description link name Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. database_cross_reference: MP:MPdatabase_cross_reference: ENVO:02000021 http://purl.obolibrary.org/obo/UBERON_0000173 Amniotic Fluid Small tissue projection existing as a cecal diverticulum with a questionable history of vestigial versus specialized organ. http://purl.obolibrary.org/obo/NCIT_C12380 Appendix CD3-, CD19+, CD20+ http://purl.obolibrary.org/obo/CL_0000236 B cell Granular leukocytes characterized by a relatively pale-staining, lobate nucleus and cytoplasm containing coarse dark-staining granules of variable size and stainable by basic dyes. A type of immune cell that has granules (small particles) with enzymes that are released during allergic reactions and asthma. A basophil is a type of white blood cell and a type of granulocyte. (UMLS CUI: C0004827) http://purl.obolibrary.org/obo/NCIT_C12531 Basophils Skeletal element that is composed of bone tissue. http://purl.obolibrary.org/obo/UBERON_0001474 Bone The soft tissue that fills the cavities of bones. http://purl.obolibrary.org/obo/UBERON_0002371 Bone Marrow The lymph nodes located along the brachial vein that receive drainage from most of the free upper limb and send efferent vessels to the central axillary lymph nodes. http://purl.obolibrary.org/obo/UBERON_0002525 Brachial lymph node The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. [database_cross_reference: http://en.wikipedia.org/wiki/Brain][database_cross_reference: https://github.com/obophenotype/uberon/issues/300] http://purl.obolibrary.org/obo/UBERON_0000955 brain Milk produced by female mammals for the purpose of feeding their young. The off-white liquid secreted by the mammary glands of humans and other mammals. It contains proteins, sugar, lipids, vitamins, and minerals. (UMLS CUI: C0026131) http://purl.obolibrary.org/obo/NCIT_C13257 Breast Milk Bronchoalveolar lavage (BAL; informally, "bronchoalveolar washing") is a medical procedure in which a bronchoscope is passed through the mouth or nose into the lungs and fluid is squirted into a small part of the lung and then collected for examination. https://en.wikipedia.org/wiki/Bronchoalveolar_lavage Bronchoalveolar Lavage Fluid Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. http://purl.obolibrary.org/obo/CHEBI_16646 Carbohydrate Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell. http://purl.obolibrary.org/obo/OBI_1000023 Cell culture supernatant A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). http://purl.obolibrary.org/obo/CLO_0000031 cell line A watery fluid that is continuously produced in the CHOROID PLEXUS and circulates around the surface of the BRAIN; SPINAL CORD; and in the CEREBRAL VENTRICLES. The fluid that flows in and around the hollow spaces of the brain and spinal cord, and between two of the meninges (the thin layers of tissue that cover and protect the brain and spinal cord). CSF is made by tissue called the choroid plexus in the ventricles (hollow spaces) in the brain. (UMLS CUI: C0007806) http://purl.obolibrary.org/obo/NCIT_C12692 Cerebrospinal Fluid Lymph nodes found in the neck. https://en.wikipedia.org/wiki/Cervical_lymph_nodes Cervical lymph nodes Last portion of the large intestine before it becomes the rectum. http://purl.obolibrary.org/obo/UBERON_0001155 Colon A lamina propria that is part of a colonic mucosa. http://purl.obolibrary.org/obo/UBERON_0007177 Colonic Lamina Propria Plasma derived from patients who have recovered from an illness. (UMLS CUI: C5383282) http://purl.obolibrary.org/obo/NCIT_C173750 Convalescent Plasma Blood that remains in the placenta and in the attached umbilical cord after childbirthWP. database_cross_reference: http://en.wikipedia.org/wiki/Cord_blood http://purl.obolibrary.org/obo/UBERON_0012168 Cord blood The hormone-responsive glandular layer of ENDOMETRIUM that sloughs off at each menstrual flow (decidua menstrualis) or at the termination of pregnancy. During pregnancy, the thickest part of the decidua forms the maternal portion of the PLACENTA, thus named decidua placentalis. The thin portion of the decidua covering the rest of the embryo is the decidua capsularis. (MSH). The epithelial tissue of the endometrium. (NCI) https://uts.nlm.nih.gov/uts/umls/concept/C0011106 Decidua CD3-, CD19, CD20, CD14-, CD16-, CD56-, HLA-DR+ http://purl.obolibrary.org/obo/CL_0000451 Dendritic cell The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis. http://purl.obolibrary.org/obo/UBERON_0002067 Dermis High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. http://purl.obolibrary.org/obo/CHEBI_16991 DNA Capillary blood collected on blotting paper, typically from heel or finger stick. (UMLS CUI: C3830395) http://purl.obolibrary.org/obo/NCIT_C113746 Dried Blood Spot A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. http://purl.bioontology.org/ontology/RCD/X7AAl Endotracheal aspirate 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]. http://purl.obolibrary.org/obo/UBERON_0000483 Epithelium The material discharged from the bowel during defecation. It consists of undigested food, intestinal mucus, epithelial cells, and bacteria. http://purl.obolibrary.org/obo/NCIT_C13234 Feces A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. http://purl.obolibrary.org/obo/CL_0000057 Fibroblast The closest term in Uberson is "Mucosa of the stomach" : The mucosal layer that lines the stomach. It consists of epithelium, lamina propria, and the muscularis mucosae. http://purl.obolibrary.org/obo/UBERON_0001199 Gastric lamina propria The portion of the small intestine that extends from the jejunum to the colon. http://purl.obolibrary.org/obo/UBERON_0002116 Ileum The lymph nodes located in the groin area. http://purl.obolibrary.org/obo/UBERON_0001542 Inguinal lymph node The portion of the small intestine that extends from the duodenum to the ileum. http://purl.obolibrary.org/obo/UBERON_0002115 Jejunum A paired organ of the urinary tract which has the production of urine as its primary function. http://purl.obolibrary.org/obo/UBERON_0002113 Kidney White blood cells. These include granular leukocytes (BASOPHILS; EOSINOPHILS; and NEUTROPHILS) as well as non-granular leukocytes (LYMPHOCYTES and MONOCYTES). Blood cells that are devoid of hemoglobin, capable of ameboid motion and phagocytosis, and act as the principal components of the immune system. (UMLS CUI: C0023516) http://purl.obolibrary.org/obo/NCIT_C12529 Leukocytes 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. http://purl.obolibrary.org/obo/CHEBI_18059 Lipid An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. http://purl.obolibrary.org/obo/UBERON_0002107 Liver Respiration organ that develops as an oupocketing of the esophagus. http://purl.obolibrary.org/obo/UBERON_0002048 Lung Bronchopulmonary segment lymph node. http://purl.obolibrary.org/obo/FMA_68286 Lung lymph node Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. http://purl.obolibrary.org/obo/UBERON_0000029 Lymph node A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. [database_cross_reference: GOC:add][database_cross_reference: ISBN:0781735149][database_cross_reference: ISBN:0683073696] http://purl.obolibrary.org/obo/CL_0000542 Lymphocyte A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse and: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, and remodelling; lineage: hematopoietic, myeloid. http://purl.obolibrary.org/obo/CL_0000235 Macrophage The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. http://purl.obolibrary.org/obo/UBERON_0002509 Mesenteric lymph node CD3-, CD19, CD20, CD56-, CD14+ http://purl.obolibrary.org/obo/CL_0000576;http://purl.obolibrary.org/obo/CL_0000860 Monocyte Mouse Ear (UMLS CUI: C1512159) http://purl.obolibrary.org/obo/NCIT_C22712 Mouse Ear The moist, inner lining of some organs and body cavities (such as the nose, mouth, lungs, and stomach). Glands in the mucosa make mucus (a thick, slippery fluid). http://purl.obolibrary.org/obo/NCIT_C13166 Mucosa A sample derived from multiple epithelial tissues. http://purl.obolibrary.org/obo/NCIT_C189133 Multiple Epithelial Tissues Sample A sample derived from multiple immune cell types isolated from blood. http://purl.obolibrary.org/obo/NCIT_C189134 Multiple Immune Cells Blood Sample A sample derived from multiple immune cell types isolated from epithelial tissues. http://purl.obolibrary.org/obo/NCIT_C189135 Multiple Immune Cells Tissue Sample Fluid obtained by irrigation or washout of the nasal cavity and nasal mucosa. [database_cross_reference: Mondofacto_Dictionary:http://www.mondofacto.com/facts/dictionary?] http://purl.obolibrary.org/obo/BTO_0004977 Nasal lavage fluid A biospecimen collected from the