ornaseq.obo

format-version: 1.2
data-version: 2019-07-08
remark: The following ontology is provided by Stephen A Fisher and Junhyong Kim to annotate next-generation sequencing experiments performed on RNA.
ontology: ornaseq
property_value: http://purl.org/dc/elements/1.1/contributor "Junhyong Kim" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Stephen A Fisher" xsd:string
property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/licenses/by/4.0/
property_value: http://purl.org/dc/elements/1.1/title "Ontology for RNA sequencing (ORNASEQ)" xsd:string
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/NCIT_C20181>))\n############################\n#   Classes\n############################\n\n# Class: <http://purl.obolibrary.org/obo/BFO_0000001> (entity)\n\nSubClassOf(<http://purl.obolibrary.org/obo/BFO_0000001> owl:Thing)\n\n# Class: <http://purl.obolibrary.org/obo/NCIT_C20181> (Conceptual Entity)\n\nSubClassOf(<http://purl.obolibrary.org/obo/NCIT_C20181> owl:Thing)\n\n\n)

[Term]
id: BFO:0000001
name: entity
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000002
name: continuant
is_a: BFO:0000001 ! entity
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000003
name: occurrent
is_a: BFO:0000001 ! entity
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000004
name: independent continuant
def: "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])" []
is_a: BFO:0000002 ! continuant
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000015
name: process
def: "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])" []
is_a: BFO:0000003 ! occurrent
property_value: IAO:0000116 "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)" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000017
name: realizable entity
is_a: BFO:0000020 ! specifically dependent continuant
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "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])" []
is_a: BFO:0000002 ! continuant
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000023
name: role
is_a: BFO:0000017 ! realizable entity
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000031
name: generically dependent continuant
def: "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])" []
is_a: BFO:0000002 ! continuant
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000040
name: material entity
is_a: BFO:0000004 ! independent continuant
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: CHEBI:16991
name: deoxyribonucleic acid
def: "High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms." []
is_a: CHEBI:23367 ! molecular entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl

[Term]
id: CHEBI:23367
name: molecular entity
def: "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl

[Term]
id: CL:0000000
name: cell
def: "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." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl

[Term]
id: CL:0000127
name: astrocyte
def: "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." []
is_a: CL:0000000 ! cell
property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl

[Term]
id: CL:0000449
name: brown fat cell
def: "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." []
is_a: CL:0000000 ! cell
property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl

[Term]
id: CL:0000540
name: neuron
def: "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." []
is_a: CL:0000000 ! cell
property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl

[Term]
id: CL:0000746
name: cardiac muscle cell
def: "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." []
is_a: CL:0000000 ! cell
property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl

[Term]
id: CL:2000029
name: central nervous system neuron
def: "Any neuron that is part of a central nervous system." []
is_a: CL:0000540 ! neuron
property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl

[Term]
id: EFO:0000683
name: replicate
def: "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." []
is_a: BFO:0000023 ! role
property_value: IAO:0000117 "James Malone" xsd:string
property_value: IAO:0000412 http://www.ebi.ac.uk/efo/efo.owl

[Term]
id: EFO:0004155
name: FASTQ format
def: "FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." []
is_a: IAO:0000098 ! data format specification
property_value: IAO:0000412 http://www.ebi.ac.uk/efo/efo.owl

[Term]
id: EFO:0004157
name: BAM format
def: "BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format" []
is_a: IAO:0000098 ! data format specification
property_value: IAO:0000412 http://www.ebi.ac.uk/efo/efo.owl

[Term]
id: EFO:0004420
name: genome
def: "A genome is the full genetic content of an organism, contained in either DNA or RNA (such as for viruses)." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000117 "James Malone" xsd:string
property_value: IAO:0000412 http://www.ebi.ac.uk/efo/efo.owl

[Term]
id: EFO:0004421
name: transcriptome
def: "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." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000412 http://www.ebi.ac.uk/efo/efo.owl

[Term]
id: EFO:0005630
name: CEL data file format
def: "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." []
is_a: IAO:0000098 ! data format specification
property_value: IAO:0000117 "James Malone" xsd:string
property_value: IAO:0000412 http://www.ebi.ac.uk/efo/efo.owl

[Term]
id: GENEPIO:0000069
name: sequencing run date
def: "date the sequencing run was performed" []
is_a: IAO:0000027 ! data item
property_value: IAO:0000119 "GROUP: IRIDA Ontology (Emma)" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/genepio.owl

[Term]
id: GENEPIO:0000081
name: sequencing kit
def: "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." []
is_a: OBI:0000047 ! processed material
property_value: IAO:0000119 "GROUP: IRIDA Ontology (Emma)" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/genepio.owl

