OWL-DL
Asiyah Yu Lin
Edison Ong
LINCS-CLOview
LINCS-CLOview: A subset of the Cell Line Ontology (CLO) that represents all known cell lines using in the NIH Library of Integrated Network-based Cellular Signatures (LINCS) project.
Qingping Liu
Yongqun "Oliver" He (YH)
Zhaohui Ni
Description
An account of the content of the resource.
Contributor
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
BFO OWL specification label
Really of interest to developers only
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Creator
Notes on the structure, composition or histology of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
Subject and Keywords
The topic of the content of the resource.
Notes on how similar or equivalent classes are represented in other ontologies.
Notes on the ontogenic development of instances of this class.
has associated axiom(nl)
An axiom associated with a term expressed using natural language
Person:Alan Ruttenberg
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
temporal interpretation
elucidation
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
person:Alan Ruttenberg
Date
Title
A name given to the resource.
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
STR profile
An annotation property that specifies an STR profile of a cell line cell.
BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
definition
PERSON:Daniel Schober
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
has curation status
PERSON:Bill Bug
PERSON:Melanie Courtot
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
Notes on the how instances of this class vary across species.
Notes on the evolved function of instances of this class.
Source
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
editor preferred term~editor preferred label
editor preferred label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
example
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
imported from
For external terms/classes, the ontology from which the term was imported
Cell line LINCS ID
An annotation property that represents an LINCS ID of a cell line.
Format
The physical or digital manifestation of the resource.
has part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
a core relation that holds between a whole and its part
has_part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
realizes
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
derives originally from patient having disease
In most cases, the patient in the relation is used to refer human patient. However, an animal patient (or veterinary patient) can also be referred.
has disease
Jie Zheng, Yongqun He, Yu Lin, Allen Xiang
is in cell line repository
an object property that specifies a cell line repository for a specifc cell line.
is disease model for
an object property that represents a relation between a cell line cell and a disease.
This object property is largely equivalent to the previous term 'is model for' (http://www.ebi.ac.uk/cellline#is_model_for).
is about
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
has_specified_input
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
is_specified_input_of
Alan Ruttenberg
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_specified_output_of
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
bearer of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
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
bearer_of
is bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
has participant
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has_participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
concretizes
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
has role
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has_role
this person has role this investigator role (more colloquially: this person has this role of investigator)
derives from
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives_from
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
derives into
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives_into
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
A reproductive system organ that produces and releases either sperm (testis) or eggs (ovary).
The part of the reproductive system that produces and releases eggs (ovaries) or sperm (testicles/testes).NCI-GLOSS
URI: http://www.ebi.ac.uk/cellline#Organ
entity
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
continuant
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
occurrent
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
An entity that has temporal parts and that happens, unfolds or develops through time.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
independent continuant
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
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])
the bottom right portion of a human torso
the interior of your mouth
process
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
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])
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
disposition
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
an atom of element X has the disposition to decay to an atom of element Y
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
realizable entity
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
specifically dependent continuant
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
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.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
role
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
generically dependent continuant
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
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])
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
material entity
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
the undetached arm of a human being
a maintaining cell culture process that keeps cell line cell alive and actively cultured.
A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures.
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters
suspension cell line culturing is a cell line culturing method where cells do not require a surface for growth and differentiation. This method is appropriate for cells that are adapted to suspension culture or cells that are non-adhesive (e.g. hematopoietic cells)
adherent cell line culturing is a cell line culturing method where cells require a surface for growth and differentiation.
a role that inheres in a cell line repository organization.
an organization that serves as a repository of cell lines.
immortal human T cell line cell
an immortal human lymphocyte cell line cell that is derived from T cell.
adherent on feeder cells cell line culturing
A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak
a immortal cell line that is dervied from human tissue.
immortal human cell line
a cell culture growth mode that indicates a cell needs to adhere to a cell culture plate to grow.
a cell culture growth mode that indicates a cell can grow when the cell is suspended in cell culture medium.
a disposition that represents a mode of cell culture growth, i.e., the cell will grow at a specific cell culture mode. For example, an adherent cell culture growh mode means that the cell will grow when the cell is adhere to a cell culture plate.
cell line
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
mixed adherent and suspension cell line culturing
clusters in suspension cell line culturing
a immortal cell line that is dervied from mouse tissue.
immortal mouse cell line
a cell line that is derived from stem cell
a immortal stem cell line that is derived from somatic stem cell
a immortal somatic stem cell line that is derived from multi fate stem cell
a immortal multi fate stem cell line that is derived from neuronal stem cell
a immortal neuronal stem cell line that is derived from neuroblast
immortal non-terminally differentiated cell line cell
a cell line that is derived from non-terminally differentiated cell
immortal non-terminally differentiated cell line
an immortal cell line cell that is derived from contractile cell
a immortal contractile cell line cell that is derived from muscle cell
immortal electrically active cell line cell
an immortal cell line cell that is derived from electrically active cell
immortal electrically responsive cell line cell
a immortal electrically active cell line cell that is derived from electrically responsive cell
a immortal electrically responsive cell line cell that is derived from neuron
a immortal neuron cell line cell that is derived from bipolar neuron
immortal peripheral neuron cell line cell
a immortal neuron cell line cell that is derived from peripheral neuron
a cell line that is derived from motile cell
a immortal motile cell line that is derived from leukocyte
immortal myeloid leukocyte cell line cell
a immortal leukocyte cell line that is derived from myeloid leukocyte
a immortal myeloid leukocyte cell line that is derived from monocyte
immortal nongranular leukocyte cell line cell
a immortal leukocyte cell line that is derived from nongranular leukocyte
immortal nongranular leukocyte cell line
a immortal nongranular leukocyte cell line that is derived from lymphocyte
a immortal lymphocyte cell line that is derived from B cell
a immortal cell line cell that is derived from eukaryotic cell
a immortal eukaryotic cell line that is derived from animal cell
a immortal animal cell line that is derived from epithelial cell
a immortal animal cell line that is derived from hematopoietic cell
a immortal hematopoietic cell line that is derived from blood cell
a immortal hematopoietic cell line that is derived from myeloid cell
immortal hematopoietic lineage restricted progenitor cell line cell
a immortal hematopoietic cell line that is derived from hematopoietic lineage restricted progenitor cell
immortal hematopoietic lineage restricted progenitor cell line
a immortal hematopoietic lineage restricted progenitor cell line that is derived from myeloblast
a immortal animal cell line that is derived from neural cell
immortal connective tissue cell line cell
a immortal animal cell line that is derived from connective tissue cell
a immortal connective tissue cell line that is derived from fibroblast
a cell line that is derived from nucleate cell
a cell line that is derived from somatic cell
immortal animal ovary-derived fibroblast cell line cell
An immortal fibroblast cell line cell that derives from animal ovary.
An immortal cell line cell that derives from skin.
An immortal cell line cell that derives from spleen.
immortal mixed endoderm/mesoderm-derived structure-derived cell line cell
An immortal cell line cell that derives from mixed endoderm/mesoderm-derived structure.
An immortal cell line cell that derives from tongue.
An immortal cell line cell that derives from pair of lungs.
An immortal cell line cell that derives from kidney.
immortal placenta-derived cell line cell
An immortal cell line cell that derives from placenta.
An immortal cell line cell that derives from embryo.
immortal prostate gland-derived cell line cell
An immortal cell line cell that derives from prostate gland.
immortal somatic nervous system-derived cell line cell
An immortal cell line cell that derives from somatic nervous system.
An immortal cell line cell that derives from liver.
An immortal cell line cell that derives from colon.
An immortal cell line cell that derives from caecum.
immortal pancreas-derived cell line cell
An immortal cell line cell that derives from pancreas.
An immortal cell line cell that derives from brain.
immortal female gonad-derived cell line cell
An immortal cell line cell that derives from female gonad.
An immortal cell line cell that derives from testis.
An immortal cell line cell that derives from stomach.
immortal bone element-derived cell line cell
An immortal cell line cell that derives from bone element.
immortal thyroid gland-derived cell line cell
An immortal cell line cell that derives from thyroid gland.
immortal urinary bladder-derived cell line cell
An immortal cell line cell that derives from urinary bladder.
immortal acetabular part of hip bone-derived cell line cell
An immortal cell line cell that derives from acetabular part of hip bone.
An immortal cell line cell that derives from breast.
immortal comma-shaped body-derived cell line cell
An immortal cell line cell that derives from comma-shaped body.
immortal supra-orbital vein-derived cell line cell
An immortal cell line cell that derives from supra-orbital vein.
An immortal cell line cell that derives from uterus.
immortal endometrium-derived cell line cell
An immortal cell line cell that derives from endometrium.
immortal uterine cervix-derived cell line cell
An immortal cell line cell that derives from uterine cervix.
immortal follicular fluid-derived cell line cell
An immortal cell line cell that derives from follicular fluid.
immortal mammary gland-derived cell line cell
An immortal cell line cell that derives from mammary gland.
immortal bone marrow-derived cell line cell
An immortal cell line cell that derives from bone marrow.
immortal uterine cervix-derived epithelial cell line cell
An immortal epithelial cell line cell that derives from uterine cervix.
immortal ileocecal junction-derived cell line cell
An immortal cell line cell that derives from ileocecal junction.
An immortal cell line cell that derives from vagina.
An immortal cell line cell that derives from larynx.
immortal esophagus-derived cell line cell
An immortal cell line cell that derives from esophagus.
An immortal cell line cell that derives from gingiva.
An immortal cell line cell that derives from mouth.
immortal round window-derived cell line cell
An immortal cell line cell that derives from round window.
immortal intestine-derived cell line cell
An immortal cell line cell that derives from intestine.
An immortal cell line cell that derives from rectum.
An immortal cell line cell that derives from tonsil.
immortal adrenal gland-derived cell line cell
An immortal cell line cell that derives from adrenal gland.
An immortal cell line cell that derives from ureter.
An immortal cell line cell that derives from cornea.
immortal mammalian vulva-derived cell line cell
An immortal cell line cell that derives from mammalian vulva.
immortal spherical lensed eye-derived cell line cell
An immortal cell line cell that derives from spherical lensed eye.
immortal cervix-derived fibroblast cell line cell
An immortal fibroblast cell line cell that derives from cervix.
immortal chordate pharynx-derived cell line cell
An immortal cell line cell that derives from chordate pharynx.
immortal pelvic fin-derived cell line cell
An immortal cell line cell that derives from pelvic fin.
immortal right ureter-derived cell line cell
An immortal cell line cell that derives from right ureter.
immortal human skin-derived cell line cell
An immortal skin-derived cell line cell that derives from human.
immortal human lymphocyte cell line cell
An immortal lymphocyte cell line cell that derives from human.
immortal human septum of telencephalon-derived cell line cell
An immortal septum of telencephalon-derived cell line cell that derives from human.
immortal human mixed endoderm/mesoderm-derived structure-derived cell line cell
An immortal mixed endoderm/mesoderm-derived structure-derived cell line cell that derives from human.
immortal human lung-derived cell line cell
An immortal lung-derived cell line cell that derives from human.
immortal mouse embryo-derived cell line cell
An immortal embryo-derived cell line cell that derives from mouse.
An immortal cell line cell that derives from human.
immortal human colon-derived cell line cell
An immortal colon-derived cell line cell that derives from human.
immortal human caecum-derived cell line cell
An immortal caecum-derived cell line cell that derives from human.
immortal human brain-derived cell line cell
An immortal brain-derived cell line cell that derives from human.
immortal mouse skin-derived cell line cell
An immortal skin-derived cell line cell that derives from mouse.
immortal human peripheral neuron cell line cell
An immortal peripheral neuron cell line cell that derives from human.
immortal human stomach-derived cell line cell
An immortal stomach-derived cell line cell that derives from human.
immortal human pancreas-derived cell line cell
An immortal pancreas-derived cell line cell that derives from human.
immortal human bone element-derived cell line cell
An immortal bone element-derived cell line cell that derives from human.
immortal human epithelial cell line cell
An immortal epithelial cell line cell that derives from human.
immortal human urinary bladder-derived cell line cell
An immortal urinary bladder-derived cell line cell that derives from human.
immortal human liver-derived cell line cell
An immortal liver-derived cell line cell that derives from human.
immortal human acetabular part of hip bone-derived cell line cell
An immortal acetabular part of hip bone-derived cell line cell that derives from human.
immortal human comma-shaped body-derived cell line cell
An immortal comma-shaped body-derived cell line cell that derives from human.
immortal human breast-derived cell line cell
An immortal breast-derived cell line cell that derives from human.
immortal human spleen-derived cell line cell
An immortal spleen-derived cell line cell that derives from human.
immortal human supra-orbital vein-derived cell line cell
An immortal supra-orbital vein-derived cell line cell that derives from human.
immortal human uterus-derived cell line cell
An immortal uterus-derived cell line cell that derives from human.
immortal human endometrium-derived cell line cell
An immortal endometrium-derived cell line cell that derives from human.
immortal human kidney-derived cell line cell
An immortal kidney-derived cell line cell that derives from human.
immortal human uterine cervix-derived cell line cell
An immortal uterine cervix-derived cell line cell that derives from human.
immortal human follicular fluid-derived cell line cell
An immortal follicular fluid-derived cell line cell that derives from human.
immortal human female gonad-derived cell line cell
An immortal female gonad-derived cell line cell that derives from human.
immortal human thyroid gland-derived cell line cell
An immortal thyroid gland-derived cell line cell that derives from human.
An immortal blood cell line cell that derives from human.
immortal human uterine cervix-derived epithelial cell line cell
An immortal uterine cervix-derived epithelial cell line cell that derives from human.
immortal human ileocecal junction-derived cell line cell
An immortal ileocecal junction-derived cell line cell that derives from human.
An immortal B cell line cell that derives from human.
immortal human vagina-derived cell line cell
An immortal vagina-derived cell line cell that derives from human.
immortal human larynx-derived cell line cell
An immortal larynx-derived cell line cell that derives from human.
immortal human esophagus-derived cell line cell
An immortal esophagus-derived cell line cell that derives from human.
immortal human gingiva-derived cell line cell
An immortal gingiva-derived cell line cell that derives from human.
An immortal muscle cell line cell that derives from human.
immortal human mouth-derived cell line cell
An immortal mouth-derived cell line cell that derives from human.
immortal human testis-derived cell line cell
An immortal testis-derived cell line cell that derives from human.
immortal human intestine-derived cell line cell
An immortal intestine-derived cell line cell that derives from human.
immortal human rectum-derived cell line cell
An immortal rectum-derived cell line cell that derives from human.
immortal human tonsil-derived cell line cell
An immortal tonsil-derived cell line cell that derives from human.
immortal human adrenal gland-derived cell line cell
An immortal adrenal gland-derived cell line cell that derives from human.
immortal human placenta-derived cell line cell
An immortal placenta-derived cell line cell that derives from human.
immortal human ovary-derived fibroblast cell line cell
An immortal animal ovary-derived fibroblast cell line cell that derives from human.
immortal human prostate gland-derived cell line cell
An immortal prostate gland-derived cell line cell that derives from human.
immortal human ureter-derived cell line cell
An immortal ureter-derived cell line cell that derives from human.
immortal human mammalian vulva-derived cell line cell
An immortal mammalian vulva-derived cell line cell that derives from human.
immortal human spherical lensed eye-derived cell line cell
An immortal spherical lensed eye-derived cell line cell that derives from human.
immortal human cervix-derived fibroblast cell line cell
An immortal cervix-derived fibroblast cell line cell that derives from human.
immortal human bone marrow-derived cell line cell
An immortal bone marrow-derived cell line cell that derives from human.
immortal human chordate pharynx-derived cell line cell
An immortal chordate pharynx-derived cell line cell that derives from human.
immortal human tongue-derived cell line cell
An immortal tongue-derived cell line cell that derives from human.
immortal human neuroblast cell line cell
An immortal neuroblast cell line cell that derives from human.
