DMID Metadata Standards Core Sample

GSCID/BRC Project and Sample Application Standard
Core Sample
v1.4
Finalized by the GSCID/BRC Metadata Working Group

How to interpret the document:
BOLD: Field Name
ITALICS: Attributes of the field
 

1. Specimen Source ID
Core Sample Field ID: CS1
Field Name: Specimen Source ID
Description: Unique identifier of the individual organism from which the initial specimen was obtained. All specimens coming from the same patient or other host must have the same Specimen Source ID. Multiple specimens from the same patient must be differentiated using the "Specimen ID" fields. Samples derived from the same initial specimen (e.g. different aliquots) can be distinguished using different Sample IDs.
Privacy Risks: Yes
Notes for Human Samples: Should be non-traceable to any individual person (i.e., de-identified); considered high risk if any of the HIPAA named Protected Health Information (PHI) identifiers are used; Medical Record Numbers should never be used.
Data Categories: Host Characterization
Allowed Values: free text
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: No
Syntax: Numerical or Alphanumerical
Example Values: AC160
Data Source: Sample Provider
Comments: It is essential that each specimen source carries a unique identifier, especially when multiple specimens may be isolated from the same specimen source, e.g. Ghedin E, et al. J Infect Dis. 2011 Jan 15;203(2):168-74. PubMed PMID: 21288815;
PubMed Central PMCID: PMC3071067. "Host" is not the preferred term since some specimens may lack any detectable pathogen
OBO Foundry Synonym: individual organism identifier
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001141
OBO Foundry Definition: a symbol used to distinguish one individual organism from another.
OBI Mapping Comments:  
BioSample Synonym: host-subject-id
BioSample Definition: a unique identifier by which each subject can be referred to, de-identified
BioSample Comments:  
MIxS Synonym: host_subject_id
Other Synonyms: Host ID; Primary Sample Source ID
2. Specimen Category
Core Sample Field ID: CS2
Field Name: Specimen Category
Description: Indicate the category of sample.
Allowed values are "clinical or host-associated pathogen" or "environmental, food or other pathogen".
Privacy Risks: No
Data Categories: Pathogen Detection
Allowed Values: "Clinical/host-associated pathogen" or "environmental/food/other" pathogen
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: No
Syntax: pick list
Example Values: clinical or host-associated pathogen
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: specimen
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0100051
OBO Foundry Definition: A material entity that has the specimen role.
OBI Mapping Comments:  
BioSample Synonym: sample category*
BioSample Definition: Specify the attribute package
BioSample Comments: Value provided in this field drives validation of other fields. Allowed values for pathogen submissions are "Pathogen.cl" (for clinical or host-associated pathogen) or "Pathogen.env" (for environmental, food or other pathogen).
MIxS Synonym:  
Other Synonyms: BioSample Category Type
3. Specimen Source Species
Core Sample Field ID: CS3
Field Name: Specimen Source Species
Description: Taxonomic species of the individual organism (host) from which the initial specimen was obtained, in as much detail as is known. Ideally this would be described using the traditional Genus species combination nomenclature.
Privacy Risks: No
Data Categories: Host Characterization
Allowed Values: NCBI taxonomy, except Avibase for avian (http://www.bsc-eoc.org/avibase/avibase.jsp)
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable
Syntax: Free text or NCBI taxonomy would be acceptable. Need "Experimental" and "Unknown" as acceptable values
Example Values: Anas platyrhynchos; Homo Sapiens; Coquillettidia perturbans
Data Source: Sample Provider
Comments: Genus and species should be combined into a single field with the use of the standard latin nomenclature.
OBO Foundry Synonym: organism
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0100026
OBO Foundry Definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
OBI Mapping Comments:  
BioSample Synonym: specific_host*
BioSample Definition: Taxid or organism name of host
BioSample Comments: Required for 'Pathogen.cl' attribute package
If taxonomic name is unknown, enter Species Source Common Name or 'Not collected', 'Not applicable' or 'Missing'
MIxS Synonym: host_taxid
Other Synonyms: Host Species; Primary Sample Source Species
4. Species Source Common Name
Core Sample Field ID: CS4
Field Name: Species Source Common Name
Description: Common name of the type of individual organism (host) from which the initial specimen was obtained.
