diff --git a/obi.owl b/obi.owl index 8c1f2eb8..77e77a99 100755 --- a/obi.owl +++ b/obi.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2022-01-03 + 2022-07-11 @@ -2245,6 +2245,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + has assay target context + + A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc. + Hector Guzman-Orozco + OBI + https://github.com/obi-ontology/obi/issues/1516 + has assay target context + + + + @@ -4225,6 +4240,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ material MaterialEntity + material entity material entity a flame a forest fire @@ -4243,6 +4259,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) @@ -4250,6 +4267,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + material entity material entity @@ -5385,7 +5403,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ fatty acid - Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. + Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. fatty acid @@ -5561,7 +5579,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium cation calcium cation @@ -5569,6 +5587,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + calcium ion + + calcium ion + + + + @@ -6831,7 +6860,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ core promoter sequence-specific DNA binding - Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. + Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. core promoter sequence-specific DNA binding @@ -7053,7 +7082,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ antigen binding - Interacting selectively and non-covalently with 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 @@ -7209,7 +7238,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ chromatin remodeling - Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. + A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication. chromatin remodeling @@ -7342,7 +7371,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ gene expression - The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. + 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. gene expression @@ -7438,7 +7467,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ protein domain specific binding - Interacting selectively and non-covalently with a specific domain of a protein. + Binding to a specific domain of a protein. protein domain specific binding @@ -7653,10 +7682,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-14 production - The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + obsolete interleukin-14 production + OBSOLETE. The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-14 production + obsolete interleukin-14 production @@ -8139,30 +8168,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - regulation of gene expression, epigenetic - Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. - - regulation of gene expression, epigenetic - - - - - - - - - regulation of molecular function, epigenetic - Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. - - regulation of molecular function, epigenetic - - - - @@ -8243,7 +8248,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ peptide antigen binding - Interacting selectively and non-covalently with an antigen peptide. + Binding to an antigen peptide. peptide antigen binding @@ -8291,7 +8296,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ sequence-specific DNA binding - Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. + Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. sequence-specific DNA binding @@ -8301,7 +8306,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 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. @@ -8754,6 +8759,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + amphiregulin production + The appearance of amphiregulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Amphiregulin (AREG) is a ligand of the epidermal growth factor receptor (EGFR), a widely expressed transmembrane tyrosine kinase. AREG is synthesized as a membrane-anchored precursor protein that can engage in juxtacrine signaling on adjacent cells. Alternatively, after proteolytic processing by cell membrane proteases, mainly TACE/ADAM17, AREG is secreted and behaves as an autocrine or paracrine factor. + + amphiregulin production + + + + + + + + + XCL1 production + The appearance of XCL1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + XCL1 production + + + + @@ -14380,7 +14409,7 @@ editor = PRS - biological vector role + obsolete biological vector role 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 @@ -14388,7 +14417,7 @@ editor = PRS GROUP: Role Branch OBI and Wikipedia - biological vector role + obsolete biological vector role true @@ -14445,6 +14474,7 @@ something taken from study subject, leaves the study and becomes the specimen. GROUP: Role Branch OBI + specimen role @@ -18426,7 +18456,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18570,7 +18600,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -22547,7 +22577,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + + + + + + + + tritiated thymidine incorporation assay @@ -23072,7 +23109,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + + + + + + + + @@ -23847,7 +23891,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + + + + + + + + @@ -23999,13 +24050,20 @@ the role 'adjuvant role' inheres in some 'material entity' a - + - + + + + + + + + @@ -24561,6 +24619,7 @@ the role 'adjuvant role' inheres in some 'material entity' a A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. + material sample role @@ -24704,6 +24763,7 @@ the role 'adjuvant role' inheres in some 'material entity' a A material entity that has the material sample role OBI: workshop sample population + sample material sample @@ -24776,7 +24836,14 @@ the role 'adjuvant role' inheres in some 'material entity' a - + + + + + + + + @@ -27083,7 +27150,7 @@ placeholder viral hemagglutination inhibition assay Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody. - An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates hemagglutination inhibition by the evaluant. + An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors. Bjoern Peters Melanie Courtot Randi Vita @@ -27466,13 +27533,20 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La - + - + + + + + + + + @@ -27999,13 +28073,20 @@ stained with fecal material and is then placed in transport medium. - + - + + + + + + + + @@ -28221,7 +28302,14 @@ Updated both textual and logical definition. Both input and output material of f - + + + + + + + + @@ -28351,7 +28439,14 @@ exudate and epithelial debris for microbiological or cellular examination. - + + + + + + + + @@ -29825,7 +29920,14 @@ In the examples above, a reagent is an operational component of a device, but th - + + + + + + + + @@ -30139,18 +30241,15 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - - - performing a diagnosis + + obsolete performing a diagnosis Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache. The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis - performing a diagnosis + + https://github.com/obi-ontology/obi/issues/623 + obsolete performing a diagnosis + true @@ -36106,18 +36205,34 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + intracellular material detection assay measuring epitope specific perforin release - A T cell epitope specific perforin release assay that uses an intracellular material detection by flow cytometry assay. + A flow cytometry assay that detects epitope specific perforin release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB perforin release|intracellular staining @@ -37179,18 +37294,34 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release - A T cell epitope specific perforin release assay that uses a detection of specific nucleic acids with complementary probes assay. + A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB perforin release|RNA/DNA detection @@ -37310,7 +37441,14 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + + + + + + + + @@ -37973,13 +38111,26 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + + + + @@ -37987,13 +38138,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific cytotoxic T cell degranulation + assay measuring epitope specific cytotoxic T cell degranulation A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB degranulation|biological activity - biological activity assay measuring epitope specific cytotoxic T cell degranulation + assay measuring epitope specific cytotoxic T cell degranulation @@ -39623,28 +39774,25 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor. @@ -39789,18 +39937,34 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses an ELISPOT assay. + An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|ELISPOT @@ -39838,7 +40002,14 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + + + + + + + + @@ -42134,7 +42305,14 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + + + + + + + + @@ -43251,18 +43429,34 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - - + + + + + + + + + + + + + + + + + + intracellular material detection measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses an intracellular material detection by flow cytometry assay. + A flow cytometry assay that detects epitope specific granzyme B release by T cells PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|intracellular staining @@ -43479,13 +43673,23 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - + + + + + + + + + + + @@ -43493,13 +43697,13 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - biological activity assay measuring epitope specific granzyme B release by T cells + assay measuring epitope specific granzyme B release by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|biological activity - biological activity assay measuring epitope specific granzyme B release by T cells + assay measuring epitope specific granzyme B release by T cells @@ -44263,18 +44467,34 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses an ELISA. + An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|ELISA @@ -44478,7 +44698,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -44529,7 +44756,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + monospecific T cell recognition assay measuring MHC ligand processing and presentation @@ -44624,7 +44858,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -44668,7 +44909,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -44712,7 +44960,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -44762,7 +45017,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -44944,7 +45206,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -45048,7 +45317,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC @@ -45107,20 +45383,32 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + + + + + + + + + + + + + + + + + + - - - - - - - radioactivity detection binding assay + binding assay using radioactivity detection A binding assay that uses radioactivity detection as an indicator of binding. Bjoern Peters Randi Vita IEDB - radioactivity detection binding assay + binding assay using radioactivity detection @@ -45134,7 +45422,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -45158,7 +45453,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -45315,13 +45617,23 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + + + + + + + + + + + @@ -45329,13 +45641,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - biological activity assay measuring epitope specific perforin release by T cells + assay measuring epitope specific perforin release by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells. IEDB IEDB perforin release|biological activity - biological activity assay measuring epitope specific perforin release by T cells + assay measuring epitope specific perforin release by T cells @@ -45357,20 +45669,32 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + + + + + + + + + + + + + + + + + + - - - - - - - fluorescence detection binding assay + binding assay using fluorescence detection - A binding assay that uses fluorescence detection as an indicator of binding + A binding assay that uses fluorescence detection as an indicator of binding. Bjoern Peters Randi Vita IEDB - fluorescence detection binding assay + binding assay using fluorescence detection @@ -45382,7 +45706,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -45618,7 +45949,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -45659,7 +45997,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + @@ -45683,7 +46028,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC @@ -45763,7 +46115,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -45886,7 +46238,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -45926,7 +46278,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex @@ -45945,7 +46297,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -45999,7 +46351,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex @@ -46045,7 +46397,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -46076,7 +46428,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex @@ -46095,7 +46447,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -46149,7 +46501,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex @@ -46268,7 +46620,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -46308,7 +46660,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex @@ -46477,7 +46829,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -46517,7 +46869,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex @@ -46591,7 +46943,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -46707,7 +47059,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -46761,7 +47113,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex @@ -46802,7 +47154,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -46856,7 +47208,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex @@ -46894,7 +47246,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -46934,7 +47286,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex @@ -46995,7 +47347,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -47054,7 +47406,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -47108,7 +47460,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex @@ -47294,7 +47646,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -47348,7 +47700,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex @@ -47574,7 +47926,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -47605,7 +47957,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex @@ -47651,7 +48003,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -47691,7 +48043,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex @@ -47710,7 +48062,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -47750,7 +48102,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex @@ -47785,7 +48137,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -47825,7 +48177,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex @@ -47908,7 +48260,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -47981,7 +48333,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -48021,7 +48373,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex @@ -48063,7 +48415,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -48103,7 +48455,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex @@ -48122,7 +48474,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -48176,7 +48528,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex @@ -48195,7 +48547,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -48235,7 +48587,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex @@ -48745,7 +49097,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -48785,7 +49137,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex @@ -48900,7 +49252,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -48968,7 +49320,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -49008,7 +49360,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex @@ -49055,7 +49407,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -49206,7 +49558,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + + + + + + + + @@ -49292,7 +49651,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -49440,7 +49799,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -49523,7 +49882,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -49563,7 +49922,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex @@ -49610,7 +49969,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -49700,7 +50059,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -49880,7 +50239,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -49934,7 +50293,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex @@ -50568,7 +50927,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + + + + + + + + @@ -51402,18 +51768,34 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + intracellular material detection assay measuring epitope specific granzyme A release by T cells - A T cell epitope specific granzyme A release assay that uses an intracellular material detection by flow cytometry assay. + A flow cytometry assay that detects epitope specific granzyme A release by T cells. IEDB IEDB granzyme A release|intracellular staining @@ -51467,7 +51849,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + + + + + + + + @@ -51503,18 +51892,34 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific granulysin release by T cells - A T cell epitope specific granulysin release assay that uses an ELISA. + An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells. IEDB IEDB granulysin release|ELISA @@ -51529,18 +51934,34 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + intracellular material detection assay measuring epitope specific granulysin release by T cells - A T cell epitope specific granulysin release assay that uses an intracellular material detection by flow cytometry assay. + A flow cytometry assay that detects epitope specific granulysin release by T cells. IEDB IEDB granulysin release|intracellular staining @@ -51555,7 +51976,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + @@ -51595,7 +52016,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex @@ -51614,7 +52035,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + @@ -51654,7 +52075,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex @@ -51673,7 +52094,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + @@ -51792,7 +52213,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + + + + + + + + @@ -52722,7 +53150,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + in vivo assay measuring B cell epitope specific protection from fertility @@ -52745,7 +53180,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + @@ -52780,7 +53222,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + @@ -52844,7 +53293,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + in vivo assay measuring B cell epitope specific protection based on survival @@ -52867,7 +53323,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + @@ -52893,7 +53356,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + @@ -53372,7 +53842,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + @@ -53398,7 +53875,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + @@ -57326,13 +57810,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -57340,13 +57834,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific granzyme A release by T cells + assay measuring epitope specific granzyme A release by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells. IEDB IEDB granzyme A release|biological activity - biological activity assay measuring epitope specific granzyme A release by T cells + assay measuring epitope specific granzyme A release by T cells @@ -57357,13 +57851,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -57371,13 +57875,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific granulysin release by T cells + assay measuring epitope specific granulysin release by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells. IEDB IEDB granulysin release|biological activity - biological activity assay measuring epitope specific granulysin release by T cells + assay measuring epitope specific granulysin release by T cells @@ -58861,13 +59365,27 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + + + + + + + + - + + + + + + + + @@ -58982,13 +59500,20 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - + + + + + + + + @@ -59123,19 +59648,26 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - + - + + + + + + + + @@ -59286,7 +59818,14 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + + + + + + + + @@ -59400,7 +59939,14 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + + + + + + + + @@ -59472,19 +60018,26 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - + - + + + + + + + + @@ -59580,19 +60133,26 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - + - + + + + + + + + @@ -59795,7 +60355,14 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + + + + + + + + @@ -61675,31 +62242,38 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + - + - + - + - + + + + + + + + @@ -61818,13 +62392,20 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + - + + + + + + + + @@ -61983,7 +62564,14 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + + + + + + + + @@ -63681,11 +64269,18 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + + + + + + + + fluorescence quenching binding assay @@ -64026,7 +64621,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64080,7 +64675,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex @@ -64848,7 +65443,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -64900,13 +65502,20 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + + + + + + + + transcription profiling by MPSS assay @@ -65001,7 +65610,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -65119,7 +65735,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -65237,7 +65860,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -65355,7 +65985,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -65621,7 +66258,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + serial analysis of gene expression assay @@ -65935,7 +66579,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + chromatin isolation by RNA purification sequencing assay @@ -66204,7 +66855,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -66241,7 +66899,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -66306,7 +66971,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -66632,7 +67304,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -66655,18 +67334,34 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific granzyme A release by T cells - A T cell epitope specific granzyme A release assay that uses a cytometric bead array assay. + A cytometric bead array assay that detects epitope specific granzyme A release by T cells. IEDB IEDB granzyme A release|cytometric bead array @@ -66681,18 +67376,34 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells - A T cell epitope specific granzyme A release assay that uses a detection of specific nucleic acids with complementary probes assay. + A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells. IEDB IEDB granzyme A release|RNA/DNA detection @@ -66707,18 +67418,34 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses a cytometric bead array assay. + A cytometric bead array assay that detects epitope specific granzyme B release by T cells. IEDB IEDB granzyme B release|cytometric bead array @@ -66733,18 +67460,34 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses a detection of specific nucleic acids with complementary probes assay. + A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells IEDB IEDB granzyme B release|RNA/DNA detection @@ -66843,18 +67586,34 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific perforin release by T cells - A T cell epitope specific perforin release assay that uses an ELISPOT assay. + An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells. IEDB IEDB perforin release|ELISPOT @@ -66872,7 +67631,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -66949,7 +67715,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -67436,7 +68209,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + @@ -67843,7 +68623,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + carboxyfluorescein succinimidyl ester staining assay @@ -68030,7 +68817,14 @@ https://www.doi.org/ - + + + + + + + + cytometry time of flight assay @@ -69792,7 +70586,14 @@ https://www.doi.org/ - + + + + + + + + ChIP-qPCR assay @@ -72167,7 +72968,14 @@ https://www.doi.org/ - + + + + + + + + RNA interactome capture @@ -72248,6 +73056,19 @@ https://www.doi.org/ + + + + + + + + + + + + + Hi-C assay A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. @@ -72803,7 +73624,14 @@ https://www.doi.org/ - + + + + + + + + genotype phasing by Hi-C assay @@ -73376,19 +74204,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -73409,19 +74233,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -73442,19 +74262,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -73475,19 +74291,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -73509,19 +74321,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -73543,19 +74351,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -73576,19 +74380,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -73609,19 +74409,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -73642,19 +74438,15 @@ https://www.doi.org/ - 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- - - - - - - - - - - - + + + + + + + + + @@ -74405,19 +75109,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74439,19 +75139,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74472,19 +75168,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74505,19 +75197,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74538,19 +75226,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74572,19 +75256,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74606,19 +75286,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74639,19 +75315,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74673,19 +75345,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74706,19 +75374,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74739,19 +75403,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74772,19 +75432,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74805,19 +75461,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74838,19 +75490,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74871,19 +75519,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74904,19 +75548,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74937,19 +75577,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -74970,19 +75606,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -75003,19 +75635,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -75036,19 +75664,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -75069,19 +75693,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -75102,19 +75722,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -75135,19 +75751,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -75168,19 +75780,15 @@ https://www.doi.org/ - - - - - - - - - - - - - + + + + + + + + + @@ -76088,25 +76696,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76127,25 +76731,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76166,25 +76766,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76205,25 +76801,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76244,25 +76836,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76283,25 +76871,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76322,25 +76906,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76361,25 +76941,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76400,25 +76976,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76439,25 +77011,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76479,25 +77047,21 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -76901,7 +77465,14 @@ https://www.doi.org/ - + + + + + + + + @@ -76928,7 +77499,14 @@ https://www.doi.org/ - + + + + + + + + @@ -76955,7 +77533,14 @@ https://www.doi.org/ - + + + + + + + + @@ -76982,7 +77567,14 @@ https://www.doi.org/ - + + + + + + + + @@ -77009,7 +77601,14 @@ https://www.doi.org/ - + + + + + + + + @@ -77066,7 +77665,14 @@ https://www.doi.org/ - + + + + + + + + @@ -77093,7 +77699,14 @@ https://www.doi.org/ - + + + + + + + + @@ -77149,7 +77762,14 @@ https://www.doi.org/ - + + + + + + + + @@ -77175,7 +77795,14 @@ https://www.doi.org/ - + + + + + + + + @@ -77257,7 +77884,14 @@ https://www.doi.org/ - + + + + + + + + Giemsa stain assay @@ -77797,7 +78431,14 @@ https://www.doi.org/ - + + + + + + + + @@ -77887,7 +78528,14 @@ https://www.doi.org/ - + + + + + + + + @@ -77920,18 +78568,34 @@ https://www.doi.org/ - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific perforin release by T cells - An assay of epitope specific perforin release by T cells that uses an ELISA. + An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells. IEDB IEDB perforin release|ELISA @@ -78040,7 +78704,14 @@ https://www.doi.org/ - + + + + + + + + @@ -79690,7 +80361,14 @@ https://www.doi.org/ - + + + + + + + + @@ -79699,7 +80377,7 @@ https://www.doi.org/ - insecticide resistance by PCR-RELP assay + insecticide resistance by PCR-RFLP assay An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. VEuPathDB @@ -79707,7 +80385,7 @@ https://www.doi.org/ MIRO:20000113 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB - insecticide resistance by PCR-RELP assay + insecticide resistance by PCR-RFLP assay @@ -81007,25 +81685,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -81046,25 +81720,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -81086,25 +81756,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -81126,25 +81792,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -81165,25 +81827,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -81204,25 +81862,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -81825,6 +82479,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + catheter + A catheter left inside the body, either temporarily or permanently, may be referred to as an "indwelling catheter". + + A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body. + https://orcid.org/0000-0002-8844-9165 + http://purl.bioontology.org/ontology/MESH/D057785 + catheter + + + + @@ -82290,7 +82959,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Centers for Disease Control and Prevention light trap - A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. + A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery. This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. John Judkins CDC light trap @@ -82609,7 +83278,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -82650,7 +83326,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -82692,7 +83375,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -82733,7 +83423,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -82774,7 +83471,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -82815,7 +83519,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -82858,7 +83569,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -82919,7 +83637,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -82959,7 +83684,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + mass spectrometry-based protein state assay @@ -83027,7 +83759,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + SWATH-MS protein profiling assay @@ -83071,7 +83810,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -83113,7 +83859,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + @@ -83258,7 +84011,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + positive/negative ion switching metabolite profiling assay @@ -84142,7 +84902,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -84150,7 +84910,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -85308,7 +86068,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + parasite species identification by PCR assay @@ -85336,7 +86103,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + parasite detection by PCR assay @@ -86068,7 +86842,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + multiplexed fluorescent antibody imaging assay @@ -86130,7 +86911,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + fluorescence in-situ hybridization assay @@ -86412,7 +87200,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + nanodroplet processing in one pot for trace samples assay @@ -86628,7 +87423,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + proximity extension assay @@ -87584,7 +88386,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - calcium cation concentration assay @@ -89167,7 +89968,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + fluorescent immunospot assay @@ -90170,7 +90978,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre virus in blood datum - A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A blood microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90191,7 +90999,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre eukaryota in blood datum - A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90233,7 +91041,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre eukaryota in feces datum - A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A feces microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90254,7 +91062,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre virus in feces datum - A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A feces microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90275,7 +91083,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre eukaryota in urine datum - A urine microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A urine microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90296,7 +91104,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre bacteria in induced sputum datum - A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + An induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90317,7 +91125,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre eukaryota in induced sputum datum - A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + An induced sputum microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90338,7 +91146,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre virus in induced sputum datum - A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + An induced sputum microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90359,7 +91167,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre bacteria in endotracheal tube aspirate datum - A endotracheal tube aspirate microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + An endotracheal tube aspirate microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90401,7 +91209,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre eukaryota in lung datum - A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A lung microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90422,7 +91230,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre virus in lung datum - A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A lung microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90464,7 +91272,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre eukaryota in nasopharyngeal or oropharyngeal swab datum - A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90485,7 +91293,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre virus in nasopharyngeal or oropharyngeal swab datum - A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90527,7 +91335,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre eukaryota in pleural fluid datum - A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A pleural fluid microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90548,7 +91356,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre virus in pleural fluid datum - A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + A pleural fluid microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90569,7 +91377,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre eukaryota in umbilical cord blood datum - A umbilical cord blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + An umbilical cord blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90956,7 +91764,823 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + mosquito membrane feeding assay + Testing the effectiveness of drugs or antibodies against parasite transmission. + + An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1439 + mosquito membrane feeding assay + + + + + + + + + in silico design + + A study design that is executed primarily on a computer. + Hector Guzman-Orozco + https://en.wikipedia.org/wiki/In_silico + https://github.com/obi-ontology/obi/issues/1430 + CMI-PB + in silico design + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific granulysin release by T cells + + A cytometric bead array assay that detects epitope specific granulysin release by T cells. + IEDB + IEDB + granulysin release|cytometric bead array + cytometric bead array assay measuring epitope specific granulysin release by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific perforin release by T cells + + A cytometric bead array assay that detects epitope specific perforin release by T cells. + IEDB + IEDB + perforin release|cytometric bead array + cytometric bead array assay measuring epitope specific perforin release by T cells + + + + + + + + + + + + + + + modified acid-fast stain microscopy assay + + A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating. + John Judkins + NCIT:C85736 + https://www.cdc.gov/dpdx/diagnosticprocedures/stool/staining.html + https://github.com/obi-ontology/obi/issues/1444 + modified acid-fast stain microscopy assay + + + + + + + + + positive binding datum + + A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex. + Bjoern Peters + Hector Guzman-Orozco + IEDB + positive binding datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + antibodies from lymphocyte secretions assay + PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes. + + An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells. + John Judkins + ALS assay + antibodies from lymphocyte supernatant assay + OBI + VEuPathDB + https://github.com/obi-ontology/obi/issues/1443 + antibodies from lymphocyte secretions assay + + + + + + + + + tyramide signal amplification sequencing assay + + A DNA sequencing assay that uses tyramide signal amplification (TSA) to assess distance of DNA regions to a targeted nuclear compartment or protein, typically on a scale of 100-1000 nm. + Michelle Giglio + Suvarna Nadendla + TSA-seq + EFO:0009971 + PMID:30154186 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + tyramide signal amplification sequencing assay + + + + + + + + + DNA adenine methyltransferase identification assay + + An assay for identifying DNA binding sites for a protein by fusing it to Dam methylase, and expressing it so that bound DNA gets methylated. The methylated DNA can then be isolated and analyzed. + Michelle Giglio + Suvarna Nadendla + DamID assay + EFO:0008704 + PMID:17545983 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + DNA adenine methyltransferase identification assay + + + + + + + + + + + + + + + + + + + + + + DamID-seq + + A DNA adenine methyltransferase identification (DamID) assay in which DamID-generated DNA fragments undergo high-throughput sequencing to determine a protein's DNA-binding site. + Michelle Giglio + Suvarna Nadendla + 4DN DCIC + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + DamID-seq + + + + + + + + + nucleolus-associated domain sequencing assay + + A DNA sequencing assay in which nucleoli are isolated and the DNA associated with them is sequenced to identify nucleoli-associating domains. + Michelle Giglio + Suvarna Nadendla + NAD-seq + EFO:0009972 + PMID:31201210 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + nucleolus-associated domain sequencing assay + + + + + + + + + DNase Hi-C assay + + A Hi-C assay in which DNase I is used for digesting DNA fragments rather than a restriction enzyme, which can result in a higher resolution of mapped chromosome contacts. + Michelle Giglio + Suvarna Nadendla + EFO:0009976 + PMID:27685100 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + DNase Hi-C assay + + + + + + + + + micro-C assay + + A Hi-C assay which uses micrococcal nuclease digestion in place of the restriction enzyme digestion step. + Michelle Giglio + Suvarna Nadendla + EFO:0008808 + PMID:26119342 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + micro-C assay + + + + + + + + + single cell combinatorial indexing Hi-C assay + + A Hi-C assay performed on massively multiplexed single-cell samples. + Michelle Giglio + Suvarna Nadendla + sci-Hi-C + EFO:0009977 + PMID:28135255 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + single cell combinatorial indexing Hi-C assay + + + + + + + + + single nucleus Hi-C assay + + A Hi-C assay performed on isolated nuclei. + Michelle Giglio + Suvarna Nadendla + sn-Hi-C + EFO:0009978 + PMID:28355183 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + single nucleus Hi-C assay + + + + + + + + + single cell Hi-C assay + + A Hi-C assay performed on a single cell. + Michelle Giglio + Suvarna Nadendla + EFO:0009979 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + single cell Hi-C assay + + + + + + + + + bulk Hi-C assay + + A Hi-C assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. + Michelle Giglio + Suvarna Nadendla + 4DN DCIC + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + bulk Hi-C assay + + + + + + + + + multi-contact Hi-C assay + + A Hi-C assay that assesses interactions between multiple DNA fragments rather than only pairwise interactions as in traditional Hi-C. The experimental procedure of cross-linking, digestion, and ligation is performed similarly to traditional Hi-C, but after DNA is purified a long-read library is produced in which many ligated fragments may be contained in a single molecule. The library is then sequenced on a long read sequencer. + Michelle Giglio + Suvarna Nadendla + MC-3C + MC-HI-C + The 4D Nucleome Network + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + multi-contact Hi-C assay + + + + + + + + + transposase-mediated analysis of chromatin looping assay + + A DNA sequencing assay designed to detect interacting genomic regions. Rather than the traditional Hi-C approach of digestion and proximity ligation, the procedure involves transposase-mediated insertion of an oligonucleotide linker between the pair of interacting regions. + Michelle Giglio + Suvarna Nadendla + TrAC-Loop + EFO:0009982 + PMID:30150754 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + transposase-mediated analysis of chromatin looping assay + + + + + + + + + split-pool recognition of interactions and tag extension assay + + A sequencing assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates are pooled together again. This sequence of splitting, tagging, and re-combining is repeated several times so that fragments with the same sequences of barcodes represent fragments that have co-associated throughout the experiment. Finally, a sequencing library is constructed and high-throughput sequencing is performed. + Michelle Giglio + Suvarna Nadendla + SPRITE + EFO:0009984 + PMID:29887377 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + split-pool recognition of interactions and tag extension assay + + + + + + + + + DNA split-pool recognition of interactions and tag extension assay + + A split-pool recognition of interactions and tag extension (SPRITE) assay that only assays interactions between regions of genomic DNA. + Michelle Giglio + Suvarna Nadendla + DNA SPRITE + EFO:0009985 + PMID:29887377 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + DNA split-pool recognition of interactions and tag extension assay + + + + + + + + + RNA-DNA split-pool recognition of interactions and tag extension assay + + A split-pool recognition of interactions and tag extension (SPRITE) assay in which RNA in the cross-linked complexes is converted to cDNA before the initial splitting step, allowing analysis of RNA-DNA interactions. + Michelle Giglio + Suvarna Nadendla + RNA-DNA SPRITE + EFO:0009986 + PMID:29887377 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + RNA-DNA split-pool recognition of interactions and tag extension assay + + + + + + + + + genome architecture mapping assay + + A DNA sequencing assay designed to analyze 3D chromatin structure without relying on digestion and ligation. The procedure involves cryosectioning samples in random orientation, and then single nuclear profiles are isolated by laser microdissection. Each nuclear profile then undergoes high-throughput sequencing, and subsequent analysis can generate a matrix of inferred proximity between genomic regions. + Michelle Giglio + Suvarna Nadendla + GAM + EFO:0009987 + PMID:28273065 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + genome architecture mapping assay + + + + + + + + + + + + + + + + + + + + + + mapping RNA-genome interactions assay + + A nuclear ligation assay for probing RNA-DNA interactions in the nucleus. Nuclei are crosslinked, and RNA fragments are ligated to proximal DNA fragments via a special linker molecule. After reverse transcription, high-throughput sequencing is performed. + Michelle Giglio + Suvarna Nadendla + MARGI + EFO:0009988 + PMID:28132817 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + mapping RNA-genome interactions assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific amphiregulin production by T cells + + A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells. + IEDB + IEDB + amphiregulin release|biological activity + assay measuring epitope specific amphiregulin production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific amphiregulin production by T cells + + An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells. + IEDB + IEDB + amphiregulin release|ELISA + ELISA measuring epitope specific amphiregulin production by T cells + + + + + + + + + + + + + + + + + + + + perforin release during T cell degranulation + + The release of perforin during cytotoxic T cell degranulation. + Bjoern Peters + Hector Guzman-Orozco + Alexander Diehl, Bjoern Peters + perforin release during T cell degranulation + + + + + + + + + + + + + + + + + + + + granzyme A release during T cell degranulation + + The release of granzyme A during cytotoxic T cell degranulation. + Bjoern Peters + Hector Guzman-Orozco + Alexander Diehl, Bjoern Peters + granzyme A release during T cell degranulation + + + + + + + + + + + + + + + + + + + + granzyme B release during T cell degranulation + + The release of granzyme B during cytotoxic T cell degranulation. + Bjoern Peters + Hector Guzman-Orozco + Alexander Diehl, Bjoern Peters + granzyme B release during T cell degranulation + + + + + + + + + + + + + + + + + + + + granulysin release during T cell degranulation + + The release of granulysin during cytotoxic T cell degranulation. + Bjoern Peters + Hector Guzman-Orozco + Alexander Diehl, Bjoern Peters + granulysin release during T cell