Gail H. Deutsch Huaqin Pan NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee Susan E Wert BFO:0000050 part of RO:0001025 located_in RO:0002202 develops_from LMMA:00001 true 2 published acinar tubule pre-alveolar acinar tubule LMMA:00001 LMHA:00002 UBERON:0004893 LMMA:00002 true published alveolar wall inter-alveolar septum primary alveolar septum gives rise to the alveolar septal crest, which develops into secondary alveolar septum interalveolar septum LMMA:00002 LMMA:00003 true 2 published acinar bud distal acinar bud distal acinar tubule peripheral acinar tubule bud peripheral acinar tubule sprout distal acinar tubule bud LMMA:00003 LMMA:00005 3 published left lung pre-alveolar parenchyma LMMA:00005 LMMA:00008 true 1 published pre-alveolar connective tissue pre-alveolar mesenchyme pre-alveolar stroma pre-alveolar interstitial tissue LMMA:00008 LMMA:00009 true 1 published proximal acinar tubule LMMA:00009 LMMA:00011 3 published right accessory lobe alveolar parenchyma LMMA:00011 LMMA:00012 2 published right accessory lobe bronchiole LMMA:00012 LMMA:00017 3 published right accessory lobe pre-alveolar parenchyma LMMA:00017 LMMA:00019 4 published right accessory lobe visceral pleura LMMA:00019 LMMA:00020 3 published right lower lobe alveolar parenchyma LMMA:00020 LMMA:00021 2 published right lower lobe bronchiole LMMA:00021 LMMA:00026 3 published right lower lobe pre-alveolar parenchyma LMMA:00026 LMMA:00028 4 published right lower lobe visceral pleura LMMA:00028 LMMA:00029 3 published right middle lobe alveolar parenchyma LMMA:00029 LMMA:00030 2 published right middle lobe bronchiole LMMA:00030 LMMA:00035 3 published right middle lobe pre-alveolar parenchyma LMMA:00035 LMMA:00037 4 published right middle lobe visceral pleura LMMA:00037 FMA:31241 LMHA:00038 LMMA:00038 3 published right upper lobe alveolar parenchyma LMMA:00038 LMHA:00039 UBERON:0005681 LMMA:00039 2 published right upper lobe bronchiole LMMA:00039 LMMA:00044 3 published right upper lobe pre-alveolar parenchyma LMMA:00044 LMHA:00046 LMMA:00046 4 published right upper lobe visceral pleura LMMA:00046 LMMA:00047 UBERON:0011148 human_anatomy2:LMHA_00047 published seromucus gland submucosal gland CL:0000136 LMHA:00054 LMMA:00054 A connective tissue cell specialized to synthesize and store fat, primarily in the form of triglycerides. published adipocyte LMMA:00054 FMA:20110 LMHA:00055 LMMA:00055 published adipose tissue LMMA:00055 LMHA:00060 LMMA:00060 true published alveolar capillary network alveolar capillary bed LMMA:00060 LMHA:00061 LMMA:00061 published alveolar capillary endothelium LMMA:00061 FMA:7341 LMHA:00062 LMMA:00062 The respiratory conducting tubes distal to the terminal bronchiole that lead to the alveolar sacs and the alveoli. true published alveolar duct respiratory alveolar duct pulmonary alveolar duct LMMA:00062 LMHA:00063 LMMA:00063 published alveolar duct lumen LMMA:00063 FMA:84476 LMHA:00064 LMMA:00064 published alveolar duct wall LMMA:00064 FMA:63915 LMHA:00065 LMMA:00065 true published alveolar epithelium LMMA:00065 LMHA:00066 LMMA:00066 A mesenchymal-derived connective tissue cell located in the interstitial space (interstitium or connective tissue compartment) of the alveolar septum (wall). published alveolar connective tissue cell alveolar stromal cell alveolar interstitial cell LMMA:00066 LMHA:00067 LMMA:00067 true published alveolar connective tissue alveolar interstitium alveolar mesenchyme alveolar stroma alveolar interstitial tissue LMMA:00067 LMHA:00068 LMMA:00068 published alveolar lumen LMMA:00068 LMHA:00071 LMMA:00071 true 2 published alveolar septal ridge secondary septal crest alveolar septal crest LMMA:00071 EFO:0001985 EMAPA:32682 FMA:7318 LMHA:00072 MA:0000420 UBERON:UBERON:0002299 LMMA:00072 true published alveoli alveolus alveolus pulmonis lung alveolus pulmonary alveolus respiratory alveoli respiratory alveolus alveolus of lung LMMA:00072 LMHA:00078 UBERON:0001916 LMMA:00078 published arteriole endothelium LMMA:00078 LMHA:00081 UBERON:0001917 LMMA:00081 published artery endothelium LMMA:00081 CL:0000236 LMHA:00086 LMMA:00086 Type of white blood cell, or leukocyte, of the B lymphocyte lineage that includes antibody secreting cells (plasma cells, memory B cells, follicular and marginal zone B cells) that function in the body's antibody-driven humoral adaptive immunity. Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). published B cell B Lymphocyte LMMA:00086 FMA:63872 LMHA:00089 LMMA:00089 published basement membrane LMMA:00089 CL:0000767 LMHA:00090 LMMA:00090 A granular leukocyte with coarse, bluish-black granules. Basophils mediate hypersensitivity reactions and contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation published basophilic granulocyte basophilic leukocyte basophil LMMA:00090 LMHA:00094 LMMA:00094 3 published bronchial adventitia LMMA:00094 LMHA:00095 LMMA:00094 2 published bronchial arteriole LMMA:00094 LMHA:00096 LMMA:00096 published bronchial arteriole tunica intima LMMA:00096 LMHA:00097 LMMA:00097 published bronchial arteriole tunica media LMMA:00097 LMHA:00098 UBERON:0002040 LMMA:00098 1 published bronchial artery LMMA:00098 LMHA:00099 LMMA:00099 published bronchial artery tunica intima LMMA:00099 LMHA:00100 LMMA:00100 published bronchial artery tunica media LMMA:00100 LMMA:00101 UBERON:0002031 human_anatomy2:LMHA_00101 true published bronchial epithelium LMHA:00104 LMMA:00104 published bronchial blood vessel LMMA:00104 LMHA:00105 UBERON:0001592 LMMA:00105 4 published bronchial vein LMMA:00105 LMHA:00106 LMMA:00106 published bronchial vein tunica adventitia LMMA:00106 LMHA:00107 LMMA:00107 published bronchial vein tunica intima LMMA:00107 LMHA:00108 LMMA:00108 published bronchial vein tunica media LMMA:00108 LMHA:00109 LMMA:00109 5 published bronchial venule LMMA:00109 LMHA:00110 LMMA:00110 published bronchial venule tunica adventitia LMMA:00110 LMHA:00111 LMMA:00111 published bronchial venule tunica intima LMMA:00111 LMHA:00112 LMMA:00112 published bronchial venule tunica media LMMA:00112 LMMA:00119 true published bronchioalveolar duct junction LMMA:00119 EMAPA:32689 FMA:7409 LMHA:00120 MA:0000436 UBERON:0002185 LMMA:00120 true 2 published bronchus LMMA:00120 LMHA:00123 UBERON:0012083 LMMA:00123 published bronchus lumen LMMA:00123 FMA:14049 LMHA:00124 LMMA:00124 published bronchus wall LMMA:00124 LMMA:00125 A rare, cholinergic, chemosensory, epithelial cell located in the upper respiratory tract, larynx, and trachea, as well as in the ducts of the submucosal glands. This cell expresses "bitter" taste receptors (TAS2R) and is responsible for detecting chemical irritants that trigger a variety of reflex responses, such as coughing, This cell also called a "brush" cell, based on a brush-like tuft of microvilli located on its apical cell surface. published brush cell chemosensory cell LMMA:00129 true published pre-alveolar capillary endothelium LMMA:00129 LMMA:00130 published capillary tunica adventitia LMMA:00130 LMMA:00131 published capillary tunica intima LMMA:00131 LMMA:00132 true published cardiac myocyte cardiomyocyte LMMA:00133 human_anatomy2:LMHA_00595 published cartilage bronchial cartilaginous ring CL:0002320 LMHA:00136 LMMA:00136 A group of cells derived from embryonic mesoderm (mesenchyme) that includes fibroblasts, cartilage cells, adipocytes, smooth muscle cells and bone cells. published connective tissue cell LMMA:00136 LMMA:00137 A mesenchymal-derived, connective tissue cell located in the interstitial space (interstitium or connective tissue compartment) between the Branching_parting acinar tubules of the peripheral fetal lung during the pseudoglandular stage of lung development (E12.5 - E16.5). published pre-alveolar acinar stromal cell pre-alveolar connective tissue cell pre-alveolar mesenchymal cell pre-alveolar interstitial cell LMMA:00137 LMMA:00138 published LMHA:00579 central bronchiolar lumen LMMA:00138 LMMA:00139 published LMHA:00580 central bronchiolar wall LMMA:00139 LMMA:00140 true published Primary bronchiole Proximal bronchiole LMHA:00578 central bronchiole LMMA:00140 BTO:0000249 LMHA:00141 LMMA:00141 A type of connective tissue cell that secretes and maintains the structural components of cartilage, primarily collagen and proteoglycans. true published chondrocyte LMMA:00141 CL:0000064 LMHA:00142 LMMA:00142 A columnar epithelial cell with microscopic hair-like processes, i.e., motile cilia, that extend from the apical cell surface. These cells are found in the epithelia of the conducting airways (trachea, bronchi, and bronchioles), where they sweep mucous, dirt, dust, bacteria and other pathogens up and out of the lung, bronchi, and trachea. true published ciliated cell LMMA:00142 CL:0000158 LMHA:00143 LMMA:00143 The club cell is a non-ciliated, dome-shaped, secretory cell with short microvilli and abundant secretory granules. Its secretory proteins function to protect the bronchiolar epithelium from environmental toxins/irritants. The club cell also has the capacity for self-renewal (maintenance of a progenitor cell pool) and regeneration of the bronchiolar epithelium after injury. true published Clara cell