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PMC:7017878 / 4424-12826 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T78 5524-5535 SO:0000673 denotes transcripts
T77 6011-6022 SO:0000673 denotes transcripts
T76 6088-6099 SO:0000673 denotes transcripts
T75 6277-6288 SO:0000673 denotes transcripts
T74 6611-6616 SP_6;NCBITaxon:9606 denotes human
T73 6635-6640 SP_6;NCBITaxon:9606 denotes human
T72 6641-6647 NCBITaxon:33208 denotes animal
T71 6684-6689 GO:0016265 denotes death
T70 6698-6704 NCBITaxon:33208 denotes animal
T69 6926-6937 SO:0000673 denotes transcripts
T68 7275-7285 NCBITaxon:1 denotes individual
T67 7311-7321 GO:0065007 denotes regulation
T66 7419-7430 NCBITaxon:1 denotes individuals
T65 3677-3682 SP_6;NCBITaxon:9606 denotes human
T64 3724-3729 SP_6;NCBITaxon:9606 denotes human
T63 3744-3749 SP_6;NCBITaxon:9606 denotes human
T62 3750-3756 NCBITaxon:33208 denotes animal
T61 3809-3814 GO:0016265 denotes death
T60 4140-4149 CHEBI:27780;CHEBI:27780 denotes detergent
T59 4379-4386 NCBITaxon:33208 denotes animals
T58 4587-4592 SP_6;NCBITaxon:9606 denotes human
T57 4593-4599 NCBITaxon:33208 denotes animal
T56 4798-4804 NCBITaxon:9606 denotes people
T55 5081-5092 SO:0000673 denotes transcripts
T54 1494-1499 SP_6;NCBITaxon:9606 denotes human
T53 1866-1872 NCBITaxon:9606 denotes people
T52 1910-1917 NCBITaxon:33208 denotes animals
T51 2020-2026 NCBITaxon:9606 denotes people
T50 2260-2271 NCBITaxon:1 denotes individuals
T49 448-451 SP_2 denotes bat
T48 456-462 NCBITaxon:9989 denotes rodent
T47 486-493 NCBITaxon:10239 denotes viruses
T46 524-530 NCBITaxon:9606 denotes humans
T45 550-555 SP_6;NCBITaxon:9606 denotes human
T44 664-675 NCBITaxon:1 denotes individuals
T43 757-764 NCBITaxon:33208 denotes animals
T42 830-837 NCBITaxon:33208 denotes animals
T41 867-874 NCBITaxon:33208 denotes animals
T40 914-917 SP_2 denotes bat
T39 939-946 NCBITaxon:33208 denotes animals
T38 963-967 CHEBI:33290;CHEBI:33290 denotes food

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 7921-7925 Body_part denotes crop http://purl.obolibrary.org/obo/UBERON_0007356
T2 7977-7981 Body_part denotes crop http://purl.obolibrary.org/obo/UBERON_0007356

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T21 208-218 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T22 3649-3665 Disease denotes zoonotic disease http://purl.obolibrary.org/obo/MONDO_0025481

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T39 327-337 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T40 338-340 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T41 448-451 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T42 486-493 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T43 524-530 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T44 550-555 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T45 722-724 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T46 757-764 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T47 830-837 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T48 867-874 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T49 914-917 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T50 939-946 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T51 991-992 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 1013-1015 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T53 1039-1045 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T54 1064-1065 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 1250-1251 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 1461-1462 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 1494-1499 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T58 1561-1571 http://purl.obolibrary.org/obo/BFO_0000030 denotes objectives
T59 1910-1917 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T60 1946-1948 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T61 2362-2363 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 2441-2442 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 2499-2504 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T64 2601-2602 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 2612-2614 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T66 2631-2632 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 3136-3137 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 3573-3581 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T69 3677-3682 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T70 3724-3729 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T71 3744-3749 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T72 3750-3756 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T73 4010-4011 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 4105-4106 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 4182-4183 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 4207-4212 http://purl.obolibrary.org/obo/UBERON_0007688 denotes Field
T77 4379-4386 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T78 4587-4592 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T79 4593-4599 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T80 4779-4780 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 4844-4845 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 5073-5080 http://www.ebi.ac.uk/efo/EFO_0000881 denotes digital
T83 5611-5617 http://purl.obolibrary.org/obo/CLO_0001929 denotes Berlin
T84 5750-5751 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85 5972-5973 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 5988-5989 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 6611-6616 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T88 6635-6640 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T89 6641-6647 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T90 6698-6704 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T91 6786-6787 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 6947-6948 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T93 6989-6990 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T94 7099-7101 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T95 7683-7687 http://purl.obolibrary.org/obo/UBERON_0003101 denotes Male