nasal passages by swabbing. http://purl.obolibrary.org/obo/NCIT_C132119 Nasal Swab A biospecimen collected from the nasal passages by swabbing. http://purl.obolibrary.org/obo/NCIT_C155833 Nasal Swab or Nose Specimen A biospecimen collected from the back of the throat by swabbing. http://purl.obolibrary.org/obo/NCIT_C155831 Nasopharyngeal Swab Specimen A control sample where a negative result is expected, to help correlate a positive result with the variable being tested. (UMLS CUI: C1947986) http://purl.obolibrary.org/obo/NCIT_C64357 Negative Control has_broad_synonym: polynuclear neutrophilic leucocyte; poly; polymorphonuclear leucocyte; PMN; polymorphonuclear neutrophil; polymorphonuclear leukocyte; polynuclear neutrophilic leukocyte Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. database_cross_reference: FMA:62860; BTO:0000130; CALOHA:TS-0688 [database_cross_reference: ISBN:0721601464] http://purl.obolibrary.org/obo/CL_0000775 Neutrophil A 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. http://purl.obolibrary.org/obo/CL_0000623 NK cell A sample of non-B-cells and non-T-cells that were obtained from a blood specimen whose cellular components were sorted first. http://purl.obolibrary.org/obo/NCIT_C189130 Non-B-cell Non T-cell Sorted Blood Sample Sample Type is not specified or not received. If no Sample Type value is received, then this is the system default value. Not Specified The nerve that carries messages from the retina to the brain. (UMLS CUI: C0029130) http://purl.obolibrary.org/obo/NCIT_C12761 Optic Nerve An organization of cells into an organ-like structure. Organoids can be generated in culture. They are also found in certain neoplasms. An organization of cells into an organ-like structure. Organoids can be generated in culture. They are also found in certain neoplasms. (UMLS CUI: C0029250) http://purl.obolibrary.org/obo/NCIT_C172259 Organoids A biospecimen collected from the oropharynx by swabbing. http://purl.obolibrary.org/obo/NCIT_C155835 Oropharyngeal Swab Specimen Bone-forming cells which secrete an EXTRACELLULAR MATRIX. HYDROXYAPATITE crystals are then deposited into the matrix to form bone. Cells which secrete an extracellular matrix into which hydroxyapaetite crystals are deposited to form bone. (UMLS CUI: C0029418) http://purl.obolibrary.org/obo/NCIT_C12568 Osteoblasts A sample type that is not provided in the preferred values list. Other A digestive organ in the abdomen that has both endocrine and exocrine functions. An organ behind the lower part of the stomach that is the shape of a fish and about the size of a hand. It is a compound gland composed of both exocrine and endocrine tissues. The endocrine pancreas makes insulin so that the body can use glucose (sugar) for energy. The exocrine pancreas makes enzymes that help the body digest food. Spread all over the pancreas are areas called the Islets of Langerhans. The cells in these areas each have a special purpose. The alpha cells make glucagon, which raises the level of glucose in the blood; the beta cells make insulin; the delta cells make somatostatin. There are also PP cells and D1 cells, about which little is known. (UMLS CUI: C0030274) http://purl.obolibrary.org/obo/NCIT_C12393 Pancreas A Star-shaped, myofibroblast-like cells located in the periacinar, perivascular, and periductal regions of the EXOCRINE PANCREAS. They play a key role in the pathobiology of FIBROSIS; PANCREATITIS; and PANCREATIC CANCER. When pancreatic stellate cells are activated in response to an injury, they proliferate and synthesize large amounts of extracellular matrix. Pancreatic cancer cells can increase the activation of pancreatic stellate cells, which leads to fibrosis. (UMLS CUI: C2936598) http://purl.obolibrary.org/obo/NCIT_C107531 Pancreatic Stellate Cells Peripheral Blood Lymphocyte (UMLS CUI:C0599819) http://purl.obolibrary.org/obo/NCIT_C12938 PBL Peripheral Blood Mononuclear Cell- A leukocyte with a single non-segmented nucleus in the mature form. http://purl.obolibrary.org/obo/CL_0000842 PBMC Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. database_cross_reference: http://en.wikipedia.org/wiki/Placenta[database_cross_reference: http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/06placenta.htm] http://purl.obolibrary.org/obo/UBERON_0001987 Placenta Body substance in liquid state