Ontology for RNA sequencing (ORNASEQ)
type: Ontology
version IRI: ornaseq.owl
contributor: Junhyong Kim
contributor: Stephen A Fisher
license: http://creativecommons.org/licenses/by/4.0/
comment: The following ontology is provided by Stephen A Fisher and Junhyong Kim to annotate next-generation sequencing experiments performed on RNA.

textual definition
type: AnnotationProperty
textual definition: English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
textual definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
textual definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: definition

editor note
type: AnnotationProperty
textual definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>

definition editor
type: AnnotationProperty
textual 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: term editor

alternative term
type: AnnotationProperty
textual definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
textual definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

imported from
type: AnnotationProperty

label
type: AnnotationProperty

part of
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
textual definition: a core relation that holds between a part and its whole
imported from: ro.owl

is_specified_output_of
type: ObjectProperty
sub property of: participates in
textual definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
imported from: obi.owl

bearer of
type: ObjectProperty
textual definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
imported from: ro.owl

participates in
type: ObjectProperty
textual definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
imported from: ro.owl

has role
type: ObjectProperty
sub property of: bearer of
textual definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
imported from: ro.owl

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
textual definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
imported from: ro.owl

starts
type: ObjectProperty
sub property of: part of
textual definition: inverse of starts with
imported from: ro.owl

mereotopologically related to
type: ObjectProperty
textual definition: A mereological relationship or a topological relationship
imported from: ro.owl

entity
type: Class
subclass of: Thing
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
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
imported from: bfo.owl

continuant
type: Class
subclass of: entity
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
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: bfo.owl

occurrent
type: Class
subclass of: entity
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
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
imported from: bfo.owl

independent continuant
type: Class
subclass of: continuant
textual definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
imported from: bfo.owl

process
type: Class
subclass of: occurrent
textual 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])
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)
imported from: bfo.owl

realizable entity
type: Class
subclass of: specifically dependent continuant
imported from: bfo.owl

specifically dependent continuant
type: Class
subclass of: continuant
textual 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])
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.
imported from: bfo.owl

role
type: Class
subclass of: realizable entity
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
imported from: bfo.owl

generically dependent continuant
type: Class
subclass of: continuant
textual definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
imported from: bfo.owl

material entity
type: Class
subclass of: independent continuant
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
imported from: bfo.owl

deoxyribonucleic acid
type: Class
subclass of: molecular entity
textual definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
imported from: chebi.owl

molecular entity
type: Class
subclass of: material entity
textual definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
imported from: chebi.owl

cell
type: Class
subclass of: material entity
textual definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
imported from: cl.owl

astrocyte
type: Class
subclass of: cell
textual definition: A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury.
imported from: cl.owl

brown fat cell
type: Class
subclass of: cell
textual definition: A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation.
imported from: cl.owl

neuron
type: Class
subclass of: cell
textual 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.
imported from: cl.owl

cardiac muscle cell
type: Class
subclass of: cell
textual definition: Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei.
imported from: cl.owl

central nervous system neuron
type: Class
subclass of: neuron
textual definition: Any neuron that is part of a central nervous system.
imported from: cl.owl

sequencing run date
type: Class
subclass of: data item
textual definition: date the sequencing run was performed
definition source: GROUP: IRIDA Ontology (Emma)
imported from: genepio.owl

sequencing kit
type: Class
subclass of: processed material
textual definition: Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications.
definition source: GROUP: IRIDA Ontology (Emma)
imported from: genepio.owl

library preparation kit
type: Class
subclass of: processed material
textual definition: Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids.
definition source: GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html
imported from: genepio.owl

organism datum
type: Class
subclass of: measurement datum
imported from: genepio.owl

cellular_component
type: Class
subclass of: material entity
textual definition: A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
imported from: go.owl

mitochondrion
type: Class
subclass of: cell part
textual definition: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
imported from: go.owl

dendrite
type: Class
subclass of: cell part
textual definition: A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
imported from: go.owl