An immortal monocyte cell line cell that derives from human.
disease: primary superficial spreading melanoma in vertical growth phase; from lung metastases in mice
ATCC: CRL-7898,COSMIC ID:910921; ATCC CRL-7898
disease: malignant melanoma (skin primary)
WEB: http://www.atcc.org/products/all/CRL-1872
ATCC: COSMIC ID:910697; ATCC CRL-7905,CRL-7905
disease: adenocarcinoma (pancreas primary)
disease: adenocarcinoma (mammary gland primary)
disease: lymphoma; EBV and KSHV positive
disease: oral cavity cancer,squamous cell carcinoma
WEB: http://capcelllines.ca/details.asp?id=132
Web: http://www.ncbi.nlm.nih.gov/pubmed/7535634
disease: clear cell carcinoma (kidney primary)
disease: tongue cancer,squamous cell carcinoma
disease: epidermoid carcinoma (lung primary)
disease: unknown, probably lung anaplastic carcinoma
disease: ductal adenocarcinoma; cystic fibrosis
DSMZ: ACC 360,COSMIC ID:910568; DSMZ ACC 360
disease: bronchogenic carcinoma (bronchus primary)
disease: promyeloblast; acute promyelocytic leukemia
disease: colorectal adenocarcinoma (colon primary)
disease: medulloblastoma (cerebellum primary)
disease: desmoplastic cerebellar medulloblastoma
disease: carcinoma; small cell lung cancer
disease: carcinoma; small cell lung cancer (lung primary)
disease: Burkitts lymphoma (B lymphocyte primary)
disease: fibrous histiocytoma (primary unknown)
disease: monoblast; myelomonoblastic leukemia
disease: primary acantholytic squamous cell carcinoma
disease: cutaneous T cell lymphoma,non-Hodgkin lymphoma
disease: gastric carcinoma (stomach primary
disease: diffuse mixed lymphoma; B lymphoblast
ATCC: HTB-63,COSMIC ID:907067; ATCC HTB-63
disease: acute T cell leukemia; CD45 deficient
disease: B cell lymphoma (metastatic site: peritoneal cavity)
disease: chronic myelo- genous leukemia (bone marrow primary)
disease: gastric carcinoma (stomach primary)
disease: myeloblast; acute lymphoblastic leukemia
disease: promyeloblast; acute lympho- blastic leukemia
DSMZ: COSMIC ID:1161992; DSMZ ACC 673,ACC 673
disease: glioblastoma; apoptosis studies; p53+, p16, p14ARF
disease: glioblastoma; p53 expression under tetracycline-induced promoter
disease: carcinoma (mammary gland primary)
disease: undifferentiated lymphoma lymphoblast
PubMed: https://www.ncbi.nlm.nih.gov/pubmed/1975513
MCF-10A is a spontaneously immortalized, but nontransformed human mammary epithelial cell line cell that was derived from the breast tissue of a 36-year-old patient with fibrocystic changes
PubMed: https://www.ncbi.nlm.nih.gov/pubmed/12798140
disease: fibrocystic disease; non-tumorigenic
CVCL: CVCL_0598; EFO: EFO_0001200; ChEMBL: CHEMBL3307364; HMSL: HMSL50583
disease: neuroepithelioma (brain primary)
disease: ductal carcinoma (mammary gland primary)
disease: epidermoid carcinoma (cervix primary)
disease: megakaryoblast; chronic myelogenous leukemia
disease: B-cell lymphocytic neoplasm,non-Hodgkin lymphoma
WEB: http://bioinformatics.hsanmartino.it/cldb/cl3535.html
disease: mesothelioma, biphasic (lung primary)
disease: biphenotypic B myelo- monocytic leukemia
disease: leukemia, acute lymphoblastic pre-B cell
disease: carcinoma; classic small cell lung cancer (lung primary)
disease: large cell neuro- endocrine carcinoma (lung primary)
disease: adenocarcinoma (lung primary)
disease: squamous cell neuro- endocrine carcinoma (lung primary)
disease: papillary adenocar- cinoma (lung primary)
disease: carcinoma; classic small cell lung cancer
disease: adenocarcinoma; non-small cell lung cancer
disease: adenocarcinoma; non-small cell lung cancer (lung primary)
disease: large cell adenocarcinoma; non-small cell lung cancer
disease: adenocarcinoma; bronchoalveolar carcinoma (lung primary)
disease: squamous cell adenocarcinoma; non-small cell lung cancer
disease: neuroendocrine carc- cinoma; non-small cell lung cancer (lung primary)
disease: squamous cell carcinoma (lung primary)
disease: large cell carcinoma; poorly differentiated (lung primary)
disease: carcinoma; variant small cell lung cancer (lung primary)
disease: non-small cell lung cancer (lung primary)
disease: carcinoma; non-small cell lung cancer
disease: squamous cell carcinoma; mesothelioma (lung primary)
disease: small cell lung cancer; adeno- carcinoma; squamous cell carcinoma
disease: alveolus); bronchioalveolar carcinoma; non-small cell lung cancer
disease: papillary adeno- carcinoma (lung primary)
disease: large cell carci- noma (lung primary)
disease: carcinoma; small cell lung cancer (unknown primary)
disease: mixed adeno- squamous and carcinoma (lung primary)
disease: bronchioalveolar carci- noma; non-small cell lung cancer (lung primary)
disease: carcinoma; large cell lung cancer (lung primary)
disease: large cell; neuroendocrine; carcinoma; non-small cell lung cancer
disease: adenocarcinoma; non- small cell lung cancer (lung primary)
disease: adenocarcinoma (ovary primary)
disease: IL-2 independent, cytotoxic to a wide range of malignant cells
disease: malignant papillary serous adenocarcinoma (ovary primary)
disease: transfected with ZAP-70 expression vector; control for P116 cells
disease: Burkitts lymphoma; B lymphoblast
disease: teratocarcinoma (ovary primary)
disease: adenocarcinoma; same patient as PL45
disease: adenocarcinoma (prostate primary)
disease: diffuse large cell non-Hodgkins lymphoma (B lymphocyte primary)
disease: malignant primitive neuroectodermal tumor
disease: ductal adenocarcinoma; same patient as Panc 10.05 cells
disease: acute lymphocytic leukemia (non-T, non-B)
disease: carcinoma; control for RKO-E6 and RKO-AS45-1 cells
disease: non-Hodgkins lymphoma; B lymphoblast
ATCC: CRL-1671,COSMIC ID:930082; ATCC CRL-1671
disease: squamous cell carcinoma (nasal septum primary)
disease: acute lymphoblastic leukemia; t(4;11) translocation
disease: carcinoma; small cell lung cancer; large cell variant
disease: neuroblastoma (brain primary)
disease: osteosarcoma; multipotential sarcoma
disease: adenocarcinoma (colon primary)
disease: sarcoma (anaplastic osteosarcoma or Ewings sarcoma)
disease: adenocarcinoma (liver primary)
ATCC: HTB-88,COSMIC ID:909720; ATCC HTB-88
WEB: http://www.atcc.org/products/all/HTB-68.aspx
ATCC: COSMIC ID:909725; ATCC HTB-71,HTB-71
disease: embryonal neuro- blastoma (brain/neuroblast primary)
disease: retroperitoneal; malignant; primitive neuroectodermal tumor
disease: mesodermal tumor (mixed); consistent with leiomyosarcoma
disease: pleomorphic hepatocellular carcinoma
disease: adenocarcinoma colon primary)
disease: large cell immuno- blastic lymphoma (unknown primary)
disease: ductal carcinoma (pancreas primary)
an immortal human B cell line cell that is derived from a 8-year-old Caucasian male human patient with an acute lymphoblastic leukemia.
WEB: http://www.atcc.org/~/ps/CRL-1929.ashx
WEB: http://www.atcc.org/products/all/CRL-1929.aspx
disease: colorectal carcinoma (colon primary)
disease: model for cytokine (IL-3) signaling pathways and myeloid progenitor cell differentiation
disease: erythroblast; erythroleukemia; CTNF responsive
disease: diffuse large cell lymphoma, non-Hodgkins
disease: primary malignant adenocarcinoma; endometrioid carcinoma
disease: primary malignant adenocarcinoma; clear cell carcinoma
ATCC: COSMIC ID:930299; ATCC CRL-1803,CRL-1803
disease: histiocytic lymphoma; neomycin resistant
disease: carcinoma, epithelioid (bone primary)
disease: primary superficial spreading melanoma in radial growth phase/vertical growth phase
disease: nodular melanoma in vertical growth phase
disease: primary superficial spreading melanoma in vertical growth phase
disease: ductal carcinoma (mammary gland epithelium primary)
immortal human pelvic fin-derived cell line cell
An immortal pelvic fin-derived cell line cell that derives from human.
immortal human round window-derived cell line cell
An immortal round window-derived cell line cell that derives from human.
immortal human bipolar neuron cell line cell
An immortal bipolar neuron cell line cell that derives from human.
immortal human right ureter-derived cell line cell
An immortal right ureter-derived cell line cell that derives from human.
immortal human myeloblast cell line cell
An immortal myeloblast cell line cell that derives from human.
immortal human mammary gland-derived cell line cell
An immortal mammary gland-derived cell line cell that derives from human.
ATCC: COSMIC ID:910401; ATCC CRL-1923,CRL-1923
ATCC: HTB-93,COSMIC ID:909759; ATCC HTB-93
ATCC: CRL-7767,COSMIC ID:924248; ATCC CRL-7767
JCRB: COSMIC ID:907314; JCRB IFO50431,IFO50431
RIKEN: COSMIC ID:925339; Riken RCB1200,RCB1200
ATCC: COSMIC ID:924247; ATCC HTB-117,HTB-117
ATCC: COSMIC ID:909758; ATCC HTB-118,HTB-118
Originator: Miyagiwa, M. (Okayama Univ.)
A immortal human cell line cell that has the characteristics: Human bile duct carcinoma. This cell line produces carbohydrate antigen 19/9 in serum-free medium. TKG0389(Deposited from Tohoku Univ.).
Derived from tissue: bile duct, ascites meta in animal: human.
Derived from tissue: epidermoid carcinoma in animal: human.
A immortal human cell line cell that has the characteristics: High level of EGF receptor
A immortal human cell line cell that has the characteristics: Human cell line derivd from epidermoid carcinoma. TKG0182 (Deposited from Tohoku Univ.).
A immortal human cell line cell that has the characteristics: It was initiated from a malignant gestational choriocarcinoma of the fetal placenta. Need to check response to hormones before use. Back up culture of ECA2687.
Derived from tissue: fetal placenta in animal: human.
A immortal human cell line cell that has the characteristics: Japanese gallbladder carcinoma established from metastated ascite. Cell growth is slow.
Derived from tissue: gallbladder, ascites meta in animal: human.
Originator: Todoroki, T. & Ohno, T. & Kim, B.
Derived from tissue: gallbladder, lymph node meta in animal: human.
A immortal human cell line cell that has the characteristics: Japanese gallbadder carcinoma metastated to lymph node from the same patient of TGBC2TKB. Cell growth is slow.
A immortal human cell line cell that has the characteristics: Lung carcinoma, refer to ATCC CCL185
Derived from tissue: lung in animal: human.
A immortal human cell line cell that has the characteristics: Lung Cancer-1/squamous, floating variant, the same patient as RCB0455 LC-1/sq.
A immortal human cell line cell that has the characteristics: Small cell carcinoma, classic type. See Lu-134-A.
Originator: Terasaki, T. & Shimosato, Y.
A immortal human cell line cell that has the characteristics: Small cell carcinoma, variant type
A immortal human cell line cell that has the characteristics: Human lung squamous cell carcinoma cell line. TKG0481(Deposited from Tohoku Univ.).
A immortal human cell line cell that has the characteristics: Japanese lung adenocarcinoma, highly metastatic in SCID mice. Also refer to RCB0444 RCRF-LC-AI. Cell growth is slow.
A immortal human cell line cell that has the characteristics: Human lung carcinoma cell line. TKG0442(Deposited from Tohoku Univ.).
A immortal human cell line cell that has the characteristics: Human lung squamous cell carcinoma cell line.TKG0494 (Deposited from Tohoku Univ.).
A immortal human cell line cell that has the characteristics: Human cell line derived from lung adenocarcinoma cells. Differentiated type. Previous name:PC-14(RCB0446)
A immortal human cell line cell that has the characteristics: Japanese lung large cell carcinoma
Originator: Miyamoto, Tadaaki & Takiguchi,Yuichi
Derived from tissue: lung, skin meta in animal: human.
Derived from tissue: lymph node, B-lymphoma in animal: human.
Originator: Miyazawa, Keisuke & Uchida, Yoshiko
A immortal human cell line cell that has the characteristics: Fas-antigen expressing. Ligation with anti-Fas mAb does not induce apoptosis.
A immortal human cell line cell that has the characteristics: Human T cell line derived from acute T cell leukemia. TKG0377 (Deposited from Tohoku Univ.).
Derived from tissue: lymphoid,T-leukemia in animal: human.
A immortal human cell line cell that has the characteristics: Human fibrous histiocytoma. Showing fibroblastic- and histiocytic features.
Derived from tissue: maxilla in animal: human.
A immortal human cell line cell that has the characteristics: Human cell line derived from osteosarcoma. TKG0452(Deposited from Tohoku Univ.).
Derived from tissue: osteosarcoma in animal: human.
Derived from tissue: pancreas in animal: human.
A immortal human cell line cell that has the characteristics: Human cell line derived from pancreatic cancer. Ductal origin. TKG0606(Deposited from Tohoku Univ.)
Derived from tissue: pelvic tumor in animal: human.
RIKEN: COSMIC ID:925342; Riken RCB0803,RCB0803
A immortal human cell line cell that has the characteristics: Isolated from a patient with hiper dopaminemia andnorepinephrinemia.
Derived from tissue: pleural effusion in animal: human.
A immortal human cell line cell that has the characteristics: Human CML derived cell line. Deposited directly from the institution that has established this cell.
Originator: Lozzio, C.B. & Lozzio, B.B.
Derived from tissue: sarcoma in animal: human.
A immortal human cell line cell that has the characteristics: Osteogenic sarcoma
Derived from tissue: T acute lymphoblastic leukemia in animal: human.
A immortal human cell line cell that has the characteristics: Human cell line derived from T cell leukemia. TKG0563(Deposited from Tohoku Univ.).
A immortal human cell line cell that has the characteristics: Human neuroblastoma cell line. TKG0460(Deposited from Tohoku Univ.).
Derived from tissue: unknown in animal: human.
A immortal somatic nervous system-derived cell line cell that has the characteristics: N-myc gene unamplified tumor. Cell growth is slow.
Derived from tissue: nervous system in animal: human.
A immortal somatic nervous system-derived cell line cell that has the characteristics: N-myc gene amplification. Cell growth is slow.
Derived from tissue: neuroblastoma in animal: human.
A immortal somatic nervous system-derived cell line cell that has the characteristics: Human cell line derived from neuroblastoma. TKG0448(Deposited from Tohoku Univ.).
A immortal somatic nervous system-derived cell line cell that has the characteristics: Neuroblastoma, a target in CTL assay
Derived from tissue: cornea in animal: human.
A immortal cornea-derived cell line cell that has the characteristics: SV40-Adeno vector transformed cornea cells. 64kD keratin producing. Choleratoxin-free medium.
