OBO: Types and relations

Classes | Datatype Properties | Annotation Properties | Object Properties | Named Individuals

Classes

obo:'dataset creating'


obo:'entity'

obo:'entity' has attributes:
  • Label: 'entity'
  • Definition:
  • obo:'entity' is a owl:Thing and has the following children: obo:'continuant', obo:'occurrent'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'
  • Editor Note: 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

obo:'continuant'

obo:'continuant' has attributes:
  • Label: 'continuant'
  • Definition: 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.
  • obo:'continuant' is a obo:'entity' and has the following children: obo:'generically dependent continuant', obo:'independent continuant', obo:'specifically dependent continuant'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'
  • Editor Note: 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

obo:'occurrent'

obo:'occurrent' has attributes:
  • Label: 'occurrent'
  • Definition: An entity that has temporal parts and that happens, unfolds or develops through time.
  • obo:'occurrent' is a obo:'entity' and has the following children: obo:'process boundary', obo:'process'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'
  • Editor Note: 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

obo:'independent continuant'

obo:'independent continuant' has attributes:

obo:'spatial region'

obo:'spatial region' has attributes:

obo:'process'

obo:'process' has attributes:
  • Label: 'process'
  • Definition: 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])
  • obo:'process' is a obo:'occurrent' and has the following children: nidm:'Blood Draw', nidm:'Image Data Reconstruction', nidm:'Model Specification', nidm:'Project', nidm:'Radioactivity', nidm:'Resting', nidm:'Session', nidm:'Task', obo:'biological_process', obo:'planned process', obo:'planned process', obo:'planning'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'
  • Editor Note: 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)

obo:'disposition'

obo:'disposition' has attributes:

obo:'realizable entity'

obo:'realizable entity' has attributes:

obo:'zero-dimensional spatial region'

obo:'zero-dimensional spatial region' has attributes:

obo:'quality'

obo:'quality' has attributes:

obo:'specifically dependent continuant'

obo:'specifically dependent continuant' has attributes:
  • Label: 'specifically dependent continuant'
  • Definition: 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])
  • obo:'specifically dependent continuant' is a obo:'continuant' and has the following children: obo:'quality', obo:'quality', obo:'realizable entity'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'
  • Editor Note: 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.

obo:'role'

obo:'role' has attributes:

obo:'one-dimensional spatial region'

obo:'one-dimensional spatial region' has attributes:

obo:'object aggregate'

obo:'object aggregate' has attributes:

obo:'three-dimensional spatial region'

obo:'three-dimensional spatial region' has attributes:

obo:'site'

obo:'site' has attributes:

obo:'object'

obo:'object' has attributes:
  • Label: 'object'
  • Definition:
  • obo:'object' is a obo:'material entity'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'
  • Editor Note: 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.

obo:'generically dependent continuant'

obo:'generically dependent continuant' has attributes:

obo:'function'

obo:'function' has attributes:

obo:'process boundary'

obo:'process boundary' has attributes:

obo:'material entity'

obo:'material entity' has attributes:

obo:'continuant fiat boundary'

obo:'continuant fiat boundary' has attributes:
  • Label: 'continuant fiat boundary'
  • Definition: 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])
  • obo:'continuant fiat boundary' is a obo:'immaterial entity'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'
  • Editor Note: 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.

obo:'immaterial entity'

obo:'immaterial entity' has attributes:

obo:'relational quality'

obo:'relational quality' has attributes:
  • Label: 'relational quality'
  • Definition: 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])
  • obo:'relational quality' is a obo:'quality'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'anatomical entity'

obo:'anatomical entity' has attributes:

obo:'connected anatomical structure'

obo:'connected anatomical structure' has attributes:

obo:'material anatomical entity'

obo:'material anatomical entity' has attributes:

obo:'immaterial anatomical entity'

obo:'immaterial anatomical entity' has attributes:

obo:'cellular organism'

obo:'cellular organism' has attributes:

obo:'polynucleotide'

obo:'polynucleotide' has attributes:

obo:'peptide'

obo:'peptide' has attributes:
  • Label: 'peptide'
  • Definition: 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..
  • obo:'peptide' is a obo:'organic amino compound' and has the following child: obo:'protein'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'deoxyribonucleic acid'

obo:'deoxyribonucleic acid' has attributes:

obo:'molecular entity'

obo:'molecular entity' has attributes:

obo:'chemical entity'

obo:'chemical entity' has attributes:

obo:'main group molecular entity'

obo:'main group molecular entity' has attributes:

obo:'carbon group molecular entity'

obo:'carbon group molecular entity' has attributes:

obo:'p-block molecular entity'

obo:'p-block molecular entity' has attributes:

obo:'biomacromolecule'

obo:'biomacromolecule' has attributes:

obo:'information biomacromolecule'

obo:'information biomacromolecule' has attributes:

obo:'nucleic acid'

obo:'nucleic acid' has attributes:

obo:'organic amino compound'

obo:'organic amino compound' has attributes:

obo:'organic molecular entity'

obo:'organic molecular entity' has attributes:

obo:'cell'

obo:'cell' has attributes:

obo:'cultured cell'

obo:'cultured cell' has attributes:

obo:'neuron'

obo:'neuron' has attributes:
  • Label: 'neuron'
  • Definition: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
  • obo:'neuron' is a obo:'neural cell'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'experimentally modified cell in vitro'

obo:'experimentally modified cell in vitro' has attributes:

obo:'neural cell'

obo:'neural cell' has attributes:

obo:'geographical location'

obo:'geographical location' has attributes:

obo:'planned process'

obo:'planned process' has attributes:

obo:'failed planned process'

obo:'failed planned process' has attributes:

obo:'evaluant role'

obo:'evaluant role' has attributes:

obo:'information representation'

obo:'information representation' has attributes:

obo:'measurement datum'

obo:'measurement datum' has attributes:

obo:GAZ_00000448

obo:GAZ_00000448 has attributes:

obo:'action potential'

obo:'action potential' has attributes:
  • Label: 'action potential'
  • Definition: A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
  • obo:'action potential' is a obo:'biological_process'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'ion channel activity'

obo:'ion channel activity' has attributes:
  • Label: 'ion channel activity'
  • Definition: Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
  • obo:'ion channel activity' is a obo:'cellular process'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'biological_process'

obo:'biological_process' has attributes:
  • Label: 'biological_process'
  • Definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
  • obo:'biological_process' is a obo:'process' and has the following children: obo:'action potential', obo:'cellular process', obo:'pathologic process'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'cellular process'

obo:'cellular process' has attributes:

obo:'conditional specification'

obo:'conditional specification' has attributes:

obo:'measurement unit label'

obo:'measurement unit label' has attributes:

obo:'objective specification'

obo:'objective specification' has attributes:

obo:'action specification'

obo:'action specification' has attributes:

obo:'datum label'

obo:'datum label' has attributes:

obo:'software'

obo:'software' has attributes:

obo:'journal article'

obo:'journal article' has attributes:

obo:'model number'

obo:'model number' has attributes:
  • Label: 'model number'
  • Definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
  • obo:'model number' is a obo:'symbol'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Person: Alan Ruttenberg
  • Editor Note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers

obo:'programming language'

obo:'programming language' has attributes:

obo:'data item'

obo:'data item' has attributes:

obo:'symbol'

obo:'symbol' has attributes:

obo:'numeral'

obo:'numeral' has attributes:

obo:'information content entity'

obo:'information content entity' has attributes:

obo:'integer numeral'

obo:'integer numeral' has attributes:

obo:'scalar measurement datum'

obo:'scalar measurement datum' has attributes:

obo:'directive information entity'

obo:'directive information entity' has attributes:

obo:'graph'

obo:'graph' has attributes:

obo:'rule'

obo:'rule' has attributes:

obo:'algorithm'

obo:'algorithm' has attributes:
  • Label: 'algorithm'
  • Definition: 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.
  • obo:'algorithm' is a obo:'plan specification'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Philippe Rocca-Serra

obo:'curation status specification'

obo:'curation status specification' has attributes:
  • Label: 'curation status specification'
  • Definition: 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.
  • obo:'curation status specification' is a obo:'data about an ontology part'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON:Bill Bug
  • Editor Note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
Examples of obo:'curation status specification' includes
  • obo:'example to be eventually removed':
  • obo:'metadata complete': Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
  • obo:'metadata incomplete': Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
  • obo:'organizational term': Term created to ease viewing/sort terms for development purpose, and will not be included in a release
  • obo:'pending final vetting': All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
  • obo:'ready for release': Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
  • obo:'requires discussion': A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
  • obo:'to be replaced with external ontology term': Terms with this status should eventually replaced with a term from another ontology.
  • obo:'uncurated': Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

obo:'report'

obo:'report' has attributes:
  • Label: 'report'
  • Definition: A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).
  • obo:'report' is a obo:'document' and has the following child: obo:'journal article'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: Alan Ruttenberg
  • Editor Note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.

obo:'data format specification'

obo:'data format specification' has attributes:
  • Label: 'data format specification'
  • Definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
  • obo:'data format specification' is a obo:'directive information entity'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: PERSON: Alan Ruttenberg
  • Editor Note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
Examples of obo:'data format specification' includes
  • obo:'tar': Tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
  • obo:'zip': Zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)

obo:'data set'

obo:'data set' has attributes:

obo:'image'

obo:'image' has attributes:
  • Label: 'image'
  • Definition: 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.
  • obo:'image' is a obo:'figure'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: person:Alan Ruttenberg

obo:'data about an ontology part'

obo:'data about an ontology part' has attributes:

obo:'plan specification'

obo:'plan specification' has attributes:

obo:'measurement datum'

obo:'measurement datum' has attributes:

obo:'version number'

obo:'version number' has attributes:
  • Label: 'version number'
  • Definition: 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.
  • obo:'version number' is a obo:'symbol'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: GROUP: IAO
  • Editor Note: 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

obo:'serial number'

obo:'serial number' has attributes:
  • Label: 'serial number'
  • Definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
  • obo:'serial number' is a obo:'symbol'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: GROUP: IAO
  • Editor Note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)

obo:'conclusion textual entity'

obo:'conclusion textual entity' has attributes:

obo:'material information bearer'

obo:'material information bearer' has attributes:

obo:'obsolescence reason specification'

obo:'obsolescence reason specification' has attributes:
  • Label: 'obsolescence reason specification'
  • Definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
  • obo:'obsolescence reason specification' is a obo:'data about an ontology part'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: Alan Ruttenberg
  • Editor Note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
Examples of obo:'obsolescence reason specification' includes

obo:'textual entity'

obo:'textual entity' has attributes:

obo:'citation'

obo:'citation' has attributes:

obo:'author identification'

obo:'author identification' has attributes:

obo:'institutional identification'

obo:'institutional identification' has attributes:

obo:'document title'

obo:'document title' has attributes:

obo:'figure'

obo:'figure' has attributes:

obo:'diagram'

obo:'diagram' has attributes:

obo:'document'

obo:'document' has attributes:

obo:'publication'

obo:'publication' has attributes:

obo:'document part'

obo:'document part' has attributes:

obo:'abstract'

obo:'abstract' has attributes:

obo:'cartesian spatial coordinate datum'

obo:'cartesian spatial coordinate datum' has attributes:
  • Label: 'cartesian spatial coordinate datum'
  • Definition: 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
  • obo:'cartesian spatial coordinate datum' is a obo:'data item' and has the following child: obo:'one dimensional cartesian spatial coordinate datum'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Alan Ruttenberg
  • Editor Note: 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

obo:'one dimensional cartesian spatial coordinate datum'

obo:'one dimensional cartesian spatial coordinate datum' has attributes:

obo:'length measurement datum'

obo:'length measurement datum' has attributes:

obo:'mass measurement datum'

obo:'mass measurement datum' has attributes:

obo:'time measurement datum'

obo:'time measurement datum' has attributes:

obo:'email address'

obo:'email address' has attributes:

obo:'author role'

obo:'author role' has attributes:
  • Label: 'author role'
  • Definition: A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
  • obo:'author role' is a obo:'role'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: Alan Ruttenberg

obo:'publishing process'

obo:'publishing process' has attributes:

obo:'document in preparation for publication'

obo:'document in preparation for publication' has attributes:

obo:'documenting'

obo:'documenting' has attributes:
  • Label: 'documenting'
  • Definition: A planned process in which a document is created or added to by including the specified input in it.
  • obo:'documenting' is a obo:'planned process' and has the following child: obo:'digital curation'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Bjoern Peters
  • Editor Note: 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

obo:'assigning a centrally registered identifier'

obo:'assigning a centrally registered identifier' has attributes:

obo:'centrally registered identifier symbol'

obo:'centrally registered identifier symbol' has attributes:

obo:'centrally registered identifier'

obo:'centrally registered identifier' has attributes:
  • Label: 'centrally registered identifier'
  • Definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
  • obo:'centrally registered identifier' is a obo:'identifier' and has the following child: obo:'ORCID identifier'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON: Alan Ruttenberg
  • Editor Note: 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').

obo:'centrally registered identifier registry'

obo:'centrally registered identifier registry' has attributes:

obo:'time stamped measurement datum'

obo:'time stamped measurement datum' has attributes:

obo:'time sampled measurement data set'

obo:'time sampled measurement data set' has attributes:
  • Label: 'time sampled measurement data set'
  • Definition: 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.
  • obo:'time sampled measurement data set' is a obo:'data set'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Alan Ruttenberg

obo:'written name'

obo:'written name' has attributes:

obo:'software module'

obo:'software module' has attributes:

obo:'software library'

obo:'software library' has attributes:
  • Label: 'software library'
  • Definition: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
  • obo:'software library' is a obo:'software'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: PERSON: Melanie Courtot

obo:'software application'

obo:'software application' has attributes:

obo:'software script'

obo:'software script' has attributes:

obo:'consent textual entity'

obo:'consent textual entity' has attributes:

obo:'ethical approval textual entity'

obo:'ethical approval textual entity' has attributes:

obo:'requirements textual entity'

obo:'requirements textual entity' has attributes:

obo:'postal code'

obo:'postal code' has attributes:

obo:'zone improvement plan code'

obo:'zone improvement plan code' has attributes:

obo:'ORCID identifier'

obo:'ORCID identifier' has attributes:
  • Label: 'ORCID identifier'
  • Definition: A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor.
  • obo:'ORCID identifier' is a obo:'centrally registered identifier'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: ns1:0000-0002-1595-3213
  • Editor Note: "You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/]

obo:'identifier'

obo:'identifier' has attributes:

obo:'identifier creating process'

obo:'identifier creating process' has attributes:

obo:'personal name'

obo:'personal name' has attributes:

obo:'given name'

obo:'given name' has attributes:
  • Label: 'given name'
  • Definition: A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
  • obo:'given name' is a obo:'personal name'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'
  • Editor: Justin Whorton

obo:'family name'

obo:'family name' has attributes:
  • Label: 'family name'
  • Definition: An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
  • obo:'family name' is a obo:'identifier'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'
  • Editor: Justin Whorton

obo:'code set'

obo:'code set' has attributes:

obo:'Viruses'

obo:'Viruses' has attributes:

obo:'Euteleostomi'

obo:'Euteleostomi' has attributes:

obo:'Bacteria'

obo:'Bacteria' has attributes:

obo:'Archaea'

obo:'Archaea' has attributes:

obo:'Eukaryota'

obo:'Eukaryota' has attributes:

obo:'Euarchontoglires'

obo:'Euarchontoglires' has attributes:

obo:'Tetrapoda'

obo:'Tetrapoda' has attributes:

obo:'Amniota'

obo:'Amniota' has attributes:

obo:'Opisthokonta'

obo:'Opisthokonta' has attributes:

obo:'Metazoa'

obo:'Metazoa' has attributes:

obo:'Bilateria'

obo:'Bilateria' has attributes:

obo:'Mammalia'

obo:'Mammalia' has attributes:

obo:'Vertebrata '

obo:'Vertebrata ' has attributes:

obo:'Homo sapiens'

obo:'Homo sapiens' has attributes:

obo:'biological attribute'

obo:'biological attribute' has attributes:

obo:'limb coordination efficacy'

obo:'limb coordination efficacy' has attributes:

obo:'upper limb coordination efficacy'

obo:'upper limb coordination efficacy' has attributes:

obo:'lower limb coordination efficacy'

obo:'lower limb coordination efficacy' has attributes:

obo:'whole organism stability'

obo:'whole organism stability' has attributes:

obo:'planned process'

obo:'planned process' has attributes:

obo:'material supplier role'

obo:'material supplier role' has attributes:

obo:'classified data set'

obo:'classified data set' has attributes:

obo:'processed material'

obo:'processed material' has attributes:

obo:'investigation'

obo:'investigation' has attributes:

obo:'evaluant role'

obo:'evaluant role' has attributes:
  • Label: 'evaluant role'
  • Definition: 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
  • obo:'evaluant role' is a obo:'role' and has the following child: obo:'magnetic resonance imaging evaluant role'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: GROUP: Role Branch
  • Editor Note: 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)

obo:'assay'

obo:'assay' has attributes:

obo:'quantitative confidence value'

obo:'quantitative confidence value' has attributes:

obo:'sample preparation for assay'

obo:'sample preparation for assay' has attributes:

obo:'culture medium'

obo:'culture medium' has attributes:
  • Label: 'culture medium'
  • Definition: A processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
  • obo:'culture medium' is a obo:'processed material'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Person: Jennifer Fostel, Jie Zheng
  • Editor Note: 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.

obo:'reagent role'

obo:'reagent role' has attributes:
  • Label: 'reagent role'
  • Definition: 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.
  • obo:'reagent role' is a obo:'role'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON:Matthew Brush

obo:'material processing'

obo:'material processing' has attributes:

obo:'participant under investigation role'

obo:'participant under investigation role' has attributes:
  • Label: 'participant under investigation role'
  • Definition: 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.
  • obo:'participant under investigation role' is a obo:'role'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: GROUP: Role Branch
  • Editor Note: 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.

obo:'specimen role'

obo:'specimen role' has attributes:
  • Label: 'specimen role'
  • Definition: 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
  • obo:'specimen role' is a obo:'role' and has the following child: obo:'material sample role'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: GROUP: Role Branch
  • Editor Note: 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.

obo:'intervention design'

obo:'intervention design' has attributes:
  • Label: 'intervention design'
  • Definition: 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.
  • obo:'intervention design' is a obo:'study design' and has the following children: obo:'randomized complete block design', obo:'repeated measure design', obo:'sequential design'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Philppe Rocca-Serra

obo:'hardware testing objective'

obo:'hardware testing objective' has attributes:

obo:'filter paper'

obo:'filter paper' has attributes:

obo:'study group role'

obo:'study group role' has attributes:
  • Label: 'study group role'
  • Definition: A study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
  • obo:'study group role' is a obo:'role'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: Jennifer Fostel

obo:'p-value'

obo:'p-value' has attributes:
  • Label: 'p-value'
  • Definition: 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.
  • obo:'p-value' is a obo:'quantitative confidence value'.
  • Type: owl:Class
  • Curation Status: obo:'organizational term'
  • Editor: PERSON:Chris Stoeckert
  • Editor Note: May be outside the scope of OBI long term, is needed so is retained

obo:'population'

obo:'population' has attributes:
  • Label: 'population'
  • Definition: 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
  • obo:'population' is a obo:'material entity'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: Philippe Rocca-Serra
  • Editor Note: 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/

obo:'imaging assay'

obo:'imaging assay' has attributes:

obo:'investigation agent role'

obo:'investigation agent role' has attributes:
  • Label: 'investigation agent role'
  • Definition: A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
  • obo:'investigation agent role' is a obo:'role' and has the following child: obo:'specimen collector role'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: GROUP: Role Branch
  • Editor Note: Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.

obo:'methodology testing objective'

obo:'methodology testing objective' has attributes:

obo:'organization'

obo:'organization' has attributes:
  • Label: 'organization'
  • Definition: 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.
  • obo:'organization' is a obo:'material entity' and has the following children: obo:'biomedical laboratory organization', obo:'clinical study center', obo:'courier organization', obo:'grant agency', obo:'molecular analysis facility organization', obo:'organization of specimen collector', obo:'specimen repository organization'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: PERSON: Alan Ruttenberg
  • Editor Note: 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.

obo:'plan'

obo:'plan' has attributes:

obo:'protocol'

obo:'protocol' has attributes:

obo:'adding a material entity into a target'

obo:'adding a material entity into a target' has attributes:

obo:'material to be added role'

obo:'material to be added role' has attributes:

obo:'drawing a conclusion based on data'

obo:'drawing a conclusion based on data' has attributes:

obo:'planning'

obo:'planning' has attributes:
  • Label: 'planning'
  • Definition: A process of creating or modifying a plan specification
  • obo:'planning' is a obo:'process'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Bjoern Peters
  • Editor Note: 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'.

obo:'histological sample preparation'

obo:'histological sample preparation' has attributes:

obo:'light emission function'

obo:'light emission function' has attributes:

obo:'magnify function'

obo:'magnify function' has attributes:

obo:'contain function'

obo:'contain function' has attributes:

obo:'heat function'

obo:'heat function' has attributes:

obo:'material separation function'

obo:'material separation function' has attributes:

obo:'excitation function'

obo:'excitation function' has attributes:
  • Label: 'excitation function'
  • Definition: A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
  • obo:'excitation function' is a obo:'function' and has the following child: obo:'light emission function'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Bill Bug

obo:'filter function'

obo:'filter function' has attributes:

obo:'mechanical function'

obo:'mechanical function' has attributes:

obo:'transfer function'

obo:'transfer function' has attributes:

obo:'electricity supply function'

obo:'electricity supply function' has attributes:

obo:'cool function'

obo:'cool function' has attributes:

obo:'energy supply function'

obo:'energy supply function' has attributes:

obo:'information processor function'

obo:'information processor function' has attributes:

obo:'signal conversion function'

obo:'signal conversion function' has attributes:

obo:'signal amplification function'

obo:'signal amplification function' has attributes:
  • Label: 'signal amplification function'
  • Definition: A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal.
  • obo:'signal amplification function' is a obo:'signal conversion function'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Bill Bug

obo:'image acquisition function'

obo:'image acquisition function' has attributes:

obo:'image creation device'

obo:'image creation device' has attributes:

obo:'solid support function'

obo:'solid support function' has attributes:

obo:'environment control function'

obo:'environment control function' has attributes:

obo:'syringe'

obo:'syringe' has attributes:
  • Label: 'syringe'
  • Definition: A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
  • obo:'syringe' is a obo:'device'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Philippe Rocca-Serra

obo:'extract'

obo:'extract' has attributes:

obo:'averaging objective'

obo:'averaging objective' has attributes:

obo:'injection'

obo:'injection' has attributes:

obo:'adding material objective'

obo:'adding material objective' has attributes:

obo:'analyte measurement objective'

obo:'analyte measurement objective' has attributes:

obo:'assay objective'

obo:'assay objective' has attributes:

obo:'analyte assay'

obo:'analyte assay' has attributes:

obo:'target of material addition role'

obo:'target of material addition role' has attributes:
  • Label: 'target of material addition role'
  • Definition: A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity.
  • obo:'target of material addition role' is a obo:'role'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: GROUP: Role Branch
  • Editor Note: From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.

obo:'intracellular electrophysiology recording assay'

obo:'intracellular electrophysiology recording assay' has attributes:

obo:'normalized data set'

obo:'normalized data set' has attributes:

obo:'measure function'

obo:'measure function' has attributes:

obo:'extracellular electrophysiology recording assay'

obo:'extracellular electrophysiology recording assay' has attributes:

obo:'consume data function'

obo:'consume data function' has attributes:

obo:'material transformation objective'

obo:'material transformation objective' has attributes:

obo:'manufacturing'

obo:'manufacturing' has attributes:
  • Label: 'manufacturing'
  • Definition: Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
  • obo:'manufacturing' is a obo:'material processing'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: PERSON: Bjoern Peters
  • Editor Note: Manufacturing implies reproducibility and responsibility AR

obo:'manufacturing objective'

obo:'manufacturing objective' has attributes:

obo:'study design execution'

obo:'study design execution' has attributes:

obo:'NMR instrument'

obo:'NMR instrument' has attributes:

obo:'manufacturer role'

obo:'manufacturer role' has attributes:

obo:'scattered molecular aggregate'

obo:'scattered molecular aggregate' has attributes:

obo:'material separation objective'

obo:'material separation objective' has attributes:

obo:'clustered data set'

obo:'clustered data set' has attributes:

obo:'data set of features'

obo:'data set of features' has attributes:
  • Label: 'data set of features'
  • Definition: A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
  • obo:'data set of features' is a obo:'data set'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: James Malone

obo:'material combination'

obo:'material combination' has attributes:

obo:'blood specimen'

obo:'blood specimen' has attributes:

obo:'data set of predicted values according to fitted curve'

obo:'data set of predicted values according to fitted curve' has attributes:

obo:'specimen collection process'

obo:'specimen collection process' has attributes:

obo:'error corrected data set'

obo:'error corrected data set' has attributes:
  • Label: 'error corrected data set'
  • Definition: 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).
  • obo:'error corrected data set' is a obo:'data set'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: James Malone

obo:'class prediction data transformation'

obo:'class prediction data transformation' has attributes:

obo:'error correction data transformation'

obo:'error correction data transformation' has attributes:

obo:'sample from organism'

obo:'sample from organism' has attributes:

obo:'center value'

obo:'center value' has attributes:

obo:'portioning objective'

obo:'portioning objective' has attributes:

obo:'average value'

obo:'average value' has attributes:

obo:'separation into different composition objective'

obo:'separation into different composition objective' has attributes:

obo:'specimen collection objective'

obo:'specimen collection objective' has attributes:

obo:'creating a mixture of molecules in solution'

obo:'creating a mixture of molecules in solution' has attributes:

obo:'material combination objective'

obo:'material combination objective' has attributes:

obo:'material sample role'

obo:'material sample role' has attributes:
  • Label: 'material sample role'
  • Definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
  • obo:'material sample role' is a obo:'specimen role'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor Note: 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.