cell body
type: Class
subclass of: cell part
textual definition: The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
imported from: go.owl

cell part
type: Class
subclass of: cellular_component
textual definition: Any constituent part of a cell, the basic structural and functional unit of all organisms.
imported from: go.owl

software
type: Class
subclass of: plan specification
textual definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
definition source: GROUP: OBI
imported from: iao.owl
imported from: obi.owl

model number
type: Class
subclass of: symbol
textual 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.
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
definition editor: Person: Alan Ruttenberg
imported from: iao.owl

data item
type: Class
subclass of: information content entity
textual definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data
imported from: iao.owl

symbol
type: Class
subclass of: information content entity
textual definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
editor note: 20091104, MC: this needs work and will most probably change
editor note: 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
definition editor: PERSON: James A. Overton
definition editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary
imported from: iao.owl

information content entity
type: Class
subclass of: generically dependent continuant
textual definition: A generically dependent continuant that is about some thing.
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: iao.owl
imported from: obi.owl

scalar measurement datum
type: Class
subclass of: measurement datum
textual definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: iao.owl

directive information entity
type: Class
subclass of: data item
textual definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
imported from: iao.owl

algorithm
type: Class
subclass of: plan specification
textual 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.
definition editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
imported from: iao.owl

data format specification
type: Class
subclass of: directive information entity
textual 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
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"
definition editor: PERSON: Alan Ruttenberg
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000187
imported from: iao.owl

plan specification
type: Class
subclass of: directive information entity
textual definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: iao.owl
imported from: obi.owl

measurement datum
type: Class
subclass of: data item
textual definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: iao.owl

time measurement datum
type: Class
subclass of: scalar measurement datum
textual definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg
imported from: iao.owl

centrally registered identifier symbol
type: Class
subclass of: symbol
textual definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: iao.owl

software application
type: Class
subclass of: software
textual definition: A software application is software that can be directly executed by some processing unit.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80
imported from: iao.owl
imported from: obi.owl

Homo sapiens
type: Class
subclass of: organism
imported from: ncbitaxon.owl

Document
type: Class
subclass of: Record
textual definition: A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable.
imported from: ncit.owl

Conceptual Entity
type: Class
subclass of: Thing
textual definition: An organizational header for concepts representing mostly abstract entities.
imported from: ncit.owl

Record
type: Class
subclass of: Conceptual Entity
textual definition: Anything (e.g., a document) providing permanent evidence of or information about past events.
imported from: ncit.owl

Identifier
type: Class
subclass of: Document
textual definition: One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing.
imported from: ncit.owl

Accession Number
type: Class
subclass of: Unique Identifier
textual definition: A control number unique to an object. It is used to identify the object among other objects in a collection.
imported from: ncit.owl

Unique Identifier
type: Class
subclass of: Identifier
textual definition: A set of characters used as a code that is unique in the context or the system for which it is created. It serves as a means of identification and reference (often instead of a name) for an entity, person, thing, function, procedure, activity, variable, or body of data.
imported from: ncit.owl

planned process
type: Class
subclass of: process
textual definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition editor: Bjoern Peters
definition source: branch derived
imported from: obi.owl

material supplier role
type: Class
subclass of: service provider role
textual definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
editor note: Supplier role is a special kind of service, e.g. biobank
definition editor: PERSON:Jennifer Fostel
alternative term: material provider role
alternative term: supplier
imported from: obi.owl

reference substance role
type: Class
subclass of: role
textual definition: a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
definition editor: Person:Jennifer Fostel
alternative term: reference substance
definition source: OBI
imported from: obi.owl

processed material
type: Class
subclass of: material entity
textual definition: Is a material entity that is created or changed during material processing.
definition editor: PERSON: Alan Ruttenberg
imported from: obi.owl

assay
type: Class
subclass of: planned process
textual definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
definition editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: obi.owl

detector reagent role
type: Class
subclass of: role
textual definition: a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.
editor note: 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances
definition source: One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009
imported from: obi.owl

material processing
type: Class
subclass of: planned process
textual definition: A planned process which results in physical changes in a specified input material
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca Serra
alternative term: material transformation
definition source: OBI branch derived
imported from: obi.owl

participant under investigation role
type: Class
subclass of: role
textual 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.
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.
definition editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

responsible party role
type: Class
subclass of: investigation agent role
textual definition: a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
definition editor: Person: Jennifer Fostel
alternative term: responsible party
definition source: OBI
imported from: obi.owl

principal investigator role
type: Class
subclass of: responsible party role
textual definition: a responsible party role played by a person responsible for the overall conduct of a study
definition editor: Person: Jennifer Fostel
alternative term: principal investigator
imported from: obi.owl

worker role
type: Class
subclass of: investigation agent role
textual definition: a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
editor note: "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
definition editor: Person:Jennifer Fostel
alternative term: worker
definition source: OBI
imported from: obi.owl

population
type: Class
subclass of: material entity
textual 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
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/
definition editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
imported from: obi.owl

biological replicate role
type: Class
subclass of: reference subject role
textual definition: a reference participant role realized by equivalent treatment of participants
definition editor: Person:Jennifer Fostel
alternative term: biological replicate
definition source: OBI
imported from: obi.owl

investigation agent role
type: Class
subclass of: role
textual 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.
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.
editor note: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
definition editor: GROUP: Role Branch
alternative term: investigator
definition source: OBI
imported from: obi.owl

reference subject role
type: Class
subclass of: participant under investigation role
textual definition: a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
definition editor: Jennifer Fostel
alternative term: reference participant
definition source: OBI
imported from: obi.owl

organization
type: Class
subclass of: material entity
textual 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.
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: obi.owl

technical replicate role
type: Class
subclass of: reference subject role
textual definition: technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
definition editor: Person: Jennifer Fostel
alternative term: technical replicate
imported from: obi.owl

protocol
type: Class
subclass of: plan specification
textual definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
imported from: obi.owl

polymerase chain reaction
type: Class
subclass of: enzymatic amplification
textual definition: PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
definition editor: OBI Plan
alternative term: PCR
definition source: adapted from wikipedai
imported from: obi.owl

DNA sequencing
type: Class
subclass of: sequencing assay
textual definition: DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
definition editor: Philippe Rocca-Serra
definition source: OBI Branch derived
imported from: obi.owl

specimen collection process
type: Class
subclass of: planned process
textual definition: A planned process with the objective of collecting a specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
definition editor: Bjoern Peters
alternative term: specimen collection
imported from: obi.owl

library preparation
type: Class
subclass of: material processing
textual definition: is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
definition editor: Philippe Rocca-Serra
alternative term: library construction
imported from: obi.owl

paired-end library
type: Class
subclass of: processed material
textual definition: is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
definition editor: Philippe Rocca-Serra
alternative term: mate-paired library
alternative term: paired-end tag (PET) library
definition source: adapted from information provided by Solid web site
imported from: obi.owl

measurement device
type: Class
subclass of: device
textual definition: A device in which a measure function inheres.
definition editor: GROUP:OBI Philly workshop
definition source: OBI
imported from: obi.owl

manufacturer
type: Class
subclass of: material entity
textual definition: A person or organization that has a manufacturer role
imported from: obi.owl

material separation device
type: Class
subclass of: device
textual definition: A device with a separation function realized in a planed process
imported from: obi.owl

service provider role
type: Class
subclass of: role
textual definition: is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
definition editor: PERSON:Helen Parkinson
imported from: obi.owl

device
type: Class
subclass of: processed material
textual definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
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…
definition editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl

sequence data
type: Class
subclass of: measurement datum
textual definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
definition editor: Person:Chris Stoeckert
definition source: GROUP: OBI
imported from: obi.owl

spike-in quality control role
type: Class
subclass of: reference substance role
textual definition: a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes
definition editor: PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
definition source: MO_937 spike_quality_control
imported from: obi.owl

age measurement datum
type: Class
subclass of: time measurement datum
textual definition: A time measurement datum that is the result of measurement of age of an organism
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
definition editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
definition source: MO_178 Age
imported from: obi.owl

age since birth measurement datum
type: Class
subclass of: age measurement datum
textual definition: An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_710 birth
imported from: obi.owl

selectively maintained organism
type: Class
subclass of: organism
textual definition: An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
definition editor: Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
alternative term: cultivar
alternative term: ecotype
alternative term: strain
definition source: MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
imported from: obi.owl