bronchiolar exocrine cell nonciliated secretory cell club cell LMMA:00143 FMA:63173 LMHA:00145 LMMA:00145 published collagen fiber LMMA:00145 CL:0000738 LMHA:00150 LMMA:00150 A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative. published dendritic cell LMMA:00150 LMMA:00155 2 published E16.5 LMMA:00157 4 published E18.5 LMHA:00158 UBERON:0002521 LMMA:00158 published elastin elastic fiber LMMA:00158 LMMA:00160 CL:0000771 LMHA:00163 LMMA:00163 A granular leukocyte with cytoplasm containing coarse, round granules which can be stained by the dye eosin. Eosinophils contain histamines and other enzymatic proteins, such as esoinophil peroxidase, RNase, DNase, and lipase, as well as plasminogen and major basic protein, which are released by degarnulation following activation. These cells play a specialized role in immunity to parasitic infections, and are the primary inflammatory cells in allergic reactions, such as asthma, hay fever, and hives. published eosinophil LMMA:00163 LMHA:00167 UBERON:0015433 LMMA:00167 published external elastic membrane LMMA:00167 LMHA:00168 MESH:D005109 LMMA:00168 published extracellular matrix LMMA:00168 FMA:62925 LMHA:00178 LMMA:00178 published glycoprotein LMMA:00178 CL:0000094 LMHA:00179 LMMA:00179 published granulocyte LMMA:00179 LMHA:00180 LMMA:00180 published ground substance LMMA:00180 CL:0000235 LMHA:00182 LMMA:00182 A mononuclear phagocyte of the myeloid lineage that is present in a variety of tissues, typically differentiated from monocytes, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. Additional functions include anitgen presentation and tissue remodeling. This phagocyte is large, highly adhesive cell with abundant cytoplasm, an eccentric nucleus, and irregularly shaped pseuodopods. Contains azurophilic granules, vacuoles and phagosomes. published histiocyte macrophage LMMA:00182 LMMA:00183 FMA:64783 human_anatomy2:LMHA_00183 true published hyaline cartilage LMMA:00184 A partially differentiated fetal club cell, whose cytoplasm contains abundant glycogen granules. Full differentiation occurs postnatally when glycogen levels decrease and secretory granules increase. true published immature Clara cell immature club cell LMMA:00184 CL:0000738 LMHA:00185 LMMA:00185 published MIC leukocyte immune cell LMMA:00185 LMMA:00187 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). published bi-potential pneumocyte intermediate alveolar epithelial cell intermediate pneumocyte LMMA:00187 LMHA:00191 UBERON:0011392 LMMA:00191 published internal elastic membrane LMMA:00191 LMMA:00196 published LMHA:00579 lateral bronchiolar lumen LMMA:00196 LMMA:00197 published LMHA:00580 lateral bronchiolar wall LMMA:00197 LMMA:00198 true published distal bronchiole secondary bronchiole LMHA:00578 lateral bronchiole LMMA:00198 LMHA:00199 UBERON:0002168 LMMA:00199 published left lung LMMA:00199 LMMA:00200 3 published LMHA:00200 LMHA:00533 left lung alveolar parenchyma LMMA:00200 LMMA:00201 2 published left lung bronchiole LMMA:00201 LMHA:00205 UBERON:0002178 LMMA:00205 published left lung mainstem bronchus left lung primary bronchus left lung main bronchus LMMA:00205 LMMA:00207 4 published left lung veceral pleura serosa serosal membrance LMHA:00207 LMHA:00537 left lung visceral pleura LMMA:00207 LMHA:00209 LMMA:00209 Lipid-containing interstitial cell located in the alveolar septum (wall). The lipofibroblast transfers neutral lipid (tryglyceride) from the capillaries to the type II pneumocyte for the synthesis of surfactant phopholipids. It also synthesizes ECM proteins, such as collagen and elastin, and contains intermediate contractile filaments. true published lipofibroblast LMMA:00209 EHDAA2:0001042 EMAPA:16728 FMA:7195 LMHA:00211 MA:0000415 UBERON:0002048 LMMA:00211 3 published lung LMMA:00211 LMMA:00213 A subset of lung macrophages which inhabit the interstitium where they interact with interstitial lymphocytes and help in mounting a specific immune response. They are CD45 pos, CD68 low, F4/80 low, CD11b+, Gr1-, CD11c low, CD14 low published lung tissue macrophage pre-alveolar interstitial macrophage interstitial macrophage LMMA:00213 CL:0002138 LMHA:00216 LMMA:00216 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). true published lymphatic endothelial cell LMMA:00216 LMHA:00217 UBERON:0004232 LMMA:00217 published lymphatic smooth muscle LMMA:00217 FMA:66259 LMHA:00220 LMMA:00220 published lymphatic vessel tunica adventitia LMMA:00220 FMA:66257 LMHA:00221 LMMA:00221 published lymphatic vessel tunica intima LMMA:00221 FMA:66258 LMHA:00222 LMMA:00222 published