[Term]
id: GENEPIO:0000085
name: library preparation kit
def: "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." []
is_a: OBI:0000047 ! processed material
property_value: IAO:0000119 "GROUP: IRIDA Ontology (Emma) and  http://applications.illumina.com/applications/sequencing/ngs-library-prep.html" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/genepio.owl

[Term]
id: GENEPIO:0001170
name: organism datum
is_a: IAO:0000109 ! measurement datum
property_value: IAO:0000412 http://purl.obolibrary.org/obo/genepio.owl

[Term]
id: GO:0005575
name: cellular_component
def: "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)." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0005739
name: mitochondrion
def: "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." []
is_a: GO:0044464 ! cell part
property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0030425
name: dendrite
def: "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." []
is_a: GO:0044464 ! cell part
property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0044297
name: cell body
def: "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections." []
is_a: GO:0044464 ! cell part
property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl

[Term]
id: GO:0044464
name: cell part
def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." []
is_a: GO:0005575 ! cellular_component
property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl

[Term]
id: IAO:0000010
name: software
def: "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." []
is_a: IAO:0000104 ! plan specification
property_value: IAO:0000116 "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000119 "GROUP: OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: IAO:0000017
name: model number
def: "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." []
is_a: IAO:0000028 ! symbol
property_value: IAO:0000116 "manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers" xsd:string
property_value: IAO:0000117 "Person: Alan Ruttenberg" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000027
name: data item
def: "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." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string
property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string
property_value: IAO:0000116 "JAR: datum     -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string
property_value: IAO:0000118 "data" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000028
name: symbol
def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000116 "20091104, MC: this needs work and will most probably change" xsd:string
property_value: IAO:0000116 "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)." xsd:string
property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string
property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string
property_value: IAO:0000119 "based on Oxford English Dictionary" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000030
name: information content entity
def: "A generically dependent continuant that is about some thing." []
is_a: BFO:0000031 ! generically dependent continuant
property_value: IAO:0000116 "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)." xsd:string
property_value: IAO:0000116 "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).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000119 "OBI_0000142" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: IAO:0000032
name: scalar measurement datum
def: "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." []
is_a: IAO:0000109 ! measurement datum
property_value: IAO:0000116 "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000033
name: directive information entity
def: "An information content entity whose concretizations indicate to their bearer how to realize them in a process." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000064
name: algorithm
def: "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." []
is_a: IAO:0000104 ! plan specification
property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000119 "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)" xsd:string
property_value: IAO:0000119 "OBI_0000270" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000098
name: data format specification
def: "A data format specification is the information content borne by the document published defining the specification.\nExample: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" []
is_a: IAO:0000033 ! directive information entity
property_value: IAO:0000116 "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes\ninformation. Example: The ISO document specifying what encompasses an\nXML document; The instructions in a XSD file\"" xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string
property_value: IAO:0000119 "OBI_0000187" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000104
name: plan specification
def: "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." []
is_a: IAO:0000033 ! directive information entity
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "2014-03-31: A plan specification can have other parts, such as conditional specifications." xsd:string
property_value: IAO:0000116 "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved" xsd:string
property_value: IAO:0000117 "Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string
property_value: IAO:0000119 "OBI_0000344" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: IAO:0000109
name: measurement datum
def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:string
property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 group:OBI xsd:string
property_value: IAO:0000119 "OBI_0000305" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000416
name: time measurement datum
def: "A scalar measurement datum that is the result of measuring a temporal interval" []
is_a: IAO:0000032 ! scalar measurement datum
property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string
property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000577
name: centrally registered identifier symbol
def: "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry." []
is_a: IAO:0000028 ! symbol
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000118 "CRID symbol" xsd:string
property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl

[Term]
id: IAO:0000594
name: software application
def: "A software application is software that can be directly executed by some processing unit." []
is_a: IAO:0000010 ! software
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000117 "PERSON: Michel Dumontier" xsd:string
property_value: IAO:0000119 https://github.com/information-artifact-ontology/IAO/issues/80 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/iao.owl
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: NCBITaxon:9606
name: Homo sapiens
is_a: OBI:0100026 ! organism
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCBITaxon:taxonomic_rank
name: taxonomic rank
is_a: IAO:0000109 ! measurement datum
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl

[Term]
id: NCIT:C19498
name: Document
def: "A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable." []
is_a: NCIT:C25198 ! Record
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncit.owl

[Term]
id: NCIT:C20181
name: Conceptual Entity
def: "An organizational header for concepts representing mostly abstract entities." []
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncit.owl