RNA-seq assay
type: Class
subclass of: sequencing assay
textual definition: An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
definition editor: PERSON: James Malone
alternative term: transcription profiling by high throughput sequencing
definition source: EFO_0002770 transcription profiling by high throughput sequencing
imported from: obi.owl

cell specimen
type: Class
subclass of: specimen
textual definition: A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
editor note: Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
definition editor: PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
definition source: MO_612 cell
imported from: obi.owl

linear amplification
type: Class
subclass of: enzymatic amplification
textual definition: An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_997 linear_amplification
imported from: obi.owl

specimen identifier
type: Class
subclass of: symbol
textual definition: A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: specimen ID
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl

transcript analysis by paired-end tag sequencing
type: Class
subclass of: sequencing assay
textual definition: An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions.
definition editor: Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
alternative term: RNA-PET
alternative term: RNA-PET assay
definition source: Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299]
imported from: obi.owl

paired-end library preparation
type: Class
subclass of: library preparation
textual definition: A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.
definition editor: Person: Venkat Malladi, Jie Zheng
definition source: Venkat Malladi, Jie Zheng
imported from: obi.owl

sequencing facility organization
type: Class
subclass of: organization
textual definition: An organization that provides sequence determination service
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl

specimen collector
type: Class
subclass of: Homo sapiens
textual definition: A person who collects the specimen
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl

value specification
type: Class
subclass of: information content entity
textual definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

sequencing library multiplexing
type: Class
subclass of: material processing
textual definition: a planned process which consists in running a set of samples as a pool in one single instrument run of data acquisition process while retaining the ability to associate individual results to each of the individual input samples thanks to the use of a multiplex identifier, introduced during the ligation step of the individual library preparation and specific to a given sample.
definition editor: PERSON:Philippe Rocca-Serra
definition source: OBI
imported from: obi.owl

multiplexing sequence identifier
type: Class
subclass of: deoxyribonucleic acid
textual definition: A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library
definition editor: PERSON:Philippe Rocca-Serra
definition source: OBI
imported from: obi.owl

single cell specimen
type: Class
subclass of: cell specimen
textual definition: A cell specimen that contains only one cell.
editor note: Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
definition editor: PERSON: Jie Zheng, Alexander Diehl
definition source: PERSON: Jie Zheng, Alexander Diehl
imported from: obi.owl

BCL format
type: Class
subclass of: data format specification
textual definition: A data format specification that is a binary file containing base calling data. These files are created by sequencing machines during the act of sequencing, and contain data about each of the nucleotide clusters on a sequencing flow cell.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

ERCC RNA spike-in
type: Class
subclass of: processed material
textual definition: A processed material developed by the External RNA Controls Consortium (ERCC) that consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://www.thermofisher.com/order/catalog/product/4456740
imported from: obi.owl

SIRV RNA spike-in
type: Class
subclass of: processed material
textual definition: A processed material that consists of transcript isoforms of 7 spike-in RNA variant (SIRV) genes and possibly the 92 External RNA Controls Consortium (ERCC) RNA spike-in genes.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://www.lexogen.com/sirvs/design/
imported from: obi.owl