lymphatic vessel tunica media LMMA:00222 CL:0000542 LMHA:00223 LMMA:00223 Subtype of white blood cells including large lymphocytes (NK cells) and small lymphocytes (T cells, B cells, and plasma cells). published lymphocyte LMMA:00223 LMHA:00224 UBERON:0000029 LMMA:00224 published lymph node LMMA:00224 CL:0000583 LMHA:00226 LMMA:00226 A tissue-resident macrophage found in the alveoli (lumen) of the lungs that is repsonsible for the clearance of inhaled particles, microorganisms, and pulmonary surfactant. Ingestion of small inhaled particles results in degradation and presentation of the antigen to immunocompetent cells. These cells are long-lived and self renewing. Marker profile: CD45 pos, CD68 high, F4/80 high, CD11b neg, CD11c high,MCHCII low, CD103 neg (1), CD64 pos and SiglecF high (2). true published alveolar macrophage LMMA:00226 CL:0000097 LMHA:00227 LMMA:00227 A leukocyte that contains numerous basophilic granules, capable of releasing large amounts of histamine and heparin upon activation. Known for their role in allergy and anaphylaxis. published mast cell LMMA:00227 CL:0000077 LMHA:00231 LMMA:00231 A flat cell of mesenchymal origin that forms the superficial layer of the serosal membranes lining the body cavities of the abdomen and thorax. true published mesothelial cell LMMA:00231 CL:0000576 LMHA:00233 LMMA:00233 A bone marrow derived circulating, mononuclear leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. published monocyte LMMA:00233 LMHA:00240 UBERON:0004515 LMMA:00240 3 published peribronchiolar smooth muscle bronchiolar smooth muscle LMMA:00240 CL:0000766 LMHA:00241 LMMA:00241 A cell of the monocyte, granulocyte, or mast cell lineage. published myeloid leukocyte LMMA:00241 CL:0000623 LMHA:00245 LMMA:00245 A type of lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells published large granular lymphocyte non-T, non-B lymphocyte natural killer cell LMMA:00245 LMHA:00247 UBERON:0006134 LMMA:00247 published nerve fiber LMMA:00247 CL:0000165 LMHA:00252 LMMA:00252 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. true published neuroendocrine cell LMMA:00252 MESH:D046568 LMMA:00253 true published Innervated clusters of NEUROEPITHELIAL CELLS found in the LUNGS. They act as airway OXYGEN sensors, releasing regulatory PEPTIDES and SEROTONIN in response to HYPOXIA. neuroepithelial body LMMA:00253 CL:0000775 LMHA:00256 LMMA:00256 A granular leukocyte that in its mature form contains a nucleus with 3-5 lobes containing fine inconspicuous granules stainable by neutral dyes in its cytoplasm. These granules contain anti-microbial substances that help combat infection when released by a process called degranulation published neutrophil LMMA:00256 LMHA:00257 LMMA:00257 published non-adrenergic and non-cholinergic nerve LMMA:00257 LMMA:00266 84 published pnd28 P28 LMMA:00268 28 published P7 pnd7 P07 LMHA:00270 UBERON:0011929 LMMA:00270 published cholinergic innervation cholinergic nerve postganglionic parasympathetic nerve LMMA:00270 LMMA:00276 published postnatal day LMHA:00279 UBERON:0005314 LMMA:00279 true 1 published primary septum primary alveolar septum gives rise to the alveolar septal crest, which develops into secondary alveolar septum primary alveolar septum LMMA:00279 FMA:63015 LMHA:00283 LMMA:00283 published proteoglycan LMMA:00283 LMMA:00284 true published epithelium, proximal acinar tubule proximal acinar tubule epithelium LMMA:00284 LMMA:00286 true 1 published proximal bronchiolar epithelium LMHA:00581 central bronchiolar epithelium LMMA:00286 LMHA:00290 LMMA:00290 true 2 published pulmonary arteriole LMMA:00290 LMHA:00291 UBERON:0002012 LMMA:00291 true 1 published pulmonary artery LMMA:00291 FMA:84914 LMHA:00292 LMMA:00292 published pulmonary artery tunica adventitia LMMA:00292 LMHA:00293 LMMA:00293 published pulmonary artery tunica intima LMMA:00293 LMHA:00294 LMMA:00294 published pulmonary artery tunica media LMMA:00294 LMHA:00297 LMMA:00297 published pulmonary distal arteriole LMMA:00297 LMHA:00298 LMMA:00298 published pulmonary distal arteriole tunica adventitia LMMA:00298 LMHA:00299 LMMA:00299 published pulmonary distal arteriole tunica intima LMMA:00299 LMHA:00300 LMMA:00300 published pulmonary distal arteriole tunica media LMMA:00300 LMHA:00301 LMMA:00301 published pulmonary distal venule LMMA:00301 LMHA:00302 LMMA:00302 published pulmonary distal venule tunica adventitia LMMA:00302 LMHA:00303 LMMA:00303 published pulmonary distal venule tunica intima LMMA:00303 LMHA:00304 LMMA:00304 published pulmonary muscular arteriole LMMA:00304 LMHA:00305 UBERON:0002016 