Guillaume Poirier-Morency Mahan Rafieenaini Paul Pavlidis Nathaniel Lim en Creative Commons Attribution Non Commercial 4.0 International Copyright 2015-2023 University of British Columbia definition has_exact_synonym has_obo_format_version has_obo_namespace has_related_synonym A relationship that holds between an organism and a disease. Used here between a fusion gene and the disease it is associated with, following the existing Gemma usage of this relation for gene-to-disease (SNCA implies Parkinson). Declared rather than imported, as RO is not loaded. The label is RO's own and must stay exact. has disease A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. Declared here rather than imported: TGEMO does not import RO, and Gemma loads it with processImports off, so a referenced-but-undeclared property has nothing to carry its label. The label is RO's own and must stay exact -- Gemma validates a supplied predicate label against this string. has role in modeling Used to indicate that the bearer was a substance provided to a subject (whether it be human, animal or cells in vitro) at the specified dose has dose delivered at dose Expresses that the bearer (a treatment or other manipulation) was applied for the stated amount of time. has duration delivered for duration Indicates that the bearer (e.g. an organism or part) was at the given stage of development has developmental stage Used to indicate that the subject (generally a cell type) expressed the product of the object (a gene). Example: CD133+ cancer cell. positive for product of gene Used to indicate that the subject (generally a cell type) does not express the product of the object (a gene). Example: CD133- cancer cell. negative for product of gene Indicates that the Subject (typically a disease or condition) was caused to occur or be present by the specified means. Examples: spinal cord injury induced by partial transection; Myocardial infarction induced by ligation of the proximal left coronary artery. "Causal relationship with disease as subject" looks at first glance to be this kind of thing, but the TGEMO term is used to indicate induction in a particular experiment, not a general statement about diseases. induced by Indicates that a genetic alteration of the Subject gene was confined to the cell type or tissue named by the Object, rather than made throughout the organism. Used for conditional / Cre-lox knockouts, cell-type-specific knockdowns and tissue-specific overexpression. The Object is a Cell Ontology (CL) cell type or an UBERON tissue. 🛑 Used on statements whose CATEGORY is genotype, and the category is what scopes the claim: under `genotype`, `Sipr1 targeted to astrocyte (CL:0000127)` asserts that the engineered alteration of Sipr1 was confined to astrocytes, NOT that the Sipr1 gene product localises there. What is targeted is the GENOTYPE, not the gene, and the category is what says so. Example: a study of an astrocyte-specific S1P1 knockout asserts, of the subject Sipr1 under the genotype category, both `has_genotype` Homozygous negative and `targeted to` astrocyte. The target of the perturbation is INDEPENDENT of the cell type the experiment profiled; the two are frequently the same and must still be stated separately, because a perturbation restricted to one population is routinely assayed in another. Minted in TGEMO because no existing relation carries this meaning: RO:0002503 ("towards") relates a relational quality to what it is a quality toward, and RO:0001025 ("located in") would assert the gene's own anatomical location rather than where the alteration acts. TGEMO:00183 ("delivered to") is the nearest sibling and deliberately not reused: it presupposes an administration event at a site, which a germline conditional allele does not have. 