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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
303 285-293 Gene denotes helicase Gene:164045
304 98-106 Disease denotes zoonoses MESH:D015047
305 1241-1258 Disease denotes zoonoses diseases MESH:D015047
307 1947-1952 Chemical denotes water MESH:D014867

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T82 181-184 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T83 281-284 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T84 331-334 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T85 435-443 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T86 573-576 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T87 996-999 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T88 1067-1070 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T89 1145-1148 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T90 1195-1198 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T91 2554-2559 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T92 2561-2566 Body_part denotes mucus http://purl.org/sig/ont/fma/fma66938
T93 2568-2574 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T94 2615-2620 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T95 2631-2634 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T96 2693-2697 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T97 2728-2731 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T14 2554-2559 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T15 2561-2566 Body_part denotes mucus http://purl.obolibrary.org/obo/UBERON_0000912
T16 2568-2574 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836
T17 2760-2773 Body_part denotes bodily fluids http://purl.obolibrary.org/obo/UBERON_0006314

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T36 98-106 Disease denotes zoonoses http://purl.obolibrary.org/obo/MONDO_0025481
T37 1241-1249 Disease denotes zoonoses http://purl.obolibrary.org/obo/MONDO_0025481

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T309 46-47 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T310 48-54 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T311 152-158 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T312 571-572 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T313 657-658 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T314 912-913 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T315 994-995 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T316 1072-1074 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T317 1143-1144 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T318 1210-1217 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T319 1219-1221 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T320 1229-1234 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T321 1273-1280 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T322 1282-1284 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T323 1305-1306 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T324 1411-1412 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T325 1484-1485 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T326 1672-1673 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T327 1709-1710 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T328 1878-1880 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T329 1936-1937 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T330 2094-2095 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T331 2333-2336 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T332 2405-2408 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T333 2554-2559 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T334 2554-2559 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T335 2615-2620 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T336 2693-2697 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T337 2760-2773 http://purl.obolibrary.org/obo/UBERON_0006314 denotes bodily fluids
T338 2945-2946 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T339 3000-3001 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T340 3050-3051 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T341 3084-3085 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T342 3086-3092 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T343 3129-3130 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T344 3174-3175 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T345 3226-3227 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T346 3290-3291 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T347 3306-3307 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T305 181-184 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T306 255-258 Chemical denotes HDA http://purl.obolibrary.org/obo/CHEBI_17314
T307 268-271 Chemical denotes HDA http://purl.obolibrary.org/obo/CHEBI_17314
T308 281-284 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T309 331-334 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T310 435-443 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T311 573-576 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T312 635-640 Chemical denotes bases http://purl.obolibrary.org/obo/CHEBI_22695
T313 836-839 Chemical denotes MDA http://purl.obolibrary.org/obo/CHEBI_566274
T314 996-999 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T315 1067-1070 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T316 1145-1148 Chemical denotes RNA http://purl.obolibrary.org/obo/CHEBI_33697
T317 1195-1198 Chemical denotes RNA http://purl.obolibrary.org/obo/CHEBI_33697
T318 1266-1272 Chemical denotes corona http://purl.obolibrary.org/obo/CHEBI_37409
T319 1947-1952 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T320 2631-2634 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T321 2728-2731 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T322 2779-2787 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T323 2882-2885 Chemical denotes MDA http://purl.obolibrary.org/obo/CHEBI_566274
T324 2895-2898 Chemical denotes HDA http://purl.obolibrary.org/obo/CHEBI_17314
T325 3105-3112 Chemical denotes essence http://purl.obolibrary.org/obo/CHEBI_48318

