diff --git a/src/ontology/OntoFox_inputs/ChEBI_input.txt b/src/ontology/OntoFox_inputs/ChEBI_input.txt index d0200298..0c9854ad 100755 --- a/src/ontology/OntoFox_inputs/ChEBI_input.txt +++ b/src/ontology/OntoFox_inputs/ChEBI_input.txt @@ -6,6 +6,7 @@ CHEBI [Low level source term URIs] http://purl.obolibrary.org/obo/CHEBI_23367 +http://purl.obolibrary.org/obo/CHEBI_4431 # deoxyribonucleotide http://purl.obolibrary.org/obo/CHEBI_4705 http://purl.obolibrary.org/obo/CHEBI_15377 http://purl.obolibrary.org/obo/CHEBI_15956 @@ -25,6 +26,7 @@ http://purl.obolibrary.org/obo/CHEBI_31624 http://purl.obolibrary.org/obo/CHEBI_31642 http://purl.obolibrary.org/obo/CHEBI_31643 http://purl.obolibrary.org/obo/CHEBI_31991 +http://purl.obolibrary.org/obo/CHEBI_32875 # methyl group http://purl.obolibrary.org/obo/CHEBI_33359 http://purl.obolibrary.org/obo/CHEBI_33375 http://purl.obolibrary.org/obo/CHEBI_33376 @@ -124,6 +126,8 @@ http://purl.obolibrary.org/obo/CHEBI_39124 # calcium ion [Top level source term URIs and target direct superclass URIs] http://purl.obolibrary.org/obo/CHEBI_23367 subClassOf http://purl.obolibrary.org/obo/BFO_0000040 +http://purl.obolibrary.org/obo/CHEBI_4431 # deoxyribonucleotide +subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 # molecular entity http://purl.obolibrary.org/obo/CHEBI_4705 subClassOf http://purl.obolibrary.org/obo/CHEBI_16991 http://purl.obolibrary.org/obo/CHEBI_15377 @@ -162,6 +166,8 @@ http://purl.obolibrary.org/obo/CHEBI_31643 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 http://purl.obolibrary.org/obo/CHEBI_31991 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +http://purl.obolibrary.org/obo/CHEBI_32875 # methyl group +subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 # molecular entity http://purl.obolibrary.org/obo/CHEBI_33359 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 http://purl.obolibrary.org/obo/CHEBI_33375 diff --git a/src/ontology/OntoFox_inputs/GO_input.txt b/src/ontology/OntoFox_inputs/GO_input.txt index a551396a..8a413b0a 100755 --- a/src/ontology/OntoFox_inputs/GO_input.txt +++ b/src/ontology/OntoFox_inputs/GO_input.txt @@ -47,7 +47,6 @@ http://purl.obolibrary.org/obo/GO_0005694 http://purl.obolibrary.org/obo/GO_0005739 # mitochondrion http://purl.obolibrary.org/obo/GO_0006006 http://purl.obolibrary.org/obo/GO_0006260 -http://purl.obolibrary.org/obo/GO_0006306 http://purl.obolibrary.org/obo/GO_0006338 http://purl.obolibrary.org/obo/GO_0006909 http://purl.obolibrary.org/obo/GO_0006955 @@ -66,7 +65,6 @@ http://purl.obolibrary.org/obo/GO_0015925 # galactosidase activity http://purl.obolibrary.org/obo/GO_0016064 http://purl.obolibrary.org/obo/GO_0016160 # amylase activity http://purl.obolibrary.org/obo/GO_0016231 # beta-N-acetylglucosaminidase activity -http://purl.obolibrary.org/obo/GO_0016570 # histone modification http://purl.obolibrary.org/obo/GO_0016788 #hydrolase activity, acting on ester bonds http://purl.obolibrary.org/obo/GO_0019814 http://purl.obolibrary.org/obo/GO_0019815 @@ -139,7 +137,6 @@ http://purl.obolibrary.org/obo/GO_0042611 http://purl.obolibrary.org/obo/GO_0043227 http://purl.obolibrary.org/obo/GO_0043316 http://purl.obolibrary.org/obo/GO_0043565 -http://purl.obolibrary.org/obo/GO_0044030 http://purl.obolibrary.org/obo/GO_0044807 # macrophage migration inhibitory factor production http://purl.obolibrary.org/obo/GO_0044808 # Oncostatin M production http://purl.obolibrary.org/obo/GO_0044809 # chemokine (C-C motif) ligand 17 production @@ -398,8 +395,6 @@ http://purl.obolibrary.org/obo/GO_0043316 subClassOf http://purl.obolibrary.org/obo/GO_0001906 http://purl.obolibrary.org/obo/GO_0043565 subClassOf http://purl.obolibrary.org/obo/OBI_0001588 -http://purl.obolibrary.org/obo/GO_0044030 -subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0048869 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0050896 @@ -458,10 +453,6 @@ http://purl.obolibrary.org/obo/GO_0097391 subClassOf http://purl.obolibrary.org/obo/GO_0032602 http://purl.obolibrary.org/obo/GO_0097392 subClassOf http://purl.obolibrary.org/obo/GO_0032602 -http://purl.obolibrary.org/obo/GO_0006306 -subClassOf http://purl.obolibrary.org/obo/GO_0008150 -http://purl.obolibrary.org/obo/GO_0016570 -subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0005739 subClassOf http://purl.obolibrary.org/obo/GO_0043227 http://purl.obolibrary.org/obo/GO_0140730 diff --git a/src/ontology/OntoFox_inputs/NCBITaxon_input.txt b/src/ontology/OntoFox_inputs/NCBITaxon_input.txt index 0c2eeb45..f93d913d 100755 --- a/src/ontology/OntoFox_inputs/NCBITaxon_input.txt +++ b/src/ontology/OntoFox_inputs/NCBITaxon_input.txt @@ -30,7 +30,6 @@ http://purl.obolibrary.org/obo/NCBITaxon_11676 http://purl.obolibrary.org/obo/NCBITaxon_11709 http://purl.obolibrary.org/obo/NCBITaxon_388799 http://purl.obolibrary.org/obo/NCBITaxon_10407 -http://purl.obolibrary.org/obo/NCBITaxon_11103 http://purl.obolibrary.org/obo/NCBITaxon_10376 http://purl.obolibrary.org/obo/NCBITaxon_10358 http://purl.obolibrary.org/obo/NCBITaxon_160 @@ -41,6 +40,7 @@ http://purl.obolibrary.org/obo/NCBITaxon_33208 #Metazoa http://purl.obolibrary.org/obo/NCBITaxon_784 http://purl.obolibrary.org/obo/NCBITaxon_12637 #Dengue http://purl.obolibrary.org/obo/NCBITaxon_37124 #Chikungunya +http://purl.obolibrary.org/obo/NCBITaxon_3052230 # Hepacivirus hominis [Top level source term URIs and target direct superclass URIs] diff --git a/src/ontology/OntoFox_outputs/CLO_imports.owl b/src/ontology/OntoFox_outputs/CLO_imports.owl index 07386bc8..411e533b 100644 --- a/src/ontology/OntoFox_outputs/CLO_imports.owl +++ b/src/ontology/OntoFox_outputs/CLO_imports.owl @@ -56,18 +56,11 @@ cell line cell - cell line cell - 细胞系细胞 A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture - - 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 - 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 cell line cell - cell line cell - 细胞系细胞 @@ -77,14 +70,9 @@ mortal cell line cell - mortal cell line cell - 非永生细胞系细胞 A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. - A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. mortal cell line cell - mortal cell line cell - 非永生细胞系细胞 @@ -94,15 +82,9 @@ immortal cell line cell - immortal cell line cell - 永生细胞系细胞 A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. - A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. - 预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。 immortal cell line cell - immortal cell line cell - 永生细胞系细胞 @@ -112,16 +94,11 @@ cell line - 细胞系 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). 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). - - 一个培养细胞群体，其代表具有共同增殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 - 培养的细胞群体代表具有共同繁殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 cell line - 细胞系 diff --git a/src/ontology/OntoFox_outputs/CL_imports.owl b/src/ontology/OntoFox_outputs/CL_imports.owl index ee5bfcbd..2e376162 100644 --- a/src/ontology/OntoFox_outputs/CL_imports.owl +++ b/src/ontology/OntoFox_outputs/CL_imports.owl @@ -32,7 +32,10 @@ definition + definition + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition + definition @@ -64,12 +67,7 @@ - - material entity - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - - material entity - + @@ -101,10 +99,10 @@ - native cell - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). + obsolete native cell + OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - native cell + obsolete native cell @@ -148,7 +146,7 @@ - + mesothelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. @@ -209,8 +207,7 @@ - - + platelet A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. @@ -282,9 +279,9 @@ - + megakaryocyte - A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. + A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release. megakaryocyte @@ -306,8 +303,7 @@ - - + band form neutrophil A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. @@ -320,7 +316,7 @@ - + nucleate erythrocyte An erythrocyte having a nucleus. @@ -333,8 +329,7 @@ - - + monocyte @@ -408,8 +403,7 @@ - - + eosinophil Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. @@ -422,8 +416,7 @@ - - + neutrophil 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. @@ -496,8 +489,7 @@ - - + promyelocyte A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. @@ -533,8 +525,7 @@ - - + metamyelocyte A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. @@ -546,8 +537,7 @@ - - + myelocyte A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. @@ -571,8 +561,7 @@ - - + segmented neutrophil of bone marrow A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface. @@ -585,7 +574,7 @@ - + peripheral blood mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. diff --git a/src/ontology/OntoFox_outputs/ChEBI_imports.owl b/src/ontology/OntoFox_outputs/ChEBI_imports.owl index 3b1dc17e..5d2120d0 100644 --- a/src/ontology/OntoFox_outputs/ChEBI_imports.owl +++ b/src/ontology/OntoFox_outputs/ChEBI_imports.owl @@ -86,7 +86,7 @@ water - An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. + An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms water @@ -352,7 +352,7 @@ cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses + A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. cortisol @@ -754,6 +754,18 @@ + + + + + methyl group + An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom. + + methyl group + + + + @@ -1097,9 +1109,22 @@ - ethylenediaminetetraacetic acid + EDTA(4-) + A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). + + EDTA(4-) + + + + + + + + + deoxyribonucleotide + A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen. - ethylenediaminetetraacetic acid + deoxyribonucleotide diff --git a/src/ontology/OntoFox_outputs/ENVO_imports.owl b/src/ontology/OntoFox_outputs/ENVO_imports.owl index 0baf7c5b..5e2a7aec 100644 --- a/src/ontology/OntoFox_outputs/ENVO_imports.owl +++ b/src/ontology/OntoFox_outputs/ENVO_imports.owl @@ -76,7 +76,7 @@ soil - Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. + An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms. soil @@ -100,7 +100,7 @@ environmental material - A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. + A material entity which other material entities in an environmental system are primarily or partially composed of. environmental material diff --git a/src/ontology/OntoFox_outputs/GO_imports.owl b/src/ontology/OntoFox_outputs/GO_imports.owl index 277cf3c7..014e607f 100644 --- a/src/ontology/OntoFox_outputs/GO_imports.owl +++ b/src/ontology/OntoFox_outputs/GO_imports.owl @@ -77,7 +77,7 @@ - + chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. @@ -198,7 +198,7 @@ adaptive immune response - An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). + An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). adaptive immune response @@ -303,7 +303,7 @@ molecular_function - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular_function @@ -315,7 +315,7 @@ antigen binding - Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. + Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. Antigen binding by an MHC protein complex allows the antigen to be displayed to a T cell or NK cell. antigen binding @@ -338,10 +338,10 @@ - L-iditol 2-dehydrogenase activity - Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+. + L-iditol 2-dehydrogenase (NAD+) activity + Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+. Acts on a number of sugar alcohols, including (but not limited to) L-iditol, D-glucitol, D-xylitol, and D-galactitol. - L-iditol 2-dehydrogenase activity + L-iditol 2-dehydrogenase (NAD+) activity @@ -399,7 +399,7 @@ alkaline phosphatase activity - Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum. + Catalysis of the reaction: a phosphate monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum. alkaline phosphatase activity @@ -435,7 +435,7 @@ creatine kinase activity - Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). + Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H+. creatine kinase activity @@ -494,10 +494,10 @@ - ribonuclease activity + RNA nuclease activity Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. - ribonuclease activity + RNA nuclease activity @@ -506,10 +506,10 @@ - ion channel activity - Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). + monoatomic ion channel activity + Enables the facilitated diffusion of a monoatomic ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). - ion channel activity + monoatomic ion channel activity @@ -519,7 +519,7 @@ cellular_component - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). cellular_component @@ -579,25 +579,13 @@ DNA replication - The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. + The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. DNA replication - - - - - DNA methylation - The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. - - DNA methylation - - - - @@ -638,10 +626,10 @@ - cellular response to DNA damage stimulus + DNA damage response Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. - cellular response to DNA damage stimulus + DNA damage response @@ -675,7 +663,7 @@ biological_process - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. biological_process @@ -747,7 +735,7 @@ gene expression - The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes. + The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. gene expression @@ -814,18 +802,6 @@ - - - - - histone modification - The covalent alteration of one or more amino acid residues within a histone protein. - - histone modification - - - - @@ -998,10 +974,10 @@ - interferon-gamma production + type II interferon production The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. - interferon-gamma production + type II interferon production @@ -1690,18 +1666,6 @@ - - - - - regulation of DNA methylation - Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. - - regulation of DNA methylation - - - - @@ -1743,7 +1707,7 @@ D-glutamyltransferase activity - Catalysis of the reaction: L(or D)-glutamine + D-glutamyl-peptide = NH3 + 5-glutamyl-D-glutamyl-peptide. + Catalysis of the reaction: D-glutamate + D-glutamine = gamma-D-glutamyl-D-glutamate + NH4+. Can also transfer additional glutamyl residues to a peptide, extending the polypeptide chain. D-glutamyltransferase activity @@ -1803,7 +1767,7 @@ ferritin complex - A protein complex that binds iron and acts as a major iron storage system. Intracellular and extracellular ferritin complexes have different ratios of two types of ferritin monomer, the L (light) chain and H (heavy) chain. + A protein complex that binds iron and acts as a major iron storage system. There are three major subclasses of ferritins: the classical ferritins (Ftn), the heme-containing bacterioferritins (Bfr) and the DNA-binding proteins from starved cells (Dps). Ftn and Bfr are made of 24 subunits, whereas Dps are smaller with 12 subunits. Ftn is found in most kindoms, while Bfr and Dps are restricted to prokaryotes. ferritin complex diff --git a/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl b/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl index eb0ca92f..cc1bfccb 100644 --- a/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl +++ b/src/ontology/OntoFox_outputs/NCBITaxon_imports.owl @@ -92,21 +92,10 @@ - - - - - Herpesviridae - - Herpesviridae - - - - - + Cytomegalovirus Cytomegalovirus @@ -117,15 +106,15 @@ - - Human gammaherpesvirus 4 + + human gammaherpesvirus 4 Epstein Barr virus Epstein-Barr virus Epstein-Barr virus EBV Human herpesvirus 4 Human herpesvirus type 4 - Human gammaherpesvirus 4 + human gammaherpesvirus 4 @@ -158,23 +147,6 @@ - - - - - Hepacivirus C - Hepatitis C virus - hepatitis C virus HCV - human hepatitis C virus - human hepatitis C virus HCV - human hepatitis virus C HCV - post-transfusion hepatitis non A non B virus - - Hepacivirus C - - - - @@ -349,6 +321,35 @@ + + + + + Orthoherpesviridae + + Orthoherpesviridae + + + + + + + + + Hepacivirus hominis + Hepacivirus C + Hepatitis C virus + hepatitis C virus HCV + human hepatitis C virus + human hepatitis C virus HCV + human hepatitis virus C HCV + post-transfusion hepatitis non A non B virus + + Hepacivirus hominis + + + + @@ -519,7 +520,7 @@ Saccharomyces cerevisiae - S. cerevisiae + Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast diff --git a/src/ontology/OntoFox_outputs/OMRSE_imports.owl b/src/ontology/OntoFox_outputs/OMRSE_imports.owl index 222d6591..2d6dadba 100644 --- a/src/ontology/OntoFox_outputs/OMRSE_imports.owl +++ b/src/ontology/OntoFox_outputs/OMRSE_imports.owl @@ -84,6 +84,12 @@ + + + + + + @@ -93,6 +99,30 @@ health care provider role + + + + + + + + hospital role + A healthcare provider role that inheres in an organization and is realized by providing inpatient care. + + hospital role + + + + + + + + + hospital organization + An organization that is the bearer of a hospital role. + + hospital organization + diff --git a/src/ontology/OntoFox_outputs/OPL_imports.owl b/src/ontology/OntoFox_outputs/OPL_imports.owl index 359d0929..e0f63af5 100644 --- a/src/ontology/OntoFox_outputs/OPL_imports.owl +++ b/src/ontology/OntoFox_outputs/OPL_imports.owl @@ -50,15 +50,6 @@ - - - - label - label - - - - - - material entity - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - - material entity - + @@ -120,7 +116,6 @@ - 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. @@ -181,7 +176,6 @@ - blood A fluid that is composed of blood plasma and erythrocytes. @@ -194,7 +188,6 @@ - amnion The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected. @@ -207,7 +200,6 @@ - breast The upper ventral region of the torso of an organism. @@ -233,7 +225,6 @@ - throat In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. @@ -330,7 +321,6 @@ - epithelium 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]. @@ -355,7 +345,6 @@ - aorta The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. @@ -489,7 +478,6 @@ - adipose tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. @@ -782,7 +770,6 @@ - cheek A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. @@ -807,7 +794,6 @@ - coronary artery @@ -821,7 +807,6 @@ - artery An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. @@ -834,7 +819,6 @@ - vein Any of the tubular branching vessels that carry blood from the capillaries toward the heart. @@ -907,7 +891,6 @@ - nasal cavity mucosa The mucous membrane that lines the nasal cavity[MP]. @@ -920,7 +903,6 @@ - minor salivary gland One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. @@ -982,7 +964,6 @@ - milk @@ -1045,7 +1026,6 @@ - areola Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. @@ -1095,7 +1075,6 @@ - dermis 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[WP]. @@ -1108,7 +1087,6 @@ - hypodermis Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. @@ -1121,7 +1099,6 @@ - skin of body The organ covering the body that consists of the dermis and epidermis. @@ -1146,7 +1123,6 @@ - liver 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]. @@ -1171,7 +1147,6 @@ - integument The dermis, epidermis and hypodermis. @@ -1184,7 +1159,6 @@ - peritoneum @@ -1308,7 +1282,6 @@ - esophagus mucosa A mucosa that is part of a esophagus [Automatically generated definition]. @@ -1345,7 +1318,6 @@ - trachea The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. @@ -1395,7 +1367,6 @@ - mucosa of nasopharynx A mucosa that is part of a nasopharynx [Automatically generated definition]. @@ -1408,7 +1379,6 @@ - mucosa of oropharynx A mucosa that is part of a oropharynx [Automatically generated definition]. @@ -1517,7 +1487,6 @@ - tibial artery @@ -1543,7 +1512,6 @@ - tendon of biceps brachii A tendon that attaches_to a biceps brachii. @@ -1630,7 +1598,6 @@ - suprapubic skin Area of skin in the hypoastric region of the abdomen. diff --git a/src/ontology/OntoFox_outputs/VO_imports.owl b/src/ontology/OntoFox_outputs/VO_imports.owl index 29867e45..186d1125 100644 --- a/src/ontology/OntoFox_outputs/VO_imports.owl +++ b/src/ontology/OntoFox_outputs/VO_imports.owl @@ -25,17 +25,9 @@ - editor preferred label - editor preferred label - editor preferred term editor preferred term - editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - editor preferred label - editor preferred label - editor preferred term editor preferred term - editor preferred term~editor preferred label @@ -43,14 +35,9 @@ - definition definition - textual definition - The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - definition definition - textual definition @@ -65,10 +52,7 @@ - - label - label - + @@ -100,7 +84,7 @@ vaccine - A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. + Material entity that is manufactured to realize the vaccine function. vaccine @@ -112,7 +96,7 @@ vaccination - a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response. + A process of administering a vaccine in vivo to a recipient (e.g., human) with the intent to invoke a protective or therapeutic adaptive immune response. vaccination diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 59254ba4..b4d47839 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -470,6 +470,12 @@ + + + + + + @@ -560,6 +566,12 @@ + + + + + + @@ -1034,12 +1046,6 @@ - - - - - - @@ -1106,12 +1112,6 @@ - - - - - - @@ -1178,12 +1178,6 @@ - - - - - - @@ -1322,12 +1316,6 @@ - - - - - - @@ -1346,6 +1334,12 @@ + + + + + + @@ -2603,6 +2597,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2625,17 +2663,6 @@ - - - - - - - - - - - @@ -2912,6 +2939,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2949,17 +3020,6 @@ - - - - - - - - - - - @@ -3647,6 +3707,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -3679,17 +3783,6 @@ - - - - - - - - - - - @@ -9287,20 +9380,53 @@ - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - + Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 @@ -9319,6 +9445,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -9331,17 +9501,6 @@ - - - - - - - - - - - @@ -10309,23 +10468,57 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - + + - - - - @@ -10337,10 +10530,20 @@ - + - - + + + + + + + + + + + + @@ -10351,10 +10554,10 @@ - + - - + + @@ -10394,17 +10597,6 @@ - - - - - - - - - - - @@ -12444,17 +12636,6 @@ - - - - - - - - - - - @@ -12566,17 +12747,6 @@ - - - - - - - - - - - @@ -14295,7 +14465,7 @@ - + @@ -14313,7 +14483,7 @@ - + @@ -14731,7 +14901,7 @@ - + @@ -14749,7 +14919,7 @@ - + @@ -21909,6 +22079,12 @@ + + + + + + @@ -26567,6 +26743,237 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR screen assay + An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. + Bjoern Peters + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR screen assay + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR screen using single-cell RNA-seq + An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression. + Bjoern Peters + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR screen using single-cell RNA-seq + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR perturbation screen using flow cytometry + An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes. + Bjoern Peters + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR screen using flow cytometry + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + single-nucleus methylcytosine and transcriptome sequencing assay + https://www.biorxiv.org/content/10.1101/434845v1 + A DNA methylation profiling by high throughput sequencing assay that measures the cytosine DNA methylation and gene expression signature of single nuclei. + Jennifer Jou + Sebastian Duesing + snmCT-seq + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1785 + Jennifer Jou + single-nucleus methylcytosine and transcriptome sequencing assay + + + + diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index 745ec45a..f876c957 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -188,9 +188,15 @@ - + - + + + + + + + @@ -6230,7 +6236,17 @@ - + + + + + + + + + + + @@ -9146,6 +9162,52 @@ + + + + + + + + + + + Illumina NovaSeq X + A DNA sequencer with three flow cell types manufactured by Illumina. The NovaSeq X provides an output of up to 8 Tb (26-52 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. + Morgana Barroso Oquendo + NovaSeq X Series + NovaSeq X System + https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html + https://github.com/obi-ontology/obi/issues/1802 + Morgana Barroso Oquendo + Illumina NovaSeq X + + + + + + + + + + + + + + + Illumina NovaSeq X Plus + A DNA sequencer with three flow cell types manufactured by Illumina. It features a dual-flow cell configuration, allowing to reach an output of up to 16 Tb (52-104 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. + Morgana Barroso Oquendo + NovaSeq X Series + NovaSeq X System + https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html + https://github.com/obi-ontology/obi/issues/1802 + Morgana Barroso Oquendo + Illumina NovaSeq X Plus + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index f0ece3b6..a3e6d377 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -2259,12 +2259,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - @@ -2339,12 +2333,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - @@ -2667,12 +2655,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 47c9115b..da996a0e 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -18,8 +18,8 @@ OBI:0000435 genotyping assay metadata complete genotype profiling|SNP analysis OBI:0000438 DNA sequence variation detection assay ready for release An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. OBI Biomaterial Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 Philippe Rocca-Serra subclass assay DNA extract measurement datum sequence feature identification objective OBI:0000443 analyte assay ready for release An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Bjoern Peters|Helen Parkinson|Philippe Rocca-Serra|Alan Ruttenberg|OBI Planned process branch example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output Bjoern Peters|Helen Parkinson|Philippe Rocca-Serra|Alan Ruttenberg subclass assay measurement datum analyte measurement objective OBI:0000445 mass measurement assay metadata complete An assay that determines the mass of an evaluant OBI The patients was weighed and mass was determined to be 47 kilograms Helen Parkinson subclass assay material entity mass measurement datum -OBI:0000447 intracellular electrophysiology recording assay metadata incomplete An electrophysiology assay where the recording location of the electrode is intracellular. Frank Gibson Frank Gibson subclass electrophysiology assay mass measurement datum ion channel activity -OBI:0000454 extracellular electrophysiology recording assay metadata complete An electrophysiology assay where the recording location of the electrode is extracellular. Frank Gibson The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron Frank Gibson|Helen Parkinson subclass electrophysiology assay mass measurement datum ion channel activity +OBI:0000447 intracellular electrophysiology recording assay metadata incomplete An electrophysiology assay where the recording location of the electrode is intracellular. Frank Gibson Frank Gibson subclass electrophysiology assay mass measurement datum monoatomic ion channel activity +OBI:0000454 extracellular electrophysiology recording assay metadata complete An electrophysiology assay where the recording location of the electrode is extracellular. Frank Gibson The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron Frank Gibson|Helen Parkinson subclass electrophysiology assay mass measurement datum monoatomic ion channel activity OBI:0000470 mass spectrometry assay An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. Philippe Rocca-Serra Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides. Philippe Rocca-Serra equivalent assay mass spectrometer OBI:0000520 clinical chemistry assay metadata complete detection of analyte in blood sample|chemical pathology An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. url:https://en.wikipedia.org/wiki/Clinical_chemistry Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. Philippe Rocca-Serra subclass analyte assay bodily fluid specimen scattered molecular aggregate OBI:0000537 copy number variation profiling assay metadata complete CNV analysis An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796 Philippe Rocca-Serra subclass assay measurement datum genetic characteristics information @@ -27,11 +27,11 @@ OBI:0000615 protein expression profiling assay metadata complete proteomic anal OBI:0000623 NMR spectroscopy assay metadata incomplete Nuclear magnetic resonance spectroscopy An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202 Philippe Rocca-Serra subclass assay OBI:0000626 DNA sequencing assay metadata incomplete nucleotide sequencing A sequencing assay which determines information on the sequence of a DNA molecule. url:https://en.wikipedia.org/wiki/DNA_sequencing Illumina (Solexa) sequencing is an example of DNA sequencing Philippe Rocca-Serra equivalent sequencing assay DNA extract DNA sequencer DNA sequence data primary structure of DNA macromolecule OBI:0000630 hematology assay metadata incomplete blood analysis|haematology An assay that studies blood and blood producing organs using a variety of techniques and instruments OBI branch derived Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 Philippe Rocca-Serra subclass assay ('information content entity' and ('is about' some hemopoiesis)) -OBI:0000634 DNA methylation profiling assay ready for release DNA methylation profiling An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. OBI branch derived Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 Philippe Rocca-Serra subclass epigenetic modification assay DNA extract (specimen and ('has part' some 'deoxyribonucleic acid')) data item DNA methylation epigenetic modification identification objective +OBI:0000634 DNA methylation profiling