x adjacent to y if and only if x and y share a boundary. Chris Mungall 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. http://www.obofoundry.org/ro/#OBO_REL:has_participant 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 http://www.obofoundry.org/ro/#OBO_REL:located_in http://purl.obolibrary.org/obo/RO_0001901 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'. http://purl.obolibrary.org/obo/RO_0001901 http://www.obofoundry.org/ro/#OBO_REL:part_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 Chris Mungall inverse of surrounded by Chris Mungall 1810036E22Rik ABC-C ABCA3 ABCC Abc3 Abca3 http://purl.obolibrary.org/obo/PR_000003541 ATP-binding_cassette_sub-family_A_member_3 http://antibodyregistry.org/search?q=AB5535 http://www.emdmillipore.com/US/en/product/Anti-Sox9-Antibody,MM_NF-AB5535 CA CALCA CGRP-1 CGRP1 Calc Calc1 Cgrp Ct Ctn http://purl.obolibrary.org/obo/PR_000027223 calcitonin http://research.bioinformatics.udel.edu/pro/visual/cytoscape/pro/PR%3AQ64314 AU040960 CD34 antigen hematopoietic progenitor cell antigen CD34 http://purl.obolibrary.org/obo/PR_000001003 CD34 2-(4-(aminoiminomethyl)phenyl)-1H-indole-6-carboximidamide, 4',6-diamidino-2-phenylindole, 4',6-diamidinophenyl-indole CHEBI:51231 DAPI https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51231 Embryonic_day_17.5 Embryonic_day_19.5 has been used for mouse but on the Sigma datasheet it says recognze human rat and canine http://antibodyregistry.org/search.php?q=AB_259000 http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Datasheet/3/c7113dat.pdf P01 P02 P03 P04 P05 P06 P07 P08 P09 P10 P11 P12 P13 P14 P15 P17 P18 P19 P20 P21 P22 P23 P24 P25 P26 P27 P28 P29 P30 P31 P32 P33 P34 P35 P36 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? http://purl.obolibrary.org/obo/CHEBI_36080 Protein lung developmental stage: late pseudoglandular http://purl.obolibrary.org/obo/MmusDv_0000033 Theiler_stage_24 lung developmental stage: early saccular http://purl.obolibrary.org/obo/MmusDv_0000035 Theiler_stage_26 http://purl.obolibrary.org/obo/MmusDv_0000036 Theiler_stage_27 lung developmental stage at age P28: mature alveoli lung developmental stage at age P7: alveolar http://purl.obolibrary.org/obo/MmusDv_0000037 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 epithelial cell no present in CL need to be added LMMA0000000052 acinar_epithelial_cell acinar tubule LungMAP ID: LMMA0000000001 acinar_tubule acinar tubule epithelium LungMap ID: LMMA0000000053 acinar_tubule_epithelium 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 No present in CL need to be added LungMAP ID: LMMA0000000599 acinar_tubule_proliferative_epithelial_cell AGER RAGE Receptor for advanced glycosylation end products http://purl.obolibrary.org/obo/PR_000003828 advanced_glycosylation_end_product-specific_receptor 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. http://purl.obolibrary.org/obo/OBI_0001169 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. http://purl.obolibrary.org/obo/OBI_0001168 ACTA2 Acta2 a-SMA actin actin, aortic smooth muscle alpha 2 alpha-smooth muscle actin aorta smooth muscle α Smooth muscle, actin α-Smooth Muscle Actin http://www.uniprot.org/uniprot/P62737 http://purl.obolibrary.org/obo/PR_P62737 alpha-actin-2 anatomical_entity 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. http://purl.obolibrary.org/obo/GO_0048856 http://antibodyregistry.org/search?q=AB5320 http://www.emdmillipore.com/US/en/product/,MM_NF-AB5320?isCountryEMD=yes 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 http://antibodyregistry.org/search?q=sc-6260 https://www.scbt.com/scbt/product/vimentin-antibody-v9 Antibody reagent that recognizes a single epitope. http://purl.obolibrary.org/obo/REO_0000002 antibody_reagent A530097K21Rik A930014M17Rik ADP-ribosylation factor-like protein 2-like 1 ARL13B ARL2-like protein 1 Arl13B Arl2l1 C530009C10Rik hnn http://purl.obolibrary.org/obo/PR_Q640N2 ADP-ribosylation factor-like protein 13B UBERON: An endothelium that is part of an arteriole [Automatically generated definition]. [database_cross_reference: OBOL:automatic] arteriole endothelium LMMA0000000078 UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001916 arteriole_endothelium UBERON: An endothelium that is part of