[Term]
id: NCIT:C25198
name: Record
def: "Anything (e.g., a document) providing permanent evidence of or information about past events." []
is_a: NCIT:C20181 ! Conceptual Entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncit.owl

[Term]
id: NCIT:C25364
name: Identifier
def: "One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing." []
is_a: NCIT:C19498 ! Document
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncit.owl

[Term]
id: NCIT:C25402
name: Accession Number
def: "A control number unique to an object.  It is used to identify the object among other objects in a collection." []
is_a: NCIT:C70663 ! Unique Identifier
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncit.owl

[Term]
id: NCIT:C70663
name: Unique Identifier
def: "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." []
is_a: NCIT:C25364 ! Identifier
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncit.owl

[Term]
id: OBI:0000011
name: planned process
def: "A processual entity that realizes a plan which is the concretization of a plan specification." []
is_a: BFO:0000015 ! process
property_value: IAO:0000116 "'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.)" xsd:string
property_value: IAO:0000116 "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 \nobjectives is a planned process." xsd:string
property_value: IAO:0000117 "Bjoern Peters" xsd:string
property_value: IAO:0000119 "branch derived" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000018
name: material supplier role
def: "a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation." []
is_a: OBI:0000947 ! service provider role
property_value: IAO:0000116 "Supplier role is a special kind of service, e.g. biobank" xsd:string
property_value: IAO:0000117 "PERSON:Jennifer Fostel" xsd:string
property_value: IAO:0000118 "material provider role" xsd:string
property_value: IAO:0000118 "supplier" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000025
name: reference substance role
def: "a role inhering in a material entity that is realized when  characteristics or responses elicited by the substance are used for comparison or reference." []
is_a: BFO:0000023 ! role
property_value: IAO:0000117 "Person:Jennifer Fostel" xsd:string
property_value: IAO:0000118 "reference substance" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000047
name: processed material
def: "Is a material entity that is created or changed during material processing." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000070
name: assay
def: "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000116 "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. " xsd:string
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000118 "measuring" xsd:string
property_value: IAO:0000118 "scientific observation" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000091
name: detector reagent role
def: "a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus." []
is_a: BFO:0000023 ! role
property_value: IAO:0000116 "19feb2009.  not clear we need this term.  originally if came from microarrays -- the probes on the array are termed detectors in some instances" xsd:string
property_value: IAO:0000119 "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" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000094
name: material processing
def: "A planned process which results in physical changes in a specified input material" []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string
property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string
property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string
property_value: IAO:0000117 "PERSON: Philippe Rocca Serra" xsd:string
property_value: IAO:0000118 "material transformation" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000097
name: participant under investigation role
def: "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." []
is_a: BFO:0000023 ! role
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000117 "GROUP:  Role Branch" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000102
name: responsible party role
def: "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" []
is_a: OBI:0000202 ! investigation agent role
property_value: IAO:0000117 "Person: Jennifer Fostel" xsd:string
property_value: IAO:0000118 "responsible party" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000103
name: principal investigator role
def: "a responsible party role played by a person responsible for the overall conduct of a study" []
is_a: OBI:0000102 ! responsible party role
property_value: IAO:0000117 "Person: Jennifer Fostel" xsd:string
property_value: IAO:0000118 "principal investigator" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000116
name: worker role
def: "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" []
is_a: OBI:0000202 ! investigation agent role
property_value: IAO:0000116 "\"executes the study plan\" includes the suppliers and manufacturers of reagents and other materials used in the study" xsd:string
property_value: IAO:0000117 "Person:Jennifer Fostel" xsd:string
property_value: IAO:0000118 "worker" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000181
name: population
def: "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" []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: \nhttp://code.google.com/p/popcomm-ontology/" xsd:string
property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string
property_value: IAO:0000119 "adapted from Oxford English Dictionnary" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000198
name: biological replicate role
def: "a reference participant role realized by equivalent treatment of participants" []
is_a: OBI:0000220 ! reference subject role
property_value: IAO:0000117 "Person:Jennifer Fostel" xsd:string
property_value: IAO:0000118 "biological replicate" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000202
name: investigation agent role
def: "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." []
is_a: BFO:0000023 ! role
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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)" xsd:string
property_value: IAO:0000117 "GROUP:  Role Branch" xsd:string
property_value: IAO:0000118 "investigator" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000220
name: reference subject role
def: "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" []
is_a: OBI:0000097 ! participant under investigation role
property_value: IAO:0000117 "Jennifer Fostel" xsd:string
property_value: IAO:0000118 "reference participant" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000245
name: organization