Privacy Risks: No
Data Categories: Host Characterization
Allowed Values: free text
Alternate Allowed Values: Source species (common name), 'Not collected', 'Not applicable', 'Missing'
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable
Syntax: Free text
Example Values: mallard; human; mosquito
Data Source: Sample Provider
Comments: This may be a situation in which m5 is preferred, and either m5 or m6 is required.
OBO Foundry Synonym: organism (alternative name)
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0100026
OBO Foundry Definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
OBI Mapping Comments:  
BioSample Synonym: host-common-name
BioSample Definition: Taxid or organism name of host
BioSample Comments: Required if Specimen Source Species is empty.
MIxS Synonym: host_common_name
Other Synonyms: Host Common Name; Primary Sample Source Common Name
5. Specimen Source Gender
Core Sample Field ID: CS5
Field Name: Specimen Source Gender
Description: Biological sex of the individual organism (host) from which the initial specimen was obtained. An organismal quality relating to sexual reproduction that differentiates the types of individuals involved in the reproductive process.
Privacy Risks: No
Data Categories: Host Characterization
Allowed Values: Drop down list - male, female, unknown
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable
Syntax:  
Example Values: male
Data Source: Sample Provider
Comments: required with unknown as an allowed value
OBO Foundry Synonym: biological sex
OBO Foundry Purl: http://purl.obolibrary.org/obo/PATO_0000047
OBO Foundry Definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
OBI Mapping Comments:  
BioSample Synonym: host-sex
BioSample Definition: Gender or physical sex of the host
BioSample Comments:  
MIxS Synonym: sex
Other Synonyms: Specimen Source Biological Sex; Host Gender/Sex; Primary Sample Source Gender/Sex
6. Specimen Source Age - Value
Core Sample Field ID: CS6
Field Name: Specimen Source Age - Value
Description: Age value of the individual organism (host) from which the initial specimen was obtained. Span of time value between birth or hatching and time of specimen collection.
Privacy Risks: Yes
Notes for Human Samples: Date of birth is a HIPAA PHI identifier; age of over 89 is also a HIPAA PHI identifier.
Data Categories: Host Characterization
Allowed Values: floating number
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable/censored
Syntax:  
Example Values: 18
Data Source: Sample Provider
Comments: required with unknown as an allowed value
OBO Foundry Synonym: age measurement datum
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001167
OBO Foundry Definition: A time measurement datum that is the result of measurement of age of an organism
OBI Mapping Comments:  
BioSample Synonym: host-age
BioSample Definition: Age of host at the time of sampling
BioSample Comments: Combined w/ Specimen Source Age - Unit
MIxS Synonym: age
Other Synonyms: Host Age; Primary Sample Source Age
7. Specimen Source Age - Unit
Core Sample Field ID: CS7
Field Name: Specimen Source Age - Unit
Description: Age unit of the individual organism (host) from which the initial specimen was obtained. Span of time unit between birth or hatching and time of specimen collection.
Privacy Risks: Yes
Notes for Human Samples: Date of birth is a HIPAA PHI identifier; age of over 89 is also a HIPAA PHI identifier.
Data Categories: Host Characterization
Allowed Values: days, weeks, months, years
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable/censored
Syntax:  
Example Values: years
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: time unit
OBO Foundry Purl: http://purl.obolibrary.org/obo/UO_0000003
OBO Foundry Definition: A unit which is a standard measure of the dimension in which events occur in sequence.
OBI Mapping Comments:  
BioSample Synonym: host-age
BioSample Definition: Age of host at the time of sampling
BioSample Comments: Combined w/ Specimen Source Age - Value
MIxS Synonym:  
Other Synonyms:  
8. Specimen Source Health Status
Core Sample Field ID: CS8
Field Name: Specimen Source Health Status
Description: A Description of whether the specimen source organism appeared healthy, sick or deceased at the time of sampling. If sick or deceased, additional details should be provided in project-specific fields.