an artery [Automatically generated definition]. [database_cross_reference: OBOL:automatic] artery endothelium LungMap ID: LMMA0000000078 UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001917 artery_endothelium UBERON definition: A vessel through which blood circulates in the body. blood_vessel UBERON http://purl.obolibrary.org/obo/UBERON_0001981 blood_vessel bronchial artery endothelium bronchial_artery_endothelium bronchiolar associated smooth muscle cell bronchiolar_associated_smooth_muscle_cell bronchiolar connective AMM: No present in UBERON need to be added LungMAp ID: LMMA0000000525 bronchiolar_connective_tissue 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. bronchiolar epithelial cell needs to be check if CL and LungMap are refering to the same term CL ID: http://purl.obolibrary.org/obo/CL_0002328 LungMAP ID: LMMA0000000582 bronchiolar_epithelial_cell 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 LMMA0000000118 http://purl.obolibrary.org/obo/UBERON_0002186 bronchiole bronchiole proliferative epithelial cell no present in CL need to be added LungMap ID: LMMA0000000599 bronchiole_proliferative_epithelial_cell cell cellular_proliferation def: "A protein that is a translation product of the human CSPG4 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. 4732461B14Rik AN2 CSPG4 NG2 chondroitin sulfate proteoglycan NG2 melanoma chondroitin sulfate proteoglycan melanoma-associated chondroitin sulfate proteoglycan proteoglycan AN2 http://purl.obolibrary.org/obo/PR_000005953 chondroitin_sulfate_proteoglycan_4 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. ciliated cell precursor LungMap ID: LMMA0000000476 ciliated_cell_precursor Anna Maria Masci and Scott White complex_structure UBERON: A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. [database_cross_reference: OBOL:automatic] connective LungMap ID: LMMA0000000147 UBERON ID: http://purl.obolibrary.org/obo/UBERON_0003570 connective http://amigo.geneontology.org/amigo/term/GO:0005737 Definition LungMAP: acinar bud, distal acinar bud, distal acinar tubule, peripheral acinar tubule bud, peripheral acinar tubule sprout. distal acinar tubule bud LungMAP ID: LMMA0000000003 distal_acinar_tubule_bud 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). distal acinar tubule epithelial cell no present in Cl need to be added LungMAP ID: LMMA0000000572 distal_acinar_tubule_epithelial_cell distal acinar tubule epithelium LMMA0000000423 distal_acinar_tubule_epithelium http://purl.obolibrary.org/obo/UBERON_0000068 embryo_stage "A protein that is a translation product of the human EMCN gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. 0610012K22Rik AI315669 EMCN Endomucin (Emcn) MUC-14 Muc14 emnc endomucin-1/2 endomucin-2 gastric cancer antigen Ga34 mucin-14 http://purl.obolibrary.org/obo/PR_000007049 endomucin 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). endothelial cell CL : http://purl.obolibrary.org/obo/CL_0000115 LungMAP ID: LMMA0000000343 endothelial_cell Definition CL: A blood vessel endothelial cell that is part of an arterial endothelium. [database_cross_reference: GOC:tfm] endothelial cell of vascular tree CL ID: http://purl.obolibrary.org/obo/CL_1001568 LungMap ID: LMMA0000000616 endothelial_cell_of_artery 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] endothelial cell of vascular tree 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 http://purl.obolibrary.org/obo/CL_0002139 endothelial_cell_of_vascular_tree 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] endothelium LungMap ID: LMMA0000000162 UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001986 endothelium 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 epithelial cell LungMap ID: LMMA0000000164 http://purl.obolibrary.org/obo/CL_0000066 epithelial_cell 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. epithelial cell of the lung CL ID: http://purl.obolibrary.org/obo/CL_0000082 LungMAP ID: LMMA0000000164 epithelial_cell_of_the_lung 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] epithelium UBERON ID: http://purl.obolibrary.org/obo/UBERON_0000483 epithelium Uberon def: An epithelium that is part of a bronchiole [Automatically generated definition]. epithelium of bronchiole 