def: "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." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "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:\n\n1) there are organization_member_roles (president, treasurer, branch\neditor), with individual persons as bearers\n\n2) there are organization_roles (employer, owner, vendor, patent holder)\n\n3) an organization has a charter / rules / bylaws, which specify what roles\nthere are, how they should be realized, and how to modify the\ncharter/rules/bylaws themselves.\n\nIt is debatable what the organization itself is (some kind of dependent\ncontinuant or an aggregate of people). This also determines who/what the\nbearer of organization_roles' are. My personal favorite is still to define\norganization as a kind of 'legal entity', but thinking it through leads to\nall kinds of questions that are clearly outside the scope of OBI.\n\nInterestingly enough, it does not seem to matter much where we place\norganization itself, as long as we can subclass it (University, Corporation,\nGovernment Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,\nW3C, University of Oklahoma), and have it play roles.\n\nThis leads to my proposal: We define organization through the statements 1 -\n3 above, but without an 'is a' statement for now. We can leave it in its\ncurrent place in the is_a hierarchy (material entity) or move it up to\n'continuant'. We leave further clarifications to BFO, and close this issue\nfor now." xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string
property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string
property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string
property_value: IAO:0000117 "PERSON: Susanna Sansone" xsd:string
property_value: IAO:0000119 "GROUP: OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000249
name: technical replicate role
def: "technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay" []
is_a: OBI:0000220 ! reference subject role
property_value: IAO:0000117 "Person: Jennifer Fostel" xsd:string
property_value: IAO:0000118 "technical replicate" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000272
name: protocol
def: "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." []
is_a: IAO:0000104 ! plan specification
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000119 "OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000415
name: polymerase chain reaction
def: "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." []
is_a: OBI:0600058 ! enzymatic amplification
property_value: IAO:0000117 "OBI Plan" xsd:string
property_value: IAO:0000118 "PCR" xsd:string
property_value: IAO:0000119 "adapted from wikipedai" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000626
name: DNA sequencing
def: "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." []
is_a: OBI:0600047 ! sequencing assay
property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string
property_value: IAO:0000119 "OBI Branch derived" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000659
name: specimen collection process
def: "A planned process with the objective of collecting a specimen." []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000116 "label  changed to 'specimen collection process' on 10/27/2014, details see tracker:\nhttp://sourceforge.net/p/obi/obi-terms/716/" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "Philly2013: The specimen_role for the specimen is created during the specimen collection process." xsd:string
property_value: IAO:0000117 "Bjoern Peters" xsd:string
property_value: IAO:0000118 "specimen collection" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000711
name: library preparation
def: "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." []
is_a: OBI:0000094 ! material processing
property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string
property_value: IAO:0000118 "library construction" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000722
name: paired-end library
def: "is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs" []
is_a: OBI:0000047 ! processed material
property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string
property_value: IAO:0000118 "mate-paired library" xsd:string
property_value: IAO:0000118 "paired-end tag (PET) library" xsd:string
property_value: IAO:0000119 "adapted from information provided by Solid web site" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000832
name: measurement device
def: "A device in which a measure function inheres." []
is_a: OBI:0000968 ! device
property_value: IAO:0000117 "GROUP:OBI Philly workshop" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000835
name: manufacturer
def: "A person or organization that has a manufacturer role" []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000932
name: material separation device
def: "A device with a separation function realized in a planed process" []
is_a: OBI:0000968 ! device
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000947
name: service provider role
def: "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" []
is_a: BFO:0000023 ! role
property_value: IAO:0000117 "PERSON:Helen Parkinson" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000968
name: device
def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." []
is_a: OBI:0000047 ! processed material
property_value: IAO:0000116 "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.\n\n2013-6-5 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:\n\n(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.\n\n(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.\n\n(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.\n\nIn 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.  " xsd:string
property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string
property_value: IAO:0000118 "instrument" xsd:string
property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0000973
name: sequence data
def: "A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.\n" []
is_a: IAO:0000109 ! measurement datum
property_value: IAO:0000117 "Person:Chris Stoeckert" xsd:string
property_value: IAO:0000119 "GROUP: OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001140
name: spike-in quality control role
def: "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" []
is_a: OBI:0000025 ! reference substance role
property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter" xsd:string
property_value: IAO:0000119 "MO_937 spike_quality_control" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001167
name: age measurement datum
def: "A time measurement datum that is the result of measurement of age of an organism" []
is_a: IAO:0000416 ! time measurement datum
property_value: IAO:0000116 "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.\nlife of bearer doesn't imply organism\nthis assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature\nage as a quality is dubious; we plan to revisit\nstages in development are currently handled with controlled vocabulary, such as 2-somite stage " xsd:string
property_value: IAO:0000117 "PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng" xsd:string
property_value: IAO:0000119 "MO_178 Age" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001169
name: age since birth measurement datum
def: "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." []
is_a: OBI:0001167 ! age measurement datum
property_value: IAO:0000117 "PERSON:Chris Stoeckert, Jie Zheng" xsd:string
property_value: IAO:0000119 "MO_710 birth" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001185
