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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T48591","span":{"begin":440,"end":452},"obj":"Body_part"},{"id":"T16532","span":{"begin":515,"end":518},"obj":"Body_part"},{"id":"T27437","span":{"begin":672,"end":675},"obj":"Body_part"},{"id":"T23683","span":{"begin":1760,"end":1765},"obj":"Body_part"},{"id":"T17125","span":{"begin":1802,"end":1806},"obj":"Body_part"}],"attributes":[{"id":"A78204","pred":"fma_id","subj":"T48591","obj":"http://purl.org/sig/ont/fma/fma82779"},{"id":"A45236","pred":"fma_id","subj":"T16532","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A10408","pred":"fma_id","subj":"T27437","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A2379","pred":"fma_id","subj":"T23683","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A86898","pred":"fma_id","subj":"T17125","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"2.1.4. 1D 31P-NMR\nWith a natural abundance of 100% and a gyromagnetic ratio of about 2.5 times smaller than 1H, one may think that phosphorus could be broadly used for NMR experiments regarding the drug discovery and development. However, the application of 31P is limited due to the fact that most of the molecules of interest simply do not contain a phosphorus atom. Therefore 31P-NMR is usually applicable for studies related to energy, phospholipid metabolism (ATP, NADP), and/or characterization of changes in DNA [94,119,120]. For example, Overall et al. conducted an experiment in which they showed that 31P solid-state NMR can be used for quantitative analysis of DNA dynamics within live bacteria [94]. For that, the researchers first prepared untreated cultures of E. coli, and measured them using a Hartmann-Hahn 1H to 31P cross-polarization (31P CP) experiment. Afterwards, they measured E. coli treated with ampicillin and maculatin 1.1 (Mac1.1) in a similar manner. Spectra obtained from treated bacteria compared to those obtained from untreated bacteria showed alterations in the lineshape, reduced signal intensity at the spectrum’s edges, and a shift in spectral density towards 0 ppm which indicated the increased dynamics of the phosphorus from nucleic acids [94].\nOver time, several innovations have been applied to expand the usage of 31P. Like in 13C and 15N labeling of specific biological compounds, incorporation of 31P can also be used. In order to achieve that, 2-chloro-4,4,5,5-tetramethyldioxaphospholane (CTMDP) can be used for tagging lipids containing hydroxyl, aldehyde, and carboxyl groups that can later be detected with better resolution [121]. Another fairly recent method enables toxicological screening of 31P in living cells for several hours without affecting cell viability [122]. This specific method can be used to observe the changes in energy metabolism in real-time while enabling the evaluation of the effects of administered drugs."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T92599","span":{"begin":23,"end":24},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T87879","span":{"begin":55,"end":56},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T52531","span":{"begin":350,"end":351},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T49797","span":{"begin":697,"end":705},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_2"},{"id":"T79755","span":{"begin":707,"end":709},"obj":"http://purl.obolibrary.org/obo/CLO_0001527"},{"id":"T36380","span":{"begin":808,"end":809},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T78941","span":{"begin":858,"end":860},"obj":"http://purl.obolibrary.org/obo/PR_000005794"},{"id":"T26738","span":{"begin":962,"end":963},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T50950","span":{"begin":1010,"end":1018},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_2"},{"id":"T83068","span":{"begin":1061,"end":1069},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_2"},{"id":"T72911","span":{"begin":1115,"end":1121},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T66455","span":{"begin":1161,"end":1162},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T71611","span":{"begin":1280,"end":1282},"obj":"http://purl.obolibrary.org/obo/CLO_0001527"},{"id":"T15967","span":{"begin":1382,"end":1390},"obj":"http://purl.obolibrary.org/obo/CLO_0007225"},{"id":"T47909","span":{"begin":1676,"end":1679},"obj":"http://purl.obolibrary.org/obo/CLO_0001053"},{"id":"T76054","span":{"begin":1760,"end":1765},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T47371","span":{"begin":1802,"end":1806},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"2.1.4. 1D 31P-NMR\nWith a natural abundance of 100% and a gyromagnetic ratio of about 2.5 times smaller than 1H, one may think that phosphorus could be broadly used for NMR experiments regarding the drug discovery and development. However, the application of 31P is limited due to the fact that most of the molecules of interest simply do not contain a phosphorus atom. Therefore 31P-NMR is usually applicable for studies related to energy, phospholipid metabolism (ATP, NADP), and/or characterization of changes in DNA [94,119,120]. For example, Overall et al. conducted an experiment in which they showed that 31P solid-state NMR can be used for quantitative analysis of DNA dynamics within live bacteria [94]. For that, the researchers first prepared untreated cultures of E. coli, and measured them using a Hartmann-Hahn 1H to 31P cross-polarization (31P CP) experiment. Afterwards, they measured E. coli treated with ampicillin and maculatin 1.1 (Mac1.1) in a similar manner. Spectra obtained from treated bacteria compared to those obtained from untreated bacteria showed alterations in the lineshape, reduced signal intensity at the spectrum’s edges, and a shift in spectral density towards 0 ppm which indicated the increased dynamics of the phosphorus from nucleic acids [94].\nOver time, several innovations have been applied to expand the usage of 31P. Like in 13C and 15N labeling of specific biological compounds, incorporation of 31P can also be used. In order to achieve that, 2-chloro-4,4,5,5-tetramethyldioxaphospholane (CTMDP) can be used for tagging lipids containing hydroxyl, aldehyde, and carboxyl groups that can later be detected with better resolution [121]. Another fairly recent method enables toxicological screening of 31P in living cells for several hours without affecting cell viability [122]. This specific method can be used to observe the changes in energy metabolism in real-time while enabling the evaluation of the effects of administered drugs."}

LitCovid-PD-CHEBI

LitCovid-PubTator

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T20318","span":{"begin":440,"end":463},"obj":"http://purl.obolibrary.org/obo/GO_0006644"},{"id":"T95169","span":{"begin":453,"end":463},"obj":"http://purl.obolibrary.org/obo/GO_0008152"},{"id":"T97670","span":{"begin":1890,"end":1900},"obj":"http://purl.obolibrary.org/obo/GO_0008152"}],"text":"2.1.4. 1D 31P-NMR\nWith a natural abundance of 100% and a gyromagnetic ratio of about 2.5 times smaller than 1H, one may think that phosphorus could be broadly used for NMR experiments regarding the drug discovery and development. However, the application of 31P is limited due to the fact that most of the molecules of interest simply do not contain a phosphorus atom. Therefore 31P-NMR is usually applicable for studies related to energy, phospholipid metabolism (ATP, NADP), and/or characterization of changes in DNA [94,119,120]. For example, Overall et al. conducted an experiment in which they showed that 31P solid-state NMR can be used for quantitative analysis of DNA dynamics within live bacteria [94]. For that, the researchers first prepared untreated cultures of E. coli, and measured them using a Hartmann-Hahn 1H to 31P cross-polarization (31P CP) experiment. Afterwards, they measured E. coli treated with ampicillin and maculatin 1.1 (Mac1.1) in a similar manner. Spectra obtained from treated bacteria compared to those obtained from untreated bacteria showed alterations in the lineshape, reduced signal intensity at the spectrum’s edges, and a shift in spectral density towards 0 ppm which indicated the increased dynamics of the phosphorus from nucleic acids [94].\nOver time, several innovations have been applied to expand the usage of 31P. Like in 13C and 15N labeling of specific biological compounds, incorporation of 31P can also be used. In order to achieve that, 2-chloro-4,4,5,5-tetramethyldioxaphospholane (CTMDP) can be used for tagging lipids containing hydroxyl, aldehyde, and carboxyl groups that can later be detected with better resolution [121]. Another fairly recent method enables toxicological screening of 31P in living cells for several hours without affecting cell viability [122]. This specific method can be used to observe the changes in energy metabolism in real-time while enabling the evaluation of the effects of administered drugs."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T133","span":{"begin":0,"end":6},"obj":"Sentence"},{"id":"T134","span":{"begin":7,"end":17},"obj":"Sentence"},{"id":"T135","span":{"begin":18,"end":229},"obj":"Sentence"},{"id":"T136","span":{"begin":230,"end":368},"obj":"Sentence"},{"id":"T137","span":{"begin":369,"end":532},"obj":"Sentence"},{"id":"T138","span":{"begin":533,"end":711},"obj":"Sentence"},{"id":"T139","span":{"begin":712,"end":873},"obj":"Sentence"},{"id":"T140","span":{"begin":874,"end":979},"obj":"Sentence"},{"id":"T141","span":{"begin":980,"end":1284},"obj":"Sentence"},{"id":"T142","span":{"begin":1285,"end":1361},"obj":"Sentence"},{"id":"T143","span":{"begin":1362,"end":1463},"obj":"Sentence"},{"id":"T144","span":{"begin":1464,"end":1681},"obj":"Sentence"},{"id":"T145","span":{"begin":1682,"end":1823},"obj":"Sentence"},{"id":"T146","span":{"begin":1824,"end":1981},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.1.4. 1D 31P-NMR\nWith a natural abundance of 100% and a gyromagnetic ratio of about 2.5 times smaller than 1H, one may think that phosphorus could be broadly used for NMR experiments regarding the drug discovery and development. However, the application of 31P is limited due to the fact that most of the molecules of interest simply do not contain a phosphorus atom. Therefore 31P-NMR is usually applicable for studies related to energy, phospholipid metabolism (ATP, NADP), and/or characterization of changes in DNA [94,119,120]. For example, Overall et al. conducted an experiment in which they showed that 31P solid-state NMR can be used for quantitative analysis of DNA dynamics within live bacteria [94]. For that, the researchers first prepared untreated cultures of E. coli, and measured them using a Hartmann-Hahn 1H to 31P cross-polarization (31P CP) experiment. Afterwards, they measured E. coli treated with ampicillin and maculatin 1.1 (Mac1.1) in a similar manner. Spectra obtained from treated bacteria compared to those obtained from untreated bacteria showed alterations in the lineshape, reduced signal intensity at the spectrum’s edges, and a shift in spectral density towards 0 ppm which indicated the increased dynamics of the phosphorus from nucleic acids [94].\nOver time, several innovations have been applied to expand the usage of 31P. Like in 13C and 15N labeling of specific biological compounds, incorporation of 31P can also be used. In order to achieve that, 2-chloro-4,4,5,5-tetramethyldioxaphospholane (CTMDP) can be used for tagging lipids containing hydroxyl, aldehyde, and carboxyl groups that can later be detected with better resolution [121]. Another fairly recent method enables toxicological screening of 31P in living cells for several hours without affecting cell viability [122]. This specific method can be used to observe the changes in energy metabolism in real-time while enabling the evaluation of the effects of administered drugs."}