LMMA:00305 4 published pulmonary vein LMMA:00305 FMA:84915 LMHA:00306 LMMA:00306 published pulmonary vein tunica adventitia LMMA:00306 FMA:84945 LMHA:00307 LMMA:00307 published pulmonary vein tunica intima LMMA:00307 FMA:85023 LMHA:00308 LMMA:00308 published pulmonary vein tunica media LMMA:00308 LMHA:00309 LMMA:00309 5 published pulmonary muscular venule LMMA:00309 LMHA:00310 LMMA:00310 published pulmonary muscular venule tunica adventitia LMMA:00310 LMHA:00311 LMMA:00311 published pulmonary muscular venule tunica intima LMMA:00311 LMHA:00312 LMMA:00312 published pulmonary muscular venule tunica media LMMA:00312 LMHA:00315 LMMA:00315 published pulmonary blood vessel LMMA:00315 LMHA:00316 LMMA:00316 true 5 published venule pulmonary venule LMMA:00316 LMHA:00320 UBERON:0006804 LMMA:00320 published reticulin reticular fiber LMMA:00320 LMMA:00322 UBERON:0004890 4 published right infra-cardiac lobe right intermediate lobe right post-caval lobe right lung accessory lobe LMMA:00323 published right infra-cardiac lobar bronchus right intermediate lobar bronchus right post-caval lobar bronchus right lung accessory lobar bronchus LMMA:00324 EHDAA2:0001740 LMHA:00324 3 published right caudal lobe right diaphragmatic lobe right lung lower lobe LMMA:00325 EHDAA2:0001744 LMHA:00325 published right caudal lobar bronchus right diaphragmatic lobar bronchus right lung lower lobar bronchus LMMA:00326 LMHA:00326 UBERON:0002167 published right lung LMMA:00329 LMHA:00329 UBERON:0002177 published right lung mainstem bronchus right lung primary bronchus right lung main bronchus LMMA:00330 LMHA:00330 UBERON:0002174 2 published right cardiac lobe right lung middle lobe LMMA:00331 LMHA:00331 UBERON:0012063 published right cardiac lobar bronchus right lung middle lobar bronchus LMMA:00332 EHDAA2:0001747 LMHA:00332 1 published right apical lobe right cranial lobe right lung upper lobe LMMA:00333 EHDAA2:0001752 LMHA:00333 published right apical lobar bronchu right cranial lobar bronchus right lung upper lobar bronchus LMMA:00338 CL:0000218 LMHA:00338 A supporting cell of the peripheral nervous system, derived from neural crest cells, which forms the insulating myelin sheaths of peripheral axons and is required for nerve maintenance and function. published Schwann cell neuroglial cell glial cell LMMA:00339 LMHA:00339 UBERON:0005315 true 3 published primary alveolar septum gives rise to the alveolar septal crest, which develops into secondary alveolar septum secondary alveolar septum LMMA:00343 CL:0000192 LMHA:00343 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). true published smooth muscle cell LMMA:00352 LMHA:00352 UBERON:0011926 published adrenergic innervation adrenergic nerve postganglionic sympathetic nerve LMMA:00354 CL:0000084 LMHA:00354 A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex (specific cell-surface antigen receptors) published T cell T Lymphocyte LMMA:00357 FMA:87486 LMHA:00357 published terminal bronchiolar lumen LMMA:00358 FMA:62792 LMHA:00358 published terminal bronchiolar wall LMMA:00359 LMHA:00359 UBERON:0002187 true published terminal bronchiole LMMA:00360 published Theiler stage LMMA:00361 EHDAA2:0002066 EMAPA:16853 FMA:7394 LMHA:00361 MA:0000441 UBERON:0003126 true 1 published trachea LMMA:00362 LMHA:00362 UBERON:0015247 3 published trachea bifurcation LMMA:00365 LMHA:00365 UBERON:0006833 1 published trachea lumen LMMA:00366 FMA:7470 LMHA:00366 2 published trachea wall LMMA:00367 LMHA:00367 3 published tracheal adventitia LMMA:00370 human_anatomy2:LMHA_00370 published membranous trachea trachealis muscle LMMA:00372 4 published TS24 LMMA:00373 6 published TS25 LMMA:00374 8 published TS26 LMMA:00375 10 published TS27 LMMA:00376 12 published TS28 LMMA:00378 LMHA:00378 A fibroblast found in the connective tissue layer located immediately under the vascular endothelium in the tunica intima of blood vessels. published subendothelial connective tissue cell LMMA:00379 CL:0002062 LMHA:00379 A thin, flat or squamous ("scale-like") alveolar epithelial cell, covering ~95% of the surface area of each alveolus, that facilitates gas exchange across the alveolar wall (septum), i.e., between the alveolus (airspace) and the capillary network. true published AEC1 AT1 cell ATI cell alveolar epithelial cell, type I alveolar type 1 cell alveolar type I cell alveolar type I epithelial cell lung type 1 cell pulmonary alveolar type I cell squamous alveolar cell squamous alveolar lining cell type I alveolar cell type I alveolar epithelial cell type I pneumocyte LMMA:00380 