tube 5mm standard tube 1mm standard tube 1.7mm standard tube Wilmad economy tube Wilmad precision tube Norell tube JEOL FID file Git: nmrML\tools\Parser_and_Converters\R R statistics to nmrML. Developed by Steffen Neumann, IPB-Halle.de nmRIO Git: nmrML\tools\Parser_and_Converters\R\rNMR-IO rNMR-IO Based on both nmrML.xsd (XML Schema Definition) and CV params (such as ontologies nmrCV, UO, CHEBI ...), a converter written in Java was developed that automatically generates nmrML files, from raw files of the major NMR vendors. The choice of Java was guided by i) the JAXB framework (Java Architecture for XML Binding), ii) its OS-platform independence and iii) strengthened by the existence of a useful java library (i.e [nmr-fid-tool](https://github.com/LuisFF/nmr-fid-tool)) for further processing and visualisation of the resulting nmrML data. As nmrML intents to gather and integrate several types of data and corresponding metadata in a single file, it is necessary to process each data source separately. Thus, two command tools were developed. The first one, nmrMLcreate allows to create a new nmrML file, based on available Bruker or Varian/Agilent raw files. The second one, nmrMLproc allows to add and fill in additional sections corresponding to the data processing step. Git: nmrML\tools\Parser_and_Converters\Java\converter Developed by Daniel Jacob at INRA Bordeaux. The recommended converter for Bruker and Varian/Agilent vendor format conversion. Vendor2nmrML_Java Agilent magnet Varian magnet premium compact narrow bore magnet premium shielded narrow bore magnet premium shielded wide bore magnet modified gaussian apodization Functional form: gmb(x_i) = exp(-a*i - b*i*i) Parameters: * data Array of spectral data. * a Exponential term. * b Gaussian term. * inv Set True for inverse apodization. modified Gaussian window function exponentially damped J-modulation apodization Functional form: jmod(x_i) = exp(-e)*sin( pi*off + pi*(end-off)*i/(size-1)) Parameters: * data Array of spectral data. * e Exponential term. * off Start of modulation in fraction of pi radians. * end End of modulation in fraction of pi radians. * inv Set True for inverse apodization exponentially damped J-modulation window function shifted sine-bell apodization Functional form: sp(x_i) = sin( (pi*off + pi*(end-off)*i/(size-1) )**pow Parameters: * data Array of spectral data. * start Start of Sine-Bell as percent of vector (0.0 -> 1.0) * end End of Sine-Bell as percent of vector (0.0 -> 1.0 ) * pow Power of Sine-Bell * inv Set True for inverse apodization. shifted sine bell window function triangle apodization Functional form: 0:loc linear increase/decrease from lHi to 1.0 loc: linear increase/decrease from 1.0 to rHi Parameters: * data Array of spectral data. * loc Location of apex, "auto" sets to middle. * lHi Left side starting height. * rHi Right side starting height. * inv Set True for inverse apodization. triangle window function The acquisition log file is a created during an acquisition and could useful for debugging an acquisition that has gone awry. acquisition log file Git: nmrML\tools\Parser_and_Converters\python A Python based vendor to nmrML converter developed by MIchael Wilson at TMIC Edmonton. PynmrML A web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. Jianguo Xia, Igor V. Sinelnikov, Beomsoo Han and David S. Wishart, MetaboAnalyst 3.0—making metabolomics more meaningful, Nucl. Acids Res. (1 July 2015) 43 (W1): W251-W257. doi: 10.1093/nar/gkv380 MetaboAnalyst software www.metaboanalyst.ca acqu2s acqu3s proc2s proc3s NMR spectrum file Bruker NMR spectrum file 1R file title file A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes. Christian Bartels, Tai-he Xia, Martin Billeter, Peter Güntert, Kurt Wüthrich, The program XEASY for computer-supported NMR spectral analysis of biological macromolecules, J Biomol NMR (1995) 6: 1. doi:10.1007/BF00417486 XEASY software NMR spectrum vizualisation software Used in NMR Assign tool for Baysil JspectraView software cryoprobe inverse detection NMR probe 5mm inverse detection cryoprobe Git: nmrML\tools\Visualizers\PMB_NMRviewer Developed by Daniel Jacob, INRA Bordeaux NMRViewer software http://services.cbib.u-bordeaux2.fr/SPECNMR/examples http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm AB multiplet pattern Use Chebi entities here. NMR solvent Use Chebi entities here. NMR buffer presat water suppression Varian VNMRS 600 data content encoding data compression scheme byte format zlib complex64 This byte format uses a consecutive array of two 32bit float numbers to represent the real and imaginary part of the complex values. complex128 This byte format uses a consecutive array of two 64bit double precision values to represent the real and imaginary part of the complex values. binary data compression type http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm AB2 multiplet pattern data encoding parameter uncompressed data DSPFVS - DSP (Digital signal processing) firmware version corresponds to the version of the digital filter, a hardware component used by the spectrometer DSPFVS digital signal processing firmware version DECIM - decimation factor is a (bruker) acquisition parameter that captures the number of raw analog points that are averaged in order to obtain a digital signal recorded in the fid. DECIM decimation factor GRPDLY - is the time delay (in number of points?) between acquiring the analog signal and producing the digital signal (i.e. "The group delay is the time necessary for the digital filter function to “walk into” the raw FID and start generating significant intensity.") GRPDLY group time delay NMR sampling strategy a type of data acquisition parameter (when recording the FID) which can be continuous/uniform or sparse/non-uniform signal acquisition. continuous sampling uniform sampling With uniform sampling, each sample is separated by the "dwell time". With uniform sampling we don't need to record the time points because we know the dwell time. We may add named strategies to the CV over time that are more specific than non-uniform http://link.springer.com/chapter/10.1007%2F1-4020-3910-7_142#page-1 sparse sampling non-uniform sampling with non-uniform, some samples are skipped, there are different strategies for which to skip, but we can simply record the time point as well as the complex data point in order to represent this type of data. Non-uniform sampling is something likely to become more important in the future, because it allows you to capture higher dimension spectra much more quickly Bruker XWIN-NMR software software attribute NMR software version http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm ABX3 multiplet pattern http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm AA'BB' multiplet pattern http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm AA'XX' multiplet pattern variable size bucketing uniform bucketing intelligent bucketing bucket importing put in as reqired by NMRProcFlow tool bucket resetting as needed for nmrProcFlow global baseline correction as needed for nmrProcFlow local baseline correction bucket fusioning JNM-ECX Series FT NMR instrument JNM-ECZR Series FT NMR instrument JNM-ECZR series is a new system that fully incorporates the latest digital and high frequency technologies. Improved reliability and a more compact size make possible by incorporating more advanced integrated circuits, it supports even greater expandability options than current models for multi-channel operation, high power amplifiers and other accessories. The bus line for control of attachments has been upgraded to high speed and enables highly accurate and rapid control. 400 MHz - 1 GHz JNM-ECZS Series FT NMR instrument The entry model ECZS spectrometer has the same basic functions, performance and capability of high-end model. The main console is amazingly small, less than 1/2 that of the current ECS series spectrometer. Coupling the use of advanced software with highly reliable automation, all routine daily measurements can be automated, while the use of the autotune Supercool probe realizes the world’s highest sensitivity in its class. Whatever your application field ECZS can demonstrate its power. 400 MHz AVANCE III HD NanoBay400 MHz Fourier 300HD DNP-NMR LC-NMR instrument LC-NMR/MS instrument Food-Screener instrument AVANCE IVDr JEOL Resonance 400MHz YH magnet JEOL Resonance 500MHz magnet JEOL Resonance 600MHz magnet JEOL Resonance 700MHz magnet JEOL Resonance 800MHz magnet single peak feature NMR instrument vendor Any organisation ort person that sells NMR instruments to customers. Avance I spectrometer Oxford Instruments Spinlock SRL General Electric Kimble Chase Phillips Siemens AG Varian Inova 500 Varian VNMRS instrument Varian Mercury plus Varian UnityInova instrument Varian 400-MR NMR instrument Varian DDR2 instrument Agilent NMR instrument Agilent 400-MR NMR instrument Varian Mercury 400 Agilent Au 400 (DDR2 Console) Agilent DDR 2 w/ HCN cryoprobe BMRB identifier TM1 0<TM1<1 left trapezoid limit trapezoid window function parameter complex64 Integer This byte format uses a consecutive array of two 32bit integer numbers to represent the real and imaginary part of the complex values (2x32bits=>2x4bytes=> 2 integers) for the FID datatype. complex128 Integer This byte format uses a consecutive array of two 64bit long integer numbers to represent the real and imaginary part of the complex values (2x64bits => 2x8bytes => 2 longs) for the FID datatype. TM2 0<TM2<1 right trapezoid limit 30 degree pulse duration thirty degree pulse duration The duration of the excitation pulse needed to rotate the magnetisation vector by 30 degrees. InChi inchikey WLN Wiswesser Line Notation ROSDAL SLN-Tripos smarts line representation 2D topological molecule representation 2D bond line structure 3D geometrical molecule representation 3D bond line structure CAS number fingerprint model molfile compound similarity measure Tanimoto similarity Gaussian window function parameter DSS 2,2-Dimethyl-2-silapentane-5-sulfonate Gaussian maximum position 2H spectrum reference compound ABX2 multiplet pattern DRX 600 instrument plot and graph generation reference deconvolution vertical alignment of on and offset of the peak of the reference compound. spectral smoothing the process of removing noisy jitters in a spectral curve to get clearer and more meaningful signals and peaks. NMR database format M. Yokochi, N. Kobayashi, E. L. Ulrich, A. R. Kinjo, T. Iwata, Y. E. Ioannidis, M. Livny, J. L. Markley, H. Nakamura, C. Kojima, T. Fujiwara, “Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins,” Journal of Biomedical Semantics, 5:7:16 (2016) BMRB/XML file format nD spectrum Terms used to describe types of data processing. data processing NMR NMR:1000452 NMR data conversion Terms used to describe types of data processing. MSI:NMR tempdef: A sample is a role that is played by an object of interest in an investigation used to obtain generalizable information about the sample source. defprov: Daniel Schober NMR NMR:1000457 sample tempdef: A sample is a role that is played by an object of interest in an investigation used to obtain generalizable information about the sample source. defprov: Daniel Schober MSI:NMR Description of the instrument or the mass spectrometer. instrument configuration NMR NMR:1000463 instrument Description of the instrument or the mass spectrometer. MSI:NMR Varian instrument model. NMR NMR:1000489 Varian/Agilent instrument model Varian instrument model. MSI:NMR Instrument properties that are associated with a value. NMR NMR:1000496 instrument attribute Instrument properties that are associated with a value. MSI:NMR Describes the data content on the file. NMR NMR:1000524 data file content Describes the data content on the file. MSI:NMR Serial Number of the instrument. value-type:xsd:string NMR NMR:1000529 instrument serial number Serial Number of the instrument. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Conversion of one file format to another. NMR NMR:1000530 file format conversion Conversion of one file format to another. MSI:NMR Object Attribute. NMR NMR:1000547 object attribute Object Attribute. MSI:NMR Sample properties that are associated with a value. NMR NMR:1000548 sample attribute Sample properties that are associated with a value. MSI:NMR Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data. NMR NMR:1000561 data file checksum type Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data. MSI:NMR MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files. value-type:xsd:string NMR NMR:1000568 MD5 MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity. value-type:xsd:string NMR NMR:1000569 SHA-1 SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Describes the type of file and its content. source file NMR NMR:1000577 NMR raw data file format Describes the type of file and its content. MSI:NMR Details about a person or organization to contact in case of concern or discussion about the file. NMR NMR:1000585 contact attribute Details about a person or organization to contact in case of concern or discussion about the file. MSI:NMR Name of the contact person or organization. value-type:xsd:string NMR NMR:1000586 contact name Name of the contact person or organization. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Postal address of the contact person or organization. value-type:xsd:string NMR NMR:1000587 contact address Postal address of the contact person or organization. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Uniform Resource Locator related to the contact person or organization. value-type:xsd:string NMR NMR:1000588 contact URL Uniform Resource Locator related to the contact person or organization. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Email address of the contact person or organization. value-type:xsd:string NMR NMR:1000589 contact email Email address of the contact person or organization. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Home institution of the contact person. value-type:xsd:string NMR NMR:1000590 contact organization Home institution of the contact person. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Data processing parameter used in the data processing performed on the data file. NMR NMR:1000630 data processing parameter Data processing parameter used in the data processing performed on the data file. MSI:NMR The time that a data processing action was finished. value-type:xsd:date NMR NMR:1000747 data processing completion time The time that a data processing action was finished. MSI:NMR value-type:xsd:date The allowed value-type for this CV term. Describes how the native spectrum identifiers are formated. nativeID format NMR NMR:1000767 FID format Describes how the native spectrum identifiers are formated. MSI:NMR file=xsd:IDREF. NMR NMR:1000773 The nativeID must be the same as the source file ID. Bruker FID format file=xsd:IDREF. MSI:NMR A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the MSI-NMR working group in order to have another CV term added. value-type:xsd:string NMR NMR:1000799 custom unreleased software A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the MSI-NMR working group in order to have another CV term added. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Description of the preparation steps which took place before the measurement was performed. NMR NMR:1000831 sample preparation information Description of the preparation steps which took place before the measurement was performed. MSI:NMR A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction. NMR NMR:1000859 molecule A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction. MSI:NMR A compound of low molecular weight that is composed of two or more amino acids. NMR NMR:1000860 peptide A compound of low molecular weight that is composed of two or more amino acids. MSI:NMR A describable property of a chemical compound. NMR NMR:1000861 chemical compound attribute A describable property of a chemical compound. MSI:NMR The pH of a solution at which a charged molecule does not migrate in an electric field. value-type:xsd:float pI NMR NMR:1000862 isoelectric point The pH of a solution at which a charged molecule does not migrate in an electric field. MSI:NMR value-type:xsd:float The allowed value-type for this CV term. The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm. value-type:xsd:float predicted pI NMR NMR:1000863 predicted isoelectric point The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm. MSI:NMR value-type:xsd:float The allowed value-type for this CV term. A combination of symbols used to express the chemical composition of a compound. NMR NMR:1000864 chemical compound formula A combination of symbols used to express the chemical composition of a compound. MSI:NMR A chemical formula which expresses the proportions of the elements present in a substance. value-type:xsd:string NMR NMR:1000865 empirical formula A chemical formula which expresses the proportions of the elements present in a substance. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked. value-type:xsd:string NMR NMR:1000866 molecular formula A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other. value-type:xsd:string NMR NMR:1000867 structural formula A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string. value-type:xsd:string NMR NMR:1000868 SMILES string The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. An identifier/accession number to an external reference database. NMR NMR:1000878 external reference identifier An identifier/accession number to an external reference database. MSI:NMR A unique identifier for a publication in the PubMed database (MIR:00000015). value-type:xsd:integer NMR NMR:1000879 PubMed identifier A unique identifier for a publication in the PubMed database (MIR:00000015). MSI:NMR value-type:xsd:integer The allowed value-type for this CV term. A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight. NMR NMR:1000881 Use Chebi entities here. chemical compound A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight. MSI:NMR A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein. NMR NMR:1000882 protein A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein. MSI:NMR A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN). value-type:xsd:string NMR NMR:1000883 protein short name A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN). MSI:NMR value-type:xsd:string The allowed value-type for this CV term. An nonphysical attribute describing a specific protein. NMR NMR:1000884 protein attribute An nonphysical attribute describing a specific protein. MSI:NMR Accession number for a specific protein in a database. value-type:xsd:string NMR NMR:1000885 protein accession Accession number for a specific protein in a database. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. A long name describing the function of the protein. value-type:xsd:string NMR NMR:1000886 protein name A long name describing the function of the protein. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. An nonphysical attribute that can be used to describe a peptide. NMR NMR:1000887 peptide attribute An nonphysical attribute that can be used to describe a peptide. MSI:NMR A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present. value-type:xsd:string NMR NMR:1000888 unmodified peptide sequence A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid mass modifications that are present using the notation where the total mass of the modified amino acid is specified in square bracketed numbers following the letter (e.g. R[162.10111] indicates an arginine whose final modified mass is 162.10111 amu). value-type:xsd:string NMR NMR:1000889 modified peptide sequence A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid mass modifications that are present using the notation where the total mass of the modified amino acid is specified in square bracketed numbers following the letter (e.g. R[162.10111] indicates an arginine whose final modified mass is 162.10111 amu). MSI:NMR value-type:xsd:string The allowed value-type for this CV term. A state description of how a peptide might be isotopically or isobarically labelled. NMR NMR:1000890 peptide labeling state A state description of how a peptide might be isotopically or isobarically labelled. MSI:NMR A peptide that has been created or labeled with some heavier-than-usual isotopes. NMR NMR:1000891 heavy labeled peptide A peptide that has been created or labeled with some heavier-than-usual isotopes. MSI:NMR A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy". light labeled peptide NMR NMR:1000892 unlabeled peptide A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy". MSI:NMR An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. value-type:xsd:string NMR NMR:1000893 peptide group label An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence. NMR NMR:1000898 data standard Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence. MSI:NMR A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard. MS_1000899 NMR NMR:1000899 de facto standard A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard. MSI:NMR A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result. MS_1000899 NMR NMR:1000900 minimum information standard A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result. MSI:NMR A file that has two or more columns of tabular data where each column is separated by a TAB character. NMR NMR:1000914 tab delimited text file A file that has two or more columns of tabular data where each column is separated by a TAB character. MSI:NMR Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation. value-type:xsd:string NMR NMR:1000933 protein modification Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Name of the gene from which the protein is translated. value-type:xsd:string NMR NMR:1000934 gene name Name of the gene from which the protein is translated. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Type of the source file, the nmrIdentML was created from. NMR NMR:1001040 intermediate analysis format Type of the source file, the nmrIdentML was created from. MSI:MI Source file for this nmrIdentML was a data set in a database. NMR NMR:1001107 data stored in database retire? Consider: "NMR database format" ? Source file for this nmrIdentML was a data set in a database. MSI:MI NMR NMR:1001267 software vendor value-type:xsd:string NMR NMR:1001268 programmer value-type:xsd:string The allowed value-type for this CV term. value-type:xsd:string NMR NMR:1001269 instrument vendor value-type:xsd:string The allowed value-type for this CV term. value-type:xsd:string NMR NMR:1001270 lab personnel value-type:xsd:string The allowed value-type for this CV term. NMR NMR:1001271 researcher Analysis software. NMR NMR:1001456 analysis software Analysis software. MSI:NMR Conversion software. NMR NMR:1001457 data processing software Conversion software. MSI:NMR Format of data files. NMR NMR:1001459 data file format Format of data files. MSI:NMR Phone number of the contact person or organization. value-type:xsd:string NMR NMR:1001755 contact phone number Phone number of the contact person or organization. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Fax number for the contact person or organization. value-type:xsd:string NMR NMR:1001756 contact fax number Fax number for the contact person or organization. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Toll-free phone number of the contact person or organization. value-type:xsd:string NMR NMR:1001757 contact toll-free phone number Toll-free phone number of the contact person or organization. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. DOI unique identifier. value-type:xsd:string NMR NMR:1001922 Digital Object Identifier (DOI) DOI unique identifier. MSI:MI value-type:xsd:string The allowed value-type for this CV term. Free text attribute that can enrich the information about an entity. value-type:xsd:string NMR NMR:1001923 external reference keyword Free text attribute that can enrich the information about an entity. MSI:MI value-type:xsd:string The allowed value-type for this CV term. Keyword present in a scientific publication. value-type:xsd:string NMR NMR:1001924 journal article keyword Keyword present in a scientific publication. MSI:MI value-type:xsd:string The allowed value-type for this CV term. Keyword assigned by the data submitter. value-type:xsd:string NMR NMR:1001925 submitter keyword Keyword assigned by the data submitter. MSI:MI value-type:xsd:string The allowed value-type for this CV term. Keyword assigned by a data curator. value-type:xsd:string NMR NMR:1001926 curator keyword Keyword assigned by a data curator. MSI:MI value-type:xsd:string The allowed value-type for this CV term. Parameters used in the NMR spectrometry acquisition. value-type:xsd:string NMR NMR:1001954 NMR acquisition parameter Parameters used in the NMR spectrometry acquisition. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. A unique identifier for a metabolite in the HMDB database (HMDB00001). value-type:xsd:integer NMR NMR:1002000 HMDB identifier A unique identifier for a metabolite in the HMDB database (HMDB00001). MSI:NMR value-type:xsd:integer The allowed value-type for this CV term. Chenomx software for data acquisition and analysis. NMR NMR:1002001 Chenomx software Chenomx software for data acquisition and analysis. MSI:NMR Chenomx software for data analysis. http://www.chenomx.com/software/ NMR NMR:1002002 Chenomx NMR Suite software Chenomx software for data analysis. MSI:NMR file=xsd:IDREF. NMR NMR:1002003 The nativeID must be the same as the source file ID. Varian FID format file=xsd:IDREF. MSI:NMR The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. NMR NMR:1002004 NMR spectrometer file format The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. MSI:NMR Simple text file of peaks. NMR NMR:1002005 text file Simple text file of peaks. MSI:PI Parameter file used to configure the acquisition of raw data on the instrument. NMR NMR:1002006 acquisition parameter file Parameter file used to configure the acquisition of raw data on the instrument. MSI:NMR tempdef: A frequency sorted array of the NMR signal frequency components. Nuclei with different resonance frequencies will show up as peaks at different corresponding frequencies in the spectrum, or 'lines'. def: A NMR spectrum is a set of chemical shifts representing a chemical analysis. synonym: NMR spectrum as designated Experiment type on http://www.bmrb.wisc.edu/tools/choose_pulse_info.php NMR NMR:1002007 NMR spectrum Conversion of a file format to Metabolomics Standards Initiative nmrData file format. NMR NMR:1002008 Conversion to nmrML Conversion of a file format to Metabolomics Standards Initiative nmrData file format. MSI:NMR Conversion of a file format to JCAMP-DX file format. NMR NMR:1002009 Conversion to JCAMP-DX Conversion of a file format to JCAMP-DX file format. MSI:NMR value-type:xsd:string NMR NMR:1002010 NMR solvent information value-type:xsd:string The allowed value-type for this CV term. pH. value-type:xsd:string NMR NMR:1002011 pH pH. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Chemical shift reference is a run attribute to designate the parts-per-million value of the peak used to reference a spectrum. It points to a fix chemical shift number, for examples 0 ppm for DSS or TSP. It can also have a calculated concentration, for examples 0.1 mM. https://github.com/nmrML/nmrML/issues/29#issue value-type:xsd:string NMR NMR:1002013 chemical shift reference Chemical shift reference is a run attribute to designate the parts-per-million value of the peak used to reference a spectrum. It points to a fix chemical shift number, for examples 0 ppm for DSS or TSP. It can also have a calculated concentration, for examples 0.1 mM. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. A bin for a spectrum. value-type:xsd:string bucketed spectrum descriptor NMR NMR:1002014 binned spectrum descriptor A bin for a spectrum. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Bin label. value-type:xsd:string NMR NMR:1002015 bin label Bin label. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. Bin start. value-type:xsd:decimal NMR NMR:1002016 bin start Bin start. MSI:NMR value-type:xsd:decimal The allowed value-type for this CV term. Bin end. value-type:xsd:decimal NMR NMR:1002017 bin end Bin end. MSI:NMR value-type:xsd:decimal The allowed value-type for this CV term. Bin area. value-type:xsd:decimal NMR NMR:1002018 bin area Bin area. MSI:NMR value-type:xsd:decimal The allowed value-type for this CV term. Name of metabolite. value-type:xsd:string NMR NMR:1002020 assigned chemical compound name Name of metabolite. MSI:NMR value-type:xsd:string The allowed value-type for this CV term. value-type:xsd:decimal NMR NMR:1002021 assigned chemical compound concentration value-type:xsd:decimal The allowed value-type for this CV term. Hilbert transformation based scaling def: Part of an NMR instrument which is not cardinally important and hence optional / facultative for the proper intended function of the instrument. synonym: optional part of NMR instrument clsdel: ontologically there is no such universal which characteristic is a possible (!) state of being a part of something... optional part of NMR instrument TODO: Discuss "obligatory_part_of". def: An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. altdef: The autosampler is an automatic sample changer. autosampler http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm multiplicity multiplicity feature tempdef: The data matrix a spectrum consists of can be projected from a higher dimension onto a lower dimension, e.g. a 3D NMR spectrum can be converted (projected) into a 2D NMR spectrum. defprov: Daniel Schober projected spectrum binned spectrum def: A post-processed NMR spectrum in which the y-values of the datapoints have been summed based on periodic ranges of the x-axis values. bucketed spectrum TODO: has spectral post processing parameter defneed peak-picked spectrum TODO: has spectral post processing parameter. def: A part of an NMR instrument which is cardinally important and hence obligatory and compulsatory for the proper intended function of the instrument. synonym: cardinal part of NMR instrument cardinal part of NMR instrument def: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. acquisition computer def: Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile “single point of failure” that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency. altdef: The instrument that transmits and recieves radiofrequency to and from the NMR sample. NMR probe def: A component of an NMR instrument that controls the activities of the other components. console TODO: same as or part of acquisition computer? tempdef: The number of data points in a data set. number of acquisition data points def: A frequency used during Hadamard encoding. hadamard frequency def: The axis onto which the spectrum was projected. projection axis 90 degree pulse duration ninety degree pulse duration The duration of the excitation pulse needed to rotate the magnetisation vector by 90 degrees. def: A digital sampling interval. alsprcls: time interval dwell time def: The temperature of an item of analysis material whilst in an autosampler. sample temperature in autosampler def: The temperature of an NMR sample whilst in the magnet of an NMR instrument. sample temperature in magnet def: The frequency of the RF radiation used to irradiate an NMR sample. irradiation frequency def: The intensity of an electric, magnetic, or other field. field strength def: The rate at which an item of analysis material is spun. spinning rate def: An indication of whether the nucleus being studied is the acquitsition nucleus. decoupled nucleus flag def: A compound added to a sample to alter its pH value. buffer information reference compound reference standard def: The compound that produced the peak used to reference a spectrum during data pre-processing. calibration compound http://www.nmrnotes.org/NMRPages/refcomps.html https://github.com/nmrML/nmrML/issues/31 https://github.com/nmrML/nmrML/issues/33 chemical shift reference compound def: A compound that is added to an NMR sample to enable the alignment of spectra. The power of NMR is that for most nuclei the NMR frequency changes very slightly with different molecular environment or chemical bonding. These shifts are very small, on the order of 1 part in 10+9. This is referred to as "Chemical Shift." Tables of chemical shifts are tabulated and used to determine molecular structure. Combining NMR chemical shift information with other NMR information such as peak integration, coupling constants and Nuclear Overhauser Enhancement (NOE) can result in complete three-dimensional molecular structures of molecules in solution without using X-ray crystallography. chemical shift standard def: The compound that produced a peak that is measured to assess the quality of a data set. quality check compound signal http://www.bmrb.wisc.edu/tools/choose_pulse_info.php https://github.com/nmrML/nmrML/issues/40 def: A sequence of excitation pulses. NMR pulse sequence May later import from http://purl.obolibrary.org/obo/CHMO_0001841 See also http://www.jcamp-dx.org/protocols/NMR%20Pulse%20Sequences%20PAC%2079(11)%20pp1748-1764%202001.pdf nmr-spectrum data processing post-FT data processing def: Automatic or manual procedures performed upon pre-processed NMR data sets that aim to summarise them or annotate them with speculative values. frequency domain data processing pre-FT data processing def: The post acquisition process of producing or refining a spectrum from raw data. defprov: Daniel Schober time domain data processing def: A data transformation that converts an NMR input data set into an output data set in a tracable and useful manner. NMR data processing tempdef: A non FT based method for converting from the time to the frequency domain. non-fourier FID transformation TODO:Exclusion guided definition. https://github.com/nmrML/nmrML/issues/37 tempdef: A data processing which alteres a data file for a specific purpose. defprov: Daniel Schober data encoding tempdef:GFT NMR allows for rapid multidimensional FT NMR spectral information gathering, avoiding sampling limitations without compromising on the precision of chemicalshift. defprov: ttp://www.nsm.buffalo.edu/Research/GFT/szyperski_publications_1st_page/Szyperski%2067.pdf synonym: GFT-projection G matrix fourier transform projection defneed synonym: TPPI time proportional phase incrementation def: A method for quadrature detection. synonym: S-TPPI states-time proportional phase incrementation defneed Hadamard encoding http://www.magnet.fsu.edu/library/publications/NHMFL_Publication-6859.pdf defneed Frydman encoding defneed echo anti-echo coherence selection def: An Instrument which is used to carry out a NMR analysis of some sample. synonym: NMR instrument NMR instrument def: The list of parameters that describe the instrument settings used for the acquisition of a spectrum. altdef: The set of variables dependent on a given pulse sequence that will be optimised in order to acquire a spectrum. synonym: NMR instrument acquisition parameter set NMR instrument acquisition parameter set Philippe Rocca Serra http://pubs.acs.org/doi/pdf/10.1021/ac0519312 10.1021/ac0519312 Scaling and Normalization Effects in NMR Spectroscopic Metabonomic Data Sets Andrew Craig , Olivier Cloarec , Elaine Holmes , Jeremy K. Nicholson , and John C. Lindon * Biological Chemistry, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ U.K. http://stats.stackexchange.com/questions/35591/normalization-vs-scaling normalisation normalization is a data transformation process which aims at making data seem roughly normally distributied by applying a mathematical function, which is most of time a continuous function. This is a row operation that is applied to the data from each sample and comprises methods to make the data from all samples directly comparable with each other. A common use is to remove or minimize the effects of variable dilution of the samples. tempdef: A technique used to suppress the water resonance peak in a spectrum. Suppression of the strong solvent signal is necessary in order to obtain high signal to noise for the peaks of the sample under investiogation, e.g. protein peaks. defprov: Daniel Schober pre-acquisition water suppression A function applied to a FID to increase the signal-to-noise ratio or the resolution. http://www.uwyo.edu/wheelernmr/nmr/window_functions.pdf https://github.com/nmrML/nmrML/issues/39 https://github.com/nmrML/nmrML/issues/67 apodization function window function for apodization The exponential function used to multiply a FID by to produce a desitred amount of line broadening. exponential apodization Functional form: em(x_i) = exp(-pi*i*lb) Parameters: * data Array of spectral data. * lp Exponential line broadening. * inv Set True for inverse apodization. exponential multiplication window function gaussian broadening defneed Gaussian window function sine sine bell window function defneed sine window function QSINE defneed sine squared window def: A method for eliminating or reducing the noise in a spectrum. spectral denoising def: A method of flattening the baseline of a spectrum. baseline correction A method of spectral projection. spectral projection defneed maximum intensity projection def: .A projection method that sums the intensities of a pre-processed 2D J-resolved NMR spectrum to obtain a projected spectrum. altdef: The adding of spectra together to produce a composite avergaed spectrum. summation projection def: A parameter used to mix real and imaginary part of an NMR spectrum that the real part of the spectrum is in pure absorption mode. altdef: The number of degrees that a central peak must be moved in order to achieve an absorptive mode line width. zero order phase correction defneed first order phase correction defneed symmetrisation def: The nucleus of an element or isotope that is being studied during an NMR analysis. Common NMR requirements include direct 1D and 2D proton-only NMR, direct observation of 13C NMR with 1H decoupling, direct observation of other nuclei such as 19F, 31P, 29Si, 31P, 27Al, and 15N (with or without 1H decoupling), triple resonance NMR (especially inverse triple resonance such as 1H observe, 13C and 15N decouple), and inverse 2D and 3D experiments such as HMQC and HMBC. acquisition nucleus def: A feature of a peak that is measured to assess the quality of a data set. quality check peak feature def: The number of repeat scans performed and summed to create the data set for an NMR sample. number of scans def: The number of scans whose data is not summed to create the data set for an NMR sample, but that are carried out to establish the steady-state of relaxation for the nuclei. number of steady state scans def: A scheme for producing a numerical representation of the environment of an atom. atom environment encoding def: The delay between repeat scans to allow nuclei to relax back to their steady state. relaxation delay def: The units of measure for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. altdef: The units used to represent either time domain (for a FID) or the frequency domain (for a spectrum). x-axis unit defneed y-axis unit def: The unit of measurement of the second dimension of a 2D NMR dataset. additional axis unit def: The starting value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. altdef: The initial time or frequency a FID or spectrum is recorded from. x start value tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. x end value def: A parameter to a window function. window function parameter Philippe Rocca-Serra http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. Hans J. Reich 2015, University of Wisconsin defneed line broadening line broadening is a process resulting in spectral peak signal becoming hard to interpret and analysed. Line broadening is affected by spin-spin relaxation and/or spin-lattice relaxation processes. When relaxation is very fast, NMR lines are broad, J-coupling may not be resolved or the signal may even be difficult or impossible to detect. The maximum repetition rate during acquisition of an NMR signal is governed by T1 - short T1 means the magnetization recovers more rapidly, and a spectrum can be acquired in less time. Line broadening may be caused by: Sample inhomogeneity (poor mixing. solid particles), Temperature gradients across sample, Paramagnetic impurities. Philippe Rocca-Serra http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. Hans J. Reich 2015, University of Wisconsin defneed line sharpening line sharpening is a data transformation process inverse to that of line broadening, which aims to improve the quality of the signal being acquired and being analyzed in order to obtain clear, sharp peaks, in turn making interpretation easier. Line sharpening can be optimized during data acquisition or performed during data analysis by applied digital processing and filtering. defneed parameter def: The data processing parameters that describe a method of translating a 2D NMR pre-processed spectrum into a 1D NMR spectrum. synonym: NMR spectral projection parameter set NMR spectral projection parameter set def: A description of the post-processing strategy used to convert a pre-processed NMR spectrum into a suitable data format for chemometric analysis. synonym: NMR spectrum post-processing parameter set NMR data post-processing parameter set TODO: altsprcls: process, not clear wether set is plural (list) or process. tempdef: A nuclear magnetic resonance spectroscopy quality check parameter set is a parameter set used for the quality check method for an NMR analysis synonym: NMR quality check parameter set NMR quality check parameter set excitation sculpting tempdef: A data processing technique used to suppress the water peak in a spectrum in order to get clearer results. defprov: Daniel Schober post-acquisition water suppression def: This Method removes the residual water and its side lobes, thereby reducing the baseline for the metabolites of interest and allowing subsequent data analysis using more sophisticated nonlinear least squares algorithms. synonym: HSVD hankel singular value decomposition defneed convolution defneed polynomial fitting def: A computational method that archieves water suppression via wavlet multi resolution analysis. WaveWat defneed synonym: NMR data pre-processing parameter set NMR data pre-processing parameter set def: The process of ensuring the quality of the raw data that results from an NMR analysis. synonym: NMR quality check NMR quality check def: A reference is a label which refers to data elsewhere, as opposed to containing the data itself. Accessing the value that a reference refers to is called dereferencing it. References are fundamental in constructing many data structures and in exchanging information between different parts of programs and databases. reference FID file reference def: A reference to a file containing the raw FID. synonym: FID file reference FID file def: A reference to a description of a pulse sequence in the literature. pulse sequence literature reference def: A reference to a file containing a specfication of the shape of an excitation pulse. shaped pulse file def: A reference to a file containing a specification of a pulse sequence. pulse sequence file def: A reference to a file of data pre-processing parameters produced by the machine. processing parameter file PRS: rename 'reference' to 'identifier' def: A reference to information on the provenance of the NMR sample. synonym: NMR sample reference NMR sample identifier def: A result of an NMR quality check. synonym: NMR quality check result NMR quality check descriptor def: A sample that has been prepared for chemical analysis by NMR. NMR samples are usually liquid solutions contained in glass tubes. NMR solution sample volume ranges from 50ul to 5ml depending on the NMR probe. Sample concentrations of solute for 1H NMR are usually in the range of 100ug to 5g, with 10 to 50mg being typical. NMR is not a chemical trace analysis technique. The NMR signal of solids and gases can be recorded but to measure solid-state NMR additional specialized hardware is required. synonym: NMR sample NMR sample tempdef: A sample introduction parameter is a parameter that describes the particular method of introducing the sample under investigation into the NMR instrument. sample introduction parameter defneed synonym: MAS rotor magic angle spinning rotor defneed flow probe The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter. http://en.wikipedia.org/wiki/NMR_tube https://github.com/nmrML/nmrML/issues/54 sample tube sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID NMR sample tube def: A software artifact used during data pre-processing. spectrum pre-processing software def: A software artifact used during spectral post-processing. spectrum post-processing software defneed peak picking binning def: A post-processing method that divides a pre-processed NMR spectrum into a series of buckets (or bins) along the x-axis, and then integrates the spectral intensity within each bucket. altdef: A type of automated integration which occurs across pre-defined regions for a spectrum. for bucket parameters see 'binned spectrum descriptor' bucketing Taking advantage of the concentration variability of each compound in a series of samples, buckets are linked together into clusters based on significant correlations.This is done i.g. in ERVA-based bucketing presaturation of the solvent resonance defneed synonym: presaturation presat pulse sequence tempdef: An improved water-suppression technique called WET (water suppression enhanced through T1 effects), developed from a Bloch equation analysis of the longitudinal magnetization over the T1 and B1 ranges of interest, achieves T1- and B1-insensitive suppression with four RF pulses, each having a numerically optimized flip angle. Once flip angles have been optimized for a given sequence, time-consuming flip-angle adjustments during clinical examinations are eliminated. defprov: Daniel Schober synonym: WET water suppression enhanced through T1 effects WET NOESY presat tempdef: The presat for an nuclear overhauser and exchange spectroscopy experiment. A 2D method used to map NOE correlations between protons within a molecule. The nuclear Overhauser effect (NOE) causes changes in peak areas, as a secondary effect of decoupling. defprov: Daniel Schober synonym: NOESY-presat nuclear overhauser and exchange spectroscopy-presat defneed watergate tempdef: A water suppression method which is used to suppress the natural water signal in a gradient selection experiment (e.g. echo/antiecho), where the water coherence is not "refocused" by the refocus gradient (therefore, is not selected). defprov: Daniel Schober coherence pathway rejection defneed flip-back watergate tempdef: A jump and return pulse sequence method is a water suppression method that uses a defined pulse sequence to make fast exchanging protons visible. jump and return pulse sequence tempdef: A jump and return 1-1 pulse sequence method is a jump and return method that uses one 90 degree pulse and one 90 degree return puls to make fast exchanging protons visible, first described by Plateau,P. and Gueron,M. (1982) J. Am. Chem. Soc., 104, 7310–7311. Compared to the 1-3-3-1 method it has a lower receiver gain and the dispersive tail of water interferes with the signals of interest. jump and return 1-1 tempdef:A jump and return 1-3-3-1 pulse sequence method is a jump and return method that uses a 1-3-3-1 pulse sequence to make fast exchanging protons visible. Compared to the 1-1 method it has better water suppression (higher receiver gain) capabilities, but with offset-dependent phase distortion (unsuitable for 2D). jump and return 1-3-3-1 defneed synonym: 1D spectrum 1D spectrum defneed synonym: 2D spectrum 2D spectrum defneed synonym: 1D NMR acquisition parameter set 1D NMR acquisition parameter set defneed synonym: 2D NMR acquisition parameter set 2D NMR acquisition parameter set tempdef: A modification of Carr-Purcell RF pulse sequence with 90° phase shift in the rotating frame of reference between the 90° pulse and the subsequent 180° pulses to reduce accumulating effects of imperfections in the 180° pulses. Suppression of effects of pulse error accumulation can alternatively be achieved by alternating phases of the 180° pulses by 180°. defprov: Daniel Schober synonym: 1D CPMG carr purcell meiboom gill pulse sequence CPMG TCOSY pulse sequence tempdef: Total Correlation Spectroscopy. A 2D homonuclear correlation experiment used to analyse scalar (J) coupling networks between protons. TOCSY is able to relay magnetisation between spins, A-B-C-D.., and can therefore show correlations amongst spins that