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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T108 158-163 Body_part denotes bowel http://purl.org/sig/ont/fma/fma7199
T109 181-186 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197
T110 199-204 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197
T111 329-334 Body_part denotes bowel http://purl.org/sig/ont/fma/fma7199
T112 1592-1597 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T113 2319-2324 Body_part denotes bowel http://purl.org/sig/ont/fma/fma7199
T114 3173-3178 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T115 3179-3182 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T116 3378-3383 Body_part denotes Joint http://purl.org/sig/ont/fma/fma7490
T117 3629-3634 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T118 4596-4601 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T83 181-186 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107
T84 199-204 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107
T85 1592-1597 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T86 3173-3178 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T87 3629-3634 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T88 4596-4601 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T239 88-96 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T240 145-171 Disease denotes inflammatory bowel disease http://purl.obolibrary.org/obo/MONDO_0005265
T241 181-194 Disease denotes liver disease http://purl.obolibrary.org/obo/MONDO_0005154
T242 316-342 Disease denotes inflammatory bowel disease http://purl.obolibrary.org/obo/MONDO_0005265
T243 476-484 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T244 918-926 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T245 1376-1384 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T246 1385-1394 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T247 1471-1479 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T248 1522-1549 Disease denotes upper respiratory infection http://purl.obolibrary.org/obo/MONDO_0024355
T249 1540-1549 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T250 1684-1692 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T251 1765-1772 Disease denotes anosmia http://purl.obolibrary.org/obo/MONDO_0010528
T252 2306-2332 Disease denotes inflammatory bowel disease http://purl.obolibrary.org/obo/MONDO_0005265
T253 2526-2534 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T254 3071-3079 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T255 3419-3428 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T256 3438-3447 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T257 3552-3571 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T258 4462-4470 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T259 4532-4540 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T353 181-186 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T354 181-186 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T355 199-204 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T356 199-204 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T357 343-345 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T358 362-363 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T359 439-448 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremely
T360 1045-1046 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T361 1085-1086 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T362 1176-1177 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T363 1212-1213 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T364 1592-1597 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T365 2514-2521 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T366 3183-3190 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T367 3251-3258 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T368 3359-3371 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T369 3378-3383 http://purl.obolibrary.org/obo/UBERON_0000982 denotes Joint
T370 3378-3383 http://purl.obolibrary.org/obo/UBERON_0004905 denotes Joint
T371 3629-3634 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T372 3842-3843 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T373 3916-3921 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T374 4420-4421 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T375 4558-4559 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T376 4596-4601 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T377 4596-4601 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T378 4627-4631 http://purl.obolibrary.org/obo/CLO_0008416 denotes peer
T379 4627-4631 http://purl.obolibrary.org/obo/CLO_0050081 denotes peer

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T134 883-885 Chemical denotes GI http://purl.obolibrary.org/obo/CHEBI_73907
T135 1662-1664 Chemical denotes GI http://purl.obolibrary.org/obo/CHEBI_73907
T6596 1799-1801 Chemical denotes GI http://purl.obolibrary.org/obo/CHEBI_73907
T30144 2280-2282 Chemical denotes GI http://purl.obolibrary.org/obo/CHEBI_73907
T15821 2487-2499 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T42671 2495-2499 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T5 3224-3226 Chemical denotes GI http://purl.obolibrary.org/obo/CHEBI_73907
T6 3479-3485 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T25880 3538-3540 Chemical denotes Hg http://purl.obolibrary.org/obo/CHEBI_16170|http://purl.obolibrary.org/obo/CHEBI_25195
T41336 3752-3754 Chemical denotes GI http://purl.obolibrary.org/obo/CHEBI_73907
T37004 4589-4591 Chemical denotes GI http://purl.obolibrary.org/obo/CHEBI_73907

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T210 145-171 Phenotype denotes inflammatory bowel disease http://purl.obolibrary.org/obo/HP_0002037
T211 181-194 Phenotype denotes liver disease http://purl.obolibrary.org/obo/HP_0001392
T212 316-342 Phenotype denotes inflammatory bowel disease http://purl.obolibrary.org/obo/HP_0002037
T213 1528-1549 Phenotype denotes respiratory infection http://purl.obolibrary.org/obo/HP_0011947
T214 1564-1569 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T215 1571-1590 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T216 1592-1602 Phenotype denotes chest pain http://purl.obolibrary.org/obo/HP_0100749
T217 1608-1613 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T218 1684-1692 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T219 1694-1710 Phenotype denotes nausea, vomiting http://purl.obolibrary.org/obo/HP_0002017
T220 1716-1730 Phenotype denotes abdominal pain http://purl.obolibrary.org/obo/HP_0002027
T221 1765-1772 Phenotype denotes anosmia http://purl.obolibrary.org/obo/HP_0000458
T222 2306-2332 Phenotype denotes inflammatory bowel disease http://purl.obolibrary.org/obo/HP_0002037
T223 3419-3428 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T224 3438-3447 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T225 3468-3477 Phenotype denotes tachypnea http://purl.obolibrary.org/obo/HP_0002789
T226 3552-3571 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T227 3613-3618 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T321 0-39 Sentence denotes Evidence Gaps and Guidance for Research
T322 40-256 Sentence denotes There is insufficient evidence on the impact of COVID-19 on subgroups of patients, such as patients with inflammatory bowel disease, chronic liver disease, or liver transplant recipients on chronic immunosuppression.