🛑 Gemma's statements are FLAT: every predicate/object pair hangs off the subject and one pair cannot qualify another. So the perturbation state (`has_genotype` -> the alteration) and this target are two INDEPENDENT assertions about the same subject; stating the perturbation alongside is expected and good practice, but it is not what makes this statement mean what it means — the category is. A nested statement shape could bind the target to the alteration itself; a flat one cannot. This is a known limitation of expressivity, the same one that prevents a dose being attached to the inducer of a disease rather than to the disease it induced. Labelled "targeted towards" when minted; renamed because RO:0002503's own label is "towards", so the two sat adjacent in the curation picker with one a suffix of the other. The former label is kept as an exact synonym so statements already written against it still resolve. restricted to cell type targeted towards engineered in perturbed in targeted to Indicates that the Subject — a cell line, an animal strain, or an engineered genotype — was derived on, or is maintained on, the genetic background named by the Object. The Object is a strain or cell line term, e.g. C57BL/6. Used to state the background separately from the thing that carries it, so that a background the submitter wrote as a constant characteristic is not recorded as the experimental strain or line itself. Example: a knockout line on an inbred background asserts, of the subject line, `has background` C57BL/6. Minted rather than adopting BCGO:0000015 (has_genetic_background_of), which asserts the SAME direction — the Object is the background of the Subject — but is defined over strains only ("strain a is derived from strain b"), and Gemma applies this to cell lines as well. BCGO:0000015 is recorded as an xref and its label as a related synonym, so a statement written against either resolves here. 🛑 Two pairs is the ceiling: a Gemma statement holds predicate/object and secondPredicate/secondObject, so a genotype subject already carrying `has_genotype` is full once this is added and a third assertion needs its own statement. The related synonym "strain background" was REMOVED when TGEMO_00217 was minted with that label: a relation-shaped string belongs on a property and a noun-shaped one on a class, and one string on both puts them side by side in the curation picker with nothing to tell them apart. This property is for a SUBJECT that has a background; the class is for a characteristic whose category is the background and whose value is the strain. Gemma's plain characteristics carry no subject, so the two are not interchangeable. has genetic background of has background Used to specify that a treatment or procedure was performed at a specific location or organism part delivered to has child with disease used in the context of experimental conditions (e.g. a treatment) where the sample taken for transcriptomic analysis followed a period of time after the condition was applied/occurred sampled after Root node for Temporary Gemma Ontology. TGEMO:00000 TGEMO Root Double negative allele. Refers both to genetic null (missing gene/knock out) and phenotypic/functional null (inactive gene product). May be overloaded for severe loss-of-function alleles also. Nullizygous Homozygous negative Parent node for all TGEMO genetic and mutation descriptors. TGEMO Genetics/Mutations true Overexpression of a gene. Includes non-canonical promoter driven expression. Overexpression Overexpression of a gene. Organism is known to have only one copy of the gene. Single-copy overexpression Overexpression of a gene. Organism is known to have only two copies of the gene. Double-copy overexpression A variant rendering the activity of the gene product (i.e. adoption of an active protein confirmation) independent of the need for activation such as ligand binding TGEMO_00008 Constitutive active mutation Parent node for all TGEMO method descriptors. TGEMO:00010 TGEMO Methods Parent node for all TGEMO internal descriptors. Used primarily for behind-the-scenes standardization. TGEMO:00011 Gemma Internals The removal of certain proteins by the use of antibodies https://en.wiktionary.org/wiki/immunodepletion Immunodepletion Samples to include in