name: selectively maintained organism
def: "An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms" []
is_a: OBI:0100026 ! organism
property_value: IAO:0000117 "Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert " xsd:string
property_value: IAO:0000118 "cultivar" xsd:string
property_value: IAO:0000118 "ecotype" xsd:string
property_value: IAO:0000118 "strain" xsd:string
property_value: IAO:0000119 "MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001271
name: RNA-seq assay
def: "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" []
is_a: OBI:0600047 ! sequencing assay
property_value: IAO:0000117 "PERSON: James Malone" xsd:string
property_value: IAO:0000118 "transcription profiling by high throughput sequencing" xsd:string
property_value: IAO:0000119 "EFO_0002770 transcription profiling by high throughput sequencing" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001468
name: cell specimen
def: "A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture." []
is_a: OBI:0100051 ! specimen
property_value: IAO:0000116 "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/" xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl" xsd:string
property_value: IAO:0000119 "MO_612 cell" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001494
name: linear amplification
def: "An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template." []
is_a: OBI:0600058 ! enzymatic amplification
property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string
property_value: IAO:0000119 "MO_997 linear_amplification" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001616
name: specimen identifier
def: "A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation." []
is_a: IAO:0000028 ! symbol
property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string
property_value: IAO:0000118 "specimen ID" xsd:string
property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001850
name: transcript analysis by paired-end tag sequencing
def: "An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions." []
is_a: OBI:0600047 ! sequencing assay
property_value: IAO:0000117 "Person: Venkat Malladi, Chris Stoeckert, Jie Zheng" xsd:string
property_value: IAO:0000118 "RNA-PET" xsd:string
property_value: IAO:0000118 "RNA-PET assay" xsd:string
property_value: IAO:0000119 "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]" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001852
name: paired-end library preparation
def: "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. " []
is_a: OBI:0000711 ! library preparation
property_value: IAO:0000117 "Person: Venkat Malladi, Jie Zheng" xsd:string
property_value: IAO:0000119 "Venkat Malladi, Jie Zheng" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001891
name: sequencing facility organization
def: "An organization that provides sequence determination service" []
is_a: OBI:0000245 ! organization
property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string
property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001895
name: specimen collector
def: "A person who collects the specimen" []
is_a: NCBITaxon:9606 ! Homo sapiens
property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string
property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001933
name: value specification
def: "An information content entity that specifies a value within a classification scheme or on a quantitative scale." []
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001959
name: sequencing library multiplexing
def: "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." []
is_a: OBI:0000094 ! material processing
property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0001967
name: multiplexing sequence identifier
def: "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" []
is_a: CHEBI:16991 ! deoxyribonucleic acid
property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra" xsd:string
property_value: IAO:0000119 "OBI" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002127
name: single cell specimen
def: "A cell specimen that contains only one cell." []
is_a: OBI:0001468 ! cell specimen
property_value: IAO:0000116 "Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/" xsd:string
property_value: IAO:0000117 "PERSON: Jie Zheng, Alexander Diehl" xsd:string
property_value: IAO:0000119 "PERSON: Jie Zheng, Alexander Diehl" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002461
name: BCL format
def: "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." []
is_a: IAO:0000098 ! data format specification
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002462
name: ERCC RNA spike-in
def: "A processed material developed by the External RNA Controls Consortium (ERCC) that  consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids." []
is_a: OBI:0000047 ! processed material
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000119 https://www.thermofisher.com/order/catalog/product/4456740 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002463
name: SIRV RNA spike-in
def: "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." []
is_a: OBI:0000047 ! processed material
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000119 https://www.lexogen.com/sirvs/design/ xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002464
name: SRS identifier
def: "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." []
is_a: NCIT:C25402 ! Accession Number
property_value: IAO:0000117 "Stephen Fisher, Dan Berrios" xsd:string
property_value: IAO:0000118 "SRA sample accession number" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002465
name: age since culture seeding measurement datum
def: "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)." []
is_a: OBI:0001167 ! age measurement datum
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000118 "age of culture" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002466
name: alignment counting algorithm
def: "An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts)." []
is_a: IAO:0000064 ! algorithm
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002467
name: alignment counting application
def: "A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes." []
is_a: IAO:0000594 ! software application
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000119 doi:10.1093/bioinformatics/btu638 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002468
name: base calling algorithm
def: "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" []
is_a: IAO:0000064 ! algorithm
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002469
name: base calling application
def: "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." []
is_a: IAO:0000594 ! software application
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002470
name: bcl2fastq software application
def: "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." []
is_a: OBI:0002469 ! base calling application
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000119 https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002471
name: date process started