T323 257-596 Sentence denotes Early data do not indicate excess risk among patients with inflammatory bowel disease.94, 95, 96, 97, 98 A number of international registries have been established that will provide extremely valuable information about COVID-19 in these potentially vulnerable populations (www.covidibd.org; covidcirrhosis.web.unc.edu; www.gi-covid19.org).
T324 597-718 Sentence denotes Other clinical decisions, including optimal medication management and treatment decisions, are still under investigation.
T325 719-834 Sentence denotes We encourage clinicians to contribute to these registries to further enhance understanding in these subpopulations.
T326 835-954 Sentence denotes Table 4 provides guidance for future studies of GI manifestations in patients with COVID-19 or other similar pathogens.
T327 955-1031 Sentence denotes Table 4 Guidance and Research Considerations for Future Studies of COVID-19a
T328 1032-1251 Sentence denotes Study design A prospective inception cohort study is a favorable study design.Another study design that is informative especially when there is a need for rapid data evaluation is a retrospective inception cohort study.
T329 1252-1614 Sentence denotes Participants Enrollment of consecutive patients beginning at pandemic onset.Specific set of symptoms that are predictive of COVID-19 infection, all symptoms should be systematically collected on presentation and before COVID-19 diagnosis is established.• Elicit typical upper respiratory infection symptoms (eg, cough, shortness of breath, chest pain, and fever)
T330 1615-1783 Sentence denotes • Inquire about less typical symptoms, such as GI-specific symptoms: diarrhea, nausea, vomiting, and abdominal pain, and also other symptoms, such as anosmia, dysguesia
T331 1784-1966 Sentence denotes • Describe the GI symptoms in detail, including initial vs late, concurrent vs isolated, duration and frequency, history, and medication initiation relating to the onset of symptoms.
T332 1967-2072 Sentence denotes Investigators should avoid:• Undefined sampling (convenience sampling), including undefined time periods.
T333 2073-2230 Sentence denotes • Overlap of the same population with other publications, which can be done by coordinating efforts between the different departments within the institution.
T334 2231-2419 Sentence denotes Investigators should consider stratification for GI comorbidities, such as inflammatory bowel disease and cirrhosisInvestigators should consider stratification by outpatients vs inpatients
T335 2420-3258 Sentence denotes Laboratory Standardized laboratory confirmation should be based on nucleic acid amplification testing for SARS-CoV-2 on respiratory specimen rather than relying on radiologic suspicion on imaging studies, which are less specificLFTs should be obtained on admission and followed throughout the hospitalization.Changes in LFTs should be reported as normal/abnormal and the cutoff for abnormal should be specified, rather than mean and median at the individual patient levelPattern of LFTs abnormalities, hepatocellular vs cholestatic, should be reported as well as the evaluation performed to work up the abnormalitiesBaseline LFTs (prior to developing COVID-19), changes during the duration of the disease, and after resolution should be reported.Report stool RNA testing, when available, and presence of GI symptoms at the time of testing
T336 3259-3447 Sentence denotes Disease severity Use of standardized disease severity definitions, for example, as per World Health Organization–China Joint Mission100:• mild-to-moderate: non-pneumonia and mild pneumonia
T337 3448-3540 Sentence denotes • severe defined as tachypnea, oxygen saturation ≤93% at rest, or PaO2/FiO2 ratio <300 mm Hg
T338 3541-3686 Sentence denotes • critical respiratory failure requiring mechanical ventilation, septic shock, or other organ dysfunction or failure that requires intensive care
T339 3687-3763 Sentence denotes Patients can be stratified by:• Disease severity and presence of GI symptoms
T340 3764-3791 Sentence denotes • Disease severity and LFTs
T341 3792-3890 Sentence denotes Symptoms and their duration before development of a severe stage of the disease should be reported
T342 3891-4177 Sentence denotes Outcomes Outcomes should focus on patient-important outcomes, such as death, clinical improvement or disease worsening/progression, hospital discharge; include clinical definitions (eg, threshold reached for intubation); select sufficient follow-up time to ensure outcome is obtainable.