obo:'material sampling process'

obo:'material sampling process' has attributes:

obo:'material sample'

obo:'material sample' has attributes:

obo:'study design independent variable'

obo:'study design independent variable' has attributes:
  • Label: 'study design independent variable'
  • Definition: 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
  • obo:'study design independent variable' is a obo:'directive information entity'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: PERSON: Alan Ruttenberg
  • Editor Note: 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.

obo:'multiple testing correction objective'

obo:'multiple testing correction objective' has attributes:

obo:'statistical model validation'

obo:'statistical model validation' has attributes:

obo:'material maintenance objective'

obo:'material maintenance objective' has attributes:

obo:'informed consent process'


obo:'primary structure of DNA macromolecule'

obo:'primary structure of DNA macromolecule' has attributes:

obo:'micro electrode'

obo:'micro electrode' has attributes:
  • Label: 'micro electrode'
  • Definition: An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system.
  • obo:'micro electrode' is a obo:'measurement device'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Helen Parkinson, Jessica Turner, Dirk Derom

obo:'measurement device'


obo:'manufacturer'

obo:'manufacturer' has attributes:
Examples of obo:'manufacturer' includes

obo:'material maintenance'

obo:'material maintenance' has attributes:

obo:'subject agrees they understand informed consent document'


obo:'record of missing knowledge'

obo:'record of missing knowledge' has attributes:
  • Label: 'record of missing knowledge'
  • Definition: An information content entity created to indicate that information about something is not available to the person recording it.
  • obo:'record of missing knowledge' is a obo:'information content entity'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Bjoern Peters
  • Editor Note: This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.

obo:'pre-mortem specimen'

obo:'pre-mortem specimen' has attributes:

obo:'post mortem specimen'

obo:'post mortem specimen' has attributes:

obo:'freezing storage'

obo:'freezing storage' has attributes:
  • Label: 'freezing storage'
  • Definition: A storage process in temperature that maintenance the frozen status of the stored entities.
  • obo:'freezing storage' is a obo:'storage'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Person: Alan Ruttenberg, Mathias Brochhausen
  • Editor Note: 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen.

obo:'frozen specimen'

obo:'frozen specimen' has attributes:

obo:'lyophilization storage'

obo:'lyophilization storage' has attributes:

obo:'study intervention'

obo:'study intervention' has attributes:

obo:'material separation device'

obo:'material separation device' has attributes:

obo:'positron emission tomography scanner'

obo:'positron emission tomography scanner' has attributes:

obo:'categorical measurement datum'

obo:'categorical measurement datum' has attributes:

obo:'training process'

obo:'training process' has attributes:

obo:'service consumer role'

obo:'service consumer role' has attributes:

obo:'handedness assay'

obo:'handedness assay' has attributes:

obo:'service provider role'

obo:'service provider role' has attributes:

obo:'paraffin specimen'

obo:'paraffin specimen' has attributes:

obo:'processed specimen'

obo:'processed specimen' has attributes:

obo:'self reported handedness assessment'

obo:'self reported handedness assessment' has attributes:

obo:'training objective'

obo:'training objective' has attributes:

obo:'categorical label'

obo:'categorical label' has attributes:
Examples of obo:'categorical label' includes

obo:'lyophilized specimen'

obo:'lyophilized specimen' has attributes:

obo:'container'

obo:'container' has attributes:
  • Label: 'container'
  • Definition: A device that can be used to restrict the location of material entities over time
  • obo:'container' is a obo:'device' and has the following children: obo:'physical store', obo:'specimen container', obo:'syringe pump'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: PERSON: Bjoern Peters
  • Editor Note: 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?)

obo:'device'

obo:'device' has attributes:
  • Label: 'device'
  • Definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
  • obo:'device' is a obo:'processed material' and has the following children: nidm:'Data Processing Device', nidm:'Phantom', nidm:'Signal Filter', nidm:'Signal Generator', nidm:'Stimulus Generator', nidm:'Stimulus Isolator', nidm:'Transmit Coil', obo:'analog-to-digital converter', obo:'assay array', obo:'assay kit', obo:'computer', obo:'container', obo:'cotton swab', obo:'digital-to-analog converter', obo:'environmental control device', obo:'light emission device', obo:'material separation device', obo:'measurement device', obo:'microscope slide', obo:'pipette', obo:'power supply', obo:'specimen collection device', obo:'syringe', obo:'voltage amplifier'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: PERSON: Helen Parkinson
  • Editor Note: 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.

obo:'scalar score from composite inputs'

obo:'scalar score from composite inputs' has attributes:

obo:'fresh specimen'

obo:'fresh specimen' has attributes:

obo:'sequence data'

obo:'sequence data' has attributes:

obo:'handedness categorical measurement datum'

obo:'handedness categorical measurement datum' has attributes:

obo:'paraffin storage'

obo:'paraffin storage' has attributes:

obo:'agar stab specimen'

obo:'agar stab specimen' has attributes:

obo:'computed tomography scanner'

obo:'computed tomography scanner' has attributes:

obo:'dose'

obo:'dose' has attributes:
  • Label: 'dose'
  • Definition: 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.
  • obo:'dose' is a obo:'measurement datum'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'

obo:'electron microscope'

obo:'electron microscope' has attributes:

obo:'Edinburgh score'

obo:'Edinburgh score' has attributes:

obo:'intravenous injection'

obo:'intravenous injection' has attributes:

obo:'administration of material to specimen'

obo:'administration of material to specimen' has attributes:

obo:'questionnaire'

obo:'questionnaire' has attributes:
  • Label: 'questionnaire'
  • Definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
  • obo:'questionnaire' is a obo:'document'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON: Jessica Turner
  • Editor Note: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Examples of obo:'questionnaire' includes

obo:'Edinburgh handedness assay'

obo:'Edinburgh handedness assay' has attributes:
  • Label: 'Edinburgh handedness assay'
  • Definition: An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
  • obo:'Edinburgh handedness assay' is a obo:'handedness assay'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Alan Ruttenberg

obo:'agar stab storage'

obo:'agar stab storage' has attributes:

obo:'image creation'

obo:'image creation' has attributes:

obo:'nucleic acid extract'

obo:'nucleic acid extract' has attributes:

obo:'feature extraction'

obo:'feature extraction' has attributes:

obo:'array image creation'

obo:'array image creation' has attributes:

obo:'light emission device'

obo:'light emission device' has attributes:

obo:'environmental control device'

obo:'environmental control device' has attributes:

obo:'SPECT scanner'

obo:'SPECT scanner' has attributes:
  • Label: 'SPECT scanner'
  • Definition: A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required.
  • obo:'SPECT scanner' is a obo:'image creation device'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON: Erik Segerdell

obo:'patch clamp device'

obo:'patch clamp device' has attributes:

obo:'ultrasound machine'

obo:'ultrasound machine' has attributes:

obo:'nucleic acid sequencer'

obo:'nucleic acid sequencer' has attributes:

obo:'voltage clamp device'

obo:'voltage clamp device' has attributes:

obo:'protein sequencer'

obo:'protein sequencer' has attributes:

obo:'age measurement datum'

obo:'age measurement datum' has attributes:
  • Label: 'age measurement datum'
  • Definition: A time measurement datum that is the result of measurement of age of an organism
  • obo:'age measurement datum' is a obo:'time measurement datum' and has the following child: obo:'age since birth measurement datum'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
  • Editor Note: note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage.

obo:'age since birth measurement datum'

obo:'age since birth measurement datum' has attributes:

obo:'service'

obo:'service' has attributes:

obo:'FWER adjusted p-value'

obo:'FWER adjusted p-value' has attributes:

obo:'q-value'

obo:'q-value' has attributes:
  • Label: 'q-value'
  • Definition: 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.
  • obo:'q-value' is a obo:'quantitative confidence value'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: PERS:Philippe Rocca-Serra

obo:'specimen with known storage state'

obo:'specimen with known storage state' has attributes:

obo:'specimen from organism'

obo:'specimen from organism' has attributes:

obo:'specimen with pre- or post-mortem status'

obo:'specimen with pre- or post-mortem status' has attributes:

obo:'sampling time measurement datum'

obo:'sampling time measurement datum' has attributes:

obo:'material maintenance service'

obo:'material maintenance service' has attributes:

obo:'material service'

obo:'material service' has attributes:

obo:'data service'

obo:'data service' has attributes:

obo:'data storage service'

obo:'data storage service' has attributes:

obo:'material analysis service'

obo:'material analysis service' has attributes:

obo:'material storage service'

obo:'material storage service' has attributes:

obo:'material processing service'

obo:'material processing service' has attributes:
  • Label: 'material processing service'
  • Definition: A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer.
  • obo:'material processing service' is a obo:'material service'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: Carlo Torniai

obo:'DNA sequence data'

obo:'DNA sequence data' has attributes:

obo:'material transport service'

obo:'material transport service' has attributes:

obo:'data maintenance service'

obo:'data maintenance service' has attributes:
  • Label: 'data maintenance service'
  • Definition: A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance.
  • obo:'data maintenance service' is a obo:'data service'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: Carlo Torniai

obo:'investigation description'

obo:'investigation description' has attributes:

obo:'specimen identifier'

obo:'specimen identifier' has attributes:

obo:'PubMed ID'

obo:'PubMed ID' has attributes:
  • Label: 'PubMed ID'
  • Definition: A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
  • obo:'PubMed ID' is a obo:'centrally registered identifier symbol'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Person: Chris Stoeckert, Jie Zheng
  • Editor Note: Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/

obo:'specimen collection time measurement datum'

obo:'specimen collection time measurement datum' has attributes:

obo:'investigation title'

obo:'investigation title' has attributes:

obo:'country name'

obo:'country name' has attributes:

obo:'investigation identifier'

obo:'investigation identifier' has attributes:

obo:'grant identifier'

obo:'grant identifier' has attributes:

obo:'grant'

obo:'grant' has attributes:
  • Label: 'grant'
  • Definition: A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role.
  • obo:'grant' is a obo:'plan specification'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Group: OBI
  • Editor Note: Discussed on Feb 13, 2012 dev call. Details see the tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178

obo:'selection criterion'

obo:'selection criterion' has attributes:

obo:'specimen collector role'

obo:'specimen collector role' has attributes:

obo:'drawing a conclusion'

obo:'drawing a conclusion' has attributes:

obo:'assay array'

obo:'assay array' has attributes:

obo:'genetic material'

obo:'genetic material' has attributes:
  • Label: 'genetic material'
  • Definition: A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants.
  • obo:'genetic material' is a obo:'nucleic acid'.
  • Type: owl:Class
  • Curation Status: obo:'requires discussion'
  • Editor Note: MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion).

obo:'number of errors'

obo:'number of errors' has attributes:

obo:'random access memory size'

obo:'random access memory size' has attributes:

obo:'random access memory'

obo:'random access memory' has attributes:
  • Label: 'random access memory'
  • Definition: Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location
  • obo:'random access memory' is a obo:'material information bearer'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Alejandra Gonzalez-Beltran

obo:'reagent'

obo:'reagent' has attributes:
  • Label: 'reagent'
  • Definition: A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
  • obo:'reagent' is a obo:'processed material'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON:Matthew Brush
  • Editor Note: 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at 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 examples, see editor note on OBI:device.