def: "A data item that is the date when a process was initiated." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000117 "Chris Stoeckert, Daniel Berrios, Stephen A. Fisher" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002472
name: dbGaP study identifier
def: "A central registered identifier symbol that denotes a specific study in dbGaP." []
is_a: IAO:0000577 ! centrally registered identifier symbol
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000118 "dbGaP accession number" xsd:string
property_value: IAO:0000119 doi:10.1038/ng1007-1181 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002473
name: material amplification role
def: "A worker role played by the person who runs the enzymatic amplifying process." []
is_a: OBI:0000116 ! worker role
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002474
name: material sequencing library preparation role
def: "A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced." []
is_a: OBI:0000116 ! worker role
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002475
name: number of PCR cycles during library construction
def: "A data item that is the number of PCR cycles used during the construction of a sequencing library." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000118 "library construction PCR cycles" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Polymerase_chain_reaction xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002476
name: number of rounds of amplification
def: "A data item that is the number of times an amplification reaction happened." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002477
name: reference genome role
def: "A reference substance role that is played by a reference genome when used during sequence alignment." []
is_a: OBI:0000025 ! reference substance role
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002478
name: reference genome-transcriptome alignment algorithm
def: "An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome." []
is_a: IAO:0000064 ! algorithm
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002479
name: sequence read length measurement datum
def: "A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence." []
is_a: IAO:0000109 ! measurement datum
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000118 "read length, read length measurement datum" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002480
name: sequencing library input quantity measurement datum
def: "A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer." []
is_a: IAO:0000032 ! scalar measurement datum
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim" xsd:string
property_value: IAO:0000118 "library input amount" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002481
name: single-end library
def: "A cDNA library that is a collection of short tags from only one end of DNA fragments." []
is_a: OBI:0000047 ! processed material
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002482
name: specimen harvest quantity
def: "A scalar measurement datum that indicates the amount of specimen collected." []
is_a: IAO:0000032 ! scalar measurement datum
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000118 "harvest quantity" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002483
name: spike-in dilution factor
def: "A data item that indicates the dilution of spike-in added to a specimen." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002484
name: star algorithm
def: "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." []
is_a: OBI:0002478 ! reference genome-transcriptome alignment algorithm
property_value: IAO:0000119 https://www.ncbi.nlm.nih.gov/pubmed/23104886 xsd:string
property_value: IAO:0000119 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002485
name: transcript analysis by single-end sequencing
def: "A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions." []
is_a: OBI:0600047 ! sequencing assay
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000119 https://www.illumina.com/science/technology/next-generation-sequencing/paired-end-vs-single-read-sequencing.html xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002486
name: verse algorithm
def: "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." []
is_a: OBI:0002466 ! alignment counting algorithm
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim" xsd:string
property_value: IAO:0000119 "http://kim.bio.upenn.edu/software/verse.shtml or http://biorxiv.org/content/early/2016/05/14/053306" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002487
name: microraft
def: "A material separation device also commerically known as Isoraft, that is used to isolate single cells." []
is_a: OBI:0000932 ! material separation device
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Microrafts xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0002488
name: pipette
def: "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." []
is_a: OBI:0000968 ! device
property_value: IAO:0000117 "Stephen A. Fisher, Junhyong Kim, Dan Berrios" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Pipette xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0100026
name: organism
def: "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." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "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')" xsd:string
property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to  when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string
property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string
property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0100051
name: specimen
def: "A material entity that has the specimen role." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000117 "PERSON: James Malone" xsd:string
property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string
property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0400099
name: flow cytometer sorter
def: "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." []
is_a: OBI:0000932 ! material separation device
property_value: IAO:0000117 "John Quinn" xsd:string
property_value: IAO:0000117 "Melanie Courtot" xsd:string
property_value: IAO:0000119 http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0400103
name: DNA sequencer
def: "A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences." []
is_a: OBI:0000832 ! measurement device
property_value: IAO:0000117 "Trish Whetzel" xsd:string
property_value: IAO:0000119 "MO" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0600047
name: sequencing assay
def: "the use of a chemical or biochemical means to infer the sequence of a biomaterial" []
is_a: OBI:0000070 ! assay
property_value: IAO:0000116 "has_output should be sequence of input; we don't have sequence well defined yet" xsd:string
property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBI:0600058
name: enzymatic amplification
def: "the use of enzymes to increase the number of molecules of a biomaterial" []
is_a: OBI:0000094 ! material processing
property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string
property_value: IAO:0000119 "OBI branch derived" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl

[Term]
id: OBIws:0000015
name: pairwise sequence alignment algorithm
def: "An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences)." []
is_a: IAO:0000064 ! algorithm
property_value: IAO:0000116 "Ready for OBI-WS : v1.0" xsd:string
property_value: IAO:0000117 "WS Annotations Group, UGA" xsd:string
property_value: IAO:0000119 "WS Annotations Group, UGA" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi/webService.owl

[Term]
id: OBIws:0000088
name: BLAST algorithm
def: "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." []
is_a: OBIws:0000015 ! pairwise sequence alignment algorithm
property_value: IAO:0000116 "Ready for OBI-WS : v1.0" xsd:string
property_value: IAO:0000117 "ITPPR" xsd:string
property_value: IAO:0000119 "Wikipedia: BLAST" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi/webService.owl

[Term]
id: OBIws:0000106
name: sequence data format specification
def: "A data format specification for molecular sequence feature information." []
is_a: IAO:0000098 ! data format specification
property_value: IAO:0000116 "Ready for OBI-WS : v1.0" xsd:string
property_value: IAO:0000117 "ITPPR" xsd:string
property_value: IAO:0000118 "sequence data format" xsd:string
property_value: IAO:0000119 "EDAM" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi/webService.owl

[Term]
id: OBIws:0000140
name: BLASTn
def: "A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a nucleotide level." []
is_a: OBIws:0000088 ! BLAST algorithm

[Term]
id: OBIws:0000192
name: RNA sequence data
def: "A sequence data that is about the primary structure of RNA." []
is_a: OBI:0000973 ! sequence data
property_value: IAO:0000117 "ITPPR" xsd:string
property_value: IAO:0000119 "ITPPR" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi/webService.owl

[Term]
id: OGMS:0000090
name: treatment
def: "A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder" []
is_a: OBI:0000011 ! planned process
property_value: IAO:0000117 "Albert Goldfain" xsd:string
property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=35 xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ogms.owl

[Term]
id: OMIABIS:0000100
name: study principle investigator or responsible
def: "The principle investigtor or responsible person for a study or a sample collection." []
is_a: NCBITaxon:9606 ! Homo sapiens
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omiabis.owl

[Term]
id: OMIABIS:0001039
name: date of specimen collection
def: "A data item that indicates the time when the collection of a specimen occurred." []
is_a: IAO:0000027 ! data item
property_value: IAO:0000117 "Alice Nzinga" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000118 "date of specimen preparation" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/omiabis.owl

[Term]
id: ORNASEQ:0000001
name: date of specimen amplification
is_a: OBI:0002471 ! date process started
relationship: RO:0002223 ORNASEQ:0000003 ! starts enzymatic amplification protocol
property_value: definition "A date process started item that indicates when a specimen was run through the amplification protocol prior to library preparation and sequencing." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000118 "amplified date" xsd:string

[Term]
id: ORNASEQ:0000002
name: date of specimen library preparation
is_a: OBI:0002471 ! date process started
relationship: RO:0002223 ORNASEQ:0000007 ! starts library preparation protocol
property_value: definition "A date process started item that indicates when a specimen was run through the library preparation protocol prior to sequencing." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000118 "library preparation date" xsd:string

[Term]
id: ORNASEQ:0000003
name: enzymatic amplification protocol
is_a: OBI:0000272 ! protocol
property_value: definition "A protocol document that contains detailed instructions on how to perform an enzymatic amplification planned process." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000118 "amplification protocol" xsd:string

[Term]
id: ORNASEQ:0000004
name: experiment name
is_a: IAO:0000028 ! symbol
property_value: definition "The name for identifying an experiment." xsd:string
property_value: IAO:0000116 "Exists in MS (Mass spectrometry ontology) with parent \"quantification object attribute\"" xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string

[Term]
id: ORNASEQ:0000005
name: Illumina TruSeq Rapid SBS Kit v2
is_a: GENEPIO:0000081 ! sequencing kit
relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing
property_value: 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." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000119 https://www.illumina.com/products/by-type/sequencing-kits/cluster-gen-sequencing-reagents/hiseq-rapid-sbs-kit.html xsd:string