A immortal cornea-derived cell line cell that has the characteristics: This cell line is provided only in Japan.
A immortal human lymphocyte cell line cell that has the characteristics: Human cell line derived from p180-BCR-ABL dependent leukemia.
Derived from tissue: peripheral blood lymphocytes in animal: human.
A immortal mouse embryo-derived cell line cell that has the characteristics: Embryonal cell line derived from wild mouse. Sensitive to leukemia viruses.
Derived from tissue: embryo in animal: mouse, wild.
Derived from tissue: colon in animal: human.
A immortal human colon-derived cell line cell that has the characteristics: Colon carcinoma. CEA-positive, nude mouse-transplantable.
A immortal human colon-derived cell line cell that has the characteristics: Described to produce serotonin, epinephrine.
Derived from tissue: colon, supraclavicular meta in animal: human.
A immortal human colon-derived cell line cell that has the characteristics: CEA-producing colon adenocarcinoma. Back up culture of ECA2739. Cell growth is slow.
A immortal human brain-derived cell line cell that has the characteristics: Human glioma separated from gliosarcoma.
Derived from tissue: brain in animal: human.
A immortal human brain-derived cell line cell that has the characteristics: Human cell line derived from glioblastoma multiforme (Caucasian). Hyperpentaploid chromosome count. TKG0471(Deposited from Tohoku Univ.).
A immortal human brain-derived cell line cell that has the characteristics: Human cell line derived from glioblastoma. TKG0183(Deposited from Tohoku Univ.).
A immortal human brain-derived cell line cell that has the characteristics: Glioma, S-100 Protein producing. Cell growth is slow.
A immortal human skin-derived cell line cell that has the characteristics: Malignant trichilemmal cyst cells. Strongly laminin positive on cell surface. Serum-free culturable.
Derived from tissue: skin in animal: human.
A immortal human skin-derived cell line cell that has the characteristics: Human melanoma producing melanin up to 50 PDL. Backup of ECA88030401.
Derived from tissue: stomach in animal: human.
A immortal human stomach-derived cell line cell that has the characteristics: Human cell line derived from signet ring cell carcinoma of stomach. TKG0449 (Deposited from Tohoku Univ.).
A immortal human stomach-derived cell line cell that has the characteristics: Stomach cancer (Borrmann IV). Mutin, CA19-9, CEA, alphafetoprotein positive Cell growth is slow.
RIKEN: COSMIC ID:906869; Riken RCB0555,RCB0555
A immortal human stomach-derived cell line cell that has the characteristics: Small cell gastrointestinal carcinoma with c-myc overexpression. Cell growth is slow.
RIKEN: COSMIC ID:906848; Riken RCB0983,RCB0983
Derived from tissue: stomach, liver meta in animal: human.
A immortal human stomach-derived cell line cell that has the characteristics: Poorly differentiated gastric adenocarcinoma. Producing high level of CEA.
A immortal human stomach-derived cell line cell that has the characteristics: Moderately differentiated adenocarcinoma. Once they were hypodiploids. Cell growth is slow.
A immortal human stomach-derived cell line cell that has the characteristics: Gastric cancer undifferentiated, mucin producing
Derived from tissue: stomach, lymph node meta in animal: human.
A immortal human stomach-derived cell line cell that has the characteristics: Japanese gastric cancer, lymph node metastated.
RIKEN: RCB1148,COSMIC ID:909770; Riken RCB1148
A immortal human stomach-derived cell line cell that has the characteristics: Potentially differentiatable to both direction of adenomatous and squamous epithelial cells.
A immortal human stomach-derived cell line cell that has the characteristics: c-erbB-2 expressing gastric adenocarcinoma. Differentiated type.
A immortal human stomach-derived cell line cell that has the characteristics: Small cell gastrointestinal carcinoma showing creatine kinase-BB and aromatic L-amino-acid decarboxy. Cell growth is slow.
Derived from tissue: stomach, subcutis in animal: human.
A immortal human bone element-derived cell line cell that has the characteristics: Osteosarcoma cell line derived from human. High yield of IFN production by induction with poly IC, cyclohexmide, actinomycin D. Antigenically, MG-63 IFN is closely related to human fibroblast IFN. TKG0294 (Deposited from Tohoku Univ.).
Derived from tissue: bone in animal: human.
A immortal human bone element-derived cell line cell that has the characteristics: Sensitive to further transformation with both virus and chemicals. Backup of ECA87070202.
A immortal human bone element-derived cell line cell that has the characteristics: Osteoid producing in vitro and in nude mice. Cell growth is slow.
Originator: Hotta, Tetsuo & Motoyama, Teiichi
Derived from tissue: bladder in animal: human.
A immortal human urinary bladder-derived cell line cell that has the characteristics: Bladder transitional-cell carcinoma
A immortal human urinary bladder-derived cell line cell that has the characteristics: Human cell line derived from bladder cancer. Transitional cell carcinoma. TKG0443 (Deposited from Tohoku Univ.).
A immortal human urinary bladder-derived cell line cell that has the characteristics: Described to produce SCF, IL-1, IL-3, IL-6, G-CSF, GM-CSF, etc.
Derived from tissue: liver in animal: human.
A immortal human liver-derived cell line cell that has the characteristics: hepatocellular carcinoma. Produce alpha-fetoprotein, albumin, etc. Back up of ECA2870. Almost equal to RCB0459, but the restriction is a. Information
A immortal human liver-derived cell line cell that has the characteristics: Human cell line derived from hepatocyte carcinoma. TKG0205 (Deposited from Tohoku Univ.). Information
Derived from tissue: breast in animal: human.
A immortal human breast-derived cell line cell that has the characteristics: Human breast carcinoma established from an effusion.
A immortal human breast-derived cell line cell that has the characteristics: Human cell line derived from breast adenocarcinoma. TKG0479 (Deposited from Tohoku Univ.).
Derived from tissue: brest, pleural fluid in animal: human.
A immortal human spleen-derived cell line cell that has the characteristics: Human cell line derived from splenic B cell lymphoma.
Derived from tissue: spleen in animal: human.
A immortal human kidney-derived cell line cell that has the characteristics: Renal tumor cell from a Japanese. Transplantable to nude mice.
Derived from tissue: kidney in animal: human.
A immortal human kidney-derived cell line cell that has the characteristics: Kidney carcinoma from a Japanese patient. Cell growth is slow.
A immortal human kidney-derived cell line cell that has the characteristics: Human renal cell carcinoma cell line. TKG0447(Deposited from Tohoku Univ.).
A immortal human uterine cervix-derived cell line cell that has the characteristics: Just like ATCC CCL 2, HeLa
Derived from tissue: cervix in animal: human.
A immortal human uterine cervix-derived cell line cell that has the characteristics: Cervical carcinoma cell line derived from human. TA-4, CA-4, TPA, placental ALP are positive. Regan isoenzyme producing. p53 normal, p51 mutation (+), HLA-A 2402/.TKG0462(Deposited from Tohoku Univ.).
A immortal human uterine cervix-derived cell line cell that has the characteristics: Human cell line derived from cervical cancer. TKG0437(Deposited from Tohoku Univ.).
A immortal human uterine cervix-derived cell line cell that has the characteristics: Human cell line derived from uterine cervical epidermoid carcinoma. TKG0366(Deposited from Tohoku Univ.).
A immortal human uterine cervix-derived cell line cell that has the characteristics: Japanese cervix squamous cell carcinoma. Once said TA-4 positive.
Derived from tissue: cervix, Virchow's lymph node in animal: human.
A immortal human thyroid gland-derived cell line cell that has the characteristics: Human thyroid anaplastic carcinoma derived cell line. TKG0446 (Deposited from Tohoku Univ.).
Derived from tissue: thyroid in animal: human.
Derived from tissue: thyroid gland in animal: human.
A immortal human thyroid gland-derived cell line cell that has the characteristics: Human cell line derived from thyroid cancer. Poorly differentiated papillary adenocarcinoma. TKG0439(Deposited from Tohoku Univ.).
Derived from tissue: blood in animal: human.
A immortal human blood cell line cell that has the characteristics: Human cell line derived from B cell leukemia. TKG0413(Deposited from Tohoku Univ.).
A immortal human blood cell line cell that has the characteristics: T cell leukemia
A immortal human blood cell line cell that has the characteristics: Chronic myelogeneous leukemia, subclone of RCB0495 KU812.
A immortal human blood cell line cell that has the characteristics: Acute lymphatic leukemia
A immortal human blood cell line cell that has the characteristics: RCB1181 ST cells transformed with human G-CSF receptor cDNA. Responds to G-CSF.
A immortal human blood cell line cell that has the characteristics: Adult T-cell leukemia. HTLV-1 pro-virus DNA(+).
A immortal human blood cell line cell that has the characteristics: Chronic myelogeneous leukemia, Ph1 chromosome (+),basophi-like cells.
A immortal human blood cell line cell that has the characteristics: T cell leukemia, the same patient as RCB1164 MOLT-3.
A immortal human blood cell line cell that has the characteristics: Human T leukemic cell line (CD4+). CR2 receptor (+). TKG0229(Deposited from Tohoku Univ.).
A immortal human blood cell line cell that has the characteristics: Differentates to macrophage-like cells after treatment with phorbol ester. The variant subline (RCB2128 A-THP-1).
A immortal human blood cell line cell that has the characteristics: Chronic myelogenous leukemia , subclone of RCB0495 KU812.
A immortal human blood cell line cell that has the characteristics: Typical human B cell leukemia.
A immortal human blood cell line cell that has the characteristics: Human cell line derived from B cell leukemia. TKG0467 (Deposited from Tohoku Univ.).
A immortal human blood cell line cell that has the characteristics: Human cell line derived from T cell leukemia. TKG0463(Deposited from Tohoku Univ.).
Derived from tissue: Peripheral blood in animal: human.
A immortal human esophagus-derived cell line cell that has the characteristics: Human cell line derived from esophageal cancer. Squamous cell carcinoma. TKG0462(Deposited from Tohoku Univ.).
Derived from tissue: esophagus in animal: human.
Originator: Nishihira, Tetsuro (Akaishi, T.)
A immortal human esophagus-derived cell line cell that has the characteristics: Human cell line derived from esophageal cancer (highly differentiated squamous cell carcinoma). Not transplantable to nude mouse. TKG0266 (Deposited from Tohoku Univ.).
A immortal human esophagus-derived cell line cell that has the characteristics: Human cell line derived from esophageal cancer. Moderately differentiated squamous cell carcinoma. TKG0259(Deposited from Tohoku Univ.).
A immortal human esophagus-derived cell line cell that has the characteristics: Human cell line derived from esophageal cancer. Highly differentiated squamous cell carcinoma. TKG0261(Deposited from Tohoku Univ.).
A immortal human esophagus-derived cell line cell that has the characteristics: Human cell line derived from esophageal cancer. Moderately differentiated squamous cell carcinoma. TKG0262(Deposited from Tohoku Univ.).
A immortal human esophagus-derived cell line cell that has the characteristics: Human cell line derived from poorly differntiated esophageal squamous cell carcinoma. Not transplantable to nude mouse. TKG0256 (Deposited from Tohoku Univ.).
A immortal human esophagus-derived cell line cell that has the characteristics: Highly differentiated squamous carcinoma (esophagus), not transplantable to nude mouse. A culture submitted to the Cell Resource Center for Biomedical Research was found to be contaminated with mycoplasma. Progeny were cured by Treatments with BM Cyclin and MC210. TKG0257 (Deposited from Tohoku Univ.).
Derived from tissue: esophagus, lymph node meta in animal: human.
A immortal human esophagus-derived cell line cell that has the characteristics: Produce hypercalcemia in nude mice. PTH-related protein, IL-1alpha producing.
A immortal human esophagus-derived cell line cell that has the characteristics: Human esophageal squamous cell carcinoma (poorly differentiated) cell line. Not transplantable to nude mouse. TKG0260 (Deposited from Tohoku Univ.).
Derived from tissue: esophagus, pleural effusion in animal: human.
A immortal human gingiva-derived cell line cell that has the characteristics: Human gingival carcinoma cell line. Expressing remarkable EGF receptor. HLA-A 2/24. TKG0485(Deposited from Tohoku Univ.).
Derived from tissue: gingiva in animal: human.
Derived from tissue: muscle in animal: human.
A immortal human muscle cell line cell that has the characteristics: Extraskeltal myxoid chondrosarcoma
A immortal human mouth-derived cell line cell that has the characteristics: Human cell line derived from oral squamous cell carcinoma occurred in 69-yo, male patient. HLA-A 24/. TKG0487 (Deposited from Tohoku Univ.).
Derived from tissue: mouth in animal: human.
Derived from tissue: mouth floor in animal: human.
A immortal human mouth-derived cell line cell that has the characteristics: Human cell line derived from squamous cell carcinoma at mouth floor. TKG0455(Deposited from Tohoku Univ.).
Derived from tissue: testis in animal: human.
A immortal human testis-derived cell line cell that has the characteristics: Embryonal carcinoma, testis.
A immortal human intestine-derived cell line cell that has the characteristics: Small-cell gastrointestinal carcinoma. High levels of creatine kinase brain isoenzyme. Cell growth is slow.
Derived from tissue: intestine in animal: human.
A immortal human adrenal gland-derived cell line cell that has the characteristics: Human cell line derived from neuroblastoma. Dibuty-cAMP (1 mM) induces differentiation. TKG0486(Deposited from Tohoku Univ.).
Derived from tissue: sympatho adrenal cell in animal: human.
Derived from tissue: ovary, ascites meta in animal: human.
A immortal human ovary-derived fibroblast cell line cell that has the characteristics: Human cell line derived from adenocarcinoma of ovary. TKG0602(Deposited from Tohoku Univ.).
A immortal human ovary-derived fibroblast cell line cell that has the characteristics: Granulosa cell tumor. Possible to produce progesterone after HCG addition. Cell growth is slow.
Originator: Nishi, Yoshihiro & Nawata, Hajime
Derived from tissue: ovary, peritoneum in animal: human.
Derived from tissue: prostate, bone meta in animal: human.
A immortal human prostate gland-derived cell line cell that has the characteristics: Human cell line derived from bone metastasis of prostatic cancer. TKG0600(Deposited from Tohoku Univ.).
A immortal human bone marrow-derived cell line cell that has the characteristics: N-myc gene amplification
Derived from tissue: bone marrow in animal: human.
RIKEN: COSMIC ID:910929; Riken RCB0478,RCB0478
A immortal human bone marrow-derived cell line cell that has the characteristics: Human T-cell line derived from acute lynphblastic leukemia. TKG0251 (Deposited from Tohoku Univ.).
A immortal human bone marrow-derived cell line cell that has the characteristics: Human acute myeloid leukemia. The variant subline (RCB1928 KG-1a) CD3-,CD13+,CD14-,CD15+,CD19-,CD33+
A immortal human bone marrow-derived cell line cell that has the characteristics: Human cell line derived from acute myelogenous leukemia. The variant subline of KG-1(RCB1166) cell line. TKG0402(Deposited from Tohoku Univ.).
A immortal human tongue-derived cell line cell that has the characteristics: Human tongue squamous cell carcinoma derived cell line. TKG0489 (Deposited from Tohoku Univ.).
Derived from tissue: tongue in animal: human.
A immortal human tongue-derived cell line cell that has the characteristics: Human cell line derived from tongue cancer. Squamous cell carcinoma. TKG0470(Deposited from Tohoku Univ.).
A immortal human tongue-derived cell line cell that has the characteristics: Human tongue squamous cell carcinoma cell line. HLA-A 2/24. TKG0484(Deposited from Tohoku Univ.).