obo:'target material in specimen specification'

obo:'target material in specimen specification' has attributes:

obo:'specimen repository organization'

obo:'specimen repository organization' has attributes:

obo:'email address of specimen collector'

obo:'email address of specimen collector' has attributes:

obo:'sequencing facility organization'

obo:'sequencing facility organization' has attributes:

obo:'organization of specimen collector'

obo:'organization of specimen collector' has attributes:

obo:'specimen collector'

obo:'specimen collector' has attributes:

obo:'comment on investigation'

obo:'comment on investigation' has attributes:

obo:'specimen identifier assigned by specimen repository'

obo:'specimen identifier assigned by specimen repository' has attributes:

obo:'specimen identifier assigned by sequencing facility'

obo:'specimen identifier assigned by sequencing facility' has attributes:

obo:'sample preparation for sequencing assay'

obo:'sample preparation for sequencing assay' has attributes:

obo:'sequencing service'

obo:'sequencing service' has attributes:

obo:'testable hypothesis'

obo:'testable hypothesis' has attributes:
  • Label: 'testable hypothesis'
  • Definition: An information content entity that expresses an assertion that is intended to be tested.
  • obo:'testable hypothesis' is a obo:'information content entity'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Group:2013 Philly Workshop group
  • Editor Note: In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.

obo:'conclusion based on data'

obo:'conclusion based on data' has attributes:

obo:'cell freezing medium'

obo:'cell freezing medium' has attributes:

obo:'computation run time'

obo:'computation run time' has attributes:
  • Label: 'computation run time'
  • Definition: Computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency.
  • obo:'computation run time' is a obo:'time measurement datum'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Alejandra Gonzalez-Beltran

obo:'selection'

obo:'selection' has attributes:
  • Label: 'selection'
  • Definition: A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
  • obo:'selection' is a obo:'planned process' and has the following children: obo:'acquisition', obo:'human subject enrollment'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Person: Philippe Rocca-Serra
  • Editor Note: this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary)

obo:'mass value specification'

obo:'mass value specification' has attributes:

obo:'categorical value specification'

obo:'categorical value specification' has attributes:

obo:'scalar value specification'

obo:'scalar value specification' has attributes:

obo:'comparing prediction to measurement'

obo:'comparing prediction to measurement' has attributes:

obo:'value specification'

obo:'value specification' has attributes:

obo:'predicted value'

obo:'predicted value' has attributes:
  • Label: 'predicted value'
  • Definition: An information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error.
  • obo:'predicted value' is a obo:'information content entity'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: PERSON:Bjoern Peters

obo:'grant agency'

obo:'grant agency' has attributes:

obo:'software pipeline'

obo:'software pipeline' has attributes:
  • Label: 'software pipeline'
  • Definition: A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements.
  • obo:'software pipeline' is a obo:'plan specification'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON: Jie Zheng, Chris Stoeckert

obo:'freezing'

obo:'freezing' has attributes:
  • Label: 'freezing'
  • Definition: A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities.
  • obo:'freezing' is a obo:'planned process'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Person: Mathias Brochhausen, Jie Zheng

obo:'hardware testing design'

obo:'hardware testing design' has attributes:

obo:'cytometry assay'

obo:'cytometry assay' has attributes:

obo:'in vivo intervention experiment'

obo:'in vivo intervention experiment' has attributes:

obo:'treatment intervention experiment'

obo:'treatment intervention experiment' has attributes:

obo:'microarray assay'

obo:'microarray assay' has attributes:

obo:'collection of specimens'

obo:'collection of specimens' has attributes:

obo:'specimens derived from shared ancestor'

obo:'specimens derived from shared ancestor' has attributes:

obo:'specimen set collection process'

obo:'specimen set collection process' has attributes:

obo:'specimens collected in one encounter'

obo:'specimens collected in one encounter' has attributes:

obo:'human specimen set'

obo:'human specimen set' has attributes:

obo:'specimens collected longitudinally'

obo:'specimens collected longitudinally' has attributes:

obo:'containing a specimen function'

obo:'containing a specimen function' has attributes:
  • Label: 'containing a specimen function'
  • Definition: A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay.
  • obo:'containing a specimen function' is a obo:'contain function'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Chris Stoeckert
  • Editor Note: For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/

obo:'specimen container'

obo:'specimen container' has attributes:

obo:'physical store'

obo:'physical store' has attributes:

obo:'specimen family creation'

obo:'specimen family creation' has attributes:

obo:'digital object identifier'

obo:'digital object identifier' has attributes:

obo:'microscopy assay'

obo:'microscopy assay' has attributes:

obo:'H&E slide staining'

obo:'H&E slide staining' has attributes:
  • Label: 'H&E slide staining'
  • Definition: A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink.
  • obo:'H&E slide staining' is a obo:'staining'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Chris Stoeckert, Ned Haubein

obo:'H&E-stained fixed tissue slide specimen'

obo:'H&E-stained fixed tissue slide specimen' has attributes:

obo:'temperature value specification'

obo:'temperature value specification' has attributes:

obo:'volume value specification'

obo:'volume value specification' has attributes:

obo:'temperature measurement assay'

obo:'temperature measurement assay' has attributes:

obo:'volume measurement assay'

obo:'volume measurement assay' has attributes:

obo:'dot blot assay'

obo:'dot blot assay' has attributes:

obo:'electrophysiology assay'

obo:'electrophysiology assay' has attributes:

obo:'patch clamp assay'

obo:'patch clamp assay' has attributes:

obo:'whole-cell patch clamp assay'

obo:'whole-cell patch clamp assay' has attributes:
  • Label: 'whole-cell patch clamp assay'
  • Definition: A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.
  • obo:'whole-cell patch clamp assay' is a obo:'patch clamp assay'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Gully Burns

obo:'cell-attached patch clamp assay'

obo:'cell-attached patch clamp assay' has attributes:
  • Label: 'cell-attached patch clamp assay'
  • Definition: A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.
  • obo:'cell-attached patch clamp assay' is a obo:'patch clamp assay'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Gully Burns

obo:'inside-out patch clamp assay'

obo:'inside-out patch clamp assay' has attributes:
  • Label: 'inside-out patch clamp assay'
  • Definition: A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations.
  • obo:'inside-out patch clamp assay' is a obo:'patch clamp assay'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Gully Burns

obo:'outside-out patch clamp assay'

obo:'outside-out patch clamp assay' has attributes:
  • Label: 'outside-out patch clamp assay'
  • Definition: A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels.
  • obo:'outside-out patch clamp assay' is a obo:'patch clamp assay'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Gully Burns

obo:'voltage clamp assay'

obo:'voltage clamp assay' has attributes:

obo:'two electrode voltage clamp assay'

obo:'two electrode voltage clamp assay' has attributes:
  • Label: 'two electrode voltage clamp assay'
  • Definition: The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation.
  • obo:'two electrode voltage clamp assay' is a obo:'voltage clamp assay'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Gully Burns

obo:'cut open oocyte voltage clamp assay'

obo:'cut open oocyte voltage clamp assay' has attributes:
  • Label: 'cut open oocyte voltage clamp assay'
  • Definition: The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques.
  • obo:'cut open oocyte voltage clamp assay' is a obo:'voltage clamp assay'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Gully Burns

obo:'current clamp assay'

obo:'current clamp assay' has attributes:
  • Label: 'current clamp assay'
  • Definition: The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels.
  • obo:'current clamp assay' is a obo:'intracellular electrophysiology recording assay'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Gully Burns

obo:'electroencephalography'

obo:'electroencephalography' has attributes:

obo:'single-unit recording'

obo:'single-unit recording' has attributes:
  • Label: 'single-unit recording'
  • Definition: An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique.
  • obo:'single-unit recording' is a obo:'extracellular electrophysiology recording assay'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Gully Burns
  • Editor Note: Can be used on any cell, not just neurons.

obo:'multi-unit recording'

obo:'multi-unit recording' has attributes:

obo:'local field potential recording'

obo:'local field potential recording' has attributes:

obo:'courier organization'

obo:'courier organization' has attributes:

obo:'courier tracking number'

obo:'courier tracking number' has attributes:

obo:'tissue section thickness'

obo:'tissue section thickness' has attributes:

obo:'molecular analysis facility organization'

obo:'molecular analysis facility organization' has attributes:

obo:'reason for lack of data item'

obo:'reason for lack of data item' has attributes:

obo:'cannot be assessed determination'

obo:'cannot be assessed determination' has attributes:

obo:'physical examination of individual'

obo:'physical examination of individual' has attributes:

obo:'measurand role'

obo:'measurand role' has attributes:
  • Label: 'measurand role'
  • Definition: A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
  • obo:'measurand role' is a obo:'role'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Person: Alan Ruttenberg, Jie Zheng

obo:'health status inclusion criterion'

obo:'health status inclusion criterion' has attributes:
  • Label: 'health status inclusion criterion'
  • Definition: An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process.
  • obo:'health status inclusion criterion' is a obo:'inclusion criterion'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: Mathias Brochhausen

obo:'gravidity inclusion criterion'

obo:'gravidity inclusion criterion' has attributes:

obo:'defined population inclusion criterion'

obo:'defined population inclusion criterion' has attributes:

obo:'date process started'

obo:'date process started' has attributes:

obo:'specimen harvest quantity'

obo:'specimen harvest quantity' has attributes:

obo:'pipette'

obo:'pipette' has attributes:
  • Label: 'pipette'
  • Definition: A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser.
  • obo:'pipette' is a obo:'device'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios

obo:'medication time value specification'

obo:'medication time value specification' has attributes:

obo:'medication dose value specification'

obo:'medication dose value specification' has attributes:

obo:'cerebrospinal fluid specimen'

obo:'cerebrospinal fluid specimen' has attributes:

obo:'saliva specimen'

obo:'saliva specimen' has attributes:

obo:'brain specimen'

obo:'brain specimen' has attributes:

obo:'age group inclusion criterion'

obo:'age group inclusion criterion' has attributes:

obo:'minimum age value specification'

obo:'minimum age value specification' has attributes:

obo:'maximum age value specification'

obo:'maximum age value specification' has attributes:

obo:'ethnicity inclusion criterion'

obo:'ethnicity inclusion criterion' has attributes:

obo:'histopathology assay'

obo:'histopathology assay' has attributes:

obo:'file merge'

obo:'file merge' has attributes:

obo:'machine learning'

obo:'machine learning' has attributes:

obo:'supervised machine learning'

obo:'supervised machine learning' has attributes:

obo:'unsupervised machine learning'

obo:'unsupervised machine learning' has attributes:

obo:'swab specimen'

obo:'swab specimen' has attributes:

obo:'collecting specimen with swab'

obo:'collecting specimen with swab' has attributes:

obo:'cheek swab specimen'

obo:'cheek swab specimen' has attributes:

obo:'nasopharyngeal swab specimen'

obo:'nasopharyngeal swab specimen' has attributes:

obo:'disease specific study design'

obo:'disease specific study design' has attributes:

obo:'ordinal value specification'

obo:'ordinal value specification' has attributes:
  • Label: 'ordinal value specification'
  • Definition: A categorical value specification in which the available categories were created with an explicit order.
  • obo:'ordinal value specification' is a obo:'categorical value specification'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Mark Andrew Miller, ORCID:0000-0001-9076-6066
  • Editor Note: https://en.wikipedia.org/wiki/Ordinal_data provides references for follow-up, but more than one OBI developer has objected to "...whose levels have natural, ordered categories and the distances between those categories is not known..." Separate from that, an OBI mechanism for asserting the order of ordinal values specification levels with OWL has not been determined yet.