contained in the lumen of arterial and venous trees, blood capillary and the cardiac chambers; constitutes the liquid phase of blood. http://purl.obolibrary.org/obo/UBERON_0001969 Plasma A sample containing a mixture of multiple individual specimens of interest that were collected in a study. (UMLS CUI: C1709595) http://purl.obolibrary.org/obo/NCIT_C165587 Pooled Sample The lymph nodes which drain the legs; contained in the popliteal fossa. http://purl.obolibrary.org/obo/UBERON_0001543 Popliteal lymph node A control sample that is known to produce a positive result if the test is working as expected. (UMLS CUI: C1883676) http://purl.obolibrary.org/obo/NCIT_C64356 Positive Control A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. http://purl.obolibrary.org/obo/CHEBI_36080 Protein A biospecimen collected from the rectum by swabbing. http://purl.obolibrary.org/obo/NCIT_C173641 Rectal Swab Specimen A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. database_cross_reference: MESH:A11.118.290database_cross_reference: GOC:tfm http://purl.obolibrary.org/obo/CL_0000232 Red Blood Cell A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. http://purl.obolibrary.org/obo/UBERON_0001836 Saliva An exocrine gland that secretes saliva. Salivary glands are mostly located in and around the oral cavity. (UMLS CUI: C0036098) http://purl.obolibrary.org/obo/NCIT_C12426 Salivary Glands Body substance derived from plasma by the elimination of fibrinogen. http://purl.obolibrary.org/obo/UBERON_0001977 Serum Nonparenchymatous organ that consists of the dermis and epidermis. Subdivisions of the skin surround various body parts; as a whole, the skin constitutes the external layer of the body. http://purl.obolibrary.org/obo/UBERON_0002097 Skin of body Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). http://purl.obolibrary.org/obo/UBERON_0002108 Small intestine A sample derived from sorted tissues. http://purl.obolibrary.org/obo/NCIT_C189132 Sorted Tissue Sample The organ that functions to filter blood and to store red corpuscles and platelets. http://purl.obolibrary.org/obo/UBERON_0002106 Spleen Material containing mucus, cellular debris, microorganisms and sometimes blood or pus. It is ejected through the mouth from the lungs, bronchi, and trachea. (UMLS CUI: C0038056) http://purl.obolibrary.org/obo/NCIT_C13278 Sputum An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. http://purl.obolibrary.org/obo/UBERON_0000945 Stomach Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae. http://purl.obolibrary.org/obo/UBERON_0001090 Synovial fluid Thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. http://purl.obolibrary.org/obo/UBERON_0007616 Synovial tissue CD3+ http://purl.obolibrary.org/obo/CL_0000084 T cell Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. http://purl.obolibrary.org/obo/UBERON_0002370 Thymus Either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx. http://purl.obolibrary.org/obo/UBERON_0002372 Tonsil The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. [database_cross_reference: GO:0060438][database_cross_reference: http://en.wikipedia.org/wiki/Vertebrate_trachea] http://purl.obolibrary.org/obo/UBERON_0003126 Trachea A tumor sample, or entire tumor that is removed for microscopic examination. http://purl.obolibrary.org/obo/NCIT_C18009 Tumor Tissue Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. [database_cross_reference: http://en.wikipedia.org/wiki/Cord_blood] http://purl.obolibrary.org/obo/UBERON_0012168 Umbilical cord blood A sample derived from multiple, unsorted tissues. http://purl.obolibrary.org/obo/NCIT_C189131 Unsorted Tissue Sample Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion http://purl.obolibrary.org/obo/UBERON_0001255 Urinary bladder Excretion that is the output of a kidney database_cross_reference: http://en.wikipedia.org/wiki/Urine[database_cross_reference: https://github.com/geneontology/go-ontology/issues/11025] http://purl.obolibrary.org/obo/UBERON_0001088 Urine A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. [database_cross_reference: http://orcid.org/0000-0002-6601-2165] [database_cross_reference: http://en.wikipedia.org/wiki/Vagina] http://purl.obolibrary.org/obo/UBERON_0000996 Vagina Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid). http://purl.obolibrary.org/obo/UBERON_0000178 Whole blood