> top > docs > PMC:7029452 > spans > 3231-10265 > annotations

PMC:7029452 / 3231-10265 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
70 607-610 Gene denotes ARS Gene:6012
71 216-223 Species denotes patient Tax:9606
72 383-390 Species denotes patient Tax:9606
73 712-719 Species denotes patient Tax:9606
74 64-72 Disease denotes COVID-19 MESH:C000657245
75 120-128 Disease denotes COVID-19 MESH:C000657245
76 297-316 Disease denotes infectious diseases MESH:D003141
77 654-663 Disease denotes infection MESH:D007239
79 1119-1122 Gene denotes ARS Gene:6012
83 1416-1424 Species denotes patients Tax:9606
84 1430-1462 Disease denotes Middle East respiratory syndrome MESH:D018352
85 1464-1468 Disease denotes MERS MESH:D018352
88 1777-1787 Species denotes SARS-CoV-2 Tax:2697049
89 1959-1969 Species denotes SARS-CoV-2 Tax:2697049
96 2661-2665 Gene denotes RdRp Gene:43740578
97 2056-2063 Species denotes patient Tax:9606
98 2247-2254 Species denotes patient Tax:9606
99 2443-2453 Species denotes SARS-CoV-2 Tax:2697049
100 2090-2111 Disease denotes respiratory infection MESH:D012141
101 2269-2288 Disease denotes respiratory illness MESH:D012140
107 2987-2994 Species denotes persons Tax:9606
108 3010-3016 Species denotes people Tax:9606
109 3373-3380 Species denotes persons Tax:9606
110 3090-3098 Disease denotes COVID-19 MESH:C000657245
111 3277-3297 Disease denotes SARS-CoV-2 infection MESH:C000657245
118 3477-3484 Species denotes persons Tax:9606
119 3543-3550 Species denotes persons Tax:9606
120 3705-3712 Species denotes persons Tax:9606
121 3431-3440 Disease denotes infection MESH:D007239
122 3509-3517 Disease denotes COVID-19 MESH:C000657245
123 3773-3782 Disease denotes infection MESH:D007239
131 5608-5615 Species denotes persons Tax:9606
132 3926-3935 Disease denotes infection MESH:D007239
133 4702-4707 Disease denotes fever MESH:D005334
134 4709-4714 Disease denotes cough MESH:D003371
135 4718-4726 Disease denotes dyspnoea MESH:D004417
136 4903-4911 Disease denotes COVID-19 MESH:C000657245
137 5213-5221 Disease denotes COVID-19 MESH:C000657245
140 3867-3876 Disease denotes infection MESH:D007239
141 3878-3886 Disease denotes COVID-19 MESH:C000657245
143 5875-5899 Disease denotes coronavirus disease 2019 MESH:C000657245
145 6121-6129 Species denotes Patients Tax:9606
149 6771-6786 Gene denotes Directive 95/46
150 6990-6998 Species denotes patients Tax:9606
151 7014-7033 Disease denotes 2019-nCoV infection MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1528-1551 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T2 1615-1638 Body_part denotes lower respiratory tract http://purl.org/sig/ont/fma/fma45662
T3 1697-1703 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T4 2666-2670 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T5 4601-4605 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T6 4981-4985 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T7 4989-4993 Body_part denotes face http://purl.org/sig/ont/fma/fma24728

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1528-1551 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T2 1534-1551 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T3 1615-1638 Body_part denotes lower respiratory tract http://purl.obolibrary.org/obo/UBERON_0001558
T4 1621-1638 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T5 1697-1703 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T6 4981-4985 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T7 4989-4993 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T26 64-72 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T27 120-128 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T28 297-307 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T29 607-610 Disease denotes ARS http://purl.obolibrary.org/obo/MONDO_0014648
T30 645-663 Disease denotes hospital infection http://purl.obolibrary.org/obo/MONDO_0043544
T31 654-663 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T32 1119-1122 Disease denotes ARS http://purl.obolibrary.org/obo/MONDO_0014648
T33 1777-1785 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 1777-1781 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T35 1959-1967 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 1959-1963 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T37 2090-2111 Disease denotes respiratory infection http://purl.obolibrary.org/obo/MONDO_0024355
T38 2102-2111 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T39 2443-2451 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 2443-2447 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T41 3090-3098 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T42 3277-3285 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 3277-3281 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T44 3288-3297 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T45 3431-3440 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T46 3509-3517 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 3773-3782 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T48 3867-3876 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T49 3878-3886 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T50 3926-3935 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T51 4903-4911 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T52 5213-5221 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T53 5865-5873 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T54 5875-5899 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T55 7014-7033 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T56 7024-7033 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T20 118-119 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 258-259 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 285-286 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 432-433 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 482-485 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T25 521-525 http://purl.obolibrary.org/obo/CLO_0001568 denotes a 24
T26 815-816 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T27 1001-1002 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 1115-1122 http://purl.obolibrary.org/obo/CLO_0001912 denotes the ARS
T29 1615-1638 http://purl.obolibrary.org/obo/UBERON_0001558 denotes lower respiratory tract