T96 7683-7687 http://www.ebi.ac.uk/efo/EFO_0000970 denotes Male
T97 7696-7702 http://purl.obolibrary.org/obo/UBERON_0003100 denotes Female
T98 7708-7710 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T99 7719-7721 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T100 7774-7776 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T101 7778-7780 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T102 7808-7810 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T103 7861-7863 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T104 8016-8018 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T105 8029-8035 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T106 8070-8076 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T107 8085-8089 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T108 8095-8101 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T109 8110-8114 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 2
T110 8130-8134 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 2
T111 8160-8162 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T112 8250-8252 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T113 8262-8266 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T114 8279-8283 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T115 8339-8341 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T116 8342-8345 http://purl.obolibrary.org/obo/CLO_0051582 denotes Has
T117 8386-8387 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 8396-8398 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T3 4140-4149 Chemical denotes detergent http://purl.obolibrary.org/obo/CHEBI_27780
T4 5156-5158 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T3 1000-1009 http://purl.obolibrary.org/obo/GO_0009056 denotes breakdown
T4 7311-7321 http://purl.obolibrary.org/obo/GO_0065007 denotes regulation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T22 0-21 Sentence denotes Materials and methods
T23 23-51 Sentence denotes Study sites and participants
T24 52-573 Sentence denotes The Yunnan, Guangxi and Guangdong provinces in southern China were selected for this study because of their historical importance in the origin of emerging infectious diseases,16 diverse wildlife population within protected forests17 and intensive wildlife farming and trade activities.18 Three sites in rural areas were identified in each province where our previous research had found numerous bat and rodent populations harbouring viruses with pathogenic potential for humans, at sites close to human communities.19–21
T25 574-978 Sentence denotes Enrolment criteria for participation in an ethnographic interview in this study included: individuals were residents of the target community, aged ≥18 y, with prior contact with live animals directly (e.g. by raising, hunting, trading or slaughtering live animals) or indirectly (e.g. through animals living in or entering dwellings/crops, bat roosts within roofs, animals invading stored food or crops).
T26 979-1174 Sentence denotes We targeted a gender breakdown of 35% of participants being female and aimed to have a diverse sample of participants from different age groups and levels of power and influence in the community.
T27 1176-1200 Sentence denotes Recruitment and sampling
T28 1201-1446 Sentence denotes In each province, project investigators provided a two-day training workshop for study staff from local provincial and city-level Centres for Disease Control and Prevention who spoke the local language and were familiar with the local community.
T29 1447-1726 Sentence denotes This included a unit on the ethical conduct of human subject research, an in-depth review of the study design and objectives, and comprehensive information on the implementation of observational research, semistructured interviews and notetaking within the context of this study.
T30 1727-2191 Sentence denotes Participants were identified through key informants and the snowball sampling method because the population size at selected sites and the people who had high-risk contacts with live animals were difficult to elucidate.22 Starting with the key informants, we asked each participant to suggest people who met the inclusion criteria and who might be interested in participating in this study; we then contacted the referrals for potential participation in our study.
T31 2192-2342 Sentence denotes Local study staff visited potential participants and provided these individuals with the participant information sheet to introduce them to the study.
T32 2343-2485 Sentence denotes We aimed to obtain a minimum sample size of 20 participants from each of the three provinces, for a total sample size of over 60 participants.
T33 2486-2641 Sentence denotes At least two field observations of local markets and household environments were conducted at each study site, for a total of 18 observations at a minimum.
T34 2642-2692 Sentence denotes Participation in the study was strictly voluntary.
T35 2693-2803 Sentence denotes Study staff reviewed the information sheet with potential participants and explained the details of the study.
T36 2804-3097 Sentence denotes This included the voluntary nature of participation, inclusion and exclusion criteria, study implementation processes (e.g. that the interview would be audio-recorded), potential risks and benefits of participation, results sharing and that they could withdraw their participation at any time.
T37 3098-3290 Sentence denotes It was also explained that an item as a token would be given as appreciation for their participation, which was identified by the study team and appropriate for the context of the study sites.