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. published immature AT1 pre-type I pneumocyte type I pneumocyte precursor cell LMMA:00381 CL:0002063 LMHA:00381 A cuboidal-like, alveolar epithelial cell that synthesizes, stores, secretes, and recycles pulmonary surfactant phospholipids and proteins, substances that reduce the surface tension in the alveolus. Pulmonary surfactant is stored in lipid-rich lamellar bodies, a distinctive feature of this cell type. The type II pneumocyte is also capable of cell division and can repopulate the alveolar epitheium after injury, differentiating into type I pneumocytes. Although this cell type covers less than 5% of the alveolar surface, it represents 60% of all alveolar epithelial cells. true published AT2 cell ATII cell TII (type II) alveolar epithelial cell, type II alveolar epithelial type II cell alveolar type II cell cuboidal type II cell granular pneumocyte lung type 2 cell type 2 alveolar epithelial cell type 2 pneumocyte type II alveolar cell type II alveolar epithelial cell type II pneumocyte LMMA:00382 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. published immature AT2 pre-type II pneumocyte type II pneumocyte precursor cell LMMA:00384 LMHA:00384 This term is used to describe an epithelial cell that cannot be classified under an existing epithelial cell type. published general epithelial cell nonspecific epithelial cell this is included for general epithelial cell markers for imaging annotation unclassified epithelial cell LMMA:00392 CL:0002139 LMHA:00392 An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. true published vascular endothelial cell LMMA:00393 LMHA:00393 UBERON:0004237 true published perivascular smooth muscle vascular smooth muscle LMMA:00395 LMHA:00395 UBERON:0003710 published vasa vasorum LMMA:00397 LMHA:00397 UBERON:0001919 published vein endothelium LMMA:00399 true published venous cardiac muscle LMMA:00403 LMHA:00403 UBERON:0007141 published venule endothelium LMMA:00406 LMHA:00406 UBERON:0007141 published visceral mesothelium LMMA:00410 LMHA:00410 published fibroelastic connective tissue fibroelastic tissue fibroelastic membrane LMMA:00412 LMHA:00412 UBERON:0002222 published perichondrium LMMA:00414 UBERON:0001901 human_anatomy2:LMHA_00288 true published tracheal epithelium LMMA:00415 UBERON:0000379 human_anatomy2:LMHA_00415 1 published tracheal mucosa LMMA:00416 2 published tracheal submucosa LMMA:00418 UBERON:0000410 human_anatomy2:LMHA_00418 1 published bronchial mucosa LMMA:00419 UBERON:0001957 human_anatomy2:LMHA_00419 2 published bronchial submucosa LMMA:00422 LMHA:00422 UBERON:0002042 true published lymphatic endothelium LMMA:00424 published epithelium, distal saccule primary saccule transitory saccule terminal saccule epithelium LMMA:00433 1 published distal bronchiolar epithelium LMHA:00581 lateral bronchiolar epithelium LMMA:00437 CL:0002089 LMHA:00437 A innate lymphoid cell that plays an important role in type 2 immune responses to helminth worm infection and in conditions such as asthma and other atopic diseases. This cell secretes the type 2 cytokines, IL-4, -5, -9 and -13. published nuocyte LMMA:00442 published pre-alveolar interstitial blood vessel LMMA:00447 LMHA:00447 UBERON:0018227 6 published pulmonary lymphatic vessel LMMA:00455 BTO:0004557 human_anatomy2:LMHA_00455 published submucosal gland duct epithelium LMMA:00457 FMA:62794 LMHA:00457 1 published terminal bronchiolar epithelium LMMA:00465 This term is used to describe an alveolar interstitial (stromal or connective tissue) cell that cannot be classified under an existing cell type. published unclassified alveolar interstitial cell LMMA:00470 CL:0002638 An epithelial cell found in the bronchioalveolar duct junction (located between the terminal bronchiole and the alveolar duct), which co-expresses specific cell markers for type II pneumocytes (SFTPC) and club cells (SCGB1A1). This putative stem/progenitor cell is self-renewing, resistant to injury, and gives rise to both alveolar pneumocytes and club cells in response to lung injury. published bronchioalveolar stem cell LMMA:00472 LMHA:00472 published bronchial arteriole tunica adventitia LMMA:00473 LMHA:00473 published bronchial artery tunica adventitia LMMA:00475 LMHA:00651 MA:0000135 published bronchus-associated lymphoid tissue LMMA:00476 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. true published ciliated cell precusor LMMA:00477 This cell is found in the fetal lung and is defined by high levels of F4/80 and low levels of CD11b. true published fetal macrophage primitive macrophage LMMA:00478 