T30 1821-1823 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T31 1884-1891 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T32 1930-1934 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T33 2016-2017 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 2054-2055 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 2069-2070 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 2153-2154 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 2245-2246 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 2320-2321 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 2361-2362 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 2379-2380 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T41 2411-2412 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 2432-2433 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 2524-2531 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T44 2666-2670 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T45 3058-3059 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 3249-3250 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 3330-3336 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T48 3488-3489 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 3554-3555 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 3622-3623 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 3813-3814 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 4041-4042 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 4167-4168 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 4323-4324 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 4378-4379 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 4399-4400 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 4624-4625 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 4755-4756 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 4891-4892 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 4981-4985 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T61 4989-4993 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T62 5018-5019 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 5133-5141 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T64 5166-5167 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 5211-5212 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 5340-5341 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 5488-5489 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 5663-5664 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 5710-5716 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T70 5780-5789 http://purl.obolibrary.org/obo/OBI_0000245 denotes organised
T71 6081-6087 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T72 6182-6183 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T73 6787-6789 http://purl.obolibrary.org/obo/CLO_0002878 denotes EC

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1180-1191 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232
T2 2721-2723 Chemical denotes IP http://purl.obolibrary.org/obo/CHEBI_74076
T3 2976-2978 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T4 3532-3534 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T5 2090-2111 Phenotype denotes respiratory infection http://purl.obolibrary.org/obo/HP_0011947
T6 2269-2288 Phenotype denotes respiratory illness http://purl.obolibrary.org/obo/HP_0002086
T7 4702-4707 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T8 4709-4714 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T9 4718-4726 Phenotype denotes dyspnoea http://purl.obolibrary.org/obo/HP_0002094

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 6730-6740 http://purl.obolibrary.org/obo/GO_0065007 denotes Regulation
T2 6742-6752 http://purl.obolibrary.org/obo/GO_0065007 denotes Regulation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T26 0-7 Sentence denotes Methods
T27 9-35 Sentence denotes French surveillance system
T28 36-346 Sentence denotes In France, according to the COVID-19 surveillance protocol, physicians suspecting a COVID-19 case have to contact immediately either the emergency hotline (SAMU-Centre 15), if the patient is seeking medical attention from a general practitioner, or a referring infectious diseases specialist at hospital level.
T29 347-460 Sentence denotes Together, they evaluate whether the patient matches the case definition criteria for a possible case (see below).
T30 461-814 Sentence denotes If they do, the case has to be reported immediately through a 24/7 available phone line to the Regional Health Agency (Agence régionale de santé, ARS), which informs without delay the hospital infection control teams involved in the management of the patient, the French Public Health Agency (Santé publique France, SpFrance) and the Ministry of Health.
T31 815-1136 Sentence denotes A standardised investigation form collecting socio-demographical information, clinical details and history of exposure (history of travel to or residence in Wuhan, China or contact with a confirmed case) is completed for each possible case at regional level, in collaboration between the clinicians, the ARS and SpFrance.
T32 1137-1221 Sentence denotes Data are entered into the secure web-based application Voozanoo (Epiconcept, Paris).
T33 1222-1474 Sentence denotes Possible cases have to be hospitalised, isolated and cared for in one of the 38 French referral hospitals designated by the Ministry of Health, according to the guidelines for the management of patients with Middle East respiratory syndrome (MERS) [3].
T34 1475-1814 Sentence denotes For each possible case, respiratory samples from the upper respiratory tract (nasopharyngeal swabs or aspirates) and when possible from the lower respiratory tract (bronchoalveolar lavage fluid, when indicated, or induced sputum) are collected and sent to one of the laboratories accredited to perform SARS-CoV-2-specific real-time RT-PCR.
T35 1815-1970 Sentence denotes Until 27 January, only the National Reference Centre for respiratory viruses (Institut Pasteur, Paris) was able to test for the presence of the SARS-CoV-2.
T36 1972-1987 Sentence denotes Case definition
T37 1988-2378 Sentence denotes From 17 to 29 January 2020, a possible case was defined either as a patient with a severe acute lower respiratory infection requiring admission to hospital and with a history of travel to or residence in Wuhan, China in the 14 days before symptom onset, or a patient with an acute respiratory illness whatever the severity and with a history of at-risk exposure, mainly to a confirmed case.
T38 2379-2523 Sentence denotes A confirmed case was defined as a possible case with a positive SARS-CoV-2 RT-PCR on respiratory samples, performed by an accredited laboratory.
T39 2524-2725 Sentence denotes Testing relied on the real-time RT-PCR procedure developed by the Charité [4] as well as on the use of real-time RT-PCR specific for the RdRp gene (four targets) designed at Institut Pasteur (RdRp-IP).
T40 2726-2799 Sentence denotes The case definition was first set up on 10 January and adapted over time.
T41 2800-2942 Sentence denotes The detailed case definition used for the cases presented here as well as the most up-to-date case definition are available in the Supplement.
T42 2944-2975 Sentence denotes Contact and co-exposure tracing
T43 2976-3099 Sentence denotes Co-exposed persons are defined as people who shared the same risks of exposure as a possible or confirmed case of COVID-19.
T44 3100-3181 Sentence denotes Contact and co-exposure identification is done for all identified possible cases.
T45 3182-3256 Sentence denotes Contacts are traced from the date of onset of clinical symptoms in a case.
T46 3257-3406 Sentence denotes If the diagnosis of SARS-CoV-2 infection is confirmed in the index case, active surveillance of contacts/co-exposed persons is initiated immediately.
T47 3407-3531 Sentence denotes Three levels of risk of infection are defined for contacts/co-exposed persons of a possible/confirmed COVID-19 case (Table).
T48 3532-3652 Sentence denotes Co-exposed persons of a confirmed case are followed-up according to the same procedure as a moderate-/high-risk contact.
T49 3653-3791 Sentence denotes The follow-up procedure for the contacts/co-exposed persons differs according to the evaluation of the level of risk of infection (Table).
T50 3792-3908 Sentence denotes Table Definition of a contact and follow-up procedure by level of risk of infection, COVID-19, France, January 2020
T51 3909-3978 Sentence denotes Level of risk of infection Contact definition Follow-up procedure
T52 3979-4244 Sentence denotes Negligible risk Person who had short (< 15 min) contact with a confirmed case in public settings such as in public transportation, restaurants and shops; healthcare personnel who treated a confirmed case while wearing appropriate PPE without any breach identified.
T53 4246-4297 Sentence denotes Neither identification nor information of contacts.
T54 4298-4563 Sentence denotes Low risk Person who had a close (within 1 m) but short (< 15 min) contact with a confirmed case, or a distant (> 1 m) but prolonged contact in public settings, or any contact in private settings that does not match with the moderate/high risk of exposure criteria.
T55 4565-4662 Sentence denotes Contacts are asked to measure their body temperature twice a day and check for clinical symptoms.
T56 4663-4917 Sentence denotes In case of occurrence of symptoms like fever, cough or dyspnoea, contacts are asked to wear a surgical mask, isolate themselves and immediately contact the emergency hotline (SAMU-centre 15) indicating that they are contacts of a confirmed COVID-19 case.
T57 4918-5306 Sentence denotes Moderate/high risk Person who had prolonged (> 15 min) direct face-to-face contact within 1 m with a confirmed case, shared the same hospital room, lived in the same household or shared any leisure or professional activity in close proximity with a confirmed case, or travelled together with a COVID-19 case in any kind of conveyance, without appropriate individual protection equipment.
T58 5307-5418 Sentence denotes Healthcare personnel who treated a confirmed case without wearing appropriate PPE or with an identified breach.
T59 5420-5680 Sentence denotes In addition to the above, contacts are asked to stay at home during a 14-day period after their last contact with the confirmed case while symptomatic and to avoid contacts with the other persons living in the same household (or at least wear a surgical mask).
T60 5681-5864 Sentence denotes The follow-up consists of an active follow-up through daily calls from the regional follow-up team organised by the Regional Health Agency in collaboration with Santé publique France.
T61 5865-5936 Sentence denotes COVID-19: coronavirus disease 2019; PPE: personal protective equipment.
T62 5937-6120 Sentence denotes During the initial implementation phase of the procedure, owing to the limited number of contacts involved, it was decided to also implement an active follow-up for low risk contacts.
T63 6121-6331 Sentence denotes Patients are interviewed by the clinicians, with the help of a translator if needed, who recover relevant information on their contacts since onset of clinical symptoms and the nature and intensity of exposure.
T64 6332-6509 Sentence denotes The involved regional health agencies work closely with the regional entities of Santé publique France (cellules régionales) in order to implement contact tracing and follow-up.
T65 6510-6627 Sentence denotes Santé publique France coordinates the surveillance at national level in liaison with the national Health Authorities.
T66 6629-6646 Sentence denotes Ethical statement
T67 6647-6886 Sentence denotes The investigations were carried out in accordance with the General Data Protection Regulation (Regulation (EU) 2016/679 and Directive 95/46/EC) and the French data protection law (Law 78–17 on 06/01/1978 and Décret 2019–536 on 29/05/2019).
T68 6887-7034 Sentence denotes Informed consent to disclosure of information relevant to this publication was obtained from the three patients confirmed with 2019-nCoV infection.