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GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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Term mismatch ENA / NCBI / MIxS #853

Open jjkoehorst opened 2 months ago

jjkoehorst commented 2 months ago

I worked a bit on the labelling matching with ENA / NCBI as I had a lot of mismatch issues with the development of the FAIR Data Station. I forked the repo and did an analysis on the terms in MIxS and what is used in ENA / NCBI.

The code can be found at the fork https://github.com/jjkoehorst/mixs/blob/rdf-validation/src/scripts/checklist_analysis.py in a new branch for rdf-validation. The code will download the XML files from the two repositories and convert it to RDF for analysis.

Please let me know if I made a mistake on the term matching or how we could improve the matches?

NCBI

ncbi_harmonized_name ncbi_name
0 typ_occupant_dens typical occupant density
1 host_infra_specific_rank host infra specific rank
2 metagenome_source metagenome source
3 isolation_source isolation source
4 virus_isolate_of_prior_infection virus isolate of prior infection
5 culture_collection culture collection
6 cell_subtype cell subtype
7 birth_date birth date
8 ww_surv_target_1_conc_unit wastewater surveillance target 1 conc unit
9 family_relationship family role
10 ww_surv_target_1_gene wastewater surveillance target 1 gene
11 host_specimen_voucher host specimen voucher
12 biospecimen_repository_sample_id biospecimen repository sample id
13 cell_line cell line
14 ww_surv_target_1_extract wastewater surveillance target 1 extract
15 subtype subtype
16 ww_sample_matrix wastewater sample matrix
17 pathovar pathovar
18 gap_change_status gap change status
19 isolate isolate
20 super_population_description Super Population Description
21 narms_isolate_number NARMS isolate number
22 host_anatomical_part host anatomical part
23 child_of child of
24 env_package environmental package
25 prior_sars_cov_2_antiviral_treat prior SARS-CoV-2 antiviral treatment
26 microb_start_taxid microbial starter NCBI taxonomy ID
27 host_variety host variety or cultivar
28 ww_flow wastewater flow
29 specimen_voucher specimen voucher
30 lab_host lab host
31 geo_loc_exposure geo loc exposure
32 non_mineral_nutr_regm non mineral nutrient regimen
33 dry_mass dry mass
34 ww_endog_control_2_protocol wastewater endogenous control 2 protocol
35 ww_surv_target_2_extract_unit wastewater surveillance target 2 extract unit
36 pulse pulse
37 treatment treatment
38 tot_mass total mass
39 sex sex
40 ww_endog_control_2_units wastewater endogenous control 2 units
41 gap_accession gap accession
42 reservoir_name reservoir name
43 ww_pre_treatment wastewater pre-treatment
44 study_disease study disease
45 morphology morphology
46 serovar serovar
47 soil_depth soil depth
48 forma forma
49 image_file image file
50 location_in_facility location or room in facility
51 extreme_salinity extreme salinity
52 reference_material reference material
53 breeding_method breeding method
54 gap_consent_code gap consent code
55 compound compound
56 submitter_handle submitter handle
57 strain strain
58 food_type_processed food type processed in facility
59 sub_species sub species
60 ww_surv_target_1_known_present wastewater surveillance target 1 known present
61 animal_env animal environment
62 biocide_admin biocide administration
63 food_industry_code FDA food industry code name
64 host_am antimicrobial name
65 source_material_id source material identifiers
66 edta_inhibitor_tested EDTA inhibitor tested
67 risk_group risk group
68 ww_surv_jurisdiction wastewater surveillance jurisdiction
69 isolate_name_alias isolate name alias
70 label_claims labeling claims
71 altitude altitude
72 collection_method collection method
73 material_condition material condition
74 biospecimen_repository biospecimen repository
75 cultivar cultivar
76 authority authority
77 subclone subclone
78 host_infra_specific_name host infra specific name
79 exposure_event exposure event
80 beta_lactamase_family beta-lactamase family
81 breed breed
82 ww_industrial_effluent_percent wastewater industrial effluent percent
83 investigation_type investigation type
84 submitted_subject_id submitted subject id
85 purpose_of_sequencing purpose of sequencing
86 annual_season_precpt annual and seasonal precipitation
87 food_processing_method food processing method
88 sars_cov_2_diag_pcr_ct_value_1 SARS-CoV-2 diagnostic pcr Ct value 1
89 purpose_of_ww_sampling purpose of wastewater sampling
90 description description
91 ww_total_suspended_solids wastewater total suspended solids
92 upstream_intervention upstream intervention
93 host_tissue_sampled host tissue sampled
94 height_or_length height or length
95 date_of_prior_sars_cov_2_infection date of prior SARS-CoV-2 infection
96 clone_lib clone lib
97 passage_number passage number
98 teleomorph teleomorph
99 ww_surv_target_1_extract_unit wastewater surveillance target 1 extract unit
100 life_stage life stage
101 derived_from derived from
102 population_description Population Description
103 water_content_soil_meth water content of soil method
104 host_blood_press_syst host blood pressure systolic
105 microbial_biomass_meth microbial biomass method
106 anamorph anamorph
107 body_mass_index body mass index
108 surface_orientation surface orientation
109 carbapenemase carbapenemase
110 serogroup serogroup
111 sample_use sample use
112 ferm_ph fermentation pH
113 sars_cov_2_diag_pcr_ct_value_2 SARS-CoV-2 diagnostic pcr Ct value 2
114 ww_surv_target_1 wastewater surveillance target 1
115 antiviral_treatment_agent antiviral treatment agent
116 passage_history passage history
117 histological_type histological type
118 ww_surv_target_2_conc_unit wastewater surveillance target 2 conc unit
119 infra_specific_rank infra specific rank
120 stud_book_number stud book number
121 prior_sars_cov_2_vaccination prior SARS-CoV-2 vaccination
122 subject_is_affected subject is affected
123 genotype genotype
124 substrain substrain
125 passage_method passage method
126 karyotype karyotype
127 family_id family id
128 ww_surv_target_2_known_present wastewater surveillance target 2 known present
129 original_subject_id original subject id
130 bio_material biological material
131 ww_surv_target_1_conc wastewater surveillance target 1 concentration
132 hiv_stat HIV status
133 host_anatomical_material host anatomical material
134 ww_surv_target_2_conc wastewater surveillance target 2 conc
135 ww_surv_target_2_extract wastewater surveillance target 2 extract
136 last_meal last meal
137 component_organism component organism
138 host_disease_stage host disease stage
139 tot_n_meth total N method
140 ww_ph wastewater pH
141 clone clone
142 growth_med growth media
143 source_type source type
144 samp_salinity sample salinity
145 haccp_term Hazard Analysis Critical Control Points (HACCP) guide food safety term
146 host_description host description
147 host_housing animal housing system
148 purpose_of_ww_sequencing purpose of wastewater sequencing
149 ww_processing_protocol wastewater processing protocol
150 study_name study name
151 infra_specific_name infra specific name
152 occupant_dens_samp occupant density at sampling
153 host host
154 omics_observ_id Omics Observatory ID
155 body_habitat body habitat
156 orgmod_note organism modifier note
157 ww_surv_target_2_protocol wastewater surveillance target 2 protocol
158 pathotype pathotype
159 submitted_sample_id submitted sample id
160 salinity_meth salinity method
161 ecotype ecotype
162 date_of_sars_cov_2_vaccination date of SARS-CoV-2 vaccination
163 host_blood_press_diast host blood pressure diastolic
164 host_disease host disease
165 sars_cov_2_diag_gene_name_1 SARS-CoV-2 diagnostic gene name 1
166 subsrc_note subsource note
167 ww_primary_sludge_retention_time wastewater primary sludge retention time
168 variety variety
169 is_tumor is tumor
170 indoor_surf_subpart indoor sampling surface or structure subpart
171 source_name source name
172 air_pm_concen air particulate matter concentration
173 gisaid_virus_name GISAID virus name
174 vaccine_received vaccine received
175 health_state health state
176 disease_stage disease stage
177 race race
178 collected_by collected by
179 ww_endog_control_1_units wastewater endogenous control 1 units
180 type_status type status
181 sanitizer_used_postharvest sanitizer used during postharvest cleaning
182 breeding_history breeding history
183 tissue_lib tissue lib
184 gap_subject_id gap subject id
185 disease disease
186 dev_stage development stage
187 sample_type sample type
188 soil_ph soil pH
189 soil_text_measure soil texture measurement
190 spikein_amr antimicrobial phenotype of spike-in bacteria
191 ww_surv_target_2_gene wastewater surveillance target 2 gene
192 host_group_size food animal group size
193 purpose_of_sampling purpose of sampling
194 body_product body product
195 prior_sars_cov_2_infection prior SARS-CoV-2 infection
196 ww_surv_system_sample_id wastewater surveillance system sample ID
197 population population
198 water_ph water pH
199 gisaid_accession GISAID accession
200 occupation occupation
201 same_as same as
202 host_recent_travel_return_date host recent travel return date
203 tissue tissue
204 haplotype haplotype
205 analyte_type analyte type
206 death_date death date
207 cell_type cell type
208 basin_name basin name
209 ww_sample_type wastewater sample type
210 ww_temperature wastewater temperature
211 serotype serotype
212 dose dose
213 repository repository
214 subgroup subgroup
215 collection_device collection device
216 ww_endog_control_2 wastewater endogenous control 2
217 type_strain submitter-asserted type strain
218 super_population_code Super Population Code
219 molecular_data_type molecular data type
220 water_content_soil water content of soil
221 wet_mass wet mass
222 date_of_prior_antiviral_treat date of prior SARS-CoV-2 antiviral treatment
223 forma_specialis forma specialis
224 ww_endog_control_1 wastewater endogenous control 1
225 substrate substrate
226 gap_study_version gap study version
227 samp_mat_type sample material type (host or environmental context)
228 growth_protocol growth protocol
229 food_industry_class FDA food industry class name
230 outbreak outbreak
231 birth_location birth location
232 ww_endog_control_2_conc wastewater endogenous control 2 concentration
233 ww_endog_control_1_conc wastewater endogenous control 1 concentration
234 ww_endog_control_1_protocol wastewater endogenous control 1 protocol
235 phenotype phenotype
236 ww_surv_target_1_protocol wastewater surveillance target 1 protocol
237 mating_type mating type
238 previous_land_use_meth previous land use method
239 gap_consent_short_name gap consent short name
240 host_recent_travel_loc host recent travel location
241 ww_population wastewater population
242 biomaterial_provider biomaterial provider
243 host_animal_breed host animal breed
244 ww_sample_site wastewater sample site
245 gap_sample_id gap sample id
246 host_family_relationship host family relationship
247 annual_season_temp annual and seasonal temperature
248 biovar biovar
249 plant_body_site plant body site
250 age age
251 host_health_state host health state
252 ifsac_category Interagency Food Safety Analytics Collaboration (IFSAC) category
253 sequenced_by sequenced by
254 host_disease_outcome host disease outcome
255 ww_sample_salinity wastewater sample salinity
256 diet diet
257 label label
258 ww_surv_target_2 wastewater surveillance target 2
259 sample_name sample name
260 sars_cov_2_diag_gene_name_2 SARS-CoV-2 diagnostic gene name 2
261 identified_by identified by
262 affection_status affection status
263 ww_sample_duration wastewater sample duration
264 ww_population_source wastewater population source
jjkoehorst commented 2 months ago

ENA

ena_label ena_name
0 host prediction approach host prediction approach
1 fermentation ph fermentation ph
2 salinity method salinity method
3 sample transportation temperature sample transportation temperature
4 sample transport container sample transport container
5 spike-in organism spike-in organism
6 sampling time point sampling time point
7 frequency of cleaning frequency of cleaning
8 growth habit growth habit
9 facility type facility type
10 annotation source annotation source
11 pooled DNA extract total pooled DNA extract total
12 single cell or viral particle lysis approach single cell or viral particle lysis approach
13 trophic level trophic level
14 relationship to oxygen relationship to oxygen
15 observed biotic relationship observed biotic relationship
16 surface material surface material
17 sample surface moisture sample surface moisture
18 indoor surface indoor surface
19 sampling room id or name sampling room id or name
20 bio_material bio_material
21 farm watering water source farm watering water source
22 food harvesting process food harvesting process
23 sequence quality check sequence quality check
24 16s recovered 16s recovered
25 completeness approach completeness approach
26 culture result culture result
27 soil texture classification soil texture classification
28 negative control type negative control type
29 extreme weather event extreme weather event
30 history/tillage history/tillage
31 geographic location (region and locality) geographic location (region and locality)
32 geographic location (longitude) geographic location (longitude)
33 geographic location (latitude) geographic location (latitude)
34 time course duration time course duration
35 geographic location (country and/or sea) geographic location (country and/or sea)
36 microbial starter ncbi taxonomy id microbial starter ncbi taxonomy id
37 food cleaning process food cleaning process
38 plant reproductive part plant reproductive part
39 food animal body condition food animal body condition
40 food traceability list category food traceability list category
41 food animal source sex category food animal source sex category
42 hazard analysis critical control points (haccp) guide food safety term hazard analysis critical control points (haccp) guide food safety term
43 interagency food safety analytics collaboration (ifsac) category interagency food safety analytics collaboration (ifsac) category
44 serotype serotype
45 isolate isolate
46 receipt date receipt date
47 isolation_source isolation_source
48 collected_by collected_by
49 Further Details Further Details
50 sub_species sub_species
51 library construction method library construction method
52 protocol protocol
53 sample transportation date sample transportation date
54 sample transportation time sample transportation time
55 instrument for DNA concentration measurement instrument for DNA concentration measurement
56 DNA concentration DNA concentration
57 read quality filter read quality filter
58 oxygenation status of sample oxygenation status of sample
59 drainage classification drainage classification
60 soil horizon soil horizon
61 profile position profile position
62 soil texture measurement soil texture measurement
63 soil_taxonomic/FAO classification soil_taxonomic/FAO classification
64 biotic relationship [deprecated] biotic relationship [deprecated]
65 previous land use method previous land use method
66 dominant hand dominant hand
67 sample storage conditions sample storage conditions
68 strain strain
69 water temperature water temperature
70 growth condition growth condition
71 culture_collection culture_collection
72 lat_lon lat_lon
73 Marine Region Marine Region
74 Chlorophyll Sensor Chlorophyll Sensor
75 Oxygen Sensor Oxygen Sensor
76 Nitrate Sensor Nitrate Sensor
77 Salinity Sensor Salinity Sensor
78 Sampling Platform Sampling Platform
79 Sampling Campaign Sampling Campaign
80 Sampling Station Sampling Station
81 Latitude End Latitude End
82 Longitude Start Longitude Start
83 Event Date/Time Start Event Date/Time Start
84 Event Date/Time End Event Date/Time End
85 Latitude Start Latitude Start
86 Longitude End Longitude End
87 Event Label Event Label
88 Citation Citation
89 Last Update Date Last Update Date
90 Protocol Label Protocol Label
91 Sample Status Sample Status
92 environmental package environmental package
93 mechanical structure mechanical structure
94 number of inoculated individuals number of inoculated individuals
95 train stop collection location train stop collection location
96 train station collection location train station collection location
97 seasonal use seasonal use
98 quadrant position quadrant position
99 wall location wall location
100 door signs of water/mold door signs of water/mold
101 wall signs of water/mold wall signs of water/mold
102 door direction of opening door direction of opening
103 interior wall condition interior wall condition
104 ceiling signs of water/mold ceiling signs of water/mold
105 window vertical position window vertical position
106 gender of restroom gender of restroom
107 door type door type
108 orientations of exterior window orientations of exterior window
109 indoor space indoor space
110 window type window type
111 door location door location
112 shading device signs of water/mold shading device signs of water/mold
113 door type, metal door type, metal
114 specifications specifications
115 rooms connected by a doorway rooms connected by a doorway
116 wall surface treatment wall surface treatment
117 furniture furniture
118 window status window status
119 window material window material
120 ceiling structure ceiling structure
121 wall texture wall texture
122 substructure type substructure type
123 window horizontal position window horizontal position
124 heating system delivery method heating system delivery method
125 space typical state space typical state
126 heating and cooling system type heating and cooling system type
127 floor structure floor structure
128 door movement door movement
129 door material door material
130 ceiling type ceiling type
131 wall construction type wall construction type
132 room sampling position room sampling position
133 window condition window condition
134 floor condition floor condition
135 filter type filter type
136 floor signs of water/mold floor signs of water/mold
137 ceiling condition ceiling condition
138 ceiling finish material ceiling finish material
139 window signs of water/mold window signs of water/mold
140 door type, composite door type, composite
141 ceiling texture ceiling texture
142 heating delivery locations heating delivery locations
143 light type light type
144 door condition door condition
145 surface-air contaminant surface-air contaminant
146 wall finish material wall finish material
147 window covering window covering
148 room condition room condition
149 window location window location
150 building setting building setting
151 fireplace type fireplace type
152 room location in building room location in building
153 water feature type water feature type
154 building occupancy type building occupancy type
155 handidness handidness
156 sampling day weather sampling day weather
157 train line train line
158 built structure setting built structure setting
159 occupancy documentation occupancy documentation
160 architectural structure architectural structure
161 shading device condition shading device condition
162 aerospace structure aerospace structure
163 shading device location shading device location
164 design, construction, and operation documents design, construction, and operation documents
165 drawings drawings
166 shading device type shading device type
167 metagenomic source metagenomic source
168 sample derived from sample derived from
169 MAG coverage software MAG coverage software
170 taxonomic identity marker taxonomic identity marker
171 binning parameters binning parameters
172 contamination screening input contamination screening input
173 source material description source material description
174 identified_by identified_by
175 sample capture status sample capture status
176 plant treatment plant treatment
177 sample disease status sample disease status
178 sample height sample height
179 sample length sample length
180 sample wet mass sample wet mass
181 sample disease stage sample disease stage
182 sample phenotype sample phenotype
183 sample health state sample health state
184 plant developmental stage plant developmental stage
185 sampled age sampled age
186 sample dry mass sample dry mass
187 organism common name organism common name
188 plant sex plant sex
189 subspecific genetic lineage rank subspecific genetic lineage rank
190 genotype genotype
191 subspecific genetic lineage name subspecific genetic lineage name
192 organism phenotype organism phenotype
193 WGA amplification approach WGA amplification approach
194 sorting technology sorting technology
195 virus identifier virus identifier
196 type exposure type exposure
197 personal protective equipment personal protective equipment
198 subject exposure subject exposure
199 illness duration illness duration
200 illness symptoms illness symptoms
201 hospitalisation hospitalisation
202 host disease outcome host disease outcome
203 host description host description
204 host habitat host habitat
205 isolation source host-associated isolation source host-associated
206 serotype (required for a seropositive sample) serotype (required for a seropositive sample)
207 definition for seropositive sample definition for seropositive sample
208 host behaviour host behaviour
209 lab_host lab_host
210 host health state host health state
211 subject exposure duration subject exposure duration
212 collecting institution collecting institution
213 collector name collector name
214 isolation source non-host-associated isolation source non-host-associated
215 area of sampling site area of sampling site
216 name of the sampling site name of the sampling site
217 surveillance target surveillance target
218 investigation type investigation type
219 population size of the catchment area population size of the catchment area
220 size of the catchment area size of the catchment area
221 tumor grading (OBI_0600002) tumor grading (OBI_0600002)
222 tissue_type tissue_type
223 sex sex
224 date of death date of death
225 diagnosis diagnosis
226 date of birth date of birth
227 treatment date treatment date
228 treatment dose treatment dose
229 treatment agent treatment agent
230 host disease stage host disease stage
231 pathotype pathotype
232 mating_type mating_type
233 Is the sequenced pathogen host associated? Is the sequenced pathogen host associated?
234 passage_history passage_history
235 sub_group sub_group
236 sub_strain sub_strain
237 serovar serovar
238 sub_type sub_type
239 specimen_voucher specimen_voucher
240 country of travel country of travel
241 clinical setting clinical setting
242 travel-relation travel-relation
243 environmental_sample environmental_sample
244 trial length trial length
245 trial timepoint trial timepoint
246 host breed host breed
247 host gutted mass host gutted mass
248 sample storage buffer sample storage buffer
249 host diet treatment concentration host diet treatment concentration
250 host storage container host storage container
251 host storage container pH host storage container pH
252 host diet treatment host diet treatment
253 host storage container temperature host storage container temperature
254 reference host genome for decontamination reference host genome for decontamination
255 virus enrichment approach virus enrichment approach
256 UViG assembly quality UViG assembly quality
257 predicted genome structure predicted genome structure
258 tidal stage tidal stage
259 sediment type sediment type
260 type of symbiosis type of symbiosis
261 route of transmission route of transmission
262 host specificity host specificity
263 symbiotic host organism life cycle type symbiotic host organism life cycle type
264 mode of transmission mode of transmission
265 host cellular location host cellular location
266 sample symbiont of sample symbiont of
267 host of the symbiont role host of the symbiont role
268 sample salinity sample salinity
269 health or disease status of specific host health or disease status of specific host
270 specific host specific host
271 finishing strategy finishing strategy
272 Sampling Site Sampling Site
273 serovar_in-silico serovar_in-silico
274 dev_stage dev_stage
275 diagnostic method diagnostic method
276 source rock depositional environment source rock depositional environment
277 source rock geological age source rock geological age
278 organism count qpcr information organism count qpcr information
279 depositional environment depositional environment
280 lithology lithology
281 hydrocarbon resource geological age hydrocarbon resource geological age
282 hydrocarbon resource type hydrocarbon resource type
283 source rock kerogen type source rock kerogen type
284 sample subtype sample subtype
285 sample material type sample material type
286 api gravity api gravity
287 hydrocarbon type produced hydrocarbon type produced
288 sample collection point sample collection point
289 depth (tvdss) of hydrocarbon resource temperature depth (tvdss) of hydrocarbon resource temperature
290 source rock lithology source rock lithology
291 sample coordinator affiliation sample coordinator affiliation
292 symbiont symbiont
293 relationship relationship
294 original geographic location (longitude) original geographic location (longitude)
295 original geographic location original geographic location
296 identifier_affiliation identifier_affiliation
297 original geographic location (latitude) original geographic location (latitude)
298 original collection date original collection date
299 habitat habitat
300 GAL GAL
301 tolid tolid
302 barcoding center barcoding center
303 sample coordinator sample coordinator
304 sample same as sample same as
305 proxy voucher proxy voucher
306 proxy biomaterial proxy biomaterial
307 specimen_id specimen_id
308 GAL_sample_id GAL_sample_id
309 culture_or_strain_id culture_or_strain_id
310 organism part organism part
311 lifestage lifestage
312 shell width shell width
313 aquaculture origin aquaculture origin
314 shell markings shell markings
315 shell length shell length
316 shellfish total weight shellfish total weight
317 shellfish soft tissue weight shellfish soft tissue weight
318 toxin burden toxin burden
319 gonad weight gonad weight
320 adductor weight adductor weight
321 age age
322 seabed habitat seabed habitat
323 chemical compound chemical compound
324 growth media growth media
325 plant body site plant body site
326 cell_type cell_type
327 time time
328 dose dose
329 infect infect
330 experimental factor 3 experimental factor 3
331 experimental factor 5 experimental factor 5
332 block block
333 experimental factor 4 experimental factor 4
334 experimental factor 1 experimental factor 1
335 experimental factor 2 experimental factor 2
336 cell_line cell_line
337 ecotype ecotype
338 cultivar cultivar
339 replicate replicate
340 cellular component cellular component
341 disease staging disease staging
342 phenotype phenotype
343 immunoprecipitate immunoprecipitate
344 individual individual
345 environmental stress environmental stress
346 environmental history environmental history
347 initial time point initial time point
348 lung/nose-throat disorder lung/nose-throat disorder
349 urine/collection method urine/collection method
350 patient tumor site of collection patient tumor site of collection
351 engrafted tumor collection site engrafted tumor collection site
352 engrafted tumor sample passage engrafted tumor sample passage
353 patient tumor type patient tumor type
354 sample material sample material
355 sample origin sample origin
356 sample unique ID sample unique ID
357 sample taxon name sample taxon name
358 patient sex patient sex
359 patient tumor primary site patient tumor primary site
360 patient age at collection of tumor patient age at collection of tumor
361 engraftment host strain name engraftment host strain name
362 Was the PDX model humanised? was the PDX model humanised?
363 patient tumor diagnosis at time of collection patient tumor diagnosis at time of collection
364 meaning of cut off value meaning of cut off value
365 other pathogens tested other pathogens tested
366 other pathogens test result other pathogens test result
367 influenza test method influenza test method
368 influenza test result influenza test result
369 inoculation route inoculation route
370 inoculation dose inoculation dose
371 inoculation stock availability inoculation stock availability
372 influenza virus type influenza virus type
373 WHO/OIE/FAO clade (required for HPAI H5N1 viruses) WHO/OIE/FAO clade (required for HPAI H5N1 viruses)
374 lineage:swl (required for H1N1 viruses) lineage:swl (required for H1N1 viruses)
375 influenza strain unique number influenza strain unique number
376 influenza vaccination type influenza vaccination type
377 source of vaccination information source of vaccination information
378 antiviral treatment dosage antiviral treatment dosage
379 antiviral treatment duration antiviral treatment duration
380 vaccine lot number vaccine lot number
381 vaccine dosage vaccine dosage
382 antiviral treatment antiviral treatment
383 influenza-like illness at the time of sample collection influenza-like illness at the time of sample collection
384 influenza vaccination date influenza vaccination date
385 illness onset date illness onset date
386 antiviral treatment initiation antiviral treatment initiation
387 vaccine manufacturer vaccine manufacturer
388 variety variety
389 germline germline
390 tissue_lib tissue_lib