A immortal human mammary gland-derived cell line cell that has the characteristics: Same as OCUB-1, OCUB-F. Chromosome = pseudotetraploid.
Derived from tissue: mammary gland, pleural fluid in animal: human.
cell
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.
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000324
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture.
A cell that will develop into a neuron often after a migration phase.
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors.
A stem cell that can give rise to multiple lineages of cells.
A precursor cell with a limited number of potential fates.
define using PATO mulit-potent or oligopotent?
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
A connective-tissue cell of mesenchymal origin that secretes proteins and especially molecular collagen from which the extracellular fibrillar matrix of connective tissue forms.
A large, flat, oval cell found in connective tissue and responsible for the formation of fibers.
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000496
These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
URI: http://www.ebi.ac.uk/cellline#fibroblast
A cell that is usually found in a two-dimensional sheet with a free surface.
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
Cell that cover the surface of the body and line its cavities.
Cell that line the inner and outer surfaces of the body by forming cellular layers (epithelium) or masses (MSH).
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000475
URI: http://www.ebi.ac.uk/cellline#epithelial_cell
A cell found predominately in the blood.
A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000208
URI: http://www.ebi.ac.uk/cellline#T_cell
A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body.
A neuron that is part of nerve found outside the central nervous system.
A cell whose primary function is to shorten.
A mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle.
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000609
Mature contractile cells, commonly known as myocytes, that form one of three kinds of muscle. The three types of muscle cells are skeletal (muscle fibers), cardiac (myocytes, cardiac), and smooth (myocytes, smooth muscle). They are derived from embryonic (precursor) muscle cells called myoblasts (MSH).
URI: http://www.ebi.ac.uk/cellline#muscle_cell
A cell whose function is determined by the generation or the reception of an electric signal.
A cell that moves by its own activities.
A lymphocyte of B lineage with the phenotype CD19-positive and surface immunoglobulin-positive.
A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000101
Immunologically important lymphocyte that is not thymus-dependent, is either short-lived and naive or long-lived and of memory phenotype, and resembles the bursa-derived lymphocyte of birds in that it is responsible for the production of immunoglobulins.
A cell whose function is determined by its response to an electric signal.
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.
These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)
Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid.
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12
A stem cell that can give rise to cell types of the body other than those of the germ-line.
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
A cell of the monocyte, granulocyte, or mast cell lineage.
The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow.
myeloid lineage restricted progenitor cell
A progenitor cell restricted to the myeloid lineage.
Note that this is a class of cell types, not an identified single cell type.
'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells.
A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
hematopoietic lineage restricted progenitor cell
A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.
A cell that is part of the nervous system.
A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
Any hematopoietic cell that is a precursor of some other hematopoietic cell type.
A cell that, by division or terminal differentiation, can give rise to other cell types.
Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.
"A hereditary disease that is the result of one or more abnormal alleles and may be dominant (a single copy of the abnormal allele is sufficient to give rise to the disease), semi-dominant, or recessive (requiring both copies of the gene to have an abnormal allele)." [DO:wk\,ls]
URI: http://www.ebi.ac.uk/cellline#simple_genetic_disease
An organ system benign neoplasm that is located_in reproductive system organs.
A cancer that is classified based on the organ it starts in.
A cancer that is classified by the type of cell from which it is derived.
A B-cell lymphocytic neoplasm characterized by an uncontrolled increase of B-cells.
A hematologic cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs.
A lymphoma that is characterized as any kind of lymphoma except Hodgkin's lymphoma.
A non-Hodgkin's lymphoma that is caused by a mutation of T cells.
A disease of cellular proliferation that results in abnormal growths in the body which lack the ability to metastasize.
An organ system cancer located_in the immune system that is characterized by uncontrolled cellular proliferation in organs of the immune system.
A benign neoplasm that is classified by the organ system from which it is arising from.
An organ system cancer located_in the muscular and skeletal organs and characterized by uncontrolled cellular proliferation of the musculoskeletal organs.
"A bone marrow cancer that affects plasma cells in which abnormal plasma cells multiply uncontrollably in the bone marrow and occasionally in other parts of the body." [url:http\://www.merck.com/mmhe/sec14/ch175/ch175c.html#sec14-ch175-ch175c-328]
URI: http://www.ebi.ac.uk/cellline#myeloma
A gastrointestinal system cancer that is located_in the intestine.
"A cancer by anatomical entity that is manifested in the pelvic region." [url:http\://www.wrongdiagnosis.com/p/pelvic_cancer/intro.htm]
"neoplasm of pelvis (disorder)" EXACT [SNOMEDCT_2005_07_31:126644004]
"pelvis neoplasm" EXACT [CSP2005:2005-4862]
URI: http://www.ebi.ac.uk/cellline#pelvic_cancer
"malignant neoplasm of pelvis NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:188370005]
"malignant neoplasm of pelvis, NOS" EXACT [SNOMEDCT_2005_07_31:93953009]
"malignant tumor of pelvis (disorder)" EXACT [SNOMEDCT_2005_07_31:363484005]
URI: http://www.ebi.ac.uk/cellline#malignant_neoplasm_of_pelvis
A prostate cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
"A hematologic cancer that is located_in lymphocytes which is composed_of white blood cell." [url:http\://www.cancer.gov/dictionary/?CdrID=46298]
"lymphoid neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414628006]
"lymphoid neoplasm" EXACT [CSP2005:2004-6589]
"lymphoid tumor" EXACT [NCI2004_11_17:C7065]
URI: http://www.ebi.ac.uk/cellline#lymphoid_cancer
Fibrocystic disease of breast (disorder)
A leukemia that has_material_basis_in lymphoblasts (immature white blood cells).
URI: http://www.ebi.ac.uk/cellline#lymphoblastic_leukemia
A lymphoblastic leukemia characterized by over production of B-cells and their accumulation in bone marrow and blood.
A gastrointestinal system cancer that is located_in the stomach.
Ca lesser curvature - stomach (disorder)
malignant neoplasm of lesser curve of stomach unspecified (disorder)
malignant tumor of body of stomach (disorder)
malignant tumor of greater curve of stomach (disorder)
malignant tumor of lesser curve of stomach (disorder)
A duodenum cancer that derives_from epithelial cells of glandular origin.
An urinary system cancer that results_in malignant growth located_in the urinary bladder.
A esophageal cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
"neoplasm of peripheral nerve (disorder)" EXACT [SNOMEDCT_2005_07_31:126980002]
"tumor of PNS" EXACT [NCI2004_11_17:C3321]
URI: http://www.ebi.ac.uk/cellline#peripheral_nervous_system_neoplasm
"A cancer of reproductive system that is manifested in the female genitals. This includes organs such as the ovaries, fallopian tubes, uterus, cervix, vagina and vulva." [url:http\://en.wikipedia.org/wiki/Template\:Female_genital_neoplasia, url:http\://www.wrongdiagnosis.com/g/genital_system_cancer/intro.htm]
A reproductive organ cancer that is manifested in the female genitals. This includes organs such as the ovaries, fallopian tubes, uterus, cervix, vagina and vulva.
URI: http://www.ebi.ac.uk/cellline#female_genital_cancer
malignant neoplasm of female genital organ
A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells.
"postpartum coagulation defect with delivery" EXACT []
"postpartum coagulation defect" EXACT []
URI: http://www.ebi.ac.uk/cellline#blood_coagulation_disorder
A leukemia that occurs when a hematopoietic stem cell undergoes malignant transformation into a primitive, undifferentiated cell with abnormal longevity. These lymphocytes (acute lymphocytic leukemia [ALL]) or myeloid cells (acute myelocytic leukemia [AML]) proliferate abnormally, replacing normal marrow tissue and hematopoietic cells and inducing anemia, thrombocytopenia, and granulocytopenia.
malignant neoplasm of genitourinary organ
URI: http://www.ebi.ac.uk/cellline#malignant_neoplasm_of_genitourinary_organ
A vulva cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
malignant neoplasm of central nervous system
"malignant neoplasm of central nervous system (disorder)" EXACT [SNOMEDCT_2005_07_31:372062007]
"malignant neoplasm of central nervous system NOS" EXACT [MTHICD9_2006:192.9]
"malignant neoplasm of central nervous system, NOS" EXACT [SNOMEDCT_2005_07_31:93744007]
"malignant neoplasm of central nervous system, unspecified (disorder)" EXACT [SNOMEDCT_2005_07_31:190135002]
"malignant tumor of CNS" EXACT [NCI2004_11_17:C4627]
URI: http://www.ebi.ac.uk/cellline#malignant_neoplasm_of_central_nervous_system
"BT - Brain tumour" EXACT [SNOMEDCT_2005_07_31:254935002]
"brain neoplasm" EXACT [CSP2005:2006-2736]
"neoplasm of brain (disorder)" EXACT [SNOMEDCT_2005_07_31:126952004]
"neoplasm of unspecified nature of brain (disorder)" EXACT [SNOMEDCT_2005_07_31:189537005]
"neoplasm of unspecified nature of brain" EXACT [ICD9CM_2006:239.6]
"tumor of the Brain" EXACT [NCI2004_11_17:C2907]
URI: http://www.ebi.ac.uk/cellline#brain_neoplasm
A respiratory system cancer that is located_in the lung.
A uterine cancer that is located_in tissues lining the uterus.
primary malignant neoplasm of endometrium
"A disease of biological process that is characterized by abnormally rapid cell division." [url:http\://en.wikipedia.org/w/index.php?title=Cell_proliferation]
A disease that is characterized by abnormally rapid cell division.
URI: http://www.ebi.ac.uk/cellline#disease_of_cellular_proliferation
A colon cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
URI: http://www.ebi.ac.uk/cellline#glandular_and_epithelial_neoplasm
"A carcinoma that derives_from the cells that line an organ." [url:http\://www.cancer.gov/dictionary/?CdrID=46422]
"Unspecified epithelial neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189559007]
"epithelial neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:118285006]
"epithelial neoplasm NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189546004]
"epithelial neoplasm, NOS" EXACT [NCI2004_11_17:C3709]
"epithelial tumor (qualifier value)" EXACT [SNOMEDCT_2005_07_31:134207000]
"skin Epithelium tumor" EXACT [NCI2004_11_17:C7342]
"tumor of surface epithelium (disorder)" EXACT [SNOMEDCT_2005_07_31:254649008]
URI: http://www.ebi.ac.uk/cellline#epithelial_carcinoma
URI: http://www.ebi.ac.uk/cellline#integumentary_system_disease
"A cancer of reproductive system that originates in the mammary gland." [url:http\://en.wikipedia.org/wiki/Mammary_tumor]
"breast tumor" EXACT [NCI2004_11_17:C2910]
"mammary tumor" EXACT [CSP2005:2016-0671]
"neoplasm of breast (disorder)" EXACT [SNOMEDCT_2005_07_31:126926005]
A thoracic cancer that originates in the mammary gland.
URI: http://www.ebi.ac.uk/cellline#mammary_cancer
"A neoplastic disease that is malignant and characterized by uncontrolled cellular proliferation, local cell invasion and metastasis." [stedman:rlc, url:http\://en.wikipedia.org/wiki/cancer, url:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=cancer]
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
URI: http://www.ebi.ac.uk/cellline#cancer
"An embryonal cancer that are masses of rapidly growing cells that originates in embryonic (fetal) tissue in the brain and spinal cord." [url:http\://www.cancer.gov/cancertopics/childCNSembryonal]
"embryonal tumor of the CNS" EXACT [NCI2004_11_17:C6990]
URI: http://www.ebi.ac.uk/cellline#embryonal_cancer_of_CNS
"primitive neuroectodermal tumour" EXACT [SNOMEDCT_2005_07_31:189925001]
URI: http://www.ebi.ac.uk/cellline#primitive_neuroectodermal_tumor
"Musculo-skeletal disorder NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:274149006]
"Musculo-skeletal disorder NOS" EXACT [SNOMEDCT_2005_07_31:156881000]
"Musculo-skeletal disorder NOS" EXACT [SNOMEDCT_2005_07_31:268142006]
"Musculoskeletal disease" EXACT [MTH:NOCODE]
"Musuloskeletal disease" EXACT [SNOMEDCT_2005_07_31:268047003]
"disorder of musculoskeletal system (disorder)" EXACT [SNOMEDCT_2005_07_31:928000]
"musculoskeletal disorder" EXACT [CSP2005:4000-0257]
URI: http://www.ebi.ac.uk/cellline#musculoskeletal_system_disease
"A cancer by anatomical entity that affects any gland in the endocrine system." [url:http\://www.wrongdiagnosis.com/e/endocrine_system_cancer/basics.htm]
"Endocrine tumor" EXACT [NCI2004_11_17:C3010]
"endocrine neoplasm" EXACT [CSP2005:2009-5861]
"neoplasm of endocrine gland (disorder)" EXACT [SNOMEDCT_2005_07_31:127015005]
"neoplasm of endocrine gland (disorder)" EXACT [SNOMEDCT_2005_07_31:387922007]
"neoplasm of endocrine system (disorder)" EXACT [SNOMEDCT_2005_07_31:387927001]
An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system.
URI: http://www.ebi.ac.uk/cellline#endocrine_gland_cancer
"Neuroectodermal tumour" EXACT [SNOMEDCT_2005_07_31:253096008]
"Neuroectodermal tumour" EXACT [SNOMEDCT_2005_07_31:73676002]
"primitive Neuroectodermal neoplasm" EXACT [NCI2004_11_17:C3716]
URI: http://www.ebi.ac.uk/cellline#neuroectodermal_tumor
A carcinoma that derives_from squamous epithelial cells.
squamous cell carcinoma (morphologic abnormality)
squamous cell carcinoma NOS (morphologic abnormality)
"neoplasm of soft tissue (disorder)" EXACT [SNOMEDCT_2005_07_31:387837005]
"neoplasm of soft tissues (disorder)" EXACT [SNOMEDCT_2005_07_31:126600002]
"tumor of the soft tissue" EXACT [NCI2004_11_17:C3377]
URI: http://www.ebi.ac.uk/cellline#soft_tissue_neoplasm
An endocrine gland cancer located_in the thryoid gland located in the neck below the thyroid cartilage.
A cell type cancer that has_material_basis_in mesothelial tissue.
An endocrine gland cancer located_in the pancreas.
URI: http://www.ebi.ac.uk/cellline#urinary_system_disease
URI: http://www.ebi.ac.uk/cellline#bone_tissue_neoplasm
A connective tissue cancer that is located_in bone and is characterized by uncontrolled cellular proliferation that destroys normal bone tissue.
A cell type cancer that has_material_basis_in abnormally proliferating cells derived_from melanocytes which are found in skin, the bowel and the eye.
"A cancer by anatomical entity that is manifested in the reproductive system." [url:http\://en.wikipedia.org/wiki/Reproductive_system#Examples_of_cancers]
"Reproductive tumor" EXACT [NCI2004_11_17:C3674]
"malignant reproductive system neoplasm" EXACT []
"reproductive system neoplasm" EXACT [CSP2005:2016-0492]
An organ system cancer that is manifested in the reproductive organs.
URI: http://www.ebi.ac.uk/cellline#cancer_of_reproductive_system
"glandular cell Epithelium neoplasm" EXACT [NCI2004_11_17:C7132]
URI: http://www.ebi.ac.uk/cellline#glandular_cell_epithelial_neoplasm
A rectum cancer that derives_from epithelial cells of glandular origin.
"Tumour of connective tissue" EXACT [SNOMEDCT_2005_07_31:254821003]
"connective tissue neoplasm" EXACT [CSP2005:2008-3809]
"neoplasm of connective tissues (disorder)" EXACT [SNOMEDCT_2005_07_31:126598008]
A musculoskeletal system cancer that is located_in connective tissue.
