Term mismatch ENA / NCBI / MIxS

[jjkoehorst]

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]

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