assay ready for release DNA methylation profiling An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. OBI branch derived Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 Philippe Rocca-Serra subclass epigenetic modification assay DNA extract ('deoxyribonucleotide' and ('has part' some 'methyl group')) (specimen and ('has part' some 'deoxyribonucleic acid')) data item epigenetic modification identification objective OBI:0000661 enzyme-linked immunosorbent assay ELISA An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. IEDB 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. IEDB subclass logical definition does not capture details of processing analyte assay immunoglobulin complex, circulating OBI:0000664 BrdU incorporation assay A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. IEDB The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. IEDB subclass logical definition does not capture how exactly BRDU is utilized cell proliferation assay ""5-bromo-2'-deoxyuridine"" OBI:0000669 tritiated thymidine incorporation assay A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. IEDB The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. IEDB subclass logical definition does not capture how exactly thymidine is utilized cell proliferation assay radioactivity detection tritiated thymidine -OBI:0000693 MeDIP-seq assay metadata complete Methylated DNA immunoprecipitation sequencing assay A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. Philippe Rocca-Serra subclass infer chip & sequecing assays DNA methylation profiling assay chromatin immunoprecipitation|library preparation sequencing assay DNA extract|('has part' some chromatin) DNA sequencer DNA extract sequence data regulation of DNA methylation epigenetic modification identification objective +OBI:0000693 MeDIP-seq assay metadata complete Methylated DNA immunoprecipitation sequencing assay A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. Philippe Rocca-Serra subclass infer chip & sequecing assays DNA methylation profiling assay chromatin immunoprecipitation|library preparation sequencing assay DNA extract|('has part' some chromatin) ('deoxyribonucleotide' and ('has part' some 'methyl group')) DNA sequencer DNA extract sequence data epigenetic modification identification objective OBI:0000695 chain termination sequencing assay metadata complete Sanger sequencing|dye terminator sequencing A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position url:https://en.wikipedia.org/wiki/Sanger_sequencing PMID: 271968. DNA sequencing with chain-terminating inhibitors. Philippe Rocca-Serra subclass DNA sequencing by synthesis assay ('ABI 377 automated sequencer' or 'Li-Cor 4300 DNA Analysis System') PCR product OBI:0000697 Helicos sequencing assay metadata complete true single molecule sequencing A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Philippe Rocca-Serra subclass DNA sequencing by synthesis assay HeliScope Single Molecule Sequencer OBI:0000699 survival assessment assay metadata incomplete An assay that measures the occurrence of death events in one or more organisms over time subclass assay organism survival rate organism @@ -44,7 +44,7 @@ OBI:0000724 Solexa sequencing assay metadata complete reversible terminator seq OBI:0000730 pyrosequencing assay metadata complete A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. url:http://en.wikipedia.org/wiki/Pyrosequencing Pyrosequencing sheds light on DNA sequencing. PMID:1115661 Philippe Rocca-Serra subclass DNA sequencing by synthesis assay ('454 Genome Sequence 20' or '454 Genome Sequencer FLX') OBI:0000734 DNA sequencing by synthesis assay metadata incomplete A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing Philippe Rocca-Serra subclass DNA sequencing assay DNA polymerase complex OBI:0000743 immune response assay metadata incomplete An assay that determines information about an immune response IEDB Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA. Bjoern Peters|Randi Vita subclass assay measurement datum immune response -OBI:0000748 bisulfite sequencing assay metadata complete A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. url:https://en.wikipedia.org/wiki/Bisulfite_sequencing PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Philippe Rocca-Serra|Sagar Jain subclass DNA meth profiling is a epigenetic mod assay, does not need inference DNA methylation profiling assay DNA sequencing assay DNA extract DNA sequencer DNA extract ('measurement datum' and 'DNA sequence data') regulation of DNA methylation epigenetic modification identification objective +OBI:0000748 bisulfite sequencing assay metadata complete A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. url:https://en.wikipedia.org/wiki/Bisulfite_sequencing PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Philippe Rocca-Serra|Sagar Jain subclass DNA meth profiling is a epigenetic mod assay, does not need inference DNA methylation profiling assay DNA sequencing assay DNA extract ('deoxyribonucleotide' and ('has part' some 'methyl group')) DNA sequencer DNA extract ('measurement datum' and 'DNA sequence data') epigenetic modification identification objective OBI:0000787 human antithrombin-III in blood assay ready for release AT-III assay An assay that measures the amount of antithrombin III in blood. url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. Alan Ruttenberg subclass analyte assay ('scattered molecular aggregate' and ('has grain' some antithrombin-III)) scalar measurement datum blood coagulation OBI:0000802 prothrombin time assay metadata complete An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). Alan Ruttenberg subclass assay scalar measurement datum blood coagulation OBI:0000805 antithrombin-III berichrome assay metadata complete AT-III assay An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 subclass human antithrombin-III in blood assay (has_specified_output some 'scalar measurement datum') and ('has participant' some 'Berichrom(r) Antithrombin III (A) Kit') and (has_specified_output exactly 1 Thing) @@ -162,8 +162,8 @@ OBI:0001680 Sos-recruitment assay ready for release SRS A binding assay that de OBI:0001681 yeast one-hybrid assay ready for release Y1H An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. PMID:22218861 Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702 Philippe Rocca-Serra|Marcus Chibucos subclass binding assay genetically modified material data item sequence-specific DNA binding OBI:0001682 bacterial one-hybrid assay ready for release B1H An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence url:http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042 Philippe Rocca-Serra|Marcus Chibucos subclass yeast one-hybrid assay genetically modified material data item sequence-specific DNA binding protein and DNA interaction identification objective OBI:0001683 chromosome organization assay by fluorescence in-situ hybridization ready for release An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity Duplication of intrachromosomal insertion segments 4q32__�q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization. PMID:22384449 Philippe Rocca-Serra|Marcus Chibucos https://github.com/obi-ontology/obi/issues/788| subclass in-situ hybridization assay ('has part' some chromosome) molecular label data item chromosome organization biological feature identification objective -OBI:0001684 methylation-specific polymerase chain reaction assay ready for release MSP An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. PMID:8790415 Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 Philippe Rocca-Serra|Marcus Chibucos subclass assay data item regulation of DNA methylation -OBI:0001685 amplification of intermethylated sites assay ready for release AIMS assay|intermethylated site amplification An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. PMID:18987810 Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 Philippe Rocca-Serra|Marcus Chibucos subclass DNA methylation profiling assay high molecular weight DNA extract data item regulation of DNA methylation epigenetic modification identification objective +OBI:0001684 methylation-specific polymerase chain reaction assay ready for release MSP An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. PMID:8790415 Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 Philippe Rocca-Serra|Marcus Chibucos subclass assay ('deoxyribonucleotide' and ('has part' some 'methyl group')) data item +OBI:0001685 amplification of intermethylated sites assay ready for release AIMS assay|intermethylated site amplification An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. PMID:18987810 Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 Philippe Rocca-Serra|Marcus Chibucos subclass DNA methylation profiling assay ('deoxyribonucleotide' and ('has part' some 'methyl group')) high molecular weight DNA extract data item epigenetic modification identification objective OBI:0001686 in-situ hybridization assay ready for release ISH|in situ hybridization An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. PMID:9021518 Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 Philippe Rocca-Serra|Marcus Chibucos subclass assay nucleic acid hybridization labeled nucleic acid extract data item macromolecule localization biological feature identification objective OBI:0001689 cytochalasin-induced inhibition of actin polymerization assay ready for release An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). Philippe Rocca-Serra|Marcus Chibucos subclass assay cytochalasin data item actin filament polymerization biological feature identification objective OBI:0001699 antibody cross-blocking assay antibody inhibition of antibody binding A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. IEDB Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format. IEDB subclass logical definition is not capturing how the different antibodies are used in