Combination: MimsHumanAssociated combined with Ancient (MimsHumanAssociatedAncient)
MIxS Data that comply with the Mims checklist, and HumanAssociated and Ancient extensions.
Composition
MimsHumanAssociated [Checklist] + Ancient [Extension]
Terms
| MIXS ID | Name | Cardinality and Range | Description |
|---|---|---|---|
| MIXS:0000092 | project_name | 1 String |
Name of the project within which the sequencing was organized |
| MIXS:0000091 | associated_resource | * recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... |
| MIXS:XXXXXXXXX | orig_site_name | * recommended String |
Designated name of the archaeological or ecological site, ancient settlement,... |
| MIXS:XXXXXXXXX | orig_site_loc | 0..1 String |
The original geographical origin of the sample, when sampled outside its orig... |
| MIXS:XXXXXXXXX | orig_site_lat | 0..1 String |
The latitude coordinate of the original geographical origin of the sample, e |
| MIXS:XXXXXXXXX | orig_site_lon | 0..1 String |
The longitude coordinate of the original geographical origin of the sample, e |
| MIXS:XXXXXXXXX | past_env_broad | 0..1 recommended String |
Report information about the general ancient broad environmental system that ... |
| MIXS:XXXXXXXXX | past_env_local | 0..1 recommended String |
Report information about the smaller-scale environmental system of the local ... |
| MIXS:XXXXXXXXX | context_retrieval_date | 0..1 recommended Datetime |
Date of excavation or retrieval from burial or depositional context, if known |
| MIXS:XXXXXXXXX | stratigraph_context | * String |
Associated stratigraphic context(s) that the sample was retrieved from, usual... |
| MIXS:0000010 | geo_loc_name | 1 String |
The geographical origin of the sample as defined by the country or sea name f... |
| MIXS:0000009 | lat_lon | 1 String |
The geographical origin of the sample as defined by latitude and longitude |
| MIXS:0000012 | env_broad_scale | 1 String |
Report the major environmental system the sample or specimen came from |
| MIXS:0000013 | env_local_scale | 1 String |
Report the entity or entities which are in the sample or specimen s local vic... |
| MIXS:0000094 | alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... |
| MIXS:0000018 | depth | 0..1 recommended String |
The vertical distance below local surface |
| MIXS:0000093 | elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... |
| MIXS:0000113 | temp | 0..1 recommended String |
Temperature of the sample at the time of sampling |
| MIXS:0000183 | salinity | 0..1 String |
The total concentration of all dissolved salts in a liquid or solid sample |
| MIXS:0000754 | perturbation | * String |
Type of perturbation, e |
| MIXS:0000008 | experimental_factor | * recommended String |
Variable aspects of an experiment design that can be used to describe an expe... |
| MIXS:0000026 | source_mat_id | * recommended String |
A unique identifier assigned to a material sample (as defined by http://rs |
| MIXS:0001107 | samp_name | 1 String |
A local identifier or name that for the material sample used for extracting n... |
| MIXS:XXXXXXXXX | samp_alt_lab_ids | * String |
An alternative sample or material ID related to the sample not already covere... |
| MIXS:XXXXXXXXX | permit_authority | * recommended String |
Name of the authorit(ies) or institution(s) that granted sampling and analysi... |
| MIXS:XXXXXXXXX | permit_id | * recommended String |
A permit ID, code, or any form of identify provided by any authority (ethical... |
| MIXS:XXXXXXXXX | permit_date | * recommended Datetime |
Date on which a permit was granted |
| MIXS:XXXXXXXXX | permit_scope | * recommended String |
Description of the original scope and permissions of the research on the gene... |
| MIXS:XXXXXXXXX | biocultural_label | * recommended BioCulturalLabelEnum |
Relevant biocultural labels defined by the local contexts project (https://lo... |
| MIXS:XXXXXXXXX | earliest_chrono_age | 1 recommended Integer |
The maximum/earliest/oldest possible age of a specimen as determined by a dat... |
| MIXS:XXXXXXXXX | earliest_chrono_sys | 1 recommended ChronoAgeSysEnum |
The reference system associated with the earliest_chrono_age |
| MIXS:XXXXXXXXX | latest_chrono_age | 1 recommended Integer |
The minimum/latest/youngest possible age of a specimen as determined by a dat... |
| MIXS:XXXXXXXXX | latest_chrono_sys | 1 recommended ChronoAgeSysEnum |
The reference system associated with the latest_chrono_age |
| MIXS:XXXXXXXXX | chrono_age_protocol | * recommended ChronoAgeProtocolEnum |
A description of or reference to the methods used to determine the earliest_c... |
| MIXS:XXXXXXXXX | chrono_age_remarks | 0..1 recommended String |
Notes or comments about the earliest_chrono_age and latest_chrono_age |
| MIXS:XXXXXXXXX | geological_epoch | 0..1 GeolEpochEnum |
The geological epoch approximating to the period within which the specimen or... |
| MIXS:XXXXXXXXX | cultural_era | 0..1 String |
The cultural era approximating to the period in which the archaeological rema... |
| MIXS:0001320 | samp_taxon_id | 1 String |
NCBI taxon id of the sample |
| MIXS:0000011 | collection_date | 1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... |
| MIXS:0000327 | store_cond | 0..1 String |
Explain how and for how long the sample was stored before DNA extraction (for... |
| MIXS:XXXXXXXXX | samp_preserv_treatm | * String |
Description of any treatment applied directly to samples for the specific pur... |
| MIXS:0000861 | host_subject_id | 0..1 String |
A unique identifier by which each subject can be referred to, de-identified |
| MIXS:0000895 | ethnicity | * String |
A category of people who identify with each other, usually on the basis of pr... |
| MIXS:0000255 | host_age | 0..1 String |
Age of host at the time of sampling; relevant scale depends on species and st... |
| MIXS:0000317 | host_body_mass_index | 0..1 String |
Body mass index, calculated as weight/(height)squared |
| MIXS:0000811 | host_sex | 0..1 String |
Gender or physical sex of the host |
| MIXS:0000264 | host_height | 0..1 String |
The height of subject |
| MIXS:0000874 | host_phenotype | 0..1 String |
Phenotype of human or other host |
| MIXS:0000333 | host_pulse | 0..1 String |
Resting pulse, measured as beats per minute |
| MIXS:0000263 | host_tot_mass | 0..1 String |
Total mass of the host at collection, the unit depends on host |
| MIXS:0000274 | host_body_temp | 0..1 String |
Core body temperature of the host when sample was collected |
| MIXS:0000869 | host_diet | * String |
Type of diet depending on the host, for animals omnivore, herbivore etc |
| MIXS:0000870 | host_last_meal | * String |
Content of last meal and time since feeding; can include multiple values |
| MIXS:0000867 | host_body_site | 0..1 String |
Name of body site where the sample was obtained from, such as a specific orga... |
| MIXS:0000888 | host_body_product | 0..1 String |
Substance produced by the body, e |
| MIXS:0000872 | host_fam_rel | * String |
Relationships to other hosts in the same study; can include multiple relation... |
| MIXS:0000326 | twin_sibling | 0..1 Boolean |
Specification of twin sibling presence |
| MIXS:0000896 | host_occupation | 0..1 String |
Most frequent job performed by subject |
| MIXS:0000365 | host_genotype | 0..1 String |
Observed genotype |
| MIXS:0001298 | host_symbiont | * String |
The taxonomic name of the organism(s) found living in mutualistic, commensali... |
| MIXS:0000031 | host_disease_stat | 0..1 String |
List of diseases with which the host has been diagnosed; can include multiple... |
| MIXS:XXXXXXXXX | palaeopath_status | 0..1 String |
Describe briefly any relevant palaeopathological or health-related observatio... |
| MIXS:0000271 | blood_blood_disord | * String |
History of blood disorders; can include multiple disorders |
| MIXS:0000277 | kidney_disord | * String |
History of kidney disorders; can include multiple disorders |
| MIXS:0000269 | pulmonary_disord | * String |
History of pulmonary disorders; can include multiple disorders |
| MIXS:0000278 | urogenit_tract_disor | * String |
History of urogenital tract disorders; can include multiple disorders |
| MIXS:0000270 | nose_throat_disord | * String |
Report any history of nose, mouth, teeth and/or throat disorders in the subje... |
| MIXS:0000265 | host_hiv_stat | 0..1 String |
HIV status of subject, if yes HAART initiation status should also be indicate... |
| MIXS:0000897 | medic_hist_perform | 0..1 Boolean |
Whether full medical history was collected |
| MIXS:0000898 | study_complt_stat | 0..1 String |
Specification of study completion status, if no the reason should be specifie... |
| MIXS:0000884 | ihmc_medication_code | * Integer |
Can include multiple medication codes |
| MIXS:0000751 | chem_administration | * String |
List of chemical compounds administered to the host or site where sampling oc... |
| MIXS:0000899 | urine_collect_meth | 0..1 UrineCollectMethEnum |
Specification of urine collection method |
| MIXS:0000894 | drug_usage | * String |
Any drug used by subject and the frequency of usage; can include multiple dru... |
| MIXS:0000262 | smoker | 0..1 Boolean |
Specification of smoking status |
| MIXS:0000295 | weight_loss_3_month | 0..1 String |
Specification of weight loss in the last three months, if yes should be furth... |
| MIXS:0000266 | diet_last_six_month | 0..1 String |
Specification of major diet changes in the last six months, if yes the change... |
| MIXS:0000268 | travel_out_six_month | * String |
Specification of the countries travelled in the last six months; can include ... |
| MIXS:0000267 | pet_farm_animal | * String |
Specification of presence of pets or farm animals in the environment of subje... |
| MIXS:0000273 | maternal_health_stat | 0..1 String |
Specification of the maternal health status |
| MIXS:0000272 | gestation_state | 0..1 String |
Specification of the gestation state |
| MIXS:0000275 | foetal_health_stat | 0..1 String |
Specification of foetal health status, should also include abortion |
| MIXS:0000276 | amniotic_fluid_color | 0..1 String |
Specification of the color of the amniotic fluid sample |
| MIXS:XXXXXXXXX | prev_pubs | * String |
Any previous publications that report non-nucleic acid data from the same sam... |
| MIXS:0000025 | ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... |
| MIXS:0000103 | organism_count | * String |
Total cell count of any organism (or group of organisms) per gram, volume or ... |
| MIXS:0000015 | rel_to_oxygen | 0..1 RelToOxygenEnum |
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... |
| MIXS:XXXXXXXXX | host_preserv_state | 0..1 String |
Description of the state of the sampled (ancient) organism/host as originally... |
| MIXS:0000753 | oxy_stat_samp | 0..1 OxyStatSampEnum |
Oxygenation status of sample |
| MIXS:0000752 | misc_param | * String |
Any other measurement performed or parameter collected, that is not listed he... |
| MIXS:XXXXXXXXX | batch_ids | * String |
Identifiers for any form of batch or 'group' that the samples is associated w... |
| MIXS:XXXXXXXXX | samp_category | 1 recommended SampCategoryEnum |
The type/category of a sample |
| MIXS:0001321 | neg_cont_type | 0..1 recommended NegContTypeEnum |
The substance or equipment used as a negative control in an investigation |
| MIXS:0001322 | pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... |
| MIXS:0000014 | env_medium | 1..* String |
Report the environmental material(s) immediately surrounding the sample or sp... |
| MIXS:0001225 | samp_collect_method | 0..1 recommended String |
The method employed for collecting the sample |
| MIXS:0000002 | samp_collect_device | 0..1 recommended String |
The device used to collect an environmental sample |
| MIXS:0000016 | samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... |
| MIXS:0000001 | samp_size | 0..1 recommended String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... |
| MIXS:0000755 | samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room |
| MIXS:0000116 | samp_store_dur | 0..1 String |
Duration for which the sample was stored |
| MIXS:0000110 | samp_store_temp | 0..1 String |
Temperature at which sample was stored, e |
| MIXS:XXXXXXXXX | samp_decont_pretreat | * String |
Protocols employed for sample surface decontamination of external modern nuc... |
| MIXS:0000017 | size_frac | 0..1 String |
Filtering pore size used in sample preparation |
| MIXS:0000111 | samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... |
| MIXS:XXXXXXXXX | nucl_acid_extr_date | 0..1 Datetime |
The date when the nucleic acid extraction was started from the sample materia... |
| MIXS:0000037 | nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:XXXXXXXXX | sop_experimental | * String |
Provide a DOI or URL to refer to the paper where the field report, nucleic ac... |
| MIXS:XXXXXXXXX | library_name | * recommended String |
Any ID or name used for referring to a nucleic acid sequencing library associ... |
| MIXS:XXXXXXXXX | damage_treatment | 1 recommended DamageTreatmentEnum |
Indication of whether characteristic ancient DNA damage has been altered or r... |
| MIXS:XXXXXXXXX | lib_strandedness | 1..* recommended LibStrandEnum |
The strandedness of the original template nucleic acid molecules used for con... |
| MIXS:0000048 | adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... |
| MIXS:0000047 | mid | 0..1 recommended String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... |
| MIXS:XXXXXXXXX | lib_mid_desc | * recommended String |
Index/barcode/primer configuration used during library building for sequencin... |
| MIXS:XXXXXXXXX | lib_gener_technique | 0..1 recommended LibTypeEnum |
The technique used to generate the library, i |
| MIXS:0000043 | lib_screen | 0..1 recommended String |
Specific enrichment or screening methods applied before and/or after creating... |
| MIXS:0000042 | lib_vector | 0..1 recommended String |
Cloning vector type(s) used in construction of libraries |
| MIXS:0000039 | lib_size | 0..1 recommended Integer |
Total number of clones in the library prepared for the project |
| MIXS:XXXXXXXXX | lib_polymerase | 0..1 recommended String |
The polymerase enzyme used for building nucleic acid libraries |
| MIXS:XXXXXXXXX | capt_probe_src_taxid | * Integer |
NCBI taxon ID(s) of all organisms included in the baits of a whole organelle ... |
| MIXS:XXXXXXXXX | capt_probe_desc | * String |
Description of target enrichment probe designs used (e |
| MIXS:XXXXXXXXX | capt_pcr_cyc_tot | * Integer |
Amplification cycles after capture enrichment total |
| MIXS:XXXXXXXXX | reamp_pcr_cyc_tot | 0..1 Integer |
Number of amplification cycles after library indexing PCR |
| MIXS:0000038 | nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000050 | seq_meth | 1 String |
Sequencing machine used |
| MIXS:0000041 | lib_layout | 0..1 recommended LibLayoutEnum |
Specify whether to expect single, paired, or other configuration of reads |
| MIXS:0000040 | lib_reads_seqd | 0..1 recommended Integer |
Total number of clones sequenced from the library |
| MIXS:XXXXXXXXX | sop_lib_preparation | * String |
Citation(s) for the nucleic acid library preparation protocol |
| MIXS:XXXXXXXXX | data_preproc_desc | 0..1 recommended String |
Description of preprocessing performed on the reads in the sequencing data fi... |
| MIXS:XXXXXXXXX | reads_removed | 0..1 recommended Boolean |
Specify whether associated data was filtered in some form prior to upload, su... |
| MIXS:0000057 | assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... |
| MIXS:0000058 | assembly_software | 0..1 recommended String |
Tool(s) used for assembly, including version number and parameters |
| MIXS:0000056 | assembly_qual | 0..1 recommended AssemblyQualEnum |
The assembly quality category is based on sets of criteria outlined for each ... |
| MIXS:0000060 | number_contig | 0..1 recommended Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... |
| MIXS:0000064 | tax_class | 0..1 String |
Method used for taxonomic classification, along with reference database used,... |
| MIXS:0000059 | annot | 0..1 recommended String |
Tool used for annotation, or for cases where annotation was provided by a com... |
| MIXS:0000061 | feat_pred | 0..1 String |
Method used to predict UViGs features such as ORFs, integration site, etc |
| MIXS:0000063 | sim_search_meth | 0..1 String |
Tool used to compare ORFs with database, along with version and cutoffs used |
| MIXS:0000062 | ref_db | 0..1 String |
List of database(s) used for ORF annotation, along with version number and re... |
| MIXS:0000090 | sop | * recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... |
LinkML Source
Direct
name: MimsHumanAssociatedAncient
description: MIxS Data that comply with the Mims checklist, and HumanAssociated and
Ancient extensions.