URI: http://www.ebi.ac.uk/cellline#connective_tissue_neoplasm
A vulva carcinoma and has_material_basis_in squamous cells and is located_in the epidermis of the vulvar tissue.
"intracranial central nervous system tumors" EXACT [NCI2004_11_17:C4953]
"intracranial tumor (disorder)" EXACT [SNOMEDCT_2005_07_31:254935002]
URI: http://www.ebi.ac.uk/cellline#intracranial_neoplasm
"HEMORRHAGIC DISORDER" EXACT [MTH:NOCODE]
"Haemorrhagic condition, unspecified" EXACT [SNOMEDCT_2005_07_31:191327000]
"Hemorrhagic condition NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:191331006]
"Hemorrhagic condition, unspecified (disorder)" EXACT [SNOMEDCT_2005_07_31:191437009]
"Hemorrhagic diathesis" EXACT [MTHICD9_2006:287.9]
"Hemorrhagic disease" EXACT [SNOMEDCT_2005_07_31:268884000]
"Unspecified hemorrhagic conditions" EXACT [ICD9CM_2006:287.9]
"hemorrhagic disorder" EXACT [CSP2005:0427-4811]
URI: http://www.ebi.ac.uk/cellline#hemorrhagic_disorder
malignant neoplasm of lymphatic and hemopoietic tissue
URI: http://www.ebi.ac.uk/cellline#malignant_neoplasm_of_lymphatic_and_hemopoietic_tissue
URI: http://www.ebi.ac.uk/cellline#female_reproductive_system_disease
A colon carcinoma that derives_from epithelial cells of glandular origin.
URI: http://www.ebi.ac.uk/cellline#disorder_of_plasma_protein_metabolism
A female reproductive organ cancer that is located_in the ovary.
"neural tumor of the skin" EXACT [NCI2004_11_17:C4479]
"skin tumor of neural origin (disorder)" EXACT [SNOMEDCT_2005_07_31:254758008]
URI: http://www.ebi.ac.uk/cellline#skin_tumor_of_neural_origin
"neoplasm of Dermis" EXACT [NCI2004_11_17:C4475]
"tumor of dermis (disorder)" EXACT [SNOMEDCT_2005_07_31:254735005]
URI: http://www.ebi.ac.uk/cellline#tumor_of_Dermis
A prostate carcinoma that derives_from epithelial cells of glandular origin.
"A cancer that affects the blood or bone marrow." [url:http\://www.cancer.gov/dictionary/?CdrID=45708]
"Hematologic malignancy (disorder)" EXACT [SNOMEDCT_2005_07_31:127221002]
"Hematologic malignancy" EXACT [SNOMEDCT_2005_07_31:269475001]
"Hematologic neoplasm (disorder)" EXACT [SNOMEDCT_2005_07_31:129154003]
"Hematological tumors" EXACT [NCI2004_11_17:C27134]
"blood cancer" EXACT [CSP2005:2004-0139]
"hematopoietic and lymphoid system tumor" EXACT []
"hematopoietic neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414388001]
"hematopoietic tumors" EXACT [NCI2004_11_17:C27134]
"malignant hematopoietic neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414644002]
An immune system cancer located_in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes.
URI: http://www.ebi.ac.uk/cellline#hematologic_cancer
hematopoietic neoplasm (morphologic abnormality)
malignant hematopoietic neoplasm (morphologic abnormality)
URI: http://www.ebi.ac.uk/cellline#neuroblastic_tumor
"kidney neoplasm" EXACT [CSP2005:2021-1116]
"neoplasm of kidney (disorder)" EXACT [SNOMEDCT_2005_07_31:126880001]
"renal tumors" EXACT [NCI2004_11_17:C3150]
A urinary system cancer that is located_in the kidney.
URI: http://www.ebi.ac.uk/cellline#kidney_neoplasm
malignant neoplasm of kidney except pelvis
A endometrial cancer that is located_in the tissue lining the uterus.
endometrioid carcinoma of female Reproductive system
A cervical cancer that is located_in the cervix uteri or located_in the cervical area and that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
"Immunoproliferative disease - morphology" EXACT [SNOMEDCT_2005_07_31:134363002]
"Immunoproliferative disease, no ICD-O subtype (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:86295000]
"Immunoproliferative disorder (disorder)" EXACT [SNOMEDCT_2005_07_31:127071007]
URI: http://www.ebi.ac.uk/cellline#immunoproliferative_disorder
"Paraproteinaemia" EXACT [SNOMEDCT_2005_07_31:35601003]
"Paraproteinemia (disorder)" EXACT [SNOMEDCT_2005_07_31:278501001]
"Paraproteinemia NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:190816000]
"Paraproteinemia" EXACT [NCI2004_11_17:C27468]
"Paraproteinemia" EXACT [SNOMEDCT_2005_07_31:123061006]
"paraproteinemia" EXACT [CSP2005:0449-2705]
URI: http://www.ebi.ac.uk/cellline#paraproteinemia
"adenocarcinoma NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189582009]
"adenocarcinoma" EXACT [CSP2005:2000-0386]
"adenocarcinoma" EXACT [NCI2004_11_17:C2852]
"adenocarcinoma, no subtype (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:35917007]
"adenocarcinomas" EXACT [SNOMEDCT_2005_07_31:189578007]
URI: http://www.ebi.ac.uk/cellline#adenocarcinoma
A breast carcinoma that derives_from the lining of milk ducts.
A cecum carcinoma that derives_from epithelial cells of glandular origin.
"A cancer that derives_from epithelial cells." [url:http\://en.wikipedia.org/wiki/Carcinoma]
"carcinoma NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189549006]
"carcinoma, no subtype (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:68453008]
"epithelial carcinoma" EXACT [NCI2004_11_17:C2916]
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
URI: http://www.ebi.ac.uk/cellline#carcinoma
An astrocytoma characterized by the presence of small areas of necrotizing tissue that is surrounded by anaplastic cells as well as the presence of hyperplastic blood vessels, and that has_material_basis_in abnormally proliferating cells derived_from multiple cell types including astrocytes and oligondroctyes.
A malignant glioma that is has_material_basis_in astocyte cells, a type of star-shaped glial cell, located_in the cerebrum.
astrocytoma, no ICD-O subtype (morphologic abnormality)
"glioma, malignant" EXACT [SNOMEDCT_2005_07_31:189909006]
"glioma, malignant, no ICD-O subtype" EXACT [SNOMEDCT_2005_07_31:74532006]
"malignant Neuroglial tumor" EXACT [NCI2004_11_17:C4822]
"malignant glioma (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:269505000]
"malignant glioma - category" EXACT [SNOMEDCT_2005_07_31:416500007]
A cell type cancer that has_material_basis_in glial cells and is located_in brain or located_in spine.
URI: http://www.ebi.ac.uk/cellline#malignant_glioma
malignant glioma (morphologic abnormality)
"A cancer that affects the nervous system." [url:http\://emedicine.medscape.com/oncology]
"neoplasm of nervous system (disorder)" EXACT [SNOMEDCT_2005_07_31:126950007]
"nervous system neoplasm" EXACT [CSP2005:2012-5157]
"tumor of the nervous system" EXACT [NCI2004_11_17:C3268]
An organ system cancer located_in the nervous sytem that affects the central or peripheral nervous system.
URI: http://www.ebi.ac.uk/cellline#cancer_of_the_nervous_system
"tumor of Neuroepithelium" EXACT [NCI2004_11_17:C3787]
URI: http://www.ebi.ac.uk/cellline#neuroepithelial_neoplasm
"germ cell and embryonal neoplasm" RELATED []
URI: http://www.ebi.ac.uk/cellline#germ_cell_and_embryonal_cancer
"renal and ureteral tumor" EXACT [NCI2004_11_17:C7514]
URI: http://www.ebi.ac.uk/cellline#kidney_and_Ureter_tumor
"gastrointestinal neoplasm" EXACT [CSP2005:2010-0179]
"neoplasm of gastrointestinal tract" EXACT [SNOMEDCT_2005_07_31:126768004]
"tumor of gastrointestinal tract (disorder)" EXACT [SNOMEDCT_2005_07_31:276806006]
An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
URI: http://www.ebi.ac.uk/cellline#gastrointestinal_neoplasm
A skin carcinoma that has_material_basis_in squamous cells.
"neoplasm of skin (disorder)" EXACT [SNOMEDCT_2005_07_31:126488004]
"neoplasm of skin by site" EXACT [SNOMEDCT_2005_07_31:363230005]
"skin neoplasm" EXACT [CSP2005:2020-0536]
"tumor of the skin" EXACT [NCI2004_11_17:C3372]
URI: http://www.ebi.ac.uk/cellline#skin_neoplasm
"neural tumor" EXACT [NCI2004_11_17:C35562]
URI: http://www.ebi.ac.uk/cellline#neural_neoplasm
A skeletal muscle cancer that arise from skeletal muscle progenitors.
"A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system." [url:http\://en.wikipedia.org/wiki/Central_nervous_system_disease]
URI: http://www.ebi.ac.uk/cellline#central_nervous_system_disease
A bone cancer that is located_in bone that has_material_basis_in cells of mesenchymal origin.
"Osteogenic tumor" EXACT [NCI2004_11_17:C6603]
URI: http://www.ebi.ac.uk/cellline#osteogenic_neoplasm
"mesenchymal tumor" EXACT [NCI2004_11_17:C7059]
URI: http://www.ebi.ac.uk/cellline#mesenchymal_cell_neoplasm
A connective tissue cancer that has_material_basis_in fibrous connective tissue and characterized by the presence of immature proliferating fibroblasts or undifferentiated anaplastic spindle cells in a storiform pattern.
A peripheral primitive neuroectodermal tumor that is located_in bone.
Ewing's sarcoma/bone peripheral primitive neuroectodermal tumor
A bone cancer that has_material_basis in neural crest cells derived_from undeveloped, undifferentiated neuroectoderm.
Ewing's sarcoma/peripheral primitive neuroectodermal tumor
Ewings sarcoma-primitive neuroectodermal tumor
localized Ewing's sarcoma/peripheral primitive neuroectodermal tumor
localized peripheral primitive neuroectodermal tumor
peripheral primitive neuroectodermal tumor
A connective tissue cancer that has_material_basis_in cells derived from transformed cells that produce cartilage.
A lipomatous cancer that arises in fat cells in deep soft tissue retroperitoneum.
"A disease that involves any biological process (GO:0008150) specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms." [DO:wk\,ls]
URI: http://www.ebi.ac.uk/cellline#disease_of_biological_process
A breast carcinoma that originates in the milk ducts and/or lobules (glandular tissue) of the breast.
A breast cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
A gastrointestinal system cancer that is located_in the liver.
malignant neoplasm of liver unspecified (disorder)
malignant neoplasm of liver, not specified as primary or secondary
non-resectable primary hepatic malignant neoplasm
primary malignant neoplasm of liver (disorder)
primary malignant neoplasm of liver NOS (disorder)
resectable malignant neoplasm of the liver
Choriocarcinoma, no ICD-O subtype (morphologic abnormality)
A cystadenocarcinoma that derives_from epithelial cells originating in glandular tissue, with a capsulated structure and mucus-producing cells.
mucinous cystadenocarcinoma (morphologic abnormality)
mucinous cystadenocarcinoma NOS (morphologic abnormality)
"CNS neoplasm" EXACT [CSP2005:2012-5421]
"central nervous system tumors" EXACT [NCI2004_11_17:C9293]
"neoplasm of central nervous system (disorder)" EXACT [SNOMEDCT_2005_07_31:126951006]
URI: http://www.ebi.ac.uk/cellline#central_nervous_system_neoplasm
A female reproductive organ cancer that is located_in the uterus.
URI: http://www.ebi.ac.uk/cellline#skin_disease
A cervix carcinoma that derives_from epithelial cells of glandular origin.
An ovarian carcinoma that derives_from epithelial cells of glandular origin.
A stomach carcinoma that derives_from epithelial cells of glandular origin.
"Myeloma - solitary" EXACT [SNOMEDCT_2005_07_31:189507001]
"Myeloma, solitary" EXACT [SNOMEDCT_2005_07_31:154644004]
"Myeloma, solitary" EXACT [SNOMEDCT_2005_07_31:269652000]
"Plasma cell tumor (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:274907000]
"Plasma cell tumor NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:190019006]
"Plasma cell tumors (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:190016004]
"Solitary myeloma (clinical)" EXACT [SNOMEDCT_2005_07_31:109987008]
"Solitary myeloma" EXACT [MTHICD9_2006:238.6]
"Solitary plasmacytoma of bone (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:10639003]
"Solitary plasmacytoma" EXACT [NCI2004_11_17:C6932]
"plasma cell neoplasm" EXACT [CSP2005:2004-8110]
"plasmacytoma - disorder" EXACT [SNOMEDCT_2005_07_31:302852008]
"plasmacytoma - disorder" EXACT [SNOMEDCT_2005_07_31:415112005]
"plasmacytoma NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:308122007]
"plasmacytoma NOS" EXACT [SNOMEDCT_2005_07_31:188720009]
"plasmacytoma NOS" EXACT [SNOMEDCT_2005_07_31:190017008]
"plasmacytoma" EXACT [NCI2004_11_17:C9349]
URI: http://www.ebi.ac.uk/cellline#plasmacytoma
A carcinoma of bladder that is manifested in squamous cells of the bladder.
Epidermoid carcinoma of the urinary bladder
squamous cell carcinoma of bladder (disorder)
A cervix carcinoma that has_material_basis_in squamous cells of the cervix.
squamous cell carcinoma of cervix (disorder)
squamous cell carcinoma of the Cervix Uteri
An esophageal carcinoma that derives_from epithelial squamous cells located_in the esophagus.
squamous cell carcinoma of esophagus (disorder)
"A cancer of reproductive system that is manifested in the male genital system. This includes organs such as the penis and scrotum." [url:http\://en.wikipedia.org/wiki/Template\:Male_genital_neoplasia, url:http\://www.wrongdiagnosis.com/g/genital_system_cancer/intro.htm]
"male reproductive system neoplasm" EXACT [CSP2005:2016-2462]
"neoplasm of male genital organ" EXACT [SNOMEDCT_2005_07_31:126895004]
"tumor of male Reproductive system" EXACT [NCI2004_11_17:C3054]
A reproductive organ cancer that is manifested in the male genital system. This includes organs such as the penis and scrotum.
URI: http://www.ebi.ac.uk/cellline#male_genital_cancer
malignant neoplasm of male genital organ or tract
malignant neoplasm of male genital organ, NOS
malignant neoplasm of male genital organ, site unspecified
malignant neoplasm of male genital organ, unspecified (disorder)
malignant neoplasm of male genital organs (disorder)
malignant tumor of male Reproductive system
malignant tumor of male genital organ (disorder)
A lung cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells and is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis.
A non-small cell lung carcinoma that has_material_basis_in the squamous cell.
A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma.
A non-small cell lung carcinoma that derives_from epithelial cells of glandular origin.
An endocrine gland cancer located_in the adrenal glands which are located above the kidneys.
An adrenalcortical carcinoma that originating in the cortex of the adrenal gland and derives_from epithelial cells of glandular origin.
A thyroid carcinoma that has_material_basis_in follicular cells.
Follicular adenocarcinoma (morphologic abnormality)
Follicular adenocarcinoma, well differentiated (morphologic abnormality)
Follicular carcinoma of the Thyroid gland
A thyroid cancer that has_material_basis_in epithelial cells.
A thyroid carcinoma that is characterized by the small mushroom shape of the tumor which has a stem attached to the epithelial layer.