are not directly coupled (eg A-C and A-D) but exist within the same spin system. defprov: Daniel Schober synonym:2D TOCSY pulse sequence total correlation spectroscopy pulse sequence def: One dimensional (referring to a FID, pre-processed spectrum, or post-processed spectrum). synonym: 1D 1D pulse sequence tempdef: In 1D NMR, as the multiplets from different chemically shifted nuclei overlap, spectral assignments become too difficult. In order to resolve the chemical shift and spin-spin coupling parameters along the different axis, 2D and 3D J-resolved NMR spectroscopies are used. defprov: Daniel Schober synonym: 2D J-resolved J-resolved pulse sequence defneed synonym: 2D hadamard TOCSY hadamard total correlation spectroscopy pulse sequence defneed synonym: 1D diffusion edited diffusion edited pulse sequence def: A magnet which induces a certain frequency (MHz) and which has a certain bore diameter. altdef: The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. NMR magnet defneed Bruker NMR magnet defneed UltraShield Ultrastabilized US 2 ??? How to model "hoch 2"? UltraShield Plus def: The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis: Significant S/N gains (with moderately salty samples also) Short pulse widths Short ring down times Linear behavior in power response Gradient capability CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher All high resolution probes have a lock circuit All high resolution probes have Z-gradient defprov: Bruker website Bruker CryoProbe def: Samples that are neither solid nor liquid, being of biological, chemical, and/or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Bruker’s high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject/insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g., 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. defprov: Bruker website altdef: High resolution MAS (hr-MAS) provides an easy means of obtaining high resolution spectra for a variety of samples that would otherwise result in poorly resolved spectra. The addition of an hr-MAS probe and a MAS pneumatic unit to a standard high resolution spectrometer is all that is needed to open the gate to the world of hr-MAS spectroscopy and gain access to a vast amount of highly interesting samples. synonyms: High resolution MAS, hr-MAS high resolution magic angle spin probe def: Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. defprov: Bruker website synonym: solid MAS probe solid magic angle spinning probe def: Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include: up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount) excellent solvent suppression properties virtually no salt effect discrete samples in tubes that can be sealed and stored automation accessory for sample preparation and handling available defprov: Bruker website 1mm MicroProbe def: Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. defprov: Bruker website synonym: flow HR-probe flow high resolution probe defneed NMR instrument parameter set defneed AVANCE II spectrometer TODO: May need no definition defneed Bruker NMR instrument https://www.bruker.com/de/products/mr/nmr.html For metabolism studies, and analysis of complex mixtures. Metabolic Profiler instrument NMR Instruments using hyphenated analytical techniques combining mass spectrometry and chromatograph. Hyphenated NMR instrument Capillary LC-NMR def: The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. defprov: Bruker website NMR Case defneed NMR tube washing system def: In today's fast-paced research environment, NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean™ system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. defprov: Bruker website Bruker AutoClean def: The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. defprov: Bruker website synonym: Bruker Efficient Sample Transfer NMR Bruker BEST NMR def: This system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back defprov: website SampleRail def: Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation. The SampleJet utilizes the modern-day industry standard for sample arrangements—the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. defprov: Bruker website SampleJet defneed Bruker autosampler def: The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. defprov: Bruker website B-ACS def: The Bruker Multiple Adjustable Tube Clamp Holder MATCH™ system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications. The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. defprov: Bruker website synonym: Bruker Multiple Adjustable Tube Clamp Holder Bruker MATCH def: A NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the NMR sample. NMR sample holder defneed NMR software defneed Bruker NMR software TODO: May need no definition. Bruker TopSpin software SampleTrack software Paravision software AURELIA software AUREMOL software AMIX VIEWER & AMIX-TOOLS def:BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. defprov: Bruker website synonym: HR Probe high resolution probe def: The ATM option for AVANCE spectrometers is available for: Double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90° pulsewidths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. defprov: Bruker website synonym: High Resolution Probes with Automatic Tuning and Matching, HR probe with ATM high resolution probe with ATM defneed micro imaging probe JEOL NMR instrument JNM-ECX Series FT NMR instrument The JNM-ECX series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials. JNM-ECA Series FT NMR instrument The JNM-ECA series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials. JEOL NMR software Delta NMR software https://www.bruker.com/products/mr/nmr/probes/probes.html Bruker NMR probe defneed JEOL NMR probe CapNMR probe Varian NMR instrument Varian MERCURY Varian INOVA Varian UNITY Varian VXR Varian GEMINI AMX instrument AC instrument liquid NMR probe defneed solid NMR probe defneed NMR imaging probe tecmag console def: The Discovery™ is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network defprov: tecmag website DISCOVERY console def: The Eagle™ is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz widebore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. defprov: website tecmag EAGLE probe defneed APOLLO console tecmag NMR instrument CAT defneed magnetic field strength defneed vendor TODO: Belongs in Ref Ontol. A manufacturer that produces (and eventually sells) NMR instruments. NMR instrument manufacturer defneed Bruker TODO: May not need definition due to its instance character. Varian JEOL MR Resources tecmag def: In some cases, it is necessary or advisable to control the temperature of the sample at some value other than ambient. The sample may be only slightly solubility at room temperatures, or it may be desirable to control some aspect of the dynamics of the system. In such cases, a default temperature, or some means of selecting this parameter, can be built into the experiment. sample temperature information Doty Scientific Wilmad JS Research data file file Any data file as generated by some acquisition computer or console. This is a class annotation exemplifying skos usage. We assume the rdfs:label to capture the skos:preferedLabel. an FID raw data file In the NMR case a file generated by an NMR acquisition computer, console or NMR processing software. Acorn NMR Inc LC NMR liquid chromatography NMR Includes the connection to a high-resolution TOF-LC-MS system. LC MS NMR SPE NMR A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE™ NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra. solid phase extraction NMR Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. Capillary LC-NMR direct detection probe indirect detection probe Continuous wave NMR spectrometers are similar in principle to optical spectrometers. The sample is held in a strong magnetic field, and the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm continuous wave NMR In FT-NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm fourier transformation NMR instrument NMR software data format ChemMagnetics format GE Omega format JEOL Lambda format JEOL Alpha format Jeol Delta format JEOL generic format JEOL AL95 format JEOL EX format TecMag format Varian VNMR format Galactic format Felix format JCAMP DX format Lybrics format Nuts format MACNMR format Nicolet GE/QE-300 format m J-coupler multiplet feature ThermoMattson FOSS Jasco Agilent Technologies micromass Waters ThermoNicolet Perkin Elmer OceanOptics ThermoFinnigan Applied Biosystems TX Net CDF format Bruker DISNMR format Bruker UXNMR/XWIN-NMR format Bruker WIN NMR format acdlabs entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000015 process process 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]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &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]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant 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]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. 0 H2O InChI=1S/H2O/h1H2 XLYOFNOQVPJJNP-UHFFFAOYSA-N 18.01530 18.011 [H]O[H] CHEBI:10743 CHEBI:13352 CHEBI:27313 CHEBI:42043 CHEBI:42857 CHEBI:43228 CHEBI:44292 CHEBI:44701 CHEBI:44819 CHEBI:5585 Beilstein:3587155 CAS:7732-18-5 Gmelin:117 HMDB:HMDB0002111 KEGG:C00001 KEGG:D00001 MetaCyc:WATER MolBase:1 PDBeChem:HOH PDBeChem:MTO Reaxys:3587155 Wikipedia:Water WATER Water oxidane water chebi_ontology BOUND WATER H2O HOH Wasser [OH2] acqua agua aqua dihydridooxygen dihydrogen oxide eau hydrogen hydroxide CHEBI:15377 water An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. 0 C10H16N2O3S InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1 YBJHBAHKTGYVGT-ZKWXMUAHSA-N 244.31172 244.088 [H][C@]12CS[C@@H](CCCCC(O)=O)[C@@]1([H])NC(=O)N2 CHEBI:13905 CHEBI:22882 CHEBI:22884 CHEBI:3108 CHEBI:41236 Beilstein:86838 CAS:58-85-5 COMe:MOL000144 DrugBank:DB00121 Drug_Central:373 Gmelin:1918703 HMDB:HMDB0000030 KEGG:C00120 KEGG:D00029 KNApSAcK:C00000756 LINCS:LSM-3994 MetaCyc:BIOTIN PDBeChem:BTN PMID:11435506 PMID:11800048 PMID:12055344 PMID:12803839 PMID:15012185 PMID:15202718 PMID:15272000 PMID:15899401 PMID:16419467 PMID:16676358 PMID:16677798 PMID:16769720 PMID:17297119 PMID:18452485 PMID:18509457 PMID:19319844 PMID:19727438 PMID:19928962 PMID:20967359 PMID:20974274 PMID:21248194 PMID:21356565 PMID:21373679 PMID:21596550 PMID:21871906 PMID:25515858 Reaxys:86838 Wikipedia:Biotin 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid BIOTIN Biotin chebi_ontology (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-valeric acid 5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid Coenzyme R D-(+)-biotin D-Biotin Vitamin H biotina biotine biotinum cis-(+)-Tetrahydro-2-oxothieno[3,4]imidazoline-4-valeric acid cis-Hexahydro-2-oxo-1H-thieno(3,4)imidazole-4-valeric acid cis-Tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid vitamin B7 CHEBI:15956 biotin An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. 0 H3N InChI=1S/H3N/h1H3 QGZKDVFQNNGYKY-UHFFFAOYSA-N 17.03056 17.027 [H]N([H])[H] CHEBI:13405 CHEBI:13406 CHEBI:13407 CHEBI:13771 CHEBI:22533 CHEBI:44269 CHEBI:44284 CHEBI:44404 CHEBI:7434 Beilstein:3587154 CAS:7664-41-7 Drug_Central:4625 Gmelin:79 HMDB:HMDB0000051 KEGG:C00014 KEGG:D02916 KNApSAcK:C00007267 MetaCyc:AMMONIA MolBase:930 PDBeChem:NH3 PMID:110589 PMID:11139349 PMID:11540049 PMID:11746427 PMID:11783653 PMID:13753780 PMID:14663195 PMID:15092448 PMID:15094021 PMID:15554424 PMID:15969015 PMID:16008360 PMID:16050680 PMID:16348008 PMID:16349403 PMID:16614889 PMID:16664306 PMID:16842901 PMID:17025297 PMID:17439666 PMID:17569513 PMID:17737668 PMID:18670398 PMID:22002069 PMID:22081570 PMID:22088435 PMID:22100291 PMID:22130175 PMID:22150211 PMID:22240068 PMID:22290316 PMID:22342082 PMID:22385337 PMID:22443779 PMID:22560242 Reaxys:3587154 Wikipedia:Ammonia AMMONIA Ammonia ammonia azane chebi_ontology Ammoniak NH3 R-717 [NH3] ammoniac amoniaco spirit of hartshorn CHEBI:16134 ammonia An azaarene comprising a benzene core in which one -CH group is replaced by a nitrogen atom. It is the parent compound of the class pyridines. 0 C5H5N InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N 79.09990 79.042 c1ccncc1 CHEBI:14974 CHEBI:26415 CHEBI:8662 Beilstein:103233 CAS:110-86-1 Gmelin:1996 HMDB:HMDB0000926 KEGG:C00747 PDBeChem:0PY PMID:24364496 PMID:24425539 PMID:8070089 Reaxys:103233 Wikipedia:Pyridine Pyridine pyridine chebi_ontology Azabenzene py CHEBI:16227 pyridine peptide 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 A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. 0 C4H7N3O InChI=1S/C4H7N3O/c1-7-2-3(8)6-4(7)5/h2H2,1H3,(H2,5,6,8) DDRJAANPRJIHGJ-UHFFFAOYSA-N 113.11800 113.059 CN1CC(=O)NC1=N CHEBI:14029 CHEBI:23406 CHEBI:3910 CAS:60-27-5 HMDB:HMDB0000562 KEGG:C00791 KEGG:D03600 MetaCyc:CREATININE PMID:11256540 PMID:11981083 PMID:17190852 PMID:17422601 PMID:18182718 PMID:19236048 PMID:19715855 PMID:19968328 PMID:21775764 PMID:22047975 PMID:22121923 PMID:22166252 PMID:22207347 PMID:22212624 PMID:22223530 PMID:22331238 PMID:22338083 PMID:22349552 PMID:22390548 PMID:22432114 PMID:22441184 PMID:22459582 PMID:22498455 Reaxys:112064 Wikipedia:Creatinine 2-imino-1-methylimidazolidin-4-one Creatinine creatinine chebi_ontology 1-Methylglycocyamidine 1-Methylhydantoin-2-imide 1-methylglycocyamidine 2-Amino-1-methylimidazolin-4-one 2-amino-1,5-dihydro-1-methyl-4H-Imidazol-4-one Creatine anhydride Kreatinin creatinina CHEBI:16737 creatinine deoxyribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. CHEBI:13302 CHEBI:21123 CHEBI:33698 CHEBI:4291 CAS:9007-49-2 KEGG:C00039 Deoxyribonucleic acid deoxyribonucleic acids chebi_ontology (Deoxyribonucleotide)m (Deoxyribonucleotide)n (Deoxyribonucleotide)n+m DNA DNAn DNAn+1 DNS Desoxyribonukleinsaeure deoxyribonucleic acids desoxyribose nucleic acid thymus nucleic acid CHEBI:16991 deoxyribonucleic acid -1 HO3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-1 LSNNMFCWUKXFEE-UHFFFAOYSA-M 81.07214 80.965 OS([O-])=O CHEBI:13367 CHEBI:5598 CAS:15181-46-1 Gmelin:1455 KEGG:C11481 PDBeChem:SO3 hydrogen(trioxidosulfate)(1-) hydrogensulfite(1-) hydrogentrioxosulfate(1-) hydrogentrioxosulfate(IV) hydroxidodioxidosulfate(1-) monohydrogentrioxosulfate chebi_ontology Bisulfite HSO3(-) HSO3- Hydrogen sulfite [SO2(OH)](-) bisulfite bisulphite hydrogen sulfite(1-) hydrosulfite anion CHEBI:17137 hydrogensulfite '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. CHEBI:14517 CHEBI:25054 CHEBI:6486 KEGG:C01356 Lipid lipids chebi_ontology CHEBI:18059 lipid 0 Cl InChI=1S/Cl ZAMOUSCENKQFHK-UHFFFAOYSA-N 35.45270 34.969 [Cl] WebElements:Cl chlorine chebi_ontology 17Cl Chlor Cl chlore chlorine chlorum cloro CHEBI:23116 chlorine atom molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function CHEBI:24432 biological role Any lipid formally derived from isoprene (2-methylbuta-1,3-diene), the skeleton of which can generally be discerned in repeated occurrence in the molecule. The skeleton of isoprenoids may differ from strict additivity of isoprene units by loss or shift of a fragment, commonly a methyl group. The class includes both hydrocarbons and oxygenated derivatives. LIPID_MAPS_class:LMPR01 PMID:12769708 PMID:19219049 isoprenoid isoprenoids chebi_ontology isoprenoids CHEBI:24913 isoprenoid Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. CHEBI:26619 CHEBI:35220 metabolite chebi_ontology metabolites primary metabolites secondary metabolites CHEBI:25212 metabolite A phosphorus oxoacid that consits of one oxo and three hydroxy groups joined covalently to a central phosphorus atom. 0 H3O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N 97.99520 97.977 [H]OP(=O)(O[H])O[H] Beilstein:1921286 CAS:7664-38-2 Drug_Central:4478 Gmelin:2000 HMDB:HMDB0002142 KEGG:C00009 KEGG:D05467 KNApSAcK:C00007408 PMID:11455380 PMID:15630224 PMID:17439666 PMID:17518491 PMID:22282755 PMID:22333268 PMID:22381614 PMID:22401268 Reaxys:1921286 Wikipedia:Phosphoric_Acid Phosphoric acid phosphoric acid tetraoxophosphoric acid trihydrogen tetraoxophosphate(3-) trihydroxidooxidophosphorus chebi_ontology H3PO4 Orthophosphoric acid Phosphate Phosphorsaeure Phosphorsaeureloesungen [PO(OH)3] acide phosphorique acidum phosphoricum orthophosphoric acid CHEBI:26078 phosphoric acid 0 P InChI=1S/P OAICVXFJPJFONN-UHFFFAOYSA-N 30.97376 30.974 [P] CHEBI:26080 CHEBI:8168 CAS:7723-14-0 Gmelin:16235 KEGG:C06262 WebElements:P phosphorus chebi_ontology 15P P Phosphor Phosphorus fosforo phosphore phosphorus CHEBI:28659 phosphorus atom The stable isotope of hydrogen with relative atomic mass 1.007825 and a natural abundance of 99.9885 atom percent (from Greek pirhoomegatauomicronsigma, first). 0 H InChI=1S/H/i1+0 YZCKVEUIGOORGS-IGMARMGPSA-N 1.00783 1.008 [1H] protium chebi_ontology (1)1H (1)H hydrogen-1 protio protium CHEBI:29236 protium atom The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). 0 D InChI=1S/H2/h1H/i1+1 UFHFLCQGNIYNRP-OUBTZVSYSA-N 2.01410 [2H] deuterium chebi_ontology (2)1H (2)H D Deuterium deuterio deuterium heavy hydrogen hidrogeno pesado hydrogen-2 schwerer Wasserstoff CHEBI:29237 deuterium atom 0 C2H3NaO2 InChI=1S/C2H4O2.Na/c1-2(3)4;/h1H3,(H,3,4);/q;+1/p-1 VMHLLURERBWHNL-UHFFFAOYSA-M 82.03379 82.003 [Na+].CC([O-])=O Beilstein:3595639 CAS:127-09-3 Gmelin:20502 Wikipedia:Sodium_Acetate sodium acetate chebi_ontology Natriumazetat acetic acid, sodium salt anhydrous sodium acetate sodium acetate anhydrous CHEBI:32954 sodium acetate atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom nucleic acid 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 acids chebi_ontology NA Nukleinsaeure Nukleinsaeuren acide nucleique acides nucleiques acido nucleico acidos nucleicos CHEBI:33696 nucleic acid ribonucleic 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 The stable isotope of oxygen with relative atomic mass 16.999131. The least abundant (0.038 atom percent) isotope of naturally occurring oxygen. 0 O InChI=1S/O/i1+1 QVGXLLKOCUKJST-OUBTZVSYSA-N 16.99913 15.995 [17O] CAS:13968-48-4 Gmelin:17561 oxygen-17 chebi_ontology (17)8O (17)O oxygen, isotope of mass 17 oxygen-17 CHEBI:33819 oxygen-17 atom macromolecule 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. polymer macromolecule 0 C4H9NO InChI=1S/C4H9NO/c1-3-6-4-2-5-1/h5H,1-4H2 YNAVUWVOSKDBBP-UHFFFAOYSA-N 87.12040 87.068 C1COCCN1 Beilstein:102549 CAS:110-91-8 Gmelin:1803 KEGG:C14452 Morpholine morpholine chebi_ontology Tetrahydro-1,4-oxazine CHEBI:34856 morpholine A one-carbon compound that is methane in which three of the hydrogens are replaced by chlorines. 0 CHCl3 InChI=1S/CHCl3/c2-1(3)4/h1H HEDRZPFGACZZDS-UHFFFAOYSA-N 119.37674 117.914 [H]C(Cl)(Cl)Cl CHEBI:23143 CHEBI:34628 Beilstein:1731042 CAS:67-66-3 Drug_Central:4363 Gmelin:1837 HMDB:HMDB0029596 KEGG:C13827 LINCS:LSM-37229 MetaCyc:CPD-843 PDBeChem:MCH PMID:10379014 PMID:15583552 PMID:20051454 PMID:21850127 PMID:23093177 PMID:8476536 PMID:8625290 Reaxys:1731042 UM-BBD_compID:c0595 Wikipedia:Chloroform Chloroform chloroform chebi_ontology 1,1,1-trichloromethane CHCl3 Trichlormethan chloroforme chloroformium pro narcosi trichloromethane CHEBI:35255 chloroform 0 P4 InChI=1S/P4/c1-2-3(1)4(1)2 OBSZRRSYVTXPNB-UHFFFAOYSA-N 123.89505 123.895 p12p3p1p23 CAS:12185-10-3 Gmelin:1856 Gmelin:25827 [Td-(13)-Delta(4)-closo]tetraphosphorus tetrahedro-tetraphosphorus tetraphosphorus chebi_ontology P4 molecular phosphorus phosphorus phosphorus tetraatomic molecule phosphorus tetramer tetraatomic phosphorus tetrameric phosphorus white phosphorus CHEBI:35895 tetraphosphorus A phosphine oxide in which the substituents on phosphorus are three phenyl groups. 0 C18H15OP InChI=1S/C18H15OP/c19-20(16-10-4-1-5-11-16,17-12-6-2-7-13-17)18-14-8-3-9-15-18/h1-15H FIQMHBFVRAXMOP-UHFFFAOYSA-N 278.28486 278.086 O=P(c1ccccc1)(c1ccccc1)c1ccccc1 Beilstein:745854 CAS:791-28-6 Gmelin:6758 PMID:24280613 PMID:24285309 Reaxys:745854 Wikipedia:Triphenylphosphine_oxide triphenyl-lambda(5)-phosphanone triphenylphosphane oxide chebi_ontology Triphenylphosphanoxid triphenyl phosphine oxide triphenyl phosphorus oxide triphenylphosphanoxide triphenylphosphine oxide CHEBI:36601 triphenylphosphane oxide 0 C InChI=1S/C/i1+1 OKTJSMMVPCPJKN-OUBTZVSYSA-N 13.00335 12.000 [13C] CAS:14762-74-4 carbon-13 carbon-13 atom chebi_ontology (13)6C (13)C carbon, isotope of mass 13 carbon-13 CHEBI:36928 carbon-13 atom 0 C InChI=1S/C/i1+0 OKTJSMMVPCPJKN-IGMARMGPSA-N 12.00000 12.000 [12C] carbon-12 chebi_ontology (12)6C (12)C carbon-12 CHEBI:36931 carbon-12 atom The stable isotope of nitrogen with relative atomic mass 15.000109. The least abundant (0.368 atom percent) isotope of naturally occurring nitrogen. N CAS:14390-96-6 nitrogen-15 chebi_ontology (15)7N (15)N nitrogen, isotope of mass 15 nitrogen-15 CHEBI:36934 nitrogen-15 atom The stable isotope of nitrogen with relative atomic mass 14.003074. The most abundant (99.63 atom percent) isotope of naturally occurring nitrogen. N nitrogen-14 chebi_ontology (14)7N (14)N nitrogen-14 CHEBI:36938 nitrogen-14 atom The stable isotope of fluorine with relative atomic mass 18.998403 and nuclear spin (1)/2. 0 F InChI=1S/F/i1+0 YCKRFDGAMUMZLT-IGMARMGPSA-N 18.99840 18.998 [19F] fluorine-19 chebi_ontology (19)9F (19)F fluorine-19 CHEBI:36940 fluorine-19 atom The stable isotope of aluminium with relative atomic mass 26.98153 and nuclear spin (5)/2. 0 Al InChI=1S/Al/i1+0 XAGFODPZIPBFFR-IGMARMGPSA-N 26.98154 26.982 [27Al] aluminium-27 chebi_ontology (27)13Al (27)Al aluminium-27 aluminum, isotope of mass 27 aluminum-27 CHEBI:37968 aluminium-27 atom The stable isotope of phosphorus with relative atomic mass 30.973762 and nuclear spin (1)/2. 0 P InChI=1S/P/i1+0 OAICVXFJPJFONN-IGMARMGPSA-N 30.97376 30.974 [31P] phosphorus-31 chebi_ontology (31)15P (31)P phosphorus-31 CHEBI:37971 phosphorus-31 atom The stable isotope of silicon with relative atomic mass 28.9764947, 4.683 atom percent natural abundancy, and nuclear spin (1)/2. 0 Si InChI=1S/Si/i1+1 XUIMIQQOPSSXEZ-OUBTZVSYSA-N 28.97649 27.977 [29Si] silicon-29 chebi_ontology (29)14Si (29)Si silicon-29 CHEBI:37974 silicon-29 atom A nitrile that is hydrogen cyanide in which the hydrogen has been replaced by a methyl group. 0 C2H3N InChI=1S/C2H3N/c1-2-3/h1H3 WEVYAHXRMPXWCK-UHFFFAOYSA-N 41.05196 41.027 CC#N CHEBI:22185 CHEBI:30972 CHEBI:41432 Beilstein:741857 CAS:75-05-8 Gmelin:895 PDBeChem:CCN PMID:17347819 PMID:19100763 PMID:20370615 PMID:985423 Reaxys:741857 Wikipedia:Acetonitrile ACETONITRILE acetonitrile chebi_ontology CH3-C#N MeCN NCMe cyanomethane ethanenitrile methyl cyanide CHEBI:38472 acetonitrile A member of the class of fluorobenzenes that is benzene in which all six hydrogen atom have been replaced by fluorine. 0 C6F6 InChI=1S/C6F6/c7-1-2(8)4(10)6(12)5(11)3(1)9 ZQBFAOFFOQMSGJ-UHFFFAOYSA-N 186.05462 185.990 Fc1c(F)c(F)c(F)c(F)c1F Beilstein:1683438 CAS:392-56-3 Gmelin:101976 hexafluorobenzene chebi_ontology 1,2,3,4,5,6-hexafluorobenzene Hexafluorbenzol perfluorobenzene CHEBI:38589 hexafluorobenzene 0 D2O InChI=1S/H2O/h1H2/i/hD2 XLYOFNOQVPJJNP-ZSJDYOACSA-N 20.02760 [2H]O[2H] CHEBI:29373 CHEBI:41979 CAS:7789-20-0 Gmelin:97 MolBase:1647 PDBeChem:DOD dideuterium oxide chebi_ontology ((2)H2)water D2O DEUTERATED WATER Deuteriumoxid [OD2] deuterium oxide heavy water schweres Wasser CHEBI:41981 dideuterium oxide A trialkyl phosphate that is the trimethyl ester of phosphoric acid. 0 C3H9O4P InChI=1S/C3H9O4P/c1-5-8(4,6-2)7-3/h1-3H3 WVLBCYQITXONBZ-UHFFFAOYSA-N 140.07492 140.024 COP(=O)(OC)OC Beilstein:1071731 CAS:512-56-1 Gmelin:49926 PDBeChem:TZZ PMID:17083219 PMID:18409209 Reaxys:1071731 Wikipedia:Trimethyl_phosphate TRIMETHYL PHOSPHATE trimethyl phosphate chebi_ontology O,O,O-Trimethyl phosphate Phosphoric acid, trimethyl ester TMP TMPA TMPO Trimethoxyphosphine oxide Trimethyl orthophosphate CHEBI:46324 trimethyl phosphate A dioxane with oxygen atoms at positions 1 and 4. 0 C4H8O2 InChI=1S/C4H8O2/c1-2-6-4-3-5-1/h1-4H2 RYHBNJHYFVUHQT-UHFFFAOYSA-N 88.10512 88.052 C1COCCO1 CHEBI:34064 CHEBI:41951 CHEBI:46925 Beilstein:102551 CAS:123-91-1 DrugBank:DB03316 KEGG:C14440 LINCS:LSM-37087 PDBeChem:DIO PMID:14550759 PMID:18044507 PMID:20598439 Reaxys:102551 Wikipedia:1,4-Dioxane 1,4-Dioxane 1,4-dioxane chebi_ontology 1,4-DIETHYLENE DIOXIDE 1,4-Dioxan 1,4-dioxacyclohexane Dioxan-1,4 di(ethylene oxide) dioxane-1,4 glycol ethylene ether p-Dioxane tetrahydro-1,4-dioxin tetrahydro-p-dioxin tetrahydro-para-dioxin CHEBI:47032 1,4-dioxane C10H17O8PR2(C5H8O5PR)n.C10H17O7PR2(C5H8O6PR)n KEGG:C00434 Double-stranded DNA chebi_ontology CHEBI:4705 double-stranded DNA A biological role played by the molecular entity or part thereof within a biochemical context. chebi_ontology CHEBI:52206 biochemical role The stable isotope of boron with relative atomic mass 11.009306, 80.1 atom percent natural abundance and nuclear spin 3/2. 