degranulation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -90964,132 +92588,344 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - mosquito membrane feeding assay - Testing the effectiveness of drugs or antibodies against parasite transmission. + venous blood microbiology assay - An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them. + A blood microbiology assay that identifies a microorganism in a venous blood specimen. John Judkins VEuPathDB - https://github.com/obi-ontology/obi/issues/1439 - mosquito membrane feeding assay + https://github.com/obi-ontology/obi/issues/1491 + venous blood microbiology assay - + - - - in silico design + + + high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex + Next-generation high-density peptide microarrays measuring antibody responses to overlapping peptides: PMID:25922409. - A study design that is executed primarily on a computer. + A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay. + IEDB + IEDB + antibody binding|High throughput multiplexed assay + high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex + + + + + + + + + high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex + Adaptive Biotech multiplexed TCR sequencing assays: PMID:32793919. + + A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay. + IEDB + IEDB + T cell binding|High throughput multiplexed assay + high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex + + + + + + + + + high throughput multiplexed assay measuring binding of a MHC:ligand complex + Peptide microarray with fluorescence detection for millions of MHC binding measurements: PMID: 33705522. + + A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay. + IEDB + IEDB + MHC binding|High throughput multiplexed assay + high throughput multiplexed assay measuring binding of a MHC:ligand complex + + + + + + + + + high throughput multiplexed assay measuring MHC ligand processing and presentation + Mass spectrometry identified 35,367 and 28,132 HLA-class I ligands witth a false discovery rate: PMID: 29789417. + + A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay. + IEDB + IEDB + ligand presentation|High throughput multiplexed assay + high throughput multiplexed assay measuring MHC ligand processing and presentation + + + + + + + + + + + + + + + milk assay datum + + A data item that is the specified output of a milk assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1515 + milk assay datum + + + + + + + + + + + + + + + organism diagnostic process + + A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has a disease, disorder, or syndrome of a certain type, or none of these as output. + Jie Zheng + https://github.com/obi-ontology/obi/issues/1505 + organism diagnostic process + + + + + + + + + + + + + + + diagnosis of an organism + + A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these. + Jie Zheng + https://github.com/obi-ontology/obi/issues/1505 + diagnosis of an organism + + + + + + + + + + + + + + + detection technique + Using a radioactivity detection assay as part of a tritiated thymidine incorporation assay to determine the degree to which cells are replicating by detecting radioactivity of tritiated thymidine, where radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. + + An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B. + Bjoern Peters Hector Guzman-Orozco - https://en.wikipedia.org/wiki/In_silico - https://github.com/obi-ontology/obi/issues/1430 - CMI-PB - in silico design + OBI + https://github.com/obi-ontology/obi/issues/1488 + detection technique - + - + + + assay kit + Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf + + A processed material that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. + John Judkins + OBI, VEuPathDB + assay kit + + + + + + + - + - - + + - - cytometric bead array assay measuring epitope specific granulysin release by T cells + + + epitope specific XCL1 release by T cells - A cytometric bead array assay that detects granulysin release by T cells. + A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope. IEDB IEDB - granulysin release|cytometric bead array - cytometric bead array assay measuring epitope specific granulysin release by T cells + epitope specific XCL1 release by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - - cytometric bead array assay measuring epitope specific perforin release by T cells + + assay measuring epitope specific lymphotactin production by T cells - A cytometric bead array assay that detects perforin release by T cells. + A T cell epitope specific cytokine production assay that detects lymphotactin production by T cells. IEDB IEDB - perforin release|cytometric bead array - cytometric bead array assay measuring epitope specific perforin release by T cells + lymphotactin release|biological activity + assay measuring epitope specific lymphotactin production by T cells - + - - - - - - - - - modified acid-fast stain microscopy assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific lymphotactin production by T cells - A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating. - John Judkins - NCIT:C85736 - https://www.cdc.gov/dpdx/diagnosticprocedures/stool/staining.html - https://github.com/obi-ontology/obi/issues/1444 - modified acid-fast stain microscopy assay + An enzyme-linked immunosorbent assay that detects lymphotactin production by T cells. + IEDB + IEDB + lymphotactin release|ELISA + ELISA measuring epitope specific lymphotactin production by T cells - + - - - positive binding datum + + + remote patient assessment + A telephone or video remote patient assessment conducted between a physician and patient. - A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex. - Bjoern Peters - Hector Guzman-Orozco - IEDB - positive binding datum + An organism diagnostic process which involves a remote assessment of a patient by a clinician. + + telehealth patient assessment + + 2022-05-02T14:15:39Z + remote patient assessment - + - - + + + + + + + + + + + + + + + + + + placental blood specimen + + A specimen that is derived from placental blood. + John Judkins + VEuPathDB + placental blood specimen + + + + + + + + @@ -91101,7 +92937,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -91112,7 +92948,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -91124,41 +92960,55 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + placental blood microbiology assay + + A blood microbiology assay that has a placental blood specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1297 + placental blood microbiology assay + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - + + + + - antibodies from lymphocyte secretions assay - PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes. + placental blood microbiology datum - An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells. + An organism identification assay that is the specified output of a placental blood microbiology assay. John Judkins - ALS assay - antibodies from lymphocyte supernatant assay - OBI VEuPathDB - https://github.com/obi-ontology/obi/issues/1443 - antibodies from lymphocyte secretions assay + https://github.com/obi-ontology/obi/issues/1297 + placental blood microbiology datum + + + + + + + + + + + + + + + eukaryota in placental blood datum + + A placental blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1297 + eukaryota in placental blood datum @@ -91486,6 +93336,7 @@ This issue is outside the scope of OBI. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch + specimen @@ -91651,7 +93502,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from obsolete_cell line A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592. - He, Tong-Chuan, et al. "Identification of c-MYC as a target of the APC pathway." Science 281.5382 (1998): 1509-1512. - "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'." + He, Tong-Chuan, et al. Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512. - To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene. Note that common usage in the literature is often of the form a human colorectal cancer cell line, as seen above. But such references to studies in a line refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'. A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). PERSON:Matthew Brush @@ -96140,7 +97991,14 @@ determinations of compounds. - + + + + + + + + @@ -100220,42 +102078,17 @@ defines and states the requirements (positive or negative) for an entity to be c - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - performing a clinical assessment + + obsolete performing a clinical assessment A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. PlanAndPlannedProcess Branch clinical diagnosis OBI branch derived - performing a clinical assessment + + https://github.com/obi-ontology/obi/issues/623 + obsolete performing a clinical assessment + true @@ -100858,13 +102691,20 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + + + + + + + + @@ -104750,7 +106590,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + + + + + + + @@ -104785,7 +106632,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + + + + + + + @@ -104835,7 +106689,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + + + + + + + @@ -105863,8 +107724,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor. @@ -105885,7 +107747,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + + + + + + + @@ -105911,7 +107780,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + + + + + + + @@ -106395,19 +108271,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106430,19 +108302,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106465,19 +108333,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106500,19 +108364,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106535,19 +108395,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106570,19 +108426,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106605,19 +108457,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106640,19 +108488,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106675,19 +108519,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106710,19 +108550,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106745,19 +108581,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106780,19 +108612,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106815,23 +108643,19 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - + umbilical cord blood specimen A specimen that is derived from some umbilical cord blood @@ -106850,19 +108674,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106885,19 +108705,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -106920,19 +108736,15 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + @@ -107960,7 +109772,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + calcium cation assay An analyte assay that measures the abundance of calcium cation @@ -111741,7 +113553,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -111961,7 +113772,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -112095,7 +113905,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -115690,7 +117499,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -116953,7 +118761,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -118010,7 +119817,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -118569,7 +120375,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -121134,7 +122939,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -122144,7 +123948,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -122948,7 +124751,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -124930,7 +126732,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -125416,7 +127217,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -126341,7 +128141,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -126780,7 +128579,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -127764,7 +129562,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -127984,7 +129781,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -130238,7 +132034,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -131922,7 +133717,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - @@ -133521,7 +135315,14 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + + + + + + + + chromium release assay @@ -135239,7 +137040,7 @@ realizes some 'host of immune response role' urethra - the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening + The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. urethra @@ -135335,7 +137136,7 @@ realizes some 'host of immune response role' renal medulla - the inner portion of the kidney consisting of the renal pyramids + The inner portion of the kidney consisting of the renal pyramids. renal medulla @@ -135443,7 +137244,7 @@ realizes some 'host of immune response role' 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 + 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. aorta @@ -135503,7 +137304,7 @@ realizes some 'host of immune response role' ovary - the gonad of a female organism which contains germ cells + The gonad of a female organism which contains germ cells. ovary @@ -135515,7 +137316,7 @@ realizes some 'host of immune response role' uterus - the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth + The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. uterus @@ -135551,7 +137352,7 @@ realizes some 'host of immune response role' adipose tissue - Portion of connective tissue composed of adipocytes enmeshed in areolar tissue + Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. adipose tissue @@ -135575,7 +137376,7 @@ realizes some 'host of immune response role' rectum - the terminal portion of the intestinal tube, terminating with the anus + The terminal portion of the intestinal tube, terminating with the anus. rectum @@ -135599,7 +137400,7 @@ realizes some 'host of immune response role' urine - Excretion that is the output of a kidney + Excretion that is the output of a kidney. urine @@ -135647,7 +137448,7 @@ realizes some 'host of immune response role' colon - Last portion of the large intestine before it becomes the rectum. + A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. colon @@ -135683,7 +137484,7 @@ realizes some 'host of immune response role' urinary bladder - distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. + Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. urinary bladder @@ -135755,7 +137556,7 @@ realizes some 'host of immune response role' lower respiratory tract - The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] + The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. lower respiratory tract @@ -135815,7 +137616,7 @@ realizes some 'host of immune response role' nasopharynx - the section of the pharynx that lies above the soft palate + The section of the pharynx that lies above the soft palate. nasopharynx @@ -135827,7 +137628,7 @@ realizes some 'host of immune response role' oropharynx - the portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis + The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. oropharynx @@ -135839,7 +137640,7 @@ realizes some 'host of immune response role' vitreous humor - A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina + A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina. vitreous humor @@ -135935,7 +137736,7 @@ realizes some 'host of immune response role' bile - vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. + Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. bile @@ -135947,7 +137748,7 @@ realizes some 'host of immune response role' placenta - organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. + Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. placenta @@ -135959,7 +137760,7 @@ realizes some 'host of immune response role' feces - Portion of semisolid bodily waste discharged through the anus[MW,modified] + Portion of semisolid bodily waste discharged through the anus[MW,modified]. feces @@ -136055,7 +137856,7 @@ realizes some 'host of immune response role' spleen - the organ that functions to filter blood and to store red corpuscles and platelets + The organ that functions to filter blood and to store red corpuscles and platelets. spleen @@ -136079,7 +137880,7 @@ realizes some 'host of immune response role' ileum - the portion of the small intestine that extends from the jejunum to the colon + The portion of the small intestine that extends from the jejunum to the colon. ileum @@ -136139,7 +137940,7 @@ realizes some 'host of immune response role' bone marrow - the soft tissue that fills the cavities of bones + The soft tissue that fills the cavities of bones. bone marrow @@ -136151,7 +137952,7 @@ realizes some 'host of immune response role' pericardial fluid - Transudate contained in the pericardial cavity.