SRS identifier
type: Class
subclass of: Accession Number
textual definition: An accession number that applies to a database record for an individual sample object in an NCBI Sequence Read Archive (SRA) submission. These records are imported from the NCBI BioSample database.
definition editor: Stephen Fisher, Dan Berrios
alternative term: SRA sample accession number
imported from: obi.owl

age since culture seeding measurement datum
type: Class
subclass of: age measurement datum
textual definition: An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish).
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
alternative term: age of culture
imported from: obi.owl

alignment counting algorithm
type: Class
subclass of: algorithm
textual definition: An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts).
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

alignment counting application
type: Class
subclass of: software application
textual definition: A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: doi:10.1093/bioinformatics/btu638
imported from: obi.owl

base calling algorithm
type: Class
subclass of: algorithm
textual definition: An algorithm that assigns nucleotides to temporal or spatial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

base calling application
type: Class
subclass of: software application
textual definition: A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

bcl2fastq software application
type: Class
subclass of: base calling application
textual definition: A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
imported from: obi.owl

date process started
type: Class
subclass of: data item
textual definition: A data item that is the date when a process was initiated.
definition editor: Chris Stoeckert, Daniel Berrios, Stephen A. Fisher
imported from: obi.owl

dbGaP study identifier
type: Class
subclass of: centrally registered identifier symbol
textual definition: A central registered identifier symbol that denotes a specific study in dbGaP.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
alternative term: dbGaP accession number
definition source: doi:10.1038/ng1007-1181
imported from: obi.owl

material amplification role
type: Class
subclass of: worker role
textual definition: A worker role played by the person who runs the enzymatic amplifying process.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

material sequencing library preparation role
type: Class
subclass of: worker role
textual definition: A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

number of PCR cycles during library construction
type: Class
subclass of: data item
textual definition: A data item that is the number of PCR cycles used during the construction of a sequencing library.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
alternative term: library construction PCR cycles
definition source: https://en.wikipedia.org/wiki/Polymerase_chain_reaction
imported from: obi.owl

number of rounds of amplification
type: Class
subclass of: data item
textual definition: A data item that is the number of times an amplification reaction happened.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

reference genome role
type: Class
subclass of: reference substance role
textual definition: A reference substance role that is played by a reference genome when used during sequence alignment.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

reference genome-transcriptome alignment algorithm
type: Class
subclass of: algorithm
textual definition: An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

sequence read length measurement datum
type: Class
subclass of: measurement datum
textual definition: A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
alternative term: read length, read length measurement datum
imported from: obi.owl

sequencing library input quantity measurement datum
type: Class
subclass of: scalar measurement datum
textual definition: A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer.
definition editor: Stephen A. Fisher, Junhyong Kim
alternative term: library input amount
imported from: obi.owl

single-end library
type: Class
subclass of: processed material
textual definition: A cDNA library that is a collection of short tags from only one end of DNA fragments.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

specimen harvest quantity
type: Class
subclass of: scalar measurement datum
textual definition: A scalar measurement datum that indicates the amount of specimen collected.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
alternative term: harvest quantity
imported from: obi.owl

spike-in dilution factor
type: Class
subclass of: data item
textual definition: A data item that indicates the dilution of spike-in added to a specimen.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
imported from: obi.owl

star algorithm
type: Class
subclass of: reference genome-transcriptome alignment algorithm
textual definition: A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference.
definition source: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23104886
imported from: obi.owl

transcript analysis by single-end sequencing
type: Class
subclass of: sequencing assay
textual definition: A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://www.illumina.com/science/technology/next-generation-sequencing/paired-end-vs-single-read-sequencing.html
imported from: obi.owl

verse algorithm
type: Class
subclass of: alignment counting algorithm
textual definition: An alignment counting algorithm that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads.
definition editor: Stephen A. Fisher, Junhyong Kim
definition source: http://kim.bio.upenn.edu/software/verse.shtml or http://biorxiv.org/content/early/2016/05/14/053306
imported from: obi.owl

microraft
type: Class
subclass of: material separation device
textual definition: A material separation device also commerically known as Isoraft, that is used to isolate single cells.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://en.wikipedia.org/wiki/Microrafts
imported from: obi.owl

pipette
type: Class
subclass of: device
textual 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.
definition editor: Stephen A. Fisher, Junhyong Kim, Dan Berrios
definition source: https://en.wikipedia.org/wiki/Pipette
imported from: obi.owl

organism
type: Class
subclass of: material entity
textual 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.
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')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
definition editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: obi.owl

specimen
type: Class
subclass of: material entity
textual definition: A material entity that has the specimen role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
imported from: obi.owl

flow cytometer sorter
type: Class
subclass of: material separation device
textual definition: A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest.
definition editor: John Quinn
definition editor: Melanie Courtot
definition source: http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
imported from: obi.owl