Privacy Risks: No
Data Categories: Host Characterization
Allowed Values: pick list - healthy, sick or deceased
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown
Syntax:  
Example Values: healthy
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: organismal quality
OBO Foundry Purl: http://purl.obolibrary.org/obo/PATO_0001995
OBO Foundry Definition: A quality that inheres in an entire organism or part of an organism.
OBI Mapping Comments: should be PATO:quality, 'manifestation of a disease' (http://purl.obolibrary.org/obo/OGMS_0000022) and 'viability' (http://purl.obolibrary.org/obo/PATO_0000169)
BioSample Synonym: host-health-state
BioSample Definition: Information regarding health state of the individual sampled at the time of sampling
BioSample Comments:  
MIxS Synonym: health_disease stat
Other Synonyms:  
9. Specimen Source Disease
Core Sample Field ID: CS9
Field Name: Specimen Source Disease
Description: Name of relevant disease thought to be related to the suspected organism in the specimen.
Privacy Risks: No
Data Categories: Host Characterization
Allowed Values: Controlled vocabulary, https://bioportal.bioontology.org/ontologies/DOID (when specimen source is human), or http://www.ncbi.nlm.nih.gov/mesh.
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable/censored
Syntax: free text
Example Values: Salmonella gastroenteritis; DOID: 8469
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: disease
OBO Foundry Purl: http://purl.obolibrary.org/obo/OGMS_0000031
OBO Foundry Definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
OBI Mapping Comments:  
BioSample Synonym: host-disease*
BioSample Definition: Name of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://www.ncbi.nlm.nih.gov/mesh
BioSample Comments: Required for 'Pathogen.cl' attribute package. If unknown, enter 'Not collected'. 'Not applicable' or 'Missing'
MIxS Synonym: disease status
Other Synonyms:  
10.  Specimen Collection Date
Core Sample Field ID: CS10
Field Name: Specimen Collection Date
Description: Date of the specimen collection event from an individual organism host (N.B. this information may be censored if derived from a human patients.), or the date of the sample collection event from an environmental material. The collection date can either be a single point in time or an interval of time.
Privacy Risks: Yes
Notes for Human Samples: Specific dates in general are an identification risk if tied to HIPAA PHI identifiers such as admission date or date of death.
Data Categories: Specimen Isolation
Allowed Values: dd-first 3 letters of month-yyyy
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not available/available upon request
Syntax: dd-first 3 letters of month-yyyy
Example Values: 40800
Data Source: Sample Provider
Comments: required with unknown as an allowed value; human subject participant confidentiality will need to be addressed
OBO Foundry Synonym: specimen creation time measurement datum (alternative term: collection date)
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001619
OBO Foundry Definition: A scalar measurement datum that is the result of measuring a temporal interval
OBI Mapping Comments:  
BioSample Synonym: collection_date*
BioSample Definition: Date of sampling, in "DD-Mmm-YYYY", "Mmm-YYYY" or "YYYY" format (single instance, eg., 05-Oct-1990, Oct-1990 or 1990) or ISO 8601 standard "YYYY-mm-dd" or "YYYY-mm-ddThh:mm:ss" (eg. 1990-11-05 or 1990-11-05T14:41:36)
BioSample Comments: If unknown, enter 'Not collected'. 'Not applicable' or 'Missing'
MIxS Synonym: collection date
Other Synonyms: Primary Sample Collection Date
11.  Specimen Collection Location - Latitude
Core Sample Field ID: CS11
Field Name: Specimen Collection Location - Latitude
Description: Latitude coordinate for the site of the specimen collection event.
Privacy Risks: Yes
Notes for Human Samples: Geographic location is a HIPAA PHI identifier when smaller than a state.
Data Categories: Specimen Isolation
Allowed Values: ISO 6709
Alternate Allowed Values: Values should be stored in signed decimal degrees format based on the WGS84 geodetic reference system. Multiple value pairs may be entered if the site is not a point.
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable/not available/ available upon request
Syntax: ISO 6709 Syntax: “+” denotes northern hemisphere or the equator and “-” denotes southern hemisphere; Need "N/A" or "Unknown" as accepted value
Example Values: +15.871732; +37.2556; unknown; censored
Data Source: Sample Provider
Comments: required with unknown, not applicable and censored as an allowed values; human subject participant confidentiality may or may not be an issue since the location of specimen collection (hospital/clinic) will not be the human subject participant's address; for NCBI submissions, since NCBI only accepts “N” or “S”, a format conversion will be needed.
OBO Foundry Synonym: latitude coordinate measurement datum
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001620
OBO Foundry Definition: A measurement datum that is the measure of the latitude coordinate of a site.
OBI Mapping Comments:  
BioSample Synonym: lat_lon*
BioSample Definition: Report values in decimal degrees and in WGS84 system
BioSample Comments: If unknown, enter 'Not collected'. 'Not applicable' or 'Missing' (Combined with Longitude)
MIxS Synonym: geographic location (latitude and longitude)
Other Synonyms: Primary Sample Collection Location – Latitude
12.  Specimen Collection Location - Longitude
Core Sample Field ID: CS12
Field Name: Specimen Collection Location - Longitude
Description: Longitude coordinate for the site of the specimen collection event.
Privacy Risks: Yes
Notes for Human Samples: Geographic location is a HIPAA PHI identifier when smaller than a state.
Data Categories: Specimen Isolation
Allowed Values: ISO 6709
Alternate Allowed Values: Values should be stored in signed decimal degrees format based on the WGS84 geodetic reference system. Multiple value pairs may be entered if the site is not a point.
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable/not available/ available upon request
Syntax: ISO 6709 Syntax: “+” denotes east longitude or the prime meridian, and “-” denotes west longitude or 180° meridian; Need "N/A" or "Unknown" as accepted value
Example Values: +100.279899; -80.4290; unknown; censored
Data Source: Sample Provider
Comments: required with unknown, not applicable and censored as an allowed values; human subject participant confidentiality may or may not be an issue since the location of specimen collection (hospital/clinic) will not be the human subject participant's address; for NCBI submissions, since NCBI only accepts “E” or “W”, a format conversion will be needed.
OBO Foundry Synonym: longitude coordinate measurement datum
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001621
OBO Foundry Definition: A measurement datum that is the measure of the longitude coordinate of a site.
OBI Mapping Comments:  
BioSample Synonym: lat_lon*
BioSample Definition: Report values in decimal degrees and in WGS84 system
BioSample Comments: If unknown, enter 'Not collected'. 'Not applicable' or 'Missing' (Combined w/ Specimen Collection Location - Latitude)
MIxS Synonym: geographic location (latitude and longitude)
Other Synonyms: Primary Sample Collection Location – Longitude
13.  Specimen Collection Location - Location
Core Sample Field ID: CS13
Field Name: Specimen Collection Location - Location
Description: The name (or Gazetteer term) of the most precise geographical location available for the site of the specimen collection event.
Privacy Risks: Yes
Notes for Human Samples: Geographic location is a HIPAA identifier when smaller than a state.
Data Categories: Specimen Isolation
Allowed Values: GAZ Ontology
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable
Syntax:  
Example Values: GAZ:00003953 (Haiti)
Data Source: Sample Provider
Comments: Recommend the use of GAZ because it allows inference of higher level location information; GAZ is not currently hamonized with lat/lon; although one can infer country from a GAZ location, decided to ask for country in addition to facilitate GenBank submission and as a type of quality control to check accurate use of GAZ; since many people will not be familar with GAZ and how to use it, we will need to facilitate it's use through our implementation strategy
OBO Foundry Synonym: geographical location
OBO Foundry Purl: http://purl.obolibrary.org/obo/GAZ_00000448
OBO Foundry Definition: A reference to a place on the Earth, by its name or by its geographical location.