Differential Expression Analysis. DE_Include Samples to exclude in Differential Expression Analysis. DE_Exclude Indicator for studies containing a collection of samples rather than a designed experiment with known covariates or pre-defined experimental groups. Sample Study Indicator for studies that have a complex experimental design, and are currently incompletely curated. Complex Design true Indicator (Temporary Placeholder) for experiments that are a collection of studies, and will be separated internally. Use the factor-level subsetRelevance field; what was actually subset is recorded on the differential expression analysis. SUBSET true Indicator for studies that contain a technical comparison, e.g. of methodological approaches to sample preparation, rather than (or in addition to) biological ones. Technique comparison study Indicator for sample studies containing a collection of various cell lines. Cell Line Sample Study Cross between C57BL/6 and 129S. Generation Unknown. B6129SF? Cross between C57BL/6J and 129S. Generation Unknown. B6J129SF? Parent node for all TGEMO terms that are currently not assigned a parent class. TGEMO:00057 TGEMO Unclassified Tissue that is spatially located adjacent to the tissue of interest. Adjacent tissue are assumed to be normal, but that is not necessarily always the case. Use "adjacent" relation Adjacent tissue true Indicator (Temporary Placeholder) for experiments that are identified to be time consuming for curation, and will be revisited at a later time. TGEMO:00088 Time Consuming true A biological system intended as a model of a human disease. Disease model An experimental procedure using direct introduction of a protein to test rescue of a phenotype rather than genetic manipulation (e.g. a transgene). Rescue by external protein true Used to signify that a particular factor has no specified value for a particular sample. Intended as a less ambiguous alternative to "NA", "null" or "none" Unspecified factor value Fusion of the human BCR and ABL1 genes Philadelphia chromosome BCR-ABL1 BCR-ABL An engineered fusion of green fluorescent protein with another gene Intention is that this would be related to a gene term via a predicate such as 'modified by' GFP-tagged GFP fusion Fusion of the human ETV6 and RUNX1 genes, associated with childhood acute lymphoblastic leukemia E/R ETV6/RUNX1 ETV6-RUNX1 A conditionally active form of murine GATA-1 made by fusing its coding region to the ligand-binding domain of the human estrogen receptor (ER) https://doi.org/10.1016/S0092-8674(00)80318-9 GATA1-ESR1 GATA1/ER GATA1-ER Fusion of the human MLL and AF9 genes, associated with acute myeloid leukemia (AML) MLL-AF9 Fusion of the human NUP98 and HOXA9 genes, associated with acute myeloid leukemia (AML) doi: 10.1093/emboj/20.3.350 NUP98-HOXA9 Fusion of the human PML and RARA genes, associated with acute myeloid leukemia (AML) doi: 10.3390/cancers12030624 PML-RARA Fusion of the human AML1 and ETO genes, associated with acute myeloid leukemia (AML) DOI: 10.1182/blood-2005-04-1656 RUNX1- RUNX1T1 AML1-ETO An engineered fusion of red fluorescent protein with another gene RFP fusion An engineered fusion of the human interleukin (IL)-4 and IL-10 genes developed as an experimentallly to inhibit pro‐inflammatory activity in arthritis models DOI: 10.1073/pnas.2009647118 doi: 10.1111/cei.13224 IL4-10 FP fusion of the human E2A and PBX1 genes, associated with prognostically favorable precursor B-subtypes of childhood acute lymphoblastic leukemia doi: 10.1016/S1470-2045(08)70339-5 E2A-PBX1 fusion of the human TEL and AML1 genes, associated with prognostically favorable precursor B-subtypes of childhood acute lymphoblastic leukemia doi: 10.1016/S1470-2045(08)70339-5 TEL-AML1 Fusion of the human TMPRSS2 and ERG genes, identified in some prostate cancers doi: 10.1126/science.1117679 TMPRSS2-ERG Alzheimer disease model. Overexpresses both mutant human amyloid beta (A4) precursor protein 695 (APP)) with the Swedish (K670N, M671L), Florida (I716V), and London (V717I) Familial Alzheimer's Disease (FAD) mutations and human PS1 harboring two FAD mutations, M146L and L286V. https://www.jax.org/strain/008730 https://www.informatics.jax.org/allele/MGI:3693208 5XFAD 5XFAD APP/PS1 5XFAD line Tg6799 Tg(APP*Swe*Fl*Lon,PSEN1*M146L*L286V)6799Vas Tg-5xFAD Tg6799 5xFAD Alzheimer disease model. Triple transgenic homozygous with genotype APP Swedish, MAPT P301L, and PSEN1 M146V. https://www.jax.org/strain/004807 https://www.alzforum.org/research-models/3xtg https://www.informatics.jax.org/strain/MGI:2673730 https://www.jax.org/strain/004807 https://www.informatics.jax.org/allele/MGI:2672831 https://www.informatics.jax.org/allele/MGI:1930937 B6.Cg-Psen1tm1Mpm Tg(APPSwe,tauP301L)1Lfa/J B6;129-Psen1tm1Mpm Tg(APPSwe,tauP301L)1Lfa/J B6;129-Psen1tm1Mpm Tg(APPSwe,tauP301L)1Lfa/Mmjax C57BL/6-Psen1tm1Mpm Tg(APPSwe, tauP301L)1Lfa/J C57BL/6-Psen1tm1Mpm Tg(APPSwe,tauP301L)1Lfa/J The LaFerla mouse 3xTg-AD Alzheimer disease model. Double transgenic mice expressing a chimeric mouse/human amyloid precursor protein (Mo/HuAPP695swe) and a mutant human presenilin 1 (PS1-dE9), both directed to CNS neurons. https://www.jax.org/strain/005864 https://www.informatics.jax.org/strain/MGI:3611279 https://www.jax.org/strain/005864 https://www.informatics.jax.org/allele/MGI:3524957 B6.Cg-Tg(APPswe,PSEN1dE9)85Dbo/J B6.Cg-Tg(APPswe,PSEN1dE9)85Dbo/Mmjax APP/PS1 Type 1 diabetes disease model. Expresses a chicken calmodulin minigene (CALM1) controlled by the rat insulin II promoter (Ins2)(Referred to as BIC). In addition, these mice express a truncated SV40 T antigen (TAg) controlled by a lens specific alpha A crystallin (Cryaa) promoter (referred to as GR19). https://www.jax.org/strain/005564 https://www.informatics.jax.org/allele/MGI:3576672 https://www.jax.org/strain/005564 FVB(Cg)-Tg(Cryaa-Tag,Ins2-CALM1)26Ove/PneJ OVE26 Alzheimer disease model. P301S Tg mice express the P301S mutant form of human microtubule-associated protein tau (MAPT), under the direction of the mouse prion protein promoter (Prnp). https://www.jax.org/strain/008169 https://www.alzforum.org/research-models/tau-p301s-line-ps19 https://www.informatics.jax.org/strain/MGI:5553124 https://www.jax.org/strain/008169 https://www.informatics.jax.org/allele/MGI:3768407 B6N.Cg-Tg(Prnp-MAPT*P301S)PS19Vle/J Tau P301S PS19 Huntington's Disease model. Are transgenic for the 5' end of the human HD gene carrying (CAG)115-(CAG)150 repeat expansions. https://www.jax.org/strain/006471 https://www.informatics.jax.org/strain/MGI:3692955 https://www.jax.org/strain/006471 https://www.informatics.jax.org/allele/MGI:2389466 B6-R6/1 B6.Cg-Tg(HDexon1)61Gpb/J HD R6/1 R6/1 Huntington's Disease model. Transgenic for the 5' end of the human HD gene carrying approximately 120 +/- 5 CAG repeat expansions. The transgene is ubiquitously expressed. https://www.jax.org/strain/006494 https://qpsneuro.com/in-vivo-services/animal-models/huntingtons-disease-mouse-models/r6-2-transgenic-mouse-model/ https://www.informatics.jax.org/strain/MGI:3688746 https://www.jax.org/strain/006494 https://www.informatics.jax.org/allele/MGI:2386951 B6CBA-R6/2 (CAG 120 +/- 5) B6CBA-Tg(HDexon1)62Gpb/3J R6/2 Down Syndrome disease model. Ts65Dn mice have three copies of most of the genes on mouse Chr 16 that are homologues of human Chr 21 genes. These extra genes, along with the centromere and about 5% of proximal Chr 17 are contained in a small extra chromosome derived from a reciprocal translocation. https://www.jax.org/strain/001924 https://www.informatics.jax.org/strain/MGI:2163627 https://www.jax.org/strain/001924 https://www.informatics.jax.org/allele/MGI:3512067 B6EiC3Sn a/A-Ts(1716)65Dn B6EiC3Sn a/A-Ts(1716)65Dn/J Ts65Dn Duchenne muscular dystrophy disease model. Point mutation in Dmd gene results in a termination codon (TAA) in place of a glutamine codon.This allele is predicted to produce a truncated protein. https://www.jax.org/strain/001801 https://www.informatics.jax.org/strain/MGI:2162540 https://www.jax.org/strain/001801 