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Merge pull request #22 from pathoplexus/use-host-field
fix: Update example data to use 'host' instead of 'hostTaxonId', 'hostName…
2 parents 6e6209c + dc4e405 commit a6b8985

8 files changed

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‎example_files/cchfv_test_metadata.tsv‎

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fastaIds ampliconPcrPrimerScheme ampliconSize anatomicalMaterial anatomicalPart authorAffiliations authors bodyProduct breadthOfCoverage cellLine collectionDevice collectionMethod consensusSequenceSoftwareName consensusSequenceSoftwareVersion cultureId dehostingMethod depthOfCoverage diagnostic_measurement_method diagnosticMeasurementUnit diagnosticMeasurementValue diagnosticTargetGeneName diagnosticTargetPresence environmentalMaterial environmentalSite experimentalSpecimenRoleType exposureDetails exposureEvent exposureSetting foodProduct foodProductProperties geoLocAdmin1 geoLocAdmin2 geoLocCity geoLocCountry geoLocSite hostAge hostAgeBin hostDisease hostGender hostHealthOutcome hostHealthState hostNameCommon hostNameScientific hostOriginCountry hostRole hostTaxonId hostVaccinationStatus passageMethod passageNumber presamplingActivity previousInfectionDisease previousInfectionOrganism purposeOfSampling purposeOfSequencing qualityControlDetails qualityControlDetermination qualityControlIssues qualityControlMethodName qualityControlMethodVersion rawSequenceDataProcessingMethod referenceGenomeAccession sampleCollectionDate sampleReceivedDate sampleType sequencedByContactEmail sequencedByContactName sequencedByOrganization sequencingAssayType sequencingDate sequencingInstrument sequencingProtocol signsAndSymptoms specimenCollectorSampleId specimenProcessing specimenProcessingDetails bioprojectAccessions id travelHistory versionComment
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test_NIHPAK-19_L test_NIHPAK-19_M test_NIHPAK-19_S "National Institute of Health, Department of Virology" "Ammar, M.; Salman, M.; Umair, M.; Ali, Q.; Hakim, R.; Haider, S.A.; Jamal, Z." Hogwarts Pakistan Homo sapiens 9606 2023-08-26 CCHF/NIHPAK-19/2023 test_NIHPAK-19 "OR964915.1,OR964926.1,OR964937.1"
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fastaIds ampliconPcrPrimerScheme ampliconSize anatomicalMaterial anatomicalPart authorAffiliations authors bodyProduct breadthOfCoverage cellLine collectionDevice collectionMethod consensusSequenceSoftwareName consensusSequenceSoftwareVersion cultureId dehostingMethod depthOfCoverage diagnostic_measurement_method diagnosticMeasurementUnit diagnosticMeasurementValue diagnosticTargetGeneName diagnosticTargetPresence environmentalMaterial environmentalSite experimentalSpecimenRoleType exposureDetails exposureEvent exposureSetting foodProduct foodProductProperties geoLocAdmin1 geoLocAdmin2 geoLocCity geoLocCountry geoLocSite hostAge hostAgeBin hostDisease hostGender hostHealthOutcome hostHealthState hostNameCommon hostOriginCountry hostRole host hostVaccinationStatus passageMethod passageNumber presamplingActivity previousInfectionDisease previousInfectionOrganism purposeOfSampling purposeOfSequencing qualityControlDetails qualityControlDetermination qualityControlIssues qualityControlMethodName qualityControlMethodVersion rawSequenceDataProcessingMethod referenceGenomeAccession sampleCollectionDate sampleReceivedDate sampleType sequencedByContactEmail sequencedByContactName sequencedByOrganization sequencingAssayType sequencingDate sequencingInstrument sequencingProtocol signsAndSymptoms specimenCollectorSampleId specimenProcessing specimenProcessingDetails bioprojectAccessions id travelHistory versionComment
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test_NIHPAK-19_L test_NIHPAK-19_M test_NIHPAK-19_S "National Institute of Health, Department of Virology" "Ammar, M.; Salman, M.; Umair, M.; Ali, Q.; Hakim, R.; Haider, S.A.; Jamal, Z." Hogwarts Pakistan 9606 2023-08-26 CCHF/NIHPAK-19/2023 test_NIHPAK-19 "OR964915.1,OR964926.1,OR964937.1"

‎example_files/dengue_test_metadata.tsv‎

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id geoLocCountry sampleCollectionDate authors authorAffiliations hostNameScientific collectionDevice collectionMethod cultureId depthOfCoverage geoLocAdmin1 geoLocAdmin2 sampleReceivedDate sequencingDate specimenProcessing sequencingInstrument sequencingProtocol specimenCollectorSampleId versionComment comment
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id geoLocCountry sampleCollectionDate authors authorAffiliations host collectionDevice collectionMethod cultureId depthOfCoverage geoLocAdmin1 geoLocAdmin2 sampleReceivedDate sequencingDate specimenProcessing sequencingInstrument sequencingProtocol specimenCollectorSampleId versionComment comment
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GU363549.1 China 2009-08-06 "Zhang, F. C.; Hu, F. Y.; Zhou, W. Z.; Wang, J.; Hong, W. X.; Liao, B. L.; Chen, W. L.; Lu, Y. C.; Tang, Y. B.; Wei, S. J." "Guangzhou No. 8 People's Hospital, Institute of Infectious Disease" Homo sapiens Guangzhou Hogwarts GZ1D3 Example data from Pathoplexus
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HM469966.1 Thailand 2007-07-27 "Lambrechts, L.; Quillery, E.; Noel, V.; Richardson, J. H.; Jarman, R. G.; Scott, T. W.; Chevillon, C." "Institut Pasteur, Virology" Homo sapiens Bangkok Hogwarts 01096-07 Example data from Pathoplexus
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JN697056.1 Malaysia 2005-01-01 "Chem, Y. K.; Chua, K. B.; Yasmin, A. M." "Natonal Public Health Laboratory, Microbiology" Homo sapiens Hogwarts DEN-1/Thailand/01096-07/2005 Example data from Pathoplexus
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EU081263.1 Singapore 2005 "Schreiber, M. J.; Holmes, E. C.; Ong, S. H.; Soh, H. S.; Liu, W.; Tanner, L.; Aw, P. P.; Tan, H. C.; Ng, L. C.; Leo, Y. S.; Low, J. G.; Ong, A.; Ooi, E. E.; Vasudevan, S. G.; Hibberd, M. L." "Novartis Institute for Tropical Diseases, Bioinformatics" Culicidae Hogwarts Samples pooled D1/SG/05K4174DK1/2005 Example data from Pathoplexus
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EU920848.1 French Guiana 2006-04 "Dussart, P.; Iteman, I.; Leduc, A.; Delannoy, A. S.; Tran, C.; Matheus, S.; Najioullah, F.; Soebhag-Ramlal, T.; Tjon Kon Fat, H.; Cesaire, R.; Caro, V.; Brisse, S.; Chevillon, C." "Institut Pasteur de la Guyane, Laboratoire de Virologie, Centre National de Reference des Arbovirus et Virus Influenza, Region Antilles Guyane" Aedes aegypti Hogwarts FGU-Apr2-06 Example data from Pathoplexus
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JN983813.1 Brazil 2010-09-08 "Naveca, F. G.; Souza, V. C.; Silva, G. A.; Maito, R. M.; Granja, F.; Siqueira, T.; Acosta, P. O.; Silva, G. A. V." "Instituto Leonidas e Maria Deane, Biodiversity Lab" Homo sapiens "Boa Vista, Roraima State" Hogwarts Br246RR_10 Example data from Pathoplexus
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KC294210.1 Peru 2011-03-23 "Williams, M.; Mayer, S. V.; Johnson, W. L.; Chen, R.; Volkova, E.; Vilcarromero, S.; Widen, S. G.; Wood, T. G.; Suarez-Ognio, L.; Long, K. C.; Hanley, K. A.; Morrison, A. C.; Vasilakis, N.; Halsey, E. S.; Wilden, S.; Wood, T." "U.S. NAMRU-6, Virology" Homo sapiens Iquitos Hogwarts DENV-2/PE/FPI1617/2011 Example data from Pathoplexus
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KC294210.1 Peru 2011-03-23 "Williams, M.; Mayer, S. V.; Johnson, W. L.; Chen, R.; Volkova, E.; Vilcarromero, S.; Widen, S. G.; Wood, T. G.; Suarez-Ognio, L.; Long, K. C.; Hanley, K. A.; Morrison, A. C.; Vasilakis, N.; Halsey, E. S.; Wilden, S.; Wood, T." "U.S. NAMRU-6, Virology" Homo sapiens Iquitos Hogwarts DENV-2/PE/FPI1617/2011 Example data from Pathoplexus

‎example_files/hmpv_metadata.xlsx‎

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