DNA sequencer
type: Class
subclass of: measurement device
textual definition: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
definition editor: Trish Whetzel
definition source: MO
imported from: obi.owl

sequencing assay
type: Class
subclass of: assay
textual definition: the use of a chemical or biochemical means to infer the sequence of a biomaterial
editor note: has_output should be sequence of input; we don't have sequence well defined yet
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

enzymatic amplification
type: Class
subclass of: material processing
textual definition: the use of enzymes to increase the number of molecules of a biomaterial
definition editor: PERSON:Kevin Clancy
definition source: OBI branch derived
imported from: obi.owl

pairwise sequence alignment algorithm
type: Class
subclass of: algorithm
textual definition: An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences).
editor note: Ready for OBI-WS : v1.0
definition editor: WS Annotations Group, UGA
definition source: WS Annotations Group, UGA
imported from: webService.owl

BLAST algorithm
type: Class
subclass of: pairwise sequence alignment algorithm
textual definition: BLAST (Basic Local Alignment Search Tool), a pairwise sequence alignment algorithm is a heuristic search algorithm for comparing primary biological sequence information, such as the amino-acid or nucleotides sequences with a database of sequences, and identify sequences that resemble the query sequence above a certain threshold.
editor note: Ready for OBI-WS : v1.0
definition editor: ITPPR
definition source: Wikipedia: BLAST
imported from: webService.owl

sequence data format specification
type: Class
subclass of: data format specification
textual definition: A data format specification for molecular sequence feature information.
editor note: Ready for OBI-WS : v1.0
definition editor: ITPPR
alternative term: sequence data format
definition source: EDAM
imported from: webService.owl

BLASTn
type: Class
subclass of: BLAST algorithm
type: NamedIndividual
type: BLAST algorithm
textual definition: A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a nucleotide level.

RNA sequence data
type: Class
subclass of: sequence data
textual definition: A sequence data that is about the primary structure of RNA.
definition editor: ITPPR
definition source: ITPPR
imported from: webService.owl

treatment
type: Class
subclass of: planned process
textual definition: A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
imported from: ogms.owl

study principle investigator or responsible
type: Class
subclass of: Homo sapiens
textual definition: The principle investigtor or responsible person for a study or a sample collection.
imported from: omiabis.owl

date of specimen collection
type: Class
subclass of: data item
textual definition: A data item that indicates the time when the collection of a specimen occurred.
definition editor: Alice Nzinga
definition editor: Mathias Brochhausen
alternative term: date of specimen preparation
imported from: omiabis.owl

date of specimen amplification
type: Class
subclass of: date process started
subclass of: Restriction
  on property: starts
  some values from: enzymatic amplification protocol
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
alternative term: amplified date
definition: A date process started item that indicates when a specimen was run through the amplification protocol prior to library preparation and sequencing.

date of specimen library preparation
type: Class
subclass of: date process started
subclass of: Restriction
  on property: starts
  some values from: library preparation protocol
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
alternative term: library preparation date
definition: A date process started item that indicates when a specimen was run through the library preparation protocol prior to sequencing.

enzymatic amplification protocol
type: Class
subclass of: protocol
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
alternative term: amplification protocol
definition: A protocol document that contains detailed instructions on how to perform an enzymatic amplification planned process.

experiment name
type: Class
subclass of: symbol
editor note: Exists in MS (Mass spectrometry ontology) with parent "quantification object attribute"
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition: The name for identifying an experiment.