https://www.informatics.jax.org/allele/MGI:1856328 C57BL/10ScSn-Dmdmdx/J mdx Down syndrome disease model. Trisomic for the mouse chromosome segment orthologus to the human chromosome 21 Down syndrome critical region (DSCR). The borders of the 3.9 Mb region are defined by the carbonyl reductase 1 gene and a site adjacent to the myxovirus (influenza virus) resistance 2 locus. https://www.jax.org/strain/005383 https://www.informatics.jax.org/strain/MGI:3574387 https://www.jax.org/strain/005383 https://www.informatics.jax.org/allele/MGI:3487283 B6.129S6-Dp(16Cbr1-Fam3b)1Rhr/J B6.129S6-Dp(16Cbr1-ORF9)1Rhr/J B6.129S6-Is(16Cbr1-ORF9)1Rhr B6.129S6-Is(16Cbr1-ORF9)1Rhr/J Ts1Rhr Down syndrome disease model. Mice have partial trisomy of chromosome 16. https://www.jax.org/strain/004861 https://www.informatics.jax.org/strain/MGI:2680524 https://www.jax.org/strain/004861 https://www.informatics.jax.org/allele/MGI:3623022 B6Ei;C3Sn-Ts(1216C-tel)1Cje B6EiC3Sn-Ts(1216C-tel)1Cje B6EiC3Sn-Ts(16C-tel)1Cje B6EiC3Sn-Ts(16C-tel)1Cje/DnJ Ts1Cje There are two mouse models referred to by the name “PS2APP” to in the literature. This entry refers to the model that was generated by co-injecting two constructs into C57/BL/6 zygotes, and is also known by the name B6.152H. The other PS2APP line was generated by crossing two single transgenic animals (PS2(N141I) x APPswe) (Richards et al., 2003). Both lines of double transgenic animals express the same transgenes and both develop a similar level of cerebral pathology (Weidensteiner et al., 2009), but only the B6.152H mice show enhanced LTP. The reasons for this are not entirely clear, but differing levels of transgene expression may be partly responsible. B6.152H mice have higher expression of transgenic human APP mRNA (1.45-fold) compared to PS2APP mice and approximately 30-fold higher levels of PSEN2 mRNA. They also have about 2-fold higher Aβ levels than PS2APP mice (Poirier et al., 2010). The B6.152H line is maintained as a homozygote line. It is on a pure C57BL/6 background and shows less variability in pathology expression. It has been used to generate the TauPS2APP triple transgenic line by crossing with the Tau-overexpressing pR5 line (Grueninger et al., 2010). https://www.alzforum.org/research-models/ps2app https://www.informatics.jax.org/allele/MGI:4412048 B6.152H B6.PS2APP TG B6.PS2APP mice (line B6.152H) PS2APP Fusion of the human TCF3 and PBX1 genes. Associated with B-cell childhood lymphoblastic lymphoma. DOI: 10.1182/blood-2009-12-253419 TCF3-PBX1 Fusion of the human MYB and GATA1 genes. Associated with acute basophilic leukaemia. DOI: 10.1002/path.4908 MYB-GATA1 Fusion of the human ZBTB16 and RARA genes. Associated with acute promyelocytic leukemia. DOI: 10.1038/nm.3441 ZBTB16-RARA Fusion of the human IRF4 and SPIB genes. Associated with the activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL). DOI: 10.1016/j.ccr.2012.05.024 IRF4-SPIB DOI: 10.4161/15592294.2014.988048 Fusion of the human EWS and FLI1 genes. Associated with Ewing sarcoma. EWS-FLI1 Fusion of the human RUNX1 and ETO genes. Associated with acute myeloid leukemia. DOI: 10.1038/leu.2012.49 RUNX1-ETO Fusion of the human YAP1 and MAMLD1 genes. Associated with supratentorial ependymoma. DOI: 10.1038/s41556-022-01069-6 MAMLD1-YAP1 YAP1-MAMLD1 Fusion of the human BIRC3 and MALT1 genes. Associated with B-cell non Hodgkin lymphoma and MALT lymphoma. BIRC3-MALT1 APP23 transgenic mice have the 6.7 kbp murine Thy1 cassette driving expression of human APP isoform 751, containing the Swedish double mutation (APP751*K670N/M671L) associated with Alzheimer's disease. https://www.jax.org/strain/030504 https://www.informatics.jax.org/allele/MGI:2447146 APP K670N/M671L APP23 Fusion of the human SH3PXD2A and HTRA1 genes. The gene product of the SH3PXD2A-HTRA1 fusion has been shown to promote proliferation, invasion and resistance to cell death in vitro and tumor growth in vivo. DOI: 10.1007/s11060-021-03796-6 SH3PXD2A-HTRA1 Fusion of the ETV6 and NTRK3 genes. ETV6-NTRK3 (EN) is reported in seven