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T20 181-199 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplifications
T21 331-346 http://purl.obolibrary.org/obo/GO_0006260 denotes DNA replication
T22 1115-1128 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T23 1115-1128 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T24 2698-2703 http://purl.obolibrary.org/obo/GO_0019835 denotes lysis
T25 2808-2813 http://purl.obolibrary.org/obo/GO_0019835 denotes lysis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T355 0-2 Sentence denotes 5.
T356 3-10 Sentence denotes Outlook
T357 11-267 Sentence denotes Future steps, which will result in a device for early-stage detection of, for example, zoonoses, include studies on the optimization of this device for sequence specific DNA amplifications (e.g., primer design and reaction optimization), i.e., HDA or LAMP.
T358 268-402 Sentence denotes HDA utilizes DNA helicase (an enzyme also used in vitro during DNA replication) to separate the dsDNA instead of thermal denaturation.
T359 403-641 Sentence denotes After separation, ssDNA binding proteins hybridize on the ssDNA strands for stabilization, ensuring that the next primer will have time to bind to the ssDNA stripe and a DNA polymerase will extend the primers with the complementary bases.
T360 642-811 Sentence denotes This method is a truly isothermal technique in which the separation of the dsDNA can be performed at the same temperature as the amplification reaction, i.e., 64 °C [9].
T361 812-891 Sentence denotes LAMP is more similar to MDA in the way it also uses heat to denature the dsDNA.
T362 892-1076 Sentence denotes After denaturation, a set of four primers (six can be used as well to achieve better selectivity) and a DNA polymerase is used at isothermal conditions (65 °C) to amplify the DNA [11].
T363 1077-1286 Sentence denotes When used in combination with reverse transcriptase, LAMP becomes a RNA amplification method, which could be used for RNA-containing viruses [11], like virus-based zoonoses diseases as the corona viruses [22].
T364 1287-1405 Sentence denotes Despite not being a truly isothermal technique, LAMP offers the possibility to use turbidity as detection method [76].
T365 1406-1565 Sentence denotes Such a detection method would simplify the required equipment even further as a decrease in transmitted light through the chip can be used as detection method.
T366 1566-1632 Sentence denotes Different amplification techniques require different temperatures.
T367 1633-1757 Sentence denotes Based on Table 1 one can conclude that a higher temperature would also give a larger temperature gradient within the system.
T368 1758-1889 Sentence denotes This can be disadvantageous for amplification reactions, as optimal denaturation temperatures are in the range 92 °C to 94 °C [77].
T369 1890-2005 Sentence denotes The denaturation in this research was done in a separate water bath, so this temperature gradient was circumvented.
T370 2006-2214 Sentence denotes However, when on-chip denaturation and/or another amplification technique will be used, a second step will be the optimization of the heater in order to create better temperature uniformity within the system.
T371 2215-2312 Sentence denotes This can be done by using different heater geometries [26,37] or using double-sided heating [28].
T372 2313-2400 Sentence denotes The third step that has to be optimized in the sample collection and work-up procedure.
T373 2401-2582 Sentence denotes One has to think of what kind of samples to collect in order to have the biggest chance of having the agent of the disease present in that sample (i.e., blood, mucus, saliva, etc.).
T374 2583-2650 Sentence denotes Such crude samples contain full cells, with the DNA present within.
T375 2651-2737 Sentence denotes There are different approaches to perform cell lysis in order to extract the DNA [78].
T376 2738-2872 Sentence denotes Various components of bodily fluids, and reagents and products of the lysis are well-known to inhibit the amplification reaction [79].
T377 2873-2944 Sentence denotes However, MDA [80] and HDA [9] could also be performed on crude samples.
T378 2945-3078 Sentence denotes A fourth step in the near-future is the development of a first prototype with all hardware integrated in a single piece of equipment.
T379 3079-3319 Sentence denotes Such a device in its pure essence will consist of a battery to power the heater and detection, a chip holder to firmly keep the chip in its place, a thermocouple for real-time monitoring of the temperature, and a LED light and a photodiode.
T380 3320-3420 Sentence denotes The lamp and photodiode could both be used for fluorescence measurements and turbidity measurements.

2_test

Id Subject Object Predicate Lexical cue
32106462-15247927-69893327 808-809 15247927 denotes 9
32106462-21157218-69893328 1072-1074 21157218 denotes 11
32106462-21157218-69893329 1219-1221 21157218 denotes 11
32106462-21479543-69893330 1282-1284 21479543 denotes 22
32106462-11708792-69893331 1401-1403 11708792 denotes 76
32106462-2003928-69893332 1885-1887 2003928 denotes 77
32106462-9327537-69893333 2868-2870 9327537 denotes 79
32106462-11959976-69893334 2887-2889 11959976 denotes 80
32106462-15247927-69893335 2900-2901 15247927 denotes 9