obo:'specimen collection device'

obo:'specimen collection device' has attributes:

obo:'cotton swab'

obo:'cotton swab' has attributes:

obo:'magnetic resonance imaging assay'

obo:'magnetic resonance imaging assay' has attributes:

obo:'computed tomography imaging assay'

obo:'computed tomography imaging assay' has attributes:

obo:'positron emission tomography imaging assay'

obo:'positron emission tomography imaging assay' has attributes:

obo:'material supplier'

obo:'material supplier' has attributes:

obo:'blood assay'

obo:'blood assay' has attributes:

obo:'clinical study center'

obo:'clinical study center' has attributes:

obo:'specimen collection protocol'

obo:'specimen collection protocol' has attributes:

obo:'participant identifier'

obo:'participant identifier' has attributes:

obo:'organismal body temperature measurement datum'

obo:'organismal body temperature measurement datum' has attributes:

obo:'common name of organism'

obo:'common name of organism' has attributes:

obo:'age since birth at time of enrollment'

obo:'age since birth at time of enrollment' has attributes:

obo:'age since birth at time of visit'

obo:'age since birth at time of visit' has attributes:

obo:'temperature measurement datum'

obo:'temperature measurement datum' has attributes:

obo:'extraction date'

obo:'extraction date' has attributes:

obo:'biomedical laboratory organization'

obo:'biomedical laboratory organization' has attributes:

obo:'in silico design'

obo:'in silico design' has attributes:

obo:'image data set'

obo:'image data set' has attributes:

obo:'magnetic resonance image data set'

obo:'magnetic resonance image data set' has attributes:

obo:'magnetic resonance imaging participant'

obo:'magnetic resonance imaging participant' has attributes:

obo:'magnetic resonance imaging evaluant role'

obo:'magnetic resonance imaging evaluant role' has attributes:

obo:'raw image data set'

obo:'raw image data set' has attributes:

obo:'magnetic resonance pulse sequence protocol'

obo:'magnetic resonance pulse sequence protocol' has attributes:

obo:'image data set analysis'

obo:'image data set analysis' has attributes:

obo:'organism diagnostic process'

obo:'organism diagnostic process' has attributes:

obo:'diagnosis of an organism'

obo:'diagnosis of an organism' has attributes:

obo:'detection technique'

obo:'detection technique' has attributes:

obo:'assay kit'

obo:'assay kit' has attributes:
  • Label: 'assay kit'
  • Definition: A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit.
  • obo:'assay kit' is a obo:'device'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: John Judkins

obo:'remote patient assessment'

obo:'remote patient assessment' has attributes:

obo:'administering substance in vivo to reduce or prevent disease'

obo:'administering substance in vivo to reduce or prevent disease' has attributes:

obo:'in vivo challenge'

obo:'in vivo challenge' has attributes:

obo:'functional assessment of individual'

obo:'functional assessment of individual' has attributes:

obo:'finger taps assessment'

obo:'finger taps assessment' has attributes:

obo:'limits of stability assessment'

obo:'limits of stability assessment' has attributes:

obo:'observational assessment of individual'

obo:'observational assessment of individual' has attributes:

obo:'blood plasma specimen'

obo:'blood plasma specimen' has attributes:
  • Label: 'blood plasma specimen'
  • Definition: A material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
  • obo:'blood plasma specimen' is a obo:'processed specimen'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON: Maura Gasparetto
  • Editor Note: 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.

obo:'blood serum specimen'

obo:'blood serum specimen' has attributes:

obo:'organism'

obo:'organism' has attributes:
  • Label: 'organism'
  • Definition: 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.
  • obo:'organism' is a obo:'material entity' and has the following children: obo:'Archaea', obo:'Bacteria', obo:'Eukaryota', obo:'Viruses', obo:'cellular organism'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: GROUP: OBI Biomaterial Branch
  • Editor Note: 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')

obo:'specimen'

obo:'specimen' has attributes:

obo:'cultured cell population'

obo:'cultured cell population' has attributes:
  • Label: 'cultured cell population'
  • Definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
  • obo:'cultured cell population' is a obo:'processed material'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON:Matthew Brush
  • Editor Note: 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.

obo:'organ section'

obo:'organ section' has attributes:
  • Label: 'organ section'
  • Definition: A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
  • obo:'organ section' is a obo:'processed material'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: Helen Parkinson

obo:'data transformation'


obo:'feature extraction objective'

obo:'feature extraction objective' has attributes:

obo:'mean centering'

obo:'mean centering' has attributes:

obo:'median centering'

obo:'median centering' has attributes:

obo:'leave one out cross validation method'

obo:'leave one out cross validation method' has attributes:
  • Label: 'leave one out cross validation method'
  • Definition: Is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
  • obo:'leave one out cross validation method' is a obo:'statistical model validation'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: Person:Helen Parkinson
  • Editor Note: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178

obo:'jackknifing method'

obo:'jackknifing method' has attributes:

obo:'boostrapping'

obo:'boostrapping' has attributes:
  • Label: 'boostrapping'
  • Definition: Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient
  • obo:'boostrapping' is a obo:'statistical model validation'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Helen Parkinson

obo:'Benjamini and Hochberg false discovery rate correction method'

obo:'Benjamini and Hochberg false discovery rate correction method' has attributes:

obo:'k-means clustering'

obo:'k-means clustering' has attributes:
  • Label: 'k-means clustering'
  • Definition: A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
  • obo:'k-means clustering' is a obo:'class discovery data transformation'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Elisabetta Manduchi

obo:'hierarchical clustering'

obo:'hierarchical clustering' has attributes:
  • Label: 'hierarchical clustering'
  • Definition: A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
  • obo:'hierarchical clustering' is a obo:'class discovery data transformation'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: James Malone

obo:'Benjamini and Yekutieli false discovery rate correction method'

obo:'Benjamini and Yekutieli false discovery rate correction method' has attributes:

obo:'dimensionality reduction'

obo:'dimensionality reduction' has attributes:

obo:'principal components analysis dimensionality reduction'

obo:'principal components analysis dimensionality reduction' has attributes:

obo:'moving average'

obo:'moving average' has attributes:

obo:'data imputation'

obo:'data imputation' has attributes:
  • Label: 'data imputation'
  • Definition: Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm.
  • obo:'data imputation' is a obo:'data transformation'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Monnie McGee

obo:'Holm-Bonferroni family-wise error rate correction method'

obo:'Holm-Bonferroni family-wise error rate correction method' has attributes:
  • Label: 'Holm-Bonferroni family-wise error rate correction method'
  • Definition: A data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction
  • obo:'Holm-Bonferroni family-wise error rate correction method' is a obo:'family wise error rate correction method'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Person:Helen Parkinson
  • Editor Note: 2011-03-14: [PRS]. Class Label has been changed to address the conflict with the definition Also added restriction to specify the output to be a FWER adjusted p-value The 'editor preferred term' should be removed

obo:'curve fitting data transformation'

obo:'curve fitting data transformation' has attributes:

obo:'family wise error rate correction method'

obo:'family wise error rate correction method' has attributes:

obo:'descriptive statistical calculation objective'

obo:'descriptive statistical calculation objective' has attributes:

obo:'arithmetic mean calculation'

obo:'arithmetic mean calculation' has attributes:
  • Label: 'arithmetic mean calculation'
  • Definition: An arithmetic mean calculation 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.
  • obo:'arithmetic mean calculation' is a obo:'averaging data transformation'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: James Malone

obo:'network analysis'

obo:'network analysis' has attributes:

obo:'sequence analysis objective'

obo:'sequence analysis objective' has attributes:

obo:'longitudinal data analysis'

obo:'longitudinal data analysis' has attributes:

obo:'multiple testing correction method'

obo:'multiple testing correction method' has attributes:

obo:'inter-rater reliability objective'

obo:'inter-rater reliability objective' has attributes:

obo:'regression analysis method'

obo:'regression analysis method' has attributes:

obo:'multiple linear regression analysis'

obo:'multiple linear regression analysis' has attributes:
  • Label: 'multiple linear regression analysis'
  • Definition: Multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression.
  • obo:'multiple linear regression analysis' is a obo:'regression analysis method'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Tina Hernandez-Boussard

obo:'principal component regression'

obo:'principal component regression' has attributes:
  • Label: 'principal component regression'
  • Definition: The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores.
  • obo:'principal component regression' is a obo:'class discovery data transformation'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Tina Hernandez-Boussard

obo:'partial least square regression analysis'

obo:'partial least square regression analysis' has attributes:
  • Label: 'partial least square regression analysis'
  • Definition: Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that Y = b0 + b1X1 + b2X2 + ... + bpXp In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data.
  • obo:'partial least square regression analysis' is a obo:'regression analysis method'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Tina Hernandez-Boussard

obo:'discriminant analysis'

obo:'discriminant analysis' has attributes:

obo:'data visualization'

obo:'data visualization' has attributes:

obo:'similarity calculation'

obo:'similarity calculation' has attributes:

obo:'euclidean distance calculation'

obo:'euclidean distance calculation' has attributes:
  • Label: 'euclidean distance calculation'
  • Definition: An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered.
  • obo:'euclidean distance calculation' is a obo:'similarity calculation'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Elisabetta Manduchi

obo:'pearson correlation coefficient calculation'

obo:'pearson correlation coefficient calculation' has attributes:
  • Label: 'pearson correlation coefficient calculation'
  • Definition: A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered.
  • obo:'pearson correlation coefficient calculation' is a obo:'similarity calculation'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Elisabetta Manduchi

obo:'data combination'

obo:'data combination' has attributes:

obo:'network graph construction'

obo:'network graph construction' has attributes:

obo:'data partitioning'

obo:'data partitioning' has attributes:

obo:'generalized family wise error rate correction method'

obo:'generalized family wise error rate correction method' has attributes:

obo:'false discovery rate correction method'

obo:'false discovery rate correction method' has attributes:

obo:'data transformation objective'


obo:'data normalization objective'

obo:'data normalization objective' has attributes:

obo:'correction objective'

obo:'correction objective' has attributes:

obo:'normalization data transformation'

obo:'normalization data transformation' has attributes:

obo:'averaging data transformation'

obo:'averaging data transformation' has attributes:

obo:'partitioning data transformation'

obo:'partitioning data transformation' has attributes:

obo:'partitioning objective'

obo:'partitioning objective' has attributes:

obo:'curve fitting objective'

obo:'curve fitting objective' has attributes:

obo:'class discovery data transformation'

obo:'class discovery data transformation' has attributes:

obo:'center calculation objective'

obo:'center calculation objective' has attributes:

obo:'class discovery objective'

obo:'class discovery objective' has attributes:
  • Label: 'class discovery objective'
  • Definition: A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
  • obo:'class discovery objective' is a obo:'data transformation objective'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: James Malone

obo:'class prediction objective'

obo:'class prediction objective' has attributes:
  • Label: 'class prediction objective'
  • Definition: A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
  • obo:'class prediction objective' is a obo:'data transformation objective'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: James Malone

obo:'center calculation data transformation'

obo:'center calculation data transformation' has attributes:

obo:'scaling objective'

obo:'scaling objective' has attributes:

obo:'descriptive statistical calculation data transformation'

obo:'descriptive statistical calculation data transformation' has attributes:

obo:'scaling data transformation'

obo:'scaling data transformation' has attributes:

obo:'error correction objective'

obo:'error correction objective' has attributes:

obo:'cross validation objective'

obo:'cross validation objective' has attributes:
  • Label: 'cross validation objective'
  • Definition: A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
  • obo:'cross validation objective' is a obo:'partitioning objective'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: James Malone

obo:'merging objective'

obo:'merging objective' has attributes:

obo:'correlation study objective'

obo:'correlation study objective' has attributes:

obo:'sequential design'

obo:'sequential design' has attributes:
  • Label: 'sequential design'
  • Definition: Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does
  • obo:'sequential design' is a obo:'intervention design'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Philippe Rocca-Serra

obo:'observation design'

obo:'observation design' has attributes:

obo:'chemical solution'

obo:'chemical solution' has attributes:

obo:'solvent role'

obo:'solvent role' has attributes:

obo:'solute role'

obo:'solute role' has attributes:

obo:'curated information'

obo:'curated information' has attributes:
  • Label: 'curated information'
  • Definition: An information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts.
  • obo:'curated information' is a obo:'information content entity'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Person:Bjoern Peters
  • Editor Note: 2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions.

obo:'randomized group participant role'

obo:'randomized group participant role' has attributes:

obo:'mean-centered data'

obo:'mean-centered data' has attributes:

obo:'edited document'

obo:'edited document' has attributes:

obo:'extraction'

obo:'extraction' has attributes:
  • Label: 'extraction'
  • Definition: A material separation in which a desired component of an input material is separated from the remainder
  • obo:'extraction' is a obo:'material component separation' and has the following child: obo:'nucleic acid extraction'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: Person:Bjoern Peters
  • Editor Note: 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.