title: MimsHumanAssociated combined with Ancient
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: Ancient
mixins:
- MimsHumanAssociated
slots:
- project_name
- associated_resource
- orig_site_name
- orig_site_loc
- orig_site_lat
- orig_site_lon
- past_env_broad
- past_env_local
- context_retrieval_date
- stratigraph_context
- geo_loc_name
- lat_lon
- env_broad_scale
- env_local_scale
- alt
- depth
- elev
- temp
- salinity
- perturbation
- experimental_factor
- source_mat_id
- samp_name
- samp_alt_lab_ids
- permit_authority
- permit_id
- permit_date
- permit_scope
- biocultural_label
- earliest_chrono_age
- earliest_chrono_sys
- latest_chrono_age
- latest_chrono_sys
- chrono_age_protocol
- chrono_age_remarks
- geological_epoch
- cultural_era
- samp_taxon_id
- collection_date
- store_cond
- samp_preserv_treatm
- host_subject_id
- ethnicity
- host_age
- host_body_mass_index
- host_sex
- host_height
- host_phenotype
- host_pulse
- host_tot_mass
- host_body_temp
- host_diet
- host_last_meal
- host_body_site
- host_body_product
- host_fam_rel
- twin_sibling
- host_occupation
- host_genotype
- host_symbiont
- host_disease_stat
- palaeopath_status
- blood_blood_disord
- kidney_disord
- pulmonary_disord
- urogenit_tract_disor
- nose_throat_disord
- host_hiv_stat
- medic_hist_perform
- study_complt_stat
- ihmc_medication_code
- chem_administration
- urine_collect_meth
- drug_usage
- smoker
- weight_loss_3_month
- diet_last_six_month
- travel_out_six_month
- pet_farm_animal
- maternal_health_stat
- gestation_state
- foetal_health_stat
- amniotic_fluid_color
- prev_pubs
- ref_biomaterial
- organism_count
- rel_to_oxygen
- host_preserv_state
- oxy_stat_samp
- misc_param
- batch_ids
- samp_category
- neg_cont_type
- pos_cont_type
- env_medium
- samp_collect_method
- samp_collect_device
- samp_mat_process
- samp_size
- samp_store_loc
- samp_store_dur
- samp_store_temp
- samp_decont_pretreat
- size_frac
- samp_vol_we_dna_ext
- nucl_acid_extr_date
- nucl_acid_ext
- sop_experimental
- library_name
- damage_treatment
- lib_strandedness
- adapters
- mid
- lib_mid_desc
- lib_gener_technique
- lib_screen
- lib_vector
- lib_size
- lib_polymerase
- capt_probe_src_taxid
- capt_probe_desc
- capt_pcr_cyc_tot
- reamp_pcr_cyc_tot
- nucl_acid_amp
- seq_meth
- lib_layout
- lib_reads_seqd
- sop_lib_preparation
- data_preproc_desc
- reads_removed
- assembly_name
- assembly_software
- assembly_qual
- number_contig
- tax_class
- annot
- feat_pred
- sim_search_meth
- ref_db
- sop
slot_usage:
project_name:
name: project_name
rank: 1
slot_group: Investigation
associated_resource:
name: associated_resource
rank: 2
slot_group: Investigation
orig_site_name:
name: orig_site_name
rank: 3
slot_group: Environment
orig_site_loc:
name: orig_site_loc
rank: 4
slot_group: Environment
orig_site_lat:
name: orig_site_lat
rank: 5
slot_group: Environment
orig_site_lon:
name: orig_site_lon
rank: 6
slot_group: Environment
past_env_broad:
name: past_env_broad
rank: 7
slot_group: Environment
past_env_local:
name: past_env_local
rank: 8
slot_group: Environment
context_retrieval_date:
name: context_retrieval_date
rank: 9
slot_group: Environment
stratigraph_context:
name: stratigraph_context
rank: 10
slot_group: Environment
geo_loc_name:
name: geo_loc_name
rank: 11
slot_group: Environment
lat_lon:
name: lat_lon
rank: 12
slot_group: Environment
env_broad_scale:
name: env_broad_scale
rank: 13
slot_group: Environment
env_local_scale:
name: env_local_scale
rank: 14
slot_group: Environment
alt:
name: alt
rank: 15
slot_group: Environment
depth:
name: depth
rank: 16
slot_group: Environment
elev:
name: elev
rank: 17
slot_group: Environment
temp:
name: temp
rank: 18
slot_group: Environment
salinity:
name: salinity
rank: 19
slot_group: Environment
perturbation:
name: perturbation
rank: 20
slot_group: Environment
experimental_factor:
name: experimental_factor
rank: 21
slot_group: Environment
source_mat_id:
name: source_mat_id
rank: 22
slot_group: Environment
samp_name:
name: samp_name
rank: 23
slot_group: Environment
samp_alt_lab_ids:
name: samp_alt_lab_ids
rank: 24
slot_group: Environment
permit_authority:
name: permit_authority
rank: 25
slot_group: Environment
permit_id:
name: permit_id
rank: 26
slot_group: Environment
permit_date:
name: permit_date
rank: 27
slot_group: Environment
permit_scope:
name: permit_scope
rank: 28
slot_group: Environment
biocultural_label:
name: biocultural_label
rank: 29
slot_group: Environment
earliest_chrono_age:
name: earliest_chrono_age
rank: 30
slot_group: Environment
earliest_chrono_sys:
name: earliest_chrono_sys
rank: 31
slot_group: Environment
latest_chrono_age:
name: latest_chrono_age
rank: 32
slot_group: Environment
latest_chrono_sys:
name: latest_chrono_sys
rank: 33
slot_group: Environment
chrono_age_protocol:
name: chrono_age_protocol
rank: 34
slot_group: Environment
chrono_age_remarks:
name: chrono_age_remarks
rank: 35
slot_group: Environment
geological_epoch:
name: geological_epoch
rank: 36
slot_group: Environment
cultural_era:
name: cultural_era
rank: 37
slot_group: Environment
samp_taxon_id:
name: samp_taxon_id
rank: 38
slot_group: Environment
collection_date:
name: collection_date
rank: 39
slot_group: Environment
store_cond:
name: store_cond
rank: 40
slot_group: Environment
samp_preserv_treatm:
name: samp_preserv_treatm
rank: 41
slot_group: Environment
host_subject_id:
name: host_subject_id
rank: 42
slot_group: Environment
ethnicity:
name: ethnicity
rank: 43
slot_group: Environment
host_age:
name: host_age
rank: 44
slot_group: Environment
host_body_mass_index:
name: host_body_mass_index
rank: 45
slot_group: Environment
host_sex:
name: host_sex
rank: 46
slot_group: Environment
host_height:
name: host_height
rank: 47
slot_group: Environment
host_phenotype:
name: host_phenotype
rank: 48
slot_group: Environment
host_pulse:
name: host_pulse
rank: 49
slot_group: Environment
host_tot_mass:
name: host_tot_mass
rank: 50
slot_group: Environment
host_body_temp:
name: host_body_temp
rank: 51
slot_group: Environment
host_diet:
name: host_diet
rank: 52
slot_group: Environment
host_last_meal:
name: host_last_meal
rank: 53
slot_group: Environment
host_body_site:
name: host_body_site
rank: 54
slot_group: Environment
host_body_product:
name: host_body_product
rank: 55
slot_group: Environment
host_fam_rel:
name: host_fam_rel
rank: 56
slot_group: Environment
twin_sibling:
name: twin_sibling
rank: 57
slot_group: Environment
host_occupation:
name: host_occupation
rank: 58
slot_group: Environment
host_genotype:
name: host_genotype
rank: 59
slot_group: Environment
host_symbiont:
name: host_symbiont
rank: 60
slot_group: Environment
host_disease_stat:
name: host_disease_stat
rank: 61
slot_group: Environment
palaeopath_status:
name: palaeopath_status
rank: 62
slot_group: Environment
blood_blood_disord:
name: blood_blood_disord
rank: 63
slot_group: Environment
kidney_disord:
name: kidney_disord
rank: 64
slot_group: Environment
pulmonary_disord:
name: pulmonary_disord
rank: 65
slot_group: Environment
urogenit_tract_disor:
name: urogenit_tract_disor
rank: 66
slot_group: Environment
nose_throat_disord:
name: nose_throat_disord
rank: 67
slot_group: Environment
host_hiv_stat:
name: host_hiv_stat
rank: 68
slot_group: Environment
medic_hist_perform:
name: medic_hist_perform
rank: 69
slot_group: Environment
study_complt_stat:
name: study_complt_stat
rank: 70
slot_group: Environment
ihmc_medication_code:
name: ihmc_medication_code
rank: 71
slot_group: Environment
chem_administration:
name: chem_administration
rank: 72
slot_group: Environment
urine_collect_meth:
name: urine_collect_meth
rank: 73
slot_group: Environment
drug_usage:
name: drug_usage
rank: 74
slot_group: Environment
smoker:
name: smoker
rank: 75
slot_group: Environment
weight_loss_3_month:
name: weight_loss_3_month
rank: 76
slot_group: Environment
diet_last_six_month:
name: diet_last_six_month
rank: 77
slot_group: Environment
travel_out_six_month:
name: travel_out_six_month
rank: 78
slot_group: Environment
pet_farm_animal:
name: pet_farm_animal
rank: 79
slot_group: Environment
maternal_health_stat:
name: maternal_health_stat
rank: 80
slot_group: Environment
gestation_state:
name: gestation_state
rank: 81
slot_group: Environment
foetal_health_stat:
name: foetal_health_stat
rank: 82
slot_group: Environment
amniotic_fluid_color:
name: amniotic_fluid_color
rank: 83
slot_group: Environment
prev_pubs:
name: prev_pubs
rank: 84
slot_group: Environment
ref_biomaterial:
name: ref_biomaterial
rank: 85
slot_group: Environment
organism_count:
name: organism_count
rank: 86
slot_group: Environment
rel_to_oxygen:
name: rel_to_oxygen
rank: 87
slot_group: Environment
host_preserv_state:
name: host_preserv_state
rank: 88
slot_group: Environment
oxy_stat_samp:
name: oxy_stat_samp
rank: 89
slot_group: Environment
misc_param:
name: misc_param
rank: 90
slot_group: Environment
batch_ids:
name: batch_ids
rank: 91
slot_group: Nucleic acid source
samp_category:
name: samp_category
rank: 92
slot_group: Nucleic acid source
neg_cont_type:
name: neg_cont_type
rank: 93
slot_group: Nucleic acid source
pos_cont_type:
name: pos_cont_type
rank: 94
slot_group: Nucleic acid source
env_medium:
name: env_medium
rank: 95
slot_group: Nucleic acid source
samp_collect_method:
name: samp_collect_method
rank: 96
slot_group: Nucleic acid source
samp_collect_device:
name: samp_collect_device
rank: 97
slot_group: Nucleic acid source
samp_mat_process:
name: samp_mat_process
rank: 98
slot_group: Nucleic acid source
samp_size:
name: samp_size
rank: 99
slot_group: Nucleic acid source
samp_store_loc:
name: samp_store_loc
rank: 100
slot_group: Nucleic acid source
samp_store_dur:
name: samp_store_dur
rank: 101
slot_group: Nucleic acid source
samp_store_temp:
name: samp_store_temp
rank: 102
slot_group: Nucleic acid source
samp_decont_pretreat:
name: samp_decont_pretreat
rank: 103
slot_group: Nucleic acid source
size_frac:
name: size_frac
rank: 104
slot_group: Nucleic acid source
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
rank: 105
slot_group: Nucleic acid source
nucl_acid_extr_date:
name: nucl_acid_extr_date
rank: 106
slot_group: Nucleic acid source
nucl_acid_ext:
name: nucl_acid_ext
rank: 107
slot_group: Nucleic acid source
sop_experimental:
name: sop_experimental
rank: 108
slot_group: Nucleic acid source
library_name:
name: library_name
rank: 109
slot_group: Sequencing
damage_treatment:
name: damage_treatment
rank: 110
slot_group: Sequencing
lib_strandedness:
name: lib_strandedness
rank: 111
slot_group: Sequencing
adapters:
name: adapters
rank: 112
slot_group: Sequencing
mid:
name: mid
rank: 113
slot_group: Sequencing
lib_mid_desc:
name: lib_mid_desc
rank: 114
slot_group: Sequencing
lib_gener_technique:
name: lib_gener_technique
rank: 115
slot_group: Sequencing
lib_screen:
name: lib_screen
rank: 116
slot_group: Sequencing
lib_vector:
name: lib_vector
rank: 117
slot_group: Sequencing
lib_size:
name: lib_size
rank: 118
slot_group: Sequencing
lib_polymerase:
name: lib_polymerase
rank: 119
slot_group: Sequencing
capt_probe_src_taxid:
name: capt_probe_src_taxid
rank: 120
slot_group: Sequencing
capt_probe_desc:
name: capt_probe_desc
rank: 121
slot_group: Sequencing
capt_pcr_cyc_tot:
name: capt_pcr_cyc_tot
rank: 122
slot_group: Sequencing
reamp_pcr_cyc_tot:
name: reamp_pcr_cyc_tot
rank: 123
slot_group: Sequencing
nucl_acid_amp:
name: nucl_acid_amp
rank: 124
slot_group: Sequencing
seq_meth:
name: seq_meth
rank: 125
slot_group: Sequencing
lib_layout:
name: lib_layout
rank: 126
slot_group: Sequencing
lib_reads_seqd:
name: lib_reads_seqd
rank: 127
slot_group: Sequencing
sop_lib_preparation:
name: sop_lib_preparation
rank: 128
slot_group: Sequencing