Illumina TruSeq Rapid SBS Kit v2
type: Class
subclass of: sequencing kit
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition source: https://www.illumina.com/products/by-type/sequencing-kits/cluster-gen-sequencing-reagents/hiseq-rapid-sbs-kit.html
definition: A processed material that is a sequencing kit used with Illumina HiSeq 2500 and 1500 sequencers allowing for single-end or paired-end sequencing.

Illumina TruSeq Stranded
type: Class
subclass of: library preparation kit
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition source: https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-mrna.html
definition: A processed material that is used to create a sequencing library that retains mRNA strand orientation.

library preparation protocol
type: Class
subclass of: protocol
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition: A protocol document that contains detailed instructions on how to perform a library preparation planned process.

number of flow cell lanes
type: Class
subclass of: data item
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition source: http://scap-t.org/
definition: A data item that indicates the number of lanes in a flow cell that were used to sequence a specimen

number of flow cells
type: Class
subclass of: data item
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition source: http://scap-t.org/
definition: A data item that indicates the number of flow cells used to sequence a specimen.

pairwise sequence alignment application
type: Class
subclass of: software application
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition: A software application that implements a pairwise sequence alignment algorithm to attempt to align two molecular sequences (nucleic acid or protein sequences).

region of material anatomical entity
type: Class
subclass of: material anatomical entity
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition: An area within a material anatomical entity that is distinct from the other areas of that entity such as the parietal cortex, hippocampus CA1 and amygdala.

RNA harvest compound
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
subclass of: Restriction
  on property: has role
  some values from: detector reagent role
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition: A molecular entity that is an engineered molecule which enables the collection of RNA from cells.

specimen harvest source type
type: Class
subclass of: material entity
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition: A material entity that contained the specimen during harvesting such as a primary culture, tissue, or fixed section.

specimen harvest source unit
type: Class
subclass of: material entity
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition: A material entity that represents the number of number of material entities used during harvesting; for example, a single cell, pooled single cells, tissue, a culture dish, or a coverslip.

star
type: Class
subclass of: pairwise sequence alignment application
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition source: https://github.com/alexdobin/STAR
definition: A software application that implements a RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference.

TIVA tag
type: Class
subclass of: RNA harvest compound
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition source: doi:10.1038/nmeth.2804
definition: A molecular entity that is an engineered molecule which upon photoactivation enables mRNA capture from single cells in live tissue.

verse
type: Class
subclass of: alignment counting application
definition editor: PERSON: Junhyong Kim
definition editor: PERSON: Stephen A. Fisher
definition source: http://kim.bio.upenn.edu/software/verse.shtml
definition: An alignment counting application that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads.

reference_genome
type: Class
subclass of: genome
textual definition: A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.
imported from: so.owl

taxonomic_rank
type: Class
subclass of: organism datum
textual definition: A level of depth of a taxon in a taxonomic hierarchy.
imported from: taxrank.owl

species
type: Class
subclass of: taxonomic_rank
imported from: taxrank.owl

material anatomical entity
type: Class
subclass of: material entity
textual definition: Anatomical entity that has mass.
imported from: uberon.owl

taxonomic rank
type: Class
subclass of: measurement datum
imported from: ncbitaxon.owl

replicate
type: Class
subclass of: role
textual definition: A role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured.
definition editor: James Malone
imported from: efo.owl

FASTQ format
type: Class
subclass of: data format specification
textual definition: FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores.
imported from: efo.owl

BAM format
type: Class
subclass of: data format specification
textual definition: BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format
imported from: efo.owl

genome
type: Class
subclass of: material entity
textual definition: A genome is the full genetic content of an organism, contained in either DNA or RNA (such as for viruses).
definition editor: James Malone
imported from: efo.owl

transcriptome
type: Class
subclass of: material entity
textual definition: The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.
imported from: efo.owl

CEL data file format
type: Class
subclass of: data format specification
textual definition: CEL data file format describes the format used in a CEL file for storing the results of the intensity calculations on the pixel values of a DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array.
definition editor: James Malone
imported from: efo.owl