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 LungMap ID: LMMA0000000115 UBERON ID: http://purl.obolibrary.org/obo/UBERON_0002051 epithelium_of_bronchiole epithelium of respiratory bronchiole epithelium_of_respiratory_bronchiole http://amigo.geneontology.org/amigo/term/GO:0005615 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. fibroblast CL ID: http://purl.obolibrary.org/obo/CL_0002553 LungMAP ID: LMMA0000000169 fibroblast 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 H3.5 p-Histone H3 pHisH3 histone H3 only when phosphorylated at Ser10 human http://purl.obolibrary.org/obo/PR_000029067??? http://purl.obolibrary.org/obo/PR_000029532 histone_H3.3C http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php?id=PR:000011241 "A protein that is a translation product of the human NKX2-1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. BCH BHC NK-2 NK2 NKX2.1 NKX21 NKX2A NMTC1 Nkx-2.1 Nkx2-1 T/EBP TEBP TITF1 TTF-1 TTF1 homeobox protein NK-2 homolog A thyroid nuclear factor 1 http://purl.obolibrary.org/obo/PR_000011241 homeobox_protein_Nkx-2.1 "A protein that is a translation product of the human HOPX gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. HOP Homeobox HOPX Hopx Odd homeobox protein 1 homeobox-only protein lung cancer-associated Y protein not expressed in choriocarcinoma protein 1 http://purl.obolibrary.org/obo/PR_000008685 homeodomain-only_protein human_embryo_stage 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. immature club cell no present in CL need to be added LungMap ID: LMMA0000000184 immature_club_cell 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. immature type II pneumocyte AMM: not present in CL need to be added 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 LungMAP ID: LMMA0000000382 immature_type_II_pneumocyte 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. immature AT1, pre-type I pneumocyte immature type I pneumocyte AMM: not present in CL need to be added 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 LungMAP ID: LMMA0000000380 immature_type_I_pneumocyte 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. http://purl.obolibrary.org/obo/GO_0019814 Definition: A generically dependent continuant that is about some thing http://purl.obolibrary.org/obo/IAO_0000030 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). intermediate pneumocyte AMM: not present in CL need to be added LungMAP ID: LMMA0000000187 intermediate_pneumocyte LungMap definition: A mesenchymal-derived, connective tissue cell located in the interstitial space (i.e., interstitium or connective tissue compartments) of the lung. not present in CL too generic LungMap ID: LMHA0000000192 interstitial_cell UBERON: Connective tissue between the cellular elements of a structure. [database_cross_reference: http://medical-dictionary.thefreedictionary.com/tissue] interstitial tissue UBERON ID: http://purl.obolibrary.org/obo/UBERON_0005169 interstitial_tissue http://purl.obolibrary.org/obo/UBERON_0000105 life_cycle_stage Definition Uberon: Respiration organ that develops as an oupocketing of the esophagus. [database_cross_reference: http://orcid.org/0000-0002-6601-2165] lung LungMap ID: LMMA0000000211 http://purl.obolibrary.org/obo/UBERON_0002048 lung UBERON: The epithelial layer of the lung. [database_cross_reference: MP:0006382] lung epithelium LungMap ID: LMMA0000000166 UBERON ID: http://purl.obolibrary.org/obo/UBERON_0000115 lung_epithelium 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. lung neuroendocrine cell LungMap ID: LMMA0000000252 http://purl.obolibrary.org/obo/CL_1000223 lung_neuroendocrine_cell 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). endothelial cell of lymphatic vessel lymphatic endothelial cell CL: http://purl.obolibrary.org/obo/CL_0002138 LungMap ID: Lung Ontology : LMMA0000000216 lymphatic_endothelial_cell lymphatic_endothelium lymphatic_tree "A protein that is a translation product of the human LYVE1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. CRSBP-1 LYVE-1 LYVE1 Lyve-1 cell surface retention sequence-binding protein 1 extracellular link domain-containing protein 1 hyaluronic acid receptor http://purl.obolibrary.org/obo/PR_000010012 lymphatic_vessel_endothelial_hyaluronic_acid_receptor_1 