0 B InChI=1S/B/i1+0 ZOXJGFHDIHLPTG-IGMARMGPSA-N 11.00931 11.009 [11B] boron-11 chebi_ontology (11)5B (11)B CHEBI:52451 boron-11 The stable isotope of sodium with relative atomic mass 22.989770, 100 atom percent natural abundance and nuclear spin 3/2. 0 Na InChI=1S/Na/i1+0 KEAYESYHFKHZAL-IGMARMGPSA-N 22.98977 22.990 [23Na] sodium-23 chebi_ontology (23)11Na (23)Na sodium-23 CHEBI:52634 sodium-23 atom The bromide salt of tetramethylammonium. 0 C4H12BrN InChI=1S/C4H12N.BrH/c1-5(2,3)4;/h1-4H3;1H/q+1;/p-1 DDFYFBUWEBINLX-UHFFFAOYSA-M 154.04900 153.015 [Br-].C[N+](C)(C)C CAS:64-20-0 PMID:24804652 PMID:6196640 Reaxys:3620955 N,N,N-trimethylmethanaminium bromide chebi_ontology TMAB CHEBI:55317 tetramethylammonium bromide A member of the class of chlorobenzenes that is benzene in which all of the hydrogens are replaced by chlorines. An agricultural fungicide introduced in the mid-1940s and formerly used as a seed treatment, its use has been banned since 1984 under the Stockholm Convention on Persistent Organic Pollutants. 0 C6Cl6 InChI=1S/C6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9 CKAPSXZOOQJIBF-UHFFFAOYSA-N 284.78040 281.813 Clc1c(Cl)c(Cl)c(Cl)c(Cl)c1Cl Beilstein:1912585 CAS:118-74-1 Gmelin:27278 HMDB:HMDB0032566 KEGG:C11042 PMID:10641019 PMID:12117784 PMID:17150971 PMID:23336922 PMID:23462309 PMID:23627767 PMID:23747559 PMID:23923419 PMID:23973543 PMID:24148401 PMID:24311623 PMID:24365113 Reaxys:1912585 Wikipedia:Hexachlorobenzene Hexachlorobenzene hexachlorobenzene chebi_ontology 1,2,3,4,5,6-hexachlorobenzene HCB Hexachlorbenzol perchlorobenzene phenyl perchloryl CHEBI:5692 hexachlorobenzene The inorganic nitrate salt of sodium. 0 NNaO3 InChI=1S/NO3.Na/c2-1(3)4;/q-1;+1 VWDWKYIASSYTQR-UHFFFAOYSA-N 84.99470 84.978 [Na+].[O-][N+]([O-])=O CAS:7631-99-4 Reaxys:11343077 Wikipedia:Sodium_nitrate sodium nitrate sodium trioxidonitrate(1-) chebi_ontology Chile saltpeter Cubic niter Niter Nitrate de sodium Nitrate of soda Nitric acid monosodium salt Nitric acid sodium salt (1:1) Nitric acid, sodium salt Sodium saltpeter Sodium(I) nitrate (1:1) CHEBI:63005 sodium nitrate Any organic molecular entity whose stucture is based on derivatives of a phenyl-substituted 1-phenylpropane possessing a C15 or C16 skeleton, or such a structure which is condensed with a C6-C3 lignan precursors. The term is a 'superclass' comprising all members of the classes of flavonoid, isoflavonoid, neoflavonoid, chalcones, dihydrochalcones, aurones, pterocarpan, coumestans, rotenoid, flavonolignan, homoflavonoid and flavonoid oligomers. Originally restricted to natural products, the term is also applied to synthetic compounds related to them. Wikipedia:Flavonoids chebi_ontology flavonoid CHEBI:72544 flavonoids A primary nitroalkane that is methane in which one of the hydrogens is replace by a nitro group. A polar solvent (b.p. 101 degreeC), it is an important starting material in organic synthesis. It is also used as a fuel for rockets and radio-controlled models. 0 CH3NO2 InChI=1S/CH3NO2/c1-2(3)4/h1H3 LYGJENNIWJXYER-UHFFFAOYSA-N 61.04000 61.016 C[N+]([O-])=O CAS:75-52-5 KEGG:C19275 MetaCyc:CPD-8133 PMID:11100413 PMID:21860501 PMID:26735907 PMID:26800205 PMID:4207867 PMID:999282 Reaxys:1698205 Wikipedia:Nitromethane nitromethane chebi_ontology CH3NO2 MeNO2 CHEBI:77701 nitromethane An N-silyl compound that is N-methyltrifluoroacetamide in which the amide nitrogen is replaced by a tert-butyldimethylsilyl group. 0 C9H18F3NOSi InChI=1S/C9H18F3NOSi/c1-8(2,3)15(5,6)13(4)7(14)9(10,11)12/h1-6H3 QRKUHYFDBWGLHJ-UHFFFAOYSA-N 241.32600 241.111 CN(C(=O)C(F)(F)F)[Si](C)(C)C(C)(C)C CAS:77377-52-7 Reaxys:3606546 N-[tert-butyl(dimethyl)silyl]-2,2,2-trifluoro-N-methylacetamide chebi_ontology N-(t-butyldimethylsilyl)-N-methyltrifluoroacetamide N-methyl-N-(t-butyldimethylsilyl)trifluoroacetamide N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide CHEBI:85060 N-(tert-butyldimethylsilyl)-N-methyltrifluoroacetamide The study of the interaction of a sample with radiation or particles for measurement or detection. spectrometry CHMO:0000228 spectroscopy Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance. MS mass spectroscopy CHMO:0000470 mass spectrometry Any method where a sample mixture is first separated by gas chromatography then ionised and characterised according to mass-to-charge ratio and relative abundance. FIX:0000921 GC MS GC-MS GC/MS GCMS gas chromatography mass spectrometry gas chromatography mass spectroscopy gas chromatography with mass spectrometric detection gas chromatography-mass spectroscopy gas chromatography/mass spectrometry CHMO:0000497 gas chromatography-mass spectrometry Mass spectrometry where the relative abundance of isotopes in a sample is determined. IR MS IR-MS IRMS isotope ratio mass spectroscopy isotope-ratio mass spectrometry isotopic ratios mass spectrometry isotopic ratios mass spectroscopy CHMO:0000506 isotope ratio mass spectrometry Mass spectrometry where the relative abundance of non-radioactive isotopes in a sample is determined. S-IRMS SIRMS stable isotope ratio mass spectroscopy CHMO:0000514 stable isotope ratio mass spectrometry A method where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterised by their mass-to-charge ratio and relative abundance. FIX:0000924 LC MS LC-MS LC/MS LCMS iquid chromatography/mass spectrometry liquid chromatography mass spectrometry CHMO:0000524 liquid chromatography-mass spectrometry Mass spectrometry where the intensities of one or more specific ion beams are recorded rather than the entire mass spectrum. SIM selected ion monitoring selected-ion monitoring selective-ion monitoring CHMO:0000571 selective ion monitoring Mass spectrometry involving multiple mass-selection steps, with some form of fragmentation occurring between each stage. MS-MS MS/MS MS2 double mass spectrometry tandem MS tandem mass spectroscopy tandem-MS CHMO:0000575 tandem mass spectrometry Spectroscopy where the energy states of spin-active nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. NMR NMR spectrometry NMR spectroscopy nuclear magnetic resonance (NMR) spectroscopy nuclear magnetic resonance spectrometry CHMO:0000591 nuclear magnetic resonance spectroscopy Spectroscopy where the energy states of spin-active nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them, and the spectrum is obtained by plotting chemical shift vs. frequency. 1-D NMR 1D NMR 1D NMR spectrometry 1D NMR spectroscopy 1D nuclear magnetic resonance spectrometry 1D nuclear magnetic resonance spectroscopy one-dimensional nuclear magnetic resonance spectrometry one-dimensional nuclear magnetic resonance spectroscopy CHMO:0000592 one-dimensional nuclear magnetic resonance spectroscopy Spectroscopy where the energy states of 1H nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them. 1H NMR 1H NMR spectroscopy 1H nuclear magnetic resonance spectrometry 1H-NMR 1H-NMR spectrometry 1H-NMR spectroscopy proton NMR proton nuclear magnetic resonance spectroscopy CHMO:0000593 1H nuclear magnetic resonance spectroscopy Spectroscopy where the energy states of 13C nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them. 13C NMR 13C NMR spectroscopy 13C nuclear magnetic resonance spectrometry 13C-NMR spectrometry 13C-NMR spectroscopy C-NMR carbon NMR CHMO:0000595 13C nuclear magnetic resonance spectroscopy An NMR experiment in which a second frequency dimension is employed to disperse the signals and reveal correlations between interacting nuclei. 2-D NMR 2D NMR 2D NMR spectrometry 2D NMR spectroscopy 2D nuclear magnetic resonance 2D nuclear magnetic resonance spectrometry two-dimensional NMR two-dimensional nuclear magnetic resonance spectrometry two-dimensional nuclear magnetic resonance spectroscopy CHMO:0000598 two-dimensional nuclear magnetic resonance spectroscopy A type of homonuclear NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between nuclei which are J-coupled (usually \leq 3 bonds apart). COSY correlated spectrometry correlated spectroscopy correlation spectrometry CHMO:0000599 correlation spectroscopy A type of NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between protons and heteronuclei. FIX:0001025 2D heteronuclear correlation spectroscopy HETCOR HETCORR HETCOSY HETEROCOR hetCOSY heteronuclear COSY two-dimensional heteronuclear correlation spectroscopy CHMO:0000600 heteronuclear correlation spectroscopy A type of homonuclear NMR spectroscopy which reveal correlations between all nuclei of a spin-system. HOHAHA spectrometry HOHAHA spectroscopy TOCSY homonuclear Hartmann Hahn spectroscopy homonuclear Hartmann,Hahn spectroscopy homonuclear Hartmann-Hahn spectroscopy total correlated spectroscopy total correlation spectrometry CHMO:0000605 total correlation spectroscopy A type of homonuclear proton--proton) NMR spectroscopy where chemical shift and J-coupling information are separated onto different frequency axes. 2D J-resolved spectroscopy 2D J-spectroscopy 2DJ spectroscopy J-RES J-resolved NMR J-resolved NMR spectrometry J-resolved NMR spectroscopy J-resolved spectrometry J-resolved spectroscopy J-resolved spectroscopy NMR spectroscopy J-spectrometry JRES JRES NMR two-dimensional J-spectroscopy CHMO:0000606 J-spectroscopy A type of homonuclear NMR spectroscopy based on the nuclear Overhauser enhancement effect in which correlations are seen between nuclei that are spatially proximate within a molecule (\leq 6 \AA apart). 2D EXSY 2D exchange spectroscopy EXSY NOE experiments NOESY NOESY NMR NOEsy exchange spectrometry exchange spectroscopy nOesy nuclear Overhauser effect spectrometry nuclear Overhauser effect spectroscopy nuclear Overhauser enhancement spectrometry CHMO:0000607 nuclear Overhauser enhancement spectroscopy Spectroscopy where the energy states of spin-active nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them. NMR NMR spectrometry NMR spectroscopy nuclear magnetic resonance spectrometry nuclear magnetic resonance spectroscopy pulsed nuclear magnetic resonance spectrometry CHMO:0000613 pulsed nuclear magnetic resonance spectroscopy A pulse sequence which is applied during nuclear magnetic resonance spectroscopy to measure spin--spin (T2) relaxation times. For the pulse sequence see Rev. Sci. Inst., (1958), 29, pg 688. FIX:0000215 CPMG CPMG pulse sequence CPMG sequence Carr, Purcell,Meiboom,Gill pulse sequence Carr-Purcell Meiboom-Gill pulse sequence Carr-Purcell-Meiboom-Gill pulse sequence CHMO:0000718 Carr-Purcell-Meiboom-Gill pulse sequence A pulse sequence which is applied during nuclear magnetic resonance spectroscopy of quadrupolar nuclei, to measure spin--spin (T2) relaxation times. In the solid state, the sequence is used to achieve sensitivity enhancement for nuclei with low gyromagnetic ratios. For the pulse sequence see J. Phys. Chem. A, (1997), 101, pg 8597. QCPMG QCPMG NMR QCPMG pulse sequence QCPMG sequence quadrupolar Carr, Purcell,Meiboom, Gill pulse sequence quadrupolar Carr-Purcell Meiboom-Gill pulse sequence CHMO:0000719 quadrupolar Carr-Purcell-Meiboom-Gill pulse sequence Any type of heteronuclear NMR spectroscopy where a second frequency dimension is employed. heteronuclear 2D NMR CHMO:0000931 heteronuclear two-dimensional nuclear magnetic resonance spectroscopy A type of homonuclear NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between protons which are J-coupled (usually \leq 3 bonds apart). burchh 2009-03-11T05:11:37Z 1H--1H COSY 1H-1H COSY 1H-1H correlated spectroscopy CHMO:0001150 1H--1H correlation spectroscopy An NMR experiment in which multiple frequencies in an NMR spectrum are excited simultaneously over a broad frequency rnage using polychromatic pulses. burchh 2009-03-19T05:34:21Z Hadamard NMR spectroscopy Hadamard encoded NMR Hadamard nuclear magnetic resonance spectroscopy Hadamard-encoded NMR CHMO:0001195 Hadamard-encoded nuclear magnetic resonance spectroscopy Any technique which detects the response of spins to a perturbing magnetic field. burchh 2009-03-25T11:36:57Z FIX:0000012 CHMO:0001215 magnetic resonance method A technique or procedure applied in nuclear magnetic resonance experiments. burchh 2009-05-22T11:04:59Z CHMO:0001806 nuclear magnetic resonance method A series of short (microsecond) bursts (pulses) of rf radiation separated by delays (of defined duration) designed to interact with, and manipulate the magnetic moments of spin-active nuclei during NMR spectroscopy. burchh 2009-05-29T01:41:59Z NMR pulse sequence pulse sequence CHMO:0001841 nuclear magnetic resonance pulse sequence An NMR pulse sequence that decouples nuclei i.e. removes the effects of (usually) J-coupling (line splitting) from the spectrum. burchh 2009-05-29T12:00:00Z CHMO:0001844 decoupling pulse sequence An NMR pulse sequence, used in magic angle spinning, that decouples nuclei i.e. removes the effects of (usually) J-coupling (line splitting) from the spectrum. burchh 2009-05-29T12:00:00Z CHMO:0001852 magic angle spinning decoupling pulse sequence A sequence of composite pulses designed to allow isotropic mixing of magnetisation between nuclei. For the pulse sequence see J. Magn.Reson., (1988), 77, pg 274. burchh 2009-05-29T12:00:00Z FLOPSY flip-flop spectroscopy CHMO:0001862 flip flop spectroscopy An NMR pulse sequence used to transfer magnetisation between protons and covalently bound (spin active) heteronuclei via isotropic mixing of their magnetisation. Used to e.g. enhance the NMR signal of heteronuclei or to correlate chemical shifts of protons with heteronuclei. For the pulse sequence see J. Magn. Reson., (1991), 91, pg 444. burchh 2009-05-29T12:00:00Z HEHAHA HEHAHA pulse sequence HEHAHA sequence heteronuclear Hartman-Hahn pulse sequence heteronuclear Hartman-Hahn sequence heteronuclear Hartmann Hahn CHMO:0001863 heteronuclear Hartmann Hahn pulse sequence An NMR pulse sequence that is used to suppress or remove the solvent signal. burchh 2009-05-29T12:00:00Z CHMO:0001864 solvent suppression pulse sequence A pulse cluster used for solvent suppression consisting of two rf pulses separated by a delay with conditions set such that the solvent signal alone is rendered unobservable by the second pulse. For the pulse sequence see J. Am. Chem. Soc., (1982), 104, pg 7310. burchh 2009-05-29T12:00:00Z JR JR pulse sequence JR sequence jump and return jump-and-return jump-and-return pulse sequence CHMO:0001865 jump and return pulse sequence A pulse cluster used to suppress solvent (water) signals exploiting the differing relaxation properties of solvent and sample. Resonances are inverted and the subsequent recovery period is chosen such that the solvent signal is at a null point when the signal is detected. For the pulse sequence see J. Chem. Phys., (1972), 56, pg 3182. burchh 2009-05-29T12:00:00Z WEFT WEFT pulse sequence WEFT sequence water-elimination Fourier transform CHMO:0001866 water elimination Fourier transform A pulse cluster used for solvent (water) suppression. The solvent resonances are selectively excited and pulsed field gradients used to destroy the signal. For the pulse sequence see J. Biomol. NMR, (1992), 2, pg 661. burchh 2009-05-29T12:00:00Z WATERGATE WATERGATE pulse sequence WATERGATE sequence CHMO:0001867 water suppression through gradient tailored excitation A pulse cluster used in NMR experiments which manipulates signals such that, at the end of the sequence, the effects of chemical shift differences have been compensated/removed. Used most simply to compensate for inhomogeneities in the magnetic field but delays in the sequence also permit various possible manipulations of the magnetisation. For the pulse sequence see Phys. Rev., (1950), 80, pg 580. burchh 2009-05-29T12:00:00Z spin echo sequence spin-echo pulse sequence spin-echo sequence CHMO:0001868 spin echo pulse sequence A pulse sequence used in magic angle spinning NMR experiments to remove additional signals resulting from spinning the sample too slowly to obtain a response composed solely of isotropic chemical shifts. burchh 2009-05-29T12:00:00Z TOSS TOSS pulse sequence TOSS sequence CHMO:0001869 total suppression of sidebands pulse sequence A 2D NMR experiment which correlates the chemical shifts of spatially proximate protons with the chemical shifts of all (of one type of) their covalently bound heteronuclei. burchh 2009-06-30T10:23:52Z 2D HSQC-NOESY 2D NOESY-HSQC two-dimensional heteronuclear single quantum coherence nuclear Overhauser effect spectroscopy CHMO:0002060 two-dimensional heteronuclear single quantum coherence-nuclear Overhauser effect spectroscopy A type of homonuclear NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between 13C nuclei that are J-coupled (usually \leq 3 bonds apart). burchh 2009-08-24T04:14:21Z 13C-13C COSY 13C-13C correlated spectroscopy CC-COSY CHMO:0002301 13C--13C correlation spectroscopy A type of NMR spectroscopy where a second frequency dimension is employed to disperse the signals and reveal correlations between protons and 13C nuclei. burchh 2009-09-15T05:40:49Z 1H--13C COSY 1H--13C HETCOR 1H--13C HETCORR 1H--13C HETCOSY 1H--13C HETEROCOR 1H-13C COSY 1H-13C HETCOR 1H-13C HETCORR 1H-13C HETCOSY 1H-13C HETEROCOR heteronuclear 13C-1H COSY CHMO:0002380 1H--13C heteronuclear correlation spectroscopy Spectroscopy where the energy states of 1H nuclei placed in a static magnetic field are interrogated by inducing transitions between the states via radio frequency irradiation. Each experiment consists of a sequence of radio frequency pulses with delay periods in between them, and the spectrum is obtained by plotting chemical shift vs. frequency. burchh 2009-09-23T02:32:09Z 1D 1H NMR 1D proton NMR CHMO:0002442 one-dimensional 1H nuclear magnetic resonance spectroscopy CHMO:0002867 selected reaction monitoring cell cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." 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DUO:0000001 consent code A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016. DUO:0000002 consent code primary category A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016. DUO:0000003 consent code secondary category This consent code primary category indicates there is no restriction on use. DUO:0000004 Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service no restriction This primary category consent code indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry. DUO:0000005 general research use and clinical care This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. DUO:0000006 health/medical/biomedical research and clinical care This primary category consent code indicates that use is allowed provided it is related to the specified disease. DUO:0000007 disease-specific research and clinical care This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. population origins/ancestry research DUO:0000011 population origins or ancestry research This secondary category consent code indicates that use is limited to studies of a certain research type. DUO:0000012 research-specific restrictions This secondary category consent code indicates that use is limited to research purposes (e.g., does not include its use in clinical care). DUO:0000014 research use only This secondary category consent code indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations. DUO:0000015 no general methods research This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) DUO:0000016 genetic studies only Requirements indicate additional conditions set for use. DUO:0000017 data use requirements This requirement indicates that use is limited to not-for-profit organizations. DUO:0000018 not-for-profit use only This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. DUO:0000019 publication required This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000020 collaboration required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 ethics approval required This requirement indicates that use is limited to within a specific geographic region. DUO:0000022 geographical restriction This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo DUO:0000024 publication moratorium This requirement indicates that use is approved for a specific number of months. DUO:0000025 time limit on use This requirement indicates that use is limited to use by approved users. DUO:0000026 user-specific restriction This requirement indicates that use is limited to use within an approved project. DUO:0000027 project-specific restriction This requirement indicates that use is limited to use within an approved institution. DUO:0000028 institution-specific restriction This requirement indicates that the requestor must return derived/enriched data to the database/resource. DUO:0000029 RTN return to database/resource geographic location A reference to a place on the Earth, by its name or by its geographical location. GAZ:00000448 geographic location molecular_function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. molecular_function catalytic activity 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. catalytic activity biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. biological_process gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. gene expression protein complex A ribosome is a protein complex Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. protein complex conditional specification a directive information entity that specifies what should happen if the trigger condition is fulfilled PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. A unit of measurement is a standardized quantity of a physical quality. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot george gkoutos unit.ontology UO:0000000 measurement unit label unit objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. Software related to the recording or transformation of spectra. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI NMR NMR:1000531 software software Software related to the recording or transformation of spectra. MSI:NMR data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity information content entity 1 1 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph rule example to be added a rule is an executable which guides, defines, restricts actions MSI PRS OBI_0500021 PRS rule algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum 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. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version number conclusion textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still Person:Alan Ruttenberg conclusion textual entity textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity table | T F --+----- T | T F F | F F A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions PERSON: Lawrence Hunter table figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document 1 A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 Alan Ruttenberg AR notes: We need to discuss whether it should include site. cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 1 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum 1 1 A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region Alan Ruttenberg two dimensional cartesian spatial coordinate datum A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. a planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting line graph A line graph is a type of graph created by connecting a series of data points together with a line. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry time stamped measurement datum pmid:20604925 - time-lapse live cell microscopy A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series time sampled measurement data set OpenFLUX2 is a MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Modern techniques like Elementary Metabolite Unit (EMU) framework, are implemented for efficient computing of fluxes. OpenFlux2 is an expanded version of OpenFLUX to support analysis of parallel labeling experiments (PLE) data, i.e. those experiments using several different tracers concomitantly. Philippe Rocca-Serra https://doi.org/10.1186/s12934-014-0152-x openFlux2 2H2O -> 2H2+ O2 a process which uses or consumes chemical/molecular entities to generate other molecular entities Philippe Rocca-Serra adapted from wikipedia: https://en.wikipedia.org/wiki/Chemical_reaction last accessed: 2018-01-11 chemical reaction buffer role is a role played by a chemical solution to dampens pH variation Philippe Rocca-Serra EU H2020 PhenoMenAl buffer role derivatization agent role is a role played by a chemical entity involved in a chemical reaction known as derivatization whereby another chemical entity is augmented, but not altered otherwise, with groups specify to the chemical entity acting as a derivatization agent. Philippe Rocca-Serra EU H2020 PhenoMenAl derivatization agent role external standard role is a role played by a material entity used as a reference point for signal acquisition. this is a type of positive control role Philippe Rocca-Serra EU H2020 PhenoMenAl external standard role internal standard role is a role played by a chemical entity added in known amount to an analytical sample Philippe Rocca-Serra EU H2020 PhenoMenAl internal standard role long term reference role is a role played by a material entity known for its stability to provide the means to compare across sets of acquisitions Philippe Rocca-Serra EU H2020 PhenoMenAl long term reference role positive control role is a role played by a material entity in the context of analytical work to provide no signal or a signal as close to baseline as technically possible (within the limits of detection) thereby providing a reference point for the noise and indicative that the detectors and signal acquisition system operate nominally. Philippe Rocca-Serra EU H2020 PhenoMenAl negative control role positive control role is a role played by a material entity in the context of analytical work to provide a signal of known intensity indicative that the detectors and signal acquisition system operate nominally. Philippe Rocca-Serra EU H2020 PhenoMenAl positive control role solvent role is a role played by a chemical entity present in a solution and providing the solvatation activity to other compounds, the solutes. Philippe Rocca-Serra EU H2020 PhenoMenAl solvent role AbsoluteIDQ p150 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling of up to 163 distinct molecular entities with quantitative accuracy on human plasma samples. Philippe Rocca-Serra http://www.biocrates.com/products/research-products/absoluteidq-p150-kit AbsoluteIDQ p150 Kit AbsoluteIDQ p180 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling of up to 188 distinct endogenous molecular entities with quantitative accuracy from 5 different compound classes (i.e. acylcarnitines, amino acids, hexoses, phospho- and sphingolipids and biogenic amines). The assay requires very small sample amounts (10 μL) and shows excellent reproducibility. Philippe Rocca-Serra http://www.biocrates.com/products/research-products/absoluteidq-p180-kit AbsoluteIDQ p180 Kit AbsoluteIDQ Stero17 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling (identification and quantification) of 17 steroid hormones (sex steroids, mineralocorticoids, glucocorticoids). Philippe Rocca-Serra http://www.biocrates.com/products/research-products/absoluteidq-p150-kit AbsoluteIDQ Stero17 Kit AbsoluteIDQ p400 kit is a reagent system manufactured by Biocrates AG, Austria which allows the targeted metabolite profiling of up to 400 distinct molecular entities with quantitative accuracy on human plasma samples. Philippe Rocca-Serra http://www.biocrates.com/products/research-products/absoluteidq-p400-hr-kit AbsoluteIDQ p400 Kit ammonium bicarbonate is kind of buffer solution where the weak base is ammonium and the weak acid carbonic acid. Philippe Rocca-Serra cosmos tracer based metabolomics working group ammonium bicarbonate buffer the bicarbonate buffering system is used to regulate the pH of blood. A buffer solution (more precisely, pH buffer or hydrogen ion buffer) is an aqueous solution consisting of a mixture of a weak acid and its conjugate base, or vice versa. Philippe Rocca-Serra https://en.wikipedia.org/wiki/Buffer_solution buffer a dilution series sample is a material entity which is part of a collection of such materials, each defined by its dilution factor with respect to a stock solution of reference sample. Dilution series samples are used to assess the linearity of the signal acquisition by providing a set of expected and known quantities. Philippe Rocca-Serra EU H2020 PhenoMenAl dilution series reference Fetal bovine serum (FBS) or fetal calf serum (spelled foetal in Commonwealth English) is a material entity which correspsonds to the blood fraction remaining after the natural coagulation of blood, followed by centrifugation to remove any remaining red blood cells. Philippe Rocca-Serra cosmos tracer based metabolomics working group https://en.wikipedia.org/wiki/Fetal_bovine_serum fetal bovine serum HEPES buffer is a buffer which uses HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) as a zwitterionic organic chemical buffering agent . Philippe Rocca-Serra cosmos tracer based metabolomics working group HEPES buffer a pooled sample made from fractions from samples collected from large, study independent collection of samples with the purpose of serving as a reference for quality control purpose. Long Term Reference Samples maybe used in ring trials to check cross facility data acquisition consistency but also to enable data integration, irrespective of data acquisition platform or study context but providing a single point of reference against which to normalize. purpose: Inter study variability(within a core facility) Alejandra Gonzalez-Beltran Philippe Rocca-Serra LTR biological pool (inter) [CEA] biological pool [MASTR-MS] inter study QC H2020 PhenoMenal long term reference Phosphated buffer saline (PBS) buffer is a buffer which is a water-based salt solution containing disodium hydrogen phosphate, sodium chloride and, in some formulations, potassium chloride and potassium dihydrogen phosphate. Philippe Rocca-Serra cosmos tracer based metabolomics working group https://en.wikipedia.org/wiki/Phosphate-buffered_saline PBS buffer quality control material (qc material) is a material entity which is used for the purpose to quality control processes such as assessing unwanted source of variations during signal acquisitions. Typically, these materials are known compounds or mixture of compounds introduced in known quantities into test samples or run as is, diluted from stock to provide reference measurements at fixed temporal intervals. Philippe Rocca-Serra QC material EU H2020 PhenoMenAl quality control material a reference compound is a chemical entity of know origin, formula and established spectral fingerprint added to a solution of unknown component in known quantities in order to provide a basis (hence the term reference) with which to establish a comparison, be used for calibration or quality control or quantitation estimate for unknown compound in spectral analysis such as NMR or mass spectrometry Philippe Rocca-Serra pure standard reference material cosmos tracer based metabolomics working group reference compound NIST reference material: https://www.nist.gov/publications/certification-standard-reference-materialr-968f-fat-soluble-vitamins-frozen-human-serum a reference compound mix is a material entity which consists of composite solution of several molecular entities acting as reference compound and present in known quantity in the mixture, with which to establish a comparison, be used for calibration or quality control or quantitation estimate for unknown compound in spectral analysis such as NMR or mass spectrometry Philippe Rocca-Serra pure standard mix reference material mix cosmos tracer based metabolomics working group reference compound mix a material entity corresponding to a sample containing no biological sample, which undergoes all laboratory process of preparation as used for test samples and used as a negative control to evaluate contamination effect and artefacts caused by reactions occurring during the sample preparation steps of test samples. method blank method reference sample preparation blank a material entity corresponding to ‘solvent’ (mobile phase in chromatography context) only, containing no biological sample and used as a negative control to evaluate carry over effect between injections of test samples. Alejandra Gonzalez-Beltran Philippe Rocca-Serra normal blank [Leiden] solvent blank solvent blank a study reference sample is a pool made up of aliquots from all the sample collected in a given study. It is meant to be used to monitor intra study variability, also known as within study variability of the signal acquisition, for instance between batches of such data acquisition. Alejandra Gonzalez-Beltran Philippe Rocca-Serra SR iQC - internal quality control [Imperial College London] study reference study reference material a carrier gas is a chemical entity in gaseous phase with is used for eluting chemical compound in a gas chromatography process. Philippe Rocca-Serra cosmos tracer based metabolomics working group carrier gas tert-Butyldimethylsilyl chloride is a derivatization agent a derivatization agent is a chemical entity which is used in a material combination process known as derivatization and which consists in adding chemical groups to a molecule in an attempt to make it more volatile and therefore amenable to gas-chromatography mass spectrometry. Philippe Rocca-Serra EU H2020 PhenoMenAl derivatization agent Philippe Rocca-Serra QDA reagent quaternary ammonium dodecyl aminooxy reagent an isotopic tracer is a molecular entity whose atoms may have entirely or partially replaced with isotopes of the normally occuring element and which can be distinguished from naturally occuring molecular entity through mass analysis or nucleic magnetic resonance analysis. Philippe Rocca-Serra cosmos tracer based metabolomics working group isotopic tracer a specificly labeled isotopic tracer is an isotopic tracer where only specific positions on the backbone have been replaced with an isotopic atom. Such molecules are often used in Fluxomics analysis and metabolic path elucidation experiments. Philippe Rocca-Serra cosmos tracer based metabolomics working group positionally labeled isotopic tracer uniformly labeled isotopic tracer is an isotopic tracer where all atoms of the backbone are replaced with the same isotope. Such molecules are often used in Fluxomics analysis and metabolic path elucidation experiments. Philippe Rocca-Serra cosmos tracer based metabolomics working group uniformly labeled isotopic tracer A single isotopologue represents a set of mass-equivalent isotopomers. It is therefore a set of chemicals representing molecules of the same chemical entity and same isotopic composition. Isotopologue can be monitored using mass spectrometry but only NMR spectroscopy can discriminate between positional isotopomer. Philippe Rocca-Serra adapted from IUPAC nomenclature cosmos tracer based metabolomics working group isotopologue OpenFLUX is a MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Modern techniques like Elementary Metabolite Unit (EMU) framework, are implemented for efficient computing of fluxes. Philippe Rocca-Serra https://www.ncbi.nlm.nih.gov/pubmed/19409084 openFlux a mass isotopomer (short for isotopic isomer) is a compound which differ from another one only by the position of an isotopic substitution in the molecular backbone. One in a collection of isomers with the same number of each isotope of each element but differing in their positions within the chemical structure. Philippe Rocca-Serra isotopic isomer mass isotopomer cosmos tracer based metabolomics working group isotopomer a solvent is a chemical entity playing a solvent role in a solution. Philippe Rocca-Serra solvent A non-radioactive, glucose molecule in which all six carbons are substituted with stable carbon 13 (13C) isotope, with potential imaging application or fluxomics studies. CAS RN 110187-42-3 submit to CHEBI Philippe Rocca-Serra uniformly-labeled [U-13C] glucose http://www.cancer.gov/drugdictionary?cdrid=739239 an isotopomer where the isotopic content of specific atoms is known for a part of the molecule should it be a relation or a class? Philippe Rocca-Serra partial isotopomer metabolic flux unit is a measurement unit datum used to qualify a metabolic flux. It is therefore an amount of matter over a temporal interval. Philippe Rocca-Serra Philippe Rocca-Serra for the COSMOS-Fluxomics Ontology (CFO) metabolic flux unit micromolar per milligram of protein per hour is a unit used to report metabolic fluxes. it denotes a measurement indicative of an amount of material over a period of time and normalized to the amount of protein present in the cellular fraction under consideration Philippe Rocca-Serra umol mg prot-1 hr-1 micromolar per milligram of protein per hour c13Fluc2 is a software suite of applications for the detailed quantification of intracellular (quasi) steady-state fluxes as explored by 13C-based metabolic flux analysis. The tool is developed and maintained by W. Wiechert at the Institute of Bio- and Geosciences, IBG-1: Biotechnology and JARA High Performance Computing, Forschungszentrum, Julich GmbH, 52428 Julich, Germany. Philippe Rocca-Serra Weitzel M, Nöh K, Dalman T, Niedenführ S, Stute B, Wiechert W 13CFLUX2 - High-Performance Software Suite for 13C-Metabolic Flux Analysis Bioinformatics 2012 doi: 10.1093/bioinformatics/bts646 http://www.13cflux.net/13cflux2/ 13cflux2 C13 is a tool for quantification of in vivo metabolic fluxes, from carbon labelling experiments. The underlying approach is metabolic flux analysis based on stationary carbon isotope labelling experiments, using fractional enrichment data. The mathematical framework adopted herein is the one developed by Wiechert and de Graaf (1997). It is developed and maintained at the Chalmers University of Technology, Department of Chemical and Biological Engineering, Systems Biology group , Kemivägen 10 412 96 Göteborg, Sweden. Philippe Rocca-Serra http://129.16.106.142/tools.php?c=c13 C13 An intuitive tool for quantitative investigations of intracellular metabolism by users that are not familiar with numerical methods or isotopic tracer experiments. The aim of this open source software is to enable non-specialists to adapt the software to their specific scientific interests, including other 13C-substrates, labeling mixtures, and organisms. FiatFlux is written in Matlab Philippe Rocca-Serra http://www.ncbi.nlm.nih.gov/pubmed/16122385 fiatFlux FIA is a software written in python, implementing the FIA (Fluxomer Iterative Algorithm) - a new effective method for 13C metabolic fluxes (tracer) experiments analysis. It is developed by Orr Srour, Jamey D. Young and Yonina C. Eldar at the Technion, Israel Institute of Technology Philippe Rocca-Serra FIA https://doi.org/10.1186/1752-0509-5-129 Fluxomer Iterative Algorithm iMAT is a software integrating transcriptomic and proteomic data with genome-scale metabolic network models to predict enzyme metabolic flux. The tool is developed by Tomer Shlomi at The Isreal Institute of Technology Philippe Rocca-Serra Integrative Metabolic Analysis Tool Bioinformatics (2010) 26 (24): 3140-3142. https://doi.org/10.1093/bioinformatics/btq602 http://www.cs.technion.ac.il/~tomersh/methods.html iMAT INCA: a computational platform for isotopically non-stationary metabolic flux analysis, Jamey D. Young. Bioinformatics, first published online January 11, 2014. INCA is a software package that can perform both steady-state metabolic flux analysis and isotopically non-stationary metabolic flux analysis. The software provides a framework for comprehensive analysis of metabolic networks using mass balances and elementary metabolite unit balances. The generation of balance equations and their computational solution is completely automated and can be performed on networks of arbitrary complexity. Philippe Rocca-Serra Isotopomer Network Compartmental Analysis http://www.ncbi.nlm.nih.gov/pubmed/24413674 INCA Iso2Flux is a Python-based flux analysis software that allows to perform 13C Metabolic Flux Analysis on a sub-network of a large scale model. Iso2flux uses constraint-based modelling to compute steady state fluxes across a large metabolic network and uses such flxues to predict 13C distribution across a subser of the newtork. Then, given a set of 13C data Iso2flux can iteratively find the steady state flux distributions that are most consistent with such fluxes. the source code is available from: https://github.com/cfoguet/iso2flux http://portal.phenomenal-h2020.eu/app-library/iso2flux https://github.com/cfoguet/iso2flux Pedro de Atauri Vitaly Selivanov iso2flux “Isodyn” is a C++-program that performs an analysis of stable isotope tracer data to assess metabolic flux profiles in living cells. Isodyn simulates the dynamics of isotopic isomer (isotopomer) distribution in central metabolic pathways, and, by changing its parameters, which reflect the characteristics of corresponding biochemical reactions, fit the simulated dynamics of mass isotopomers to that observed experimentally. The simulated metabolic fluxes that correspond to the best fit are assumed to reproduce the real fluxes in the analyzed biological object and conditions. Isodyn contains tools that check the goodness of fit and perform a statistical analysis of obtained metabolic fluxes. the source code is available from: https://github.com/seliv55/isodyn Philippe Rocca-Serra http://portal.phenomenal-h2020.eu/app-library/isodyn Pedro de Atauri Vitaly Selivanov isodyn IsoDesign, a software that enables these parameters to be maximized by optimizing the isotopic composition of the label input. It can be applied to (13) C-MFA investigations using a broad panel of analytical tools (MS, MS/MS, (1) H NMR, (13) C NMR, etc.) individually or in combination. It includes a visualization module to intuitively select the optimal label input depending on the biological question to be addressed. The software is available from: http://metasys.insa-toulouse.fr/software/isodes/ Philippe Rocca-Serra https://doi.org/10.1002/bit.24997 isodesign Metran is a software for Metabolic Flux Analysis implementing the Elementary Metabolite Units. Metabolic Flux Analysis (MFA) has emerged as a tool of great significance for metabolic engineering and quantitative cell physiology. An important limitation of MFA, as carried out via stable isotope labeling and GC-MS measurements, is the large number of isotopomer/cumomer equations that need to be solved, especially when multiple isotopic tracers are used for the labeling of the system. This restriction reduces the ability of MFA to fully utilize the power of multiple isotopic tracers in elucidating the physiology of realistic situations comprising complex bioreaction networks. To address this limitation, we have developed a novel framework for modeling of isotopic tracer distributions that significantly reduces the number of variables, without any loss of information. The EMU framework is based on a highly efficient decomposition method that identifies the minimum amount of information needed to simulate isotopic labeling within a reaction network using the knowledge of atomic transitions occurring in the network reactions. The functional units generated by the decomposition algorithm, called elementary metabolite units (EMUs), form the new basis for generating system equations that describe the relationship between fluxes and isotopomer abundances. The EMU decomposition algorithm is completely unsupervised and converges within seconds even for very genome-wide network models. Isotopomer abundances simulated using the EMU framework are identical to those obtained using the isotopomer and cumomer frameworks, however, requiring significantly less computation time. For a typical carbon labeling system the total number of equations that needs to be solved is reduced by one order-of-magnitude (100s EMUs vs. 1000s cumomers). As such, the EMU framework is most efficient for the analysis of labeling by multiple isotopic tracers. For example, the analysis of gluconeogenesis network model with 2H, 13C, and 18O tracers requires only 354 EMUs compared to >2,000,000 isotopomers Philippe Rocca-Serra http://www.ncbi.nlm.nih.gov/pubmed/17088092 metran “midcor.R” is an “R”-program that performs a primary analysis of isotopic isomers (isotopomers) distribution obtained by Gas Chromatography coupled with Mass Spectrometry (GCMS). The aim of this analysis is to have a correct distribution of isotopes originated from substrates that are artificially enriched with specific isotopes (usually 13C). To this end the program performs a correction for natural occurring isotopes and also correction for “impurities” of the assay media that give peaks overlapping with the spectra of analyzed labeled metabolites. This program offers two ways of corrections of “impurities” resulted from overlapping the assayed mass isotopomer distribution with peaks produced either by unknown metabolites in the media, or by different fragments produced by the assayed metabolite. The source code is available from https://github.com/seliv55/midcor Philippe Rocca-Serra http://portal.phenomenal-h2020.eu/app-library/midcor Pedra de Atauri Vitaly Selivanov midcor an isotopically non-stationary labeling experiment is a material processing used in fluxomics studies where cells cultures are grown in the presence of radiolabeled tracer compound for relatively short amount of time and samples collection before the system can reach an isotopic and metabolic steady state, and is therefore in a non-stationary phase. Such experiment are shorter to run that steady-state labeling experiment and usually allow to determine fluxes with increased precision. Alejandra Gonzalez-Beltran Philippe Rocca-Serra EU H2020 PhenoMenAl non-stationary isotopic labeling experiment A non-radioactive, glutamine molecule in which 5 carbons are substituted with stable carbon 13 (13C) isotope and both glutamin nitrogen atoms are substituted with 15N ones, with potential imaging application or fluxomics studies. submit to CHEBI Alejandra Gonzalez-Beltran Philippe Rocca-Serra 184161-19-1 13C5-15N2-glutamine OpenMoebius is an integrated software for conventional 13C-Metabolic Flux Analysis and isotopically nonstationary 13C-Metabolic Flux Analysis (INST-13C-MFA). This work is partially supported by JST, Strategic International Collaborative Research Program, SICORP for JP-US Metabolomics. Philippe Rocca-Serra http://www-shimizu.ist.osaka-u.ac.jp/hp/en/software/OpenMebius.html openMoebius RaMID is a computer program designed to read the machine-generated files saved in netCDF format containing registered time course of m/z chromatograms. It evaluates the peaks of mass isotopomer distribution (MID) making them ready for further correction for natural isotope occurrence. RaMID is written in “R”, uses library “ncdf4” (it should be installed before the first use of RaMID) and contains several functions, located in the files “ramid.R” and "libcdf.R," designed to read CDF files, and analyze and visualize the spectra that they contain. the source code is available from: https://github.com/seliv55/RaMID Philippe Rocca-Serra https://github.com/seliv55/RaMID Pedro de Atauri Vitaly Selivanov ramid a software produced by Nicolas Zamboni and colleagues for flux ratio estimation based on a 5 step workflow known as SUMOFLUX and which relies on surrogate modeling. Matlab code available from: http://www.imsb.ethz.ch/research/zamboni/resources.html Philippe Rocca-Serra http://ncbi.nlm.nih.gov/pubmed/27626798 sumoflux The chemical compounds of a living cell are connected by biochemical reactions which convert one compound into another. The reactions are catalyzed by enzymes. Thus, all compounds in a cell are parts of an intricate biochemical network of reactions which is called metabolic network. It is possible to use network analyses to infer how selection acts on metabolic pathways. Philippe Rocca-Serra adapted from wikipedia: https://en.wikipedia.org/wiki/Biological_network network a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes. Philippe Rocca-Serra https://en.wikipedia.org/wiki/Metabolic_pathway pathway CH4 + 2 O2 → CO2 + 2 H2O, the stoichiometric coefficient of CH4 is -1, the stoichiometric coefficient of O2 is -2, for CO2 it would be +1 and for H2O it is +2 a stoichiometric coefficient is an information object which is part of an equation describing a chemical reaction and which corresponds to the number of molecules of a reactant taking part in a reaction. Philippe Rocca-Serra http://en.wikipedia.org/wiki/Stoichiometry#Stoichiometric_coefficient stoichiometric coefficient the amount of time elapsed for a cell culture to growth twice its initial size, usually expressed in hour Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group cell culture doubling time Cell seeding density is a measurement datum which denotes the number of cells per surface area in the case of adherent cells or number of cells per volume in the case of free cells deposited in the culture vessel to start a cell culture. The cell seeding density is therefore stated in number of cells per cm2 or number of cells per ml. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group cell seeding density average cell volume is a measurement datum used to report over physcal occupancy of cells under study. This information is used for as input for kinetic modeling. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group cell volume when cells reach 50% confluence level, replenish medium confluence level is a measurement datum denotes the status of a cell culture and how cells are occupying the space available in a plate. confluence levels are stated in %. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group confluence level dilution factor is a measurement data item which indicates in percentage the level of purity of a material in the context of dilution such as a dilution series. Philippe Rocca-Serra EU H2020 PhenoMenAl dilution factor the amount of dideoxyribonucleic acids present in a cell culture or tissue. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group DNA content intracellular metabolite average content is a measurement provided of metabolite concentration normalized against cell average volume or DNA content or protein content or dry weight Philippe Rocca-Serra metabolite content EU H2020 PhenoMenAl cosmos tracer based metabolomics working group Barcelona meeting, march 2015 interacellular metabolite average content the concentration of a molecular entity acting as metabolite and stated in standard concentration units, such molar, micromolar and so on Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolite concentration metabolite pool size estimate is an information entity used in fluxomics studies to estimate the amount of molecular entity available to a particular metabolic process. It is usually reported in umol per mg of protein. can be also computed from simulation and be output of such simulation (then provide confidence indicator) Alejandra Gonzalez-Beltran Philippe Rocca-Serra pool size EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolite pool size estimate passage number is a measurement data item denoting how many times a cell culture has been split and transferred to a new culture vessel. It can also be considered to be equivalent to how many times a cell culture has reached 100% confluence Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group passage number ratio of protein content over a reference standard element (usually bovine serum albumin (BSA)) Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group protein concentration the amount of (soluble) protein from cell culture or tissue. the quantity of total protein recovered from an extraction process varies depending on the solvent and buffers used during the extraction phase. the amount is usuall expressed in milligram (refer to Unit Ontology) Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group protein content signal intensity is a kind of measurement providing an estimate of the strength of a phenomena as it is recorded. For digital detector instrument, the signal intensity is usually a electric intensity or a field strength of the electromagnetic wave transmitting a signal. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group signal intensity Signal intensity of all m/z values at the maximum of the peak (also known as maximum signal intensity) and subtracting baseline. Philippe Rocca-Serra peak height as signal intensity EU H2020 PhenoMenAl cosmos tracer based metabolomics working group maximum m/z values signal intensity with baseline substraction total volume of cell culture is a measurement data item which denotes the volume occupied by a cell culture Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group total volume of cell culture https://github.com/ISA-tools/isa-matrix-datapackages/tree/master/src/sirm_datapkg an isotopologue distribution matrix is an information object used in tracer based metabolomics experiments to report the amount of possible isotopologues (sets of isotopomers) derived from the tracer in a metabolic network. the matrix hold the mass isotopomer distributions (MIDs) of Elementary Metabolite Unit (EMU) which will be used as state variables. An EMU is defined as a distinct subset of a metabolite’s atoms. EMUs can exist in a variety of mass states depending on their isotopic compositions. An EMU in its lowest mass state is referred to as M+0, while an EMU that contains one additional atomic mass unit (e.g., due to the presence of a 13C atom in place of a 12C atom) is referred to as M+1, with higher mass states described accordingly. An MID is a vector that contains the fractional abundance of each mass state of an EMU. Philippe Rocca-Serra DOI 10.1002/bit.21632 An Elementary Metabolite Unit (EMU) BasedMethod of Isotopically Nonstationary Flux Analysis, Jamey D. Young, Jason L. Walther, Maciek R. Antoniewicz, Hyuntae Yoo,Gregory Stephanopoulos, Department of Chemical Engineering, Massachusetts Institute of Technology. http://onlinelibrary.wiley.com/doi/10.1002/bit.21632/epdf EU H2020 PhenoMenAl cosmos tracer based metabolomics working group isotopologue distribution matrix a metabolic flux rate matrix is an information content entity which is defined as a 2 dimensional table associating chemical species with uptake and excretion rate in the cell Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolic flux rate matrix 1 a stoichiometry matrix is an information content entity holding arrays of stoichiometric coefficients, each associated to a specific chemical reactions Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group stoichiometry matrix a CHEBI identifier for chemical or an HMDB identifier a centrally registered identifier to denote a metabolite chemical entity Philippe Rocca-Serra EU H2020 PhenoMenAl metabolite identifier a KEGG pathway identifier such as map00010 (http://www.genome.jp/dbget-bin/www_bget?map00010) a centrally registered identifier which denotes a pathway data item Philippe Rocca-Serra EU H2020 PhenoMenAl pathway identifier a uniprot identifier such P20248 (http://www.uniprot.org/uniprot/P20248) a centrally registered identifier to denote a molecular entity of the type Protein. Philippe Rocca-Serra EU H2020 PhenoMenAl protein identifier a reactome identifier such as R-HSA-174054 a centrally registered identifier which denotes a chemical reaction. Philippe Rocca-Serra EU H2020 PhenoMenAl reaction identifier calibration is a process which relies on comparison between measurements in order to estimate the reliability of the measurements performed on a particular device or instrument configuration. a calibration process may be used to identify a systematic error in measurement and possibly include it into an error model. a calibration process may be used to detect degradation of parts of instruments when long data acquisition times are needed (e.g. degradation of a chromatography column in a GC-MS chain). Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group calibration quality control is a process which aims to ensure that procedures for producing a material or a measurement remain within established error tolerance margins. Quality control often relies on the use of references or standards against which readings are gauged. those standards can be 'negative control' which should produce in an absence of signal or 'positive control', which should result in the presence of a signal of known quality and intensity. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group quality control assessing across studies variability is a quality control process which aims at monitoring the consistency of signal acquisitions between different studies (for instance in the context of meta-analysis and data integration) in order to detect unwanted causes of variation (i.e. variation that was not planned and that should be taken into account). Philippe Rocca-Serra EU H2020 PhenoMenAl assessing across studies variability assessing instrument conditionning is a quality control process which aims at monitoring the stability of the analytical instrument prior to running data acquisition on specimen of interest by running a set of control runs. Philippe Rocca-Serra EU H2020 PhenoMenAl assessing instrument conditioning assessing within study variability is a quality control process which aims at monitoring the consistency of signal acquisition throughout the course of a study in order to detect unwanted causes of variation (i.e. variation that was not planned and that should be taken into account). Philippe Rocca-Serra EU H2020 PhenoMenAl assessing within study variability assessing study batch-to-batch variation is a within study variably quality control which specifically looks at how batching of data acquisition contributes to adding unwanted noice and how to account for it. Philippe Rocca-Serra EU H2020 PhenoMenAl assessing study batch to batch variation detecting carry over event is a quality control process which aims to determine if measurements in one sample are affected to earlier measurements made on different samples and indicative of insufficient matrix regeneration between 2 data acquisition events. this is usually assessed by running solvent blanks or sample preparation blank between analytical runs. Philippe Rocca-Serra carry over detection EU H2020 PhenoMenAl detecting carry over event detecting departure from linearity event is a quality control process which aims to determine if measurements respond in a linear fashion of a linear increase of concentration of analytes. this is usually assessed by running a dilution series between analytical runs. Philippe Rocca-Serra linearity departure detection EU H2020 PhenoMenAl detecting departure from linearity event detecting sample degradation event is a quality control process which aims to determine if measurements in samples are affected by their run order or time of acquisition. This is usually assessed by running the same analytical samples at different points along the data acquistion plan (technical replication at the begining and end of runs). Philippe Rocca-Serra sample degradatation detection EU H2020 PhenoMenAl detecting sample degradation event an investigation which focused on measuring small biological molecules known as metabolite with the goal of understanding biochemical process underlying normal or pathological biological processes Philippe Rocca-Serra EU H2020 PhenoMenAl metabolomics investigation lipidomics investigation is an investigation which aims at determining the lipid content of a biological system under given experimental conditions using data acquisition techniques such as mass spectrometry, nmr spectroscopy or chromatography techniques. Philippe Rocca-Serra EU H2020 PhenoMenAl lipidomics investigation stable isotope resolved metabolomics study is a kind of investigation which uses non-radioactive isotope for labeling compounds which are precursors in key metabolic reaction. These studies therefore allow deciphering reaction and understanding the fluxes in cells. Tracer based pathway discovery study is a specific type of fluxomics study which aims at discovery new metabolic routes and their associated signature metabolites by using isotopically labeled tracers Philippe Rocca-Serra SIRMS tracer based metabolite profiling cosmos tracer based metabolomics working group stable isotope resolved metabolomics study A kind of assay which attempts to identify and measure relative concentration of all possible metabolites using the method high-performance liquid chromatography (HPLC; formerly referred to as high-pressure liquid chromatography), is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture. Alejandra Gonzalez-Beltran Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group https://en.wikipedia.org/wiki/High-performance_liquid_chromatography metabolite quantitation using high performance liquid chromatography a kind of assay which attempts to identify and measure specific compound/ metabolites (known in advance) expressed as concentration or relative abundance ratio to a standard in a extract derived from a specimen using techniques such as gas chromatography mass spectrometry, liquid chromatography mass spectrometry, NMR spectroscopy or liquid chromatography DAD Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group targeted metabolite profiling a kind of assay which attempts to identify and measure relative concentration of all possible metabolites present in a extract derived from a specimen using techniques such as gas chromatography mass spectrometry, liquid chromatography mass spectrometry, NMR spectroscopy. Alejandra Gonzalez-Beltran Philippe Rocca-Serra global metabolite profiling EU H2020 PhenoMenAl cosmos tracer based metabolomics working group untargeted metabolite profiling a fresh culture medium is a culture medium which presents its nominal characteristisc in terms of molecular concentration of its components, pH, and physical chemical expected properties. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group fresh culture medium spent culture medium is a culture medium which has been added to a cell culture and which has been depleted of its component as used by the growing cell and which has received the by products of cell metabolites excreted by the cells. Therefore, spent culture medium will different significantly in pH and physical chemical properties from the initial fresh culture medium added to the cell as the begining of the cell culture. Spent culture medium is usually recovered by aspiration or mild centrifugation (as not to distrupt cell membrane) of the cell culture. Philippe Rocca-Serra cell culture supernatant spent medium EU H2020 PhenoMenAl cosmos tracer based metabolomics working group spent culture medium metabolism quenching is a planned processed whose objective is a quick extinction of all biochemical reactions occuring in a biological system in order to fix molecular entity concentrations for downstream quantitation and analysis. An array of physical or chemical agent may be used to achieve that goal. Philippe Rocca-Serra metabolism immediate extinction EU H2020 PhenoMenAl metabolism quenching direct metabolism quenching by solvent is a kind biochemical reaction extinction process which relies on organic solvents to denature enzymatic machinery and inactivate it. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group direct metabolism quenching by solvent a type of metabolism immediate extinction using cold acetonitrile Philippe Rocca-Serra metabolism quenching using QDA EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolism quenching by 13 CD3-QDA in cold CH3CN a type of metabolism extinction which uses refrigerated buffer containing 60% of methanol ammonium bicarbonate solution Philippe Rocca-Serra cooled 60% methanol NH4HCO3 metabolism quenching EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolism quenching using precooled 60 percent methanol ammonium bicarbonate buffer a type of metabolism extinction which uses refrigerated buffer containing 60% of methanol HEPES solution Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolism quenching using precooled 60 percent methanol HEPES buffer a type of metabolism extinction which uses refrigerated PBS buffer Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolism quenching using precooled PBS buffer acetonitrile 5%, isopropanol 95% for 15 minutes at flow rate 1 ml/min, an elution program is a set of recorded instructions which determine the mobile phase (gas or liquid) composition, pressure, temperature and flow rate during the chromatography separation. Philippe Rocca-Serra cosmos tracer based metabolomics working group elution program derivatization is a technique used in chemistry which transforms a chemical compound into a product (the reaction's derivate) of similar chemical structure, called a derivative. That compound has properties more amenable to a particular analytical method. Some samples analyzed by GC require derivatization in order to make them suitable for analysis. Compounds that have poor volatility, poor thermal stability, or that can be adsorbed in the injector will exhibit nonreproducible peak areas, heights, and shapes. Other compounds that respond poorly on a specific detector may need to be “tagged” with a different functional group to improve detection. Philippe Rocca-Serra EU H2020 PhenoMenAl adapted from https://en.wikipedia.org/wiki/Derivatization and https://www.restek.com/pdfs/CFTS1269.pdf. Last accessed: 2018-01-11 derivatization a kind of derivatization which results in the addition of acetyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment. Philippe Rocca-Serra EU H2020 PhenoMenAl EU cosmos tracer based metabolomics working group acetylation a kind of derivatization which results in the addition of trifluoroacetyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment. Alejandra Gonzalez-Beltran Philippe Rocca-Serra EU H2020 PhenoMenal trifluoroacetylation a kind of derivatization which results in the addition of alkyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment. Philippe Rocca-Serra EU H2020 PhenoMenal alkylation a kind of derivatization which results in the addition of methyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment. Philippe Rocca-Serra EU H2020 PhenoMenal methylation a kind of derivatization which results in the addition of oxime group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment. Philippe Rocca-Serra EU H2020 PhenoMenal oximation a kind of derivatization which results in the addition of silyl group to molecules in an attempt to make ions derived from it more volatile in a gas-chromatography experiment. Philippe Rocca-Serra EU H2020 PhenoMenal silylation Isotopic labeling (or isotopic labelling) is a technique used to track the passage of an isotope (an atom with a detectable variation) through a reaction, metabolic pathway, or cell. The reactant is 'labeled' by replacing specific atoms by their isotope. Philippe Rocca-Serra https://en.wikipedia.org/wiki/Isotopic_labeling isotopic labeling Specific isotopic labeling refers to the placement of a single label (e.g., 2H, 13C, or 15N) in a specified location in a molecule. Philippe Rocca-Serra specific isotopic labeling EU H2020 PhenoMenAl http://www.sigmaaldrich.com/content/dam/sigma-aldrich/articles/stable-isotopes/biomolecular_nmr.pdf isotopic labeling with positional labeled tracer Uniform labeling refers to biosynthetic labeling of all carbon, nitrogen, or hydrogen sites with stable isotopes. Uniform labeling of proteins with 15N is particularly convenient because of the strategic locations of nitrogens in the backbone and the absence of homonuclear couplings due to the intervening carbons. It is also possible to replace all of the carbons with 13C, although in this case the spectroscopy has to deal with the network of couplings among bonded carbons. Similarly, all of the hydrogens can be replaced with deuterons in order to attenuate the dipolar couplings among the hydrogens that often present complications and difficulties in the experiments. Philippe Rocca-Serra EU H2020 PhenoMenAl http://www.sigmaaldrich.com/content/dam/sigma-aldrich/articles/stable-isotopes/biomolecular_nmr.pdf isotopic labeling with uniformly labeled tracer a process of collecting a sample when the cells of cell culture growth are collected at a specific phase of the cell division cycle (e.g collection at G2/G1). This often requires a cell synchronization step. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group collection at cell cycle phase a process of collecting a sample when the cells of a cell culture growth are not dividing Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group collection at cytostatic phase a process of collecting a sample when the cell culture growth can be approximated by a logarithm function. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group collection at logarithmic phase collection at specific cell culture passage is a kind of specimen collection which occurs after a strictly defined number of cell culture splitting, defined to control how many cell divisions have been performed. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group collection at specific cell culture passage collection at stabilization phase before experiment is a kind of specimen collection process which takes places once cells have reached a stationary growth phase and prior the main experimental intervention is applied. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group collection at stabilization phase before experiment a process of collecting a sample when the cell culture growth has reached a plateau, indicative of a steady state Alejandra Gonzalez-Beltran Philippe Rocca-Serra collection at steady state phase EU H2020 PhenoMenAl cosmos tracer based metabolomics working group collection at stationary phase Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. Flux balance analysis calculates the flow of metabolites through a metabolic network, thereby making it possible to predict the growth rate of an organism or the rate of production of a biotechnologically important metabolite. Philippe Rocca-Serra What is flux balance analysis? Jeffrey D. Orth, Ines Thiele, and Bernhard Ø. Palsson Nat Biotechnol. 2010 Mar; 28(3): 245–248. doi: 10.1038/nbt.1614 cosmos tracer based metabolomics working group flux balance analysis Philippe Rocca-Serra cosmos tracer based metabolomics working group 13C-constrained flux balance analysis an isotopomer data matrix is a table resulting from the analysis of NMR data acquired in the context of tracer based studies and which contains information about chemical entity assignment Philippe Rocca-Serra MSIO isotopomer data matrix Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry. BMC Bioinformatics. 2010 Mar 17;11:139. doi: 10.1186/1471-2105-11-139. natural abundance correction is a data transformation which aims to take into account the contribution of natural random variation in isotopic composition in the environment and adjust for it during the calculation of mass isotopologue distribution in a tracer based metabolomics experiment Hunter Moseley Philippe Rocca-Serra BMC Bioinformatics. 2010 Mar 17;11:139. doi: 10.1186/1471-2105-11-139. Correcting for the effects of natural abundance in stable isotope resolved metabolomics experiments involving ultra-high resolution mass spectrometry. cosmos tracer based metabolomics working group isotope natural abundance correction metabolic flux analysis is a type of investigation which uses data from tracer based studies to provide insights into cellular metabolites creation and destruction. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolic flux analysis steady-state 13C metabolic flux analysis is a metabolic flux analysis approach which relies on 13C tracer experiments and requires long incubation period necessary to meet methodological requirements that all reactions under study have reach steady state. By feeding cells a 13C-labeled substrate and subsequently measuring the patterns of isotope incorporation in downstream metabolic products, extensive information about the intracellular distribution of carbon flux can be obtained. This enables system-wide quantification of reversible, parallel, and cyclic metabolic pathways that would be otherwise unidentifiable based solely upon measurements of extracellular nutrient uptake and product excretion (Zamboni et al., 2009). While 13C MFA provides a rich source of phenotypic information, the application of this technique to mammalian systems presents unique challenges. In particular, the presence of subcellular compartmentation, complex media formulations, and slow labeling dynamics can lead to significant difficulties in experimental design and data interpretation (Zamboni, 2011). Philippe Rocca-Serra conventional 13C metabolic flux analysis conventional 13C-MFA EU H2020 PhenoMenAl cosmos tracer based metabolomics working group https://www.ncbi.nlm.nih.gov/pubmed/22140245 steady state 13C metabolic flux analysis Isotopically non-stationary MFA (INST-MFA) is a metabolic flux analysis which provides an approach to circumvent limitations from other methods through computational analysis of metabolite labeling patterns obtained during the transient labeling period prior to isotopic steady state (Wiechert and Noh, 2005). This approach offers several advantages over steady-state MFA, including shorter experimental times and the ability to determine fluxes with increased precision (Nöh and Wiechert, 2011; Young and Walther, 2008). Philippe Rocca-Serra INST-13C-MFA EU H2020 PhenoMenAl cosmos tracer based metabolomics working group https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535509/ isotopically non-stationary 13C-metabolic flux analysis a tracer analysis is a type of experimental procedure which relies on tracer molecules, usually non radioactive, to probe metabolic pathways and biochemical routes Philippe Rocca-Serra EU H2020 PhenoMenAl tracer analysis a normalization process which relies on the signal intensity measured for several reference compounds (internal standards) injected or added to the test samples in known quantities, thereby allowing sample comparison which have been placed on equal footing. Philippe Rocca-Serra cosmos tracer based metabolomics working group normalization by optimal selection with multiple internal standards a normalization process which relies on the computing to total signal intensity by simply summing up those signals and then for each sample measurements, dividing it by the total signal. The total sum is used as reference to which sample signals are then compared. Philippe Rocca-Serra cosmos tracer based metabolomics working group normalization to a total sum a normalization process used in mass spectrometry signal processing which takes into account the fact that analytes can interact with internal standards and impair accurate estimatation of these. The interaction phenomenon is known as cross contribution and needs to be compensated for. Philippe Rocca-Serra Compensation for Systematic Cross-Contribution Improves Normalization of Mass Spectrometry Based Metabolomics Data. Henning Redestig, Atsushi Fukushima, Hans Stenlund, Thomas Moritz, Masanori Arita, Kazuki Saito and Miyako Kusano. RIKEN Plant Science Center, Tsurumi-ku, Suehiro-cho, 1-7-22 Yokohama, Kanagawa, 230-0045, Japan, and Umea Plant Science Center, Umea University, 901 87 Umea, Sweden. Anal. Chem., 2009, 81 (19), pp 7974–7980 DOI: 10.1021/ac901143w cosmos tracer based metabolomics working group normalization to multiple standard with cross contribution compensation ruv_starter_analysis(Y,X,ctl) http://www-personal.umich.edu/~johanngb/ruv/howto/howto.html the 2 step normalization is a normalization process which uses 2 complementary steps provided suitable quality controls have been supplied. The process attempts to remove overall unwanted variation given suitable controls and uses factors of interest in the normalization. It relies on linear mixed effects model which utilizes quality control metabolites to obtain normalized data in typical metabolomics experiments. Philippe Rocca-Serra RUV RUV-2 Statistical Methods for Handling Unwanted Variation in Metabolomics Data. Alysha M. De Livera, Marko Sysi-Aho, Laurent Jacob, Johann A. Gagnon-Bartsch, Sandra Castillo, Julie A. Simpson, and Terence P. Speed Biostatistics Unit, Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC 3800, Australia Zora Biosciences Oy, FIN-02150 Espoo, Finland VTT Technical Research Centre of Finland, P. O. Box 1000, FI-02044 VTT Espoo, Finland Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, INRA, UMR5558, Villeurbanne, France Department of Statistics, University of California, Berkeley, California United States, 94720 Bioinformatics Division, Walter and Eliza Hall Institute, 1 G Royal Parade, Parkville, Victoria 3052, Australia Department of Mathematics and Statistics, University of Melbourne, VIC 3800, Melbourne, Australia Anal. Chem., 2015, 87 (7), pp 3606–3615 DOI: 10.1021/ac502439y Using control genes to correct for unwanted variation in microarray data. Gagnon-Bartsch and Speed, 2012. Available at: http://biostatistics.oxfordjournals.org/content/13/3/539.full. Removing Unwanted Variation from High Dimensional Data with Negative Controls. GagnonBartsch, Jacob, and Speed, 2013. Available at: http://statistics.berkeley.edu/tech-reports/820. cosmos tracer based metabolomics working group http://www-personal.umich.edu/~johanngb/ruv/index.html remove unwanted variation 2-step normalization a normalization process which relies on the signal intensity measured for one reference compound (an internal standard) injected or added to the test samples in known quantity, thereby allowing sample comparison which have been placed on equal footing based on this reference. Philippe Rocca-Serra cosmos tracer based metabolomics working group normalization to a single internal standard ribose extraction metabolite extraction is an extraction process which aims to retrieve small molecules known as metabolites, from a specimen Philippe Rocca-Serra EU H2020 PhenoMenAl metabolite extraction lipid extraction is an extraction which aims to retrieve lipid (hydrophobic carbohydrate) from a specimen Philippe Rocca-Serra EU H2020 PhenoMenAl lipid extraction polar metabolite extraction is a metabolite extraction which aims to retrieve water soluble or metabolites with polar solvent solubility properties. This is usually exclusive of hydrophobique, lipophile and lipid like metabolites. Philippe Rocca-Serra EU H2020 PhenoMenAl polar metabolite extraction cell layer enzymatic digestion is a material component separation process which uses an enzyme, usually a protease, to lyse the bonds between cultured cells and their substrates (usually a microplate, which may be coated with anchoring material such as collagen). Once the digestion is complete, cell layers can be harvested with minimal damage to the cells themselves. Philippe Rocca-Serra cosmos tracer based metabolomics working group cell layer enzymatic digestion cell scraping is a material component separation technique which uses mechanism means (as opposed to enzymatic ones) to detach cultured cells from the growth substrate. The technique is thought to be more aggressive and cause cellular breakage but has the benefit of avoiding use of enzymes, which may have their own side effects on cellular content. Philippe Rocca-Serra cosmos tracer based metabolomics working group cell scraping centrifugation is a material component separation process which relies on centrifugational forces applied by means of high velocity rotation to a sample placed in a vial or tube in a rotor, fixed to an centrifugation instrument. Philippe Rocca-Serra EU H2020 PhenoMenAl centrifugation gas chromatography is a material component separation process which use a mobile phase in gaseous form to force a mixture of chemical through chromatography columns and associated detecting equipment, which may be a mass spectrometry in GC-MS applications. Philippe Rocca-Serra GC EU H2020 PhenoMenAl gas chromatography high performance liquid chromatography is a kind of material component separation process which uses a mobile phase in liquid form to force a mixture of chemical through chromatography columns and associated detecting equipment, which may be a mass spectrometry in LC-MS applications. the notion of high performance comes from the fact that higher pressure is applied to the liquid phase to pass material with adsorbant properties. Those may vary depending on the composition of the mobile phase (gradients between 2 solutions may be used). Philippe Rocca-Serra HPLC EU H2020 PhenoMenAl adapted from https://en.wikipedia.org/wiki/High-performance_liquid_chromatography high performance liquid chromatography biomass is a rate measurement datum of how much biochemical or biological material is produced over a period of time. it is usually reported in 'per hour'. Philippe Rocca-Serra COSMOS EU H2020 PhenoMenAl biomass Flux, or metabolic flux is the rate of turnover of molecules through a metabolic pathway. Flux is regulated by the enzymes involved in a pathway. Within cells, regulation of flux is vital for all metabolic pathways to regulate the metabolic pathway's activity under different conditions. Flux is therefore of great interest in metabolic network modelling, where it is analysed via flux balance analysis. amount per unit of time maybe normalized by protein content Philippe Rocca-Serra metabolic rate http://en.wikipedia.org/wiki/Flux_%28metabolism%29 metabolic flux An extracellular flux is a metabolic flux indicating the rate of absortion or release of a molecular entity by a cell system from or to its surroundings, respectively. Philippe Rocca-Serra https://www.microbialcellfactories.com/content/13/1/152 EU H2020 PhenoMenAl cosmos tracer based metabolomics working group extracellular flux an excretion flux is a metabolic flux indicating the rate of release of a metabolite by a cell system to its surroundings. Alejandra Gonzalez-Beltran Philippe Rocca-Serra excretion rate EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolite excretion flux an uptake flux is a metabolic flux indicating the rate of absorption of a molecular entity by a cell system from its surroundings Philippe Rocca-Serra consumption rate uptake rate EU H2020 PhenoMenAl cosmos tracer based metabolomics working group metabolite uptake flux the reaction rate is a rate measurement datum denoting a biochemical reaction as measured according to standard experimental methods. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group reaction rate continuous fermentation cell culture is a type of processed material which involved a bacterial or yeast cell stock grown in conditions such as nutrients are added and product removed at a steady rate throughout the culture process. This is usually achieved using the specific type of fermenter known as a fed-batch culture reactor). classes could be moved to become subclasses of 'cell culture process' Philippe Rocca-Serra EU H2020 PhenoMenAl http://ib.bioninja.com.au/options/untitled/b1-microbiology-organisms/batch-versus-continuous.html continuous fermentation cell culture a cell culture population where cells are grown on top of each other, producing two layers of cells on the surface of the growth substrate, usually a flask or a petri dish classes could be moved to become subclasses of 'cell culture process' Philippe Rocca-Serra EU H2020 PhenoMenAl double layer cell culture a cell culture population where no cells are grown on top of each other, producing a single layer of cells on the surface of the growth substrate, usually a flask or a petri dish classes could be moved to become subclasses of 'cell culture process' Philippe Rocca-Serra EU H2020 PhenoMenAl monolayer cell culture https://www.ncbi.nlm.nih.gov/pubmed/20109035 a sandwich cell culture is a type of cell culture population where the grown cells are in contact with a substratum at the bottom and the top, thereby providing a more defined boundary and level of interaction than in suspension grown cells or in classic monolayer cell cultures. classes could be moved to become subclasses of 'cell culture process' Philippe Rocca-Serra EU H2020 PhenoMenAl sandwich cell culture a 3D cell culture is a cultured cell population grown in conditions which better mimicks in-vivo growth environment (i.e. more effectively than a 2D culture) allowing more complex recapitulation of cellular processes. These cell cultures are achieved by used of scaffolding agents. classes could be moved to become subclasses of 'cell culture process' Philippe Rocca-Serra spheroid culture EU H2020 PhenoMenAl https://www.thermofisher.com/blog/cellculture/3d-culturing-leads-parkinsons-breakthrough/ 3D cell culture A Chromatography column is a device used in chromatography for the separation of chemical compounds. A chromatography column contains the stationary phase, allowing the mobile phase to pass through it. Chromatography columns of different types are used in both gas and liquid chromatography. Alejandra Gonzalez-Beltran Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group https://en.wikipedia.org/wiki/Chromatography_column chromatography column Alejandra Gonzalez-Beltran Philippe Rocca-Serra An Instrument which is used to carry out a high performance liquid chromatography (HPLC; formerly referred to as high-pressure liquid chromatography) technique. HPLC is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture. It relies on pumps to pass a pressurized liquid solvent containing the sample mixture through a column filled with a solid adsorbent material. The schematic of an HPLC instrument typically includes a degasser, sampler, pumps, and a detector. The sampler brings the sample mixture into the mobile phase stream which carries it into the column. The pumps deliver the desired flow and composition of the mobile phase through the column. The detector generates a signal proportional to the amount of sample component emerging from the column, hence allowing for quantitative analysis of the sample components. A digital microprocessor and user software control the HPLC instrument and provide data analysis. EU H2020 PhenoMenAl https://en.wikipedia.org/wiki/High-performance_liquid_chromatography HPLC instrument 96-well microplate is an array of wells usually arranged in 8 rows of 12 columns whose volume range from 0.2 ml to 1.5 ml and which are used to grow cell or perform biochemical, in-vitro reactions. The material making up the plate may vary and may be surface treated in many custom way. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group 96-well microplate a chemostat is a device to which fresh medium is continuously added, while culture liquid is continuously removed to keep the culture volume constant. By changing the rate with which medium is added to the bioreactor the growth rate of the microorganism can be easily controlled. It allows culture to reach physiological steady state and chemostat is often used to gather steady state data about an organism in order to generate a mathematical model relating to its metabolic processes. The name chemostat stems from "Chemical environment is static". The most striking advantages of chemostats are two-fold: microorganisms can be kept at a constant environmental conditions until the cultivated microorganisms reach steady state, defined by their specific growth rate (μ) being in balance with the dilution rate (D). Once the system is equilibrated, the steady state data can be used for quantification of physiological parameters and metabolic rates of organisms, which are eventually required for the parameterization of mathematical models. Philippe Rocca-Serra 10.4319/lom.2014.12.432 http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.432/epdf EU H2020 PhenoMenAl cosmos tracer based metabolomics working group http://en.wikipedia.org/wiki/Chemostat chemostat a coated microplate is a kind of microplate whom surface has been treated in some, for instance by covalently attaching protein such as antibodies and cell matrix molecules to favor cell growth or induce speficic cellular behavior. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group coated microplate a constantly fed-btach culture reactor is a device in which the feed rate of a growth-limiting substrate is constant, i.e. the feed rate is invariant during the culture. Philippe Rocca-Serra CFBC EU H2020 PhenoMenAl cosmos tracer based metabolomics working group http://en.wikipedia.org/wiki/Fed-batch_culture#Constantly-fed-batch_culture http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.432/epdf constantly fed-batch culture reactor an exponentially fed-batch culture reactor is a device which deliver the ability to grow cells in a way non too dissimilar to that of a chemostat based culture, meaning that the cells are in a quasi steady-state condition. Philippe Rocca-Serra EFBC EU H2020 PhenoMenAl cosmos tracer based metabolomics working group http://onlinelibrary.wiley.com/doi/10.4319/lom.2014.12.432/epdf exponentially fed-batch culture reactor A container in which fermentation takes place. Alejandra Gonzalez-Beltran Philippe Rocca-Serra COSMOS tracer based metabolomics working group EU H2020 PhenoMenAl fermenter a flask is a kind of container used for cell culture, and which is available in an array of material (usually transparent plastic polymer) which may be surface treated. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group flask a petri dish is a container used to grow cells or perform biochemical reactions, which used to be made of glass, but which is now available in a variety of surface treated or non-treated plastic polymers. a petri dish is a thin cylinder with the upper part acting as a lid, resting on small peg, large enough to enable gaseaous exchanges but still preventing water evaporation. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group petri dish a uncoated microplate is a kind of microplate whom surface has not received any treatment and is uniquely made of polymer. Philippe Rocca-Serra EU H2020 PhenoMenAl cosmos tracer based metabolomics working group uncoated microplate EU H2020 PhenoMenAl mass spectrometry instrument import from NMRMLCV NMR instrument high dose is a dose specifically set to trigger strong response in the system it is administered to, those effects may be toxic. Also, the denomination allows a discrete, categorical classification of the dose points, irrespective of the actual quantity administered thereby allowing to capture the intent of the operator, something which is not necessary explicit when reading the quantitative dose reading (specific to a chemical entity and a system). Philippe Rocca-Serra EU H2020 PhenoMenAl high dose low dose is a dose specifically set to trigger no or very limited response in the system it is administered to, those effects are not expected to be toxic. Also, the denomination allows a discrete, categorical classification of the dose points, irrespective of the actual quantity administered thereby allowing to capture the intent of the operator, something which is not necessary explicit when reading the quantitative dose reading (specific to a chemical entity and a system). Philippe Rocca-Serra EU H2020 PhenoMenAl low dose a "lethal dose" represents a dose (usually recorded as dose per kilogram of subject body weight) at which a given percentage of subjects will die. Philippe Rocca-Serra EU H2020 PhenoMenAl https://en.wikipedia.org/wiki/Lethal_dose lethal dose the "lethal dose 50" represents a dose (usually recorded as dose per kilogram of subject body weight) at which 50% of subjects will die. Alejandra Gonzalez-Beltran Philippe Rocca-Serra LD50 EU H2020 PhenoMenAl https://en.wikipedia.org/wiki/Lethal_dose lethal dose 50 medium dose is a dose specifically set to trigger limited but clear response in the system it is administered to, those effects are not expected to be toxic but may be. Also, the denomination allows a discrete, categorical classification of the dose points, irrespective of the actual quantity administered thereby allowing to capture the intent of the operator, something which is not necessary explicit when reading the quantitative dose reading (specific to a chemical entity and a system). Philippe Rocca-Serra EU H2020 PhenoMenAl medium dose noael dose is a dose defined as the highest experimental point that is without adverse effect. Alejandra Gonzalez-Beltran Philippe Rocca-Serra No Observed Adverse Effect Level dose https://en.wikipedia.org/wiki/No-observed-adverse-effect_level NOAEL dose continuous fermentation cell culture is a type of processed material which involved a bacterial or yeast cell stock grown in conditions such as nutrients are added at the begining of the culture process and products removed at the end. classes could be moved to become subclasses of 'cell culture process' Alejandra Gonzalez-Beltran Philippe Rocca-Serra EU H2020 PhenoMenAl batch cell culture fluxomics is a kind of investigation which aims at identifying, quantifying the fluxes of molecules in cellular systems and understanding the cellular metabolism. Philippe Rocca-Serra cosmos tracer based metabolomics working group fluxomics investigation mass isotopomer fractional abundance is a measurement data item corresponding to the following: the most abundant species is given the value 100 and all other species are normalized relative to 100 and expressed as percent relative abundance. fractional abundance of Mx=Ax= (abundance Mx) / ∑(i=0..n) abundance Mi, where Mx represents mass isotopomer Mx. Alejandra Gonzalez-Beltran Philippe Rocca-Serra mass isotopomer distribution https://www.ncbi.nlm.nih.gov/pubmed/10362629 mass isotopomer fractional abundance steady state labeling experiment is a material processing used in fluxomics studies where cells cultures are grown continuously in the presence of radiolabeled tracer compound throughout multiple platings. The redistribution of the label into metabolic intermediates and end-products is analysed when the system has reached an isotopic and metabolic steady state. Philippe Rocca-Serra EU H2020 PhenoMenAl steady state isotopic labeling experiment the m/z notation is used for the independent variable in a mass spectrum. The mass-to-charge ratio (m/Q) is a physical quantity that is most widely used in the electrodynamics of charged particles, e.g. in electron optics and ion optics. It appears in the scientific fields of electron microscopy, cathode ray tubes, accelerator physics, nuclear physics, Auger electron spectroscopy, cosmology and mass spectrometry. Philippe Rocca-Serra adapted from wikipedia: https://en.wikipedia.org/wiki/Mass-to-charge_ratio m over z a m over z ratio which underwent a correction data transformation to take into account variations caused by a specific aspects of the data acquisition process. Philippe Rocca-Serra MSIO corrected m/z a m over z ratio which underwent a correction data transformation that takes into account the signal obtained from a reference compound and its spectral characteristics. Philippe Rocca-Serra MSIO reference corrected m/z a m over z ratio which underwent a correction data transformation that takes into account the signal obtained from a reference compound, its spectral characteristics as well as the contributions caused by adducts generated during the ionization process. Philippe Rocca-Serra MSIO reference and adduct corrected m/z Retention time (RT) is a measure of the time taken for a solute to pass through a chromatography column. It is calculated as the time from injection to detection. Philippe Rocca-Serra https://www.chromatographytoday.com/news/autosamplers/36/breaking-news/understanding-the-difference-between-retention-time-and-relative-retention-time/31166 retention time The area of a peak is a kind of data derived from a spectrum which is proportional to the product of its height and its width of a spectrum peak, but the proportionality constant depends on the peak shape. Philippe Rocca-Serra adapted from: https://terpconnect.umd.edu/~toh/spectrum/Integration.html peak area a normalized corrected peak area is a type of peak area which is produced followed a normalization data transformation and correction in order to make spectra comparable. Philippe Rocca-Serra MSIO normalized corrected peak area Signal intensity of all m/z values after integrating the whole peak and subtracting baseline Philippe Rocca-Serra peak area as signal intensity EU H2020 PhenoMenAl cosmos tracer based metabolomics working group total m/z signal intensity integrating over the whole peak with baseline substraction chemical entity assignment is an annotation which uses spectral information to assign and identify and molecular entity/chemical compound. Various methods manual and computer assisted may be used. Philippe Rocca-Serra chemical entity assignment assignment by database search is a type of chemical entity assignment which relies on probing chemical electronic libraries and chemical databases to determine matching structure and thereby attempt to assign a chemical identity. Searches may rely on InChi string or keys for instance. Philippe Rocca-Serra MSIO assignment by database search chemical entity assignment by direct assignment to standards is a data transformation process which uses spectral information from a known compound (ie. the standard) to match the signature and affirm identity based on the spectral features found in the sample. Philippe Rocca-Serra MSIO direct assignment to standard chemical entity assignment by indirect assignment to standards is a data transformation process which uses spectral information from a known compound (ie. the standard) to infer chemical properties about another compound found in the sample. Philippe Rocca-Serra MSIO indirect assignment to standard Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence. MS MS:1000898 standard A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard. MS MS:1000899 de facto standard A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result. MS MS:1000900 minimum information standard Viruses Viruses Euteleostomi bony vertebrates Euteleostomi Bacteria eubacteria Bacteria Archaea Archaea Eukaryota eucaryotes eukaryotes Eukaryota Euarchontoglires Euarchontoglires Tetrapoda tetrapods Tetrapoda Amniota amniotes Amniota Opisthokonta Opisthokonta Bilateria Bilateria Mammalia mammals Mammalia Vertebrata <Metazoa> Vertebrata vertebrates Vertebrata <Metazoa> Homo sapiens human human being man Homo sapiens planned process planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) CHMO:0001840 OBI:0000011 planned process planned process processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method CHMO:0000000 CHMO:0001133 measurement method OBI:0000070 assay assay quantitative confidence value A data item which is used to indicate the degree of uncertainty about a measurement. person:Chris Stoeckert group:OBI quantitative confidence value culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI culture medium reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush reagent PERSON:Matthew Brush Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent role material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing study subject role Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. 