adjacent to
type: ObjectProperty
definition: x adjacent to y if and only if x and y share a boundary.
term editor: Chris Mungall

derived from
type: ObjectProperty
inverse of: derives into
IAO_0000115: 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
IAO_0000116: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.

derives into
type: ObjectProperty
IAO_0000115: 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
IAO_0000116: 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'.

has participant
type: ObjectProperty
inverse of: participates in
IAO_0000115: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: 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.
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

located in
type: ObjectProperty
inverse of: location of
type: TransitiveProperty
IAO_0000115: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
IAO_0000116: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
source: http://www.obofoundry.org/ro/#OBO_REL:located_in

part of
type: ObjectProperty
comment: IAO_0000116 Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.

participates in
type: ObjectProperty
IAO_0000115: a relation between a continuant and a process, in which the continuant is somehow involved in the process

surrounded by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds
definition: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
term editor: Chris Mungall

surrounds
type: ObjectProperty
sub property of: adjacent to
definition: inverse of surrounded by
term editor: Chris Mungall

ATP-binding_cassette_sub-family_A_member_3
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: plasmamembrane
has synonym: 1810036E22Rik
has synonym: ABC-C
has synonym: ABCA3
has synonym: ABCC
has synonym: Abc3
has synonym: Abca3

calcitonin
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: extracellular space
has synonym: CA
has synonym: CALCA
has synonym: CGRP-1
has synonym: CGRP1
has synonym: Calc
has synonym: Calc1
has synonym: Cgrp
has synonym: Ct
has synonym: Ctn

CD34
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: cytoplasm
subclass of: Restriction
  on property: localizes to
  some values from: extracellular space
subclass of: Restriction
  on property: localizes to
  some values from: plasmamembrane
cytoscape view in PRO: http://research.bioinformatics.udel.edu/pro/visual/cytoscape/pro/PR%3AQ64314
has synonym: AU040960
has synonym: CD34 antigen
has synonym: hematopoietic progenitor cell antigen CD34

DAPI
type: Class
subclass of: macromolecule
has synonym: 2-(4-(aminoiminomethyl)phenyl)-1H-indole-6-carboximidamide, 4',6-diamidino-2-phenylindole, 4',6-diamidinophenyl-indole

Embryonic_day_16.5
type: Class
subclass of: mouse_embryo_age
type: NamedIndividual
type: bronchiole
type: mouse_embryo_age
type: neuroepithelial_body
definition: 16.5 days after fertilization
term editor: Person: Chris Stoeckert, Jie Zheng

Embryonic_day_17.5
type: Class
subclass of: mouse_embryo_age

Embryonic_day_19.5
type: Class
subclass of: mouse_embryo_age

Monoclonal Anti-Calcitonin Gene-Related Peptide antibody
type: Class
subclass of: mouse IgG1 antibody
subclass of: Restriction
  on property: recognizes
  some values from: calcitonin
comment: has been used for mouse but on the Sigma datasheet it says recognze human rat and canine

P01
type: Class
subclass of: mouse_postnatal_age

P02
type: Class
subclass of: mouse_postnatal_age

P03
type: Class
subclass of: mouse_postnatal_age

P04
type: Class
subclass of: mouse_postnatal_age

P05
type: Class
subclass of: mouse_postnatal_age

P06
type: Class
subclass of: mouse_postnatal_age

P07
type: Class
subclass of: mouse_postnatal_age

P08
type: Class
subclass of: mouse_postnatal_age

P09
type: Class
subclass of: mouse_postnatal_age

P10
type: Class
subclass of: mouse_postnatal_age

P11
type: Class
subclass of: mouse_postnatal_age

P12
type: Class
subclass of: mouse_postnatal_age

P13
type: Class
subclass of: mouse_postnatal_age

P14
type: Class
subclass of: mouse_postnatal_age

P15
type: Class
subclass of: mouse_postnatal_age

P17
type: Class
subclass of: mouse_postnatal_age

P18
type: Class
subclass of: mouse_postnatal_age

P19
type: Class
subclass of: mouse_postnatal_age

P20
type: Class
subclass of: mouse_postnatal_age

P21
type: Class
subclass of: mouse_postnatal_age

P22
type: Class
subclass of: mouse_postnatal_age

P23
type: Class
subclass of: mouse_postnatal_age

P24
type: Class
subclass of: mouse_postnatal_age

P25
type: Class
subclass of: mouse_postnatal_age

P26
type: Class
subclass of: mouse_postnatal_age

P27
type: Class
subclass of: mouse_postnatal_age

P28
type: Class
subclass of: mouse_postnatal_age

P29
type: Class
subclass of: mouse_postnatal_age

P30
type: Class
subclass of: mouse_postnatal_age

P31
type: Class
subclass of: mouse_postnatal_age

P32
type: Class
subclass of: mouse_postnatal_age

P33
type: Class
subclass of: mouse_postnatal_age

P34
type: Class
subclass of: mouse_postnatal_age

P35
type: Class
subclass of: mouse_postnatal_age

P36
type: Class
subclass of: mouse_postnatal_age

Protein
type: Class
subclass of: macromolecule
comment: general questions: for now we are going to have ponly mouse proteins but in the future we will have humans one. Each of the proteins we are using have a Protein ontology ID specific for mouse. Do we need to have in the future the ability to distinguish human adn maouse in the ontology? should we have to put m o h in front of each protein name so we will know which is human and which is mouse?

Theiler_stage_24
type: Class
subclass of: mouse_embryo_stage
comment: lung developmental stage: late pseudoglandular

Theiler_stage_26
type: Class
subclass of: mouse_embryo_stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: Theiler stage 25
comment: lung developmental stage: early saccular

Theiler_stage_27
type: Class
subclass of: mouse_embryo_stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: Theiler_stage_26

Theiler stage 28
type: Class
subclass of: mouse_embryo_stage
subclass of: Restriction
  on property: immediately preceded by
  some values from: Theiler_stage_27
comment: lung developmental stage at age P28: mature alveoli
comment: lung developmental stage at age P7: alveolar

acinar_epithelial_cell
type: Class
subclass of: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: part of
  some values from: acinar_tubule_epithelium
definition: Definition in Lung Ontology: A cuboidal epithelial cell that lines the branching acinar tubules of the peripheral fetal lung. These tubules are formed during the pseudoglandular stage of lung development (E12.5 - E16.5). They are called "acinar tubules", since they will become the mature pulmonary acinus (alveolar duct and alveoli) in the adult lung.
definition: proposed definition AMM: An epithelial cell of the lung acinus.
lungmap preferred label: acinar epithelial cell
comment: no present in CL need to be added

acinar_tubule
type: Class
subclass of: complex_structure
subclass of: Restriction
  on property: has part
  some values from: acinar_tubule_epithelium
lungmap preferred label: acinar tubule
is defined by: LungMAP ID: LMMA0000000001

acinar_tubule_epithelium
type: Class
subclass of: lung_epithelium
subclass of: Restriction
  on property: has part
  some values from: acinar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell_of_the_lung
lungmap preferred label: acinar tubule epithelium
is defined by: LungMap ID: LMMA0000000053

acinar_tubule_proliferative_epithelial_cell
type: Class
subclass of: distal_acinar_tubule_epithelial_cell
subclass of: Class
  complement of: Restriction
    on property: has part
    some values from: homeodomain-only_protein
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: histone_H3.3C
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-9
subclass of: Restriction
  on property: participates in
  some values from: cellular_proliferation
lungmap preferred label: acinar tubule proliferative epithelial cell
comment: AMM: something is wrong in the lungmap hierarchy since the pneumocyte type I and type II and proliferative epithelial cell are both listed as children of distal acinar cell and proximal acinar cell. That is inconsistent
comment: No present in CL need to be added
is defined by: LungMAP ID: LMMA0000000599

advanced_glycosylation_end_product-specific_receptor
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: cytoplasm
subclass of: Restriction
  on property: localizes to
  some values from: extracellular space
subclass of: Restriction
  on property: localizes to
  some values from: plasmamembrane
has synonym: AGER
has synonym: RAGE
has synonym: Receptor for advanced glycosylation end products

age since birth measurement datum
type: Class
subclass of: measurament datum
definition: OBI: An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.

age since fertilization measurement datum
type: Class
subclass of: measurament datum
definition: Definition: An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.

alpha-actin-2
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: cytoplasm
has synonym: ACTA2
has synonym: Acta2
has synonym: a-SMA
has synonym: actin
has synonym: actin, aortic smooth muscle
has synonym: alpha 2
has synonym: alpha-smooth muscle actin
has synonym: aorta
has synonym: smooth muscle
has synonym: α Smooth muscle, actin
has synonym: α-Smooth Muscle Actin
comment: http://www.uniprot.org/uniprot/P62737

anatomical_entity
type: Class

anatomical structure development
type: Class
subclass of: process
definition: Definition GO: The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.

anti ABCA3
type: Class
subclass of: antibody_reagent
subclass of: Restriction
  on property: recognizes
  some values from: ATP-binding_cassette_sub-family_A_member_3
see also: is an in house antibody CCHMC In House: BL3/10/05

anti NKX2.1
type: Class
subclass of: mouse IgG1 antibody
see also: is an antibody produced in house CCHMC In House: BL 10/7/11

anti Pecam
type: Class
subclass of: antibody_reagent
subclass of: Restriction
  on property: recognizes
  some values from: platelet_endothelial_cell_adhesion_molecule
see also: Baylor College of Medicine in-house probe

anti SOX2
type: Class
subclass of: antibody_reagent
subclass of: Restriction
  on property: recognizes
  some values from: transcription_factor_SOX-2
see also: is an in house antibody CCHMC In House: BL 5/7/09

anti uteroglobin
type: Class
subclass of: antibody_reagent
subclass of: Restriction
  on property: recognizes
  some values from: uteroglobin
see also: is an in house antibody CCHMC In House: BL 1/27/11

antibody_reagent
type: Class
subclass of: immunoglobulin complex
subclass of: Restriction
  on property: has role
  some values from: reagent
definition: Antibody reagent that recognizes a single epitope.

ADP-ribosylation factor-like protein 13B
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: plasmamembrane
has synonym: A530097K21Rik
has synonym: A930014M17Rik
has synonym: ADP-ribosylation factor-like protein 2-like 1
has synonym: ARL13B
has synonym: ARL2-like protein 1
has synonym: Arl13B
has synonym: Arl2l1
has synonym: C530009C10Rik
has synonym: hnn

arteriole_endothelium
type: Class
subclass of: endothelium
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell_of_vascular_tree
definition: UBERON: An endothelium that is part of an arteriole [Automatically generated definition]. [database_cross_reference: OBOL:automatic]
lungmap preferred label: arteriole endothelium
is defined by: UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001916

artery_endothelium
type: Class
subclass of: endothelium
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell_of_artery
definition: UBERON: An endothelium that is part of an artery [Automatically generated definition]. [database_cross_reference: OBOL:automatic]
lungmap preferred label: artery endothelium
is defined by: LungMap ID: LMMA0000000078
is defined by: UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001917

blood_vessel
type: Class
subclass of: vascular_tree
subclass of: Restriction
  on property: has part
  some values from: endothelium
subclass of: Restriction
  on property: has part
  some values from: vascular_tree_endothelium
subclass of: Restriction
  on property: surrounded by
  some values from: vascular smooth muscle tissue
definition: UBERON definition: A vessel through which blood circulates in the body.
lungmap preferred label: blood_vessel
is defined by: UBERON http://purl.obolibrary.org/obo/UBERON_0001981

bronchial_artery_endothelium
type: Class
subclass of: artery_endothelium
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell_of_artery
lungmap preferred label: bronchial artery endothelium

bronchiolar_associated_smooth_muscle_cell
type: Class
subclass of: smooth_muscle_cell
subclass of: Restriction
  on property: has part
  some values from: alpha-actin-2
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
lungmap preferred label: bronchiolar associated smooth muscle cell

bronchiolar_connective_tissue
type: Class
subclass of: connective
subclass of: Restriction
  on property: has part
  some values from: interstitial_cell
lungmap preferred label: bronchiolar connective
comment: AMM: No present in UBERON need to be added
is defined by: LungMAp ID: LMMA0000000525

bronchiolar_epithelial_cell
type: Class
subclass of: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-2
definition: Definition CL: An epithelial cell of the bronchus. [database_cross_reference: GOC:tfm]
definition: Definition in LungMAP: An epithelial cell that lines the intrapulmonary conducting airway, or bronchioles. The more proximal bronchioles are lined predominantly by ciliated cells with a greater proportion of club cells in the distal bronchioles.
lungmap preferred label: bronchiolar epithelial cell
comment: needs to be check if CL and LungMap are refering to the same term
is defined by: CL ID: http://purl.obolibrary.org/obo/CL_0002328
is defined by: LungMAP ID: LMMA0000000582

bronchiole
type: Class
subclass of: complex_structure
subclass of: Restriction
  on property: has part
  some values from: bronchiolar_connective_tissue
subclass of: Restriction
  on property: has part
  some values from: epithelium_of_bronchiole
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_16.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_17.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic day 18.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_19.5
subclass of: Restriction
  on property: identifiable at
  some values from: P01
subclass of: Restriction
  on property: identifiable at
  some values from: P02
subclass of: Restriction
  on property: identifiable at
  some values from: P03
subclass of: Restriction
  on property: identifiable at
  some values from: P04
subclass of: Restriction
  on property: identifiable at
  some values from: P05
subclass of: Restriction
  on property: identifiable at
  some values from: P06
subclass of: Restriction
  on property: identifiable at
  some values from: P07
subclass of: Restriction
  on property: identifiable at
  some values from: P08
subclass of: Restriction
  on property: identifiable at
  some values from: P09
subclass of: Restriction
  on property: identifiable at
  some values from: P10
subclass of: Restriction
  on property: identifiable at
  some values from: P11
subclass of: Restriction
  on property: identifiable at
  some values from: P12
subclass of: Restriction
  on property: identifiable at
  some values from: P13
subclass of: Restriction
  on property: identifiable at
  some values from: P14
subclass of: Restriction
  on property: identifiable at
  some values from: P15
subclass of: Restriction
  on property: identifiable at
  some values from: P17
subclass of: Restriction
  on property: identifiable at
  some values from: P18
subclass of: Restriction
  on property: identifiable at
  some values from: P19
subclass of: Restriction
  on property: identifiable at
  some values from: P20
subclass of: Restriction
  on property: identifiable at
  some values from: P21
subclass of: Restriction
  on property: identifiable at
  some values from: P22
subclass of: Restriction
  on property: identifiable at
  some values from: P23
subclass of: Restriction
  on property: identifiable at
  some values from: P24
subclass of: Restriction
  on property: identifiable at
  some values from: P25
subclass of: Restriction
  on property: identifiable at
  some values from: P26
subclass of: Restriction
  on property: identifiable at
  some values from: P27
subclass of: Restriction
  on property: identifiable at
  some values from: P28
subclass of: Restriction
  on property: identifiable at
  some values from: P29
subclass of: Restriction
  on property: identifiable at
  some values from: P30
subclass of: Restriction
  on property: identifiable at
  some values from: P31
subclass of: Restriction
  on property: identifiable at
  some values from: P32
subclass of: Restriction
  on property: identifiable at
  some values from: P33
subclass of: Restriction
  on property: identifiable at
  some values from: P34
subclass of: Restriction
  on property: identifiable at
  some values from: P35
subclass of: Restriction
  on property: identifiable at
  some values from: P36
subclass of: Restriction
  on property: identifiable at
  some values from: PO
subclass of: Restriction
  on property: part of
  some values from: lung
subclass of: Restriction
  on property: surrounded by
  some values from: smooth_muscle_tissue_of_bronchiole
definition: Uberon Definition: The conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching
lungmap preferred label: bronchiole

bronchiole_proliferative_epithelial_cell
type: Class
subclass of: bronchiolar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: histone_H3.3C
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-2
subclass of: Restriction
  on property: participates in
  some values from: cellular_proliferation
lungmap preferred label: bronchiole proliferative epithelial cell
comment: no present in CL need to be added
is defined by: LungMap ID: LMMA0000000599

cell
type: Class
subclass of: anatomical_entity
disjoint with: complex_structure
disjoint with: macromolecule
disjoint with: tissue

cellular_proliferation
type: Class
subclass of: process

chondroitin_sulfate_proteoglycan_4
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: plasmamembrane
definition: def: "A protein that is a translation product of the human CSPG4 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: 4732461B14Rik
has synonym: AN2
has synonym: CSPG4
has synonym: NG2
has synonym: chondroitin sulfate proteoglycan NG2
has synonym: melanoma chondroitin sulfate proteoglycan
has synonym: melanoma-associated chondroitin sulfate proteoglycan
has synonym: proteoglycan AN2

ciliated_cell_precursor
type: Class
subclass of: bronchiolar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-2
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_16.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_17.5
definition: Definition LungMap: An epithelial cell that is located in the conducting airways of the fetal lung in the late pseudoglandular stage of lug development (E15.5-E16.5). This cell is committed to the ciliated cell lineage, but is not fully differentiated. It expresses FOXJ1, a marker for ciliated cells, but does not have fully formed, functional. motile cilia.
lungmap preferred label: ciliated cell precursor
is defined by: LungMap ID: LMMA0000000476

complex_structure
type: Class
subclass of: multicellular_anatomical_structure
subclass of: Restriction
  on property: has part
  some values from: tissue
disjoint with: organ
disjoint with: tissue
term editor: Anna Maria Masci and Scott White

connective
type: Class
subclass of: tissue
definition: UBERON: A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. [database_cross_reference: OBOL:automatic]
lungmap preferred label: connective
is defined by: LungMap ID: LMMA0000000147
is defined by: UBERON ID: http://purl.obolibrary.org/obo/UBERON_0003570

distal_acinar_tubule_bud
type: Class
subclass of: complex_structure
subclass of: Restriction
  on property: has part
  some values from: distal_acinar_tubule_epithelium
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_16.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_17.5
subclass of: Restriction
  on property: part of
  some values from: acinar_tubule
definition: Definition LungMAP: acinar bud, distal acinar bud, distal acinar tubule, peripheral acinar tubule bud, peripheral acinar tubule sprout.
lungmap preferred label: distal acinar tubule bud
is defined by: LungMAP ID: LMMA0000000003

distal_acinar_tubule_epithelial_cell
type: Class
subclass of: epithelial_cell_of_the_lung
subclass of: Class
  complement of: Restriction
    on property: has part
    some values from: homeodomain-only_protein
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-9
definition: Definition LungMAP: A cuboidal epithelial cell located in the distal acinar tubule, or bud, of the peripheral fetal lung in the pseudoglandular stage of lung development (E12.5-E16.5). These cells express cell-specific proteins (or markers) for pre-type II pneumocytes, such as surfactant protein C (SFTPC).
lungmap preferred label: distal acinar tubule epithelial cell
comment: no present in Cl need to be added
is defined by: LungMAP ID: LMMA0000000572

distal_acinar_tubule_epithelium
type: Class
subclass of: lung_epithelium
subclass of: Restriction
  on property: has part
  some values from: acinar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: acinar_tubule_proliferative_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: ciliated_cell_precursor
subclass of: Restriction
  on property: has part
  some values from: distal_acinar_tubule_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: immature_type_II_pneumocyte
subclass of: Restriction
  on property: has part
  some values from: immature_type_I_pneumocyte
lungmap preferred label: distal acinar tubule epithelium

embryo_stage
type: Class
subclass of: life_cycle_stage

endomucin
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: plasmamembrane
definition: "A protein that is a translation product of the human EMCN gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: 0610012K22Rik
has synonym: AI315669
has synonym: EMCN
has synonym: Endomucin (Emcn)
has synonym: MUC-14
has synonym: Muc14
has synonym: emnc
has synonym: endomucin-1/2
has synonym: endomucin-2
has synonym: gastric cancer antigen Ga34
has synonym: mucin-14

endothelial_cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: has part
  some values from: CD34
subclass of: Restriction
  on property: has part
  some values from: endomucin
subclass of: Restriction
  on property: part of
  some values from: endothelium
definition: Definition in CL: An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. [database_cross_reference: MESH:D042783][database_cross_reference: GOC:tfm][database_cross_reference: http://en.wikipedia.org/wiki/Endothelial_cell][database_cross_reference: https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855][database_cross_reference: PMID:21275341]
definition: Definition in LungMAP: A mesenchymal-derived, polygonal, rounded, flat, or squamous ("scale-like") cell that lines the inner (luminal) surface of the blood vessels and lymphaic vessels. These cells contain vimentin filaments and are held together by junctional complexes to form a thin, continuous, endothelial cell layer or sheath (endothelium).
lungmap preferred label: endothelial cell
is defined by: CL : http://purl.obolibrary.org/obo/CL_0000115
is defined by: LungMAP ID: LMMA0000000343

endothelial_cell_of_artery
type: Class
subclass of: endothelial_cell_of_vascular_tree
subclass of: Restriction
  on property: has part
  some values from: CD34
subclass of: Restriction
  on property: has part
  some values from: endomucin
subclass of: Restriction
  on property: has part
  some values from: platelet_endothelial_cell_adhesion_molecule
subclass of: Restriction
  on property: part of
  some values from: artery_endothelium
definition: Definition CL: A blood vessel endothelial cell that is part of an arterial endothelium. [database_cross_reference: GOC:tfm]
lungmap preferred label: endothelial cell of vascular tree
is defined by: CL ID: http://purl.obolibrary.org/obo/CL_1001568
is defined by: LungMap ID: LMMA0000000616

endothelial_cell_of_vascular_tree
type: Class
subclass of: endothelial_cell
subclass of: Restriction
  on property: has part
  some values from: platelet_endothelial_cell_adhesion_molecule
subclass of: Restriction
  on property: part of
  some values from: vascular_tree_endothelium
definition: Definition CL: An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. [database_cross_reference: GOC:tfm][database_cross_reference: GOC:dsd][database_cross_reference: PMID:12768659]
lungmap preferred label: endothelial cell of vascular tree
comment: comment in CL: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive.
is defined by: Definition: An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. LMMA0000000392

endothelium
type: Class
subclass of: tissue
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell
definition: UBERON: A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] [database_cross_reference: https://github.com/obophenotype/uberon/issues/225][database_cross_reference: FMA:63916][database_cross_reference: MESH:A10.272.491]
lungmap preferred label: endothelium
is defined by: LungMap ID: LMMA0000000162
is defined by: UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001986

epithelial_cell
type: Class
subclass of: cell
definition: Definition CL: 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. [database_cross_reference: GOC:tfm][database_cross_reference: FB:ma][database_cross_reference: MESH:A11.436]
definition: Definition LungMap: Cells that line the inner and outer surfaces of the body by forming single or mutliple cell layers or sheets (epithelia). Epithelial cells lining the respiratory system are derived from endoderm. Epithelial cells can be classified by cell shape into squamous, cuboidal, columnar, and transitional epithelial cells. They have a cytoskeleton that allows for tight cell-to-cell contact and cell polarity
lungmap preferred label: epithelial cell
is defined by: LungMap ID: LMMA0000000164

epithelial_cell_of_the_lung
type: Class
subclass of: epithelial_cell
definition: Definition LungMAP: Cells that line the inner and outer surfaces of the body by forming single or mutliple cell layers or sheets (epithelia). Epithelial cells lining the respiratory system are derived from endoderm. Epithelial cells can be classified by cell shape into squamous, cuboidal, columnar, and transitional epithelial cells. They have a cytoskeleton that allows for tight cell-to-cell contact and cell polarity.
lungmap preferred label: epithelial cell of the lung
is defined by: CL ID: http://purl.obolibrary.org/obo/CL_0000082
is defined by: LungMAP ID: LMMA0000000164

epithelium
type: Class
subclass of: tissue
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell
definition: UBERON: Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. [database_cross_reference: http://orcid.org/0000-0001-9114-8737][database_cross_reference: http://en.wikipedia.org/wiki/Epithelium]
lungmap preferred label: epithelium
is defined by: UBERON ID: http://purl.obolibrary.org/obo/UBERON_0000483

epithelium_of_bronchiole
type: Class
subclass of: lung_epithelium
subclass of: Restriction
  on property: has part
  some values from: bronchiole_proliferative_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: neuroepithelial_body
subclass of: Restriction
  on property: surrounded by
  some values from: bronchiolar_associated_smooth_muscle_cell
definition: Uberon def: An epithelium that is part of a bronchiole [Automatically generated definition].
lungmap preferred label: epithelium of bronchiole
comment: Age Range(s): E16.5, E18.5, P0-P3, P4-P36 Theiler Stage(s): TS24, TS26, TS27, TS28 Developmental Stage(s): alveolar stage, canalicular stage, saccular stage
is defined by: LungMap ID: LMMA0000000115
is defined by: UBERON ID: http://purl.obolibrary.org/obo/UBERON_0002051

epithelium_of_respiratory_bronchiole
type: Class
subclass of: epithelium_of_bronchiole
subclass of: Restriction
  on property: has part
  some values from: bronchiolar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: bronchiole_proliferative_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: neuroepithelial_body
subclass of: Restriction
  on property: has part
  some values from: unclassified_epithelial_cell
lungmap preferred label: epithelium of respiratory bronchiole

fibroblast
type: Class
subclass of: cell
subclass of: Restriction
  on property: has part
  some values from: vimentin
definition: definition CL: A fibroblast that is part of lung. [database_cross_reference: GOC:tfm]
definition: definition LungMap: A connective tissue cell that secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
lungmap preferred label: fibroblast
is defined by: CL ID: http://purl.obolibrary.org/obo/CL_0002553
is defined by: LungMAP ID: LMMA0000000169

histone_H3.3C
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: nucleus
cytoscape view in PRO: http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php?id=PR:000029067??? https://proconsortium.org/app/visual/cytoscape/pro/PR%3A000029532
has synonym: Histone H3.5
has synonym: p-Histone H3
has synonym: pHisH3
comment: histone H3 only when phosphorylated at Ser10 human

homeobox_protein_Nkx-2.1
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: nucleus
cytoscape view in PRO: http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php
definition: "A protein that is a translation product of the human NKX2-1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: BCH
has synonym: BHC
has synonym: NK-2
has synonym: NK2
has synonym: NKX2.1
has synonym: NKX21
has synonym: NKX2A
has synonym: NMTC1
has synonym: Nkx-2.1
has synonym: Nkx2-1
has synonym: T/EBP
has synonym: TEBP
has synonym: TITF1
has synonym: TTF-1
has synonym: TTF1
has synonym: homeobox protein NK-2 homolog A
has synonym: thyroid nuclear factor 1

homeodomain-only_protein
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: cytoplasm
subclass of: Restriction
  on property: localizes to
  some values from: nucleus
definition: "A protein that is a translation product of the human HOPX gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: HOP Homeobox
has synonym: HOPX
has synonym: Hopx
has synonym: Odd homeobox protein 1
has synonym: homeobox-only protein
has synonym: lung cancer-associated Y protein
has synonym: not expressed in choriocarcinoma protein 1

human_embryo_stage
type: Class
subclass of: embryo_stage

immature_club_cell
type: Class
subclass of: bronchiolar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-2
subclass of: Restriction
  on property: has part
  some values from: uteroglobin
definition: Definition LungMap: A partially differentiated fetal club cell, whose cytoplasm contains abundant glycogen granules. Full differentiation occurs postnatally when glycogen levels decrease and secretory granules increase.
lungmap preferred label: immature club cell
comment: no present in CL need to be added
is defined by: LungMap ID: LMMA0000000184

immature_type_II_pneumocyte
type: Class
subclass of: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: ATP-binding_cassette_sub-family_A_member_3
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: pulmonary_surfactant-associated_protein_C
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-9
definition: Definition LungMAP: A fetal type II peumocyte that is structurally and biochemically immature. This cell is glycogen-rich with lamellar bodies in various stages of formation. Metabolically, large stores of glycogen are required to support surfactant lipid synthesis and lamellar body formation in this cell.
lungmap preferred label: immature type II pneumocyte
comment: AMM: not present in CL need to be added
comment: AMM: something is wrong in the lungmap hierarchy since the pneumocyte type I and type II and proliferative epithelial cell are both listed as children of distal acinar cell and proximal acinar cell. That is inconsistent
is defined by: LungMAP ID: LMMA0000000382

immature_type_I_pneumocyte
type: Class
subclass of: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: advanced_glycosylation_end_product-specific_receptor
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: homeodomain-only_protein
definition: Definition LungMAP: A fetal type I pneumocytes that is structurally immature. This former cuboidal-like cell changes shape to a flat, squamous-like cell, thinning and spreading over the luminal surface of the expanding terminal and/or primary alveolar saccule during late fetal lung development (E17.5 - E19.5). This process requires extensive membrane enlargement and reorganization of the cytoskeleton.
has synonym: immature AT1, pre-type I pneumocyte
lungmap preferred label: immature type I pneumocyte
comment: AMM: not present in CL need to be added
comment: AMM: something is wrong in the lungmap hierarchy since the pneumocyte type I and type II and proliferative epithelial cell are both listed as children of distal acinar cell and proximal acinar cell. That is inconsistent
is defined by: LungMAP ID: LMMA0000000380

immunoglobulin complex
type: Class
subclass of: protein complex
definition: A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.

information content entity
type: Class
definition: Definition: A generically dependent continuant that is about some thing

intermediate_pneumocyte
type: Class
subclass of: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: homeodomain-only_protein
subclass of: Restriction
  on property: has part
  some values from: pulmonary_surfactant-associated_protein_C
definition: Definition LungMAP: A pneumocyte with characteristics of both type I and type II precursor cells, identified by co-expression of SFTPC (a type II cell marker) and HOPX (a type I cell marker).
lungmap preferred label: intermediate pneumocyte
comment: AMM: not present in CL need to be added
is defined by: LungMAP ID: LMMA0000000187

interstitial_cell
type: Class
subclass of: bronchiolar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-2
definition: LungMap definition: A mesenchymal-derived, connective tissue cell located in the interstitial space (i.e., interstitium or connective tissue compartments) of the lung.
comment: not present in CL too generic
is defined by: LungMap ID: LMHA0000000192

interstitial_tissue
type: Class
subclass of: tissue
subclass of: Restriction
  on property: has part
  some values from: fibroblast
subclass of: Restriction
  on property: has part
  some values from: myofibroblast
subclass of: Restriction
  on property: has part
  some values from: unclassified_fibroblast
definition: UBERON: Connective tissue between the cellular elements of a structure. [database_cross_reference: http://medical-dictionary.thefreedictionary.com/tissue]
lungmap preferred label: interstitial tissue
is defined by: UBERON ID: http://purl.obolibrary.org/obo/UBERON_0005169

life_cycle_stage
type: Class
subclass of: process

lung
type: Class
subclass of: organ
subclass of: Restriction
  on property: has part
  some values from: cell
subclass of: Restriction
  on property: has part
  some values from: complex_structure
subclass of: Restriction
  on property: has part
  some values from: lung_epithelium
subclass of: Restriction
  on property: has part
  some values from: pulmonary_lymphatic_vessel
subclass of: Restriction
  on property: has part
  some values from: tissue
definition: Definition Uberon: Respiration organ that develops as an oupocketing of the esophagus. [database_cross_reference: http://orcid.org/0000-0002-6601-2165]
lungmap preferred label: lung
is defined by: LungMap ID: LMMA0000000211

lung_epithelium
type: Class
subclass of: epithelium
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: immature_club_cell
definition: UBERON: The epithelial layer of the lung. [database_cross_reference: MP:0006382]
lungmap preferred label: lung epithelium
is defined by: LungMap ID: LMMA0000000166
is defined by: UBERON ID: http://purl.obolibrary.org/obo/UBERON_0000115

lung_neuroendocrine_cell
type: Class
subclass of: bronchiolar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: calcitonin
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-2
definition: Definition CL: An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals. [database_cross_reference: MESH:A06.688]
definition: Definition LungMap:An endocrine cell that produces and secretes neurotransmitters and neuropeptide hormones in response to neuronal signals. In the lung, these cells are found as single cells or in cell clusters (neuroepithelial bodies) and are located in the epithelium of the conducting airways, including trachea, bronchi, and bronchioles.
lungmap preferred label: lung neuroendocrine cell
is defined by: LungMap ID: LMMA0000000252

lymphatic_endothelial_cell
type: Class
subclass of: endothelial_cell_of_vascular_tree
subclass of: Restriction
  on property: has part
  some values from: CD34
subclass of: Restriction
  on property: has part
  some values from: endomucin
subclass of: Restriction
  on property: has part
  some values from: lymphatic_vessel_endothelial_hyaluronic_acid_receptor_1
subclass of: Restriction
  on property: has part
  some values from: platelet_endothelial_cell_adhesion_molecule
subclass of: Restriction
  on property: part of
  some values from: lymphatic_endothelium
definition: Definition CL: A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions. [database_cross_reference: PMID:17846148][database_cross_reference: GOC:tfm]
definition: Definition LungMap: A mesenchymal-derived, squamous (flat), endothelial cell that lines the inner (i.e., luminal) surface of lymphatic vessels, forming a continuous, thin, endothelial cell layer or sheath (endothelium).
has synonym: endothelial cell of lymphatic vessel
lungmap preferred label: lymphatic endothelial cell
is defined by: CL: http://purl.obolibrary.org/obo/CL_0002138
is defined by: LungMap ID: Lung Ontology : LMMA0000000216

lymphatic_endothelium
type: Class
subclass of: endothelium
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell
subclass of: Restriction
  on property: has part
  some values from: lymphatic_endothelial_cell

lymphatic_tree
type: Class
subclass of: complex_structure
subclass of: Restriction
  on property: has part
  some values from: lymphatic_endothelium

lymphatic_vessel_endothelial_hyaluronic_acid_receptor_1
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: plasmamembrane
definition: "A protein that is a translation product of the human LYVE1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: CRSBP-1
has synonym: LYVE-1
has synonym: LYVE1
has synonym: Lyve-1
has synonym: cell surface retention sequence-binding protein 1
has synonym: extracellular link domain-containing protein 1
has synonym: hyaluronic acid receptor

macromolecular_complex
type: Class
definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.

macromolecule
type: Class
disjoint with: tissue

monoclonal antibody
type: Class
subclass of: antibody_reagent
subclass of: Restriction
  on property: derived from
  all values from: Class
    intersection of: cell
    intersection of: Restriction
      on property: has number
      cardinality: 1
definition: An antibody reagent produced by clonal hybridoma cells deriving from the fusion of a single activasted B-cell with a neoplastic cell, such that antibodies isolated from such cells are monospecific for a single epitope. A collection of such antibodies has specificity for a single epitopes on its target antigen - versus a collection of 'polyclonal antibodies', which recognize various different epitopes. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies.
imported from: http://purl.obolibrary.org/obo/reo.owl

mouse_embryo_age
type: Class
subclass of: age since fertilization measurement datum
comment: has synonim age since fertilization measurement datum

mouse_embryo_stage
type: Class
subclass of: embryo_stage

mouse_postnatal_age
type: Class
subclass of: age since birth measurement datum

multicellular_anatomical_structure
type: Class
subclass of: anatomical_entity
definition: UBERON: An anatomical structure that has more than one cell as a part. [database_cross_reference: CARO:0010000]

myofibroblast
type: Class
subclass of: fibroblast
subclass of: Restriction
  on property: has part
  some values from: alpha-actin-2
definition: Definition in LungMAP: A stromal cell combining the features of a fibroblast and a smooth muscle cell, such as alpha-smooth-muscle-actin positive, contractile myofilaments
definition: definition CL: A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis. [database_cross_reference: GOC:tfm]
lungmap preferred label: myofibroblast
is defined by: CL ID: http://purl.obolibrary.org/obo/CL_0002241
is defined by: LungMAP ID: LMHA0000000243

nerve_fiber
type: Class
subclass of: complex_structure
subclass of: Restriction
  on property: has part
  some values from: tubulin_alpha-1A_chain
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_16.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_17.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic day 18.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_19.5
subclass of: Restriction
  on property: identifiable at
  some values from: P01
subclass of: Restriction
  on property: identifiable at
  some values from: P02
subclass of: Restriction
  on property: identifiable at
  some values from: P03
subclass of: Restriction
  on property: identifiable at
  some values from: P04
subclass of: Restriction
  on property: identifiable at
  some values from: P05
subclass of: Restriction
  on property: identifiable at
  some values from: P06
subclass of: Restriction
  on property: identifiable at
  some values from: P07
subclass of: Restriction
  on property: identifiable at
  some values from: P08
subclass of: Restriction
  on property: identifiable at
  some values from: P09
subclass of: Restriction
  on property: identifiable at
  some values from: P10
subclass of: Restriction
  on property: identifiable at
  some values from: P11
subclass of: Restriction
  on property: identifiable at
  some values from: P12
subclass of: Restriction
  on property: identifiable at
  some values from: P13
subclass of: Restriction
  on property: identifiable at
  some values from: P14
subclass of: Restriction
  on property: identifiable at
  some values from: P15
subclass of: Restriction
  on property: identifiable at
  some values from: P17
subclass of: Restriction
  on property: identifiable at
  some values from: P18
subclass of: Restriction
  on property: identifiable at
  some values from: P19
subclass of: Restriction
  on property: identifiable at
  some values from: P20
subclass of: Restriction
  on property: identifiable at
  some values from: P21
subclass of: Restriction
  on property: identifiable at
  some values from: P22
subclass of: Restriction
  on property: identifiable at
  some values from: P23
subclass of: Restriction
  on property: identifiable at
  some values from: P24
subclass of: Restriction
  on property: identifiable at
  some values from: P25
subclass of: Restriction
  on property: identifiable at
  some values from: P26
subclass of: Restriction
  on property: identifiable at
  some values from: P27
subclass of: Restriction
  on property: identifiable at
  some values from: P28
subclass of: Restriction
  on property: identifiable at
  some values from: P29
subclass of: Restriction
  on property: identifiable at
  some values from: P30
subclass of: Restriction
  on property: identifiable at
  some values from: P31
subclass of: Restriction
  on property: identifiable at
  some values from: P32
subclass of: Restriction
  on property: identifiable at
  some values from: P33
subclass of: Restriction
  on property: identifiable at
  some values from: P34
subclass of: Restriction
  on property: identifiable at
  some values from: P35
subclass of: Restriction
  on property: identifiable at
  some values from: P36
subclass of: Restriction
  on property: identifiable at
  some values from: PO
subclass of: Restriction
  on property: part of
  some values from: lung
definition: Uberon Definition: A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system. [database_cross_reference: http://en.wikipedia.org/wiki/Nervous_system_fiber]

neuroepithelial_body
type: Class
subclass of: complex_structure
subclass of: Restriction
  on property: has part
  some values from: lung_neuroendocrine_cell
definition: UNBERON: Corpuscular, organoid structures composed of PNECs, found as distinctive innervated clusters only within intrapulmonary airways, where they appear concentrated at airway branch points; NEBs reach from the basement membrane to the airway lumen and are thought to function as oxygen sensors. [database_cross_reference: MP:0010921]
lungmap preferred label: neuroepithelial body
comment: AMM: For me is an anatomical entity e not a cell since is a group of cell
comment: are those really part of the bronchiole epithelium or more general part of the lung epithelium?
is defined by: LungMap ID: LMMA0000000253
is defined by: Uberon ID: http://purl.obolibrary.org/obo/UBERON_0010002

organ
type: Class
subclass of: multicellular_anatomical_structure
disjoint with: tissue

periarterial_connective_tissue
type: Class
subclass of: connective
subclass of: Restriction
  on property: has part
  some values from: intermediate_pneumocyte

pericyte
type: Class
subclass of: cell
subclass of: Restriction
  on property: has part
  some values from: chondroitin_sulfate_proteoglycan_4
definition: Definition CL: An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells. [database_cross_reference: PMID:20024907][database_cross_reference: MESH:D020286][database_cross_reference: PMID:17986482][database_cross_reference: GOC:dsd][database_cross_reference: ISBN:0721662544][database_cross_reference: PMID:16807374][database_cross_reference: GOC:tfm]
definition: Definition LungMAP: Unique slender cells with multiple processes extending along the capillary vessel and encircling the vascular wall to form a net around the vessel. These cells are embedded in the basement membrane shared with the endothelial cells of the vessel. They are are important in maintaining vessel integrity, angiogenesis, and vascular remodeling.
lungmap preferred label: pericyte
is defined by: LungMAP ID: LMMA0000000273

phosphorylated_histone_H3.3C
type: Class
subclass of: histone_H3.3C
comment: AM: the phosphorylated from has been isolated in Human

platelet_endothelial_cell_adhesion_molecule
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: plasmamembrane
has synonym: CD31
has synonym: EndoCAM
has synonym: GPIIA'
has synonym: PECA1
has synonym: PECAM-1
has synonym: Pecam-1
has synonym: Pecam1

policlonal antibody
type: Class
subclass of: antibody_reagent
definition: REO* an antibody reagent that is output from an antibody production process that yields a heterogenous collection of antibodies that are not mono-specific (ie individual antibodies in the collection may recognize different epitopes becasue they arise from more than one clone of B-lymphocyte cells). Polyclonal antibodies are typically manufactured through an antibody production technique in which a host organism is immunized with a specific immunogen and antibodies purified from serum collected following the induced immune response. A collection of such antibodies has specificity for various different epitopes on its target antigen - versus a collection of 'monoclonal antibodies', which all recognize a single epitope. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies.
imported from: http://purl.obolibrary.org/obo/reo.owl

process
type: Class

protein complex
type: Class
subclass of: macromolecular_complex
definition: Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

proximal_acinar_tubule
type: Class
subclass of: complex_structure
subclass of: Restriction
  on property: has part
  some values from: proximal_acinar_tubule_epithelium
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_16.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_17.5
subclass of: Restriction
  on property: part of
  some values from: acinar_tubule
lungmap preferred label: proximal acinar tubule
is defined by: LungMAP ID: LMMA0000000009

proximal_acinar_tubule_epithelial_cell
type: Class
subclass of: epithelial_cell_of_the_lung
subclass of: Class
  complement of: Restriction
    on property: has part
    some values from: transcription_factor_SOX-9
subclass of: Restriction
  on property: has part
  some values from: advanced_glycosylation_end_product-specific_receptor
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: homeodomain-only_protein
definition: Definition LungMAP: A cuboidal epithelial cell that lines the proximal acinar tubule of the peripheral fetal lung in the pseudoglandular stage of lung development (E12.5 - E16.5). These cells express cell-specific proteins (or markers) for pre-type I pneumocytes, such as HOPX.
lungmap preferred label: proximal acinar tubule epithelial cell
comment: no present in CL need to be added
is defined by: lungMAP ID: LMMA0000000573

proximal_acinar_tubule_epithelium
type: Class
subclass of: lung_epithelium
subclass of: Restriction
  on property: has part
  some values from: acinar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: intermediate_pneumocyte
subclass of: Restriction
  on property: has part
  some values from: proximal_acinar_tubule_epithelial_cell
lungmap preferred label: proximal acinar tubule epithelium

pulmonary_artery
type: Class
subclass of: blood_vessel
subclass of: Restriction
  on property: has part
  some values from: artery_endothelium
subclass of: Restriction
  on property: has part
  some values from: endothelium
subclass of: Restriction
  on property: has part
  some values from: vascular_tree_endothelium
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_16.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_17.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic day 18.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_19.5
subclass of: Restriction
  on property: identifiable at
  some values from: P01
subclass of: Restriction
  on property: identifiable at
  some values from: P02
subclass of: Restriction
  on property: identifiable at
  some values from: P03
subclass of: Restriction
  on property: identifiable at
  some values from: P04
subclass of: Restriction
  on property: identifiable at
  some values from: P05
subclass of: Restriction
  on property: identifiable at
  some values from: P06
subclass of: Restriction
  on property: identifiable at
  some values from: P07
subclass of: Restriction
  on property: identifiable at
  some values from: P08
subclass of: Restriction
  on property: identifiable at
  some values from: P09
subclass of: Restriction
  on property: identifiable at
  some values from: P10
subclass of: Restriction
  on property: identifiable at
  some values from: P11
subclass of: Restriction
  on property: identifiable at
  some values from: P12
subclass of: Restriction
  on property: identifiable at
  some values from: P13
subclass of: Restriction
  on property: identifiable at
  some values from: P14
subclass of: Restriction
  on property: identifiable at
  some values from: P15
subclass of: Restriction
  on property: identifiable at
  some values from: P17
subclass of: Restriction
  on property: identifiable at
  some values from: P18
subclass of: Restriction
  on property: identifiable at
  some values from: P19
subclass of: Restriction
  on property: identifiable at
  some values from: P20
subclass of: Restriction
  on property: identifiable at
  some values from: P21
subclass of: Restriction
  on property: identifiable at
  some values from: P22
subclass of: Restriction
  on property: identifiable at
  some values from: P23
subclass of: Restriction
  on property: identifiable at
  some values from: P24
subclass of: Restriction
  on property: identifiable at
  some values from: P25
subclass of: Restriction
  on property: identifiable at
  some values from: P26
subclass of: Restriction
  on property: identifiable at
  some values from: P27
subclass of: Restriction
  on property: identifiable at
  some values from: P28
subclass of: Restriction
  on property: identifiable at
  some values from: P29
subclass of: Restriction
  on property: identifiable at
  some values from: P30
subclass of: Restriction
  on property: identifiable at
  some values from: P31
subclass of: Restriction
  on property: identifiable at
  some values from: P32
subclass of: Restriction
  on property: identifiable at
  some values from: P33
subclass of: Restriction
  on property: identifiable at
  some values from: P34
subclass of: Restriction
  on property: identifiable at
  some values from: P35
subclass of: Restriction
  on property: identifiable at
  some values from: P36
subclass of: Restriction
  on property: identifiable at
  some values from: PO
subclass of: Restriction
  on property: part of
  some values from: lung
subclass of: Restriction
  on property: surrounded by
  some values from: vascular smooth muscle tissue
lungmap preferred label: pulmonary artery
comment: additional information that can be imported from uberon: develops_from some pharyngeal arch artery 6 great vessel of heart develops_from some outflow tract pulmonary component continuous_with some pulmonary trunk develops_from some truncus arteriosus artery
is defined by: LungMAP ID: LMMA0000000291