[FMA] + Transudate contained in the pericardial cavity.[FMA]. pericardial fluid @@ -136163,7 +137964,7 @@ realizes some 'host of immune response role' tail - An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail + An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. tail @@ -136378,7 +138179,7 @@ realizes some 'host of immune response role' esophagogastric junction - The junction between the esophagus and the stomach epithelium + The junction between the esophagus and the stomach epithelium. esophagogastric junction @@ -136390,7 +138191,7 @@ realizes some 'host of immune response role' omental fat pad - encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon + Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon. omental fat pad @@ -136400,9 +138201,9 @@ realizes some 'host of immune response role' - + umbilical cord blood - blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. + Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. umbilical cord blood @@ -136469,6 +138270,18 @@ realizes some 'host of immune response role' + + + + + placental blood + Blood located in the placenta. + + placental blood + + + + @@ -137709,8 +139522,7 @@ realizes some 'host of immune response role' eBioscience - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.ebioscience.com/@2011/04/11 eBioscience @@ -137723,8 +139535,7 @@ realizes some 'host of immune response role' Cytopeia - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.cytopeia.com/@2011/04/11 Cytopeia @@ -137737,8 +139548,7 @@ realizes some 'host of immune response role' Exalpha Biological - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.exalpha.com/@2011/04/11 Exalpha Biological @@ -137751,8 +139561,7 @@ realizes some 'host of immune response role' Apogee Flow Systems - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.apogeeflow.com/@2011/04/11 Apogee Flow Systems @@ -137765,8 +139574,7 @@ realizes some 'host of immune response role' Exbio Antibodies - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.exbio.cz/@2011/04/11 Exbio Antibodies @@ -137779,8 +139587,7 @@ realizes some 'host of immune response role' Becton Dickinson (BD Biosciences) - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.bdbiosciences.com/@2011/04/11 Becton Dickinson (BD Biosciences) @@ -137793,8 +139600,7 @@ realizes some 'host of immune response role' Dako Cytomation - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.dakousa.com/@2011/04/11 Dako Cytomation @@ -137807,8 +139613,7 @@ realizes some 'host of immune response role' Millipore - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.guavatechnologies.com/@2011/04/11 Millipore @@ -137821,8 +139626,7 @@ realizes some 'host of immune response role' Antigenix - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.antigenix.com/@2011/04/11 Antigenix @@ -137835,8 +139639,7 @@ realizes some 'host of immune response role' Partec - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.partec.de/@2011/04/11 Partec @@ -137849,8 +139652,7 @@ realizes some 'host of immune response role' Beckman Coulter - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.beckmancoulter.com/@2011/04/11 Beckman Coulter @@ -137863,8 +139665,7 @@ realizes some 'host of immune response role' Advanced Instruments Inc. (AI Companies) - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.aicompanies.com/@2011/04/11 Advanced Instruments Inc. (AI Companies) @@ -137877,8 +139678,7 @@ realizes some 'host of immune response role' Miltenyi Biotec - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.miltenyibiotec.com/@2011/04/11 Miltenyi Biotec @@ -137891,8 +139691,7 @@ realizes some 'host of immune response role' AES Chemunex - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.aeschemunex.com/@2011/04/11 AES Chemunex @@ -137905,8 +139704,7 @@ realizes some 'host of immune response role' Bentley Instruments - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://bentleyinstruments.com/@2011/04/11 Bentley Instruments @@ -137919,8 +139717,7 @@ realizes some 'host of immune response role' Invitrogen - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.invitrogen.com/@2011/04/11 Invitrogen @@ -137933,8 +139730,7 @@ realizes some 'host of immune response role' Luminex - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.luminexcorp.com/@2011/04/11 Luminex @@ -137947,8 +139743,7 @@ realizes some 'host of immune response role' CytoBuoy - - A supplier of flow cytometry analyzers + Karin Breuer WEB:http://www.cytobuoy.com/@2011/04/11 CytoBuoy @@ -140941,9 +142736,6 @@ binary, and takes no temporal argument. - - 2 - diff --git a/views/NIAID-GSC-BRC.owl b/views/NIAID-GSC-BRC.owl index 30b20497..44aedb81 100644 --- a/views/NIAID-GSC-BRC.owl +++ b/views/NIAID-GSC-BRC.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg @@ -77,7 +77,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2022-01-03 + 2022-07-11 @@ -1527,6 +1527,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ material MaterialEntity + material entity material entity a flame a forest fire @@ -1545,7 +1546,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + + material entity material entity diff --git a/views/obi.obo b/views/obi.obo index fe71962a..3ee9a31f 100644 --- a/views/obi.obo +++ b/views/obi.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: obi/2022-01-03/obi.obo -date: 03:01:2022 13:09 +data-version: obi/2022-07-11/obi.obo +date: 11:07:2022 15:37 remark: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. ontology: obi.obo property_value: defaultLanguage "en" xsd:string @@ -67,7 +67,7 @@ property_value: http://purl.org/dc/elements/1.1/subject "An ontology for the ann property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/ xsd:string property_value: http://purl.org/dc/terms/title "Ontology for Biomedical Investigations" xsd:string property_value: IAO:0000589 "Ontology for Biomedical Investigations" xsd:string -property_value: owl:versionInfo "2022-01-03" xsd:string +property_value: owl:versionInfo "2022-07-11" xsd:string [Term] id: APOLLO_SV:00000008 @@ -715,7 +715,7 @@ is_a: CHEBI:33839 ! macromolecule [Term] id: CHEBI:35366 name: fatty acid -def: "Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax." [] +def: "Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids." [] is_a: CHEBI:23367 ! molecular entity [Term] @@ -791,6 +791,11 @@ is_a: CHEBI:6495 ! lipoprotein [Term] id: CHEBI:39123 name: calcium cation +is_a: CHEBI:39124 ! calcium ion + +[Term] +id: CHEBI:39124 +name: calcium ion is_a: CHEBI:23367 ! molecular entity [Term] @@ -1332,7 +1337,7 @@ is_a: GO:0005575 ! cellular_component [Term] id: GO:0001046 name: core promoter sequence-specific DNA binding -def: "Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon." [] +def: "Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon." [] is_a: GO:0003674 ! molecular_function is_a: GO:0043565 ! sequence-specific DNA binding @@ -1443,7 +1448,7 @@ is_a: BFO:0000015 ! process [Term] id: GO:0003823 name: antigen binding -def: "Interacting selectively and non-covalently with 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." [] +def: "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." [] is_a: GO:0003674 ! molecular_function [Term] @@ -1521,7 +1526,7 @@ is_a: GO:0008150 ! biological_process [Term] id: GO:0006338 name: chromatin remodeling -def: "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [] +def: "A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication." [] is_a: GO:0009987 ! cellular process [Term] @@ -1588,7 +1593,7 @@ is_a: GO:0008150 ! biological_process [Term] id: GO:0010467 name: gene expression -def: "The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [] +def: "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." [] is_a: GO:0008150 ! biological_process [Term] @@ -1636,7 +1641,7 @@ is_a: GO:0008150 ! biological_process [Term] id: GO:0019904 name: protein domain specific binding -def: "Interacting selectively and non-covalently with a specific domain of a protein." [] +def: "Binding to a specific domain of a protein." [] is_a: OBI:0001588 ! binding [Term] @@ -1743,8 +1748,8 @@ is_a: GO:0001816 ! cytokine production [Term] id: GO:0032617 -name: interleukin-14 production -def: "The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] +name: obsolete interleukin-14 production +def: "OBSOLETE. The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] @@ -1984,18 +1989,6 @@ name: chemokine (C-C motif) ligand 20 production def: "The appearance of chemokine (C-C motif) ligand 20 (CCL20) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production -[Term] -id: GO:0040029 -name: regulation of gene expression, epigenetic -def: "Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [] -is_a: GO:0040030 ! regulation of molecular function, epigenetic - -[Term] -id: GO:0040030 -name: regulation of molecular function, epigenetic -def: "Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [] -is_a: GO:0008150 ! biological_process - [Term] id: GO:0042098 name: T cell proliferation @@ -2032,7 +2025,7 @@ is_a: OBI:0000427 ! enzyme [Term] id: GO:0042605 name: peptide antigen binding -def: "Interacting selectively and non-covalently with an antigen peptide." [] +def: "Binding to an antigen peptide." [] is_a: GO:0003823 ! antigen binding [Term] @@ -2056,14 +2049,14 @@ is_a: GO:0001906 ! cell killing [Term] id: GO:0043565 name: sequence-specific DNA binding -def: "Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding." [] +def: "Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding." [] is_a: OBI:0001588 ! binding [Term] id: GO:0044030 name: regulation of DNA methylation def: "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." [] -is_a: GO:0040030 ! regulation of molecular function, epigenetic +is_a: GO:0008150 ! biological_process [Term] id: GO:0044807 @@ -2287,6 +2280,18 @@ name: chemokine (C-X-C motif) ligand 16 production def: "The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production +[Term] +id: GO:0140730 +name: amphiregulin production +def: "The appearance of amphiregulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Amphiregulin (AREG) is a ligand of the epidermal growth factor receptor (EGFR), a widely expressed transmembrane tyrosine kinase. AREG is synthesized as a membrane-anchored precursor protein that can engage in juxtacrine signaling on adjacent cells. Alternatively, after proteolytic processing by cell membrane proteases, mainly TACE/ADAM17, AREG is secreted and behaves as an autocrine or paracrine factor." [] +is_a: GO:0001816 ! cytokine production + +[Term] +id: GO:0140779 +name: XCL1 production +def: "The appearance of XCL1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] +is_a: GO:0001816 ! cytokine production + [Term] id: HP:0000855 name: Insulin resistance @@ -4305,7 +4310,7 @@ is_a: OBI:0000094 ! material processing [Term] id: OBI:0000109 -name: biological vector role +name: obsolete biological vector role def: "a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true @@ -5423,7 +5428,7 @@ is_obsolete: true id: OBI:0000447 name: intra cellular electrophysiology recording assay def: "An electrophysiology recording assay where the recording location of the electrode is intracellular" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0002176 ! electrophysiology assay [Term] id: OBI:0000448 @@ -5460,7 +5465,7 @@ is_a: BFO:0000034 ! function id: OBI:0000454 name: extracellular electrophysiology recording assay def: "An electrophysiology recording assay where the recording location of the electrode is extracellular" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0002176 ! electrophysiology assay [Term] id: OBI:0000455 @@ -7728,7 +7733,7 @@ is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000875 name: viral hemagglutination inhibition assay -def: "An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates hemagglutination inhibition by the evaluant." [] +def: "An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors." [] synonym: "biological activity" EXACT [] synonym: "HAI" EXACT [] synonym: "hemagglutination inhibition" EXACT [] @@ -8394,9 +8399,10 @@ is_obsolete: true [Term] id: OBI:0000988 -name: performing a diagnosis +name: obsolete performing a diagnosis def: "The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis" [] -is_a: OBI:0200000 ! data transformation +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true [Term] id: OBI:0000989 @@ -9797,9 +9803,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001215 name: intracellular material detection assay measuring epitope specific perforin release -def: "A T cell epitope specific perforin release assay that uses an intracellular material detection by flow cytometry assay." [] +def: "A flow cytometry assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|intracellular staining" EXACT [] -is_a: OBI:0001497 ! biological activity assay measuring epitope specific perforin release by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells [Term] id: OBI:0001216 @@ -10008,9 +10015,10 @@ is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production b [Term] id: OBI:0001245 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release -def: "A T cell epitope specific perforin release assay that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|RNA/DNA detection" EXACT [] -is_a: OBI:0001497 ! biological activity assay measuring epitope specific perforin release by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells [Term] id: OBI:0001246 @@ -10176,7 +10184,7 @@ is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production b [Term] id: OBI:0001269 -name: biological activity assay measuring epitope specific cytotoxic T cell degranulation +name: assay measuring epitope specific cytotoxic T cell degranulation def: "A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation." [] synonym: "degranulation|biological activity" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding @@ -10531,9 +10539,10 @@ is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production [Term] id: OBI:0001322 name: ELISPOT assay measuring epitope specific granzyme B release by T cells -def: "A T cell epitope specific granzyme B release assay that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells." [] synonym: "granzyme B release|ELISPOT" EXACT [] -is_a: OBI:0001436 ! biological activity assay measuring epitope specific granzyme B release by T cells +is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001323 @@ -11200,9 +11209,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001423 name: intracellular material detection measuring epitope specific granzyme B release by T cells -def: "A T cell epitope specific granzyme B release assay that uses an intracellular material detection by flow cytometry assay." [] +def: "A flow cytometry assay