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. A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. GROUP: Role Branch OBI Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS participant under investigation role specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role intervention design PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. 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. Philppe Rocca-Serra OBI branch derived intervention design p-value PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2). A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. May be outside the scope of OBI long term, is needed so is retained PERSON:Chris Stoeckert WEB: http://en.wikipedia.org/wiki/P-value p-value population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass 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 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process population imaging assay An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. PlanAndPlannedProcess Branch OBI branch derived imaging assay organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization dye role A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. Jennifer Fostel dye A substance used to color materials www.answers.com/topic/dye 19feb09 dye role protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol analyte role Glucose in blood (measured in an assay to determine the concentration of glucose). A 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 interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. qualities such as weight, color are not assayed but measured, so they do not fall into this category. GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. analyte role interpreting data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data planning The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning contain function A syringe, a beaker A contain function is a function to constrain a material entities location in space Bill Bug Daniel Schober Frank Gibson Melanie Courtot contain function material separation function A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. Bill Bug Daniel Schober Frank Gibson Melanie Courtot material separation function averaging objective A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi averaging objective enzyme (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. person: Melanie Courtot GROUP:OBI enzyme analyte measurement objective The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant PERSON: Bjoern Peters PPPB branch analyte measurement objective assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective 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. 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 PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch analyte assay normalized data set A data set that is produced as the output of a normalization data transformation. PERSON: James Malone PERSON: Melanie Courtot normalized data set measure function A glucometer measures blood glucose concentration, the glucometer has a measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that carries out a study design removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. study design execution material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. bp bp material combination specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process error corrected data set A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for). PERSON: James Malone PERSON: Monnie McGee error corrected data set error correction data transformation An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. James Malone Monnie McGee EDITORS error correction data transformation center value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. PERSON: James Malone PERSON: Monnie McGee median center value portioning objective The objective to obtain multiple aliquots of an enzyme preparation. A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value separation into different composition objective The objective to obtain cells contained in a sample of blood. 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). We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective material combination objective is an objective to obtain an output material that contains several input materials. PPPB branch bp material combination objective material sample role a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. material sample role material sampling process A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity material sampling process material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample population sample material sample independent variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. 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 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) 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. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert experimental factor independent variable Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 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 thisdefinition please notify OBI. study factor study design independent variable dependent variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. 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. 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) 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. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert dependent variable WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 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 thisdefinition please notify OBI. study design dependent variable survival rate A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. Oliver He adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate survival rate multiple testing correction objective Application of the Bonferroni correction A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously multiple comparison correction objective http://en.wikipedia.org/wiki/Multiple_Testing_Correction multiple testing correction objective material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective primary structure of DNA macromolecule a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO BP et al primary structure of DNA macromolecule 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 process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance study intervention the part of the execution of an intervention design study which is varied between two or more subjects in the study PERSON: Bjoern Peters GROUP: OBI study intervention material separation device flow cytometer A device with a separation function realized in a planed process material separation device categorical measurement datum A measurement datum that is reported on a categorical scale Bjoern Peters nominal mesurement datum Bjoern Peters categorical measurement datum categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label container A device that can be used to restrict the location of material entities over time 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) PERSON: Bjoern Peters container device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device dose An organism has been injected 1ml of vaccine 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 dose response curve A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. Bjoern Peters; Randi Vita dose response curve genetic population background information genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information a genetic characteristics information which is a part of genotype information that identifies the population of organisms proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic population background information genotype information Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genotype information allele information genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_58 Allele allele information genetic alteration information a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic alteration information genetic characteristics information a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. Person: Chris Stoeckert, Jie Zheng MO_66 IndividualGeneticCharacteristics MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) genetic characteristics information q-value PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)" A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level. PERS:Philippe Rocca-Serra FDR adjusted p-value Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html q-value rate measurement datum The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. A scalar measurement datum that represents the number of events occuring over a time interval PERSON: Bjoern Peters, Randi Vita IEDB rate measurement datum selection criterion rats should be aged between 6 and 8 weeks and weight between 180-250grams A directive information entity which defines and states a principle of standard by which selection process may take place. Person: Philippe Rocca-Serra selection rule OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ selection criterion drawing a conclusion Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. A planned process in which new information is inferred from existing information. drawing a conclusion conclusion based on data The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group 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. PERSON: Matthew Brush cell freezing medium categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification 1 1 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. cultured cell population data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors method defneed data transformation altspcls: process ??? Benjamini and Hochberg false discovery rate correction method Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate) A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate 2011-03-31: [PRS]. specified input and output of dt which were missing Helen Parkinson Philippe Rocca-Serra Helen Parkinson Benjamini and Hochberg false discovery rate correction method Benjamini and Yekutieli false discovery rate correction method The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate 2011-03-31: [PRS]. specified input and output of dt which were missing Helen Parkinson Philippe Rocca-Serra Helen Parkinson Benjamini and Yekutieli false discovery rate correction method multiple testing correction method A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate Monnie McGee multiple testing procedure PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. multiple testing correction method logarithmic transformation A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm. Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Logarithm logarithmic transformation regression analysis method Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. Tina Hernandez-Boussard BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 regression analysis method data visualization Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data visualization false discovery rate correction method The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. . 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt Monnie McGee Philippe Rocca-Serra FDR correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate false discovery rate correction method data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective data normalization objective Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. 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. Elisabetta Manduchi Helen Parkinson James Malone PERSON: Elisabetta Manduchi PERSON: Helen Parkinson PERSON: James Malone data normalization objective correction objective Type I error correction A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself James Malone PERSON: James Malone PERSON: Melanie Courtot correction objective normalization data transformation A normalization data transformation is a data transformation that has objective normalization. James Malone PERSON: James Malone normalization data transformation averaging data transformation An averaging data transformation is a data transformation that has objective averaging. James Malone PERSON: James Malone averaging data transformation center calculation objective A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. James Malone PERSON: James Malone center calculation objective center calculation data transformation A center calculation data transformation is a data transformation that has objective of center calculation. James Malone PERSON: James Malone center calculation data transformation error correction objective Application of a multiple testing correction method An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. James Malone, Helen Parkinson PERSON: James Malone error correction objective observation design PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. Philippe Rocca-Serra OBI branch derived observation design extraction nucleic acid extraction using phenol chloroform A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. Person:Bjoern Peters Philippe Rocca-Serra extraction group randomization PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] group randomization study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design repeated measure design PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. 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 PlanAndPlannedProcess Branch http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design cross over design PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. 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 Philippe Rocca-Serra (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) cross over design time series design PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. Groups of assays that are related as part of a time series. Philippe Rocca-Serra on behalf of MO MO_887 time series design material component separation Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification a material processing in which components of an input material become segregated in space Bjoern Peters IEDB material component separation group assignment Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation group assignment is a process which has an organism as specified input and during which a role is assigned Philippe Rocca-Serra cohort assignment study assignment OBI Plan group assignment maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing PlanAndPlannedProcess Branch 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 PERSON:Matthew Brush A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. establishing cell culture 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. phenotype mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass protein antithrombin III is a protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. protein molecular label role a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role) molecular tracer role OBI developer call, 3-12-12 molecular label role 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. primary structure of sequence macromolecule sequence region length unit A unit which is a standard measure of the distance between two points. length unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. george gkoutos kg unit.ontology UO:0000009 kilogram 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. george gkoutos s unit.ontology UO:0000010 second A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water. george gkoutos K unit.ontology UO:0000012 kelvin A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. george gkoutos g unit.ontology UO:0000021 gram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. george gkoutos mg unit.ontology UO:0000022 milligram A mass unit which is equal to one millionth of a gram or 10^[-6] g. george gkoutos ug unit.ontology UO:0000023 microgram 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. george gkoutos C unit.ontology UO:0000027 degree Celsius A time unit which is equal to 60 seconds. george gkoutos min unit.ontology UO:0000031 minute A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. george gkoutos unit.ontology UO:0000036 year A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. george gkoutos mM unit.ontology UO:0000063 millimolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. george gkoutos uM unit.ontology UO:0000064 micromolar A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. george gkoutos millilitre ml unit.ontology UO:0000098 milliliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. george gkoutos microlitre ul unit.ontology UO:0000101 microliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. george gkoutos mg/ml milligram per millilitre unit.ontology UO:0000176 milligram per milliliter A dimensionless ratio unit which denotes numbers as fractions of 100. george gkoutos % unit.ontology UO:0000187 percent A magnetic flux density unit which is equal to one weber per square meter. george gkoutos T Wb/m2 unit.ontology UO:0000228 tesla A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters. George Gkoutos 2011-03-21T10:40:21Z ug/ml unit.ontology microgram per millilitre UO:0000274 microgram per milliliter A frequency unit which is equal to one million hertz or 10^[6] V. gkoutos 2013-12-06T12:17:48Z unit.ontology mH UO:0000325 megaHertz A category denoting a rather broad domain or field of interest, study, application, work, data, or technology. Topics have no clearly defined borders between each other. topic:0003 Topic Philippe Rocca-Serra isotopomer analysis Philippe Rocca-Serra isotopologue distribution analysis metabolism quenching by snap freeing in liquid nitrogen is a kind biochemical reaction extinction process which relies on extremely low temperature afforded by nitrogen in liquid state to denature enzymatic machinery of live cells or live tissue and inactivate it. Philippe Rocca-Serra LN2 snap freezing EU H2020 PhenoMenAl metabolism quenching by snap freezing in liquid nitrogen a normalization process which relies on the computing to arithmetic mean signal intensity over all measurements (controls and samples) and then for each sample measurements, adjusting the signal with the mean (by substracting the mean, allowing to retain measurement unit, which is not the case with dividing with the mean). The arithmetic mean is used as reference to which sample signals are then compared. Philippe Rocca-Serra cosmos tracer based metabolomics working group normalization to the mean import from PATO example to be eventually removed The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term 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 term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term 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 Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated 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 Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. other true Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term 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 Biocrates Life Sciences AG, a biotechnology company, develops and markets targeted metabolic phenotyping solutions that support the discovery and validation of biomarkers for complex multifactorial diseases in pre-clinical and clinical research. The company offers mass-spectrometry based reproducible and quantitative kits and services that analyze various endogenous metabolites; and tools for insight into pathways and metabolic signatures of diseases, such as cancer or neurodegenerative diseases. It also offers metabolic phenotyping, and biomarker discovery and development services. Alejandra Gonzalez-Beltran Philippe Rocca-Serra Biocrates Life Sciences AG https://www.bloomberg.com/research/stocks/private/snapshot.asp?privcapId=20741978 Biocrates AG Agilent Technologies is an American public research, development and manufacturing company established in 1999 as a spin-off from Hewlett-Packard. The resulting IPO of Agilent stock was the largest in the history of Silicon Valley at the time. The company provides analytical instruments, software, services and consumables for the entire laboratory workflow. Alejandra Gonzalez-Beltran Philippe Rocca-Serra Agilent https://en.wikipedia.org/wiki/Agilent_Technologies Agilent Technologies Bruker Corporation is a manufacturer of scientific instruments for molecular and materials research, as well as for industrial and applied analysis. It is headquartered in Billerica, Massachusetts and is the publicly traded parent company of Bruker Scientific Instruments (Bruker AXS, Bruker BioSpin, Bruker Daltonics and Bruker Optics) and Bruker Energy & Supercon Technologies (BEST) divisions. Bruker Bruker Corporation https://en.wikipedia.org/wiki/Bruker Bruker AG Thermo Fisher Scientific is an American multinational biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Alejandra Gonzalez-Beltran Philippe Rocca-Serra https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific Thermo Fisher Scientific ## 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 en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg Allyson Lister Barry Smith Bill Bug Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Chris Taylor Christian Bolling Cristian Cocos Daniel Rubin Daniel Schober Dawn Field Dirk Derom Elisabetta Manduchi Eric Deutsch Frank Gibson Gilberto Fragoso Helen C. Causton Helen Parkinson Holger Stenzhorn James A. Overton James Malone Jay Greenbaum Jeffrey Grethe Jennifer Fostel Jessica Turner Jie Zheng Joe White John Westbrook Kevin Clancy Larisa Soldatova Lawrence Hunter Liju Fan Luisa Montecchi Matthew Brush Matthew Pocock Melanie Courtot Melissa Haendel Mervi Heiskanen Monnie McGee Norman Morrison Philip Lord Philippe Rocca-Serra Pierre Grenon Richard Bruskiewich Richard Scheuermann Robert Stevens Ryan R. Brinkman Stefan Wiemann Susanna-Assunta Sansone Tanya Gray Tina Hernandez-Boussard Trish Whetzel Yongqun He 2009-07-31 The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. OWL-DL An ontology for the annotation of biomedical and functional genomics experiments. Ontology for Biomedical Investigation Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. 2017-09-03 SVN $Revision: 717 $ IAO Release 2015-02-23 Person:Alan Ruttenberg To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])