Papillary carcinoma of the Thyroid gland
An organ system cancer that is located_in the kidneys, ureteres, bladder or urethra.
URI: http://www.ebi.ac.uk/cellline#cancer_of_urinary_tract
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A bladder carcinoma that has_material_basis_in transitional cells located_in the lining of the bladder.
transitional cell carcinoma of bladder (disorder)
A urinary bladder cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
A pancreatic carcinoma that derives_from epithelial cells of glandular origin.
Ewings sarcoma-primitive neuroectodermal tumor (PNET)
"peripheral Neuroectodermal neoplasm" EXACT [NCI2004_11_17:C9341]
"peripheral neuroectodermal tumor (disorder)" EXACT [SNOMEDCT_2005_07_31:253096008]
"peripheral neuroectodermal tumor (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:73676002]
"peripheral neuroepithelioma (disorder)" EXACT [SNOMEDCT_2005_07_31:254764001]
URI: http://www.ebi.ac.uk/cellline#Ewings_sarcoma-primitive_neuroectodermal_tumor_(PNET)
"malignant neoplasm of skin (disorder)" EXACT [SNOMEDCT_2005_07_31:372130007]
"malignant neoplasm of skin NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:188143008]
"malignant neoplasm of skin" EXACT [MTH:NOCODE]
"malignant neoplasm of skin, unspecified (disorder)" EXACT [SNOMEDCT_2005_07_31:190107001]
"melanoma and Non-melanoma skin cancer" EXACT [NCI2004_11_17:C2920]
URI: http://www.ebi.ac.uk/cellline#cancer_of_skin
URI: http://www.ebi.ac.uk/cellline#tissue_disease
A renal carcinoma that has_material_basis_in the lining of the proximal convoluted renal tubule of the kidney.
A kidney cancer that derives_from the lining of the proximal convoluted tubule (the very small tubes in the kidney that filter the blood and remove waste products).
A renal cell carcinoma that has_material_basis_in cells that appear very pale or clear when examined under microscope.
Clear cell carcinoma of kidney (disorder)
Clear-cell metastatic renal cell carcinoma
MSH:C538445 added from NeuroDevNet [WAK].
conventional (Clear cell) renal cell carcinoma
A thyroid cancer that is located_in the supporting cells of the thyroid.
A gastrointestinal system cancer that results_in malignant growth located_in the gallbladder or located_in the bile duct.
"A cancer that affects an anatomical entity." [DO:lh]
"malignant neoplasm of aortic body and other paraganglia (disorder)" EXACT [SNOMEDCT_2005_07_31:188343003]
"malignant neoplasm of aortic body and other paraganglia" EXACT []
URI: http://www.ebi.ac.uk/cellline#cancer_by_anatomical_entity
URI: http://www.ebi.ac.uk/cellline#malignant_neoplasm_of_nervous_system
URI: http://www.ebi.ac.uk/cellline#male_reproductive_system_disease
"vascular hemostatic disease (disorder)" EXACT [SNOMEDCT_2005_07_31:21112004]
URI: http://www.ebi.ac.uk/cellline#vascular_hemostatic_disorder
A bile duct cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
A pancreas cancer that derives_from epithelial cells located_in the pancreas.
An esophageal carcinoma that derives_from epithelial cells of glandular origin.
A gallbladder cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
"A bone marrow disease and hematopoietic cancer that derives_from the blood-forming stem cells of the bone marrow." [url:http\://nci.nih.gov/dictionary/?CdrID=430857]
"Myeloid neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414792005]
"Myeloproliferative disease NOS" EXACT [MTHICD9_2006:238.7]
"Myeloproliferative disease, NOS" EXACT [SNOMEDCT_2005_07_31:20921005]
"Myeloproliferative disease, no ICD-O subtype (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:128925001]
"Myeloproliferative disorder (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414794006]
"Myeloproliferative disorder" EXACT [SNOMEDCT_2005_07_31:188772004]
"Myeloproliferative tumors" EXACT [NCI2004_11_17:C9290]
"bone Marrow tumor" EXACT [NCI2004_11_17:C35370]
"bone marrow neoplasm" EXACT [CSP2005:2004-0492]
"malignant bone Marrow tumor" EXACT [NCI2004_11_17:C35501]
"malignant neoplasm of bone marrow" EXACT []
"myeloproliferative neoplasm" EXACT [CSP2005:2004-0893]
"neoplasm of bone marrow (disorder)" EXACT [SNOMEDCT_2005_07_31:414824005]
"primary malignant neoplasm of bone marrow (disorder)" EXACT [SNOMEDCT_2005_07_31:93720005]
URI: http://www.ebi.ac.uk/cellline#bone_marrow_cancer
"bone Marrow disorder" EXACT [NCI2004_11_17:C34433]
"bone marrow disorder (disorder)" EXACT [SNOMEDCT_2005_07_31:127035006]
"bone marrow disorder" EXACT [CSP2005:0427-3773]
URI: http://www.ebi.ac.uk/cellline#bone_marrow_disease
A gastrointestinal system cancer that is located_in the esophagus.
malignant neoplasm of distal third of esophagus
malignant neoplasm of lower third of oesophagus
malignant neoplasm of middle third of oesophagus
malignant neoplasm of proximal third of esophagus
malignant neoplasm of upper third esophagus
malignant tumor of Distal Third of esophagus
malignant tumor of Proximal Third of esophagus
malignant tumor of the middle Third of the esophagus
"A cancer by anatomical entity that develops in the different types of cells within the lungs, as well as less common cancers of the esophagus, the trachea, or the chest wall." [url:http\://www.advocatehealth.com/cmc/body.cfm?id=203]
"Thoracic tumor" EXACT [NCI2004_11_17:C3406]
"thorax neoplasm" EXACT [CSP2005:2005-5041]
"tumor of thorax (disorder)" EXACT [SNOMEDCT_2005_07_31:255058005]
An organ system cancer located_in the thoracic cavity that develops in the different types of cells within the lungs, as well as less common cancers of the esophagus, the trachea, or the chest wall.
URI: http://www.ebi.ac.uk/cellline#thoracic_cancer
An uterine corpus cancer that is located_in the muscles of the uterus or located_in other tissues that support the uterus.
Clear cell carcinoma of the Cervix Uteri
A lung carcinoma that has_material_basis_in primitive-appearing cells that are smaller than normal cells.
small cell neuroendocrine carcinoma of lung
Oat cell carcinoma (morphologic abnormality)
poorly differentiated Endocrine neoplasm
A synovium cancer which develops in the synovial membrane of the joints.
A stomach cancer that is located_in the stomach.
A testicular cancer that has_material_basis_in germ cells.
URI: http://www.ebi.ac.uk/cellline#kidney_disease
A lung carcinoma that is located_in large undifferentiated cells.
T-cell acute lymphoblastic leukemia (disorder)
An intestinal cancer that effects the long, tube-like organ that is connected to the small intestine at one end and the anus at the other.
An adrenal gland cancer that derives_from immature neuroblastic cells.
renal pelvis transitional cell carcinoma
Urothelial cell carcinoma of renal Pelvis
"Duncan's syndrome" EXACT [SNOMEDCT_2005_07_31:77121009]
"Lymphoproliferative disease NOS" EXACT [MTHICD9_2006:238.7]
"Lymphoproliferative disease, no ICD-O subtype (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:84631004]
"Lymphoproliferative disorder (disorder)" EXACT [SNOMEDCT_2005_07_31:277466009]
"Lymphoproliferative disorder (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:414629003]
"Lymphoproliferative disorder" EXACT [NCI2004_11_17:C9308]
URI: http://www.ebi.ac.uk/cellline#lymphoproliferative_disorder
"blood protein disorder" EXACT [CSP2005:0449-0541]
URI: http://www.ebi.ac.uk/cellline#blood_protein_disorder
"Hereditary disease (disorder)" EXACT [SNOMEDCT_2005_07_31:32895009]
"Hereditary disease" EXACT [SNOMEDCT_2005_07_31:264530000]
"Molecular disease" EXACT [NCI2004_11_17:C3101]
"hereditary disorder" EXACT [CSP2005:1254-7727]
URI: http://www.ebi.ac.uk/cellline#hereditary_disease
"Connective tissue dis." EXACT [SNOMEDCT_2005_07_31:268048008]
"Connective tissue disease" EXACT [MTH:NOCODE]
"Connective tissue disease" EXACT [SNOMEDCT_2005_07_31:201432001]
"Connective tissue disorder" EXACT [NCI2004_11_17:C26729]
"Other musculoskelet/connectiv" EXACT [SNOMEDCT_2005_07_31:268126004]
"connective tissue disorder" EXACT [CSP2005:0729-7208]
"disorder of connective tissue (disorder)" EXACT [SNOMEDCT_2005_07_31:105969002]
URI: http://www.ebi.ac.uk/cellline#connective_tissue_disease
"Plasma cell disorder (disorder)" EXACT [SNOMEDCT_2005_07_31:277576009]
"Plasma cell dyscrasia (disorder)" EXACT [SNOMEDCT_2005_07_31:71390001]
"Plasma cell neoplasm (disorder)" EXACT [SNOMEDCT_2005_07_31:415111003]
"Plasma cell neoplasm (morphology)" EXACT [SNOMEDCT_2005_07_31:127580003]
"Plasma cell tumour" EXACT [SNOMEDCT_2005_07_31:274907000]
"Plasmacytic tumor" EXACT [NCI2004_11_17:C4665]
URI: http://www.ebi.ac.uk/cellline#plasma_cell_neoplasm
"A simple genetic disease that comprises a large class of genetic diseases involving disorders of metabolism." [url:http\://en.wikipedia.org/wiki/Inborn_errors_of_metabolism]
"Inborn Errors of Metabolism" EXACT [NCI2004_11_17:C34816]
"Inborn error of metabolism (disorder)" EXACT [SNOMEDCT_2005_07_31:86095007]
"Metabolic hereditary disorder" EXACT [SNOMEDCT_2005_07_31:363205007]
"inborn metabolism disorder" EXACT [CSP2005:1849-0057]
URI: http://www.ebi.ac.uk/cellline#inborn_errors_of_metabolism
A liver carcinoma that has_material_basis_in undifferentiated hepatocytes.
"A germ cell cancer that is associated with an embryo." [url:http\://www.cancer.gov/dictionary/?CdrID=44250]
"embryo neoplasm" EXACT [CSP2005:2000-3997]
"embryonal neoplasm" EXACT [NCI2004_11_17:C3264]
URI: http://www.ebi.ac.uk/cellline#embryonal_cancer
"A disease that manifests in a defined anatomical structure." [DO:wk\,ls, URL:http\://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic]
"acellular anatomical structure disease" EXACT []
"disease of anatomical structure" EXACT []
"disease of material anatomical entity" EXACT []
"disease of physical anatomical entity" EXACT []
"disease of set of heterogenous clusters" EXACT []
URI: http://www.ebi.ac.uk/cellline#disease_of_anatomical_entity
URI: http://www.ebi.ac.uk/cellline#mature_B-cell_lymphocytic_neoplasm
"B-cell neoplasm (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:413616009]
A non-Hodgkin lymphoma that has_material_basis_in B cells.
URI: http://www.ebi.ac.uk/cellline#B-cell_lymphocytic_neoplasm
"neoplasm of urinary system (disorder)" EXACT [SNOMEDCT_2005_07_31:126879004]
"tumor of the urinary system" EXACT [NCI2004_11_17:C3431]
"tumor of urinary tract (disorder)" EXACT [SNOMEDCT_2005_07_31:254913005]
"urinary tract neoplasm" EXACT [CSP2005:2021-0179]
URI: http://www.ebi.ac.uk/cellline#Urologic_neoplasm
"Blood disease (disorder)" EXACT [SNOMEDCT_2005_07_31:267552000]
"Blood disease NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:267573000]
"Blood disease NOS" EXACT [SNOMEDCT_2005_07_31:154842002]
"Blood disease" EXACT [SNOMEDCT_2005_07_31:154785002]
"Blood dyscrasia NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:191402006]
"Blood dyscrasia NOS" EXACT [MTHICD9_2006:289.9]
"Blood/blood forming organ NOS" EXACT [SNOMEDCT_2005_07_31:191446003]
"DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS" EXACT [ICD9CM_2006:280-289.99]
"Hematological disease" EXACT [MTH:NOCODE]
"Unspecified disease of blood and blood-forming organs" EXACT [ICD9CM_2006:289.9]
"blood disorder" EXACT [CSP2005:0427-3600]
"disease of blood and/or blood-forming organ (navigational concept)" EXACT [SNOMEDCT_2005_07_31:191124002]
"disease of hematopoietic system" EXACT []
"disorder of hematopoietic system (navigational concept)" EXACT [SNOMEDCT_2005_07_31:34093004]
URI: http://www.ebi.ac.uk/cellline#hematopoietic_system_disease
"Lymphangiopathy, NOS" EXACT [SNOMEDCT_2005_07_31:3305006]
"Lymphatic disease" EXACT [SNOMEDCT_2005_07_31:155452000]
"Lymphatic disease" EXACT [SNOMEDCT_2005_07_31:266326002]
"Lymphatic disorder" EXACT [NCI2004_11_17:C3206]
"disorder of lymph node and lymphatics (disorder)" EXACT [SNOMEDCT_2005_07_31:234087005]
"disorder of lymphatic system" EXACT [SNOMEDCT_2005_07_31:362971004]
"disorder of lymphoid system" EXACT [SNOMEDCT_2005_07_31:111590001]
"lymphatic disorder" EXACT [CSP2005:0427-7757]
URI: http://www.ebi.ac.uk/cellline#lymphatic_system_disease
An autonomic nervous system neoplasm that derives_from immature nerve cells.
"GIT disorder NOS" EXACT [SNOMEDCT_2005_07_31:155806004]
"GIT disorder NOS" EXACT [SNOMEDCT_2005_07_31:266534007]
"Gastroenteropathy" EXACT [SNOMEDCT_2005_07_31:25374005]
"Non-neoplastic gastrointestinal disorder" EXACT [NCI2004_11_17:C27550]
"disease of digestive tract (disorder)" EXACT [SNOMEDCT_2005_07_31:84410009]
"disorder of gastrointestinal tract (disorder)" EXACT [SNOMEDCT_2005_07_31:119292006]
"gastrointestinal disease and Manifestations" EXACT [NCI2004_11_17:C2990]
"gastrointestinal disorder" EXACT [CSP2005:1248-3545]
"gastrointestinal tract disorder NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:286978000]
"gastrointestinal tract disorder NOS" EXACT [SNOMEDCT_2005_07_31:155799006]
URI: http://www.ebi.ac.uk/cellline#gastrointestinal_system_disease
Signet Ring cell adenocarcinoma of the stomach
"A cancer by anatomical entitiy that is manifested in any part of the digestive system." [url:http\://www.wrongdiagnosis.com/d/digestive_system_cancer/intro.htm]
"Digestive system neoplasm" EXACT [MTH:NOCODE]
"digestive neoplasm" EXACT [CSP2005:4000-0164]
"neoplasm of digestive system (disorder)" EXACT [SNOMEDCT_2005_07_31:128348002]
"neoplasm of digestive tract" EXACT [SNOMEDCT_2005_07_31:128415001]
"neoplasm of unspecified nature of digestive system (disorder)" EXACT [SNOMEDCT_2005_07_31:189527000]
"neoplasm of unspecified nature of digestive system" EXACT [ICD9CM_2006:239.0]
URI: http://www.ebi.ac.uk/cellline#digestive_system_cancer
A myeloid leukemia that is characterized by over production of white blood cells.
A lymphoma that is marked by the presence of a type of cell called the Reed-Sternberg cell.
stage I Subdiaphragmatic Hodgkin Lymphoma
stage II Subdiaphragmatic Hodgkin Lymphoma
A mature B-cell neoplasm of B-cells found in the germinal center.
small Non-Cleaved cell Lymphoma, Burkitt's type
malignant neoplasm of gum NOS (disorder)
malignant neoplasm of other sites of gum
malignant neoplasm of other sites of gum (disorder)
A gastrointestinal system cancer that is located_in the oral cavity.
malignant neoplasm of anterior portion of floor of mouth
malignant neoplasm of lateral floor of mouth
malignant neoplasm of lateral portion of floor of mouth
malignant tumor of anterior floor of mouth (disorder)
malignant tumor of lateral floor of mouth (disorder)
malignant tumor of the Floor of the Mouth
URI: http://www.ebi.ac.uk/cellline#nervous_system_disease
Tongue neoplasm malignant stage Unspecified
malignant neoplasm of anterior 2/3 of tongue unspecified (disorder)
malignant neoplasm of anterior two-thirds of tongue, part unspecified
malignant neoplasm of dorsal surface of tongue
malignant neoplasm of dorsum of tongue NOS (disorder)
malignant neoplasm of fixed part of tongue NOS
malignant neoplasm of fixed part of tongue NOS (disorder)
malignant neoplasm of junctional zone of tongue
malignant neoplasm of mobile part of tongue NOS
malignant neoplasm of other sites of tongue
malignant neoplasm of other sites of tongue (disorder)
malignant neoplasm of tip and lateral border of tongue
malignant neoplasm of tip and/or lateral border of tongue
malignant neoplasm of tongue NOS (disorder)
malignant neoplasm of tongue, tip and lateral border (disorder)
malignant neoplasm of ventral surface of tongue
malignant neoplasm of ventral tongue surface NOS (disorder)
malignant tumor of anterior two-thirds of tongue (disorder)
malignant tumor of base of tongue (disorder)
malignant tumor of lingual tonsil (disorder)
malignant tumor of mobile part of tongue
A leukemia that is located_in myeloid tissue.
Myeloid leukemia in remission (disorder)
Myeloid leukemia, NOS, without mention of remission
Myeloid leukemia, no ICD-O subtype (morphologic abnormality)
Myeloid leukemias (morphologic abnormality)
Other myeloid leukemia (morphologic abnormality)
Other myeloid leukemia NOS (morphologic abnormality)
Other myeloid leukemia without mention of remission
Unspecified myeloid leukemia in remission
Unspecified myeloid leukemia without mention of remission
"Neuropathy (disorder)" EXACT [SNOMEDCT_2005_07_31:264554005]
"Neuropathy (disorder)" EXACT [SNOMEDCT_2005_07_31:386033004]
"Neuropathy, NOS" EXACT [SNOMEDCT_2005_07_31:42658009]
URI: http://www.ebi.ac.uk/cellline#neuropathy
"Connective and soft tissue disease" EXACT [NCI2004_11_17:C27574]
"Connective and soft tissue disorder" EXACT [MTH:NOCODE]
"disease of deep fascial system" EXACT []
URI: http://www.ebi.ac.uk/cellline#soft_tissue_disease
acute Monoblastic Leukemia and acute Monocytic Leukemia
acute monocytic leukemia without mention of remission
acute monocytic leukemia, FAB M5 (disorder)
acute monocytic leukemia, morphology (morphologic abnormality)
A myeloid leukemia that is characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells.
malignant neoplasm of submaxillary gland
malignant tumor of submandibular gland (disorder)
malignant tumor of the Submandibular gland
A large intestine cancer that is located_in the colon and/or located_in the rectum.
URI: http://www.ebi.ac.uk/cellline#brain_disease
multiple myeloma and immunoproliferative neoplasm
URI: http://www.ebi.ac.uk/cellline#multiple_myeloma_and_immunoproliferative_neoplasm
A lymphoblastic leukemia that is characterized by over production of lymphoblasts.
objective specification
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
OBI Plan and Planned Process/Roles Branch
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
goal specification
action specification
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
data item
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.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
Data items include counts of things, analyte concentrations, and statistical summaries.
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
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.
data
information content entity
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).
A generically dependent continuant that is about some thing.
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
directive information entity
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
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.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
"house mouse" EXACT genbank_common_name []
"mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling []
URI: http://www.ebi.ac.uk/cellline#Mus_musculus
"Rodents and rabbits" EXACT genbank_common_name []
URI: http://www.ebi.ac.uk/cellline#Glires
URI: http://www.ebi.ac.uk/cellline#Hominoidea
URI: http://www.ebi.ac.uk/cellline#Mammalia
URI: http://www.ebi.ac.uk/cellline#Primates
URI: http://www.ebi.ac.uk/cellline#Hominidae
URI: http://www.ebi.ac.uk/cellline#Homo_sapiens
URI: http://www.ebi.ac.uk/cellline#Rodentia
planned process
'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.)
6/11/9: Edited at workshop. Used to include: is initiated by an agent
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
culture medium
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
OBI
Person: Jennifer Fostel, Jie Zheng
material processing
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
OBI branch derived
material transformation
organization
An organization is a continuant entity which can play 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.
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0002010
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.
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
material transformation objective
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
The objective to obtain multiple aliquots of an enzyme preparation.
separation into different composition objective
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
The objective to obtain cells contained in a sample of blood.
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
An objective specification maintains some or all of the qualities of a material over time.
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.
A cultured cell population that is derived through one or more passages in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
cell freezing medium
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
culture media or serum + 10% DMSO is often used as cell freezing media.
organism
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')
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.
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. E.g Drosophila melanogaster
EFO_URI: http://www.ebi.ac.uk/efo/EFO_0000634
WEB: http://en.wikipedia.org/wiki/Organism
animal
fungus
plant
virus
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
material component separation
Bjoern Peters
IEDB
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
maintaining cell culture
PlanAndPlannedProcess Branch
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
cell culture splitting
An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]
The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors.
somatic nervous system, somatic division
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
An organ that is capable of transducing sensory stimulus to the nervous system.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
Major subdivision of an organism that protrudes from the body[DOS, CARO].
Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
this is currently a subtype of organism subdivision - which would exclude feathers
The fluid surrounding the ovum and granulosa cells in the ovarian follicle..
The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
simple eye that consists of a lens of one refractive index
A tubular structure that contains, conveys body fluid, such as blood or lymph.
Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.
The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]
in humans, consists of adventitial, muscular and mucoa layers
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA].
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the endoderm and the mesoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
A spatiotemporal region encompassing some part of the life cycle of an organism.
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
Paired fin located in the abdominal position of the body.
Paired fin located in the abdominal position of the body.[TAO]
Paired fin located in the abdominal position of the body.[VSAO]
In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Anatomical conduit that connects two adjacent body spaces, surrounded by two or more subdivisions of two or more organs. Examples: right atrioventricular orifice, orifice of artery, hilum of kidney, porta hepatis[FMA,modified].
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
The breasts of a female primate’s body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
The upper ventral region of an animal's torso.
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
Gray matter structure located on the midline of the forebrain consisting of the septum pellucidum (in some species) and the septal nuclei (Heimer, 1996).
Subdivision of the telencephalon on the midline between the lateral ventricles which contains the septum pellucidum and the septal nuclei[FMA][FMA:61842].
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
A gonad of a male animal. A gonad produces and releases sperm.
The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical group that has its parts adjacent to one another.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
see also conceptus extraembryonic component in EHDAA2.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
Compound organ that contains one or more macroscopic anatomical spaces.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
requires review for applicability to invertebrate structures, e.g. synganglion
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman’s membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
In MA, is_a cavity lining. In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See http://purl.obolibrary.org/obo/uberon/tracker/86
The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
the serous membrane surrounding the lungs and lining the walls of the pleural cavity
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
female organism reproductive system gonad
female organism reproductive system gonada
gonad of female organism reproductive system
gonad of reproductive system of female organism
gonada of female organism reproductive system
gonada of reproductive system of female organism
reproductive system of female organism gonad
reproductive system of female organism gonada
the gonad of a female organism which contains germ cells
An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.
The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]
Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688
A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]
The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]
The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]
The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]
external genital organs of the female mammal[WP].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
Consider generalizing to deuterostome pharynx
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
the terminal portion of the intestinal tube, terminating with the anus
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice
A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
Kardong: in some herbivorous lizards, a cecum is present between small and large intestines
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
Last portion of the large intestine before it becomes the rectum.
TODO - abstract this such that it legitimately covers all vertebrates
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
it extracts water and salt from solid wastes before they are eliminated from the body[WP]
An ureter that is part of a right side of organism [Automatically generated definition].
This class was created automatically from a combination of ontologies
A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]
distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans
The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
Cavity for the articulation of the proximal bone of the hind limb.[AAO]
During the transformation from the osteolepiform fins to tetrapod limbs, the appendages and girdles underwent a number of radical changes. The pelvic girdle became a weight-bearing structure by evolution of an ischium, a full mesio-ventral contact between the two sides of the girdle, an ilium, and a contact between the vertebral column and the girdle through a sacral rib. Fore- and hindlimbs shifted laterally by reorientation of the glenoid and the acetabulum.[well established][VHOG]
In reptiles and in birds, the acetabula are deep sockets.
The acetabulum is a concave surface of the pelvis. The head of the femur meets with the pelvis at the acetabulum, forming the hip joint. There are three bones of the os coxae (hip bone) that come together to form the acetabulum. Contributing a little more than two-fifths of the structure is the ischium, which provides lower and side boundaries to the acetabulum. The ilium forms the upper boundary, providing a little less than two-fifths of the structure of the acetabulum. The rest is formed by the pubis, near the midline. It is bounded by a prominent uneven rim, which is thick and strong above, and serves for the attachment of the acetabular labrum, which reduces its opening, and deepens the surface for formation of the hip joint. At the lower part of the acetabulum is the acetabular notch, which is continuous with a circular depression, the acetabular fossa, at the bottom of the cavity of the acetabulum. The rest of the acetabulum is formed by a curved, crescent-moon shaped surface, the lunate surface, where the joint is made with the head of the femur. Its counterpart in the pectoral girdle is the glenoid fossa.[WP,unvetted].
whilst WP defines this as a surface, MA treats it as a bone. There are other FMA classes that may be better suited to representing the surface.
Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead
The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG]
The mucous membrane lining the uterus. [TFD][VHOG]
in FMA this is subdivided into basal and outer
the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
TODO - check with MA - vein vs venous blood vessel
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
The supraorbital vein begins on the forehead where it communicates with the frontal branch of the superficial temporal vein. It runs downward superficial to the Frontalis muscle, and joins the frontal vein at the medial angle of the orbit to form the angular vein. Previous to its junction with the frontal vein, it sends through the supraorbital notch into the orbit a branch which communicates with the ophthalmic vein; as this vessel passes through the notch, it receives the frontal diploic vein through a foramen at the bottom of the notch. The areas drained by this vessel are the forehead, eyebrow and upper eyelid. [WP,unvetted].
A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG]
A muscular organ in the floor of the mouth.
Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods
Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]
Muscular organ in the floor of the mouth.[FEED]
The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions
The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586].
in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence.
(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]
An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED]
Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO]
Heterogeneous cluster that connects the pharynx to the tracheobronchial tree[FMA].
Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP].
FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton.
The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001].
A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts
A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males.
Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG]
Originally this was classified as a female reproductive structure, as it was in the MP in 2011
The BTO class represents the combination of nipple plus lobe
The FMA class represents an individule lobe. The nipple is not a part
The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts
The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]
The male Dayak fruit bat has lactating mammary glands
The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges.
A vessel through which blood circulates in the body.
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
annelids have blood vessels, but this class is not applicable to annelids.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN10:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: http://dx.doi.org/10.1002/jmor.11011
Marsupials possess only a rudimentary placenta, with reduced nutrient and oxygen exchanging capabilities.
Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]
organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]
In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes
In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)
In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs
An organ involved in red blood cell filtration and immune response.[AAO]
In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron
It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells
Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)
With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]
the organ that functions to filter blood and to store red corpuscles and platelets
All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
A paired organ of the urinary tract which has the production of urine as its primary function.
One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
TODO - FMA treats the gland as part of the prostate - see also FMA:74119.
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]
Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]
Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole
suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.
In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]
TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
the soft tissue that fills the cavities of bones
either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx
the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region
round window of petrous part of temporal bone
the opening on the medial wall of the middle ear leading into the cochlea, closed in life by the secondary tympanic membrane; serves to regulate fluid pressure in the inner ear
an organ that functions as a secretory or excretory organ
Fin that is one of a pair located ventrally on the organism.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
GO uses genitalia for the singular organ
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
Organ that is part of the hematopoietic system.
consider splitting out lymph organ, compare with lymph node
the FMA class 'lymphoid organ' is a general anatomical term
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
A portions of the gut that is derived from endoderm.
The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron
in MA this groups pericardium, pleura and periotoneal cavity lining
An appendage that is part of a appendage girdle complex.
this class is the union of the classes limb, pectoral fin and pelvic fin.
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
A portion of the gut that is derived from ectoderm.
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
A part of a wall of an organ that forms a layer.
An organ that is part of a immune system [Automatically generated definition].
An anatomical structure that is part of the reproductive system.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
A tube that is part of a excretory system.
This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]
keep this grouping class so long as it is required for GO
A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion.
Branch or outpocketing of the digestive tract.
An anatomical structure that has more than one cell as a part.
An anatomical structure that develops from the neural crest.
structure with developmental contribution from neural crest
An anatomical structure that has some part that develops from the neural crest.
central nervous system cell part cluster
A multi cell part structure that is part of a central nervous system.
Anatomical structure, which consists of a specific set of the members of (predominantly) one organ or organ part subclass interconnected by zones of continuity or body substances; is demarcated from other subdivisions of the same organ system by one or more zones of continuity or anatomical lines; together with other subdivisions of the same organ system, it constitutes an organ system. Examples: rib cage, facial skeleton, portal system, central nervous system, upper respiratory tract, muscle group of back.
Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue
Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue
FMA class may only represent the uterine portion
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
An exocrine gland that is part of a integumental system.
A malignant tumor of the bone which always arises in the medullary tissue, occurring more often in cylindrical bones. There are conspicuous foci of necrosis in association with irregular masses of small, regular, rounded or ovoid cells with very scanty cytoplasm. The tumor occurs usually before the age of 20, about twice as frequently in males as in females. (From Dorland, 27th ed; Stedman, 25th ed)
A small round cell tumor that lacks morphologic, immunohistochemical, and electron microscopic evidence of neuroectodermal differentiation. It represents one of the two ends of the spectrum called Ewing's sarcoma/peripheral neuroectodermal tumor. It affects mostly males under age 20, and it can occur in soft tissue or bone. Pain and the presence of a mass are the most common clinical symptoms.
A spectrum of malignant tumors, affecting mostly males under age 20, characterized morphologically by the presence of small round cells. Ewing sarcoma and peripheral primitive neuroectodermal tumor represent the ends of a spectrum, with Ewing sarcoma lacking evidence of neural differentiation and the markers that characterize the peripheral primitive neuroectodermal tumor. Ewing sarcoma and peripheral primitive neuroectodermal tumor may share cytogenetic abnormalities, proto-oncogene expression, cell culture and immunohistochemical abnormalities. These tumors may occur in the soft tissues or the bones. Pain and the presence of a mass are the most common clinical symptoms.
Ewing Sarcoma/Peripheral Primitive Neuroectodermal Tumor
Ewing's sarcoma (morphologic abnormality)
URI: http://www.ebi.ac.uk/cellline#Ewing_sarcoma
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.