different cancers. DOI: 10.3390/cancers15174246 ETV6-NTRK3 Fusion of the human EWSR1 and FLI1 genes. Associated with Ewing Sarcoma. DOI: 10.3390/cancers13153783 EWSR1-FLI1 Fusion of the human CALM and AF10 genes. Associated with acute leukemia. DOI: 10.1038/sj.leu.2405074 CALM-AF10 Fusion of the human AF4 and MLL genes. Associated with infant pro-B acute lymphoblastic leukemia. DOI: 10.18632/oncotarget.19567 MLL-AF4 AF4-MLL Fusion of the human MOZ and TIF2 genes. Associated with acute myeloid leukemia. DOI: 10.1016/s1535-6108(03)00051-5 MOZ-TIF2 Fusion of the human CBFB and MYH11 genes. Associated with acute myeloid leukemia subtype M4Eo, which is characterized by the presence of myelomonocytic blasts and atypical eosinophils. DOI: 10.1097/00062752-200107000-00004 CBFB-MYH11 A substrain of C57BL/6 mice with unknown supplier. https://www.informatics.jax.org/strain/MGI:2159965 C57BL/6N A three dimensional mass comprised of a cultured cell or tissue sample that resembles an in vivo tissue or organ. Organoids are grown in vitro from a combination of cells or tissue fragments cultured in medium containing a variety of biochemical factors. http://purl.obolibrary.org/obo/NCIT_C172259 3D organoid organoid Down's syndrome model. Cre mediated chromosomal rearrangement between loxP sites in regions proximal to Prmt2 and distal to Pdxk results in duplication of the genes, including Prmt2 and Pdxk, in this approximately 2.3 Mb region that is syntenic with the distal part of human 21q22.3. https://www.informatics.jax.org/marker/MGI:4461397 https://www.informatics.jax.org/allele/MGI:4461400 Dp(10)1Yey Dp(10Prmt2-Pdxk)1Yey Dp(10Prmt2-Pdxk)2Yey Ts2Yey Dp(10)2Yey Retinitis pigmentosa model. Retinal degeneration 10 (rd10) is a spontaneous missense point mutation in Pde6b (cGMP phosphodiesterase 6B, rod receptor, beta polypeptide). Although similar to rd1, the rd10 phenotype has a later onset and milder retinal degeneration and may provide a better experimental drug therapy model for retinitis pigmentosa. https://www.informatics.jax.org/strain/MGI:2173852 https://www.informatics.jax.org/allele/MGI:2388259 B6.CXB1-Pde6brd10/J Pde6brd1-J rd10 An experiment where an identified transcription regulator has been perturbed. TF Pert Transcription Factor Perturbation Experiment Transcriptional Regulator Perturbation Experiment The zQ175 neo-deleted knock-in allele (zQ175DN KI) has the mouse Htt exon 1 replaced by the human HTT exon 1 sequence with a ~190 CAG repeat tract. These B6J.zQ175DN KI mice (Stock No. 029928) are useful for studying Huntington's disease pathogenesis and for the assessment of potential therapeutic interventions. This zQ175DN KI allele is the same design as the zQ175 KI allele (Stock No. 027410), with the exception that this zQ175DN KI has had the floxed neo cassette removed. It is not specifically characterized if deletion of the neo cassette alters the zQ175DN KI phenotype compared to the zQ175 KI phenotype. https://www.jax.org/strain/029928# https://www.informatics.jax.org/allele/MGI:5789600 B6.129S1-Htttm1.1Mfc/190ChdiJ B6J.zQ175DN KI zQ175 neo-deleted knock-in zQ175DN KI A behavioural or psychological stressor applied to an experimental subject. Combines with severity modifiers (mild / moderate / severe), temporal-pattern modifiers (acute / chronic), and `delivered for duration` for the experimental time course. Parent EFO:0000470 is provisional; the concept is a stressor / protocol rather than a treatment effect and may move to a more appropriate parent in a future revision. behavioral stress psychological stress stress stressor stressful experience behavioural stress A material entity which results from the transplantation of living cells, tissues or organs between genetically non-identical individuals of the same species. Sibling of OBI:0100058 (xenograft), which is the equivalent material entity for transplantation between different species; use this term when donor and recipient are the same species. The donor is frequently not recorded as a sample attribute