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. http://purl.obolibrary.org/obo/GO_0032991 macromolecular_complex macromolecule http://purl.obolibrary.org/obo/IAO_0000109 http://antibodyregistry.org/search.php?q=AB_609894 http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Datasheet/8/t7451dat.pdf 1 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. http://purl.obolibrary.org/obo/reo.owl http://purl.obolibrary.org/obo/REO_0000501 has synonim age since fertilization measurement datum http://purl.obolibrary.org/obo/OBI_0001168 mouse_embryo_age http://purl.obolibrary.org/obo/MmusDv_0000002 mouse_embryo_stage http://antibodyregistry.org/search?q=AF4666 https://www.rndsystems.com/products/mouse-endomucin-antibody_af4666 mouse_postnatal_age UBERON: An anatomical structure that has more than one cell as a part. [database_cross_reference: CARO:0010000] http://purl.obolibrary.org/obo/UBERON_0010000 multicellular_anatomical_structure 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] myofibroblast CL ID: http://purl.obolibrary.org/obo/CL_0002241 LungMAP ID: LMHA0000000243 myofibroblast 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] http://purl.obolibrary.org/obo/UBERON_0006134 nerve_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] neuroepithelial body 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? LungMap ID: LMMA0000000253 Uberon ID: http://purl.obolibrary.org/obo/UBERON_0010002 neuroepithelial_body http://amigo.geneontology.org/amigo/term/GO:0005634 organ periarterial_connective_tissue 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. pericyte LungMAP ID: LMMA0000000273 http://purl.obolibrary.org/obo/CL_0000669 pericyte AM: the phosphorylated from has been isolated in Human http://purl.obolibrary.org/obo/PR_000045314 phosphorylated_histone_H3.3C http://amigo.geneontology.org/amigo/term/GO:0005886 CD31 EndoCAM GPIIA' PECA1 PECAM-1 Pecam-1 Pecam1 http://purl.obolibrary.org/obo/PR_000001904 platelet_endothelial_cell_adhesion_molecule 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. http://purl.obolibrary.org/obo/reo.owl http://purl.obolibrary.org/obo/REO_0000502 process 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. http://purl.obolibrary.org/obo/GO_0043234 proximal acinar tubule LungMAP ID: LMMA0000000009 proximal_acinar_tubule 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. proximal acinar tubule epithelial cell no present in CL need to be added lungMAP ID: LMMA0000000573 proximal_acinar_tubule_epithelial_cell proximal acinar tubule epithelium LMMA0000000284 proximal_acinar_tubule_epithelium pulmonary artery 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 LungMAP ID: LMMA0000000291 http://purl.obolibrary.org/obo/UBERON_0002012 pulmonary_artery pulmonary lymphatic endothelial cell pulmonary_lymphatic_endothelial_cell pulmonary lymphatic endothelium AMM : not present in UBERON need to be added and could be a child of http://purl.obolibrary.org/obo/UBERON_0003529 Lungmap ID: LMMA0000000446 pulmonary_lymphatic_endothelium A lymphatic vessel that is part of a lung. pulmonary lymphatic vessel 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 LungMAP ID: LMMA0000000447 http://purl.obolibrary.org/obo/UBERON_0018227 pulmonary_lymphatic_vessel http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php?id=PR:000014774 "A protein that is a translation product of the human SFTPC gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Bricd6 Pro SP-C SFTPC SP-C SP5 SPC Sftp-2 Sftp2 Sftpc pro-SpC proSpC pulmonary surfactant-associated proteolipid SPL(Val) http://purl.obolibrary.org/obo/PR_000014774 pulmonary_surfactant-associated_protein_C Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO pulmonary vein 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) LungMAP ID: LMMA0000000305 http://purl.obolibrary.org/obo/UBERON_0002016 pulmonary_vein 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] http://purl.obolibrary.org/obo/UBERON_0002188 respiratory_bronchiole 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). smooth muscle cell CL ID: http://purl.obolibrary.org/obo/CL_0000192 LungMap ID: LMMA0000000343 smooth_muscle_cell UBERON definition: A portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition]. [database_cross_reference: OBOL:automatic] http://purl.obolibrary.org/obo/UBERON_0004515 smooth_muscle_tissue_of_bronchiole subendothelial connective tissue AMM: not found in LungMAP need to added AMM: not present in UBEROn need to added subendothelial_connective_tissue UBERON: http://purl.obolibrary.org/obo/UBERON_0002187 LungMap: LMMA0000000359 terminal_bronchiole UBERON: An epithelium that lines a terminal bronchiole. [database_cross_reference: http://orcid.org/0000-0002-6601-2165] terminal bronchiole epithelium UBERON ID: http://purl.obolibrary.org/obo/UBERON_0001958 terminal_bronchiole_epithelium 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 tissue http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php?id=PR:000015426 http://pir.georgetown.edu/cgi-bin/pro/browser_pro?ids=PR:000015426 "A protein that is a translation product of the human SOX2 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. SOCX2 Sox2 sox2 http://purl.obolibrary.org/obo/PR_000015426 transcription_factor_SOX-2 http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php?id=PR:000015435 http://pir.georgetown.edu/cgi-bin/pro/browser_pro?ids=PR:000015435 "A protein that is a translation product of the human SOX9 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. SOX9 Sox9 http://purl.obolibrary.org/obo/PR_000015435 transcription_factor_SOX-9 http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php?id=PR:000016807 http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php?id=PR:000016807 "A tubulin that is a translation product of the human TUBA1A gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. TUBA1A Tuba-1 Tuba1 alpha-tubulin 3 alpha-tubulin isotype M-alpha-1 tubulin B-alpha-1 http://purl.obolibrary.org/obo/PR_000016807 tubulin_alpha-1A_chain Acetylated Tubulin AMM new term Definition LungMap: This term is used to describe an epithelial cell that cannot be classified under an existing epithelial cell type. unclassified epithelial cell not present in CL need to be added LungMAp ID: LMMA0000000384 unclassified_epithelial_cell Definition LungMAP: This term is used to describe a fibroblast that cannot be classified under an existing fibroblast cell type. unclassified fibroblast AMM: not present in CL need to be added LungMAP ID: LMMA0000000386 unclassified_fibroblast A protein that is a translation product of the human SCGB1A1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. CC10 CC16 CCPBP CCSP PCB-BP PCB-binding protein PCBBP SCGB1A1 UG UGB UP-1 UP1 Utg clara cell 17 kDa protein clara cell phospholipid-binding protein clara cells 10 kDa secretory protein secretoglobin family 1A member 1 urinary protein 1 urine protein 1 http://purl.obolibrary.org/obo/PR_000014505 uteroglobin CL : A smooth muscle cell assocatiated with the vasculature. [database_cross_reference: GOC:dsd][database_cross_reference: GOC:tfm] vascular associated smooth muscle cell CL ID: http://purl.obolibrary.org/obo/CL_0000359 LungMap ID: LMMA0000000393 vascular_associated_smooth_muscle_cell 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. http://purl.obolibrary.org/obo/FMA_3710 vascular_tree vascular tree endothelium vascular_tree_endothelium http://research.bioinformatics.udel.edu/visualization/pro/view/entry_cw_pro.php?id=PR:000017298 http://pir.georgetown.edu/cgi-bin/pro/browser_pro?ids=PR:000017298 "A protein that is a translation product of the human VIM gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. VIM Vimentin http://purl.obolibrary.org/obo/PR_000017298 vimentin http://antibodyregistry.org/search?q=ab14917 http://www.abcam.com/lyve1-antibody-ab14917.html http://antibodyregistry.org/search?q=sc-30216 http://datasheets.scbt.com/sc-30216.pdf Mouse/Rat RAGE Antibody anti ager mouse_rat RAGE antibody http://antibodyregistry.org/search?q=MAB1179 https://www.rndsystems.com/products/mouse-rat-rage-antibody-175410_mab1179 anti acta2 http://antibodyregistry.org/search.php?q=AB_262054 http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Datasheet/6/a5228dat.pdf http://antibodyregistry.org/search?q=sc-8656-R https://www.citeab.com/antibodies/3431105-sc-8656-r-p-histone-h3-antibody-ser-10-r 18.5 days after fertilization Person: Chris Stoeckert, Jie Zheng embryonic day 18.5 Embryonic_day_16.5 16.5 days after fertilization Person: Chris Stoeckert, Jie Zheng