data_preproc_desc:
name: data_preproc_desc
rank: 129
slot_group: Data analysis
reads_removed:
name: reads_removed
rank: 130
slot_group: Data analysis
assembly_name:
name: assembly_name
rank: 131
slot_group: Data analysis
assembly_software:
name: assembly_software
rank: 132
slot_group: Data analysis
assembly_qual:
name: assembly_qual
rank: 133
slot_group: Data analysis
number_contig:
name: number_contig
rank: 134
slot_group: Data analysis
tax_class:
name: tax_class
rank: 135
slot_group: Data analysis
annot:
name: annot
rank: 136
slot_group: Data analysis
feat_pred:
name: feat_pred
rank: 137
slot_group: Data analysis
sim_search_meth:
name: sim_search_meth
rank: 138
slot_group: Data analysis
ref_db:
name: ref_db
rank: 139
slot_group: Data analysis
sop:
name: sop
rank: 140
slot_group: Data analysis
class_uri: MIXS:10007_16003_9999903
Induced
name: MimsHumanAssociatedAncient
description: MIxS Data that comply with the Mims checklist, and HumanAssociated and
Ancient extensions.
title: MimsHumanAssociated combined with Ancient
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: Ancient
mixins:
- MimsHumanAssociated
slot_usage:
project_name:
name: project_name
rank: 1
slot_group: Investigation
associated_resource:
name: associated_resource
rank: 2
slot_group: Investigation
orig_site_name:
name: orig_site_name
rank: 3
slot_group: Environment
orig_site_loc:
name: orig_site_loc
rank: 4
slot_group: Environment
orig_site_lat:
name: orig_site_lat
rank: 5
slot_group: Environment
orig_site_lon:
name: orig_site_lon
rank: 6
slot_group: Environment
past_env_broad:
name: past_env_broad
rank: 7
slot_group: Environment
past_env_local:
name: past_env_local
rank: 8
slot_group: Environment
context_retrieval_date:
name: context_retrieval_date
rank: 9
slot_group: Environment
stratigraph_context:
name: stratigraph_context
rank: 10
slot_group: Environment
geo_loc_name:
name: geo_loc_name
rank: 11
slot_group: Environment
lat_lon:
name: lat_lon
rank: 12
slot_group: Environment
env_broad_scale:
name: env_broad_scale
rank: 13
slot_group: Environment
env_local_scale:
name: env_local_scale
rank: 14
slot_group: Environment
alt:
name: alt
rank: 15
slot_group: Environment
depth:
name: depth
rank: 16
slot_group: Environment
elev:
name: elev
rank: 17
slot_group: Environment
temp:
name: temp
rank: 18
slot_group: Environment
salinity:
name: salinity
rank: 19
slot_group: Environment
perturbation:
name: perturbation
rank: 20
slot_group: Environment
experimental_factor:
name: experimental_factor
rank: 21
slot_group: Environment
source_mat_id:
name: source_mat_id
rank: 22
slot_group: Environment
samp_name:
name: samp_name
rank: 23
slot_group: Environment
samp_alt_lab_ids:
name: samp_alt_lab_ids
rank: 24
slot_group: Environment
permit_authority:
name: permit_authority
rank: 25
slot_group: Environment
permit_id:
name: permit_id
rank: 26
slot_group: Environment
permit_date:
name: permit_date
rank: 27
slot_group: Environment
permit_scope:
name: permit_scope
rank: 28
slot_group: Environment
biocultural_label:
name: biocultural_label
rank: 29
slot_group: Environment
earliest_chrono_age:
name: earliest_chrono_age
rank: 30
slot_group: Environment
earliest_chrono_sys:
name: earliest_chrono_sys
rank: 31
slot_group: Environment
latest_chrono_age:
name: latest_chrono_age
rank: 32
slot_group: Environment
latest_chrono_sys:
name: latest_chrono_sys
rank: 33
slot_group: Environment
chrono_age_protocol:
name: chrono_age_protocol
rank: 34
slot_group: Environment
chrono_age_remarks:
name: chrono_age_remarks
rank: 35
slot_group: Environment
geological_epoch:
name: geological_epoch
rank: 36
slot_group: Environment
cultural_era:
name: cultural_era
rank: 37
slot_group: Environment
samp_taxon_id:
name: samp_taxon_id
rank: 38
slot_group: Environment
collection_date:
name: collection_date
rank: 39
slot_group: Environment
store_cond:
name: store_cond
rank: 40
slot_group: Environment
samp_preserv_treatm:
name: samp_preserv_treatm
rank: 41
slot_group: Environment
host_subject_id:
name: host_subject_id
rank: 42
slot_group: Environment
ethnicity:
name: ethnicity
rank: 43
slot_group: Environment
host_age:
name: host_age
rank: 44
slot_group: Environment
host_body_mass_index:
name: host_body_mass_index
rank: 45
slot_group: Environment
host_sex:
name: host_sex
rank: 46
slot_group: Environment
host_height:
name: host_height
rank: 47
slot_group: Environment
host_phenotype:
name: host_phenotype
rank: 48
slot_group: Environment
host_pulse:
name: host_pulse
rank: 49
slot_group: Environment
host_tot_mass:
name: host_tot_mass
rank: 50
slot_group: Environment
host_body_temp:
name: host_body_temp
rank: 51
slot_group: Environment
host_diet:
name: host_diet
rank: 52
slot_group: Environment
host_last_meal:
name: host_last_meal
rank: 53
slot_group: Environment
host_body_site:
name: host_body_site
rank: 54
slot_group: Environment
host_body_product:
name: host_body_product
rank: 55
slot_group: Environment
host_fam_rel:
name: host_fam_rel
rank: 56
slot_group: Environment
twin_sibling:
name: twin_sibling
rank: 57
slot_group: Environment
host_occupation:
name: host_occupation
rank: 58
slot_group: Environment
host_genotype:
name: host_genotype
rank: 59
slot_group: Environment
host_symbiont:
name: host_symbiont
rank: 60
slot_group: Environment
host_disease_stat:
name: host_disease_stat
rank: 61
slot_group: Environment
palaeopath_status:
name: palaeopath_status
rank: 62
slot_group: Environment
blood_blood_disord:
name: blood_blood_disord
rank: 63
slot_group: Environment
kidney_disord:
name: kidney_disord
rank: 64
slot_group: Environment
pulmonary_disord:
name: pulmonary_disord
rank: 65
slot_group: Environment
urogenit_tract_disor:
name: urogenit_tract_disor
rank: 66
slot_group: Environment
nose_throat_disord:
name: nose_throat_disord
rank: 67
slot_group: Environment
host_hiv_stat:
name: host_hiv_stat
rank: 68
slot_group: Environment
medic_hist_perform:
name: medic_hist_perform
rank: 69
slot_group: Environment
study_complt_stat:
name: study_complt_stat
rank: 70
slot_group: Environment
ihmc_medication_code:
name: ihmc_medication_code
rank: 71
slot_group: Environment
chem_administration:
name: chem_administration
rank: 72
slot_group: Environment
urine_collect_meth:
name: urine_collect_meth
rank: 73
slot_group: Environment
drug_usage:
name: drug_usage
rank: 74
slot_group: Environment
smoker:
name: smoker
rank: 75
slot_group: Environment
weight_loss_3_month:
name: weight_loss_3_month
rank: 76
slot_group: Environment
diet_last_six_month:
name: diet_last_six_month
rank: 77
slot_group: Environment
travel_out_six_month:
name: travel_out_six_month
rank: 78
slot_group: Environment
pet_farm_animal:
name: pet_farm_animal
rank: 79
slot_group: Environment
maternal_health_stat:
name: maternal_health_stat
rank: 80
slot_group: Environment
gestation_state:
name: gestation_state
rank: 81
slot_group: Environment
foetal_health_stat:
name: foetal_health_stat
rank: 82
slot_group: Environment
amniotic_fluid_color:
name: amniotic_fluid_color
rank: 83
slot_group: Environment
prev_pubs:
name: prev_pubs
rank: 84
slot_group: Environment
ref_biomaterial:
name: ref_biomaterial
rank: 85
slot_group: Environment
organism_count:
name: organism_count
rank: 86
slot_group: Environment
rel_to_oxygen:
name: rel_to_oxygen
rank: 87
slot_group: Environment
host_preserv_state:
name: host_preserv_state
rank: 88
slot_group: Environment
oxy_stat_samp:
name: oxy_stat_samp
rank: 89
slot_group: Environment
misc_param:
name: misc_param
rank: 90
slot_group: Environment
batch_ids:
name: batch_ids
rank: 91
slot_group: Nucleic acid source
samp_category:
name: samp_category
rank: 92
slot_group: Nucleic acid source
neg_cont_type:
name: neg_cont_type
rank: 93
slot_group: Nucleic acid source
pos_cont_type:
name: pos_cont_type
rank: 94
slot_group: Nucleic acid source
env_medium:
name: env_medium
rank: 95
slot_group: Nucleic acid source
samp_collect_method:
name: samp_collect_method
rank: 96
slot_group: Nucleic acid source
samp_collect_device:
name: samp_collect_device
rank: 97
slot_group: Nucleic acid source
samp_mat_process:
name: samp_mat_process
rank: 98
slot_group: Nucleic acid source
samp_size:
name: samp_size
rank: 99
slot_group: Nucleic acid source
samp_store_loc:
name: samp_store_loc
rank: 100
slot_group: Nucleic acid source
samp_store_dur:
name: samp_store_dur
rank: 101
slot_group: Nucleic acid source
samp_store_temp:
name: samp_store_temp
rank: 102
slot_group: Nucleic acid source
samp_decont_pretreat:
name: samp_decont_pretreat
rank: 103
slot_group: Nucleic acid source
size_frac:
name: size_frac
rank: 104
slot_group: Nucleic acid source
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
rank: 105
slot_group: Nucleic acid source
nucl_acid_extr_date:
name: nucl_acid_extr_date
rank: 106
slot_group: Nucleic acid source
nucl_acid_ext:
name: nucl_acid_ext
rank: 107
slot_group: Nucleic acid source
sop_experimental:
name: sop_experimental
rank: 108
slot_group: Nucleic acid source
library_name:
name: library_name
rank: 109
slot_group: Sequencing
damage_treatment:
name: damage_treatment
rank: 110
slot_group: Sequencing
lib_strandedness:
name: lib_strandedness
rank: 111
slot_group: Sequencing
adapters:
name: adapters
rank: 112
slot_group: Sequencing
mid:
name: mid
rank: 113
slot_group: Sequencing
lib_mid_desc:
name: lib_mid_desc
rank: 114
slot_group: Sequencing
lib_gener_technique:
name: lib_gener_technique
rank: 115
slot_group: Sequencing
lib_screen:
name: lib_screen
rank: 116
slot_group: Sequencing
lib_vector:
name: lib_vector
rank: 117
slot_group: Sequencing
lib_size:
name: lib_size
rank: 118
slot_group: Sequencing
lib_polymerase:
name: lib_polymerase
rank: 119
slot_group: Sequencing
capt_probe_src_taxid:
name: capt_probe_src_taxid
rank: 120
slot_group: Sequencing
capt_probe_desc:
name: capt_probe_desc
rank: 121
slot_group: Sequencing
capt_pcr_cyc_tot:
name: capt_pcr_cyc_tot
rank: 122
slot_group: Sequencing
reamp_pcr_cyc_tot:
name: reamp_pcr_cyc_tot
rank: 123
slot_group: Sequencing
nucl_acid_amp:
name: nucl_acid_amp
rank: 124
slot_group: Sequencing
seq_meth:
name: seq_meth
rank: 125
slot_group: Sequencing
lib_layout:
name: lib_layout
rank: 126
slot_group: Sequencing
lib_reads_seqd:
name: lib_reads_seqd
rank: 127
slot_group: Sequencing
sop_lib_preparation:
name: sop_lib_preparation
rank: 128
slot_group: Sequencing
data_preproc_desc:
name: data_preproc_desc
rank: 129
slot_group: Data analysis
reads_removed:
name: reads_removed
rank: 130
slot_group: Data analysis
assembly_name:
name: assembly_name
rank: 131
slot_group: Data analysis
assembly_software:
name: assembly_software
rank: 132
slot_group: Data analysis
assembly_qual:
name: assembly_qual
rank: 133
slot_group: Data analysis
number_contig:
name: number_contig
rank: 134
slot_group: Data analysis
tax_class:
name: tax_class
rank: 135
slot_group: Data analysis
annot:
name: annot
rank: 136
slot_group: Data analysis
feat_pred:
name: feat_pred
rank: 137
slot_group: Data analysis
sim_search_meth:
name: sim_search_meth
rank: 138
slot_group: Data analysis
ref_db:
name: ref_db
rank: 139
slot_group: Data analysis
sop:
name: sop
rank: 140
slot_group: Data analysis
attributes:
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
examples:
- value: Forest soil metagenome
in_subset:
- investigation
from_schema: https://w3id.org/mixs
rank: 1
keywords:
- project
slot_uri: MIXS:0000092
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Investigation
range: string
required: true
associated_resource:
name: associated_resource
annotations:
Expected_value:
tag: Expected_value
value: reference to resource
description: A related resource that is referenced, cited, or otherwise associated
to the sequence