in clinical transplant cohorts, so the allogeneic relationship cannot be derived from the annotation and is stated here directly. Minted in TGEMO because no standalone allograft class exists in the ontologies Gemma loads (2026-08-08: OBI carries `xenograft` OBI:0100058 and EFO uses "allograft" only inside compound labels such as EFO:0008497 chronic lung allograft dysfunction), while NCIT, SNOMED and MeSH all define it. http://purl.obolibrary.org/obo/NCIT_C60701 allogeneic graft allogeneic transplant homograft allograft A material entity which results from the transplantation of living cells, tissues or organs between individuals of the same species with an identical, or immunologically compatible, genetic profile — for example between animals of the same inbred strain. Narrower than TGEMO:00211 (allograft), where donor and recipient are genetically non-identical. Sibling of OBI:0100058 (xenograft). Minted in TGEMO because no such class exists in the ontologies Gemma loads. http://purl.obolibrary.org/obo/NCIT_C122939 isograft syngeneic transplant syngraft syngeneic graft A material entity which results from the transplantation of living cells, tissues or organs from one location to another within the same individual, so that donor and recipient are the same organism. Sibling of OBI:0100058 (xenograft). Minted in TGEMO because no such class exists in the ontologies Gemma loads. http://purl.obolibrary.org/obo/NCIT_C75339 autologous graft autotransplant autograft strain cell line The strain on which an experimental line, genotype or animal was derived or is maintained, recorded as a characteristic in its own right. The VALUE is a strain, e.g. C57BL/6. Used as a CATEGORY, where the submitter stated the background separately from the experimental strain or line that carries it. A nuance of strain, and used the way `strain` itself is used: as a category whose value is a strain term. Parented at EFO_0005135 rather than beside the strain values, because EFO_0005135 has no children and the particular strains do not hang off it (C57BL/6 EFO_0022397 sits under C57BL EFO_0005181, BALB/c EFO_0000602 under NCBITaxon_10090). The same shape EFO already uses for `population` OBI_0000181 -> `strain`, both of which Gemma lists as categories. 🛑 NOT expressible with TGEMO_00216 (`has background`): that is a relation and needs a SUBJECT, and a plain Gemma characteristic has only a category and a value. Minted 2026-09-15 against 24,179 corpus rows whose category is a spelling of this and whose CATEGORY_URI is NULL. Cell lines are the sibling TGEMO_00218, not this class, because the parents differ. background strain genetic background strain/background background/strain background mouse strain mouse background host strain background background strain background The cell line from which an experimental line was derived, recorded as a characteristic in its own right. The VALUE is a cell line, e.g. HEK-293. Used as a CATEGORY, where the submitter stated the parental line separately from the line the experiment used. Sibling of TGEMO_00217 (`strain background`), split from it rather than folded in because the two parent at different categories: this one at CLO_0000031 (`cell line`), that one at EFO_0005135 (`strain`). One class could not sit under both without asserting that a cell line is a strain. Minted 2026-09-15 against 759 corpus rows. 🛑 `background cell type` is NOT a synonym: its values are cell types, not lines, and it would pull them under a cell-line category. background cell line cell background cell line background Strain family. MGI:2159768. RESTORED 2026-09-16. Removed in 0702ecf as a strain "recently added to EFO 3.60.0", but EFO added the SUBSTRAIN DBA/2J (EFO_0005184), not this family, and no ontology OLS indexes carries DBA/2 at all. So the retirement swapped a family for one of its substrains and left the family with no term: the corpus holds 80 rows valued plain `DBA/2`, plus DBA/2NTac, DBA/2Crl and DBA2/J variants that EFO_0005184 would misground. MGI:2159768 resolves and is titled "DBA/2 Strain Detail", so the original xref was correct. 🛑 Re-parented to NCBITaxon_10090 because its former parent TGEMO_00019 ("DBA", the strain group) went in the same commit; that is also how the surviving strain terms here are parented, e.g. TGEMO_00172. 🛑 NOT the term for `C57BL/6 x DBA/2`: that is a B6D2 F1 hybrid, not this family, and the three corpus rows bound to this URI under that label were mis-bound before the removal. No ontology has a term for the hybrid. https://www.informatics.jax.org/strain/MGI:2159768 D2 DBA/2 An RNA assay based on identification of molecules associated with ribosomes. Encompasses all methods whether sequencing-based or array-based, including as ribo-seq, TRAP-seq, polysome-purification. Ribosome-associated RNA profiling RNA that is associated with polysomes. Can be used to annotate samples that emerged from polysome purification, but the method of purification itself is another concept. polysome-associated RNA A relation linking a parent and their child possessing a specified disease. A exposure event involving the interaction of an exposure receptor to radiation. exposure to radiation A exposure event involving the interaction of an exposure receptor to electromagnetic radiation. exposure to electromagnetic radiation A exposure event involving the interaction of an exposure receptor to ultraviolet radiation. exposure to ultraviolet radiation A exposure event involving the interaction of an exposure receptor to ionizing radiation. exposure to ionizing radiation A exposure event involving the interaction of an exposure receptor to gamma-ray radiation. exposure to gamma radiation A exposure event involving the interaction of an exposure receptor to X-ray radiation. exposure to x-ray radiation A exposure event involving the interaction of an exposure receptor to infrared radiation. exposure to infrared radiation A exposure event involving the interaction of an exposure receptor to microwave radiation. exposure to microwave radiation A exposure event involving the interaction of an exposure receptor to particle radiation. exposure to particle radiation A exposure event involving the interaction of an exposure receptor to acoustic radiation. exposure to sound radiation A exposure event involving the interaction of an exposure receptor to ultrasound radiation. exposure to ultrasound radiation An exposure to radiation therapy. exposure to radiation therapy A exposure event involving the interaction of an exposure receptor to decreased temperature. exposure to decreased temperature A exposure event involving the interaction of an exposure receptor to increased temperature. exposure to increased temperature Includes individuals who either self-report or have been described by authors as European, Caucasian, White or one of the sub-populations from this region (e.g Dutch). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CEU, FIN, GBR, IBS and TSI populations. European ancestry Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian. Asian ancestry Includes individuals that either self-report or have been described as African, but there was not sufficient information to allow classification as African American, AfroCaribbean or Sub-Saharan African. African ancestry Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations Latin or Admixed American ancestry Japanese Chinese Individuals who self-identify or are reported by authors as belonging to the Han people, an East Asian ethnic group native to Greater China. Han Chinese Ancestry which is an admixture of more than one defined ancestral population. The degree and type of admixture may vary within a population and the accuracy of classification requires well-defined reference samples admixed ancestry British Indian Individuals who self-identify or are reported by authors as African American. Term used by some communities to describe themselves and some US government and other institutions on official forms used to collect demographic information. African American