that detects epitope specific granzyme B release by T cells" [] synonym: "granzyme B release|intracellular staining" EXACT [] -is_a: OBI:0001436 ! biological activity assay measuring epitope specific granzyme B release by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells [Term] id: OBI:0001425 @@ -11256,10 +11266,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001436 -name: biological activity assay measuring epitope specific granzyme B release by T cells +name: assay measuring epitope specific granzyme B release by T cells def: "A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells." [] synonym: "granzyme B release|biological activity" EXACT [] -is_a: OBI:0001269 ! biological activity assay measuring epitope specific cytotoxic T cell degranulation +is_a: OBI:0001269 ! assay measuring epitope specific cytotoxic T cell degranulation [Term] id: OBI:0001437 @@ -11418,9 +11428,10 @@ is_a: OBI:0000115 ! intervention design [Term] id: OBI:0001461 name: ELISA measuring epitope specific granzyme B release by T cells -def: "A T cell epitope specific granzyme B release assay that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells." [] synonym: "granzyme B release|ELISA" EXACT [] -is_a: OBI:0001436 ! biological activity assay measuring epitope specific granzyme B release by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells [Term] id: OBI:0001462 @@ -11618,7 +11629,7 @@ is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001491 -name: radioactivity detection binding assay +name: binding assay using radioactivity detection def: "A binding assay that uses radioactivity detection as an indicator of binding." [] is_a: OBI:0001146 ! binding assay @@ -11659,10 +11670,10 @@ is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production b [Term] id: OBI:0001497 -name: biological activity assay measuring epitope specific perforin release by T cells +name: assay measuring epitope specific perforin release by T cells def: "A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells." [] synonym: "perforin release|biological activity" EXACT [] -is_a: OBI:0001269 ! biological activity assay measuring epitope specific cytotoxic T cell degranulation +is_a: OBI:0001269 ! assay measuring epitope specific cytotoxic T cell degranulation [Term] id: OBI:0001498 @@ -11672,8 +11683,8 @@ is_a: OBI:0000997 ! growth environment [Term] id: OBI:0001499 -name: fluorescence detection binding assay -def: "A binding assay that uses fluorescence detection as an indicator of binding" [] +name: binding assay using fluorescence detection +def: "A binding assay that uses fluorescence detection as an indicator of binding." [] is_a: OBI:0001146 ! binding assay [Term] @@ -11766,7 +11777,7 @@ id: OBI:0001513 name: radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|purified MHC/competitive/radioactivity" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] @@ -11787,7 +11798,7 @@ id: OBI:0001516 name: radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001991 ! assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex [Term] @@ -11795,7 +11806,7 @@ id: OBI:0001517 name: radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] @@ -11810,7 +11821,7 @@ id: OBI:0001519 name: fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex def: "A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "qualitative binding|lysate MHC/direct/fluorescence" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001579 ! assay measuring binding of a cell-lysate-MHC:ligand complex [Term] @@ -11818,7 +11829,7 @@ id: OBI:0001520 name: fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] @@ -11849,7 +11860,7 @@ id: OBI:0001524 name: fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "association constant KA|cellular MHC/direct/fluorescence|1/M" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001987 ! assay measuring the association constant [KA] of a MHC:ligand complex [Term] @@ -11895,7 +11906,7 @@ id: OBI:0001531 name: fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand." [] synonym: "half life|purified MHC/direct/fluorescence|min" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] @@ -11917,7 +11928,7 @@ id: OBI:0001534 name: fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|purified MHC/competitive/fluorescence" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] @@ -11938,7 +11949,7 @@ id: OBI:0001537 name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|purified MHC/competitive/fluorescence|nM" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] @@ -11952,7 +11963,7 @@ id: OBI:0001539 name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|cellular MHC/competitive/fluorescence|nM" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] @@ -11969,7 +11980,7 @@ id: OBI:0001541 name: fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex." [] synonym: "on rate|purified MHC/direct/fluorescence|nM^-1s^-1" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001994 ! assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex [Term] @@ -11993,7 +12004,7 @@ id: OBI:0001544 name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|lysate MHC/competitive/radioactivity|nM" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] @@ -12028,7 +12039,7 @@ id: OBI:0001549 name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|cellular MHC/competitive/radioactivity|nM" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] @@ -12077,7 +12088,7 @@ id: OBI:0001556 name: radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "qualitative binding|lysate MHC/direct/radioactivity" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001579 ! assay measuring binding of a cell-lysate-MHC:ligand complex [Term] @@ -12091,7 +12102,7 @@ id: OBI:0001558 name: radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "half life|cellular MHC/direct/radioactivity|min" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] @@ -12099,7 +12110,7 @@ id: OBI:0001559 name: fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "half life|cellular MHC/direct/fluorescence|min" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] @@ -12114,7 +12125,7 @@ id: OBI:0001561 name: fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001991 ! assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex [Term] @@ -12144,7 +12155,7 @@ id: OBI:0001565 name: radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "half life|lysate MHC/direct/radioactivity|min" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] @@ -12159,7 +12170,7 @@ id: OBI:0001567 name: radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "off rate|lysate MHC/direct/radioactivity|1/s" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001993 ! assay measuring the off rate measurement [koff] of a MHC:ligand complex [Term] @@ -12167,7 +12178,7 @@ id: OBI:0001568 name: radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] @@ -12175,7 +12186,7 @@ id: OBI:0001569 name: fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand." [] synonym: "off rate|purified MHC/direct/fluorescence|1/s" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001993 ! assay measuring the off rate measurement [koff] of a MHC:ligand complex [Term] @@ -12299,7 +12310,7 @@ id: OBI:0001586 name: radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand." [] synonym: "half life|purified MHC/direct/radioactivity|min" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] @@ -12328,7 +12339,7 @@ id: OBI:0001590 name: fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC/direct/fluorescence" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] @@ -12342,7 +12353,7 @@ id: OBI:0001592 name: fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand." [] synonym: "half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001991 ! assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex [Term] @@ -12356,7 +12367,7 @@ id: OBI:0001594 name: fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|cellular MHC/competitive/fluorescence" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] @@ -12391,7 +12402,7 @@ id: OBI:0001599 name: radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|cellular MHC/competitive/radioactivity" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] @@ -12414,7 +12425,7 @@ id: OBI:0001602 name: radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "qualitative binding|cellular MHC/direct/radioactivity" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] @@ -12429,7 +12440,7 @@ id: OBI:0001604 name: fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand." [] synonym: "50% dissociation temperature|purified MHC/direct/fluorescence|°C" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0003145 ! assay measuring quantitative binding of a MHC:ligand complex [Term] @@ -12444,7 +12455,7 @@ id: OBI:0001606 name: fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "qualitative binding|cellular MHC/direct/fluorescence" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] @@ -12459,7 +12470,7 @@ id: OBI:0001608 name: radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC/direct/radioactivity" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] @@ -12498,7 +12509,7 @@ id: OBI:0001613 name: fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] @@ -12833,9 +12844,10 @@ is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:anti [Term] id: OBI:0001660 name: intracellular material detection assay measuring epitope specific granzyme A release by T cells -def: "A T cell epitope specific granzyme A release assay that uses an intracellular material detection by flow cytometry assay." [] +def: "A flow cytometry assay that detects epitope specific granzyme A release by T cells." [] synonym: "granzyme A release|intracellular staining" EXACT [] -is_a: OBI:0001809 ! biological activity assay measuring epitope specific granzyme A release by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001809 ! assay measuring epitope specific granzyme A release by T cells [Term] id: OBI:0001661 @@ -12855,23 +12867,25 @@ is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:anti [Term] id: OBI:0001663 name: ELISA measuring epitope specific granulysin release by T cells -def: "A T cell epitope specific granulysin release assay that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells." [] synonym: "granulysin release|ELISA" EXACT [] -is_a: OBI:0001810 ! biological activity assay measuring epitope specific granulysin release by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001810 ! assay measuring epitope specific granulysin release by T cells [Term] id: OBI:0001664 name: intracellular material detection assay measuring epitope specific granulysin release by T cells -def: "A T cell epitope specific granulysin release assay that uses an intracellular material detection by flow cytometry assay." [] +def: "A flow cytometry assay that detects epitope specific granulysin release by T cells." [] synonym: "granulysin release|intracellular staining" EXACT [] -is_a: OBI:0001810 ! biological activity assay measuring epitope specific granulysin release by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001810 ! assay measuring epitope specific granulysin release by T cells [Term] id: OBI:0001665 name: fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "off rate|cellular MHC/direct/fluorescence|1/s" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001993 ! assay measuring the off rate measurement [koff] of a MHC:ligand complex [Term] @@ -12879,7 +12893,7 @@ id: OBI:0001666 name: fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "on rate|cellular MHC/direct/fluorescence|nM^-1s^-1" EXACT [] -is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001994 ! assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex [Term] @@ -13942,17 +13956,17 @@ is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by [Term] id: OBI:0001809 -name: biological activity assay measuring epitope specific granzyme A release by T cells +name: assay measuring epitope specific granzyme A release by T cells def: "A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells." [] synonym: "granzyme A release|biological activity" EXACT [] -is_a: OBI:0001269 ! biological activity assay measuring epitope specific cytotoxic T cell degranulation +is_a: OBI:0001269 ! assay measuring epitope specific cytotoxic T cell degranulation [Term] id: OBI:0001810 -name: biological activity assay measuring epitope specific granulysin release by T cells +name: assay measuring epitope specific granulysin release by T cells def: "A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells." [] synonym: "granulysin release|biological activity" EXACT [] -is_a: OBI:0001269 ! biological activity assay measuring epitope specific cytotoxic T cell degranulation +is_a: OBI:0001269 ! assay measuring epitope specific cytotoxic T cell degranulation [Term] id: OBI:0001811 @@ -15093,7 +15107,7 @@ is_a: OBI:0000443 ! analyte assay id: OBI:0001979 name: fluorescence quenching binding assay def: "A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other." [] -is_a: OBI:0001146 ! binding assay +is_a: OBI:0001499 ! binding assay using fluorescence detection [Term] id: OBI:0001980 @@ -15156,7 +15170,7 @@ id: OBI:0001989 name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|purified MHC/direct/radioactivity|nM" EXACT [] -is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] @@ -15709,30 +15723,34 @@ is_a: OBI:1110130 ! biological activity assay measuring epitope specific T cell [Term] id: OBI:0002063 name: cytometric bead array assay measuring epitope specific granzyme A release by T cells -def: "A T cell epitope specific granzyme A release assay that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects epitope specific granzyme A release by T cells." [] synonym: "granzyme A release|cytometric bead array" EXACT [] -is_a: OBI:0001809 ! biological activity assay measuring epitope specific granzyme A release by T cells +is_a: OBI:0001809 ! assay measuring epitope specific granzyme A release by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002064 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells -def: "A T cell epitope specific granzyme A release assay that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells." [] synonym: "granzyme A release|RNA/DNA detection" EXACT [] -is_a: OBI:0001809 ! biological activity assay measuring epitope specific granzyme A release by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001809 ! assay measuring epitope specific granzyme A release by T cells [Term] id: OBI:0002065 name: cytometric bead array assay measuring epitope specific granzyme B release by T cells -def: "A T cell epitope specific granzyme B release assay that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects epitope specific granzyme B release by T cells." [] synonym: "granzyme B release|cytometric bead array" EXACT [] -is_a: OBI:0001436 ! biological activity assay measuring epitope specific granzyme B release by T cells +is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002066 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells -def: "A T cell epitope specific granzyme B release assay that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells" [] synonym: "granzyme B release|RNA/DNA detection" EXACT [] -is_a: OBI:0001436 ! biological activity assay measuring epitope specific granzyme B release by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells [Term] id: OBI:0002067 @@ -15753,9 +15771,10 @@ is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002069 name: ELISPOT assay measuring epitope specific perforin release by T cells -def: "A T cell epitope specific perforin release assay that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|ELISPOT" EXACT [] -is_a: OBI:0001497 ! biological activity assay measuring epitope specific perforin release by T cells +is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0002070 @@ -18705,9 +18724,10 @@ is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response a [Term] id: OBI:0002672 name: ELISA measuring epitope specific perforin release by T cells -def: "An assay of epitope specific perforin release by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|ELISA" EXACT [] -is_a: OBI:0001497 ! biological activity assay measuring epitope specific perforin release by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells [Term] id: OBI:0002673 @@ -19095,7 +19115,7 @@ is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002726 -name: insecticide resistance by PCR-RELP assay +name: insecticide resistance by PCR-RFLP assay def: "An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay." [] synonym: "PCR-RFLP" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay @@ -19725,6 +19745,12 @@ name: surface wipe def: "A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces." [] is_a: OBI:0002814 ! specimen collection device +[Term] +id: OBI:0002830 +name: catheter +def: "A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body." [] +is_a: OBI:0000968 ! device + [Term] id: OBI:0002897 name: surveillance process @@ -19916,7 +19942,7 @@ is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002926 name: Centers for Disease Control and Prevention light trap -def: "A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant." [] +def: "A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery." [] synonym: "CDC light trap" EXACT [] is_a: OBI:0002930 ! light trap @@ -21323,7 +21349,6 @@ is_a: OBI:0003021 ! basophil assay id: OBI:0003150 name: calcium cation concentration assay def: "A calcium cation assay that measures the concentration of calcium cations in a specimen." [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -21948,13 +21973,13 @@ is_a: OBI:0003244 ! blood microbiology datum [Term] id: OBI:0003262 name: virus in blood datum -def: "A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A blood microbiology datum that is interpreted as an indication of the presence of viruses in the specimen." [] is_a: OBI:0003244 ! blood microbiology datum [Term] id: OBI:0003263 name: eukaryota in blood datum -def: "A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] is_a: OBI:0003244 ! blood microbiology datum [Term] @@ -21966,43 +21991,43 @@ is_a: OBI:0003246 ! feces microbiology datum [Term] id: OBI:0003265 name: eukaryota in feces datum -def: "A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A feces microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] is_a: OBI:0003246 ! feces microbiology datum [Term] id: OBI:0003266 name: virus in feces datum -def: "A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A feces microbiology datum that is interpreted as an indication of the presence of viruses in the specimen." [] is_a: OBI:0003246 ! feces microbiology datum [Term] id: OBI:0003267 name: eukaryota in urine datum -def: "A urine microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A urine microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] is_a: OBI:0003248 ! urine microbiology datum [Term] id: OBI:0003268 name: bacteria in induced sputum datum -def: "A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "An induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] is_a: OBI:0003251 ! induced sputum microbiology datum [Term] id: OBI:0003269 name: eukaryota in induced sputum datum -def: "A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "An induced sputum microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] is_a: OBI:0003251 ! induced sputum microbiology datum [Term] id: OBI:0003270 name: virus in induced sputum datum -def: "A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "An induced sputum microbiology datum that is interpreted as an indication of the presence of viruses in the specimen." [] is_a: OBI:0003251 ! induced sputum microbiology datum [Term] id: OBI:0003271 name: bacteria in endotracheal tube aspirate datum -def: "A endotracheal tube aspirate microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "An endotracheal tube aspirate microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] is_a: OBI:0003255 ! endotracheal tube aspirate microbiology datum [Term] @@ -22014,13 +22039,13 @@ is_a: OBI:0003256 ! lung microbiology datum [Term] id: OBI:0003273 name: eukaryota in lung datum -def: "A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A lung microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] is_a: OBI:0003256 ! lung microbiology datum [Term] id: OBI:0003274 name: virus in lung datum -def: "A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A lung microbiology datum that is interpreted as an indication of the presence of viruses in the specimen." [] is_a: OBI:0003256 ! lung microbiology datum [Term] @@ -22032,13 +22057,13 @@ is_a: OBI:0003257 ! nasopharyngeal or oropharyngeal swab microbiology datum [Term] id: OBI:0003276 name: eukaryota in nasopharyngeal or oropharyngeal swab datum -def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] is_a: OBI:0003257 ! nasopharyngeal or oropharyngeal swab microbiology datum [Term] id: OBI:0003277 name: virus in nasopharyngeal or oropharyngeal swab datum -def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of viruses in the specimen." [] is_a: OBI:0003257 ! nasopharyngeal or oropharyngeal swab microbiology datum [Term] @@ -22050,19 +22075,19 @@ is_a: OBI:0003258 ! pleural fluid microbiology datum [Term] id: OBI:0003279 name: eukaryota in pleural fluid datum -def: "A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A pleural fluid microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] is_a: OBI:0003258 ! pleural fluid microbiology datum [Term] id: OBI:0003280 name: virus in pleural fluid datum -def: "A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "A pleural fluid microbiology datum that is interpreted as an indication of the presence of viruses in the specimen." [] is_a: OBI:0003258 ! pleural fluid microbiology datum [Term] id: OBI:0003281 name: eukaryota in umbilical cord blood datum -def: "A umbilical cord blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +def: "An umbilical cord blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] is_a: OBI:0003260 ! umbilical cord blood microbiology datum [Term] @@ -22131,16 +22156,18 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0003292 name: cytometric bead array assay measuring epitope specific granulysin release by T cells -def: "A cytometric bead array assay that detects granulysin release by T cells." [] +def: "A cytometric bead array assay that detects epitope specific granulysin release by T cells." [] synonym: "granulysin release|cytometric bead array" EXACT [] -is_a: OBI:0001810 ! biological activity assay measuring epitope specific granulysin release by T cells +is_a: OBI:0001810 ! assay measuring epitope specific granulysin release by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0003293 name: cytometric bead array assay measuring epitope specific perforin release by T cells -def: "A cytometric bead array assay that detects perforin release by T cells." [] +def: "A cytometric bead array assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|cytometric bead array" EXACT [] -is_a: OBI:0001497 ! biological activity assay measuring epitope specific perforin release by T cells +is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0003294 @@ -22162,6 +22189,277 @@ synonym: "ALS assay" EXACT [] synonym: "antibodies from lymphocyte supernatant assay" EXACT [] is_a: OBI:0003040 ! blood assay +[Term] +id: OBI:0003297 +name: tyramide signal amplification sequencing assay +def: "A DNA sequencing assay that uses tyramide signal amplification (TSA) to assess distance of DNA regions to a targeted nuclear compartment or protein, typically on a scale of 100-1000 nm." [] +synonym: "TSA-seq" EXACT [] +is_a: OBI:0000626 ! DNA sequencing assay + +[Term] +id: OBI:0003298 +name: DNA adenine methyltransferase identification assay +def: "An assay for identifying DNA binding sites for a protein by fusing it to Dam methylase, and expressing it so that bound DNA gets methylated. The methylated DNA can then be isolated and analyzed." [] +synonym: "DamID assay" EXACT [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003299 +name: DamID-seq +def: "A DNA adenine methyltransferase identification (DamID) assay in which DamID-generated DNA fragments undergo high-throughput sequencing to determine a protein's DNA-binding site." [] +is_a: OBI:0003298 ! DNA adenine methyltransferase identification assay + +[Term] +id: OBI:0003300 +name: nucleolus-associated domain sequencing assay +def: "A DNA sequencing assay in which nucleoli are isolated and the DNA associated with them is sequenced to identify nucleoli-associating domains." [] +synonym: "NAD-seq" EXACT [] +is_a: OBI:0000626 ! DNA sequencing assay + +[Term] +id: OBI:0003301 +name: DNase Hi-C assay +def: "A Hi-C assay in which DNase I is used for digesting DNA fragments rather than a restriction enzyme, which can result in a higher resolution of mapped chromosome contacts." [] +is_a: OBI:0002440 ! Hi-C assay + +[Term] +id: OBI:0003302 +name: micro-C assay +def: "A Hi-C assay which uses micrococcal nuclease digestion in place of the restriction enzyme digestion step." [] +is_a: OBI:0002440 ! Hi-C assay + +[Term] +id: OBI:0003303 +name: single cell combinatorial indexing Hi-C assay +def: "A Hi-C assay performed on massively multiplexed single-cell samples." [] +synonym: "sci-Hi-C" EXACT [] +is_a: OBI:0002440 ! Hi-C assay + +[Term] +id: OBI:0003304 +name: single nucleus Hi-C assay +def: "A Hi-C assay performed on isolated nuclei." [] +synonym: "sn-Hi-C" EXACT [] +is_a: OBI:0002440 ! Hi-C assay + +[Term] +id: OBI:0003305 +name: single cell Hi-C assay +def: "A Hi-C assay performed on a single cell." [] +is_a: OBI:0002440 ! Hi-C assay + +[Term] +id: OBI:0003306 +name: bulk Hi-C assay +def: "A Hi-C assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells." [] +is_a: OBI:0002440 ! Hi-C assay + +[Term] +id: OBI:0003307 +name: multi-contact Hi-C assay +def: "A Hi-C assay that assesses interactions between multiple DNA fragments rather than only pairwise interactions as in traditional Hi-C. The experimental procedure of cross-linking, digestion, and ligation is performed similarly to traditional Hi-C, but after DNA is purified a long-read library is produced in which many ligated fragments may be contained in a single molecule. The library is then sequenced on a long read sequencer." [] +synonym: "MC-3C" EXACT [] +synonym: "MC-HI-C" EXACT [] +is_a: OBI:0002440 ! Hi-C assay + +[Term] +id: OBI:0003309 +name: transposase-mediated analysis of chromatin looping assay +def: "A DNA sequencing assay designed to detect interacting genomic regions. Rather than the traditional Hi-C approach of digestion and proximity ligation, the procedure involves transposase-mediated insertion of an oligonucleotide linker between the pair of interacting regions." [] +synonym: "TrAC-Loop" EXACT [] +is_a: OBI:0000626 ! DNA sequencing assay + +[Term] +id: OBI:0003310 +name: split-pool recognition of interactions and tag extension assay +def: "A sequencing assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates are pooled together again. This sequence of splitting, tagging, and re-combining is repeated several times so that fragments with the same sequences of barcodes represent fragments that have co-associated throughout the experiment. Finally, a sequencing library is constructed and high-throughput sequencing is performed." [] +synonym: "SPRITE" EXACT [] +is_a: OBI:0600047 ! sequencing assay + +[Term] +id: OBI:0003311 +name: DNA split-pool recognition of interactions and tag extension assay +def: "A split-pool recognition of interactions and tag extension (SPRITE) assay that only assays interactions between regions of genomic DNA." [] +synonym: "DNA SPRITE" EXACT [] +is_a: OBI:0003310 ! split-pool recognition of interactions and tag extension assay + +[Term] +id: OBI:0003312 +name: RNA-DNA split-pool recognition of interactions and tag extension assay +def: "A split-pool recognition of interactions and tag extension (SPRITE) assay in which RNA in the cross-linked complexes is converted to cDNA before the initial splitting step, allowing analysis of RNA-DNA interactions." [] +synonym: "RNA-DNA SPRITE" EXACT [] +is_a: OBI:0003310 ! split-pool recognition of interactions and tag extension assay + +[Term] +id: OBI:0003313 +name: genome architecture mapping assay +def: "A DNA sequencing assay designed to analyze 3D chromatin structure without relying on digestion and ligation. The procedure involves cryosectioning samples in random orientation, and then single nuclear profiles are isolated by laser microdissection. Each nuclear profile then undergoes high-throughput sequencing, and subsequent analysis can generate a matrix of inferred proximity between genomic regions." [] +synonym: "GAM" EXACT [] +is_a: OBI:0000626 ! DNA sequencing assay + +[Term] +id: OBI:0003314 +name: mapping RNA-genome interactions assay +def: "A nuclear ligation assay for probing RNA-DNA interactions in the nucleus. Nuclei are crosslinked, and RNA fragments are ligated to proximal DNA fragments via a special linker molecule. After reverse transcription, high-throughput sequencing is performed." [] +synonym: "MARGI" EXACT [] +is_a: OBI:0002438 ! nuclear ligation assay + +[Term] +id: OBI:0003315 +name: assay measuring epitope specific amphiregulin production by T cells +def: "A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells." [] +synonym: "amphiregulin release|biological activity" EXACT [] +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells + +[Term] +id: OBI:0003316 +name: ELISA measuring epitope specific amphiregulin production by T cells +def: "An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells." [] +synonym: "amphiregulin release|ELISA" EXACT [] +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0003315 ! assay measuring epitope specific amphiregulin production by T cells + +[Term] +id: OBI:0003317 +name: perforin release during T cell degranulation +def: "The release of perforin during cytotoxic T cell degranulation." [] +is_a: GO:0035944 ! perforin production + +[Term] +id: OBI:0003318 +name: granzyme A release during T cell degranulation +def: "The release of granzyme A during cytotoxic T cell degranulation." [] +is_a: GO:0035746 ! granzyme A production + +[Term] +id: OBI:0003319 +name: granzyme B release during T cell degranulation +def: "The release of granzyme B during cytotoxic T cell degranulation." [] +is_a: GO:0071613 ! granzyme B production + +[Term] +id: OBI:0003320 +name: granulysin release during T cell degranulation +def: "The release of granulysin during cytotoxic T cell degranulation." [] +is_a: GO:0036262 ! granulysin production + +[Term] +id: OBI:0003321 +name: venous blood microbiology assay +def: "A blood microbiology assay that identifies a microorganism in a venous blood specimen." [] +is_a: OBI:0002649 ! blood microbiology assay + +[Term] +id: OBI:0003323 +name: high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex +def: "A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay." [] +synonym: "antibody binding|High throughput multiplexed assay" EXACT [] +is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex + +[Term] +id: OBI:0003324 +name: high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex +def: "A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay." [] +synonym: "T cell binding|High throughput multiplexed assay" EXACT [] +is_a: OBI:1110037 ! assay measuring binding of a T cell epitope:MHC:TCR complex + +[Term] +id: OBI:0003325 +name: high throughput multiplexed assay measuring binding of a MHC:ligand complex +def: "A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay." [] +synonym: "MHC binding|High throughput multiplexed assay" EXACT [] +is_a: OBI:1110126 ! assay measuring binding of a MHC:ligand complex + +[Term] +id: OBI:0003326 +name: high throughput multiplexed assay measuring MHC ligand processing and presentation +def: "A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay." [] +synonym: "ligand presentation|High throughput multiplexed assay" EXACT [] +is_a: OBI:1110125 ! assay measuring MHC ligand processing and presentation + +[Term] +id: OBI:0003365 +name: milk assay datum +def: "A data item that is the specified output of a milk assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003366 +name: organism diagnostic process +def: "A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has a disease, disorder, or syndrome of a certain type, or none of these as output." [] +is_a: OBI:0000338 ! drawing a conclusion based on data + +[Term] +id: OBI:0003367 +name: diagnosis of an organism +def: "A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these." [] +is_a: OBI:0001909 ! conclusion based on data + +[Term] +id: OBI:0003368 +name: detection technique +def: "An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003369 +name: assay kit +def: "A processed material that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit." [] +is_a: OBI:0000047 ! processed material + +[Term] +id: OBI:0003371 +name: epitope specific XCL1 release by T cells +def: "A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope." [] +is_a: GO:0140779 ! XCL1 production +is_a: OBI:0001193 ! epitope specific cytokine production by T cells + +[Term] +id: OBI:0003372 +name: assay measuring epitope specific lymphotactin production by T cells +def: "A T cell epitope specific cytokine production assay that detects lymphotactin production by T cells." [] +synonym: "lymphotactin release|biological activity" EXACT [] +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells + +[Term] +id: OBI:0003373 +name: ELISA measuring epitope specific lymphotactin production by T cells +def: "An enzyme-linked immunosorbent assay that detects lymphotactin production by T cells." [] +synonym: "lymphotactin release|ELISA" EXACT [] +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0003372 ! assay measuring epitope specific lymphotactin production by T cells + +[Term] +id: OBI:0003374 +name: remote patient assessment +def: "An organism diagnostic process which involves a remote assessment of a patient by a clinician." [] +synonym: "telehealth patient assessment" EXACT [] +is_a: OBI:0003366 ! organism diagnostic process + +[Term] +id: OBI:0003380 +name: placental blood specimen +def: "A specimen that is derived from placental blood." [] +is_a: OBI:2000009 ! bodily fluid specimen + +[Term] +id: OBI:0003381 +name: placental blood microbiology assay +def: "A blood microbiology assay that has a placental blood specimen as evaluant." [] +is_a: OBI:0002649 ! blood microbiology assay + +[Term] +id: OBI:0003382 +name: placental blood microbiology datum +def: "An organism identification assay that is the specified output of a placental blood microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003383 +name: eukaryota in placental blood datum +def: "A placental blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] +is_a: OBI:0003382 ! placental blood microbiology datum + [Term] id: OBI:0005246 name: injection function @@ -24802,10 +25100,11 @@ is_a: OBI:0000070 ! assay [Term] id: OBI:0600003 -name: performing a clinical assessment +name: obsolete performing a clinical assessment def: "A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition." [] synonym: "clinical diagnosis" EXACT [] -is_a: OBI:0000011 ! planned process +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true [Term] id: OBI:0600004 @@ -25990,8 +26289,9 @@ id: OBI:1110179 name: MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex def: "A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor." [] synonym: "qualitative binding|multimer/tetramer" EXACT [] -is_a: OBI:0001317 ! flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex +is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:1110124 ! assay measuring qualitative binding of a T cell epitope:MHC:TCR complex [Term] id: OBI:1110180 @@ -26205,7 +26505,7 @@ is_a: OBI:0002503 ! feces specimen id: OBI:2000012 name: umbilical cord blood specimen def: "A specimen that is derived from some umbilical cord blood" [] -is_a: OBI:2000009 ! bodily fluid specimen +is_a: OBI:2000013 ! arterial blood specimen [Term] id: OBI:2000013 @@ -26385,7 +26685,7 @@ is_a: OBI:0000443 ! analyte assay id: OBI:2100024 name: calcium cation assay def: "An analyte assay that measures the abundance of calcium cation" [] -is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003012 ! ionized calcium assay [Term] id: OBI:2100025 @@ -26793,7 +27093,6 @@ is_a: OBI:2100020 ! glucose assay id: OBI:2100092 name: basic metabolic panel venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -26812,7 +27111,6 @@ is_a: OBI:2100025 ! creatine kinase assay id: OBI:2100095 name: venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -26825,7 +27123,6 @@ is_a: OBI:0003009 ! ferritin assay id: OBI:2100097 name: total venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a total order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -27144,7 +27441,6 @@ is_a: OBI:2100001 ! carbon dioxide assay id: OBI:2100149 name: comprehensive metabolic panel venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -27253,7 +27549,6 @@ is_a: OBI:2100036 ! elemental oxygen assay id: OBI:2100167 name: ionized venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -27344,7 +27639,6 @@ is_a: OBI:2100004 ! potassium(1+) assay id: OBI:2100182 name: ionized arterial blood calcium assay def: "An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -27393,7 +27687,6 @@ is_a: OBI:0003018 ! hematocrit assay id: OBI:2100190 name: GEM premier blood gas venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -27611,7 +27904,6 @@ is_a: OBI:2100004 ! potassium(1+) assay id: OBI:2100226 name: chem11 venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -27696,7 +27988,6 @@ is_a: OBI:2100020 ! glucose assay id: OBI:2100240 name: chem16 venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -27763,7 +28054,6 @@ is_a: OBI:2100020 ! glucose assay id: OBI:2100251 name: POC chem8 arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -27934,7 +28224,6 @@ is_a: OBI:0003018 ! hematocrit assay id: OBI:2100279 name: ABL90 panel arterial blood calcium assay def: "An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -27977,7 +28266,6 @@ is_a: OBI:2100014 ! hemoglobin assay id: OBI:2100286 name: ABL90 panel venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -28057,7 +28345,6 @@ is_a: OBI:2100022 ! albumin assay id: OBI:2100299 name: bone profile venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -28094,7 +28381,6 @@ is_a: OBI:2100036 ! elemental oxygen assay id: OBI:2100305 name: ABG/electrolytes arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -28179,7 +28465,6 @@ is_a: OBI:2100020 ! glucose assay id: OBI:2100319 name: GEM4000 ANLCOOX arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -28198,7 +28483,6 @@ is_a: OBI:2100002 ! sodium(1+) assay id: OBI:2100322 name: ionized venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -28397,7 +28681,6 @@ is_a: OBI:2100014 ! hemoglobin assay id: OBI:2100355 name: venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -28549,7 +28832,6 @@ is_a: OBI:0003018 ! hematocrit assay id: OBI:2100380 name: GEM4 arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order" [] -is_a: OBI:0003012 ! ionized calcium assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -29534,7 +29816,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000057 name: urethra -def: "the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening" [] +def: "The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -29582,7 +29864,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000362 name: renal medulla -def: "the inner portion of the kidney consisting of the renal pyramids" [] +def: "The inner portion of the kidney consisting of the renal pyramids." [] is_a: UBERON:0000481 ! multi-tissue structure [Term] @@ -29636,7 +29918,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000947 name: aorta -def: "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" [] +def: "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." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -29666,13 +29948,13 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000992 name: ovary -def: "the gonad of a female organism which contains germ cells" [] +def: "The gonad of a female organism which contains germ cells." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000995 name: uterus -def: "the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth" [] +def: "The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -29690,7 +29972,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001013 name: adipose tissue -def: "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue" [] +def: "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue." [] is_a: UBERON:0000479 ! tissue [Term] @@ -29702,7 +29984,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001052 name: rectum -def: "the terminal portion of the intestinal tube, terminating with the anus" [] +def: "The terminal portion of the intestinal tube, terminating with the anus." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -29714,7 +29996,7 @@ is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0001088 name: urine -def: "Excretion that is the output of a kidney" [] +def: "Excretion that is the output of a kidney." [] is_a: UBERON:0000463 ! organism substance [Term] @@ -29738,7 +30020,7 @@ is_a: UBERON:0000479 ! tissue [Term] id: UBERON:0001155 name: colon -def: "Last portion of the large intestine before it becomes the rectum." [] +def: "A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -29756,7 +30038,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001255 name: urinary bladder -def: "distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]." [] +def: "Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -29792,7 +30074,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001558 name: lower respiratory tract -def: "The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]" [] +def: "The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -29822,19 +30104,19 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001728 name: nasopharynx -def: "the section of the pharynx that lies above the soft palate" [] +def: "The section of the pharynx that lies above the soft palate." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001729 name: oropharynx -def: "the portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis" [] +def: "The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001797 name: vitreous humor -def: "A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina" [] +def: "A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina." [] is_a: UBERON:0000463 ! organism substance [Term] @@ -29882,19 +30164,19 @@ is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0001970 name: bile -def: "vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium." [] +def: "Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0001987 name: placenta -def: "organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell." [] +def: "Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001988 name: feces -def: "Portion of semisolid bodily waste discharged through the anus[MW,modified]" [] +def: "Portion of semisolid bodily waste discharged through the anus[MW,modified]." [] is_a: UBERON:0000463 ! organism substance [Term] @@ -29942,7 +30224,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002106 name: spleen -def: "the organ that functions to filter blood and to store red corpuscles and platelets" [] +def: "The organ that functions to filter blood and to store red corpuscles and platelets." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -29954,7 +30236,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002116 name: ileum -def: "the portion of the small intestine that extends from the jejunum to the colon" [] +def: "The portion of the small intestine that extends from the jejunum to the colon." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -29984,19 +30266,19 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002371 name: bone marrow -def: "the soft tissue that fills the cavities of bones" [] +def: "The soft tissue that fills the cavities of bones." [] is_a: UBERON:0000479 ! tissue [Term] id: UBERON:0002409 name: pericardial fluid -def: "Transudate contained in the pericardial cavity.[FMA]" [] +def: "Transudate contained in the pericardial cavity.[FMA]." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0002415 name: tail -def: "An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail" [] +def: "An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -30103,20 +30385,20 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0007650 name: esophagogastric junction -def: "The junction between the esophagus and the stomach epithelium" [] +def: "The junction between the esophagus and the stomach epithelium." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0010414 name: omental fat pad -def: "encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon" [] +def: "Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon." [] is_a: UBERON:0001013 ! adipose tissue [Term] id: UBERON:0012168 name: umbilical cord blood -def: "blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]." [] -is_a: UBERON:0000178 ! blood +def: "Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]." [] +is_a: UBERON:0013755 ! arterial blood [Term] id: UBERON:0013755 @@ -30148,6 +30430,12 @@ name: anterior nasal wall def: "Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule." [] is_a: UBERON:0000465 ! material anatomical entity +[Term] +id: UBERON:8470000 +name: placental blood +def: "Blood located in the placenta." [] +is_a: UBERON:0000178 ! blood + [Term] id: UO:0000001 name: length unit @@ -30675,6 +30963,12 @@ name: has performer domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant +[Typedef] +id: OBI:0003385 +name: has assay target context +def: "A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc." [] +range: BFO:0000040 ! material entity + [Typedef] id: OBI:1110060 name: process is result of diff --git a/views/obi_core.owl b/views/obi_core.owl index 28d116fd..e64cfed4 100644 --- a/views/obi_core.owl +++ b/views/obi_core.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -78,7 +78,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2022-01-03 + 2022-07-11 @@ -1577,6 +1577,7 @@ every c that is a concretization of g specifically denotes r material MaterialEntity + material entity material entity a flame a forest fire @@ -1595,6 +1596,7 @@ every c that is a concretization of g specifically denotes r BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) @@ -1602,6 +1604,7 @@ every c that is a concretization of g specifically denotes r (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + material entity material entity @@ -2868,6 +2871,7 @@ something taken from study subject, leaves the study and becomes the specimen. GROUP: Role Branch OBI + specimen role @@ -3799,6 +3803,7 @@ This issue is outside the scope of OBI. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch + specimen