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added Samule Piquer addition of 1252 sams, new grammar
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paolinomanghi committed Jan 21, 2024
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79 changes: 79 additions & 0 deletions inst/curated/AverinaOV_2020/AverinaOV_2020_metadata.tsv
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91 changes: 91 additions & 0 deletions inst/curated/JacobsonDK_2021/JacobsonDK_2021_metadata.tsv
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study_name sample_id subject_id control control_ontology_term_id target_condition target_condition_ontology_term_id sequencing_platform DNA_extraction_kit PMID NCBI_accession curator body_site body_site_ontology_term_id disease disease_ontology_term_id disease_subtype age age_unit age_group age_group_ontology_term_id age_min age_max country sex sex_ontology_term_id location non_westernized antibiotics_current_use number_bases number_reads minimum_read_length median_read_length
MejiaR_2020 SRR11294813 SRR11294813 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294813 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 6 Year Children 2-11 Years Old NCIT:C49683 6 6 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 5837411756 38658356 151 151
MejiaR_2020 SRR11294815 SRR11294815 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294815 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 5 Year Children 2-11 Years Old NCIT:C49683 5 5 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 7497336183 49651233 151 151
MejiaR_2020 SRR11294816 SRR11294816 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294816 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 4 Year Children 2-11 Years Old NCIT:C49683 4 4 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 7311897009 48423159 151 151
MejiaR_2020 SRR11294818 SRR11294818 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294818 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 3922615184 25977584 151 151
MejiaR_2020 SRR11294826 SRR11294826 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294826 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 5048126451 33431301 151 151
MejiaR_2020 SRR11294834 SRR11294834 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294834 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 3 Year Children 2-11 Years Old NCIT:C49683 3 3 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 1841571085 12195835 151 151
MejiaR_2020 SRR11294835 SRR11294835 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294835 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 1798557678 11910978 151 151
MejiaR_2020 SRR11294836 SRR11294836 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294836 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 9244168509 61219659 151 151
MejiaR_2020 SRR11294838 SRR11294838 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294838 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 6 Year Children 2-11 Years Old NCIT:C49683 6 6 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 7955171052 52683252 151 151
MejiaR_2020 SRR11294842 SRR11294842 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294842 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 1848954834 12244734 151 151
MejiaR_2020 SRR11294844 SRR11294844 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294844 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia NCIT:C77213 Giardia duodenalis 3 Year Children 2-11 Years Old NCIT:C49683 3 3 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 3674868880 24336880 151 151
MejiaR_2020 SRR11294814 SRR11294814 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294814 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia;Helminth NCIT:C77213;NCIT:C125642 Giardia duodenalis 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 4542856442 30085142 151 151
MejiaR_2020 SRR11294817 SRR11294817 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294817 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia;Helminth NCIT:C77213;NCIT:C125642 Giardia duodenalis 8 Year Children 2-11 Years Old NCIT:C49683 8 8 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 6644609738 44004038 151 151
MejiaR_2020 SRR11294837 SRR11294837 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294837 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia;Helminth NCIT:C77213;NCIT:C125642 Giardia duodenalis 8 Year Children 2-11 Years Old NCIT:C49683 8 8 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 7285073822 48245522 151 151
MejiaR_2020 SRR11294840 SRR11294840 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294840 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia;Helminth NCIT:C77213;NCIT:C125642 Giardia duodenalis 3 Year Children 2-11 Years Old NCIT:C49683 3 3 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 2657395999 17598649 151 151
MejiaR_2020 SRR11294843 SRR11294843 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294843 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia;Helminth NCIT:C77213;NCIT:C125642 Giardia duodenalis 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 1839306991 12180841 151 151
MejiaR_2020 SRR11294848 SRR11294848 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294848 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia;Helminth NCIT:C77213;NCIT:C125642 Giardia duodenalis 4 Year Children 2-11 Years Old NCIT:C49683 4 4 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 4911863749 32528899 151 151
MejiaR_2020 SRR11294849 SRR11294849 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294849 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Giardia;Helminth NCIT:C77213;NCIT:C125642 Giardia duodenalis 8 Year Children 2-11 Years Old NCIT:C49683 8 8 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 8229250548 54498348 151 151
MejiaR_2020 SRR11294832 SRR11294832 Study Control NCIT:C142703 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294832 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Healthy NCIT:C115935 healthy 3 Year Children 2-11 Years Old NCIT:C49683 3 3 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 5442106289 36040439 151 151
MejiaR_2020 SRR11294833 SRR11294833 Study Control NCIT:C142703 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294833 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Healthy NCIT:C115935 healthy 6 Year Children 2-11 Years Old NCIT:C49683 6 6 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 1774519384 11751784 151 151
MejiaR_2020 SRR11294845 SRR11294845 Study Control NCIT:C142703 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294845 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Healthy NCIT:C115935 healthy 4 Year Children 2-11 Years Old NCIT:C49683 4 4 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 3077079963 20378013 151 151
MejiaR_2020 SRR11294846 SRR11294846 Study Control NCIT:C142703 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294846 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Healthy NCIT:C115935 healthy 3 Year Children 2-11 Years Old NCIT:C49683 3 3 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 2837850814 18793714 151 151
MejiaR_2020 SRR11294847 SRR11294847 Study Control NCIT:C142703 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294847 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Healthy NCIT:C115935 healthy 6 Year Children 2-11 Years Old NCIT:C49683 6 6 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 3474463794 23009694 151 151
MejiaR_2020 SRR11294819 SRR11294819 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294819 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 4586091967 33939222 35 150
MejiaR_2020 SRR11294820 SRR11294820 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294820 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 4035507775 29970136 35 150
MejiaR_2020 SRR11294821 SRR11294821 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294821 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 3868049156 28639714 35 150
MejiaR_2020 SRR11294822 SRR11294822 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294822 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 3856718651 28836688 35 150
MejiaR_2020 SRR11294823 SRR11294823 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294823 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 4 Year Children 2-11 Years Old NCIT:C49683 4 4 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 3862636649 29307400 35 149
MejiaR_2020 SRR11294824 SRR11294824 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294824 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 3 Year Children 2-11 Years Old NCIT:C49683 3 3 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 5842551809 45469476 35 149
MejiaR_2020 SRR11294825 SRR11294825 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294825 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 5 Year Children 2-11 Years Old NCIT:C49683 5 5 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 3616321686 27663926 35 150
MejiaR_2020 SRR11294827 SRR11294827 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294827 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 4 Year Children 2-11 Years Old NCIT:C49683 4 4 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 2502486578 18604506 35 150
MejiaR_2020 SRR11294828 SRR11294828 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294828 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 7 Year Children 2-11 Years Old NCIT:C49683 7 7 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 1569408706 11809088 35 150
MejiaR_2020 SRR11294829 SRR11294829 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294829 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 4 Year Children 2-11 Years Old NCIT:C49683 4 4 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 6388629252 51227354 35 140
MejiaR_2020 SRR11294830 SRR11294830 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294830 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 3 Year Children 2-11 Years Old NCIT:C49683 3 3 ARG Male NCIT:C20197 periurban locale at Orán department, Salta Province, Argentina yes No 4562418335 34448790 35 150
MejiaR_2020 SRR11294831 SRR11294831 Case NCIT:C49152 human gut microbiome;Helminth;Giardia OHMI:0000020;NCIT:C125642;NCIT:C77213 IlluminaNextSeq MPBio 32306993 SRR11294831 Samuel_Piquer-Esteban;Paolo_Manghi feces UBERON:0001988 Helminth NCIT:C125642 3 Year Children 2-11 Years Old NCIT:C49683 3 3 ARG Female NCIT:C16576 periurban locale at Orán department, Salta Province, Argentina yes No 3149252822 24447978 35 150
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