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Merge pull request #254 from LabKey/fb_merge_25.3_to_develop
Merge discvr-25.3 to develop
2 parents bfa60f8 + 88dd5a6 commit 5c625e5

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‎IDR/resources/queries/bimber_data/idrAnchorDateSource.sql‎

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SELECT
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Rh as subjectId,
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PID0 as date,
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'SIV Infection' as eventLabel,
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'Hansen/IDR' as dataSource
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FROM bimber_data.subjects
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WHERE PID0 IS NOT NULL
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UNION ALL
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SELECT
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Rh as subjectId,
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D0 as date,
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'Vaccination Start' as eventLabel,
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'Hansen/IDR' as dataSource
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FROM bimber_data.subjects
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WHERE D0 IS NOT NULL

‎IDR/resources/queries/bimber_data/idrOutcomeSource.sql‎

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SELECT
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Rh as Id,
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cohortStart as date,
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CASE
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WHEN contprog = 'C' THEN 'Controller'
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WHEN contprog = 'P' THEN 'Progressor'
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END as outcome,
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'Hansen/IDR' as dataSource
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FROM bimber_data.subjects
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WHERE contprog IS NOT NULL AND contprog != ''

‎IDR/resources/queries/bimber_data/idrPvlSource.sql‎

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SELECT
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i_rh as Id,
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d_PVLDate as date,
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c_PVL as result,
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'Copies/mL' as units,
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'Plasma' as sampleType,
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'SIVmac239' as assayType,
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'SIV' as target,
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'Hansen/IDR' as dataSource
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FROM bimber_data.pvl
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WHERE c_PVL != 'missing from box'

‎IDR/resources/queries/bimber_data/idrSampleSource.sql‎

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SELECT
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MonkeyId as Id,
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ID as sampleid,
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SampleDate as date,
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Tissue as sampleType,
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CellCnt as quantity,
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'Hansen/IDR' as dataSource
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FROM bimber_data.ln_loc
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WHERE SampleDate IS NOT NULL
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UNION ALL
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SELECT
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Rh as Id,
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ID as sampleid,
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SampleDate as date,
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Tissue as sampleType,
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null as quantity,
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'Hansen/IDR' as dataSource
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FROM bimber_data.ult_loc
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WHERE SampleDate IS NOT NULL

‎SivStudies/resources/data/gender_codes.tsv‎

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v meaning origgender
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value meaning origgender
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f Female f
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m Male m
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u Unknown

‎SivStudies/resources/data/labwork_types.tsv‎

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value title units sort_order category
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GLUC Glucose mg/dL 1 Chemistry
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BUN Blood urea nitrogen mg/dL 2 Chemistry
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CREAT Creatinine mg/dL 3 Chemistry
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CPK Creatine phosphokinase U/L 4 Chemistry
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CHOL Cholesterol mg/dl 5 Chemistry
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TRIG Triglyceride mg/dL 6 Chemistry
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SGOT Serum glutamic oxaloacetic transaminase IU/L 7 Chemistry
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LDL Low-Density Lipoprotein mg/dL 8 Chemistry
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LDH Lactate dehydrogenase IU/L 9 Chemistry
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TB Total Bilirubin mg/dL 10 Chemistry
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GGT Gamma-glutamyltransferase IU/L 11 Chemistry
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SGPT Serum glutamic pyruvic transaminase IU/L 12 Chemistry
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TP Total Protein g/dL 13 Chemistry
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ALB Albumin g/dL 14 Chemistry
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ALKP Alkaline Phosphatase IU/L 15 Chemistry
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CA Calcium mg/dL 16 Chemistry
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PHOS Phosphorus mg/dL 17 Chemistry
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FE Iron ?g/dL 18 Chemistry
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K Potassium mmol/L 20 Chemistry
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UA Uric Acid mg/dL 22 Chemistry
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A/P Albumin/Protein Ratio ratio 999 Chemistry
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B/C BUN/Creatinine Ratio ratio 999 Chemistry
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CL Chloride mEq/L 999 Chemistry
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FIBR Fibrinogen mg/dL 999 Chemistry
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HDL High-Density Lipoprotein mg/dL 999 Chemistry
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WBC White Blood Cells 10^3/uL 1 Hematology
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NEUT% Neutrophils % 2 Hematology
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BAND% Bands 3 Hematology
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LYMPH% Lymphocytes % 4 Hematology
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MONO% Monocytes % 5 Hematology
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EOS% Eosinophils % 6 Hematology
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BASO% Basophils % 7 Hematology
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HCT Hematocrit % 8 Hematology
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HGB Hemoglobin 9 Hematology
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RBC Red Blood Cells 10^6/uL 10 Hematology
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MCV Mean corpuscular volume fL 11 Hematology
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MCH Mean corpuscular hemoglobin picograms 12 Hematology
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MCHC Mean corpuscular hemoglobin concentration g/dL 13 Hematology
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RETIC Reticulocytes % 14 Hematology
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PLT Platelets 10^3/uL 15 Hematology
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MYELO Myelocytes % 999 Hematology
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MPV Mean platelet volume fl 999 Hematology
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Anisocytosis Anisocytosis 999 Hematology
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GLOB Globulin g/dL 999 Hematology
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Hypochromic RBC Hypochromic RBC 999 Hematology
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LUC Large unstained cells 999 Hematology
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Macrocytic RBC Macrocytic RBC 999 Hematology
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METAMYELO Metamyelocytes % 999 Hematology
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Microcytic RBC Microcytic RBC 999 Hematology
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NRBC Nucleated red blood cells 999 Hematology
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PCV Packed cell volume % 999 Hematology
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Polychromasia RBC Polychromasia RBC 999 Hematology
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MPMN Neutrophils 999 Hematology
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SEDRate Sedimentation rate 999 Hematology
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RDW % 999 Hematology
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NEUT# Neutrophil # 10^3/uL 16 Hematology
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LYMPH# Lymphocyte # 10^3/uL 17 Hematology
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MONO# Monocyte # 10^3/uL 18 Hematology
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EOS# Eosinophil # 10^3/uL 19 Hematology
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BASO# Basophil # 10^3/uL 20 Hematology

‎SivStudies/resources/data/lookup_sets.tsv‎

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@@ -6,4 +6,6 @@ dosage_units Dosage Units unit
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gender_codes Gender Codes
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geographic_origins Geographic Origins origin
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routes Routes route
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volume_units Volume Units unit
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volume_units Volume Units unit
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labwork_types Lab Tests test title
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vl_sample_types Lab Tests test

‎SivStudies/resources/data/reports.tsv‎

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reportname category reporttype reporttitle visible containerpath schemaname queryname viewname report datefieldname todayonly queryhaslocation sort_order QCStateLabelFieldName description
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activeAssignments Assignments and Groups query Active Assignments true study Assignment Active Assignments date false false qcstate/publicdata This report shows the active assignments for each animal
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assignmentHistory Assignments and Groups query Assignment History true study Assignment date false false qcstate/publicdata This report shows all assignments records for the animals
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activeGroups Assignments and Groups query Active Groups true study animal_group_members Active Members date false false qcstate/publicdata This report shows the active assignments for each animal
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groupHistory Assignments and Groups query Group History true study animal_group_members date false false qcstate/publicdata This report shows all assignments records for the animals
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microbiology Lab Results query Microbiology true study Microbiology Results date false false qcstate/publicdata
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biochemistry Lab Results js Biochemistry true study bloodChemistry date false false Contains results of chemistry panels. Can be displayed either by panel, or showing reference ranges
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clinPathRuns Lab Results query Lab Runs true study Clinpath Runs date false false qcstate/publicdata Contains all clinpath requests
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iStat Lab Results js iStat true study iStat date false false qcstate/publicdata Contains iStat results
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hematology Lab Results js Hematology true study hematology date false false Contains hematology data showing cell subsets
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parasitology Lab Results query Parasitology true study Parasitology Results date false false qcstate/publicdata Contains results of parasitology testing
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urinalysis Lab Results js Urinalysis true study urinalysisResults date false false Contains urinalysis results
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reporttype category schemaname queryname viewname reporttitle subjectfieldname
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query General study additionalDatatypes Additional Data
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query Clinical study weight Weights
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query Clinical study treatments Treatments/Medications
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query Clinical study chemistryPivot Blood Chemistry
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query Clinical study hematologyPivot CBC/Hematology
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query Study Design study assignment Project/Study Assignment
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query Research study flow Flow Cytometry
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query Research study outcomes Study Outcomes/Phenotypes
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query Research study genetics Genetic Data / MHC
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query Clinical study procedures Procedures
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query Research study viralLoads Viral Loads
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query General study samples Samples
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query Research study immunizations Immunizations
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query General study flags Flags/Misc Information
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query General study demographics Demographics
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query General study demographics Project Summary Project Summary
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query General study demographics MHC Type MHC Typing
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query General study demographics Expanded Expanded Information
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query Study Design studies timepointToDate Timepoints subjectId
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query Study Design studies subjectAnchorDates Anchor Dates subjectId

‎SivStudies/resources/data/species.tsv‎

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common scientific_name id_prefix mhc_prefix blood_per_kg max_draw_pct blood_draw_interval cites_code dateDisabled
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common_name scientific_name id_prefix mhc_prefix blood_per_kg max_draw_pct blood_draw_interval cites_code dateDisabled
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Baboon 60 0.2 30
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Cotton-top Tamarin Saguinus oedipus so Saoe 60 0.2 30
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Cynomolgus Macaca fascicularis cy Mafa 60 0.2 30

‎SivStudies/resources/data/vl_sample_types.tsv‎

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value
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Plasma
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Cells

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