title: relevant electronic resources
examples:
- value: http://www.earthmicrobiome.org/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 2
keywords:
- resource
slot_uri: MIXS:0000091
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Investigation
range: string
recommended: true
multivalued: true
structured_pattern:
syntax: ^({PMID}|{DOI}|{URL})$
interpolated: true
orig_site_name:
name: orig_site_name
annotations:
Expected_value:
tag: Expected_value
value: Name of site or location where sample was originated
description: Designated name of the archaeological or ecological site, ancient
settlement, or location etc. where the sample was originally collected. Can
be a non-geographical name, such as a field-specific name or code, the official
name of an excavation, or a colloquial name that is used in academic literature.
Typically names that would not be found on official maps. If the site name is
unclear please use the name of the closest location or region as best as possible.
Can also include different transliterations or languages used in the literature.
title: name of site or location where sample originated
examples:
- value: Valley of the Kings
- value: Krakow Spadzista B
- value: Coopers Cave
- value: Cutler Fossil Site
- value: Kap København Formation
- value: Northern Italy, Lombardy, exact location unknown
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 3
keywords:
- environment
- sample
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: true
multivalued: true
orig_site_loc:
name: orig_site_loc
annotations:
Expected_value:
tag: Expected_value
value: Name of original geographic origin of the sample
description: The original geographical origin of the sample, when sampled outside
its original natural environment (e.g. sampled in a museum collection), as defined
by the country or sea name followed by specific region name. Country or sea
names should be chosen from the INSDC country list (http://insdc.org/country.html),
or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ).
title: original site location
examples:
- value: 'South Africa: Western Cape'
- value: 'Germany: Baden-Württemberg, Geißenklösterle Cave'
- value: 'Northern Italy: Lombardy'
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 4
keywords:
- location
- site
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: false
structured_pattern:
syntax: '^{country}: {region}, {specific_location}$'
orig_site_lat:
name: orig_site_lat
description: The latitude coordinate of the original geographical origin of the
sample, e.g. the original place the sample was buried, deposited, or formed.
In cases where the sample was directly sampled in the burial environment for
the purposes of scientific investigation, this will be the same as geo_loc_name,
and lat_lon. For samples kept in collections, the geo_loc_name and lat_lon terms
are used to refer to the collection where the sample is stored, but this term
is used for the original geographic location the sample existed in prior to
archiving in a collection (i.e., should correspond to orig_site_loc, not the
collection itself as recorded in site_name). The values should be reported in
decimal degrees, limited to 8 decimal points, and in WGS84 system.
title: original geographic location (latitude)
examples:
- value: '50.586825'
- value: '-0.123'
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 5
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: false
structured_pattern:
syntax: ^{lat}$
interpolated: true
partial_match: true
orig_site_lon:
name: orig_site_lon
description: The longitude coordinate of the original geographical origin of the
sample, e.g. the original place the sample was buried, deposited, or formed.
In cases where the sample was directly sampled in the burial environment for
the purposes of scientific investigation, this will be the same as geo_loc_name,
and lat_lon. For samples kept in collections, the geo_loc_name and lat_lon terms
are used to refer to the collection where the sample is stored, but this term
is used for the original geographic location the sample existed in prior to
archiving in a collection (i.e., should correspond to orig_site_loc, not the
collection itself, as recorded in site_name). The values should be reported
in decimal degrees, limited to 8 decimal points, and in WGS84 system.
title: original geographic location (longitude)
examples:
- value: '6.408977'
- value: '-12.12'
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 6
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: false
structured_pattern:
syntax: ^{lon}$
interpolated: true
partial_match: true
past_env_broad:
name: past_env_broad
description: 'Report information about the general ancient broad environmental
system that the sample or specimen existed or lived within, as it was at the
time of deposition or burial (e.g. in the desert or a forest). This should not
describe the environment as it is today (e.g. farmland), but specifically the
state as it was in the past (i.e. the palaeo- or (pre)historical ecosystem).
Compared to `env_broad_scale` which is taken from direct observation, the information
about the past environment will normally be derived from inference from archaeological,
palaeontological, geological, or other scientific methods. We recommend using
subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.
EnvO documentation about how to use the field for present day equivalents: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\""'
title: broad-scale past environmental context
examples:
- value: dessert biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 7
keywords:
- context
- environmental
- ancient
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
past_env_local:
name: past_env_local
annotations:
Expected_value:
tag: Expected_value
value: Report information about smaller environmental entities having causal
influences upon the sample or specimen at/during the time of burial
description: 'Report information about the smaller-scale environmental system
of the local vicinity of the sample or specimen at the time of deposition or
burial (e.g. in hillside, burial mound, or midden). This should not describe
the environment as it is today (e.g. carpark), but specifically the entity or
entities surrounding the sample that may have significant causal influences
as it was in the past. Compared to `env_local_scale` which is taken from direct
observation, the information about the past environment will normally be derived
from inference from archaeological, palaeontological, geological, or other scientific
methods. We recommend using EnvO terms which are of smaller than your entry
for past_env_broad. Terms, such as anatomical sites, from other OBO Library
ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field.
EnvO documentation about how to use the field for present day equivalents: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\'
title: local past environmental context
examples:
- value: hillside [ENVO:01000333]
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 8
keywords:
- context
- environmental
- ancient
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: true
context_retrieval_date:
name: context_retrieval_date
annotations:
Preferred_unit:
tag: Preferred_unit
value: year
description: 'Date of excavation or retrieval from burial or depositional context,
if known. If excavations were done during a longer period, report its midpoint
at a month or year level. In case no exact time is available, the date can be right
truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant.'
title: date of retrieval from depositional context
examples:
- value: '2023'
- value: 1972-11
- value: '2001-09-25'
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 9
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: datetime
required: false
recommended: true
stratigraph_context:
name: stratigraph_context
annotations:
Expected_value:
tag: Expected_value
value: Stratigraphic context that the sample was retrieved from
description: Associated stratigraphic context(s) that the sample was retrieved
from, usually from an archaeological or palaeontological excavation. Description(s)
or identifier(s) of stratigraphic units or layer names within and/or relative
to the site (e.g., stratigraphic unit ID, archaeological feature ID, layer name
or a description, grid location).
title: stratigraphic context
examples:
- value: Layer 5
- value: Layer UE
- value: Horizon IIc, Quadrant 77
- value: HF_23447_77_410_IIc
- value: KrSp C2/2011/B5
- value: US10
- value: YSL
- value: Subunit 1
- value: Black Mousterian (BM)
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 10
keywords:
- identifiers
- excavation
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: true
geo_loc_name:
name: geo_loc_name
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name. Country or sea names should be chosen
from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
(http://purl.bioontology.org/ontology/GAZ)
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 11
keywords:
- geographic
- location
slot_uri: MIXS:0000010
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: true
structured_pattern:
syntax: '^{country}: {region}, {specific_location}$'
interpolated: true
partial_match: true
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees, limited to 8 decimal
points, and in WGS84 system
title: geographic location (latitude and longitude)
examples:
- value: 50.586825 6.408977
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 12
keywords:
- geographic
- location
slot_uri: MIXS:0000009
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: true
structured_pattern:
syntax: ^{lat} {lon}$
interpolated: true
partial_match: true
env_broad_scale:
name: env_broad_scale
description: 'Report the major environmental system the sample or specimen came
from. The system(s) identified should have a coarse spatial grain, to provide
the general environmental context of where the sampling was done (e.g. in the
desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.
EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: broad-scale environmental context
examples:
- value: rangeland biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 13
keywords:
- context
- environmental
slot_uri: MIXS:0000012
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: true
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
env_local_scale:
name: env_local_scale
annotations:
Expected_value:
tag: Expected_value
value: Environmental entities having causal influences upon the entity at
time of sampling
description: 'Report the entity or entities which are in the sample or specimen
s local vicinity and which you believe have significant causal influences on
your sample or specimen. We recommend using EnvO terms which are of smaller
spatial grain than your entry for env_broad_scale. Terms, such as anatomical
sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
UBERON) are accepted in this field. EnvO documentation about how to use the
field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: local environmental context
examples:
- value: hillside [ENVO:01000333]
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 14
keywords:
- context
- environmental
slot_uri: MIXS:0000013
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: true
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
alt:
name: alt
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
balloons and heights of places such as atmospheric layers and clouds. It is
used to measure the height of an object which is above the earth's surface.
In this context, the altitude measurement is the vertical distance between the
earth's surface above sea level and the sampled position in the air
title: altitude
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 15
slot_uri: MIXS:0000094
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- HostAssociated
- MiscellaneousNaturalOrArtificialEnvironment
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
recommended: true
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
depth:
name: depth
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: The vertical distance below local surface. For sediment or soil samples
depth is measured from sediment or soil surface, respectively. Depth can be
reported as an interval for subsurface samples
title: depth
examples:
- value: 10 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 16
keywords:
- depth
slot_uri: MIXS:0000018
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
recommended: true
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
elev:
name: elev
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit
title: elevation
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 17
keywords:
- elevation
slot_uri: MIXS:0000093
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- HostAssociated
- HydrocarbonResourcesCores
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
recommended: true
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
temp:
name: temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature of the sample at the time of sampling
title: temperature
examples:
- value: 25 degree Celsius
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 18
keywords:
- temperature
slot_uri: MIXS:0000113
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
recommended: true
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
salinity:
name: salinity
annotations:
Preferred_unit:
tag: Preferred_unit
value: practical salinity unit, percentage
description: The total concentration of all dissolved salts in a liquid or solid
sample. While salinity can be measured by a complete chemical analysis, this
method is difficult and time consuming. More often, it is instead derived from
the conductivity measurement. This is known as practical salinity. These derivations
compare the specific conductance of the sample to a salinity standard such as
seawater
title: salinity
examples:
- value: 25 practical salinity unit
from_schema: https://w3id.org/mixs
rank: 19
keywords:
- salinity
slot_uri: MIXS:0000183
owner: MimsHumanAssociatedAncient
domain_of:
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
perturbation:
name: perturbation
annotations:
Expected_value:
tag: Expected_value
value: perturbation type name;perturbation interval and duration
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
examples:
- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
from_schema: https://w3id.org/mixs
rank: 20
keywords:
- perturbation
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
multivalued: true
experimental_factor:
name: experimental_factor
annotations:
Expected_value:
tag: Expected_value
value: text or EFO and/or OBI
description: Variable aspects of an experiment design that can be used to describe
an experiment, or set of experiments, in an increasingly detailed manner. This
field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
Ontology for Biomedical Investigations (OBI)
title: experimental factor
examples:
- value: time series design [EFO:0001779]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
rank: 21
keywords:
- experimental
- factor
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
recommended: true
multivalued: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
source_mat_id:
name: source_mat_id
annotations:
Expected_value:
tag: Expected_value
value: 'for cultures of microorganisms: identifiers for two culture collections;
for other material a unique arbitrary identifer'
description: A unique identifier assigned to a material sample (as defined by
http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
digital record of a material sample) used for extracting nucleic acids, and
subsequent sequencing. The identifier can refer either to the original material
collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
/bio_material, or /culture_collection may or may not share the same value as
the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
sampled tissue with the same identifier. However, the /culture_collection qualifier
may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
would refer to an identifier from some derived culture from which the nucleic
acids were extracted (e.g. xatc123 or ark:/2154/R2)
title: source material identifiers
examples:
- value: MPI012345
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 22
keywords:
- identifier
- material
- source
slot_uri: MIXS:0000026
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
recommended: true
multivalued: true
samp_name:
name: samp_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
description: A local identifier or name that for the material sample used for
extracting nucleic acids, and subsequent sequencing. It can refer either to
the original material collected or to any derived sub-samples. It can have any
format, but we suggest that you make it concise, unique and consistent within
your lab, and as informative as possible. INSDC requires every sample name from
a single Submitter to be unique. Use of a globally unique identifier for the
field source_mat_id is recommended in addition to sample_name
title: sample name
examples:
- value: ISDsoil1
in_subset:
- investigation
from_schema: https://w3id.org/mixs
rank: 23
keywords:
- sample
slot_uri: MIXS:0001107
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: true
samp_alt_lab_ids:
name: samp_alt_lab_ids
description: 'An alternative sample or material ID related to the sample not already
covered by terms samp_name and source_mat_id, including from associated other
non-genetic analyses of the same sample, that can be used synonymously with
the main ID. For example: external database IDs, internal lab sample ID from
sampling such as bone drilling, or IDs from other scientific analyses. Can be
specified multiple times for different ID contexts.'
title: alternative sample IDs
examples:
- value: ABC_24
- value: Grave 6
- value: 'Museum ID: NHM_AR_123, Drilling ID: DRL_001, Extraction ID: ABC_24'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 24
string_serialization: '{text}'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: true
permit_authority:
name: permit_authority
annotations:
Expected_value:
tag: Expected_value
value: Name of authority providing permission or ethical approval.
description: Name of the authorit(ies) or institution(s) that granted sampling
and analysis (e.g. human remains) and/or export permission (e.g. animal remains),
as well any form of ethical approval (whether from institutional research ethics
boards such as REB or IRBs, or indigenous or native community associations),
if available.
title: permit authority
examples:
- value: University of Copenhagen
- value: Federal Foreign Office (Germany)
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
close_mappings:
- dc:rightsHolder
rank: 25
keywords:
- ethics
- location
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: true
multivalued: true
permit_id:
name: permit_id
description: A permit ID, code, or any form of identify provided by any authority
(ethical, local, legal, academic etc.) associated with the approval of the analysis
of this particular sample, if available.
title: permit or approval ID
examples:
- value: DE-123-JK
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 26
keywords:
- ethics
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: true
multivalued: true
permit_date:
name: permit_date
description: 'Date on which a permit was granted. The date can be right truncated
i.e. all of these are valid times: 2008-01-23; 2008-01; 2008; Except: 2008-01;
2008 all are ISO8601 compliant.'
title: date of permit approval
examples:
- value: '2023-12-01'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 27
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: datetime
required: false
recommended: true
multivalued: true
permit_scope:
name: permit_scope
annotations:
Expected_value:
tag: Expected_value
value: Description of the scope of ethical permissions for data use.
description: Description of the original scope and permissions of the research
on the genetic material, as was approved by a legal, ethical, or relevant authority
(e.g. bacteria only, DNA only, bacteria and human, no host read analysis allowed).
Note this description is only informative, and will not necessarily automatically
apply restrictions to associated data to other researchers.
title: permit scope
examples:
- value: Defined scope only includes the study of bacterial sequences and any
human sequence is not covered under the agreement.
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
close_mappings:
- dc:accessRights
- dc:license
rank: 28
keywords:
- ethics
string_serialization: '{text}'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: true
multivalued: true
biocultural_label:
name: biocultural_label
annotations:
Expected_value:
tag: Expected_value
value: Relevant biocultural label from https://localcontexts.org/labels/biocultural-labels/
description: Relevant biocultural labels defined by the local contexts project
(https://localcontexts.org/label/bc-provenance/) that describe in what ways
this data can be reused, as permitted by any associated native or indigenous
peoples or communities.
title: biocultural label
examples:
- value: BC R
- value: BC MC
- value: BC MC;BC CV
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 29
keywords:
- ethics
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: BioCulturalLabelEnum
required: false
recommended: true
multivalued: true
earliest_chrono_age:
name: earliest_chrono_age
annotations:
Expected_value:
tag: Expected_value
value: age value corresponding to unit
description: The maximum/earliest/oldest possible age of a specimen as determined
by a dating method. If multiple dating measurements available, use the most
earliest/oldest date to provide widest range of age possibilities. The specific
age unit should be specified by the term earliest_chrono_sys. More information
on specific dates (e.g. radiocarbon lab codes) can be specified in the term
chrono_age_remarks.
title: earliest chronometric age
examples:
- value: '120000'
- value: '1900'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
broad_mappings:
- chrono:earliestChronometricAge
rank: 30
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: integer
required: true
recommended: true
multivalued: false
earliest_chrono_sys:
name: earliest_chrono_sys
description: The reference system associated with the earliest_chrono_age.
title: earliest chronometric age reference system
examples:
- value: cal BP
- value: CE
- value: Ma
- value: ka
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
broad_mappings:
- chrono:earliestChronometricAgeReferenceSystem
rank: 31
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: ChronoAgeSysEnum
required: true
recommended: true
multivalued: false
latest_chrono_age:
name: latest_chrono_age
annotations:
Expected_value:
tag: Expected_value
value: age value corresponding to unit
description: The minimum/latest/youngest possible age of a specimen as determined
by a dating method. If multiple dating measurements available, use the most
latest/youngest date to provide widest range of age possibilities. The specific
age unit should be specified by the term latest_chrono_sys. More information
on specific dates (e.g. radiocarbon lab codes) can be specified in the term
chrono_age_remarks.
title: latest chronometric age
examples:
- value: '100000'
- value: '1700'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
broad_mappings:
- chrono:latestChronometricAge
rank: 32
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: integer
required: true
recommended: true
multivalued: false
latest_chrono_sys:
name: latest_chrono_sys
description: The reference system associated with the latest_chrono_age.
title: latest chronometric age reference system
examples:
- value: cal BP
- value: CE
- value: Ma
- value: ka
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
broad_mappings:
- chrono:latestChronometricAgeReferenceSystem
rank: 33
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: ChronoAgeSysEnum
required: true
recommended: true
multivalued: false
chrono_age_protocol:
name: chrono_age_protocol
description: A description of or reference to the methods used to determine the
earliest_chrono_age and latest_chrono_age.
title: chronometric age protocol
examples:
- value: radiocarbon dating
- value: optically stimulated infrared luminescence
- value: contextual dating
- value: historical records
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
broad_mappings:
- chrono:chronometricAgeProtocol
rank: 34
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: ChronoAgeProtocolEnum
required: false
recommended: true
multivalued: true
chrono_age_remarks:
name: chrono_age_remarks
description: Notes or comments about the earliest_chrono_age and latest_chrono_age.
For more detail use Chronometric Age Protocol to point to original publication
describing method. Useful to specify confidence and/or accuracy of reported
date.
title: chronometric age remarks
examples:
- value: radiocarbon dating, calibrated with OxCal v4.3 with 95% confidence interval
- value: based on proxy dating from other bone samples of stratigraphic layer
- value: a coin found in the burial was from the 3rd century was found in the
mouth of the skeleton
- value: age taken from previous publication Doe et al. 2019
- value: 'radiocarbon age ID: OxA-12345'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
close_mappings:
- chrono:chronometricAgeRemarks
rank: 35
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: true
multivalued: false
geological_epoch:
name: geological_epoch
annotations:
Expected_value:
tag: Expected_value
value: ontology term; text
description: 'The geological epoch approximating to the period within which the
specimen or sample existed. Where possible use terms from ontologies. NOTE:
This term is for geological timescales. For more precise or anthropogenic defined
periods, use `Cultural Era`.'
title: geological epoch
examples:
- value: Pleistocene
- value: Upper Cretaceous
- value: Pliocene
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 36
keywords:
- ancient
- age
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: GeolEpochEnum
required: false
recommended: false
multivalued: false
cultural_era:
name: cultural_era
annotations:
Expected_value:
tag: Expected_value
value: chronotology or PeriodO term; text
description: The cultural era approximating to the period in which the archaeological
remains existed in. Where possible use terms from ontologies such as Chronontology
(https://chronontology.dainst.org/) or PeriodO (https://perio.do/en/).
title: cultural era or period
examples:
- value: 'Copper Age [Chronotology: NW6hofAScJSE]'
- value: Upper Middle Palaeolthic
- value: Not collected
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 37
keywords:
- ancient
- age
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: false
samp_taxon_id:
name: samp_taxon_id
description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa
sample. Use 'synthetic metagenome for mock community/positive controls, or
'blank sample' for negative controls
title: taxonomy ID of DNA sample
examples:
- value: Gut Metagenome [NCBITaxon:749906]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
rank: 38
keywords:
- dna
- identifier
- sample
- taxon
slot_uri: MIXS:0001320
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: true
structured_pattern:
syntax: ^{text} \[{NCBItaxon_id}\]$
interpolated: true
partial_match: true
collection_date:
name: collection_date
description: 'The time of sampling, either as an instance (single point in time)
or interval. In case no exact time is available, the date/time can be right
truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
title: collection date
examples:
- value: '2013-03-25T12:42:31+01:00'
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 39
keywords:
- date
slot_uri: MIXS:0000011
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: datetime
required: true
store_cond:
name: store_cond
description: Explain how and for how long the sample was stored before DNA extraction
(for example, fresh/frozen/other). Include factors that may influence nucleic
acid recovery or library construction. For example, specify temperature, humidity,
presence of microbial overgrowth etc..
title: storage conditions
examples:
- value: -20 degree Celsius freezer;P2Y10D
- value: climate-controlled
- value: Mould growth in storage box observed
- value: Stored at -20oC until 2025-05-15
- value: Stored in the museum from 1924 to 2021
from_schema: https://w3id.org/mixs
rank: 40
keywords:
- condition
- storage
slot_uri: MIXS:0000327
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- Ancient
- Soil
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^{storage_condition_type};{duration}$
samp_preserv_treatm:
name: samp_preserv_treatm
description: Description of any treatment applied directly to samples for the
specific purpose of maximising longevity of sample preservation in archives
and/or collections by curators that may influence downstream nucleic acid recovery
or library construction, such as storage fluid or reconstructive glue.
title: preservational treatment
examples:
- value: stored in formalin
- value: reconstructive glue applied
- value: alcohol preserved
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 41
keywords:
- ancient
string_serialization: '{text}'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: true
host_subject_id:
name: host_subject_id
description: A unique identifier by which each subject can be referred to, de-identified
title: host subject id
examples:
- value: MPI123
from_schema: https://w3id.org/mixs
rank: 42
keywords:
- host
- host.
- identifier
slot_uri: MIXS:0000861
owner: MimsHumanAssociatedAncient
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
ethnicity:
name: ethnicity
annotations:
Expected_value:
tag: Expected_value
value: text recommend from Wikipedia list
description: A category of people who identify with each other, usually on the
basis of presumed similarities such as a common language, ancestry, history,
society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups
title: ethnicity
examples:
- value: native american
from_schema: https://w3id.org/mixs
rank: 43
slot_uri: MIXS:0000895
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
multivalued: true
host_age:
name: host_age
annotations:
Preferred_unit:
tag: Preferred_unit
value: year, day, hour
description: Age of host at the time of sampling; relevant scale depends on species
and study, e.g. Could be seconds for amoebae or centuries for trees
title: host age
examples:
- value: 30 years
from_schema: https://w3id.org/mixs
rank: 44
keywords:
- age
- host
- host.
slot_uri: MIXS:0000255
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_body_mass_index:
name: host_body_mass_index
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram per square meter
description: Body mass index, calculated as weight/(height)squared
title: host body-mass index
examples:
- value: 22 kilogram per square meter
from_schema: https://w3id.org/mixs
rank: 45
keywords:
- host
- host.
slot_uri: MIXS:0000317
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_sex:
name: host_sex
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Gender or physical sex of the host
title: host sex
comments:
- example of non-binary from Excel sheets does not match any of the enumerated
values
from_schema: https://w3id.org/mixs
rank: 46
keywords:
- host
- host.
string_serialization: '[female|hermaphrodite|non-binary|male|transgender|transgender
(female to male)|transgender (male to female) |undeclared]'
slot_uri: MIXS:0000811
owner: MimsHumanAssociatedAncient
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
host_height:
name: host_height
annotations:
Preferred_unit:
tag: Preferred_unit
value: centimeter, millimeter, meter
description: The height of subject
title: host height
examples:
- value: 1.75 meter
from_schema: https://w3id.org/mixs
rank: 47
keywords:
- height
- host
- host.
slot_uri: MIXS:0000264
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_phenotype:
name: host_phenotype
annotations:
Expected_value:
tag: Expected_value
value: PATO or HP
description: Phenotype of human or other host. Use terms from the phenotypic quality
ontology (pato) or the Human Phenotype Ontology (HP)
title: host phenotype
examples:
- value: Tinnitus [HP:0000360]
from_schema: https://w3id.org/mixs
rank: 48
keywords:
- host
- host.
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000874
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
host_pulse:
name: host_pulse
annotations:
Preferred_unit:
tag: Preferred_unit
value: beats per minute
description: Resting pulse, measured as beats per minute
title: host pulse
examples:
- value: 65 beats per minute
from_schema: https://w3id.org/mixs
rank: 49
keywords:
- host
- host.
slot_uri: MIXS:0000333
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_tot_mass:
name: host_tot_mass
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram, gram
description: Total mass of the host at collection, the unit depends on host
title: host total mass
examples:
- value: 65 kilogram
from_schema: https://w3id.org/mixs
rank: 50
keywords:
- host
- host.
- mass
- total
slot_uri: MIXS:0000263
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_body_temp:
name: host_body_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Core body temperature of the host when sample was collected
title: host body temperature
examples:
- value: 36.5 degree Celsius
from_schema: https://w3id.org/mixs
rank: 51
keywords:
- body
- host
- host.
- temperature
slot_uri: MIXS:0000274
owner: MimsHumanAssociatedAncient
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_diet:
name: host_diet
description: Type of diet depending on the host, for animals omnivore, herbivore
etc., for humans high-fat, meditteranean etc.; can include multiple diet types
title: host diet
examples:
- value: high-fat
from_schema: https://w3id.org/mixs
rank: 52
keywords:
- diet
- host
- host.
slot_uri: MIXS:0000869
owner: MimsHumanAssociatedAncient
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
multivalued: true
host_last_meal:
name: host_last_meal
annotations:
Expected_value:
tag: Expected_value
value: content;duration
description: Content of last meal and time since feeding; can include multiple
values
title: host last meal
examples:
- value: french fries;P5H30M
from_schema: https://w3id.org/mixs
rank: 53
keywords:
- host
- host.
string_serialization: '{text};{duration}'
slot_uri: MIXS:0000870
owner: MimsHumanAssociatedAncient
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
multivalued: true
host_body_site:
name: host_body_site
annotations:
Expected_value:
tag: Expected_value
value: FMA or UBERON
description: Name of body site where the sample was obtained from, such as a specific
organ or tissue (tongue, lung etc...). Use terms from the foundational model
of anatomy ontology (fma) or the Uber-anatomy ontology (UBERON)
title: host body site
examples:
- value: Lung parenchyma [fma27360]
from_schema: https://w3id.org/mixs
rank: 54
keywords:
- body
- host
- site
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000867
owner: MimsHumanAssociatedAncient
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
host_body_product:
name: host_body_product
annotations:
Expected_value:
tag: Expected_value
value: FMA or UBERON
description: Substance produced by the body, e.g. Stool, mucus, where the sample
was obtained from. Use terms from the foundational model of anatomy ontology
(fma) or Uber-anatomy ontology (UBERON)
title: host body product
examples:
- value: mucus [FMA:66938]
from_schema: https://w3id.org/mixs
rank: 55
keywords:
- body
- host
- host.
- product
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000888
owner: MimsHumanAssociatedAncient
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
host_fam_rel:
name: host_fam_rel
annotations:
Expected_value:
tag: Expected_value
value: relationship type;arbitrary identifier
description: Relationships to other hosts in the same study; can include multiple
relationships
title: host family relationship
examples:
- value: mother;ID298
from_schema: https://w3id.org/mixs
rank: 56
keywords:
- family
- host
- host.
- relationship
string_serialization: '{text};{text}'
slot_uri: MIXS:0000872
owner: MimsHumanAssociatedAncient
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
multivalued: true
twin_sibling:
name: twin_sibling
description: Specification of twin sibling presence
title: twin sibling presence
examples:
- value: 'yes'
from_schema: https://w3id.org/mixs
rank: 57
keywords:
- presence
slot_uri: MIXS:0000326
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: boolean
host_occupation:
name: host_occupation
description: Most frequent job performed by subject
title: host occupation
comments:
- Couldn't convert host_occupation with value veterinary to integer
- almost all host_occupation values in the NCBI biosample_set are strings, not
integers
examples:
- value: veterinary
from_schema: https://w3id.org/mixs
rank: 58
keywords:
- host
- host.
slot_uri: MIXS:0000896
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: string
host_genotype:
name: host_genotype
description: Observed genotype
title: host genotype
examples:
- value: ST1
from_schema: https://w3id.org/mixs
rank: 59
keywords:
- host
- host.
slot_uri: MIXS:0000365
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
host_symbiont:
name: host_symbiont
annotations:
Expected_value:
tag: Expected_value
value: species name or common name
description: The taxonomic name of the organism(s) found living in mutualistic,
commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont
can have its own symbionts. For example, parasites may have hyperparasites (=parasites
of the parasite)
title: observed host symbionts
examples:
- value: flukeworms
from_schema: https://w3id.org/mixs
rank: 60
keywords:
- host
- host.
- observed
- symbiosis
slot_uri: MIXS:0001298
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
multivalued: true
host_disease_stat:
name: host_disease_stat
annotations:
Expected_value:
tag: Expected_value
value: disease name or Disease Ontology term
description: List of diseases with which the host has been diagnosed; can include
multiple diagnoses. The value of the field depends on host; for humans the terms
should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
non-human host diseases are free text
title: host disease status
examples:
- value: measles [DOID:8622]
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 61
keywords:
- disease
- host
- host.
- status
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000031
owner: MimsHumanAssociatedAncient
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
palaeopath_status:
name: palaeopath_status
annotations:
Expected_value:
tag: Expected_value
value: description of health related observation on ancient remains
description: Describe briefly any relevant palaeopathological or health-related
observations of the remains of the individual or subject under study.
title: palaeopathology status
examples:
- value: Osteoporosis.
- value: Parasites found in pelvic area.
- value: Caries on right upper molar.
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 62
keywords:
- palaeopathology
- host health
- ancient
string_serialization: '{text}'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: false
blood_blood_disord:
name: blood_blood_disord
description: History of blood disorders; can include multiple disorders. The
terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
hematopoietic system disease (https://disease-ontology.org/?id=DOID:74)
title: blood/blood disorder
from_schema: https://w3id.org/mixs
rank: 63
keywords:
- disorder
slot_uri: MIXS:0000271
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
multivalued: true
kidney_disord:
name: kidney_disord
description: History of kidney disorders; can include multiple disorders. The
terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
kidney disease (https://disease-ontology.org/?id=DOID:557)
title: urine/kidney disorder
from_schema: https://w3id.org/mixs
rank: 64
keywords:
- disorder
slot_uri: MIXS:0000277
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
multivalued: true
pulmonary_disord:
name: pulmonary_disord
description: History of pulmonary disorders; can include multiple disorders. The
terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
lung disease (https://disease-ontology.org/?id=DOID:850)
title: lung/pulmonary disorder
from_schema: https://w3id.org/mixs
rank: 65
keywords:
- disorder
slot_uri: MIXS:0000269
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
multivalued: true
urogenit_tract_disor:
name: urogenit_tract_disor
description: History of urogenital tract disorders; can include multiple disorders.
The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
urinary system disease (https://disease-ontology.org/?id=DOID:18)
title: urine/urogenital tract disorder
from_schema: https://w3id.org/mixs
rank: 66
keywords:
- disorder
slot_uri: MIXS:0000278
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
multivalued: true
nose_throat_disord:
name: nose_throat_disord
description: 'Report any history of nose, mouth, teeth and/or throat disorders
in the subject. May include multiple disorders.
'
title: nose throat disorder
comments:
- 'The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory
tract disease (https://disease-ontology.org/?id=DOID:974)
'
from_schema: https://w3id.org/mixs
aliases:
- nose_mouth_teeth_throat_disord
rank: 67
keywords:
- disorder
slot_uri: MIXS:0000270
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
multivalued: true
host_hiv_stat:
name: host_hiv_stat
annotations:
Expected_value:
tag: Expected_value
value: HIV status;HAART initiation status
description: HIV status of subject, if yes HAART initiation status should also
be indicated as [YES or NO]
title: host HIV status
examples:
- value: yes;yes
from_schema: https://w3id.org/mixs
rank: 68
keywords:
- host
- host.
- status
string_serialization: '{boolean};{boolean}'
slot_uri: MIXS:0000265
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
medic_hist_perform:
name: medic_hist_perform
description: Whether full medical history was collected
title: medical history performed
examples:
- value: '1'
from_schema: https://w3id.org/mixs
rank: 69
keywords:
- history
slot_uri: MIXS:0000897
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: boolean
study_complt_stat:
name: study_complt_stat
annotations:
Expected_value:
tag: Expected_value
value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow
up (4)other-specify
description: Specification of study completion status, if no the reason should
be specified
title: study completion status
examples:
- value: no;non-compliance
from_schema: https://w3id.org/mixs
rank: 70
keywords:
- status
slot_uri: MIXS:0000898
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^{boolean};(?:adverse event|non-compliance|lost to follow up|other)$
interpolated: true
ihmc_medication_code:
name: ihmc_medication_code
description: Can include multiple medication codes
title: IHMC medication code
examples:
- value: '810'
from_schema: https://w3id.org/mixs
rank: 71
keywords:
- code
slot_uri: MIXS:0000884
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
slot_group: Environment
range: integer
multivalued: true
chem_administration:
name: chem_administration
annotations:
Expected_value:
tag: Expected_value
value: CHEBI;timestamp
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
examples:
- value: agar [CHEBI:2509];2018-05-11T20:00Z
from_schema: https://w3id.org/mixs
rank: 72
keywords:
- administration
string_serialization: '{termLabel} [{termID}];{timestamp}'
slot_uri: MIXS:0000751
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
multivalued: true
urine_collect_meth:
name: urine_collect_meth
description: Specification of urine collection method
title: urine/collection method
examples:
- value: catheter
from_schema: https://w3id.org/mixs
rank: 73
keywords:
- method
slot_uri: MIXS:0000899
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: UrineCollectMethEnum
drug_usage:
name: drug_usage
annotations:
Expected_value:
tag: Expected_value
value: drug name;frequency
description: Any drug used by subject and the frequency of usage; can include
multiple drugs used
title: drug usage
examples:
- value: Lipitor;2/day
from_schema: https://w3id.org/mixs
rank: 74
keywords:
- drug
- use
string_serialization: '{text};{integer}/[year|month|week|day|hour]'
slot_uri: MIXS:0000894
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
multivalued: true
smoker:
name: smoker
description: Specification of smoking status
title: smoker
examples:
- value: 'yes'
from_schema: https://w3id.org/mixs
rank: 75
slot_uri: MIXS:0000262
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: boolean
weight_loss_3_month:
name: weight_loss_3_month
annotations:
Expected_value:
tag: Expected_value
value: weight loss specification;measurement value
Preferred_unit:
tag: Preferred_unit
value: kilogram, gram
description: Specification of weight loss in the last three months, if yes should
be further specified to include amount of weight loss
title: weight loss in last three months
examples:
- value: yes;5 kilogram
from_schema: https://w3id.org/mixs
rank: 76
keywords:
- months
- weight
string_serialization: '{boolean};{float} {unit}'
slot_uri: MIXS:0000295
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
diet_last_six_month:
name: diet_last_six_month
annotations:
Expected_value:
tag: Expected_value
value: diet change;current diet
description: Specification of major diet changes in the last six months, if yes
the change should be specified
title: major diet change in last six months
examples:
- value: yes;vegetarian diet
from_schema: https://w3id.org/mixs
rank: 77
keywords:
- diet
- months
string_serialization: '{boolean};{text}'
slot_uri: MIXS:0000266
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
travel_out_six_month:
name: travel_out_six_month
annotations:
Expected_value:
tag: Expected_value
value: country name
description: Specification of the countries travelled in the last six months;
can include multiple travels
title: travel outside the country in last six months
from_schema: https://w3id.org/mixs
rank: 78
keywords:
- months
slot_uri: MIXS:0000268
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
multivalued: true
pet_farm_animal:
name: pet_farm_animal
annotations:
Expected_value:
tag: Expected_value
value: presence status;type of animal or pet
description: Specification of presence of pets or farm animals in the environment
of subject, if yes the animals should be specified; can include multiple animals
present
title: presence of pets or farm animals
examples:
- value: yes; 5 cats
from_schema: https://w3id.org/mixs
rank: 79
keywords:
- animal
- farm
- presence
string_serialization: '{boolean};{text}'
slot_uri: MIXS:0000267
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
multivalued: true
maternal_health_stat:
name: maternal_health_stat
description: Specification of the maternal health status
title: amniotic fluid/maternal health status
from_schema: https://w3id.org/mixs
rank: 80
keywords:
- status
slot_uri: MIXS:0000273
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
gestation_state:
name: gestation_state
description: Specification of the gestation state
title: amniotic fluid/gestation state
from_schema: https://w3id.org/mixs
rank: 81
slot_uri: MIXS:0000272
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
foetal_health_stat:
name: foetal_health_stat
description: Specification of foetal health status, should also include abortion
title: amniotic fluid/foetal health status
from_schema: https://w3id.org/mixs
rank: 82
keywords:
- status
slot_uri: MIXS:0000275
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
amniotic_fluid_color:
name: amniotic_fluid_color
description: Specification of the color of the amniotic fluid sample
title: amniotic fluid/color
from_schema: https://w3id.org/mixs
rank: 83
slot_uri: MIXS:0000276
owner: MimsHumanAssociatedAncient
domain_of:
- HumanAssociated
- MimsHumanAssociatedAncient
slot_group: Environment
range: string
prev_pubs:
name: prev_pubs
description: Any previous publications that report non-nucleic acid data from
the same sample or ultimate source of the sample
title: previous publications
examples:
- value: doi:10.1016/j.jas.2015.02.0181
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 84
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report
title: reference for biomaterial
examples:
- value: doi:10.1016/j.syapm.2018.01.009
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 85
slot_uri: MIXS:0000025
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
structured_pattern:
syntax: ^({PMID}|{DOI}|{URL})$
interpolated: true
partial_match: true
organism_count:
name: organism_count
annotations:
Expected_value:
tag: Expected_value
value: organism name;measurement value;enumeration
description: 'Total cell count of any organism (or group of organisms) per gram,
volume or area of sample, should include name of organism followed by count.
The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
title: organism count
examples:
- value: total prokaryotes;3.5e7 cells per milliliter;qPCR
from_schema: https://w3id.org/mixs
rank: 86
keywords:
- count
- organism
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0000103
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
multivalued: true
rel_to_oxygen:
name: rel_to_oxygen
description: Is this organism an aerobe, anaerobe? Please note that aerobic and
anaerobic are valid descriptors for microbial environments
title: relationship to oxygen
examples:
- value: aerobe
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 87
keywords:
- oxygen
- relationship
slot_uri: MIXS:0000015
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: RelToOxygenEnum
host_preserv_state:
name: host_preserv_state
annotations:
Expected_value:
tag: Expected_value
value: Description of the preservation of the sampled (ancient) organism/host
at time/immediately after death.
description: Description of the state of the sampled (ancient) organism/host as
originally preserved in the burial environment at the time of or immediately
following death. This can be both natural or artificial, such as mummification
or burning for funerary purposes.
title: preservation state of sampled host at death
examples:
- value: complete artificial mummification.
- value: natural partial mummification.
- value: fully skeletonised.
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 88
keywords:
- ancient
string_serialization: '{text}'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
required: false
recommended: false
multivalued: false
oxy_stat_samp:
name: oxy_stat_samp
description: Oxygenation status of sample
title: oxygenation status of sample
examples:
- value: aerobic
from_schema: https://w3id.org/mixs
rank: 89
keywords:
- oxygen
- sample
- status
slot_uri: MIXS:0000753
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- Air
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: OxyStatSampEnum
misc_param:
name: misc_param
annotations:
Expected_value:
tag: Expected_value
value: parameter name;measurement value
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/mixs
rank: 90
keywords:
- parameter
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Environment
range: string
multivalued: true
batch_ids:
name: batch_ids
annotations:
Expected_value:
tag: Expected_value
value: list any batch_ids the sample, nucleic acids, or library was associated
with during processing and sequencing
description: 'Identifiers for any form of batch or ''group'' that the samples
is associated with, examples including: individual/skeleton ID, sediment core
IDs, extract batch, library batch, sequencing run etc.. These IDs should always
act as ''umbrella'' IDs that allow association with entries processed together,
to allow for downstream analyses of batch effects. Ideally, the information
should indicate or specify what type of batch the ID is describing.'
title: batch identifiers
examples:
- value: EXTB1;LIBB2;SeqRun1
- value: 'Extraction batch: 1'
- value: 20260501-A2 (extraction);20202607-B2 (library)
- value: ExtrMG;LibMG;SeqMG
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 91
keywords:
- identifiers
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
required: false
recommended: false
multivalued: true
samp_category:
name: samp_category
description: The type/category of a sample. "Sample" includes biological and technical
replicates.
title: sample category
examples:
- value: sample
- value: negative control
- value: positive control
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 92
keywords:
- control
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: SampCategoryEnum
required: true
recommended: true
neg_cont_type:
name: neg_cont_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration or text
description: The substance or equipment used as a negative control in an investigation
title: negative control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs
rank: 93
keywords:
- type
slot_uri: MIXS:0001321
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: NegContTypeEnum
recommended: true
pos_cont_type:
name: pos_cont_type
description: The substance, mixture, product, or apparatus used to verify that
a process which is part of an investigation delivers a true positive
title: positive control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs
rank: 94
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
recommended: true
env_medium:
name: env_medium
description: 'Report the environmental material(s) immediately surrounding the
sample or specimen at the time of sampling. We recommend using subclasses of
''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. a tree, a leaf, a table top)'
title: environmental medium
examples:
- value: bluegrass field soil [ENVO:00005789]
in_subset:
- environment
from_schema: https://w3id.org/mixs
rank: 95
keywords:
- environmental
slot_uri: MIXS:0000014
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
required: true
multivalued: true
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_collect_method:
name: samp_collect_method
description: The method employed for collecting the sample
title: sample collection method
examples:
- value: swabbing
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 96
keywords:
- method
- sample
slot_uri: MIXS:0001225
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
recommended: true
structured_pattern:
syntax: ^({PMID}|{DOI}|{URL}|{text})$
interpolated: true
partial_match: true
samp_collect_device:
name: samp_collect_device
annotations:
Expected_value:
tag: Expected_value
value: device name
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 97
keywords:
- device
- sample
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
recommended: true
samp_mat_process:
name: samp_mat_process
description: A brief description of any processing applied to the sample during
or after retrieving the sample from environment, or a link to the relevant protocol(s)
performed
title: sample material processing
examples:
- value: filtering of seawater, storing samples in ethanol
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 98
keywords:
- material
- process
- sample
slot_uri: MIXS:0000016
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
recommended: true
samp_size:
name: samp_size
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected
title: amount or size of sample collected
examples:
- value: 5 liter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 99
keywords:
- sample
- size
slot_uri: MIXS:0000001
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
recommended: true
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_store_loc:
name: samp_store_loc
annotations:
Expected_value:
tag: Expected_value
value: location name
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
examples:
- value: Freezer no:5
from_schema: https://w3id.org/mixs
rank: 100
keywords:
- location
- sample
- storage
slot_uri: MIXS:0000755
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
samp_store_dur:
name: samp_store_dur
description: Duration for which the sample was stored. Indicate the duration for
which the sample was stored written in ISO 8601 format
title: sample storage duration
examples:
- value: P1Y6M
from_schema: https://w3id.org/mixs
rank: 101
keywords:
- duration
- period
- sample
- storage
slot_uri: MIXS:0000116
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
samp_store_temp:
name: samp_store_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature at which sample was stored, e.g. -80 degree Celsius
title: sample storage temperature
examples:
- value: -80 degree Celsius
from_schema: https://w3id.org/mixs
rank: 102
keywords:
- sample
- storage
- temperature
slot_uri: MIXS:0000110
owner: MimsHumanAssociatedAncient
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_decont_pretreat:
name: samp_decont_pretreat
description: Protocols employed for sample surface decontamination of external modern
nucleic acids; Treatment used on the samples immediately prior to nucleic acid
extraction. Dependant on the sample type. More relevant for bones than environmental
samples. E.g. buffers, EDTA, etc.
title: sample decontamination pretreatment
examples:
- value: doi:10.1016/j.jas.2015.02.0181
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 103
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
multivalued: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
size_frac:
name: size_frac
annotations:
Expected_value:
tag: Expected_value
value: filter size value range
description: Filtering pore size used in sample preparation
title: size fraction selected
examples:
- value: 0-0.22 micrometer
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 104
keywords:
- fraction
- size
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
annotations:
Preferred_unit:
tag: Preferred_unit
value: milliliter, gram, milligram, square centimeter
description: 'Volume (ml) or mass (g) of total collected sample processed for
DNA extraction. Note: total sample collected should be entered under the term
Sample Size (MIXS:0000001)'
title: sample volume or weight for DNA extraction
examples:
- value: 1500 milliliter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 105
keywords:
- dna
- sample
- volume
- weight
slot_uri: MIXS:0000111
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
nucl_acid_extr_date:
name: nucl_acid_extr_date
description: 'The date when the nucleic acid extraction was started from the sample
material. In case no exact time is available, the date can be right truncated
i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
title: date of extraction of nucleic acids from sample
examples:
- value: '2023-12-01'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 106
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: datetime
required: false
recommended: false
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
examples:
- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 107
slot_uri: MIXS:0000037
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
recommended: true
structured_pattern:
syntax: ^({PMID}|{DOI}|{URL})$
interpolated: true
partial_match: true
sop_experimental:
name: sop_experimental
description: Provide a DOI or URL to refer to the paper where the field report,
nucleic acid extraction, library construction, and other procedures are explained
in more detail, e.g. the paper reporting the data.
title: experimental standard operating procedure
examples:
- value: doi:10.1093/nar/gkr771
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
rank: 108
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Nucleic acid source
range: string
required: false
recommended: false
multivalued: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
library_name:
name: library_name
annotations:
Expected_value:
tag: Expected_value
value: name of sequencing library
description: Any ID or name used for referring to a nucleic acid sequencing library
associated with the sample.
title: library name
examples:
- value: JK1234
- value: JFC001.A0101
- value: A003-1-SG1
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 109
keywords:
- sequencing
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
required: false
recommended: true
multivalued: true
damage_treatment:
name: damage_treatment
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Indication of whether characteristic ancient DNA damage has been
altered or removed from a DNA extract in a laboratory. If damage has been removed,
but whether it was fully or partially removed is unknown (e.g. with UDG treatment)
- specify 'other', and describe known information in `sop_experimental` and
related free text descriptive terms.
title: damage treatment type
examples:
- value: none
- value: partial-removal
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 110
keywords:
- ancient
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: DamageTreatmentEnum
required: true
recommended: true
multivalued: false
lib_strandedness:
name: lib_strandedness
annotations:
Expected_value:
tag: Expected_value
value: nucleic acid library strandedness
description: The strandedness of the original template nucleic acid molecules
used for constructing the sequencing library
title: nucleic acid strandedness in library creation
examples:
- value: single
- value: double
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 111
keywords:
- library
- preparation
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: LibStrandEnum
required: true
recommended: true
multivalued: true
adapters:
name: adapters
description: Adapters provide priming sequences for both amplification and sequencing
of the sample-library fragments. Both adapters should be reported; in uppercase
letters
title: adapters
examples:
- value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 112
slot_uri: MIXS:0000048
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
recommended: true
structured_pattern:
syntax: ^{dna_bases};{dna_bases}$
interpolated: true
partial_match: true
mid:
name: mid
description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
used to specifically tag unique samples in a sequencing run. Sequence should
be reported in uppercase letters
title: multiplex identifiers
examples:
- value: GTGAATAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 113
keywords:
- identifier
slot_uri: MIXS:0000047
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
recommended: true
structured_pattern:
syntax: ^{dna_bases}$
interpolated: true
partial_match: true
lib_mid_desc:
name: lib_mid_desc
annotations:
Expected_value:
tag: Expected_value
value: Description of the indexing configuration of the library
description: Index/barcode/primer configuration used during library building for
sequencing. This includes information such as the number, type and location
of indexes, the index/primer kit/list, or if 'inline' barcodes or UMIs were
ligated directly onto the template molecules.
title: description of library multiplex identifiers or indexing configuration
examples:
- value: dual index with single internal barcode.
- value: UDI index sequences.
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 114
keywords:
- library
- preparation
string_serialization: '{text}'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
required: false
recommended: true
multivalued: true
lib_gener_technique:
name: lib_gener_technique
description: The technique used to generate the library, i.e., amplicon, enriched,
or shotgun. An amplicon library is a library that has been amplified to target
a single specific region of a genome (e.g. a specific gene). An enriched library
is a library that has had a particular genome or multiple genomic regions/positions
'captured' or enriched typically via baits/probes. A shotgun library has undergone
no type of targeted amplification/enrichment for a particular genomic region
or genome, i.e., random sequencing of any nucleic acid molecule contained in
a genomic library.
title: library generation technique
examples:
- value: shotgun
- value: amplicon
- value: enriched
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 115
keywords:
- library
- preparation
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: LibTypeEnum
required: false
recommended: true
lib_screen:
name: lib_screen
annotations:
Expected_value:
tag: Expected_value
value: screening strategy name
description: Specific enrichment or screening methods applied before and/or after
creating libraries
title: library screening strategy
examples:
- value: enriched, screened, normalized
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 116
keywords:
- library
slot_uri: MIXS:0000043
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
recommended: true
lib_vector:
name: lib_vector
annotations:
Expected_value:
tag: Expected_value
value: vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
examples:
- value: Bacteriophage P1
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 117
keywords:
- library
slot_uri: MIXS:0000042
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
recommended: true
lib_size:
name: lib_size
description: Total number of clones in the library prepared for the project
title: library size
examples:
- value: '50'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 118
keywords:
- library
- size
slot_uri: MIXS:0000039
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: integer
recommended: true
lib_polymerase:
name: lib_polymerase
annotations:
Expected_value:
tag: Expected_value
value: name of polymerase used during library construction
description: The polymerase enzyme used for building nucleic acid libraries. Include
formal identifier e.g. SKU or the manufacturers name at minimum.
title: library polymerase
examples:
- value: Agilent PfuTurbo Cx HotStart
- value: KAPA HiFi HotStart
- value: AmpliTaq Gold DNA Polymerase
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 119
keywords:
- polymerase
- library
- preparation
string_serialization: '{text}'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
required: false
recommended: true
capt_probe_src_taxid:
name: capt_probe_src_taxid
annotations:
Expected_value:
tag: Expected_value
value: Taxonomic IDs corresponding to organism(s) included in target enrichment
(a.k.a. capture) probe design
description: NCBI taxon ID(s) of all organisms included in the baits of a whole
organelle or whole genome-level capture panel. There should be an (ideally)
species level taxonomic ID entry for each organism that had sequences included
in the design. If whole genera were targeted, you can instead use a single genus
level taxonomic ID or that of any relevant higher taxonomic unit.
title: Genomic capture probe source taxonomy IDs
examples:
- value: '9606'
- value: '632'
- value: '9789'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 120
keywords:
- sequencing
- library
- enrichment
- capture
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: integer
required: false
recommended: false
multivalued: true
capt_probe_desc:
name: capt_probe_desc
annotations:
Expected_value:
tag: Expected_value
value: Description of probe set used for target enrichment/library selection
(a.k.a. capture)
description: Description of target enrichment probe designs used (e.g., species
included, sequences, type, company). This can include custom kits (please provide
a general description and DOI if available) or commercially available kit (provide
ID and company).
title: capture probe design description
examples:
- value: Custom probe design (70 bp biotinylated RNA probes) covering 500 full
E. Coli genomes; company TE-Science
- value: Commercial RNA baits kit ABC001-EC from company TE-Science, purchased
2020
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 121
keywords:
- library
- enrichment
string_serialization: '{text}'
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
required: false
recommended: false
multivalued: true
capt_pcr_cyc_tot:
name: capt_pcr_cyc_tot
description: Amplification cycles after capture enrichment total. Provide additional
information about PCR conditions in pcr_cond
title: post capture PCR reamplication cycles total
examples:
- value: '12'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 122
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: integer
required: false
recommended: false
multivalued: true
reamp_pcr_cyc_tot:
name: reamp_pcr_cyc_tot
description: Number of amplification cycles after library indexing PCR. If capture
data, this refers to amplifications prior to the capture experiments.
title: number of reamplification cycles
examples:
- value: '12'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 123
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: integer
nucl_acid_amp:
name: nucl_acid_amp
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the enzymatic amplification (PCR,
TMA, NASBA) of specific nucleic acids
title: nucleic acid amplification
examples:
- value: https://phylogenomics.me/protocols/16s-pcr-protocol/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 124
slot_uri: MIXS:0000038
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
recommended: true
structured_pattern:
syntax: ^({PMID}|{DOI}|{URL})$
interpolated: true
partial_match: true
seq_meth:
name: seq_meth
description: Sequencing machine used. Where possible the term should be taken
from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
title: sequencing method
examples:
- value: 454 Genome Sequencer FLX [OBI:0000702]
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 125
keywords:
- method
slot_uri: MIXS:0000050
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
required: true
structured_pattern:
syntax: ^{text}|({termLabel} \[{termID}\])$
interpolated: true
partial_match: true
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
examples:
- value: paired
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 126
keywords:
- library
slot_uri: MIXS:0000041
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: LibLayoutEnum
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
examples:
- value: '20'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 127
keywords:
- library
slot_uri: MIXS:0000040
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: integer
recommended: true
sop_lib_preparation:
name: sop_lib_preparation
description: Citation(s) for the nucleic acid library preparation protocol.
title: library preparation protocols
examples:
- value: doi:10.1093/nar/gkr771
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 128
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Sequencing
range: string
required: false
recommended: false
multivalued: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
data_preproc_desc:
name: data_preproc_desc
annotations:
Expected_value:
tag: Expected_value
value: description of any modifications to data away from original raw files
description: Description of preprocessing performed on the reads in the sequencing
data file. Describe any in silico processing or modification of the sequencing
reads away from the original state as received from the sequencer. This should
include details such as adapter-, barcode-, and/or quality- trimming, or any
filtering such as for read length or of off-target reads.
title: description of sequencing reads preprocessing
examples:
- value: Adapter trimmed, quality filtered, and host reads removed through mapping
for ethical reasons.
- value: Adapters removed by Trimmomatic (v0.39), and off-target reads removed
after mapping to the HG19 Human reference with bwa aln (v0.7.19).
- value: Demultiplexed with bcl2fastq, inline barcodes removed, and reads quality
filtered with fastp (v1.0.0).
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 129
keywords:
- data analysis
- data
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: string
required: false
recommended: true
multivalued: false
reads_removed:
name: reads_removed
annotations:
Expected_value:
tag: Expected_value
value: Whether any sequencing reads were removed from the data files after
sequencing
description: Specify whether associated data was filtered in some form prior to
upload, such as host reads removal. Detailed description of the the data filtering
that was carried out should be described in term 'preprocessing of sequencing
reads description'.
title: description of reads removal
examples:
- value: 'no'
- value: 'yes'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 130
keywords:
- data analysis
slot_uri: MIXS:XXXXXXXXX
owner: MimsHumanAssociatedAncient
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: boolean
required: false
recommended: true
multivalued: false
assembly_name:
name: assembly_name
annotations:
Expected_value:
tag: Expected_value
value: name and version of assembly
description: Name/version of the assembly provided by the submitter that is used
in the genome browsers and in the community
title: assembly name
examples:
- value: HuRef, JCVI_ISG_i3_1.0
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 131
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: string
recommended: true
assembly_software:
name: assembly_software
description: Tool(s) used for assembly, including version number and parameters
title: assembly software
examples:
- value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 132
keywords:
- software
slot_uri: MIXS:0000058
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: string
recommended: true
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
assembly_qual:
name: assembly_qual
description: 'The assembly quality category is based on sets of criteria outlined
for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the large subunit (LSU) RNA,
small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether
it is a eukaryotic or prokaryotic genome, respectively. Medium Quality Draft:Many
fragments with little to no review of assembly other than reporting of standard
assembly statistics. Low Quality Draft:Many fragments with little to no review
of assembly other than reporting of standard assembly statistics. Assembly statistics
include, but are not limited to total assembly size, number of contigs, contig
N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities, with extensive
manual review and editing to annotate putative gene functions and transcriptional
units. High-quality draft genome: One or multiple fragments, totaling 90%
of the expected genome or replicon sequence or predicted complete. Genome fragment(s):
One or multiple fragments, totalling < 90% of the expected genome or replicon
sequence, or for which no genome size could be estimated'
title: assembly quality
examples:
- value: High-quality draft genome
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 133
keywords:
- quality
slot_uri: MIXS:0000056
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: AssemblyQualEnum
recommended: true
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
examples:
- value: '40'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 134
keywords:
- number
slot_uri: MIXS:0000060
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: integer
recommended: true
tax_class:
name: tax_class
description: Method used for taxonomic classification, along with reference database
used, classification rank, and thresholds used to classify new genomes
title: taxonomic classification
examples:
- value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification,
default parameters)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 135
keywords:
- classification
- taxon
slot_uri: MIXS:0000064
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: string
annot:
name: annot
annotations:
Expected_value:
tag: Expected_value
value: name of tool or pipeline used, or annotation source description
description: Tool used for annotation, or for cases where annotation was provided
by a community jamboree or model organism database rather than by a specific
submitter
title: annotation
examples:
- value: prokka
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 136
slot_uri: MIXS:0000059
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: string
recommended: true
feat_pred:
name: feat_pred
description: Method used to predict UViGs features such as ORFs, integration site,
etc
title: feature prediction
examples:
- value: Prodigal;2.6.3;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 137
keywords:
- feature
- predict
slot_uri: MIXS:0000061
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: string
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
examples:
- value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 138
keywords:
- method
slot_uri: MIXS:0000063
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: string
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
ref_db:
name: ref_db
annotations:
Expected_value:
tag: Expected_value
value: names, versions, and references of databases
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
examples:
- value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017
doi:10.1093/nar/gkw975
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 139
keywords:
- database
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: string
sop:
name: sop
annotations:
Expected_value:
tag: Expected_value
value: reference to SOP
description: Standard operating procedures used in assembly and/or annotation
of genomes, metagenomes or environmental sequences
title: relevant standard operating procedures
examples:
- value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
rank: 140
keywords:
- procedures
slot_uri: MIXS:0000090
owner: MimsHumanAssociatedAncient
domain_of:
- MimsMisip
- MimarksCMisip
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
slot_group: Data analysis
range: string
recommended: true
multivalued: true
structured_pattern:
syntax: ^({PMID}|{DOI}|{URL})$
interpolated: true
class_uri: MIXS:10007_16003_9999903