[Term]
id: ORNASEQ:0000006
name: Illumina TruSeq Stranded
is_a: GENEPIO:0000085 ! library preparation kit
relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing
property_value: definition "A processed material that is used to create a sequencing library that retains mRNA strand orientation." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000119 https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-mrna.html xsd:string

[Term]
id: ORNASEQ:0000007
name: library preparation protocol
is_a: OBI:0000272 ! protocol
property_value: definition "A protocol document that contains detailed instructions on how to perform a library preparation planned process." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string

[Term]
id: ORNASEQ:0000008
name: number of flow cell lanes
is_a: IAO:0000027 ! data item
property_value: definition "A data item that indicates the number of lanes in a flow cell that were used to sequence a specimen" xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000119 http://scap-t.org/?q=content/sample-attributes-data-dictionary xsd:string

[Term]
id: ORNASEQ:0000009
name: number of flow cells
is_a: IAO:0000027 ! data item
property_value: definition "A data item that indicates the number of flow cells used to sequence a specimen." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000119 http://scap-t.org/?q=content/sample-attributes-data-dictionary xsd:string

[Term]
id: ORNASEQ:0000010
name: pairwise sequence alignment application
is_a: IAO:0000594 ! software application
property_value: definition "A software application that implements a pairwise sequence alignment algorithm to attempt to align two molecular sequences (nucleic acid or protein sequences)." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string

[Term]
id: ORNASEQ:0000011
name: region of material anatomical entity
is_a: UBERON:0000465 ! material anatomical entity
property_value: 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." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string

[Term]
id: ORNASEQ:0000012
name: RNA harvest compound
is_a: CHEBI:23367 ! molecular entity
relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing
relationship: RO:0000087 OBI:0000091 ! has role detector reagent role
property_value: definition "A molecular entity that is an engineered molecule which enables the collection of RNA from cells." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string

[Term]
id: ORNASEQ:0000013
name: specimen harvest source type
is_a: BFO:0000040 ! material entity
property_value: definition "A material entity that contained the specimen during harvesting such as a primary culture, tissue, or fixed section." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string

[Term]
id: ORNASEQ:0000014
name: specimen harvest source unit
is_a: BFO:0000040 ! material entity
property_value: 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." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string

[Term]
id: ORNASEQ:0000015
name: star
is_a: ORNASEQ:0000010 ! pairwise sequence alignment application
property_value: 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." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000119 https://github.com/alexdobin/STAR xsd:string

[Term]
id: ORNASEQ:0000016
name: TIVA tag
is_a: ORNASEQ:0000012 ! RNA harvest compound
property_value: definition "A molecular entity that is an engineered molecule which upon photoactivation enables mRNA capture from single cells in live tissue." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000119 doi:10.1038/nmeth.2804 xsd:string

[Term]
id: ORNASEQ:0000017
name: verse
is_a: OBI:0002467 ! alignment counting application
property_value: 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." xsd:string
property_value: IAO:0000117 "PERSON: Junhyong Kim" xsd:string
property_value: IAO:0000117 "PERSON: Stephen A. Fisher" xsd:string
property_value: IAO:0000119 http://kim.bio.upenn.edu/software/verse.shtml xsd:string

[Term]
id: SO:0001505
name: reference_genome
def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." []
is_a: EFO:0004420 ! genome
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: TAXRANK:0000000
name: taxonomic_rank
def: "A level of depth of a taxon in a taxonomic hierarchy." []
is_a: GENEPIO:0001170 ! organism datum
property_value: IAO:0000412 http://purl.obolibrary.org/obo/taxrank.owl

[Term]
id: TAXRANK:0000006
name: species
is_a: TAXRANK:0000000 ! taxonomic_rank
property_value: IAO:0000412 http://purl.obolibrary.org/obo/taxrank.owl

[Term]
id: UBERON:0000465
name: material anatomical entity
def: "Anatomical entity that has mass." []
is_a: BFO:0000040 ! material entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl

[Typedef]
id: BFO:0000050
name: part of
def: "a core relation that holds between a part and its whole" []
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl
is_transitive: true
is_a: RO:0002131 ! overlaps

[Typedef]
id: OBI:0000312
name: is_specified_output_of
def: "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." []
property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl
is_a: RO:0000056 ! participates in

[Typedef]
id: RO:0000053
name: bearer of
def: "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" []
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl

[Typedef]
id: RO:0000056
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl

[Typedef]
id: RO:0000087
name: has role
def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" []
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0002131
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002223
name: starts
def: "inverse of starts with" []
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl
is_a: BFO:0000050 ! part of

[Typedef]
id: RO:0002323
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []
property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl