x adjacent to y if and only if x and y share a boundary.
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
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 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
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 a process and a continuant, in which the continuant is somehow involved in the process
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 two independent continuants, the target and the location, in which the target is entirely within the location
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
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'.
a relation between a continuant and a process, in which the continuant is somehow involved in the process
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
hematopoietic progenitor cell antigen CD34
2-(4-(aminoiminomethyl)phenyl)-1H-indole-6-carboximidamide, 4',6-diamidino-2-phenylindole, 4',6-diamidinophenyl-indole
has been used for mouse but on the Sigma datasheet it says recognze human rat and canine
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?
lung developmental stage: late pseudoglandular
lung developmental stage: early saccular
lung developmental stage at age P28: mature alveoli
lung developmental stage at age P7: alveolar
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.
proposed definition AMM: An epithelial cell of the lung acinus.
acinar tubule proliferative epithelial cell
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
Receptor for advanced glycosylation end products
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.
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.
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.
is an in house antibody CCHMC In House: BL3/10/05
is an antibody produced in house CCHMC In House: BL 10/7/11
Baylor College of Medicine in-house probe
is an in house antibody CCHMC In House: BL 5/7/09
is an in house antibody CCHMC In House: BL 1/27/11
Antibody reagent that recognizes a single epitope.
ADP-ribosylation factor-like protein 2-like 1
ADP-ribosylation factor-like protein 13B
UBERON: An endothelium that is part of an arteriole [Automatically generated definition]. [database_cross_reference: OBOL:automatic]
UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001916
UBERON: An endothelium that is part of an artery [Automatically generated definition]. [database_cross_reference: OBOL:automatic]
UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001917
UBERON definition: A vessel through which blood circulates in the body.
UBERON http://purl.obolibrary.org/obo/UBERON_0001981
bronchiolar associated smooth muscle cell
AMM: No present in UBERON need to be added
Definition CL: An epithelial cell of the bronchus. [database_cross_reference: GOC:tfm]
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.
needs to be check if CL and LungMap are refering to the same term
CL ID: http://purl.obolibrary.org/obo/CL_0002328
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
bronchiole proliferative epithelial cell
def: "A protein that is a translation product of the human CSPG4 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
melanoma chondroitin sulfate proteoglycan
melanoma-associated chondroitin sulfate proteoglycan
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.
UBERON: A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. [database_cross_reference: OBOL:automatic]
UBERON ID: http://purl.obolibrary.org/obo/UBERON_0003570
Definition LungMAP: acinar bud, distal acinar bud, distal acinar tubule, peripheral acinar tubule bud, peripheral acinar tubule sprout.
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).
"A protein that is a translation product of the human EMCN gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
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 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).
CL : http://purl.obolibrary.org/obo/CL_0000115
Definition CL: A blood vessel endothelial cell that is part of an arterial endothelium. [database_cross_reference: GOC:tfm]
CL ID: http://purl.obolibrary.org/obo/CL_1001568
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]
comment in CL: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive.
Definition: An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. LMMA0000000392
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]
UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001986
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 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
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.
CL ID: http://purl.obolibrary.org/obo/CL_0000082
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]
UBERON ID: http://purl.obolibrary.org/obo/UBERON_0000483
Uberon def: An epithelium that is part of a bronchiole [Automatically generated definition].
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
UBERON ID: http://purl.obolibrary.org/obo/UBERON_0002051
definition CL: A fibroblast that is part of lung. [database_cross_reference: GOC:tfm]
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.
CL ID: http://purl.obolibrary.org/obo/CL_0002553
http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php?id=PR:000029067??? https://proconsortium.org/app/visual/cytoscape/pro/PR%3A000029532
histone H3 only when phosphorylated at Ser10 human
http://purl.obolibrary.org/obo/PR_000029067??? http://purl.obolibrary.org/obo/PR_000029532
"A protein that is a translation product of the human NKX2-1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
"A protein that is a translation product of the human HOPX gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
not expressed in choriocarcinoma protein 1
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.
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.
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.
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.
Definition: A generically dependent continuant that is about some thing
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 definition: A mesenchymal-derived, connective tissue cell located in the interstitial space (i.e., interstitium or connective tissue compartments) of the lung.
UBERON: Connective tissue between the cellular elements of a structure. [database_cross_reference: http://medical-dictionary.thefreedictionary.com/tissue]
UBERON ID: http://purl.obolibrary.org/obo/UBERON_0005169
Definition Uberon: Respiration organ that develops as an oupocketing of the esophagus. [database_cross_reference: http://orcid.org/0000-0002-6601-2165]
UBERON: The epithelial layer of the lung. [database_cross_reference: MP:0006382]
UBERON ID: http://purl.obolibrary.org/obo/UBERON_0000115
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 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.
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 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).
CL: http://purl.obolibrary.org/obo/CL_0002138
LungMap ID: Lung Ontology : LMMA0000000216
"A protein that is a translation product of the human LYVE1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
cell surface retention sequence-binding protein 1
extracellular link domain-containing protein 1
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
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.
has synonim age since fertilization measurement datum
UBERON: An anatomical structure that has more than one cell as a part. [database_cross_reference: CARO:0010000]
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 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]
CL ID: http://purl.obolibrary.org/obo/CL_0002241
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]
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]
AMM: For me is an anatomical entity e not a cell since is a group of cell
are those really part of the bronchiole epithelium or more general part of the lung epithelium?
Uberon ID: http://purl.obolibrary.org/obo/UBERON_0010002
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 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.
AM: the phosphorylated from has been isolated in Human
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.
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.
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.
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
AMM : not present in UBERON need to be added and could be a child of http://purl.obolibrary.org/obo/UBERON_0003529
A lymphatic vessel that is part of a lung.
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
"A protein that is a translation product of the human SFTPC gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
pulmonary surfactant-associated proteolipid SPL(Val)
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO
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)
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]
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).
CL ID: http://purl.obolibrary.org/obo/CL_0000192
UBERON definition: A portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition]. [database_cross_reference: OBOL:automatic]
AMM: not present in UBEROn need to added
UBERON: http://purl.obolibrary.org/obo/UBERON_0002187 LungMap: LMMA0000000359
UBERON: An epithelium that lines a terminal bronchiole. [database_cross_reference: http://orcid.org/0000-0002-6601-2165]
UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001958
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]
Uberon ID: http://purl.obolibrary.org/obo/UBERON_0000479
"A protein that is a translation product of the human SOX2 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
"A protein that is a translation product of the human SOX9 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
"A tubulin that is a translation product of the human TUBA1A gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
Definition LungMap: This term is used to describe an epithelial cell that cannot be classified under an existing epithelial cell type.
Definition LungMAP: This term is used to describe a fibroblast that cannot be classified under an existing fibroblast cell type.
A protein that is a translation product of the human SCGB1A1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.
CL : A smooth muscle cell assocatiated with the vasculature. [database_cross_reference: GOC:dsd][database_cross_reference: GOC:tfm]
CL ID: http://purl.obolibrary.org/obo/CL_0000359
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.
"A protein that is a translation product of the human VIM gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene.