From fead81f6237b8c53bde6b798c8867a24bd4cd86b Mon Sep 17 00:00:00 2001 From: bedroesb Date: Mon, 13 May 2024 13:16:35 +0000 Subject: [PATCH] Update ENA Sample Checklists --- .../ENA_template_samples_ERC000055.xml | 1135 +++++++++++ .../ENA_template_samples_ERC000056.xml | 1796 +++++++++++++++++ .../ENA_template_samples_ERC000057.xml | 746 +++++++ .../ENA_template_samples_ERC000058.xml | 1009 +++++++++ 4 files changed, 4686 insertions(+) create mode 100644 ena_upload/templates/ENA_template_samples_ERC000055.xml create mode 100644 ena_upload/templates/ENA_template_samples_ERC000056.xml create mode 100644 ena_upload/templates/ENA_template_samples_ERC000057.xml create mode 100644 ena_upload/templates/ENA_template_samples_ERC000058.xml diff --git a/ena_upload/templates/ENA_template_samples_ERC000055.xml b/ena_upload/templates/ENA_template_samples_ERC000055.xml new file mode 100644 index 0000000..b008d16 --- /dev/null +++ b/ena_upload/templates/ENA_template_samples_ERC000055.xml @@ -0,0 +1,1135 @@ + + + + + + + ${row.title} + + + + ${row.taxon_id} + + ${row.scientific_name} + + ${row.common_name} + + + + ${row.sample_description} + + + + + biotic relationship [deprecated] + ${row['biotic relationship [deprecated]']} + + + + + trophic level + ${row['trophic level']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + propagation + ${row['propagation']} + + + + + observed host symbionts + ${row['observed host symbionts']} + + + + + sample collection device + ${row['sample collection device']} + + + + + sample collection method + ${row['sample collection method']} + + + + + sample storage temperature + ${row['sample storage temperature']} + °C + + + + + sample storage location + ${row['sample storage location']} + + + + + size-fraction lower threshold + ${row['size-fraction lower threshold']} + µm + + + + + size-fraction upper threshold + ${row['size-fraction upper threshold']} + µm + + + + + soil_taxonomic/FAO classification + ${row['soil_taxonomic/FAO classification']} + + + + + soil_taxonomic/local classification + ${row['soil_taxonomic/local classification']} + + + + + soil_taxonomic/local classification method + ${row['soil_taxonomic/local classification method']} + + + + + soil type + ${row['soil type']} + + + + + soil type method + ${row['soil type method']} + + + + + soil texture measurement + ${row['soil texture measurement']} + % sand/silt/clay + + + + + soil texture method + ${row['soil texture method']} + + + + + soil pH + ${row['soil pH']} + + + + + soil cover + ${row['soil cover']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + microbial biomass + ${row['microbial biomass']} + g/kg + + + + + project name + ${row['project name']} + + + + + farm equipment sanitization + ${row['farm equipment sanitization']} + + + + + equipment shared with other farms + ${row['equipment shared with other farms']} + + + + + farm equipment used + ${row['farm equipment used']} + + + + + farm watering water source + ${row['farm watering water source']} + + + + + food production system characteristics + ${row['food production system characteristics']} + + + + + animal water delivery method + ${row['animal water delivery method']} + + + + + plant water delivery method + ${row['plant water delivery method']} + + + + + food harvesting process + ${row['food harvesting process']} + + + + + food production characteristics + ${row['food production characteristics']} + °C + + + + + fertilizer administration date + ${row['fertilizer administration date']} + + + + + crop yield + ${row['crop yield']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check software + ${row['chimera check software']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + 16s recovered + ${row['16s recovered']} + + + + + 16S recovery software + ${row['16S recovery software']} + + + + + collection date + ${row['collection date']} + + + + + altitude + ${row['altitude']} + m + + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + DD + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + DD + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + broad-scale environmental context + ${row['broad-scale environmental context']} + + + + + local environmental context + ${row['local environmental context']} + + + + + environmental medium + ${row['environmental medium']} + + + + + elevation + ${row['elevation']} + m + + + + + culture isolation date + ${row['culture isolation date']} + + + + + sieving + ${row['sieving']} + + + + + microbial biomass method + ${row['microbial biomass method']} + + + + + organism count + ${row['organism count']} + + + + + horizon method + ${row['horizon method']} + + + + + extreme_unusual_properties/heavy metals + ${row['extreme_unusual_properties/heavy metals']} + + + + + extreme_unusual_properties/heavy metals method + ${row['extreme_unusual_properties/heavy metals method']} + + + + + plant structure + ${row['plant structure']} + + + + + host disease status + ${row['host disease status']} + + + + + host common name + ${row['host common name']} + + + + + host age + ${row['host age']} + years + + + + + host taxid + ${row['host taxid']} + + + + + host life stage + ${row['host life stage']} + + + + + host height + ${row['host height']} + mm + + + + + host length + ${row['host length']} + mm + + + + + host total mass + ${row['host total mass']} + kg + + + + + host phenotype + ${row['host phenotype']} + + + + + host scientific name + ${row['host scientific name']} + + + + + host subspecific genetic lineage + ${row['host subspecific genetic lineage']} + + + + + link to climate information + ${row['link to climate information']} + + + + + link to classification information + ${row['link to classification information']} + + + + + climate environment + ${row['climate environment']} + + + + + presence of pets, animals, or insects + ${row['presence of pets, animals, or insects']} + + + + + current vegetation + ${row['current vegetation']} + + + + + gaseous environment + ${row['gaseous environment']} + + + + + humidity + ${row['humidity']} + g/m3 + + + + + current vegetation method + ${row['current vegetation method']} + + + + + seasonal environment + ${row['seasonal environment']} + + + + + soil horizon + ${row['soil horizon']} + + + + + solar irradiance + ${row['solar irradiance']} + W/m2 + + + + + drainage classification + ${row['drainage classification']} + + + + + temperature + ${row['temperature']} + ºC + + + + + pH method + ${row['pH method']} + + + + + slope gradient + ${row['slope gradient']} + % + + + + + slope aspect + ${row['slope aspect']} + + + + + profile position + ${row['profile position']} + + + + + total organic carbon method + ${row['total organic carbon method']} + + + + + total nitrogen content method + ${row['total nitrogen content method']} + + + + + total phosphate + ${row['total phosphate']} + µmol/L + + + + + total nitrogen concentration + ${row['total nitrogen concentration']} + µmol/L + + + + + total carbon + ${row['total carbon']} + µg/L + + + + + total organic carbon + ${row['total organic carbon']} + g/kg + + + + + water pH + ${row['water pH']} + + + + + photosynthetic activity method + ${row['photosynthetic activity method']} + + + + + photosynthetic activity + ${row['photosynthetic activity']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + history/previous land use + ${row['history/previous land use']} + + + + + previous land use method + ${row['previous land use method']} + + + + + history/crop rotation + ${row['history/crop rotation']} + + + + + history/agrochemical additions + ${row['history/agrochemical additions']} + + + + + history/tillage + ${row['history/tillage']} + + + + + history/fire + ${row['history/fire']} + + + + + history/flooding + ${row['history/flooding']} + + + + + history/extreme events + ${row['history/extreme events']} + + + + + mean seasonal humidity + ${row['mean seasonal humidity']} + g/m3 + + + + + mean seasonal temperature + ${row['mean seasonal temperature']} + °C + + + + + mean seasonal precipitation + ${row['mean seasonal precipitation']} + mm + + + + + season + ${row['season']} + + + + + mean annual precipitation + ${row['mean annual precipitation']} + mm + + + + + mean annual temperature + ${row['mean annual temperature']} + ºC + + + + + host genotype + ${row['host genotype']} + + + + + host specificity or range + ${row['host specificity or range']} + + + + + host dry mass + ${row['host dry mass']} + mg + + + + + spike-in microbial strain + ${row['spike-in microbial strain']} + + + + + perturbation + ${row['perturbation']} + + + + + negative control type + ${row['negative control type']} + + + + + positive control type + ${row['positive control type']} + + + + + experimental factor + ${row['experimental factor']} + + + + + encoded traits + ${row['encoded traits']} + + + + + genetic modification + ${row['genetic modification']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + ancestral data + ${row['ancestral data']} + + + + + taxonomic classification + ${row['taxonomic classification']} + + + + + plant growth medium + ${row['plant growth medium']} + + + + + rooting medium macronutrients + ${row['rooting medium macronutrients']} + + + + + rooting medium carbon + ${row['rooting medium carbon']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + annotation source + ${row['annotation source']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + sequencing location + ${row['sequencing location']} + + + + + enrichment protocol + ${row['enrichment protocol']} + + + + + library preparation kit + ${row['library preparation kit']} + % + + + + + sample pooling + ${row['sample pooling']} + + + + + lot number + ${row['lot number']} + % + + + + + single cell or viral particle lysis approach + ${row['single cell or viral particle lysis approach']} + + + + + single cell or viral particle lysis kit protocol + ${row['single cell or viral particle lysis kit protocol']} + + + + + pooled DNA extract total + ${row['pooled DNA extract total']} + + + + + sample material processing + ${row['sample material processing']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + ng + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library construction method + ${row['library construction method']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + + pcr primers + ${row['pcr primers']} + + + + + adapters + ${row['adapters']} + + + + + food shipping transportation vehicle + ${row['food shipping transportation vehicle']} + + + + + water source shared + ${row['water source shared']} + + + + + food source + ${row['food source']} + + + + + food shipping transportation method + ${row['food shipping transportation method']} + + + + + food product type + ${row['food product type']} + + + + + relative location of sample + ${row['relative location of sample']} + + + + + porosity + ${row['porosity']} + + + + + depth + ${row['depth']} + mm + + + + + environment adjacent to site + ${row['environment adjacent to site']} + + + + + fungicide regimen + ${row['fungicide regimen']} + + + + + herbicide regimen + ${row['herbicide regimen']} + + + + + non-mineral nutrient regimen + ${row['non-mineral nutrient regimen']} + + + + + pesticide regimen + ${row['pesticide regimen']} + + + + + pH regimen + ${row['pH regimen']} + + + + + salt regimen + ${row['salt regimen']} + + + + + standing water regimen + ${row['standing water regimen']} + + + + + watering regimen + ${row['watering regimen']} + + + + + water temperature regimen + ${row['water temperature regimen']} + + + + + chemical administration + ${row['chemical administration']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/ena_upload/templates/ENA_template_samples_ERC000056.xml b/ena_upload/templates/ENA_template_samples_ERC000056.xml new file mode 100644 index 0000000..bc6dc8e --- /dev/null +++ b/ena_upload/templates/ENA_template_samples_ERC000056.xml @@ -0,0 +1,1796 @@ + + + + + + + ${row.title} + + + + ${row.taxon_id} + + ${row.scientific_name} + + ${row.common_name} + + + + ${row.sample_description} + + + + + culture result + ${row['culture result']} + + + + + culture result organism + ${row['culture result organism']} + m2 + + + + + culture target microbial analyte + ${row['culture target microbial analyte']} + + + + + biological sample replicate + ${row['biological sample replicate']} + year + + + + + technical sample replicate + ${row['technical sample replicate']} + + + + + purpose of sampling + ${row['purpose of sampling']} + + + + + trophic level + ${row['trophic level']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + propagation + ${row['propagation']} + + + + + sample transportation temperature + ${row['sample transportation temperature']} + °C + + + + + sample transport container + ${row['sample transport container']} + J/°C + + + + + sample transport duration + ${row['sample transport duration']} + year + + + + + sample collection device + ${row['sample collection device']} + + + + + sample collection method + ${row['sample collection method']} + + + + + sample storage temperature + ${row['sample storage temperature']} + °C + + + + + sample storage device + ${row['sample storage device']} + + + + + sample storage location + ${row['sample storage location']} + + + + + size-fraction lower threshold + ${row['size-fraction lower threshold']} + µm + + + + + size-fraction upper threshold + ${row['size-fraction upper threshold']} + µm + + + + + soil type + ${row['soil type']} + + + + + soil type method + ${row['soil type method']} + + + + + soil texture method + ${row['soil texture method']} + + + + + soil pH + ${row['soil pH']} + + + + + soil cover + ${row['soil cover']} + + + + + soil texture classification + ${row['soil texture classification']} + °C + + + + + soil sediment porosity + ${row['soil sediment porosity']} + + + + + soil conductivity + ${row['soil conductivity']} + + + + + facility type + ${row['facility type']} + + + + + collection site geographic feature + ${row['collection site geographic feature']} + m2 + + + + + area sampled size + ${row['area sampled size']} + ml + + + + + sample name + ${row['sample name']} + + + + + study design + ${row['study design']} + kg s−3 + + + + + project name + ${row['project name']} + + + + + farm equipment sanitization + ${row['farm equipment sanitization']} + + + + + equipment shared with other farms + ${row['equipment shared with other farms']} + + + + + farm equipment used + ${row['farm equipment used']} + + + + + farm equipment sanitization frequency + ${row['farm equipment sanitization frequency']} + m2 + + + + + farm watering water source + ${row['farm watering water source']} + + + + + food production system characteristics + ${row['food production system characteristics']} + + + + + animal water delivery method + ${row['animal water delivery method']} + + + + + plant water delivery method + ${row['plant water delivery method']} + + + + + food harvesting process + ${row['food harvesting process']} + + + + + food animal source diet + ${row['food animal source diet']} + + + + + food production characteristics + ${row['food production characteristics']} + °C + + + + + food animal group size + ${row['food animal group size']} + year + + + + + fertilizer administration date + ${row['fertilizer administration date']} + + + + + animal feeding equipment + ${row['animal feeding equipment']} + + + + + crop yield + ${row['crop yield']} + + + + + water delivery frequency + ${row['water delivery frequency']} + + + + + animal housing system + ${row['animal housing system']} + + + + + environmental feature adjacent water source + ${row['environmental feature adjacent water source']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check software + ${row['chimera check software']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + 16s recovered + ${row['16s recovered']} + + + + + 16S recovery software + ${row['16S recovery software']} + + + + + completeness score + ${row['completeness score']} + % + + + + + completeness software + ${row['completeness software']} + + + + + completeness approach + ${row['completeness approach']} + + + + + assembly quality + ${row['assembly quality']} + + + + + assembly name + ${row['assembly name']} + + + + + collection date + ${row['collection date']} + + + + + altitude + ${row['altitude']} + m + + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + DD + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + DD + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + broad-scale environmental context + ${row['broad-scale environmental context']} + + + + + local environmental context + ${row['local environmental context']} + + + + + environmental medium + ${row['environmental medium']} + + + + + elevation + ${row['elevation']} + m + + + + + culture isolation date + ${row['culture isolation date']} + + + + + time course duration + ${row['time course duration']} + year + + + + + number of samples collected + ${row['number of samples collected']} + + + + + surface material + ${row['surface material']} + + + + + ventilation rate + ${row['ventilation rate']} + m3/min + + + + + indoor surface + ${row['indoor surface']} + + + + + ventilation type + ${row['ventilation type']} + + + + + sampling room sterilization method + ${row['sampling room sterilization method']} + + + + + sampling floor + ${row['sampling floor']} + °C + + + + + average daily occupancy + ${row['average daily occupancy']} + °C + + + + + sample surface moisture + ${row['sample surface moisture']} + year + + + + + sampling room id or name + ${row['sampling room id or name']} + year + + + + + fermentation relative humidity + ${row['fermentation relative humidity']} + g/m3 + + + + + room dimensions + ${row['room dimensions']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + m3 + + + + + organism count + ${row['organism count']} + + + + + sampling time point + ${row['sampling time point']} + + + + + growth habit + ${row['growth habit']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + sequencing kit + ${row['sequencing kit']} + + + + + host disease status + ${row['host disease status']} + + + + + host age + ${row['host age']} + years + + + + + host taxid + ${row['host taxid']} + + + + + host height + ${row['host height']} + mm + + + + + host length + ${row['host length']} + mm + + + + + host total mass + ${row['host total mass']} + kg + + + + + host phenotype + ${row['host phenotype']} + + + + + host scientific name + ${row['host scientific name']} + + + + + host subspecific genetic lineage + ${row['host subspecific genetic lineage']} + + + + + serovar or serotype + ${row['serovar or serotype']} + + + + + humidity + ${row['humidity']} + g/m3 + + + + + conductivity + ${row['conductivity']} + mS/cm + + + + + solar irradiance + ${row['solar irradiance']} + W/m2 + + + + + wind direction + ${row['wind direction']} + + + + + wind speed + ${row['wind speed']} + m/s + + + + + temperature + ${row['temperature']} + ºC + + + + + turbidity + ${row['turbidity']} + NTU + + + + + pH + ${row['pH']} + + + + + pH method + ${row['pH method']} + + + + + fermentation vessel + ${row['fermentation vessel']} + + + + + fermentation headspace oxygen + ${row['fermentation headspace oxygen']} + m2 + + + + + frequency of cleaning + ${row['frequency of cleaning']} + year + + + + + total organic carbon method + ${row['total organic carbon method']} + + + + + air particulate matter concentration + ${row['air particulate matter concentration']} + µg/m3 + + + + + total nitrogen content method + ${row['total nitrogen content method']} + + + + + total nitrogen concentration + ${row['total nitrogen concentration']} + µmol/L + + + + + salinity + ${row['salinity']} + psu + + + + + total carbon + ${row['total carbon']} + µg/L + + + + + total organic carbon + ${row['total organic carbon']} + g/kg + + + + + total nitrogen content + ${row['total nitrogen content']} + µmol/L + + + + + water pH + ${row['water pH']} + + + + + fermentation ph + ${row['fermentation ph']} + + + + + bacteria density + ${row['bacteria density']} + g/m3 + + + + + salinity method + ${row['salinity method']} + + + + + bio_material + ${row['bio_material']} + + + + + source material identifiers + ${row['source material identifiers']} + + + + + sample source material category + ${row['sample source material category']} + + + + + history/previous land use + ${row['history/previous land use']} + + + + + history/crop rotation + ${row['history/crop rotation']} + + + + + history/tillage + ${row['history/tillage']} + + + + + mean seasonal humidity + ${row['mean seasonal humidity']} + g/m3 + + + + + mean seasonal temperature + ${row['mean seasonal temperature']} + °C + + + + + mean seasonal precipitation + ${row['mean seasonal precipitation']} + mm + + + + + extreme weather date + ${row['extreme weather date']} + J/°C + + + + + extreme weather event + ${row['extreme weather event']} + m + + + + + season + ${row['season']} + + + + + host genotype + ${row['host genotype']} + + + + + host specificity or range + ${row['host specificity or range']} + + + + + host dry mass + ${row['host dry mass']} + mg + + + + + host prediction approach + ${row['host prediction approach']} + + + + + host prediction estimated accuracy + ${row['host prediction estimated accuracy']} + + + + + spike-in microbial strain + ${row['spike-in microbial strain']} + + + + + fermentation chemical additives + ${row['fermentation chemical additives']} + J/°C + + + + + fermentation chemical additives percentage + ${row['fermentation chemical additives percentage']} + % + + + + + study treatment + ${row['study treatment']} + % + + + + + spike-in organism + ${row['spike-in organism']} + g/m3 + + + + + spike-in organism count + ${row['spike-in organism count']} + mm + + + + + fermentation temperature + ${row['fermentation temperature']} + °C + + + + + spike-in with heavy metals + ${row['spike-in with heavy metals']} + year + + + + + microbial starter inoculation + ${row['microbial starter inoculation']} + m3/day + + + + + microbial starter source + ${row['microbial starter source']} + year + + + + + microbial starter preparation + ${row['microbial starter preparation']} + year + + + + + spike-in bacterial serovar or serotype + ${row['spike-in bacterial serovar or serotype']} + year + + + + + antimicrobial phenotype of spike-in bacteria + ${row['antimicrobial phenotype of spike-in bacteria']} + + + + + fermentation time + ${row['fermentation time']} + year + + + + + microbial starter organism count + ${row['microbial starter organism count']} + m2 + + + + + spike-in with antibiotics + ${row['spike-in with antibiotics']} + m2 + + + + + study incubation temperature + ${row['study incubation temperature']} + °C + + + + + perturbation + ${row['perturbation']} + + + + + study incubation duration + ${row['study incubation duration']} + year + + + + + biocide + ${row['biocide']} + °C + + + + + negative control type + ${row['negative control type']} + + + + + positive control type + ${row['positive control type']} + + + + + experimental factor + ${row['experimental factor']} + + + + + encoded traits + ${row['encoded traits']} + + + + + genetic modification + ${row['genetic modification']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + ancestral data + ${row['ancestral data']} + + + + + taxonomic classification + ${row['taxonomic classification']} + + + + + plant growth medium + ${row['plant growth medium']} + + + + + rooting conditions + ${row['rooting conditions']} + + + + + rooting medium macronutrients + ${row['rooting medium macronutrients']} + + + + + rooting medium micronutrients + ${row['rooting medium micronutrients']} + + + + + rooting medium carbon + ${row['rooting medium carbon']} + + + + + rooting medium pH + ${row['rooting medium pH']} + + + + + microbiological culture medium + ${row['microbiological culture medium']} + Pa + + + + + spike-in growth medium + ${row['spike-in growth medium']} + W/m2 + + + + + fermentation medium + ${row['fermentation medium']} + m + + + + + growth medium + ${row['growth medium']} + year + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + annotation source + ${row['annotation source']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + sequencing location + ${row['sequencing location']} + + + + + enrichment protocol + ${row['enrichment protocol']} + + + + + library preparation kit + ${row['library preparation kit']} + % + + + + + nucleic acid extraction kit + ${row['nucleic acid extraction kit']} + ppm + + + + + sample pooling + ${row['sample pooling']} + + + + + lot number + ${row['lot number']} + % + + + + + single cell or viral particle lysis approach + ${row['single cell or viral particle lysis approach']} + + + + + single cell or viral particle lysis kit protocol + ${row['single cell or viral particle lysis kit protocol']} + + + + + pooled DNA extract total + ${row['pooled DNA extract total']} + + + + + sample material processing + ${row['sample material processing']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + ng + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + + assembly software + ${row['assembly software']} + + + + + pcr primers + ${row['pcr primers']} + + + + + adapters + ${row['adapters']} + + + + + food animal antimicrobial + ${row['food animal antimicrobial']} + + + + + food shipping transportation vehicle + ${row['food shipping transportation vehicle']} + + + + + water source shared + ${row['water source shared']} + + + + + food source + ${row['food source']} + + + + + food shipping transportation method + ${row['food shipping transportation method']} + + + + + material of contact prior to food packaging + ${row['material of contact prior to food packaging']} + + + + + food product name legal status + ${row['food product name legal status']} + + + + + food quality date + ${row['food quality date']} + + + + + food cleaning process + ${row['food cleaning process']} + m + + + + + hygienic food production area + ${row['hygienic food production area']} + kg s−3 + + + + + food contact surface + ${row['food contact surface']} + J/°C + + + + + food cooking process + ${row['food cooking process']} + % + + + + + food product by quality + ${row['food product by quality']} + year + + + + + food animal antimicrobial route of administration + ${row['food animal antimicrobial route of administration']} + m2 + + + + + food allergen labeling + ${row['food allergen labeling']} + W/m2 + + + + + food product type + ${row['food product type']} + + + + + food animal source sex category + ${row['food animal source sex category']} + °C + + + + + animal intrusion near sample source + ${row['animal intrusion near sample source']} + °C + + + + + food packing medium integrity + ${row['food packing medium integrity']} + °C + + + + + microbial starter + ${row['microbial starter']} + °C + + + + + food treatment process + ${row['food treatment process']} + + + + + food preservation process + ${row['food preservation process']} + J/°C + + + + + microbial starter ncbi taxonomy id + ${row['microbial starter ncbi taxonomy id']} + + + + + interagency food safety analytics collaboration (ifsac) category + ${row['interagency food safety analytics collaboration (ifsac) category']} + + + + + food animal body condition + ${row['food animal body condition']} + + + + + food product synonym + ${row['food product synonym']} + + + + + food ingredient + ${row['food ingredient']} + year + + + + + food stored by consumer (storage duration) + ${row['food stored by consumer (storage duration)']} + year + + + + + food animal antimicrobial duration + ${row['food animal antimicrobial duration']} + year + + + + + part of plant or animal + ${row['part of plant or animal']} + year + + + + + hazard analysis critical control points (haccp) guide food safety term + ${row['hazard analysis critical control points (haccp) guide food safety term']} + year + + + + + dietary claim or use + ${row['dietary claim or use']} + + + + + degree of plant part maturity + ${row['degree of plant part maturity']} + year + + + + + food production environmental monitoring zone + ${row['food production environmental monitoring zone']} + + + + + plant reproductive part + ${row['plant reproductive part']} + + + + + food traceability list category + ${row['food traceability list category']} + mm + + + + + food animal antimicrobial frequency + ${row['food animal antimicrobial frequency']} + m2 + + + + + intended consumer + ${row['intended consumer']} + m2 + + + + + quantity purchased + ${row['quantity purchased']} + + + + + food container or wrapping + ${row['food container or wrapping']} + °C + + + + + food additive + ${row['food additive']} + g/m3 + + + + + food source age + ${row['food source age']} + year + + + + + food animal antimicrobial intended use + ${row['food animal antimicrobial intended use']} + year + + + + + food packing medium + ${row['food packing medium']} + m2 + + + + + specific intended consumer + ${row['specific intended consumer']} + m2 + + + + + purchase date + ${row['purchase date']} + m2 + + + + + food stored by consumer (storage temperature) + ${row['food stored by consumer (storage temperature)']} + °C + + + + + food package capacity + ${row['food package capacity']} + year + + + + + food distribution point geographic location (city) + ${row['food distribution point geographic location (city)']} + + + + + food product origin geographic location + ${row['food product origin geographic location']} + m + + + + + food distribution point geographic location + ${row['food distribution point geographic location']} + m + + + + + production labeling claims + ${row['production labeling claims']} + + + + + relative location of sample + ${row['relative location of sample']} + + + + + depth + ${row['depth']} + mm + + + + + environment adjacent to site + ${row['environment adjacent to site']} + + + + + fertilizer administration + ${row['fertilizer administration']} + + + + + biotic regimen + ${row['biotic regimen']} + + + + + mechanical damage + ${row['mechanical damage']} + + + + + chemical administration + ${row['chemical administration']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/ena_upload/templates/ENA_template_samples_ERC000057.xml b/ena_upload/templates/ENA_template_samples_ERC000057.xml new file mode 100644 index 0000000..6eb68af --- /dev/null +++ b/ena_upload/templates/ENA_template_samples_ERC000057.xml @@ -0,0 +1,746 @@ + + + + + + + ${row.title} + + + + ${row.taxon_id} + + ${row.scientific_name} + + ${row.common_name} + + + + ${row.sample_description} + + + + + trophic level + ${row['trophic level']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + propagation + ${row['propagation']} + + + + + host of the symbiont role + ${row['host of the symbiont role']} + + + + + sample symbiont of + ${row['sample symbiont of']} + + + + + sample collection method + ${row['sample collection method']} + + + + + sample storage temperature + ${row['sample storage temperature']} + °C + + + + + sample storage location + ${row['sample storage location']} + + + + + sample storage solution + ${row['sample storage solution']} + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + project name + ${row['project name']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check software + ${row['chimera check software']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + 16s recovered + ${row['16s recovered']} + + + + + 16S recovery software + ${row['16S recovery software']} + + + + + collection date + ${row['collection date']} + + + + + altitude + ${row['altitude']} + m + + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + DD + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + DD + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + broad-scale environmental context + ${row['broad-scale environmental context']} + + + + + local environmental context + ${row['local environmental context']} + + + + + environmental medium + ${row['environmental medium']} + + + + + elevation + ${row['elevation']} + m + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + m3 + + + + + organism count + ${row['organism count']} + + + + + sample storage duration + ${row['sample storage duration']} + + + + + host disease status + ${row['host disease status']} + + + + + host of the symbiotic host disease status + ${row['host of the symbiotic host disease status']} + + + + + host common name + ${row['host common name']} + + + + + host subject id + ${row['host subject id']} + + + + + host age + ${row['host age']} + years + + + + + host taxid + ${row['host taxid']} + + + + + host body habitat + ${row['host body habitat']} + + + + + host body site + ${row['host body site']} + + + + + host life stage + ${row['host life stage']} + + + + + host height + ${row['host height']} + mm + + + + + host length + ${row['host length']} + mm + + + + + host growth conditions + ${row['host growth conditions']} + + + + + host substrate + ${row['host substrate']} + + + + + host total mass + ${row['host total mass']} + kg + + + + + host infra-specific name + ${row['host infra-specific name']} + + + + + host infra-specific rank + ${row['host infra-specific rank']} + + + + + host phenotype + ${row['host phenotype']} + + + + + host color + ${row['host color']} + + + + + host shape + ${row['host shape']} + + + + + host sex + ${row['host sex']} + + + + + host scientific name + ${row['host scientific name']} + + + + + host of the symbiotic host subject id + ${row['host of the symbiotic host subject id']} + year + + + + + host of the symbiotic host taxon id + ${row['host of the symbiotic host taxon id']} + + + + + duration of association with the host + ${row['duration of association with the host']} + year + + + + + temperature + ${row['temperature']} + ºC + + + + + sample salinity + ${row['sample salinity']} + psu + + + + + source material identifiers + ${row['source material identifiers']} + + + + + host family relationship + ${row['host family relationship']} + + + + + host genotype + ${row['host genotype']} + + + + + gravidity + ${row['gravidity']} + + + + + host specificity or range + ${row['host specificity or range']} + + + + + host of the symbiotic host phenotype + ${row['host of the symbiotic host phenotype']} + + + + + mode of transmission + ${row['mode of transmission']} + + + + + symbiotic host organism life cycle type + ${row['symbiotic host organism life cycle type']} + + + + + host specificity + ${row['host specificity']} + + + + + host cellular location + ${row['host cellular location']} + % + + + + + host of the symbiotic host infra-specific rank + ${row['host of the symbiotic host infra-specific rank']} + °C + + + + + type of symbiosis + ${row['type of symbiosis']} + °C + + + + + observed coinfecting organisms in host of host + ${row['observed coinfecting organisms in host of host']} + year + + + + + host of the symbiotic host infra-specific name + ${row['host of the symbiotic host infra-specific name']} + year + + + + + host of the symbiotic host total mass + ${row['host of the symbiotic host total mass']} + µg + + + + + host of the symbiotic host local environmental context + ${row['host of the symbiotic host local environmental context']} + g/m3 + + + + + host of the symbiotic host common name + ${row['host of the symbiotic host common name']} + °C + + + + + host of the symbiotic host genotype + ${row['host of the symbiotic host genotype']} + year + + + + + route of transmission + ${row['route of transmission']} + mm + + + + + host dry mass + ${row['host dry mass']} + mg + + + + + host body product + ${row['host body product']} + + + + + host number individual + ${row['host number individual']} + + + + + perturbation + ${row['perturbation']} + + + + + negative control type + ${row['negative control type']} + + + + + positive control type + ${row['positive control type']} + + + + + experimental factor + ${row['experimental factor']} + + + + + encoded traits + ${row['encoded traits']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + taxonomic classification + ${row['taxonomic classification']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + annotation source + ${row['annotation source']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + single cell or viral particle lysis approach + ${row['single cell or viral particle lysis approach']} + + + + + single cell or viral particle lysis kit protocol + ${row['single cell or viral particle lysis kit protocol']} + + + + + sample material processing + ${row['sample material processing']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + ng + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + + pcr primers + ${row['pcr primers']} + + + + + adapters + ${row['adapters']} + + + + + depth + ${row['depth']} + mm + + + + + chemical administration + ${row['chemical administration']} + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file diff --git a/ena_upload/templates/ENA_template_samples_ERC000058.xml b/ena_upload/templates/ENA_template_samples_ERC000058.xml new file mode 100644 index 0000000..5556dae --- /dev/null +++ b/ena_upload/templates/ENA_template_samples_ERC000058.xml @@ -0,0 +1,1009 @@ + + + + + + + ${row.title} + + + + ${row.taxon_id} + + ${row.scientific_name} + + ${row.common_name} + + + + ${row.sample_description} + + + + + sample true vertical depth subsea + ${row['sample true vertical depth subsea']} + + + + + trophic level + ${row['trophic level']} + + + + + observed biotic relationship + ${row['observed biotic relationship']} + + + + + known pathogenicity + ${row['known pathogenicity']} + + + + + relationship to oxygen + ${row['relationship to oxygen']} + + + + + propagation + ${row['propagation']} + + + + + sample transport conditions + ${row['sample transport conditions']} + m2 + + + + + sample collection device + ${row['sample collection device']} + + + + + sample collection method + ${row['sample collection method']} + + + + + sample storage temperature + ${row['sample storage temperature']} + °C + + + + + sample storage location + ${row['sample storage location']} + + + + + source rock depositional environment + ${row['source rock depositional environment']} + + + + + sample measured depth + ${row['sample measured depth']} + mm + + + + + corrosion rate at sample location + ${row['corrosion rate at sample location']} + + + + + sample collection point + ${row['sample collection point']} + + + + + depth (tvdss) of hydrocarbon resource temperature + ${row['depth (tvdss) of hydrocarbon resource temperature']} + m + + + + + oxygenation status of sample + ${row['oxygenation status of sample']} + + + + + density + ${row['density']} + g/m3 + + + + + sample well name + ${row['sample well name']} + + + + + project name + ${row['project name']} + + + + + ploidy + ${row['ploidy']} + + + + + number of replicons + ${row['number of replicons']} + + + + + extrachromosomal elements + ${row['extrachromosomal elements']} + + + + + estimated size + ${row['estimated size']} + + + + + target gene + ${row['target gene']} + + + + + target subfragment + ${row['target subfragment']} + + + + + multiplex identifiers + ${row['multiplex identifiers']} + + + + + sequence quality check + ${row['sequence quality check']} + + + + + chimera check software + ${row['chimera check software']} + + + + + relevant electronic resources + ${row['relevant electronic resources']} + + + + + relevant standard operating procedures + ${row['relevant standard operating procedures']} + + + + + 16s recovered + ${row['16s recovered']} + + + + + well identification number + ${row['well identification number']} + year + + + + + water cut + ${row['water cut']} + year + + + + + production rate + ${row['production rate']} + °C + + + + + field name + ${row['field name']} + + + + + collection date + ${row['collection date']} + + + + + altitude + ${row['altitude']} + m + + + + + geographic location (country and/or sea) + ${row['geographic location (country and/or sea)']} + + + + + geographic location (latitude) + ${row['geographic location (latitude)']} + DD + + + + + geographic location (longitude) + ${row['geographic location (longitude)']} + DD + + + + + geographic location (region and locality) + ${row['geographic location (region and locality)']} + + + + + broad-scale environmental context + ${row['broad-scale environmental context']} + + + + + local environmental context + ${row['local environmental context']} + + + + + environmental medium + ${row['environmental medium']} + + + + + elevation + ${row['elevation']} + m + + + + + secondary and tertiary recovery methods and start date + ${row['secondary and tertiary recovery methods and start date']} + + + + + amount or size of sample collected + ${row['amount or size of sample collected']} + m3 + + + + + organism count + ${row['organism count']} + + + + + organism count qpcr information + ${row['organism count qpcr information']} + year + + + + + hydrocarbon type produced + ${row['hydrocarbon type produced']} + year + + + + + api gravity + ${row['api gravity']} + °C + + + + + sample storage duration + ${row['sample storage duration']} + + + + + host disease status + ${row['host disease status']} + + + + + host scientific name + ${row['host scientific name']} + + + + + pressure + ${row['pressure']} + bar + + + + + temperature + ${row['temperature']} + ºC + + + + + pH + ${row['pH']} + + + + + viscosity + ${row['viscosity']} + + + + + permeability + ${row['permeability']} + mm + + + + + oil water contact depth + ${row['oil water contact depth']} + m + + + + + hydrocarbon resource original pressure + ${row['hydrocarbon resource original pressure']} + Pa + + + + + source rock geological age + ${row['source rock geological age']} + °C + + + + + ammonium + ${row['ammonium']} + µmol/L + + + + + sample salinity + ${row['sample salinity']} + psu + + + + + calcium + ${row['calcium']} + µmol/L + + + + + chloride + ${row['chloride']} + mg/L + + + + + suspended solids + ${row['suspended solids']} + parts/million + + + + + dissolved carbon dioxide + ${row['dissolved carbon dioxide']} + µmol/L + + + + + dissolved inorganic carbon + ${row['dissolved inorganic carbon']} + µg/L + + + + + dissolved inorganic phosphorus + ${row['dissolved inorganic phosphorus']} + µg/L + + + + + dissolved organic carbon + ${row['dissolved organic carbon']} + µmol/L + + + + + magnesium + ${row['magnesium']} + parts/million + + + + + nitrate + ${row['nitrate']} + µmol/L + + + + + nitrite + ${row['nitrite']} + µmol/L + + + + + total nitrogen concentration + ${row['total nitrogen concentration']} + µmol/L + + + + + potassium + ${row['potassium']} + µmol/L + + + + + salinity + ${row['salinity']} + psu + + + + + sodium + ${row['sodium']} + µmol/L + + + + + sulfate + ${row['sulfate']} + µmol/L + + + + + sulfide + ${row['sulfide']} + µmol/L + + + + + total phosphorus + ${row['total phosphorus']} + µmol/L + + + + + total iron + ${row['total iron']} + + + + + volatile fatty acids + ${row['volatile fatty acids']} + + + + + dissolved iron + ${row['dissolved iron']} + µl/L + + + + + resins wt% + ${row['resins wt%']} + + + + + dissolved oxygen in fluids + ${row['dissolved oxygen in fluids']} + µmol/kg + + + + + total sulfur + ${row['total sulfur']} + µmol/L + + + + + injection water fraction + ${row['injection water fraction']} + % + + + + + ethylbenzene + ${row['ethylbenzene']} + µmol/L + + + + + vfa in formation water + ${row['vfa in formation water']} + + + + + total acid number + ${row['total acid number']} + year + + + + + sulfate in formation water + ${row['sulfate in formation water']} + year + + + + + toluene + ${row['toluene']} + year + + + + + asphaltenes wt% + ${row['asphaltenes wt%']} + % + + + + + xylene + ${row['xylene']} + m2 + + + + + alkalinity method + ${row['alkalinity method']} + m2 + + + + + benzene + ${row['benzene']} + m2 + + + + + alkalinity + ${row['alkalinity']} + mEq/L + + + + + source material identifiers + ${row['source material identifiers']} + + + + + source rock lithology + ${row['source rock lithology']} + year + + + + + sample material type + ${row['sample material type']} + + + + + host of the symbiotic host phenotype + ${row['host of the symbiotic host phenotype']} + + + + + biocide administration method + ${row['biocide administration method']} + + + + + chemical treatment + ${row['chemical treatment']} + + + + + biocide administration + ${row['biocide administration']} + year + + + + + chemical treatment method + ${row['chemical treatment method']} + J/K + + + + + negative control type + ${row['negative control type']} + + + + + positive control type + ${row['positive control type']} + + + + + experimental factor + ${row['experimental factor']} + + + + + encoded traits + ${row['encoded traits']} + + + + + subspecific genetic lineage + ${row['subspecific genetic lineage']} + + + + + taxonomic classification + ${row['taxonomic classification']} + + + + + isolation and growth condition + ${row['isolation and growth condition']} + + + + + annotation source + ${row['annotation source']} + + + + + reference for biomaterial + ${row['reference for biomaterial']} + + + + + sample subtype + ${row['sample subtype']} + m2 + + + + + preservative added to sample + ${row['preservative added to sample']} + + + + + single cell or viral particle lysis approach + ${row['single cell or viral particle lysis approach']} + + + + + single cell or viral particle lysis kit protocol + ${row['single cell or viral particle lysis kit protocol']} + + + + + sample material processing + ${row['sample material processing']} + + + + + sample volume or weight for DNA extraction + ${row['sample volume or weight for DNA extraction']} + ng + + + + + nucleic acid extraction + ${row['nucleic acid extraction']} + + + + + nucleic acid amplification + ${row['nucleic acid amplification']} + + + + + library size + ${row['library size']} + + + + + library reads sequenced + ${row['library reads sequenced']} + + + + + library vector + ${row['library vector']} + + + + + library screening strategy + ${row['library screening strategy']} + + + + + pcr conditions + ${row['pcr conditions']} + + + + + pcr primers + ${row['pcr primers']} + + + + + adapters + ${row['adapters']} + + + + + production start date + ${row['production start date']} + m + + + + + aromatics wt% + ${row['aromatics wt%']} + % + + + + + saturates wt% + ${row['saturates wt%']} + % + + + + + porosity + ${row['porosity']} + + + + + formation water salinity + ${row['formation water salinity']} + ppm + + + + + basin name + ${row['basin name']} + g/m3 + + + + + pour point + ${row['pour point']} + °C + + + + + reservoir name + ${row['reservoir name']} + °C + + + + + hydrocarbon resource geological age + ${row['hydrocarbon resource geological age']} + + + + + depositional environment + ${row['depositional environment']} + m + + + + + source rock kerogen type + ${row['source rock kerogen type']} + year + + + + + hydrocarbon resource type + ${row['hydrocarbon resource type']} + year + + + + + water production rate + ${row['water production rate']} + m3/day + + + + + lithology + ${row['lithology']} + year + + + + + hydrocarbon resource original temperature + ${row['hydrocarbon resource original temperature']} + °C + + + + + depth + ${row['depth']} + mm + + + + + injection water breakthrough date of specific well + ${row['injection water breakthrough date of specific well']} + % + + + + SUBMISSION_TOOL + ${tool_name} + + + SUBMISSION_TOOL_VERSION + ${tool_version} + + + + + \ No newline at end of file