This cell is found in the fetal lung and is defined by high levels of Ly6C (a monocte marker) and high levels of CD11b true published fetal monocyte LMMA:00485 3 published distal terminal saccule lung saccule proximal terminal saccule smooth-walled saccule terminal air sac terminal lung saccule terminal saccule pre-alveolar terminal saccule LMMA:00486 LMHA:00486 published pulmonary muscular arteriole tunica adventitia LMMA:00488 LMHA:00488 published pulmonary muscular arteriole tunica intima LMMA:00489 LMHA:00489 published pulmonary muscular arteriole tunica media LMMA:00507 CL:0002543 A vascular endothelial cell that forms the endothelial lining of veins. true published venous endothelial cell LMMA:00509 5 published P04-P36 alveolar stage LMMA:00510 3 published E16-E17 canalicular stage LMMA:00511 published developmental stage LMMA:00513 2 published E12-E16 pseudoglandular stage LMMA:00514 4 published E17-E19 prenatal saccular stage LMMA:00515 5 published P0-P03 postnatal saccular stage LMMA:00516 FMA:7428 3 published bronchial capillary LMMA:00520 LMHA:00546 4 published respiratory autonomic nervous system LMMA:00521 CL:0000107 LMHA:00521 A neuron whose cell body is located within an autonomic ganglion, i.e., part of a cluster of nerve cell bodies in the peripheral nervous system. Each neuron consists of a body, an axon, and dendrites. Its purpose is to receive, conduct, and transmit impulses between the central nervous system and its target organs/tissues. published autonomic ganglion cell autonomic ganglion neuron autonomic neuron LMMA:00522 LMHA:00547 5 published respiratory immune system LMMA:00523 LMHA:00548 UBERON:0003504 6 published respiratory vascular system LMMA:00525 FMA:7507 2 published peribronchiolar connective tissue LMHA:00114 LMHA:00589 bronchiolar connective tissue LMMA:00527 LMHA:00540 UBERON:0002182 1 published mainstem bronchus primary bronchus main bronchus LMMA:00528 LMHA:00538 UBERON:0002183 2 published secondary bronchus lobar bronchus LMMA:00529 FMA:63011 LMHA:00576 published glycosaminoglycan LMMA:00573 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. published proximal acinar epithelial cell proximal acinar tubule epithelial cell LMMA:00574 FMA:62499 LMHA:00586 An epithelial cell that lines the peripheral gas exchange region (epithelial lining of the alveolar duct and alveoli) of the lungs. Includes both alveolar type I and type II pneumocytes. published alveolar epithelial cell LMMA:00576 An epithelial cell that lines the terminal saccule of the peripheral lung in the saccular stage of lung development (E18.5 - P0). The terminal saccule is an epithelial-lined, pre-alveolar structure with an immature, double capillary network in its septum (wall). At E18.5, it can be distinguished from the transitory duct by its relative location (distal), morphology (low cuboidal-like epithelium with more closely space nuclei), and immunohistochemical and/or immunofluorescence marker analysis. published terminal saccule epithelial cell LMMA:00582 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. published LMHA:00629 LMHA:00630 bronchiolar epithelial cell LMMA:00583 published pre-alveolar capillary network pre-alveolar capillary bed LMMA:00590 CL:0000307 human_anatomy2:LMHA_00583 An epithelial cell that lines the trachea. The trachea is lined by pseudostratified columnar epithelial cells, including ciliated cells, club cells, basal cells, and neuroepithelial cells. published tracheal epithelial cell LMMA:00591 CL:0002328 human_anatomy2:LMHA_00577 An epithelial cell that lines the bronchus. Bronchi are lined by pseudostratified columnar epithelial cells, including ciliated cells, club cells, basal cells, and neuroepithelial cells. published bronchial epithelial cell LMMA:00592 UBERON:2002141 human_anatomy2:LMHA_00587 published annular ligament LMMA:00599 published proliferating epithelial cell proliferative epithelial cell LMMA:00601 true 1 published left lung hilum LMMA:00602 true 1 published right accessory lobe hilum LMMA:00603 LMHA:00022 true 1 published right lower lobe hilum LMMA:00604 true 1 published right middle lobe hilum LMMA:00605 LMHA:00040 true 1 published right upper lobe hilum LMMA:00606 human_anatomy2:LMHA_00133 true published tracheal cartilaginous ring LMMA:00609 This cell is found in the perinatal lung and is CD11b+,F4/80+ with intermediate levels of CD11c and CD64 and low levels of SiglecF true published fetal macrophage immature alveolar macrophage immature macrophage LMMA:00610 true 2 published smooth-walled channel transitory duct pre-alveolar