obo:'filtration'

obo:'filtration' has attributes:

obo:'centrifugation'

obo:'centrifugation' has attributes:

obo:'staining'

obo:'staining' has attributes:

obo:'storage'

obo:'storage' has attributes:

obo:'group randomization'

obo:'group randomization' has attributes:

obo:'document editing'

obo:'document editing' has attributes:

obo:'validation'

obo:'validation' has attributes:

obo:'digital curation'

obo:'digital curation' has attributes:
  • Label: 'digital curation'
  • Definition: Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
  • obo:'digital curation' is a obo:'documenting'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Philippe Rocca-Serra

obo:'analog-to-digital converter'

obo:'analog-to-digital converter' has attributes:

obo:'band pass filter'

obo:'band pass filter' has attributes:
  • Label: 'band pass filter'
  • Definition: A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others.
  • obo:'band pass filter' is a obo:'optical filter'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: Person:John Quinn

obo:'laser'

obo:'laser' has attributes:
  • Label: 'laser'
  • Definition: A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer.
  • obo:'laser' is a obo:'light source'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: Daniel Schober

obo:'light source'

obo:'light source' has attributes:
  • Label: 'light source'
  • Definition: A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
  • obo:'light source' is a obo:'light emission device' and has the following child: obo:'laser'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: Elizabeth M. Goralczyk

obo:'optical filter'

obo:'optical filter' has attributes:
  • Label: 'optical filter'
  • Definition: An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
  • obo:'optical filter' is a obo:'material separation device' and has the following child: obo:'band pass filter'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: John Quinn

obo:'preamplifier'

obo:'preamplifier' has attributes:

obo:'syringe pump'

obo:'syringe pump' has attributes:
  • Label: 'syringe pump'
  • Definition: Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates.
  • obo:'syringe pump' is a obo:'container'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: Person:John Quinn

obo:'voltage amplifier'

obo:'voltage amplifier' has attributes:

obo:'DNA sequencer'

obo:'DNA sequencer' has attributes:

obo:'centrifuge'

obo:'centrifuge' has attributes:

obo:'computer'

obo:'computer' has attributes:

obo:'power supply'

obo:'power supply' has attributes:
  • Label: 'power supply'
  • Definition: A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
  • obo:'power supply' is a obo:'device'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Daniel Schober

obo:'microarray'

obo:'microarray' has attributes:
  • Label: 'microarray'
  • Definition: A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
  • obo:'microarray' is a obo:'assay array'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Daniel Schober

obo:'digital-to-analog converter'

obo:'digital-to-analog converter' has attributes:

obo:'microtome'

obo:'microtome' has attributes:
  • Label: 'microtome'
  • Definition: A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
  • obo:'microtome' is a obo:'material separation device'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON: Phillippe Rocca-Serra

obo:'microscope'

obo:'microscope' has attributes:
  • Label: 'microscope'
  • Definition: A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
  • obo:'microscope' is a obo:'image creation device' and has the following child: obo:'electron microscope'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: PERSON: Phillippe Rocca-Serra

obo:'microscope slide'

obo:'microscope slide' has attributes:
  • Label: 'microscope slide'
  • Definition: A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
  • obo:'microscope slide' is a obo:'device'.
  • Type: owl:Class
  • Curation Status: obo:'metadata incomplete'
  • Editor: PERSON: Phillippe Rocca-Serra

obo:'study design'

obo:'study design' has attributes:

obo:'clinical study design'

obo:'clinical study design' has attributes:
  • Label: 'clinical study design'
  • Definition: Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
  • obo:'clinical study design' is a obo:'study design'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: PlanAndPlannedProcess Branch
  • Editor Note: The definition needs to be extended to other things than simply patients

obo:'repeated measure design'

obo:'repeated measure design' has attributes:

obo:'cross over design'

obo:'cross over design' has attributes:
  • Label: 'cross over design'
  • Definition: 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
  • obo:'cross over design' is a obo:'repeated measure design'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: Philippe Rocca-Serra

obo:'matched pairs design'

obo:'matched pairs design' has attributes:
  • Label: 'matched pairs design'
  • Definition: A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
  • obo:'matched pairs design' is a obo:'study design'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Philippe Rocca-Serra

obo:'parallel group design'

obo:'parallel group design' has attributes:
  • Label: 'parallel group design'
  • Definition: A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
  • obo:'parallel group design' is a obo:'study design'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Philippe Rocca-Serra

obo:'randomized complete block design'

obo:'randomized complete block design' has attributes:
  • Label: 'randomized complete block design'
  • Definition: A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
  • obo:'randomized complete block design' is a obo:'intervention design'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Philippe Rocca-Serra

obo:'balanced incomplete block design'

obo:'balanced incomplete block design' has attributes:

obo:'loop design'

obo:'loop design' has attributes:

obo:'reference design'

obo:'reference design' has attributes:

obo:'factorial design'

obo:'factorial design' has attributes:
  • Label: 'factorial design'
  • Definition: Factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
  • obo:'factorial design' is a obo:'study design' and has the following child: obo:'balanced incomplete block design'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Philippe Rocca-Serra

obo:'replicate design'

obo:'replicate design' has attributes:
  • Label: 'replicate design'
  • Definition: A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
  • obo:'replicate design' is a obo:'study design'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Philippe Rocca-Serra on behalf of MO

obo:'time series design'

obo:'time series design' has attributes:

obo:'stopping rule'

obo:'stopping rule' has attributes:

obo:'compliance rule'

obo:'compliance rule' has attributes:

obo:'standard compliance rule'

obo:'standard compliance rule' has attributes:

obo:'ethical standard compliance rule'

obo:'ethical standard compliance rule' has attributes:

obo:'eligibility criterion'

obo:'eligibility criterion' has attributes:

obo:'inclusion criterion'

obo:'inclusion criterion' has attributes:

obo:'exclusion criterion'

obo:'exclusion criterion' has attributes:
  • Label: 'exclusion criterion'
  • Definition: An exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
  • obo:'exclusion criterion' is a obo:'eligibility criterion'.
  • Type: owl:Class
  • Curation Status: obo:'pending final vetting'
  • Editor: Person: Philippe Rocca-Serra

obo:'human subject enrollment'

obo:'human subject enrollment' has attributes:
  • Label: 'human subject enrollment'
  • Definition: A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
  • obo:'human subject enrollment' is a obo:'selection'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Bjoern Peters
  • Editor Note: As with group assignment, should the specified output here be an organism which bears a role

obo:'collecting specimen from organism'

obo:'collecting specimen from organism' has attributes:

obo:'administering substance in vivo'

obo:'administering substance in vivo' has attributes:

obo:'acquisition'

obo:'acquisition' has attributes:

obo:'material acquisition'

obo:'material acquisition' has attributes:
  • Label: 'material acquisition'
  • Definition: An acquisition in which possession of a material entity is gained.
  • obo:'material acquisition' is a obo:'acquisition'.
  • Type: owl:Class
  • Curation Status: obo:'ready for release'
  • Editor: Bjoern Peters, Alan Ruttenberg, Helen Parkinson
  • Editor Note: The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation

obo:'information acquisition'

obo:'information acquisition' has attributes:

obo:'material component separation'

obo:'material component separation' has attributes:

obo:'group assignment'

obo:'group assignment' has attributes:

obo:'material portioning'

obo:'material portioning' has attributes:

obo:'histological assay'

obo:'histological assay' has attributes:

obo:'cell fixation'

obo:'cell fixation' has attributes:

obo:'maintaining cell culture'

obo:'maintaining cell culture' has attributes:

obo:'establishing cell culture'

obo:'establishing cell culture' has attributes:
  • Label: 'establishing cell culture'
  • Definition: 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).
  • obo:'establishing cell culture' is a obo:'material processing'.
  • Type: owl:Class
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON:Matthew Brush

obo:'sequencing assay'

obo:'sequencing assay' has attributes:

obo:'dialysis'

obo:'dialysis' has attributes:

obo:'nucleic acid extraction'

obo:'nucleic acid extraction' has attributes:

obo:'blood harvesting'

obo:'blood harvesting' has attributes:

obo:'pathologic process'

obo:'pathologic process' has attributes:

obo:'bodily fluid specimen'

obo:'bodily fluid specimen' has attributes:

obo:'arterial blood specimen'

obo:'arterial blood specimen' has attributes:

obo:'venous blood specimen'

obo:'venous blood specimen' has attributes:

obo:'clinical history'

obo:'clinical history' has attributes:

obo:'phenotype'

obo:'phenotype' has attributes:
  • Label: 'phenotype'
  • Definition: 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.
  • obo:'phenotype' is a obo:'quality'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'disease'

obo:'disease' has attributes:

obo:'diagnosis'

obo:'diagnosis' has attributes:

obo:'treatment'

obo:'treatment' has attributes:
  • Label: 'treatment'
  • Definition: A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
  • obo:'treatment' is a obo:'planned process'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'fixed tissue specimen'

obo:'fixed tissue specimen' has attributes:

obo:'fixed tissue slide specimen'

obo:'fixed tissue slide specimen' has attributes:

obo:'quality'

obo:'quality' has attributes:

obo:'age'

obo:'age' has attributes:

obo:'concentration of'

obo:'concentration of' has attributes:

obo:'distance'

obo:'distance' has attributes:

obo:'biological sex'

obo:'biological sex' has attributes:

obo:'morphology'

obo:'morphology' has attributes:

obo:'size'

obo:'size' has attributes:

obo:'length'

obo:'length' has attributes:

obo:'mass'

obo:'mass' has attributes:

obo:'position'

obo:'position' has attributes:

obo:'structure'

obo:'structure' has attributes:
  • Label: 'structure'
  • Definition: A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
  • obo:'structure' is a obo:'morphology'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'temperature'

obo:'temperature' has attributes:

obo:'time'

obo:'time' has attributes:

obo:'viability'

obo:'viability' has attributes:

obo:'behavioral quality'

obo:'behavioral quality' has attributes:

obo:'female'

obo:'female' has attributes:

obo:'male'

obo:'male' has attributes:

obo:'volume'

obo:'volume' has attributes:

obo:'physical quality'

obo:'physical quality' has attributes:

obo:'lateral to'

obo:'lateral to' has attributes:

obo:'ventral to'

obo:'ventral to' has attributes:

obo:'dorsal to'

obo:'dorsal to' has attributes:
  • Label: 'dorsal to'
  • Definition: A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity.
  • obo:'dorsal to' is a obo:'position'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'process quality'

obo:'process quality' has attributes:

obo:'physical object quality'

obo:'physical object quality' has attributes:

obo:'mixed sex'

obo:'mixed sex' has attributes:

obo:'hermaphrodite'

obo:'hermaphrodite' has attributes:

obo:'alive'

obo:'alive' has attributes:

obo:'dead'

obo:'dead' has attributes:

obo:'quality of a solid'

obo:'quality of a solid' has attributes:

obo:'quality of a gas'

obo:'quality of a gas' has attributes:

obo:'quality of a liquid'

obo:'quality of a liquid' has attributes:

obo:'flow rate'

obo:'flow rate' has attributes:

obo:'anterior to'

obo:'anterior to' has attributes:

obo:'3-D extent'

obo:'3-D extent' has attributes:

obo:'radiation quality'

obo:'radiation quality' has attributes:

obo:'activity (of a radionuclide)'

obo:'activity (of a radionuclide)' has attributes:

obo:'radioactive'

obo:'radioactive' has attributes:

obo:'left side of'

obo:'left side of' has attributes:

obo:'right side of'

obo:'right side of' has attributes:

obo:'phenotypic sex'

obo:'phenotypic sex' has attributes:

obo:'movement quality'

obo:'movement quality' has attributes:

obo:'frozen'

obo:'frozen' has attributes:

obo:'organismal quality'

obo:'organismal quality' has attributes:

obo:'population quality'

obo:'population quality' has attributes:

obo:'molecular quality'

obo:'molecular quality' has attributes:

obo:'charge'

obo:'charge' has attributes:

obo:'quality of a substance'

obo:'quality of a substance' has attributes:

obo:'handedness'

obo:'handedness' has attributes:

obo:'left handedness'

obo:'left handedness' has attributes:

obo:'right handedness'

obo:'right handedness' has attributes:

obo:'ambidextrous handedness'

obo:'ambidextrous handedness' has attributes:

obo:'fluid flow rate'

obo:'fluid flow rate' has attributes:

obo:'population process quality'

obo:'population process quality' has attributes:
  • Label: 'population process quality'
  • Definition: A quality inhering in a process by virtue of that process having a population or part of a population, where population is defined as a collection of individuals from the same taxonomic class distinguished by one or more characteristics, as participants.
  • obo:'population process quality' is a obo:'process quality'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'protein'

obo:'protein' has attributes:

obo:'system'

obo:'system' has attributes:

obo:'agent role'

obo:'agent role' has attributes:

obo:'region'

obo:'region' has attributes:

obo:'blood'

obo:'blood' has attributes:

obo:'organism substance'

obo:'organism substance' has attributes:

obo:'material anatomical entity'


obo:'anatomical cluster'

obo:'anatomical cluster' has attributes:

obo:'tissue'

obo:'tissue' has attributes:
  • Label: 'tissue'
  • Definition: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
  • obo:'tissue' is a obo:'material anatomical entity'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'multi-tissue structure'

obo:'multi-tissue structure' has attributes:
  • Label: 'multi-tissue structure'
  • Definition: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
  • obo:'multi-tissue structure' is a obo:'material anatomical entity'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'heart'

obo:'heart' has attributes:

obo:'brain'

obo:'brain' has attributes:
  • Label: 'brain'
  • Definition: The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
  • obo:'brain' is a obo:'material anatomical entity'.
  • Type: owl:Class
  • Curation Status: obo:'uncurated'

obo:'cerebral cortex'

obo:'cerebral cortex' has attributes:

obo:'cerebrospinal fluid'

obo:'cerebrospinal fluid' has attributes:

obo:'cheek'

obo:'cheek' has attributes:

obo:'coronary artery'

obo:'coronary artery' has attributes:

obo:'vein'

obo:'vein' has attributes:

obo:'nasopharynx'

obo:'nasopharynx' has attributes:

obo:'saliva'

obo:'saliva' has attributes:

obo:'manual digit'

obo:'manual digit' has attributes:

obo:'bodily fluid'

obo:'bodily fluid' has attributes:

obo:'arterial blood'

obo:'arterial blood' has attributes:

obo:'venous blood'

obo:'venous blood' has attributes:

obo:'length unit'

obo:'length unit' has attributes:
Examples of obo:'length unit' includes
  • obo:'angstrom': A length unit which is equal to 10 [-10] m.
  • obo:'centimeter': A length unit which is equal to one hundredth of a meter or 10^[-2] m.
  • obo:'meter': A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
  • obo:'micrometer': A length unit which is equal to one millionth of a meter or 10^[-6] m.
  • obo:'millimeter': A length unit which is equal to one thousandth of a meter or 10^[-3] m.
  • obo:'nanometer': A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.