The hard form of connective tissue that constitutes the majority of the skeleton of most vertebrates; it consists of an organic component (the cells and matrix) and an inorganic, or mineral, component; the matrix contains a framework of collagenous fibers and is impregnated with the mineral component, chiefly calcium phosphate (85 per cent) and calcium carbonate (10 per cent), which imparts the quality of rigidity to bone.
A carcinoma arising from the breast, most commonly the terminal ductal-lobular unit. It is the most common malignant tumor in females. Risk factors include country of birth, family history, menstrual and reproductive history, fibrocystic disease and epithelial hyperplasia, exogenous estrogens, contraceptive agents, and ionizing radiation. The vast majority of breast carcinomas are adenocarcinomas (ductal or lobular). Breast carcinoma spreads by direct invasion, by the lymphatic route, and by the blood vessel route. The most common site of lymph node involvement is the axilla.
A carcinoma that originates from breast tissue.
URI: http://www.ebi.ac.uk/cellline#breast_carcinoma
A body system disease which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
A non-neoplastic or neoplastic disorder affecting the heart or the vessels (arteries, veins and lymph vessels). Representative examples of non-neoplastic cardiovascular disorders are endocarditis and hypertension. Representative examples of neoplastic cardiovascular disorders are endocardial myxoma and angiosarcoma.
Circulatory system disease NOS (disorder)
Disease affecting entire cardiovascular system
Disease affecting entire cardiovascular system (disorder)
Disease of cardiovascular system (disorder)
Disorder of cardiovascular system (disorder)
Other diseases of endocardium (disorder)
Other diseases of pericardium (disorder)
Other ill-defined heart disease (disorder)
Other ill-defined heart disease NOS (disorder)
Other pericardial disease NOS (disorder)
Other sequelae of myocardial infarction, not elsewhere classified
Other specified pericardial disease NOS (disorder)
Pathological conditions involving the CARDIOVASCULAR SYSTEM including the HEART; the BLOOD VESSELS; or the PERICARDIUM.
URI: http://www.ebi.ac.uk/cellline#cardiovascular_disease
[X]Cardiovascular disease, unspecified (disorder)
[X]Other forms of heart disease (disorder)
[X]Other ill-defined heart diseases (disorder)
[X]Other specified diseases of pericardium
[X]Other specified diseases of pericardium (disorder)
disease of subdivision of hemolymphoid system
A disease is a disposition that describes states of disease associated with a particular sample and/or organism.
Disorder of reproductive system (disorder)
Non-neoplastic Reproductive system disease
URI: http://www.ebi.ac.uk/cellline#reproductive_system_disease
A cancer that is derived from germ cells.
Germ cell neoplasm (morphologic abnormality)
Germ cell neoplasm NOS (morphologic abnormality)
Germ cell neoplasms (morphologic abnormality)
Neoplasms composed of primordial GERM CELLS of embryonic GONADS or of elements of the germ layers of the EMBRYO, MAMMALIAN. The concept does not refer to neoplasms located in the gonads or present in an embryo or FETUS.
URI: http://www.ebi.ac.uk/cellline#germ_cell_tumor
[M]Germ cell neoplasm NOS (morphologic abnormality)
[M]Germ cell neoplasms (morphologic abnormality)
A benign or malignant brain and spinal cord tumor that arises from glial cells (astrocytes, oligodendrocytes, ependymal cells). Tumors that arise from astrocytes are called astrocytic tumors or astrocytomas. Tumors that arise from oligodendrocytes are called oligodendroglial tumors. Tumors that arise from ependymal cells are called ependymomas.
Benign and malignant central nervous system neoplasms derived from glial cells (i.e., astrocytes, oligodendrocytes, and ependymocytes). Astrocytes may give rise to astrocytomas (ASTROCYTOMA) or glioblastoma multiforme (see GLIOBLASTOMA). Oligodendrocytes give rise to oligodendrogliomas (OLIGODENDROGLIOMA) and ependymocytes may undergo transformation to become EPENDYMOMA; CHOROID PLEXUS NEOPLASMS; or colloid cysts of the third ventricle. (From Escourolle et al., Manual of Basic Neuropathology, 2nd ed, p21)
Glioma (except Nasal glioma, not neoplastic)
Glioma, NOS (except Nasal glioma, not neoplastic)
Glioma, malignant (morphologic abnormality)
Replaced with central nervous system cancer (EFO_0000326)
URI: http://www.ebi.ac.uk/cellline#obsolete_glioma
Autoimmune disease, not elsewhere classified
Disorder of the immune mechanism NOS (disorder)
Immunodeficiency and Immunosuppression Disorders
Immunodeficiency with predominant T-cell defect, unspecified
Other deficiency of cell-mediated immunity
Other specified disorders involving the immune mechanism
Other specified disorders of the immune mechanism
Other specified disorders of the immune mechanism (disorder)
URI: http://www.ebi.ac.uk/cellline#immune_system_disease
Unspecified disorder of immune mechanism
[X]Disorder involving the immune mechanism, unspecified
[X]Disorder involving the immune mechanism, unspecified (disorder)
A cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs.
A general term for various neoplastic diseases of the lymphoid tissue.
A malignant (clonal) proliferation of B- lymphocytes or T- lymphocytes which involves the lymph nodes, bone marrow and/or extranodal sites. This category includes Non-Hodgkin lymphomas and Hodgkin lymphomas.
Malignant lymphoma NOS of unspecified site
Malignant lymphoma NOS of unspecified site (disorder)
This is potentially too broad as well as overlaps with leukemia and should be obsoleted.
URI: http://www.ebi.ac.uk/cellline#lymphoma
malignant lymphoma, no ICD-O subtype (morphologic abnormality)
A congenital (due to inherited enzyme abnormality) or acquired (due to failure of a metabolic important organ) disorder resulting from an abnormal metabolic process. -- 2003
Generalized metabolic disorder (disorder)
Generic term for diseases caused by an abnormal metabolic process. It can be congenital due to inherited enzyme abnormality (METABOLISM, INBORN ERRORS) or acquired due to disease of an endocrine organ or failure of a metabolically important organ such as the liver. (Stedman, 26th ed)
URI: http://www.ebi.ac.uk/cellline#metabolic_disease
(Neuroblastoma NOS) or (sympathicoblastoma)
A common neoplasm of early childhood arising from neural crest cells in the sympathetic nervous system, and characterized by diverse clinical behavior, ranging from spontaneous remission to rapid metastatic progression and death. This tumor is the most common intraabdominal malignancy of childhood, but it may also arise from thorax, neck, or rarely occur in the central nervous system. Histologic features include uniform round cells with hyperchromatic nuclei arranged in nests and separated by fibrovascular septa. Neuroblastomas may be associated with the opsoclonus-myoclonus syndrome (MeSH).
A common neoplasm of early childhood arising from neural crest cells in the sympathetic nervous system, and characterized by diverse clinical behavior, ranging from spontaneous remission to rapid metastatic progression and death. This tumor is the most common intraabdominal malignancy of childhood, but it may also arise from thorax, neck, or rarely occur in the central nervous system. Histologic features include uniform round cells with hyperchromatic nuclei arranged in nests and separated by fibrovascular septa. Neuroblastomas may be associated with the opsoclonus-myoclonus syndrome. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, pp2099-2101; Curr Opin Oncol 1998 Jan;10(1):43-51)
A neuroblastic tumor characterized by the presence of neuroblastic cells, the absence of ganglion cells, and the absence of a prominent Schwannian stroma formation.
URI: http://www.ebi.ac.uk/cellline#neuroblastoma
[M]Neuroblastoma NOS (morphologic abnormality)
neuroblastoma NOS (morphologic abnormality)
The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).
URI: http://www.ebi.ac.uk/cellline#organism_part
tissue, organ, system, sperm, blood or body location (arm).
A malignant mesenchymal tumor arising from the bone.
A sarcoma originating in bone-forming cells, affecting the ends of long bones. It is the most common and most malignant of sarcomas of the bones, and occurs chiefly among 10- to 25-year-old youths. (From Stedman, 25th ed)
A usually aggressive malignant bone-forming mesenchymal tumor, predominantly affecting adolescents and young adults. It usually involves bones and less frequently extraosseous sites. It often involves the long bones (particularly distal femur, proximal tibia, and proximal humerus). Pain with or without a palpable mass is the most frequent clinical symptom. It may spread to other anatomic sites, particularly the lungs.
Osteosarcoma, no ICD-O subtype (morphologic abnormality)
URI: http://www.ebi.ac.uk/cellline#osteosarcoma
A cancer that affects connective tissue resulting in mesoderm proliferation.
A malignant mesenchymal neoplasm arising exclusively from the soft tissues. Representative examples include soft tissue sarcoma, extraosseous Ewing sarcoma/peripheral primitive neuroectodermal tumor, and malignant hemangiopericytoma.
A malignant mesenchymal neoplasm arising from muscle tissue, adipose tissue, blood vessels, fibrous tissue, or other supportive tissues excluding the bones.
Malignant neoplasm of connective and other soft tissue
Malignant neoplasm of connective and other soft tissue (disorder)
Malignant neoplasm of connective and other soft tissue of abdomen
Malignant neoplasm of connective and other soft tissue of head, face, and neck
Malignant neoplasm of connective and other soft tissue of lower limb, including hip
Malignant neoplasm of connective and other soft tissue of pelvis
Malignant neoplasm of connective and other soft tissue of thorax
Malignant neoplasm of connective and other soft tissue of trunk, unspecified
Malignant neoplasm of connective and other soft tissue of upper limb, including shoulder
Malignant neoplasm of connective and other soft tissue, site unspecified
Malignant neoplasm of other specified sites of connective and other soft tissue
Malignant neoplasm of soft tissue (disorder)
Sarcoma, no ICD-O subtype (morphologic abnormality)
Type of cancer of the bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue.
URI: http://www.ebi.ac.uk/cellline#sarcoma
[M]Sarcoma NOS (morphologic abnormality)
Organ system which consists of the heart, the systemic and pulmonary arterial and venous system, the lymphatic and the portal venous system.
URI: http://www.ebi.ac.uk/cellline#cardiovascular_system
The organ system involved in the absorption of nutrients.
URI: http://www.ebi.ac.uk/cellline#digestive_system_component
A cell, group of cells, or organ of endothelial origin that selectively removes materials from the blood, concentrates or alters them, and secretes them for further use in the body or for elimination from the body.
URI: http://www.ebi.ac.uk/cellline#gland
URI: http://www.ebi.ac.uk/cellline#haemopoietic_system
The bodily system that is composed of skeletal, smooth, and cardiac muscle tissue and functions in movement of the body or of materials through the body, maintenance of posture, and heat production.
URI: http://www.ebi.ac.uk/cellline#muscular_system
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS).
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)
All the nerve centers and nerve fibers in the central, visceral and peripheral nervous systems.
The nervous system is essentially a biological information highway, and is responsible for controlling all the biological processes and movement in the body, and can also receive information and interpret it via electrical signals which are used in this nervous system. It consists of the Central Nervous System (CNS), essentially the processing area and the Peripheral Nervous System which detects and sends electrical impulses that are used in the nervous system.
URI: http://www.ebi.ac.uk/cellline#nervous_system
A system of organs subserving the function of respiration and in air-breathing vertebrates consisting typically of the lungs and their nervous and circulatory supply and the channels by which these are continuous with the outer air.
Functional system which consists of structures involved in respiration.
URI: http://www.ebi.ac.uk/cellline#respiratory_system_structure
URI: http://www.ebi.ac.uk/cellline#skeleton_structure
A division of the whole organism into specialized systems.
Something that covers or encloses; especially: an enveloping layer (as a skin, membrane, or husk) of an organism or one of its parts.
The taxon-independent term for the outer covering of an organism
URI: http://www.ebi.ac.uk/cellline#integumental_system
URI: http://www.ebi.ac.uk/cellline#animal_reproductive_system
The fluid-feeding habit of adult mosquitoes is reflected in the structure and ultrastructure of the alimentary canal.
The tubular part of the alimentary canal that extends from the stomach to the anus.
URI: http://www.ebi.ac.uk/cellline#intestine
Lobular organ which consist of a lactiferous duct tree and the set of lactiferous acini that are connected to duct tree. Examples: There are variable numbers of lactiferous duct trees.
The specialized accessory gland of the skin of female mammals that secretes milk. In the human female, it is a compound tubuloalveolar gland composed of 15 to 25 lobes arranged radially about the nipple and separated by connective and adipose tissue, each lobe having its own excretory (lactiferous) duct opening on the nipple. The lobes are subdivided into lobules, with the alveolar ducts and alveoli being the secretory portion of the gland.
URI: http://www.ebi.ac.uk/cellline#mammary_gland
URI: http://www.ebi.ac.uk/cellline#lymphatic_system
The outer parts of the nervous system that perform sensory and motor functions.
The peripheral nervous system (PNS) connects the central nervous system (CNS) to sensory organs (such as the eye and ear), other organs of the body, muscles, blood vessels and glands.
URI: http://www.ebi.ac.uk/cellline#peripheral_nervous_system
Nervous structures including ganglia outside of the central nervous system.
One of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord, and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera, and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter.
Sympathetic part of autonomic division of nervous system
URI: http://www.ebi.ac.uk/cellline#sympathetic_nervous_system
Lobular organ which has as its parts alveoli connected to the tracheobronchial tree. Examples: There are only two instances, right lung and left lung.
One of the usually paired compound saccular thoracic organs that constitute the basic respiratory organ of air-breathing vertebrates.
The tissue which binds together and is the support of the various structures of the body. It is made up of fibroblasts, fibroglia, collagen fibrils, and elastic fibrils. It is derived from the mesoderm and in a broad sense includes the collagenous, elastic, mucous, reticular, osseous, and cartilaginous tissue. Some also include the blood in this group of tissues. Connective tissue is classified according to concentration of fibers as loose (areolar) and dense, the latter having more abundant fibers than the former.
Tissue which consists of fibroblasts, osteocytes or chondrocytes and intercellular matrix produced by these cells. Examples: bone (tissue), dense regular elastic tissue, areolar tissue, neuroglia, adipose tissue.
URI: http://www.ebi.ac.uk/cellline#connective_tissue
Nonparenchymatous organ that consists of the epidermis, dermis and sets of hair and nails and which surrounds the entire body. Subdivisions of the skin surround various body parts; as a whole, the skin constitutes the external layer of the body. Examples: There is only one skin.
The integument of an animal (as a fur-bearing mammal or a bird) separated from the body usually with its hair or feathers.
Gonochoristic organism that can produce female gametes.
The reproductive system in women includes the ovaries, the fallopian tubes, the uterus (womb), the cervix, and the vagina (birth canal).
URI: http://www.ebi.ac.uk/cellline#female_reproductive_system
URI: http://www.ebi.ac.uk/cellline#animal_ovary
A constricted portion of an organ or part; especially: the narrow outer end of the uterus.
URI: http://www.ebi.ac.uk/cellline#cervix
Multiple myeloma without mention of remission
Multiple myeloma, morphology (morphologic abnormality)
Multiple myeloma, no ICD-O subtype (morphologic abnormality)
URI: http://www.ebi.ac.uk/cellline#multiple_myeloma
Pathological processes of the ENDOCRINE GLANDS, and diseases resulting from abnormal level of available HORMONES.
URI: http://www.ebi.ac.uk/cellline#endocrine_system_disease
URI: http://www.ebi.ac.uk/cellline#endocrine_system
RIKEN Cell Bank
an organization that serves as a cell ine repository. Its website is: http://www.brc.riken.jp/lab/cell/english/.
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
axiom holds for all times