pulmonary_lymphatic_endothelial_cell
type: Class
subclass of: lymphatic_endothelial_cell
subclass of: Restriction
  on property: has part
  some values from: CD34
subclass of: Restriction
  on property: has part
  some values from: endomucin
subclass of: Restriction
  on property: has part
  some values from: lymphatic_vessel_endothelial_hyaluronic_acid_receptor_1
subclass of: Restriction
  on property: has part
  some values from: platelet_endothelial_cell_adhesion_molecule
subclass of: Restriction
  on property: part of
  some values from: pulmonary_lymphatic_endothelium
lungmap preferred label: pulmonary lymphatic endothelial cell

pulmonary_lymphatic_endothelium
type: Class
subclass of: lymphatic_endothelium
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell
subclass of: Restriction
  on property: has part
  some values from: lymphatic_endothelial_cell
subclass of: Restriction
  on property: has part
  some values from: pulmonary_lymphatic_endothelial_cell
lungmap preferred label: pulmonary lymphatic endothelium
comment: AMM : not present in UBERON need to be added and could be a child of http://purl.obolibrary.org/obo/UBERON_0003529
is defined by: Lungmap ID: LMMA0000000446

pulmonary_lymphatic_vessel
type: Class
subclass of: complex_structure
subclass of: Restriction
  on property: has part
  some values from: pulmonary_lymphatic_endothelium
definition: A lymphatic vessel that is part of a lung.
lungmap preferred label: pulmonary lymphatic vessel
comment: additional information that can be imported from uberon: lymphatic vessel and (part of some lung) endoderm-derived structure part of some pulmonary part of lymphatic system respiratory system lymphatic vessel pulmonary part of lymphatic system subClassOf : has part some pulmonary lymphatic vessel
is defined by: LungMAP ID: LMMA0000000447

pulmonary_surfactant-associated_protein_C
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: cytoplasm
subclass of: Restriction
  on property: localizes to
  some values from: extracellular space
cytoscape view in PRO: http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php
definition: "A protein that is a translation product of the human SFTPC gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: Bricd6
has synonym: Pro SP-C
has synonym: SFTPC
has synonym: SP-C
has synonym: SP5
has synonym: SPC
has synonym: Sftp-2
has synonym: Sftp2
has synonym: Sftpc
has synonym: pro-SpC
has synonym: proSpC
has synonym: pulmonary surfactant-associated proteolipid SPL(Val)

pulmonary_vein
type: Class
subclass of: blood_vessel
subclass of: Restriction
  on property: has part
  some values from: endothelium
subclass of: Restriction
  on property: has part
  some values from: vascular_tree_endothelium
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_16.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_17.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic day 18.5
subclass of: Restriction
  on property: identifiable at
  some values from: Embryonic_day_19.5
subclass of: Restriction
  on property: identifiable at
  some values from: P01
subclass of: Restriction
  on property: identifiable at
  some values from: P02
subclass of: Restriction
  on property: identifiable at
  some values from: P03
subclass of: Restriction
  on property: identifiable at
  some values from: P04
subclass of: Restriction
  on property: identifiable at
  some values from: P05
subclass of: Restriction
  on property: identifiable at
  some values from: P06
subclass of: Restriction
  on property: identifiable at
  some values from: P07
subclass of: Restriction
  on property: identifiable at
  some values from: P08
subclass of: Restriction
  on property: identifiable at
  some values from: P09
subclass of: Restriction
  on property: identifiable at
  some values from: P10
subclass of: Restriction
  on property: identifiable at
  some values from: P11
subclass of: Restriction
  on property: identifiable at
  some values from: P12
subclass of: Restriction
  on property: identifiable at
  some values from: P13
subclass of: Restriction
  on property: identifiable at
  some values from: P14
subclass of: Restriction
  on property: identifiable at
  some values from: P15
subclass of: Restriction
  on property: identifiable at
  some values from: P17
subclass of: Restriction
  on property: identifiable at
  some values from: P18
subclass of: Restriction
  on property: identifiable at
  some values from: P19
subclass of: Restriction
  on property: identifiable at
  some values from: P20
subclass of: Restriction
  on property: identifiable at
  some values from: P21
subclass of: Restriction
  on property: identifiable at
  some values from: P22
subclass of: Restriction
  on property: identifiable at
  some values from: P23
subclass of: Restriction
  on property: identifiable at
  some values from: P24
subclass of: Restriction
  on property: identifiable at
  some values from: P25
subclass of: Restriction
  on property: identifiable at
  some values from: P26
subclass of: Restriction
  on property: identifiable at
  some values from: P27
subclass of: Restriction
  on property: identifiable at
  some values from: P28
subclass of: Restriction
  on property: identifiable at
  some values from: P29
subclass of: Restriction
  on property: identifiable at
  some values from: P30
subclass of: Restriction
  on property: identifiable at
  some values from: P31
subclass of: Restriction
  on property: identifiable at
  some values from: P32
subclass of: Restriction
  on property: identifiable at
  some values from: P33
subclass of: Restriction
  on property: identifiable at
  some values from: P34
subclass of: Restriction
  on property: identifiable at
  some values from: P35
subclass of: Restriction
  on property: identifiable at
  some values from: P36
subclass of: Restriction
  on property: identifiable at
  some values from: PO
subclass of: Restriction
  on property: part of
  some values from: lung
subclass of: Restriction
  on property: surrounded by
  some values from: vascular smooth muscle tissue
definition: Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO
lungmap preferred label: pulmonary vein
comment: additional information that can be imported from uberon: vein great vessel of heart part of some pulmonary vascular system develops_from some truncus arteriosus left pulmonary vein equivalentClass : pulmonary vein and ( drains some left lung) pulmonary myocardium subClassOf : part of some pulmonary vein pulmonary vascular system subClassOf : has part some pulmonary vein right pulmonary vein equivalentClass : pulmonary vein and ( drains some right lung)
is defined by: LungMAP ID: LMMA0000000305

respiratory_bronchiole
type: Class
subclass of: bronchiole
subclass of: Restriction
  on property: has part
  some values from: bronchiolar_connective_tissue
subclass of: Restriction
  on property: has part
  some values from: epithelium_of_bronchiole
subclass of: Restriction
  on property: has part
  some values from: epithelium_of_respiratory_bronchiole
subclass of: Restriction
  on property: proximally connected to
  some values from: terminal_bronchiole
definition: UBERON Definition: A bronchiole that is the first segment of the respiratory zone. [database_cross_reference: http://en.wikipedia.org/wiki/Respiratory_bronchiole][database_cross_reference: ISBN10:0123813611]