obo:'mass unit'

obo:'mass unit' has attributes:
Examples of obo:'mass unit' includes
  • obo:'gram': A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
  • obo:'kilogram': A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
  • obo:'microgram': A mass unit which is equal to one millionth of a gram or 10^[-6] g.
  • obo:'milligram': A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
  • obo:'nanogram': A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
  • obo:'picogram': A mass unit which is equal to 10^[-12] g.

obo:'time unit'

obo:'time unit' has attributes:
Examples of obo:'time unit' includes
  • obo:'day': A time unit which is equal to 24 hours.
  • obo:'hour': A time unit which is equal to 3600 seconds or 60 minutes.
  • obo:'minute': A time unit which is equal to 60 seconds.
  • obo:'month': A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
  • obo:'second': A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
  • obo:'week': A time unit which is equal to 7 days.
  • obo:'year': A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.

obo:'temperature unit'

obo:'temperature unit' has attributes:
Examples of obo:'temperature unit' includes
  • obo:'degree Celsius': A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
  • obo:'degree Fahrenheit': A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.

obo:'substance unit'

obo:'substance unit' has attributes:
Examples of obo:'substance unit' includes
  • obo:'micromole': A substance unit equal to a millionth of a mol or 10^[-6] mol.
  • obo:'nanomole': A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
  • obo:'picomole': A substance unit equal to 10^[-12] mol.

obo:'concentration unit'

obo:'concentration unit' has attributes:
Examples of obo:'concentration unit' includes
  • obo:'gram per deciliter': A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
  • obo:'gram per liter': A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
  • obo:'mass percentage': A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
  • obo:'mass volume percentage': A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
  • obo:'micromolar': A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
  • obo:'milligram per milliliter': A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
  • obo:'milliliter per liter': A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
  • obo:'millimolar': A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
  • obo:'molar': A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
  • obo:'nanomolar': A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
  • obo:'pH': A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
  • obo:'picomolar': A unit of molarity which is equal to 10^[-12] M.
  • obo:'volume percentage': A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.

obo:'volume unit'

obo:'volume unit' has attributes:
Examples of obo:'volume unit' includes
  • obo:'cubic centimeter': A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
  • obo:'cubic decimeter': A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
  • obo:'liter': A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
  • obo:'microliter': A volume unit which is equal to one millionth of a liter or 10^[-6] L.
  • obo:'milliliter': A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
  • obo:'nanoliter': A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
  • obo:'picoliter': A volume unit which is equal to 10^[-12] L.

obo:'frequency unit'

obo:'frequency unit' has attributes:
Examples of obo:'frequency unit' includes
  • obo:'hertz': A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.

obo:'pressure unit'

obo:'pressure unit' has attributes:

obo:'volumetric flow rate unit'

obo:'volumetric flow rate unit' has attributes:

obo:'rate unit'

obo:'rate unit' has attributes:

obo:'phenotype'

obo:'phenotype' has attributes:

Datatype Properties

obo:'has quantity'

obo:'has quantity' has attributes:

obo:'has measurement value'

obo:'has measurement value' has attributes:

obo:'has x coordinate value'

obo:'has x coordinate value' has attributes:

obo:'has z coordinate value'

obo:'has z coordinate value' has attributes:

obo:'has y coordinate value'

obo:'has y coordinate value' has attributes:

obo:'has specified numeric value'

obo:'has specified numeric value' has attributes:

obo:'has specified value'

obo:'has specified value' has attributes:
  • Label: 'has specified value'
  • Definition: A relation between a value specification and a literal.
  • obo:'has specified value' is a owl:DatatypeProperty.
  • Type: owl:DatatypeProperty
  • Domain: obo:OBI_0001933
  • Curation Status: obo:'metadata incomplete'
  • Editor Note: 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.

Annotation Properties

obo:'BFO OWL specification label'

obo:'BFO OWL specification label' has attributes:

obo:'BFO CLIF specification label'

obo:'BFO CLIF specification label' has attributes:

obo:'editor preferred term'

obo:'editor preferred term' has attributes:

obo:'example of usage'

obo:'example of usage' has attributes:
  • Label: 'example of usage'
  • Definition: 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.
  • obo:'example of usage' is a owl:AnnotationProperty.
  • Type: owl:AnnotationProperty
  • Curation Status: obo:'ready for release'
  • Editor: PERSON:Daniel Schober

obo:'has curation status'

obo:'has curation status' has attributes:

obo:'definition'

obo:'definition' has attributes:
  • Label: 'definition'
  • Definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
  • obo:'definition' is a owl:AnnotationProperty.
  • Type: owl:AnnotationProperty
  • Curation Status: obo:'ready for release'
  • Editor: PERSON:Daniel Schober
  • Editor Note: 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.

obo:'editor note'

obo:'editor note' has attributes:

obo:'term editor'

obo:'term editor' has attributes:
  • Label: 'term editor'
  • Definition: 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
  • obo:'term editor' is a owl:AnnotationProperty.
  • Type: owl:AnnotationProperty
  • Curation Status: obo:'ready for release'
  • Editor: PERSON:Daniel Schober
  • Editor Note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.

obo:'alternative label'

obo:'alternative label' has attributes:

obo:'definition source'

obo:'definition source' has attributes:

obo:'is about'


obo:'curator note'

obo:'curator note' has attributes:

obo:'term tracker item'

obo:'term tracker item' has attributes:

obo:'ontology term requester'

obo:'ontology term requester' has attributes:

obo:'imported from'

obo:'imported from' has attributes:

obo:'OBO foundry unique label'

obo:'OBO foundry unique label' has attributes:
  • Label: 'OBO foundry unique label'
  • Definition: An alternative name for a class or property which is unique across the OBO Foundry.
  • obo:'OBO foundry unique label' is a owl:AnnotationProperty.
  • Type: owl:AnnotationProperty
  • Curation Status: obo:'pending final vetting'
  • Editor: PERSON:Alan Ruttenberg
  • Editor Note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .

obo:'elucidation'

obo:'elucidation' has attributes:

obo:'has associated axiom(nl)'

obo:'has associated axiom(nl)' has attributes:

obo:'has associated axiom(fol)'

obo:'has associated axiom(fol)' has attributes:

obo:'may be identical to'

obo:'may be identical to' has attributes:

obo:'has axiom label'

obo:'has axiom label' has attributes:

obo:'ISA alternative term'

obo:'ISA alternative term' has attributes:

obo:'NIAID GSCID-BRC alternative term'

obo:'NIAID GSCID-BRC alternative term' has attributes:

obo:'IEDB alternative term'

obo:'IEDB alternative term' has attributes:

obo:'temporal interpretation'

obo:'temporal interpretation' has attributes:

obo:'defined by inverse'

obo:'defined by inverse' has attributes:

obo:'logical macro assertion'

obo:'logical macro assertion' has attributes:

obo:'logical macro assertion on a property'

obo:'logical macro assertion on a property' has attributes:

obo:'logical macro assertion on an object property'

obo:'logical macro assertion on an object property' has attributes:

obo:'logical macro assertion on an annotation property'


obo:'is direct form of'

obo:'is direct form of' has attributes:
  • Label: 'is direct form of'
  • Definition: Relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
  • obo:'is direct form of' is a obo:'logical macro assertion on an object property'.
  • Type: owl:AnnotationProperty
  • Curation Status: obo:'uncurated'
  • Editor Note: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"

obo:'is directional form of'

obo:'is directional form of' has attributes:

obo:'is positive form of'

obo:'is positive form of' has attributes:

obo:'is negative form of'

obo:'is negative form of' has attributes:

obo:'is homeomorphic for'

obo:'is homeomorphic for' has attributes:

Object Properties

obo:'part of'

obo:'part of' has attributes:

obo:'has part'

obo:'has part' has attributes:

obo:'realized in'

obo:'realized in' has attributes:

obo:'realizes'

obo:'realizes' has attributes:

obo:'precedes'

obo:'precedes' has attributes:

obo:'occurs in'

obo:'occurs in' has attributes:

obo:'contains process'

obo:'contains process' has attributes:

obo:'executed by'

obo:'executed by' has attributes:

obo:'intended to realize'

obo:'intended to realize' has attributes:

obo:'has plan'

obo:'has plan' has attributes:

obo:'intended plan process type'

obo:'intended plan process type' has attributes:

obo:'realizes'

obo:'realizes' has attributes:

obo:'has measurement unit label'

obo:'has measurement unit label' has attributes:

obo:'is about'


obo:'denotes'

obo:'denotes' has attributes:
  • Label: 'denotes'
  • Definition: 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
  • obo:'denotes' is a obo:'is about'.
  • Type: owl:ObjectProperty
  • Range: obo:BFO_0000001
  • Domain: obo:IAO_0000030
  • Curation Status: obo:'uncurated'
  • Editor: person:Alan Ruttenberg
  • Editor Note: 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

obo:'is quality measurement of'

obo:'is quality measurement of' has attributes:
  • Label: 'is quality measurement of'
  • Definition: 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
  • obo:'is quality measurement of' is a obo:'is about'.
  • Type: owl:ObjectProperty
  • Range: obo:BFO_0000019
  • Domain: obo:IAO_0000109
  • Curation Status: obo:'uncurated'
  • Editor: Alan Ruttenberg
  • Editor Note: 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

obo:'denoted by'

obo:'denoted by' has attributes:

obo:'has coordinate unit label'

obo:'has coordinate unit label' has attributes:

obo:'is duration of'

obo:'is duration of' has attributes:

obo:'is quality measured as'

obo:'is quality measured as' has attributes:

obo:'has time stamp'

obo:'has time stamp' has attributes:

obo:'has measurement datum'

obo:'has measurement datum' has attributes:

obo:'provides_service_consumer_with'

obo:'provides_service_consumer_with' has attributes:

obo:'is_supported_by_data'

obo:'is_supported_by_data' has attributes:

obo:'has specified input'

obo:'has specified input' has attributes:

obo:'is specified input of'

obo:'is specified input of' has attributes:

obo:'has specified output'

obo:'has specified output' has attributes:

obo:'is_manufactured_by'

obo:'is_manufactured_by' has attributes:
  • Label: 'is_manufactured_by'
  • Definition: C is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
  • obo:'is_manufactured_by' is a owl:ObjectProperty.
  • Type: owl:ObjectProperty
  • Domain: obo:BFO_0000040
  • Curation Status: obo:'metadata incomplete'
  • Editor: Alan Ruttenberg

obo:'is specified output of'

obo:'is specified output of' has attributes:

obo:'achieves_planned_objective'

obo:'achieves_planned_objective' has attributes:

obo:'has grain'

obo:'has grain' has attributes:
  • Label: 'has grain'
  • Definition: 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.
  • obo:'has grain' is a obo:'has part'.
  • Type: owl:ObjectProperty
  • Curation Status: obo:'metadata complete'
  • Editor: PERSON: Alan Ruttenberg
  • Editor Note: 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

obo:'objective_achieved_by'

obo:'objective_achieved_by' has attributes:

obo:'is member of organization'

obo:'is member of organization' has attributes:
  • Label: 'is member of organization'
  • Definition: 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.
  • obo:'is member of organization' is a owl:ObjectProperty.
  • Type: owl:ObjectProperty
  • Range: obo:OBI_0000245
  • Domain: nca0dba935a234f8e8234f1264f410475b53
  • Curation Status: obo:'metadata complete'
  • Editor: Person:Alan Ruttenberg
  • Editor Note: 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

obo:'has category label'

obo:'has category label' has attributes:

obo:'has organization member'

obo:'has organization member' has attributes:

obo:'specifies value of'

obo:'specifies value of' has attributes:

obo:'has value specification'

obo:'has value specification' has attributes:

obo:'characteristic of'

obo:'characteristic of' has attributes:

obo:'has characteristic'

obo:'has characteristic' has attributes:

obo:'participates in'

obo:'participates in' has attributes:

obo:'has participant'

obo:'has participant' has attributes:
  • Label: 'has participant'
  • Definition: A relation between a process and a continuant, in which the continuant is somehow involved in the process
  • obo:'has participant' is a owl:ObjectProperty.
  • Type: owl:ObjectProperty
  • Range: obo:BFO_0000002
  • Domain: obo:BFO_0000003
  • Curation Status: obo:'uncurated'
  • Editor Note: 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.