T38 3291-3348 Sentence denotes Figure 1 Coding themes, subthemes and analysis framework
T39 3349-3438 Sentence denotes Figure 2 Nine study sites in the Yunnan, Guangxi and Guangdong Provinces, Southern China
T40 3440-3470 Sentence denotes Data collection and management
T41 3471-3838 Sentence denotes After completion of the informed consent process, one-on-one semistructured interviews were conducted focusing on the five core themes outlined in the interview guide related to zoonotic disease emergence: human movement, socioeconomics, biosecurity in human environments, human–animal contact and illness, and medical care/treatment and death (Supplementary Data I).
T42 3839-3946 Sentence denotes All interviews were conducted in the local language and audio-recorded without any identifying information.
T43 3947-4043 Sentence denotes Confidentiality was maintained by conducting the interviews in a private and secure environment.
T44 4044-4206 Sentence denotes At the end of the interview, each study participant received a bottle of cooking oil or laundry detergent valued at no more than US$10 as a token of appreciation.
T45 4207-4288 Sentence denotes Field observations were conducted by study staff at each study site concurrently.
T46 4289-4643 Sentence denotes Observations were general and implemented in three settings: (1) local markets where live animals were traded, (2) in and/or around the dwellings of study participants and, if applicable, (3) community centres, to obtain an overview of the study site and the communities, and supplementary data on human-animal interactions and environmental biosecurity.
T47 4644-4726 Sentence denotes The observed information was narrated by study staff and audio-recorded on site.23
T48 4727-5207 Sentence denotes To enhance saturation, efforts were made to include a large variety of people with different backgrounds, to conduct a maximized number of interviews during the 8 wk study period in each province and to cover as many themes and subthemes from the interview guide as possible in each interview.24 All data generated, including notes, audio files, digital transcripts and the interviewer checklist, were coded with an alphanumeric ID to preserve the confidentiality of participants.
T49 5208-5266 Sentence denotes Paper files were scanned electronically and then shredded.
T50 5267-5388 Sentence denotes All electronic data were encrypted and password-protected, and access was limited to the study staff conducting analyses.
T51 5390-5403 Sentence denotes Data analysis
T52 5404-5519 Sentence denotes All interviews and observations were transcribed from the local language into Mandarin and translated into English.
T53 5520-5661 Sentence denotes All transcripts were imported into MAXQDA release 12 statistical software (VERBI Software, Berlin, Germany) for data management and analysis.
T54 5662-5981 Sentence denotes The analysis process incorporated both deductive and inductive approaches, and followed a process of initial coding, identification of new themes, primary coding and identification and analysis of emerging themes.25 An initial codebook associated with the five core themes of the interview guide was developed a priori.
T55 5982-6175 Sentence denotes After a close reading of the transcripts, two authors used the initial codebook to independently code two transcripts in their entirety, making notes on emerging themes and specified subthemes.
T56 6176-6289 Sentence denotes Subsequently, the two authors adapted the codebook and used the modified codebook to code all of the transcripts.
T57 6290-6517 Sentence denotes During the coding process, the two authors met when any major new themes or concepts emerged to decide on any necessary revisions to the codebook, until no new themes emerged and no new information was obtained from the coding.
T58 6518-6753 Sentence denotes The final codebook was restructured with five sections: (1) demographics, (2) biosecurity in human environments, (3) human–animal contact, (4) illness, treatment and death and (5) animal taxa; subthemes were defined under each section.
T59 6754-6826 Sentence denotes After completion of the coding, a code report was generated from MAXQDA.
T60 6827-7560 Sentence denotes Internal reliability was assessed by comparing the coded segments from two authors on the same two transcripts to reach a minimum code interaction rate of 80%.26 A saturation grid was built using the ‘Segment Retrieval’ function in MAXQDA to ensure saturation was reached.27 Coded segments were categorized into protective factors and risk factors based on their known associations with disease transmission, and the analysis was stratified at the individual, community and policy or regulation level.28 At the individual level, both risk and protective factors were analysed in terms of the individuals' knowledge, attitudes and practices to better understand the risk factors for identifying context-based strategies.29 (Figure 1).
T61 7561-7623 Sentence denotes Table 1 Demographic characteristics of the study participants
T62 7624-7659 Sentence denotes Characteristic Participants (n=88)
T63 7660-7675 Sentence denotes Frequency, n %
T64 7676-7682 Sentence denotes Gender
T65 7683-7695 Sentence denotes Male 58 66
T66 7696-7710 Sentence denotes Female 30 34
T67 7711-7718 Sentence denotes Age (y)
T68 7719-7730 Sentence denotes 18–30 8 9
T69 7731-7744 Sentence denotes 31–50 55 63
T70 7745-7756 Sentence denotes >50 25 28
T71 7757-7765 Sentence denotes Province
T72 7766-7780 Sentence denotes Yunnan 36 41
T73 7781-7796 Sentence denotes Guangxi 25 28
T74 7797-7814 Sentence denotes Guangdong 27 31
T75 7815-7835 Sentence denotes Source of livelihood
T76 7836-7863 Sentence denotes Government employee 10 11
T77 7864-7894 Sentence denotes Private company employee 7 8
T78 7895-7915 Sentence denotes School teacher 5 6
T79 7916-7970 Sentence denotes Cash crop production (e.g. fruit tree, bamboo) 23 26
T80 7971-8018 Sentence denotes Grain crop production (e.g. corn, rice) 32 36
T81 8019-8060 Sentence denotes Household animal raising for sale 13 15
T82 8061-8089 Sentence denotes Domestic animal farmer 1 1
T83 8090-8114 Sentence denotes Wild animal farmer 2 2
T84 8115-8134 Sentence denotes Health worker 2 2
T85 8135-8162 Sentence denotes Construction worker 10 11
T86 8163-8190 Sentence denotes Nature reserve worker 8 9
T87 8191-8252 Sentence denotes Small business (e.g. restaurant, grocery store owner) 16 18
T88 8253-8266 Sentence denotes Student 1 1
T89 8267-8283 Sentence denotes Mineworker 1 1
T90 8284-8341 Sentence denotes Other casual or out-migrating work (non-specific) 30 34
T91 8342-8402 Sentence denotes Has worked or work on multiple jobs to make a living 35 40

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
102 448-451 Gene denotes bat Gene:570
103 524-530 Species denotes humans Tax:9606
104 550-555 Species denotes human Tax:9606
105 208-227 Disease denotes infectious diseases MESH:D003141
109 914-917 Gene denotes bat Gene:570
110 1020-1032 Species denotes participants Tax:9606
111 1084-1096 Species denotes participants Tax:9606
113 1494-1499 Species denotes human Tax:9606
122 1727-1739 Species denotes Participants Tax:9606
123 1866-1872 Species denotes people Tax:9606
124 1997-2008 Species denotes participant Tax:9606
125 2020-2026 Species denotes people Tax:9606
126 2228-2240 Species denotes participants Tax:9606
127 2281-2292 Species denotes participant Tax:9606
128 2390-2402 Species denotes participants Tax:9606
129 2472-2484 Species denotes participants Tax:9606
131 2751-2763 Species denotes participants Tax:9606
139 3677-3682 Species denotes human Tax:9606
140 3724-3729 Species denotes human Tax:9606
141 3744-3749 Species denotes human Tax:9606
142 4084-4095 Species denotes participant Tax:9606
143 4125-4128 Chemical denotes oil MESH:D009821
144 3649-3657 Disease denotes zoonotic MESH:D015047
145 3809-3814 Disease denotes death MESH:D003643
149 4444-4456 Species denotes participants Tax:9606
150 4587-4592 Species denotes human Tax:9606
151 4617-4630 Species denotes environmental Tax:1275957
154 4798-4804 Species denotes people Tax:9606
155 5194-5206 Species denotes participants Tax:9606
159 6611-6616 Species denotes human Tax:9606
160 6635-6640 Species denotes human Tax:9606
161 6684-6689 Disease denotes death MESH:D003643
164 7640-7652 Species denotes Participants Tax:9606
165 8005-8009 Species denotes rice Tax:4530

2_test

Id Subject Object Predicate Lexical cue
32040190-23200502-48103168 228-230 23200502 denotes 16
32040190-28137858-48103169 338-340 28137858 denotes 18
32040190-29614074-48103170 571-573 29614074 denotes 21
32040190-19784865-48103171 7099-7101 19784865 denotes 27
32040190-29486714-48103172 7546-7548 29486714 denotes 29
T27139 228-230 23200502 denotes 16
T66879 338-340 28137858 denotes 18
T82467 571-573 29614074 denotes 21
T88965 7099-7101 19784865 denotes 27
T87475 7546-7548 29486714 denotes 29