smooth_muscle_cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: has part
  some values from: alpha-actin-2
definition: LungMap: A non-striated, elongated, spindle-shaped, involuntary contractile cell found in internal organs and blood vessels. Smooth muscle cells are found in the walls of the conducting airways (trachea, bronchi, bronchioles) and of the pulmonary and bronchial blood vessels (vascular smooth muscle).
lungmap preferred label: smooth muscle cell
is defined by: CL ID: http://purl.obolibrary.org/obo/CL_0000192
is defined by: LungMap ID: LMMA0000000343

smooth_muscle_tissue_of_bronchiole
type: Class
subclass of: smooth muscle tissue
subclass of: Restriction
  on property: has part
  some values from: smooth_muscle_cell
definition: UBERON definition: A portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition]. [database_cross_reference: OBOL:automatic]

subendothelial_connective_tissue
type: Class
subclass of: connective
subclass of: Restriction
  on property: has part
  some values from: pericyte
lungmap preferred label: subendothelial connective tissue
comment: AMM: not found in LungMAP need to added
comment: AMM: not present in UBEROn need to added

terminal_bronchiole
type: Class
subclass of: bronchiole
subclass of: Restriction
  on property: has part
  some values from: bronchiolar_connective_tissue
subclass of: Restriction
  on property: has part
  some values from: epithelium_of_bronchiole
subclass of: Restriction
  on property: has part
  some values from: terminal_bronchiole_epithelium
subclass of: Restriction
  on property: proximally connected to
  some values from: respiratory_bronchiole
is defined by: UBERON: http://purl.obolibrary.org/obo/UBERON_0002187 LungMap: LMMA0000000359

terminal_bronchiole_epithelium
type: Class
subclass of: epithelium_of_bronchiole
subclass of: Restriction
  on property: has part
  some values from: bronchiolar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: bronchiole_proliferative_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: epithelial_cell_of_the_lung
subclass of: Restriction
  on property: has part
  some values from: neuroepithelial_body
definition: UBERON: An epithelium that lines a terminal bronchiole. [database_cross_reference: http://orcid.org/0000-0002-6601-2165]
lungmap preferred label: terminal bronchiole epithelium
is defined by: UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001958

tissue
type: Class
subclass of: multicellular_anatomical_structure
definition: UBERON: 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. [database_cross_reference: CARO:0000043]
is defined by: Uberon ID: http://purl.obolibrary.org/obo/UBERON_0000479

transcription_factor_SOX-2
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: nucleus
cytoscape view in PRO: http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php
PRO hierarchy: http://pir.georgetown.edu/cgi-bin/pro/browser_pro
definition: "A protein that is a translation product of the human SOX2 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: SOCX2
has synonym: Sox2
has synonym: sox2

transcription_factor_SOX-9
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: nucleus
cytoscape view in PRO: http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php
PRO hierarchy: http://pir.georgetown.edu/cgi-bin/pro/browser_pro
definition: "A protein that is a translation product of the human SOX9 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: SOX9
has synonym: Sox9

tubulin_alpha-1A_chain
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: cytoplasm
cytoscape view in PRO: http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php
PRO hierarchy: http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php
definition: "A tubulin that is a translation product of the human TUBA1A gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: TUBA1A
has synonym: Tuba-1
has synonym: Tuba1
has synonym: alpha-tubulin 3
has synonym: alpha-tubulin isotype M-alpha-1
has synonym: tubulin B-alpha-1

tubulin alpha 1A chain acetylated
type: Class
subclass of: tubulin_alpha-1A_chain
subclass of: Restriction
  on property: is a specific output
  some values from: acetylation
has synonym: Acetylated Tubulin
is defined by: AMM new term

unclassified_epithelial_cell
type: Class
subclass of: bronchiolar_epithelial_cell
subclass of: Restriction
  on property: has part
  some values from: ADP-ribosylation factor-like protein 13B
subclass of: Restriction
  on property: has part
  some values from: homeobox_protein_Nkx-2.1
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-2
definition: Definition LungMap: This term is used to describe an epithelial cell that cannot be classified under an existing epithelial cell type.
lungmap preferred label: unclassified epithelial cell
comment: not present in CL need to be added
is defined by: LungMAp ID: LMMA0000000384

unclassified_fibroblast
type: Class
subclass of: fibroblast
subclass of: Restriction
  on property: has part
  some values from: transcription_factor_SOX-9
definition: Definition LungMAP: This term is used to describe a fibroblast that cannot be classified under an existing fibroblast cell type.
lungmap preferred label: unclassified fibroblast
comment: AMM: not present in CL need to be added
is defined by: LungMAP ID: LMMA0000000386

uteroglobin
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: cytoplasm
subclass of: Restriction
  on property: localizes to
  some values from: extracellular space
definition: A protein that is a translation product of the human SCGB1A1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: CC10
has synonym: CC16
has synonym: CCPBP
has synonym: CCSP
has synonym: PCB-BP
has synonym: PCB-binding protein
has synonym: PCBBP
has synonym: SCGB1A1
has synonym: UG
has synonym: UGB
has synonym: UP-1
has synonym: UP1
has synonym: Utg
has synonym: clara cell 17 kDa protein
has synonym: clara cell phospholipid-binding protein
has synonym: clara cells 10 kDa secretory protein
has synonym: secretoglobin family 1A member 1
has synonym: urinary protein 1
has synonym: urine protein 1

vascular_associated_smooth_muscle_cell
type: Class
subclass of: smooth_muscle_cell
subclass of: Restriction
  on property: has part
  some values from: alpha-actin-2
definition: CL : A smooth muscle cell assocatiated with the vasculature. [database_cross_reference: GOC:dsd][database_cross_reference: GOC:tfm]
lungmap preferred label: vascular associated smooth muscle cell
is defined by: CL ID: http://purl.obolibrary.org/obo/CL_0000359
is defined by: LungMap ID: LMMA0000000393

vascular_tree
type: Class
subclass of: complex_structure
definition: Hollow tree, the organ parts of which are arteries, veins or lymphatic vessels. Examples: systemic arterial tree (organ), portal venous tree (organ), thoracic duct tree.

vascular_tree_endothelium
type: Class
subclass of: endothelium
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell
subclass of: Restriction
  on property: has part
  some values from: endothelial_cell_of_vascular_tree
lungmap preferred label: vascular tree endothelium

vimentin
type: Class
subclass of: Protein
subclass of: Restriction
  on property: localizes to
  some values from: cytoplasm
subclass of: Restriction
  on property: localizes to
  some values from: plasmamembrane
cytoscape view in PRO: http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php
PRO hierarchy: http://pir.georgetown.edu/cgi-bin/pro/browser_pro
definition: "A protein that is a translation product of the human VIM gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
has synonym: VIM
has synonym: Vimentin

mouse_rat RAGE antibody
type: Class
subclass of: monoclonal rat IgG2a
subclass of: Restriction
  on property: recognizes
  some values from: advanced_glycosylation_end_product-specific_receptor
has synonym: Mouse/Rat RAGE Antibody
has synonym: anti ager

anti-actin, α-smooth muscle antibody
type: Class
subclass of: mouse IgG2a antibody
subclass of: Restriction
  on property: recognizes
  some values from: alpha-actin-2
has synonym: anti acta2

embryonic day 18.5
type: NamedIndividual
type: mouse_embryo_age
definition: 18.5 days after fertilization
term editor: Person: Chris Stoeckert, Jie Zheng