obo:'is concretized as'

obo:'is concretized as' has attributes:
  • Label: 'is concretized as'
  • Definition: 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.
  • obo:'is concretized as' is a owl:ObjectProperty.
  • Type: owl:ObjectProperty
  • Range: obo:BFO_0000020
  • Domain: obo:BFO_0000031
  • Curation Status: obo:'uncurated'

obo:'concretizes'

obo:'concretizes' has attributes:
  • Label: 'concretizes'
  • Definition: 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.
  • obo:'concretizes' is a owl:ObjectProperty.
  • Type: owl:ObjectProperty
  • Range: obo:BFO_0000031
  • Domain: obo:BFO_0000020
  • Curation Status: obo:'uncurated'

obo:'function of'

obo:'function of' has attributes:
  • Label: 'function of'
  • Definition: A relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
  • obo:'function of' is a obo:'characteristic of'.
  • Type: owl:ObjectProperty
  • Domain: obo:BFO_0000034
  • Curation Status: obo:'uncurated'
  • Editor Note: 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.

obo:'quality of'

obo:'quality of' has attributes:
  • Label: 'quality of'
  • Definition: A relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
  • obo:'quality of' is a obo:'characteristic of'.
  • Type: owl:ObjectProperty
  • Curation Status: obo:'uncurated'
  • Editor Note: A quality inheres in its bearer at all times for which the quality exists.

obo:'role of'

obo:'role of' has attributes:
  • Label: 'role of'
  • Definition: A relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
  • obo:'role of' is a obo:'characteristic of'.
  • Type: owl:ObjectProperty
  • Curation Status: obo:'uncurated'
  • Editor Note: 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.

obo:'has function'

obo:'has function' has attributes:
  • Label: 'has function'
  • Definition: A relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
  • obo:'has function' is a obo:'has characteristic'.
  • Type: owl:ObjectProperty
  • Range: obo:BFO_0000034
  • Domain: obo:BFO_0000004
  • Curation Status: obo:'uncurated'
  • Editor Note: 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.

obo:'has quality'

obo:'has quality' has attributes:
  • Label: 'has quality'
  • Definition: A relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
  • obo:'has quality' is a obo:'has characteristic'.
  • Type: owl:ObjectProperty
  • Range: obo:BFO_0000019
  • Curation Status: obo:'uncurated'
  • Editor Note: 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.

obo:'has role'

obo:'has role' has attributes:
  • Label: 'has role'
  • Definition: A relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
  • obo:'has role' is a obo:'has characteristic'.
  • Type: owl:ObjectProperty
  • Range: obo:BFO_0000023
  • Domain: obo:BFO_0000004
  • Curation Status: obo:'uncurated'
  • Editor Note: 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.

obo:'derives from'

obo:'derives from' has attributes:
  • Label: 'derives from'
  • Definition: 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
  • obo:'derives from' is a owl:ObjectProperty.
  • Type: owl:ObjectProperty
  • Curation Status: obo:'pending final vetting'
  • Editor Note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.

obo:'derives into'

obo:'derives into' has attributes:
  • Label: 'derives into'
  • Definition: 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
  • obo:'derives into' is a owl:ObjectProperty.
  • Type: owl:ObjectProperty
  • Curation Status: obo:'pending final vetting'
  • Editor Note: 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'.

obo:'location of'

obo:'location of' has attributes:

obo:'contained in'

obo:'contained in' has attributes:

obo:'contains'

obo:'contains' has attributes:

obo:'located in'

obo:'located in' has attributes:
  • Label: 'located in'
  • Definition: A relation between two independent continuants, the target and the location, in which the target is entirely within the location
  • obo:'located in' is a owl:ObjectProperty, owl:TransitiveProperty.
  • Type: owl:ObjectProperty, owl:TransitiveProperty
  • Range: obo:BFO_0000004
  • Domain: nca0dba935a234f8e8234f1264f410475b8obo:BFO_0000004
  • Curation Status: obo:'uncurated'
  • Editor Note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus

obo:'immediately precedes'

obo:'immediately precedes' has attributes:

obo:'overlaps'

obo:'overlaps' has attributes:

obo:'connected to'

obo:'connected to' has attributes:

obo:'connects'

obo:'connects' has attributes:
  • Label: 'connects'
  • Definition: C connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
  • obo:'connects' is a obo:'mereotopologically related to'.
  • Type: owl:ObjectProperty
  • Domain: obo:BFO_0000004
  • Curation Status: obo:'uncurated'

obo:'has phenotype'

obo:'has phenotype' has attributes:
  • Label: 'has phenotype'
  • Definition: A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
  • obo:'has phenotype' is a obo:'has phenotype or disease'.
  • Type: owl:ObjectProperty
  • Range: obo:UPHENO_0001001
  • Domain: nca0dba935a234f8e8234f1264f410475b23
  • Curation Status: obo:'pending final vetting'
  • Editor: ns2:0000-0002-6601-2165

obo:'phenotype of'

obo:'phenotype of' has attributes:

obo:'temporally related to'


obo:'starts'

obo:'starts' has attributes:

obo:'starts with'

obo:'starts with' has attributes:

obo:'ends with'

obo:'ends with' has attributes:

obo:'has input'

obo:'has input' has attributes:

obo:'has output'

obo:'has output' has attributes:

obo:'characteristic of part of'

obo:'characteristic of part of' has attributes:

obo:'mereotopologically related to'


obo:'functionally related to'


obo:'enabled by'

obo:'enabled by' has attributes:

obo:'member of'

obo:'member of' has attributes:

obo:'has member'

obo:'has member' has attributes:

obo:'input of'

obo:'input of' has attributes:

obo:'output of'

obo:'output of' has attributes:

obo:'has direct input'

obo:'has direct input' has attributes:

obo:'causally related to'


obo:'causally upstream of'

obo:'causally upstream of' has attributes:

obo:'immediately causally upstream of'

obo:'immediately causally upstream of' has attributes:

obo:'provides input for'

obo:'provides input for' has attributes:

obo:'transitively provides input for'

obo:'transitively provides input for' has attributes:

obo:'causally upstream of or within'

obo:'causally upstream of or within' has attributes:

obo:'causally downstream of or within'

obo:'causally downstream of or within' has attributes:

obo:'receives input from'

obo:'receives input from' has attributes:

obo:'sends output to'

obo:'sends output to' has attributes:

obo:'causal relation between processes'

obo:'causal relation between processes' has attributes:

obo:'depends on'

obo:'depends on' has attributes:

obo:'has model'

obo:'has model' has attributes:

obo:'produces'

obo:'produces' has attributes:

obo:'produced by'

obo:'produced by' has attributes:

obo:'has role in modeling'

obo:'has role in modeling' has attributes:

obo:'causally upstream of or within, positive effect'


obo:'has phenotype or disease'

obo:'has phenotype or disease' has attributes:

obo:'executes'

obo:'executes' has attributes:

Named Individuals

obo:'example to be eventually removed'

obo:'example to be eventually removed' has attributes:

obo:'failed exploratory term'

obo:'failed exploratory term' has attributes:

obo:'metadata complete'

obo:'metadata complete' has attributes:

obo:'organizational term'

obo:'organizational term' has attributes:

obo:'ready for release'

obo:'ready for release' has attributes:
  • Label: 'ready for release'
  • Definition: 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."
  • obo:'ready for release' is a obo:'curation status specification', owl:Thing.
  • Type: owl:NamedIndividual
  • Curation Status: obo:'uncurated'

obo:'metadata incomplete'

obo:'metadata incomplete' has attributes:

obo:'uncurated'

obo:'uncurated' has attributes:

obo:'pending final vetting'

obo:'pending final vetting' has attributes:

obo:'placeholder removed'

obo:'placeholder removed' has attributes:

obo:'terms merged'

obo:'terms merged' has attributes:

obo:'term imported'

obo:'term imported' has attributes:

obo:'term split'

obo:'term split' has attributes:

obo:'to be replaced with external ontology term'

obo:'to be replaced with external ontology term' has attributes:

obo:'requires discussion'

obo:'requires discussion' has attributes:

obo:'zip'

obo:'zip' has attributes:

obo:'tar'

obo:'tar' has attributes:

obo:'Bruker Corporation'

obo:'Bruker Corporation' has attributes:

obo:'right handed'

obo:'right handed' has attributes:

obo:'ambidexterous'

obo:'ambidexterous' has attributes:

obo:'left handed'

obo:'left handed' has attributes:

obo:'Edingburgh handedness inventory'

obo:'Edingburgh handedness inventory' has attributes:

obo:'axiom holds for all times'

obo:'axiom holds for all times' has attributes:
  • Label: 'axiom holds for all times'
  • Definition: ## 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
  • obo:'axiom holds for all times' is a owl:NamedIndividual.
  • Type: owl:NamedIndividual
  • Curation Status: obo:'uncurated'

obo:'meter'

obo:'meter' has attributes:

obo:'kilogram'

obo:'kilogram' has attributes:

obo:'second'

obo:'second' has attributes:
  • Label: 'second'
  • Definition: 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.
  • obo:'second' is a obo:'time unit'.
  • Type: owl:NamedIndividual
  • Curation Status: obo:'uncurated'

obo:'centimeter'

obo:'centimeter' has attributes:

obo:'millimeter'

obo:'millimeter' has attributes:

obo:'micrometer'

obo:'micrometer' has attributes:

obo:'nanometer'

obo:'nanometer' has attributes:

obo:'angstrom'

obo:'angstrom' has attributes:

obo:'gram'

obo:'gram' has attributes:

obo:'milligram'

obo:'milligram' has attributes:

obo:'microgram'

obo:'microgram' has attributes:

obo:'nanogram'

obo:'nanogram' has attributes:

obo:'picogram'

obo:'picogram' has attributes:

obo:'degree Celsius'

obo:'degree Celsius' has attributes:

obo:'minute'

obo:'minute' has attributes:

obo:'hour'

obo:'hour' has attributes:

obo:'day'

obo:'day' has attributes:

obo:'week'

obo:'week' has attributes:

obo:'month'

obo:'month' has attributes:

obo:'year'

obo:'year' has attributes:

obo:'micromole'

obo:'micromole' has attributes:

obo:'nanomole'

obo:'nanomole' has attributes:

obo:'picomole'

obo:'picomole' has attributes:

obo:'molar'

obo:'molar' has attributes:

obo:'millimolar'

obo:'millimolar' has attributes:

obo:'micromolar'

obo:'micromolar' has attributes:

obo:'nanomolar'

obo:'nanomolar' has attributes:

obo:'picomolar'

obo:'picomolar' has attributes:

obo:'cubic centimeter'

obo:'cubic centimeter' has attributes:

obo:'milliliter'

obo:'milliliter' has attributes:

obo:'liter'

obo:'liter' has attributes:

obo:'cubic decimeter'

obo:'cubic decimeter' has attributes:

obo:'microliter'

obo:'microliter' has attributes:

obo:'nanoliter'

obo:'nanoliter' has attributes:

obo:'picoliter'

obo:'picoliter' has attributes:

obo:'hertz'

obo:'hertz' has attributes:

obo:'mass percentage'

obo:'mass percentage' has attributes:

obo:'mass volume percentage'

obo:'mass volume percentage' has attributes:

obo:'volume percentage'

obo:'volume percentage' has attributes:

obo:'gram per liter'

obo:'gram per liter' has attributes:

obo:'milligram per milliliter'

obo:'milligram per milliliter' has attributes:

obo:'degree Fahrenheit'

obo:'degree Fahrenheit' has attributes:

obo:'pH'

obo:'pH' has attributes:

obo:'milliliter per liter'

obo:'milliliter per liter' has attributes:

obo:'gram per deciliter'

obo:'gram per deciliter' has attributes: