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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1816-1832 Body_part denotes neurotransmitter http://purl.org/sig/ont/fma/fma302832
T2 1848-1852 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T3 2114-2131 Body_part denotes neurotransmitters http://purl.org/sig/ont/fma/fma302832
T4 2193-2201 Body_part denotes dopamine http://purl.org/sig/ont/fma/fma67238
T5 2203-2212 Body_part denotes serotonin http://purl.org/sig/ont/fma/fma67245
T6 2242-2255 Body_part denotes acetylcholine http://purl.org/sig/ont/fma/fma61789
T7 2382-2387 Body_part denotes brain http://purl.org/sig/ont/fma/fma50801
T8 2452-2466 Body_part denotes frontal cortex http://purl.org/sig/ont/fma/fma61824
T9 2472-2480 Body_part denotes striatum http://purl.org/sig/ont/fma/fma77618
T10 2508-2516 Body_part denotes dopamine http://purl.org/sig/ont/fma/fma67238
T11 2521-2535 Body_part denotes norepinephrine http://purl.org/sig/ont/fma/fma61799
T12 2741-2749 Body_part denotes dopamine http://purl.org/sig/ont/fma/fma67238
T13 2886-2889 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T14 2917-2925 Body_part denotes dopamine http://purl.org/sig/ont/fma/fma67238
T15 3019-3027 Body_part denotes dopamine http://purl.org/sig/ont/fma/fma67238
T16 3042-3050 Body_part denotes dopamine http://purl.org/sig/ont/fma/fma67238
T17 3068-3076 Body_part denotes striatum http://purl.org/sig/ont/fma/fma77618
T18 3156-3164 Body_part denotes dopamine http://purl.org/sig/ont/fma/fma67238
T917 125-128 Body_part denotes CNS http://purl.org/sig/ont/fma/fma55675
T918 541-550 Body_part denotes pituitary http://purl.org/sig/ont/fma/fma13889
T919 565-569 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T920 609-617 Body_part denotes dopamine http://purl.org/sig/ont/fma/fma67238
T921 728-732 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T922 734-764 Body_part denotes corticotropin releasing factor http://purl.org/sig/ont/fma/fma83354
T923 1472-1476 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T924 1517-1520 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T925 1560-1564 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T926 1573-1576 Body_part denotes CNS http://purl.org/sig/ont/fma/fma55675
T927 1590-1598 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T178 125-128 Body_part denotes CNS http://purl.obolibrary.org/obo/UBERON_0001017
T179 1573-1576 Body_part denotes CNS http://purl.obolibrary.org/obo/UBERON_0001017
T180 1883-1886 Body_part denotes NAc http://purl.obolibrary.org/obo/UBERON_0001882
T181 1887-1892 Body_part denotes shell http://purl.obolibrary.org/obo/UBERON_0006612
T182 2382-2387 Body_part denotes brain http://purl.obolibrary.org/obo/UBERON_0000955
T183 2447-2450 Body_part denotes NAc http://purl.obolibrary.org/obo/UBERON_0001882
T184 2452-2466 Body_part denotes frontal cortex http://purl.obolibrary.org/obo/UBERON_0001870
T185 2460-2466 Body_part denotes cortex http://purl.obolibrary.org/obo/UBERON_0001851
T186 2472-2480 Body_part denotes striatum http://purl.obolibrary.org/obo/UBERON_0002435
T187 2690-2693 Body_part denotes NAc http://purl.obolibrary.org/obo/UBERON_0001882
T188 3068-3076 Body_part denotes striatum http://purl.obolibrary.org/obo/UBERON_0002435

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T205 541-550 Disease denotes pituitary http://purl.obolibrary.org/obo/MONDO_0021156
T206 1301-1319 Disease denotes immune suppression http://purl.obolibrary.org/obo/MONDO_0007816
T207 1517-1530 Disease denotes HIV infection http://purl.obolibrary.org/obo/MONDO_0005109
T208 1521-1530 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T209 3189-3201 Disease denotes opioid abuse http://purl.obolibrary.org/obo/MONDO_0001225

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 1848-1852 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T2 2136-2142 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T3 2193-2201 http://purl.obolibrary.org/obo/CHEBI_18243 denotes dopamine
T4 2203-2212 http://purl.obolibrary.org/obo/CHEBI_28790 denotes serotonin
T5 2382-2387 http://purl.obolibrary.org/obo/UBERON_0000955 denotes brain
T6 2382-2387 http://www.ebi.ac.uk/efo/EFO_0000302 denotes brain
T7 2460-2466 http://purl.obolibrary.org/obo/UBERON_0001851 denotes cortex
T8 2508-2516 http://purl.obolibrary.org/obo/CHEBI_18243 denotes dopamine
T9 2674-2682 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T10 2710-2711 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 2741-2749 http://purl.obolibrary.org/obo/CHEBI_18243 denotes dopamine
T12 2917-2925 http://purl.obolibrary.org/obo/CHEBI_18243 denotes dopamine
T13 3019-3027 http://purl.obolibrary.org/obo/CHEBI_18243 denotes dopamine
T14 3042-3050 http://purl.obolibrary.org/obo/CHEBI_18243 denotes dopamine
T15 3156-3164 http://purl.obolibrary.org/obo/CHEBI_18243 denotes dopamine
T972 125-128 http://www.ebi.ac.uk/efo/EFO_0000302 denotes CNS
T973 125-128 http://www.ebi.ac.uk/efo/EFO_0000908 denotes CNS
T974 125-128 http://purl.obolibrary.org/obo/UBERON_0001017 denotes CNS
T975 184-185 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T976 609-617 http://purl.obolibrary.org/obo/CHEBI_18243 denotes dopamine
T977 710-719 http://purl.obolibrary.org/obo/CLO_0001658 denotes activates
T978 800-801 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T979 1071-1081 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T980 1244-1254 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T981 1573-1576 http://www.ebi.ac.uk/efo/EFO_0000302 denotes CNS
T982 1573-1576 http://www.ebi.ac.uk/efo/EFO_0000908 denotes CNS
T983 1573-1576 http://purl.obolibrary.org/obo/UBERON_0001017 denotes CNS

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T389 207-211 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T93960 242-246 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T19189 453-457 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T97969 560-563 Chemical denotes HPA http://purl.obolibrary.org/obo/CHEBI_29031|http://purl.obolibrary.org/obo/CHEBI_53393|http://purl.obolibrary.org/obo/CHEBI_61431|http://purl.obolibrary.org/obo/CHEBI_64342
T44514 609-617 Chemical denotes dopamine http://purl.obolibrary.org/obo/CHEBI_18243|http://purl.obolibrary.org/obo/CHEBI_59905
T14707 724-727 Chemical denotes HPA http://purl.obolibrary.org/obo/CHEBI_29031|http://purl.obolibrary.org/obo/CHEBI_53393|http://purl.obolibrary.org/obo/CHEBI_61431|http://purl.obolibrary.org/obo/CHEBI_64342
T29525 734-764 Chemical denotes corticotropin releasing factor http://purl.obolibrary.org/obo/CHEBI_65311
T403 734-747 Chemical denotes corticotropin http://purl.obolibrary.org/obo/CHEBI_3892
T13587 959-967 Chemical denotes cortisol http://purl.obolibrary.org/obo/CHEBI_17650
T405 1067-1070 Chemical denotes HPA http://purl.obolibrary.org/obo/CHEBI_29031|http://purl.obolibrary.org/obo/CHEBI_53393|http://purl.obolibrary.org/obo/CHEBI_61431|http://purl.obolibrary.org/obo/CHEBI_64342
T18273 1240-1243 Chemical denotes HPA http://purl.obolibrary.org/obo/CHEBI_29031|http://purl.obolibrary.org/obo/CHEBI_53393|http://purl.obolibrary.org/obo/CHEBI_61431|http://purl.obolibrary.org/obo/CHEBI_64342
T40484 1393-1397 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T60355 1398-1407 Chemical denotes methadone http://purl.obolibrary.org/obo/CHEBI_6807
T52802 1468-1471 Chemical denotes HPA http://purl.obolibrary.org/obo/CHEBI_29031|http://purl.obolibrary.org/obo/CHEBI_53393|http://purl.obolibrary.org/obo/CHEBI_61431|http://purl.obolibrary.org/obo/CHEBI_64342
T84484 1556-1559 Chemical denotes HPA http://purl.obolibrary.org/obo/CHEBI_29031|http://purl.obolibrary.org/obo/CHEBI_53393|http://purl.obolibrary.org/obo/CHEBI_61431|http://purl.obolibrary.org/obo/CHEBI_64342
T21762 1816-1832 Chemical denotes neurotransmitter http://purl.obolibrary.org/obo/CHEBI_25512
T99163 1967-1973 Chemical denotes heroin http://purl.obolibrary.org/obo/CHEBI_27808
T98849 2114-2131 Chemical denotes neurotransmitters http://purl.obolibrary.org/obo/CHEBI_25512
T88345 2158-2166 Chemical denotes morphine http://purl.obolibrary.org/obo/CHEBI_17303|http://purl.obolibrary.org/obo/CHEBI_58097
T94074 2193-2201 Chemical denotes dopamine http://purl.obolibrary.org/obo/CHEBI_18243|http://purl.obolibrary.org/obo/CHEBI_59905
T30597 2203-2212 Chemical denotes serotonin http://purl.obolibrary.org/obo/CHEBI_28790|http://purl.obolibrary.org/obo/CHEBI_350546
T23157 2229-2233 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T53196 2235-2239 Chemical denotes GABA http://purl.obolibrary.org/obo/CHEBI_16865
T93729 2242-2255 Chemical denotes acetylcholine http://purl.obolibrary.org/obo/CHEBI_15355
T22491 2257-2266 Chemical denotes aspartate http://purl.obolibrary.org/obo/CHEBI_132943|http://purl.obolibrary.org/obo/CHEBI_29995|http://purl.obolibrary.org/obo/CHEBI_72314
T393 2272-2281 Chemical denotes glutamate http://purl.obolibrary.org/obo/CHEBI_14321|http://purl.obolibrary.org/obo/CHEBI_29987
T66783 2301-2309 Chemical denotes morphine http://purl.obolibrary.org/obo/CHEBI_17303|http://purl.obolibrary.org/obo/CHEBI_58097
T81259 2508-2516 Chemical denotes dopamine http://purl.obolibrary.org/obo/CHEBI_18243|http://purl.obolibrary.org/obo/CHEBI_59905
T41515 2521-2535 Chemical denotes norepinephrine http://purl.obolibrary.org/obo/CHEBI_18357|http://purl.obolibrary.org/obo/CHEBI_33569
T87195 2623-2629 Chemical denotes Heroin http://purl.obolibrary.org/obo/CHEBI_27808
T2127 2741-2749 Chemical denotes dopamine http://purl.obolibrary.org/obo/CHEBI_18243|http://purl.obolibrary.org/obo/CHEBI_59905
T24088 2917-2925 Chemical denotes dopamine http://purl.obolibrary.org/obo/CHEBI_18243|http://purl.obolibrary.org/obo/CHEBI_59905
T62096 3019-3027 Chemical denotes dopamine http://purl.obolibrary.org/obo/CHEBI_18243|http://purl.obolibrary.org/obo/CHEBI_59905
T44600 3042-3050 Chemical denotes dopamine http://purl.obolibrary.org/obo/CHEBI_18243|http://purl.obolibrary.org/obo/CHEBI_59905
T93735 3156-3164 Chemical denotes dopamine http://purl.obolibrary.org/obo/CHEBI_18243|http://purl.obolibrary.org/obo/CHEBI_59905
T22751 3217-3221 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
3397 734-764 Gene denotes corticotropin releasing factor Gene:1392
3398 609-617 Chemical denotes dopamine MESH:D004298
3399 959-967 Chemical denotes cortisol MESH:D006854
3400 1398-1407 Chemical denotes methadone MESH:D008691
3401 528-558 Disease denotes hypothalamic-pituitary-adrenal MESH:D007029
3402 560-563 Disease denotes HPA MESH:D010661
3403 724-727 Disease denotes HPA MESH:D010661
3404 1067-1070 Disease denotes HPA MESH:D010661
3405 1240-1243 Disease denotes HPA MESH:D010661
3406 1468-1471 Disease denotes HPA MESH:D010661
3407 1517-1530 Disease denotes HIV infection MESH:D015658
3408 1556-1559 Disease denotes HPA MESH:D010661
3409 1577-1585 Disease denotes toxicity MESH:D064420
3431 2886-2889 Species denotes HIV Tax:12721
3432 2945-2949 Gene denotes Nath Gene:80155
3433 1967-1973 Chemical denotes heroin MESH:D003932
3434 2158-2166 Chemical denotes morphine MESH:D009020
3435 2193-2201 Chemical denotes dopamine MESH:D004298
3436 2203-2212 Chemical denotes serotonin MESH:D012701
3437 2214-2233 Chemical denotes γ-aminobutyric acid MESH:D005680
3438 2235-2239 Chemical denotes GABA MESH:D005680
3439 2242-2255 Chemical denotes acetylcholine MESH:D000109
3440 2257-2266 Chemical denotes aspartate MESH:D001224
3441 2272-2281 Chemical denotes glutamate MESH:D018698
3442 2301-2309 Chemical denotes morphine MESH:D009020
3443 2508-2516 Chemical denotes dopamine MESH:D004298
3444 2521-2535 Chemical denotes norepinephrine MESH:D009638
3445 2623-2629 Chemical denotes Heroin MESH:D003932
3446 2741-2749 Chemical denotes dopamine MESH:D004298
3447 2917-2925 Chemical denotes dopamine MESH:D004298
3448 3019-3027 Chemical denotes dopamine MESH:D004298
3449 3042-3050 Chemical denotes dopamine MESH:D004298
3450 3156-3164 Chemical denotes dopamine MESH:D004298
3451 3189-3212 Disease denotes opioid abuse tendencies MESH:D009293

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1816-1843 http://purl.obolibrary.org/obo/GO_0042133 denotes neurotransmitter metabolism
T2 1833-1843 http://purl.obolibrary.org/obo/GO_0008152 denotes metabolism
T3 1848-1863 http://purl.obolibrary.org/obo/GO_0010467 denotes gene expression
T4 2741-2762 http://purl.obolibrary.org/obo/GO_0042416 denotes dopamine biosynthesis
T5 2750-2762 http://purl.obolibrary.org/obo/GO_0009058 denotes biosynthesis
T6 2926-2943 http://purl.obolibrary.org/obo/GO_0007268 denotes neurotransmission
T7 3042-3060 http://purl.obolibrary.org/obo/GO_0015872 denotes dopamine transport
T8 3051-3060 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T9 3230-3239 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviors
T182 781-796 http://purl.obolibrary.org/obo/GO_0006694 denotes steroidogenesis
T183 1590-1609 http://purl.obolibrary.org/obo/GO_0001816 denotes cytokine production

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1235 0-55 Sentence denotes Modeling the Pharmacology of Opioid Self-Administration
T1236 56-278 Sentence denotes Opiate self-administration as seen with addiction can have different CNS consequences than “steady-state” (e.g., continuous via a pump or time-release drug implant) exposure to the same drug (Kreek 1987, 2001; Kreek et al.
T1237 279-394 Sentence denotes 2002), and we predict the pharmacokinetic differences in opiate exposure will markedly impact neuroHIV progression.
T1238 395-650 Sentence denotes Differential effects based on “on-off” and “steady-state” drug administration schedules have been reported for the stress-responsive hypothalamic-pituitary-adrenal (HPA) axis, the endogenous opioid system, and the dopamine system (Kreek 1973; Kreek et al.
T1239 651-670 Sentence denotes 2002; George et al.
T1240 671-677 Sentence denotes 2012).
T1241 678-872 Sentence denotes Acute opiate exposure typically activates the HPA axis, corticotropin releasing factor, and peripheral steroidogenesis in a species-dependent manner (Koob and Kreek 2007; Cleck and Blendy 2008).
T1242 873-999 Sentence denotes Alternatively, chronic self-administration of short-acting opiates suppresses diurnal cortisol rhythmicity (Facchinetti et al.
T1243 1000-1018 Sentence denotes 1984; Vuong et al.
T1244 1019-1140 Sentence denotes 2010), while opiate withdrawal typically evokes HPA activation (Culpepper-Morgan and Kreek 1997; Kreek 2007; Paris et al.
T1245 1141-1147 Sentence denotes 2020).
T1246 1148-1338 Sentence denotes The daily, repeated bouts of relative withdrawal seen with opiate addiction cause sustained HPA activation, stress (Koob and Kreek 2007; Koob 2020), and immune suppression (Eisenstein 2019).
T1247 1339-1490 Sentence denotes Importantly, maintenance therapy with the long-acting drug methadone achieves steady-dose opiate levels and normalization of the HPA axis (Kreek 1973).
T1248 1491-1623 Sentence denotes Further, it is known that HIV infection significantly alters the HPA axis, due to CNS toxicity and cytokine production (Costa et al.
T1249 1624-1682 Sentence denotes 2000; George and Bhangoo 2013; Chrousos and Zapanti 2014).
T1250 1683-1864 Sentence denotes Additionally, the nature of opiate exposure in the context of neuroHIV needs to be considered as it may induce different outcomes on neurotransmitter metabolism and gene expression.
T1251 1865-2008 Sentence denotes Specifically, the NAc shell demonstrates molecular and structural changes associated with intravenous heroin self-administration (Jacobs et al.
T1252 2009-2015 Sentence denotes 2005).
T1253 2016-2323 Sentence denotes Moreover, earlier studies have reported differential alterations in the turnover rates of various neurotransmitters for active versus passive morphine administration, including dopamine, serotonin, γ-aminobutyric acid (GABA), acetylcholine, aspartate, and glutamate during exposure to morphine (Smith et al.
T1254 2324-2336 Sentence denotes 1982, 1984).
T1255 2337-2615 Sentence denotes The disruptions were noticed specifically in brain regions involved in reinforcement processes, including the NAc, frontal cortex, and striatum, and encompassed increased dopamine and norepinephrine levels and turnover, which are central in opiate reward processes (Smith et al.
T1256 2616-2622 Sentence denotes 1982).
T1257 2623-2864 Sentence denotes Heroin abuse is known to downregulate dopaminergic activity in the NAc and may reflect a compensatory reduction in of dopamine biosynthesis in response to excessive dopaminergic stimulation resulting from chronic opiate exposure (Kish et al.
T1258 2865-2871 Sentence denotes 2001).
T1259 2872-2956 Sentence denotes Additionally, HIV is known to interfere with dopamine neurotransmission (Nath et al.
T1260 2957-2978 Sentence denotes 2000b; Gaskill et al.
T1261 2979-3089 Sentence denotes 2017) causing reductions in presynaptic dopamine terminals and dopamine transport in the striatum (Wang et al.
T1262 3090-3108 Sentence denotes 2004; Chang et al.
T1263 3109-3127 Sentence denotes 2008; Midde et al.
T1264 3128-3140 Sentence denotes 2012, 2015).
T1265 3141-3303 Sentence denotes The decline in dopamine function may exacerbate opioid abuse tendencies and drug-seeking behaviors as the rewarding effects of opioids are discounted by neuroHIV.

2_test

Id Subject Object Predicate Lexical cue
32876803-3125471-62958318 254-258 3125471 denotes 1987
32876803-11458539-62958319 260-264 11458539 denotes 2001
32876803-12209151-62958320 279-283 12209151 denotes 2002
32876803-4739193-62958321 632-636 4739193 denotes 1973
32876803-12209151-62958322 651-655 12209151 denotes 2002
32876803-22108506-62958323 671-675 22108506 denotes 2012
32876803-17671276-62958324 843-847 17671276 denotes 2007
32876803-18246196-62958325 866-870 18246196 denotes 2008
32876803-6320568-62958326 1000-1004 6320568 denotes 1984
32876803-19903933-62958327 1019-1023 19903933 denotes 2010
32876803-9030816-62958328 1110-1114 9030816 denotes 1997
32876803-18286797-62958329 1122-1126 18286797 denotes 2007
32876803-17671276-62958330 1279-1283 17671276 denotes 2007
32876803-31400808-62958331 1290-1294 31400808 denotes 2020
32876803-31921165-62958332 1332-1336 31921165 denotes 2019
32876803-4739193-62958333 1484-1488 4739193 denotes 1973
32876803-11085902-62958334 1624-1628 11085902 denotes 2000
32876803-23728720-62958335 1649-1653 23728720 denotes 2013
32876803-15849023-62958336 2009-2013 15849023 denotes 2005
32876803-6123120-62958337 2324-2328 6123120 denotes 1982
32876803-6538688-62958338 2330-2334 6538688 denotes 1984
32876803-6123120-62958339 2616-2620 6123120 denotes 1982
32876803-11282256-62958340 2865-2869 11282256 denotes 2001
32876803-15319273-62958342 3090-3094 15319273 denotes 2004
32876803-18579413-62958343 3109-3113 18579413 denotes 2008