T343 4178-4419 Sentence denotes Analysis Analysis should attempt to control for confounding variables; analysis of risk factors should include univariate followed by multivariate analyses to identify independent risk factors predicting more severe disease and poor outcomes
T344 4420-4617 Sentence denotes a aIn the table, we specifically refer to COVID-19, but this guidance applies to any future pathogen similar to COVID-19 that presents as a viral illness with potential GI and liver manifestations.
T345 4618-4700 Sentence denotes Finally, peer-review remains critical to the process of disseminating information.
T346 4701-5012 Sentence denotes Journals should add resources to expedite reviews by increasing the number of editors and reviewers to shorten the review process; maintain accuracy, high quality, and details of the data reported; as well as to avoid overlap in patients between studies or multiple studies being published on the same cohort.99

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1322 3224-3226 Gene denotes GI Gene:2770
1323 2280-2282 Gene denotes GI Gene:2770
1324 1662-1664 Gene denotes GI Gene:2770
1325 1252-1264 Species denotes Participants Tax:9606
1326 1291-1299 Species denotes patients Tax:9606
1327 2526-2536 Species denotes SARS-CoV-2 Tax:2697049
1328 2878-2885 Species denotes patient Tax:9606
1329 3925-3932 Species denotes patient Tax:9606
1330 2540-2551 Species denotes respiratory Tax:12814
1331 1376-1384 Disease denotes COVID-19 MESH:C000657245
1332 1385-1394 Disease denotes infection MESH:D007239
1333 1471-1479 Disease denotes COVID-19 MESH:C000657245
1334 1528-1549 Disease denotes respiratory infection MESH:D012141
1335 1564-1569 Disease denotes cough MESH:D003371
1336 1571-1590 Disease denotes shortness of breath MESH:D004417
1337 1592-1602 Disease denotes chest pain MESH:D002637
1338 1608-1613 Disease denotes fever MESH:D005334
1339 1684-1692 Disease denotes diarrhea MESH:D003967
1340 1694-1700 Disease denotes nausea MESH:D009325
1341 1702-1710 Disease denotes vomiting MESH:D014839
1342 1716-1730 Disease denotes abdominal pain MESH:D015746
1343 1765-1772 Disease denotes anosmia MESH:D000857
1344 1774-1810 Disease denotes dysguesia • Describe the GI symptoms MESH:D051271
1345 2306-2332 Disease denotes inflammatory bowel disease MESH:D015212
1346 2337-2359 Disease denotes cirrhosisInvestigators
1347 2902-2920 Disease denotes LFTs abnormalities MESH:D018376
1348 2922-2951 Disease denotes hepatocellular vs cholestatic MESH:D006528
1349 3071-3079 Disease denotes COVID-19 MESH:C000657245
1350 3415-3428 Disease denotes non-pneumonia MESH:D011014
1351 3468-3477 Disease denotes tachypnea MESH:D059246
1352 3538-3571 Disease denotes Hg • critical respiratory failure MESH:D012131
1353 3606-3618 Disease denotes septic shock MESH:D012772
1354 3629-3657 Disease denotes organ dysfunction or failure MESH:D009102
1355 3961-3966 Disease denotes death MESH:D003643
1357 1022-1027 Disease denotes COVID MESH:C000657245
1362 4589-4591 Gene denotes GI Gene:2770
1363 4462-4470 Disease denotes COVID-19 MESH:C000657245
1364 4532-4540 Disease denotes COVID-19 MESH:C000657245
1365 4560-4573 Disease denotes viral illness
1379 883-885 Gene denotes GI Gene:2770
1380 580-582 Gene denotes gi Gene:2770
1381 113-121 Species denotes patients Tax:9606
1382 131-139 Species denotes patients Tax:9606
1383 302-310 Species denotes patients Tax:9606
1384 904-912 Species denotes patients Tax:9606
1385 88-96 Disease denotes COVID-19 MESH:C000657245
1386 145-171 Disease denotes inflammatory bowel disease MESH:D015212
1387 173-194 Disease denotes chronic liver disease MESH:D058625
1388 316-342 Disease denotes inflammatory bowel disease MESH:D015212
1389 476-484 Disease denotes COVID-19 MESH:C000657245
1390 548-562 Disease denotes covidcirrhosis
1391 918-926 Disease denotes COVID-19 MESH:C000657245
1393 4930-4938 Species denotes patients Tax:9606