transitory duct LMMA:00611 true published transitory duct epithelium LMMA:00612 true published transitory duct epithelial cell LMMA:00614 BTO:0001096 LMHA:00614 Cells derived from stem cells of the lymphoid lineage. Responsible for the production of immunity mediated by cells or antibodies true published lymphoid cell LMMA:00616 true published arterial endothelial cell LMMA:00619 CL:0000232 LMHA:00622 A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. published RBC red blood cell erythrocyte LMMA:00620 CL:0001065 LMHA:00623 A cell of the lymphoid lineage that lacks expression of rearranged antigen-specific receptors, existing mainly in non-lymphoid tissues as tissue-resident cells. These cells have physiological functions analogous to helper T cells, while also including the cytotoxic NK cells. They can be divided into 3 groups based on the cytokines they produce: Group 1 (ILC and NK cells) produces type 1 cytokines (IFNgamma and TNF); Group 2 (nuocytes) produces type 2 cytokines (IL-4, -5, -9, and -13); and Group 3 (ILC3 and lymphoid tissue-inducer cells) produces IL-17A and/or IL-22. They play an important role in protective immunity and in the regulation of homeostasis and inflammation. Dysregulation can result in allergic responses (asthma) and autoimmune disease. published innate lymphoid cell LMMA:00626 LMHA:00626 UBERON:0001744 true published lymphoid tissue LMMA:00632 LMHA:00632 true 3 published intra-parenchymal blood vessel LMMA:00633 LMHA:00633 UBERON:0002009 true published extrapulmonary plexus; associated with left and right bronchi at root of left and right lung in mediastinum pulmonary nerve plexus LMMA:00634 LMHA:00634 true published nerve cell cluster intrapulmonary; adjacent to bronchi and blood vessels pulmonary autonomic ganglion LMMA:00635 FMA:223443 LMHA:00635 true published left pulmonary nerve plexus LMMA:00636 FMA:6657 LMHA:00636 true published left anterior pulmonary nerve plexus LMMA:00637 FMA:6659 LMHA:00637 true published left posterior pulmonary nerve plexus LMMA:00638 FMA:223441 LMHA:00638 true published right pulmonary nerve plexus LMMA:00639 FMA:6656 LMHA:00639 true published right anterior pulmonary nerve plexus LMMA:00640 FMA:6658 LMHA:00640 true published right posterior pulmonary nerve plexus LMMA:00641 LMHA:00641 true published pulmonary autonomic nerve LMMA:00642 LMHA:00642 UBERON:0011930 true published preganglionic parasympathetic nerve LMMA:00643 FMA:9905 LMHA:00643 true published general visceral nervous system LMMA:00644 FMA:80114 LMHA:00644 true published sensory nerve general visceral afferent nerve LMMA:00645 LMHA:00645 true published visceral afferent sensory nerve receptor visceral afferent sensory nerve terminal LMMA:00655 published proliferative smooth muscle cell LMMA:00669 P0 is defined as 0-24 hours, P01 as 24-48 hours, P02 as 48-72 hours, P03 as 72-96 hours post birth. 5 published P0-P3 LMMA:00670 16 published P4-P36 LMMA:00677 CL:0000786 LMHA:00574 published plasma cell LMMA:00678 LMHA:00678 published connective tissue capsule LMMA:00679 LMHA:00679 UBERON:0000440 published trabecula LMMA:00680 LMHA:00680 UBERON:0001851 published cortex LMMA:00681 published lymphoid follicle LMMA:00682 FMA:61108 LMHA:00682 published medulla LMMA:00683 LMHA:00683 UBERON:0009745 published medullary cord LMMA:00684 published interfollicular area of the lymph node subcortical zone paracortex LMMA:00685 CL:0000432 published reticular cell LMMA:00686 LMHA:00686 MESH:D042783 published endothelial sinus LMMA:00687 LMHA:00687 published cortical sinus LMMA:00688 LMHA:00688 UBERON:0009744 published medullary sinus LMMA:00689 LMHA:00689 published paratrabecular sinus LMMA:00690 LMHA:00690 UBERON:0005463 published subcapsular sinus LMMA:00692 CL:0000081 LMHA:00692 published blood cell LMMA:00693 published submucosal gland duct epithelial cell LMMA:00698 CL:0000868 LMHA:00681 published mucosa-associated lymphoid tissue macrophage LMMA:00699 LMHA:00570 UBERON:0010754 published central zone of follicle reactive center of follicle germinal center LMMA:00704 2 published E16.5 – E17.5 LMMA:00705 3 published E17.5 – E19.5 LMMA:00817 EMAPA:35119 FMA:7317 MA:0000418 UBERON:0002169 UMLS:C0225691 human_anatomy2:LMHA_00817 true published alveolar sac LMMA:00818 human_anatomy2:LMHA_00817 true published alveolar sac lumen obo:Other mouse mus musculus breath_database:organism RO:0002150 continuous_with RO:0002220 adjacent_to RO:0002380 branching_part_of Gail H. Deutsch Huaqin Pan NHLBI Molecular Atlas of Lung Development Program Consortium Ontology Subcommittee Susan E Wert