relation to each other. competitive inhibition of binding assay immunoglobulin complex, circulating ('immunoglobulin complex, circulating' and ('has role' some 'positive reference substance role')) @@ -175,7 +175,7 @@ OBI:0001853 DNase I hypersensitive sites sequencing assay metadata complete An OBI:0001857 RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay metadata complete RIP-seq assay|RIP-seq An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). PMID:21172659 Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer sequencing assay analyte assay immunoprecipitation|library preparation|cross linking RNA sequencing assay protein-containing complex DNA sequencer|sonicator DNA sequence data protein and RNA interaction identification objective OBI:0001858 cross-linking immunoprecipitation high-throughput sequencing assay metadata complete HITS-CLIP|CLIP-seq|CLIP-seq assay An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. PMID:18978773 Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer sequencing assay analyte assay immunoprecipitation|library preparation|cross linking RNA sequencing assay protein-containing complex DNA sequencer DNA sequence data protein and RNA interaction identification objective OBI:0001859 formaldehyde-assisted isolation of regulatory elements assay metadata complete FAIRE-seq assay|FAIRE-seq An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. url:http://en.wikipedia.org/wiki/FAIRE-Seq Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass sequencing assay library preparation|cross linking DNA sequencing assay DNA extract DNA sequence data regulatory_region protein and DNA interaction identification objective -OBI:0001861 methylation-sensitive restriction enzyme sequencing assay metadata complete MRE-seq|MRE-seq assay An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. PMID:20613842 Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer DNA sequencing assay DNA methylation profiling by high throughput sequencing assay library preparation|specific enzymatic cleavage DNA sequencing assay DNA extract DNA sequencer DNA sequence data regulation of DNA methylation epigenetic modification identification objective +OBI:0001861 methylation-sensitive restriction enzyme sequencing assay metadata complete MRE-seq|MRE-seq assay An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. PMID:20613842 Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer DNA sequencing assay DNA methylation profiling by high throughput sequencing assay library preparation|specific enzymatic cleavage DNA sequencing assay DNA extract ('deoxyribonucleotide' and ('has part' some 'methyl group')) DNA sequencer DNA sequence data epigenetic modification identification objective OBI:0001862 reduced representation bisulfite sequencing assay metadata complete reduced representation bisulfite-seq|RRBS|RRBS assay A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. PMC:1258174 Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868_�_5877. [PMCID: PMC1258174] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass bisulfite sequencing assay library preparation|specific enzymatic cleavage OBI:0001863 shotgun bisulfite-seq assay metadata complete WGBS|Shotgun bisulfite sequencing|whole genome bisulfite sequencing|WGSBS|whole-genome shotgun bisulfite sequencing A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. PMID:18278030 Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. Venkat Malladi|Chris Stoeckert|Jie Zheng subclass bisulfite sequencing assay library preparation sonicator OBI:0001864 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay metadata complete RAMPAGE An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. PMID:22936248 Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] Venkat Malladi|Chris Stoeckert|Jie Zheng subclass infer sequencing assay transcription profiling assay library preparation|non specific enzymatic cleavage sequencing assay RNA extract DNA sequencer DNA sequence data transcription start site identification objective @@ -205,8 +205,8 @@ OBI:0001985 microarray assay An analyte assay where binding of the analyte to OBI:0001986 immunohistochemistry An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. IEDB Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. IEDB equivalent immuno staining assay specimen from organism material entity OBI:0002014 DNA methylation profiling by ChIP-chip assay DNA methylation ChIP-chip An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-chip assay epigenetic modification assay chromatin immunoprecipitation ChIP-chip assay ('has part' some chromatin) DNA microarray epigenetic modification identification objective OBI:0002015 transcription profiling by MPSS assay expression MPSS A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). url:http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing Chris Stoeckert|Jie Zheng subclass transcription profiling assay library preparation DNA sequencing assay assay bead -OBI:0002016 histone modification identification by ChIP-chip assay histone modification ChIP-chip An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-chip assay epigenetic modification assay chromatin immunoprecipitation ChIP-chip assay ('has part' some chromatin) DNA microarray information content entity histone modification epigenetic modification identification objective -OBI:0002017 histone modification identification by ChIP-Seq assay histone modification ChIP-Seq An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-seq assay epigenetic modification assay chromatin immunoprecipitation ChIP-seq assay ('has part' some chromatin) DNA sequencer DNA sequence data histone modification epigenetic modification identification objective +OBI:0002016 histone modification identification by ChIP-chip assay histone modification ChIP-chip An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-chip assay epigenetic modification assay chromatin immunoprecipitation ChIP-chip assay ('has part' some chromatin) DNA microarray information content entity epigenetic modification identification objective +OBI:0002017 histone modification identification by ChIP-Seq assay histone modification ChIP-Seq An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-seq assay epigenetic modification assay chromatin immunoprecipitation ChIP-seq assay ('has part' some chromatin) DNA sequencer DNA sequence data epigenetic modification identification objective OBI:0002018 transcription factor binding site identification by ChIP-chip assay TF Binding ChIP-chip A transcription factor binding site assay that utilizes ChIP-chip technology. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-chip assay transcription factor binding site assay chromatin immunoprecipitation ChIP-chip assay ('has part' some chromatin) DNA microarray information content entity TF_binding_site protein and DNA interaction identification objective OBI:0002019 transcription factor binding site identification by ChIP-Seq assay TF Binding ChIP-Seq A transcription factor binding site assay that utilizes ChIP-seq technology. Penn group Chris Stoeckert|Jie Zheng subclass infer chip-seq assay transcription factor binding site assay chromatin immunoprecipitation ChIP-seq assay ('has part' some chromatin) DNA sequencer DNA sequence data TF_binding_site protein and DNA interaction identification objective OBI:0002020 epigenetic modification assay An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. Penn group Chris Stoeckert|Jie Zheng equivalent assay epigenetic modification identification objective @@ -260,15 +260,15 @@ OBI:0002147 HIV group O antibody assay HIV I/II Plus O assay An antigen specif OBI:0002148 surface HBV antibody assay HBsAb assay An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepatitis B virus')) OBI:0002149 core HBV antibody assay HBcAb assay An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepatitis B virus')) OBI:0002150 core HBV IgM antibody assay HBcAb-IgM assay An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepatitis B virus')) -OBI:0002151 HCV antibody assay HCV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepacivirus C')) -OBI:0002152 EBV IgG antibody assay EBV IgG Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4')) -OBI:0002153 EBV IgM antibody assay EBV IgM Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4')) +OBI:0002151 HCV antibody assay HCV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Hepacivirus hominis')) +OBI:0002152 EBV IgG antibody assay EBV IgG Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'human gammaherpesvirus 4')) +OBI:0002153 EBV IgM antibody assay EBV IgM Ab assay An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'human gammaherpesvirus 4')) OBI:0002154 CMV antibody assay CMV Ab assay An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass antigen specific antibodies assay ('immunoglobulin complex' and ('has disposition to bind' some 'Cytomegalovirus')) OBI:0002155 venereal disease research laboratory test VDRL test An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay immunoglobulin complex OBI:0002156 rapid plasma reagin test RPR assay An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. url:http://www.differencebetween.net/science/health/difference-between-vdlr-and-rpr/ Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay immunoglobulin complex OBI:0002157 HBV surface antigen assay HBsAg assay An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay Hepatitis B virus OBI:0002158 HIV-1 nucleic acid testing HIV-1 NAT An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay ('nucleic acid' and ('part of' some 'Human immunodeficiency virus 1')) -OBI:0002159 HCV nucleic acid testing HCV NAT An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay ('nucleic acid' and ('part of' some 'Hepacivirus C')) +OBI:0002159 HCV nucleic acid testing HCV NAT An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. OBI Chris Stoeckert|Bjoern Peters|Randi Vita|James Overton NCI BBRB https://github.com/obi-ontology/obi/issues/825 subclass analyte assay ('nucleic acid' and ('part of' some 'Hepacivirus hominis')) OBI:0002160 multiplexed indexed T7 ChIP-seq assay ready for release Mint-ChIP|Mint-ChIP-seq A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. url:http://www.cell.com/molecular-cell/abstract/S1097-2765(15)00863-1 Jason Hilton|Chris Stoeckert ENCODE DCC https://github.com/obi-ontology/obi/issues/829 subclass ChIP-seq assay OBI:0002161 systematic evolution of ligands by exponential enrichment assay SELEX A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ PMID:21720957 Rebecca Jackson subclass binding assay OBI:0002162 footprinting assay An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. doi:10.1002/3527600906.mcb.200300025 Bjoern Peters subclass assay @@ -624,10 +624,10 @@ OBI:0003430 gamma-glutamyltransferase activity level assay An enzymatic activ OBI:0003431 glutamate dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay glutamate dehydrogenase [NAD(P)+] activity OBI:0003432 isocitrate dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay isocitrate dehydrogenase [NAD(P)+] activity OBI:0003433 lactate dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay lactate dehydrogenase activity -OBI:0003434 sorbitol dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay L-iditol 2-dehydrogenase activity +OBI:0003434 sorbitol dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. James A. Overton equivalent enzymatic activity level assay L-iditol 2-dehydrogenase (NAD+) activity OBI:0003435 acyl-CoA oxidase activity level assay An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample. James A. Overton equivalent enzymatic activity level assay acyl-CoA oxidase activity OBI:0003436 N-acetyl-beta-glucosaminidase activity level assay An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample. James A. Overton equivalent enzymatic activity level assay beta-N-acetylglucosaminidase activity -OBI:0003437 ribonuclease activity level assay An enzymatic activity level assay that measures the activity of ribonuclease in a sample. James A. Overton equivalent enzymatic activity level assay ribonuclease activity +OBI:0003437 ribonuclease activity level assay An enzymatic activity level assay that measures the activity of ribonuclease in a sample. James A. Overton equivalent enzymatic activity level assay RNA nuclease activity OBI:0003438 galactosidase activity level assay An enzymatic activity level assay that measures the activity of galactosidase in a sample. James A. Overton equivalent enzymatic activity level assay galactosidase activity OBI:0003457 epitope protection from infectious challenge experiment based on survival survival after infectious challenge An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. IEDB Hector Guzman-Orozco https://github.com/obi-ontology/obi/issues/1594 subclass epitope protection from infectious challenge experiment OBI:0003458 epitope protection from tumor challenge experiment based on burden burden after tumor challenge An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls. IEDB Hector Guzman-Orozco https://github.com/obi-ontology/obi/issues/1594 subclass epitope protection from tumor challenge experiment @@ -649,14 +649,18 @@ OBI:0003582 cell proliferation assay using carboxyfluorescein succinimidyl ester OBI:0003583 cell viability assay A cytometry assay which measures the number of living cells in a population. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 equivalent cytometry assay viability OBI:0003584 cell viability assay using Annexin V staining A cell viability assay that uses Annexin V staining to detect apoptotic cells. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 equivalent cell viability assay Annexin V staining OBI:0003587 cell culture assay An assay that has cell culture as an input. Sebastian Duesing|Randi Vita equivalent assay cultured cell population -OBI:0003589 serum anti-Epstein-Barr virus antibody level assay EBV An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. Sebastian Duesing|Randi Vita equivalent antigen specific antibodies assay blood serum specimen ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4')) +OBI:0003589 serum anti-Epstein-Barr virus antibody level assay EBV An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. Sebastian Duesing|Randi Vita equivalent antigen specific antibodies assay blood serum specimen ('immunoglobulin complex' and ('has disposition to bind' some 'human gammaherpesvirus 4')) OBI:0003590 serum anti-cytomegalovirus antibody level assay CMV A CMV antibody assay that has serum as an input. Sebastian Duesing|Randi Vita equivalent CMV antibody assay blood serum specimen OBI:0003598 single cell B cell receptor repertoire sequencing assay single cell B cell receptor repertoire sequencing assay single-cell BCR assay A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin. Sebastian Duesing|Randi Vita subclass B cell receptor repertoire sequencing assay nucleic acid extract OBI:0003599 single cell T cell receptor repertoire sequencing assay single cell T cell receptor repertoire sequencing assay single-cell TCR assay A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin. Sebastian Duesing|Randi Vita subclass T cell receptor repertoire sequencing assay nucleic acid extract OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay QCM An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. http://www.ncbi.nlm.nih.gov/pubmed/23504432|https://en.wikipedia.org/wiki/Quartz_crystal_microbalance Randi Vita|Bjoern Peters|Sebastian Duesing subclass assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay -OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus +OBI:0003659 in vitro CRISPR screen assay in vitro CRISPR screen assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell +OBI:0003660 in vitro CRISPR screen using single-cell RNA-seq in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay single-cell RNA sequencing assay +OBI:0003661 in vitro CRISPR screen using flow cytometry in vitro CRISPR perturbation screen using flow cytometry An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay flow cytometry assay +OBI:0003662 single-nucleus methylcytosine and transcriptome sequencing assay single-nucleus methylcytosine and transcriptome sequencing assay snmCT-seq A DNA methylation profiling by high throughput sequencing assay that measures the cytosine DNA methylation and gene expression signature of single nuclei. Jennifer Jou https://www.biorxiv.org/content/10.1101/434845v1 Sebastian Duesing|Jennifer Jou Jennifer Jou https://github.com/obi-ontology/obi/issues/1785 equivalent DNA methylation profiling by high throughput sequencing assay artificially induced reverse transcription RNA extract DNA sequencer RNA extract sequence data primary structure of RNA molecule +OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity DNA damage response OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course OBI:0600017 assay detecting a molecular label pending final vetting An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached OBI developer call, 3-12-12 Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present Matthew Brush subclass assay molecular-labeled material measurement datum molecular-labeled material @@ -666,7 +670,7 @@ OBI:0600026 longitudinal mass measurement assay metadata complete An assay tha OBI:0600031 enzyme-linked immunospot assay ELISPOT assay A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. IEDB Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell. IEDB subclass logical definition does not capture details of processing cytometry assay cultured cell population immunoglobulin complex, circulating OBI:0600045 3D structure determination assay An assay that determines the 3-dimensional configuration of an input material. IEDB The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein. IEDB equivalent assay 3D structural organization datum OBI:0600047 sequencing assay pending final vetting An assay the uses chemical or biochemical means to infer the sequence of a biomaterial OBI branch derived The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template PlanAndPlannedProcess Branch equivalent assay ('nucleic acid extract' or ('has part' some protein)) ('protein sequencer' or 'nucleic acid sequencer' or 'DNA sequencer') sequence data region -OBI:1110207 assay detecting IFN-gamma production ready for release IFNg release An assay that determines information about the production of the cytokine interferon gamma IEDB An IFN-g ELISPOT is an assay detecting ifn-gamma production Bjoern Peters equivalent assay ('measurement datum' and ('is about' some 'interferon-gamma production')) +OBI:1110207 assay detecting IFN-gamma production ready for release IFNg release An assay that determines information about the production of the cytokine interferon gamma IEDB An IFN-g ELISPOT is an assay detecting ifn-gamma production Bjoern Peters equivalent assay ('measurement datum' and ('is about' some 'type II interferon production')) OBI:2100001 carbon dioxide assay An analyte assay that measures the abundance of carbon dioxide PennTURBO team Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X https://github.com/obi-ontology/obi/issues/1253 equivalent analyte assay carbon dioxide OBI:2100002 sodium(1+) assay An analyte assay that measures the abundance of sodium(1+) PennTURBO team Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X https://github.com/obi-ontology/obi/issues/1253 equivalent analyte assay 'sodium(1+)' OBI:2100003 creatinine assay An analyte assay that measures the abundance of creatinine PennTURBO team Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X https://github.com/obi-ontology/obi/issues/1253 equivalent analyte assay creatinine diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index ee8e777e..2023d36f 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -309,7 +309,7 @@ OBI:0001204 SNP microarray SNP microarray metadata complete A DNA microarray us OBI:0001307 tiling microarray tiling microarray metadata complete genome tiling array A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. EFO_0002704: tiling array Person: Helen Parkinson DNA microarray OBI:0001865 assay array metadata complete A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg device solid support function OBI:0001869 Illumina BeadChip metadata complete An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. http://www.illumina.com/technology/beadarray_technology.ilmn PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi assay array Illumina -OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg equivalent Illumina BeadChip ('bearer of' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some 'DNA methylation'))))))) +OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg equivalent Illumina BeadChip ('bearer of' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some (deoxyribonucleotide and ('has part' some 'methyl group'))))))))) OBI:0001871 LSRFortessa X-20 metadata complete A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg Anna Maria Masci flow cytometer analyzer Becton Dickinson (BD Biosciences) OBI:0001971 Ion 316 Chip v2 Ion 316 Chip v2 Ion PGM 316 Chip|Ion 316 Chip|Ion PGM 316 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ ion semiconductor chip OBI:0001972 Ion 318 Chip v2 Ion 318 Chip v2 Ion 318 Chip|Ion PGM 318 Chip|Ion PGM 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ ion semiconductor chip @@ -469,6 +469,8 @@ OBI:0003550 odor baited CDC light trap human odour baited light trap A CDC lig OBI:0003551 resting clay pot trap resting clay pot catch A resting arthropod trap that consists of a container composed primarily of clay. John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1651 resting arthropod trap OBI:0003606 Illumina NextSeq 1000 NextSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html Sebastian Duesing GENEPIO https://github.com/obi-ontology/obi/issues/1711 subclass DNA sequencer Illumina OBI:0003650 Illumina Infinium MethylationEPIC v2.0 BeadChip Illumina Infinium MethylationEPIC v2.0 BeadChip An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html Sebastian Duesing https://github.com/obi-ontology/obi/issues/1665 Illumina methylation BeadChip +OBI:0003663 Illumina NovaSeq X Illumina NovaSeq X NovaSeq X System|NovaSeq X Series A DNA sequencer with three flow cell types manufactured by Illumina. The NovaSeq X provides an output of up to 8 Tb (26-52 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html Morgana Barroso Oquendo Morgana Barroso Oquendo https://github.com/obi-ontology/obi/issues/1802 subclass DNA sequencer Illumina +OBI:0003664 Illumina NovaSeq X Plus Illumina NovaSeq X Plus NovaSeq X System|NovaSeq X Series A DNA sequencer with three flow cell types manufactured by Illumina. It features a dual-flow cell configuration, allowing to reach an output of up to 16 Tb (52-104 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html Morgana Barroso Oquendo Morgana Barroso Oquendo https://github.com/obi-ontology/obi/issues/1802 subclass DNA sequencer Illumina OBI:0400005 A10-Analyzer A10-Analyzer ready for release A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400006 A40-MiniFCM A40-MiniFCM ready for release A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400007 analog-to-digital converter analog-to-digital converter metadata incomplete A2D|A-D An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. http://en.wiktionary.org/wiki/Analog-to-Digital_Converter The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. John Quinn|Melanie Courtot device signal conversion function diff --git a/src/ontology/templates/epitope-assays.tsv b/src/ontology/templates/epitope-assays.tsv index bdd2534c..df7eb494 100644 --- a/src/ontology/templates/epitope-assays.tsv +++ b/src/ontology/templates/epitope-assays.tsv @@ -68,7 +68,7 @@ OBI:0001309 intracellular cytokine staining assay measuring epitope specific int OBI:0001311 X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex 3D structure|x-ray crystallography|angstroms A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent X-ray crystallography 3D molecular structure determination assay 3D structural organization datum epitope:MHC:TCR complex angstrom OBI:0001315 ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells CCL1/TCA-3 release|ELISA An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('chemokine (C-C motif) ligand 1 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001317 flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex T cell- APC binding|binding assay A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass flow cytometry assay categorical binding datum MHC:epitope complex binding to TCR -OBI:0001319 cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells IFNg release|bioassay A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent reporter cell line analyte detection bioassay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001319 cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells IFNg release|bioassay A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent reporter cell line analyte detection bioassay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001322 ELISPOT assay measuring epitope specific granzyme B release by T cells granzyme B release|ELISPOT An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('granzyme B release during T cell degranulation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001324 in vivo assay measuring T cell epitope specific tolerance induction tolerance|in vivo assay An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent epitope tolerance induction experiment ('T cell tolerance induction' and ('process is result of' some 'MHC:epitope complex binding to TCR')) (Metazoa and ('has quality' some alive)) OBI:0001325 detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells CCL5/RANTES release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells. IEDB IEDB equivalent detection of specific nucleic acid polymers with complementary probes ('chemokine (C-C motif) ligand 5 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -85,7 +85,7 @@ OBI:0001345 assay measuring epitope specific chemokine (C-C motif) ligand 4 prod OBI:0001346 ELISA measuring epitope specific interleukin-21 production by T cells IL-21 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interleukin-21 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001348 in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity type IV hypersensitivity (DTH)|in vivo skin test An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent efficacy of epitope intervention experiment ('type IV hypersensitivity' and ('process is result of' some 'MHC:epitope complex binding to TCR')) (Metazoa and ('has quality' some alive)) OBI:0001349 cytometric bead array assay measuring epitope specific interleukin-13 production by T cells IL-13 release|cytometric bead array A cytometric bead array assay that detects interleukin-13 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('interleukin-13 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:0001350 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells IFNg release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001350 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells IFNg release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001353 cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells TNFa release|cytometric bead array A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('tumor necrosis factor production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001354 ELISPOT assay measuring epitope specific interleukin-17 production by T cells IL-17 release|ELISPOT An enzyme-linked immunospot assay that detects interleukin-17 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interleukin-17 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001356 detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells IFNb release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('interferon-beta production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -98,7 +98,7 @@ OBI:0001368 cytometric bead array assay measuring epitope specific tumor necrosi OBI:0001370 intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells CCL4/MIP-1b release|ICS A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('chemokine (C-C motif) ligand 4 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001376 intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells IL-3 release|ICS A flow cytometry assay that detects interleukin-3 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('interleukin-3 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001378 ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells CCL4/MIP-1b release|ELISA An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('chemokine (C-C motif) ligand 4 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:0001379 cytometric bead array assay measuring epitope specific interferon-gamma production by T cells IFNg release|cytometric bead array A cytometric bead array assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001379 cytometric bead array assay measuring epitope specific interferon-gamma production by T cells IFNg release|cytometric bead array A cytometric bead array assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001380 assay measuring epitope specific interleukin-18 production by T cells IL-18 release|biological activity A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('interleukin-18 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001382 detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells IL-27 release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('interleukin-27 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001383 detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells CXCL10/IP-10 release|RNA/DNA detection A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent detection of specific nucleic acid polymers with complementary probes ('IP-10 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -118,10 +118,10 @@ OBI:0001406 assay measuring epitope specific interleukin-3 production by T cells OBI:0001407 assay measuring epitope specific T cell activation activation|biological activity A T cell epitope dependent biological activity assay that detects T cell activation. IEDB IEDB equivalent assay ('T cell activation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001412 cytometric bead array assay measuring epitope specific RANTES production by T cells CCL5/RANTES release|cytometric bead array A cytometric bead array assay that detects RANTES production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('chemokine (C-C motif) ligand 5 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001413 cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells IL-6 release|bioassay A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent reporter cell line analyte detection bioassay ('interleukin-6 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:0001414 assay measuring epitope specific interferon-gamma production by T cells IFNg release|biological activity A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001414 assay measuring epitope specific interferon-gamma production by T cells IFNg release|biological activity A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001416 assay measuring epitope specific tumor necrosis factor alpha production by T cells TNFa release|biological activity An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('tumor necrosis factor production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001423 intracellular material detection measuring epitope specific granzyme B release by T cells granzyme B release|intracellular staining A flow cytometry assay that detects epitope specific granzyme B release by T cells IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('granzyme B release during T cell degranulation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:0001433 radio immuno assay measuring epitope specific interferon-gamma production by T cells IFNg release|radio immuno assay (RIA) A radio immuno assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent radio immuno assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:0001433 radio immuno assay measuring epitope specific interferon-gamma production by T cells IFNg release|radio immuno assay (RIA) A radio immuno assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent radio immuno assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001436 assay measuring epitope specific granzyme B release by T cells granzyme B release|biological activity A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('granzyme B release during T cell degranulation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001437 intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells CXCL9/MIG release|ICS A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('chemokine (C-X-C motif) ligand 9 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001438 ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells CCL9/MIP-1g release|ELISA An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('macrophage inflammatory protein-1 gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -504,7 +504,7 @@ OBI:0003612 electron microscopy assay determining the 3D structure of a T cell e OBI:0003613 electron microscopy assay determining the 3D structure of a MHC:ligand complex 3D structure|electron microscopy An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a MHC:ligand complex. IEDB PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters equivalent electron-microscopy 3D molecular structure determination assay 3D structural organization datum MHC:ligand complex OBI:1110013 ELISPOT assay measuring epitope specific interleukin-2 production by T cells IL-2 release|ELISPOT An enzyme-linked immunospot assay that detects interleukin-2 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interleukin-2 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110037 assay measuring binding of a T cell epitope:MHC:TCR complex T cell binding|any method A T cell epitope assay that measures the binding of T cell receptor to an epitope. IEDB IEDB equivalent assay binding datum MHC:epitope complex binding to TCR -OBI:1110059 ELISPOT assay measuring epitope specific interferon-gamma production by T cells IFNg release|ELISPOT An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:1110059 ELISPOT assay measuring epitope specific interferon-gamma production by T cells IFNg release|ELISPOT An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110124 assay measuring qualitative binding of a T cell epitope:MHC:TCR complex qualitative binding|binding assay An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a qualitative measurement of the binding as an output. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay categorical binding datum MHC:epitope complex binding to TCR OBI:1110125 assay measuring MHC ligand processing and presentation ligand presentation|any method A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. IEDB IEDB equivalent assay cell ('MHC protein complex binding to ligand' and ('process is result of' some 'antigen processing and presentation')) OBI:1110126 assay measuring binding of a MHC:ligand complex MHC binding|any method A MHC ligand assay that detects the binding of a ligand to an MHC molecule. IEDB IEDB equivalent assay binding datum MHC protein complex binding to ligand @@ -514,7 +514,7 @@ OBI:1110129 assay measuring epitope specific cytokine production by T cells c OBI:1110130 assay measuring epitope specific T cell killing cytotoxicity|biological activity A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. IEDB IEDB equivalent cell-cell killing assay ('T cell mediated cytotoxicity' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110131 assay measuring epitope specific proliferation of T cells proliferation|biological activity A T cell epitope dependent biological activity assay that detects T cell proliferation. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('T cell proliferation' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110150 51 chromium assay measuring epitope specific T cell killing cytotoxicity|51 chromium A chromium release assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. IEDB IEDB equivalent chromium release assay ('T cell mediated cytotoxicity' and ('process is result of' some 'MHC:epitope complex binding to TCR')) cell culture -OBI:1110151 ELISA measuring epitope specific interferon-gamma production by T cells IFNg release|ELISA An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:1110151 ELISA measuring epitope specific interferon-gamma production by T cells IFNg release|ELISA An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110152 ELISA measuring epitope specific interleukin-2 production by T cells IL-2 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interleukin-2 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110153 ELISA measuring epitope specific interleukin-4 production by T cells IL-4 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interleukin-4 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110154 ELISA measuring epitope specific interleukin-5 production by T cells IL-5 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunosorbent assay ('interleukin-5 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) @@ -531,7 +531,7 @@ OBI:1110167 ELISPOT assay measuring epitope specific interleukin-4 production by OBI:1110168 ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells TNFa release|ELISPOT An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells IEDB IEDB equivalent enzyme-linked immunospot assay ('tumor necrosis factor production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110170 ELISPOT assay measuring epitope specific interleukin-10 production by T cells IL-10 release|ELISPOT An enzyme-linked immunospot assay that detects interleukin-10 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interleukin-10 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110171 ELISPOT assay measuring epitope specific interleukin-13 production by T cells IL-13 release|ELISPOT An enzyme-linked immunospot assay that detects interleukin-13 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interleukin-13 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) -OBI:1110172 intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells IFNg release|ICS A flow cytometry assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) +OBI:1110172 intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells IFNg release|ICS A flow cytometry assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('type II interferon production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110173 intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells IL-2 release|ICS A flow cytometry assay that detects interleukin-2 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('interleukin-2 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110174 intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells TNFa release|ICS A flow cytometry assay that detects tumor necrosis factor alpha production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('tumor necrosis factor production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:1110175 intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells IL-4 release|ICS A flow cytometry assay that detects interleukin-4 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent flow cytometry assay ('interleukin-4 production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))