OBI Mapping Comments:  
BioSample Synonym: geo_loc_name*
BioSample Definition: Geographical origin of the sample
BioSample Comments: If unknown, enter 'Not collected'. 'Not applicable' or 'Missing' (Combined w/ Specimen Collection Location - Country)
MIxS Synonym:  
Other Synonyms: Primary Sample Collection Geographical Location
14.  Specimen Collection Location - Country
Core Sample Field ID: CS14
Field Name: Specimen Collection Location - Country
Description: Country location of the site of the specimen collection event.
Privacy Risks: No
Data Categories: Specimen Isolation
Allowed Values: ISO 3166 standard abbreviation (2-alpha), www.iso.org/iso/iso-3166-1_decoding_table
Alternate Allowed Values: NCBI country
Unknown/Not Applicable/Censored Allowed: Unknown
Syntax: Currently is free text, but ISO3166 standard abbreviations would be acceptable
Example Values: US
Data Source: Sample Provider
Comments: see Comments to Specimen Collection Location - Longitude
OBO Foundry Synonym: country name
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001627
OBO Foundry Definition: A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
OBI Mapping Comments:  
BioSample Synonym: geo_loc_name*
BioSample Definition: Geographical origin of the sample
BioSample Comments: If unknown, enter 'Not collected'. 'Not applicable' or 'Missing' (Combined w/ Specimen Collection Location - Location)
MIxS Synonym: geographic location (country and/or sea,region)
Other Synonyms: Primary Sample Collection Location – Country
15.  Specimen ID
Core Sample Field ID: CS15
Field Name: Specimen ID
Description: Unique identifier of the initial specimen collected from the specimen source.
Privacy Risks: No
Data Categories: Specimen Isolation
Allowed Values: free text
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: No
Syntax:  
Example Values: CRIP1123455
Data Source: Sample Provider
Comments: It is essential that each specimen carries a unique identifier, especially when multiple pathogen isolates may be identified in the same specimen. Each independent specimen should be given a different Specimen ID even if isolated from the same source organism.
OBO Foundry Synonym: specimen identifier
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001616
OBO Foundry Definition: A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
OBI Mapping Comments:  
BioSample Synonym: sample name*
BioSample Definition: Submitter-supplied Sample Name or identifier.
BioSample Comments: Must be unique within a submitter name space.
MIxS Synonym:  
Other Synonyms:  
16.  Specimen Type
Core Sample Field ID: CS16
Field Name: Specimen Type
Description: Tissue or bodily fluid type of initial specimen obtained. A material sample isolated from a host organism for the purpose of target organism isolation or the experimental measurement of some other property of that material entity.
Privacy Risks: No
Data Categories: Specimen Isolation
Allowed Values: pick list: blood, X tissue, CSF, nasal swab, BAL, feather, hair, fur, nasal secretion
Alternate Allowed Values: Term of organism appropriate anatomy ontology, e.g. Foundational Model of Anatomy Ontology or Mosquito Gross Anatomy Ontology.
Unknown/Not Applicable/Censored Allowed: No
Syntax: pick list would be acceptable; currently we use Whole Blood or Serum or Plasma or PBMC or Cell Supernatant or Tissue
Example Values: lung tissue; fma:Skin; fma:Lung; TGMA:0000136 (adult thorax of mosquito); whole worms
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: tissue specimen
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001479
OBO Foundry Definition: A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
OBI Mapping Comments:  
BioSample Synonym: host-tissue-sampled
BioSample Definition: Type of tissue the initial sample was taken from. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1005)
BioSample Comments:  
MIxS Synonym: body habitat, body site, body product
Other Synonyms: Isolation Site on Host; Primary Sample Type
17.  Suspected Organism(s) in Specimen - Species
Core Sample Field ID: CS17
Field Name: Suspected Organism(s) in Specimen - Species
Description: Anticipated species of the organism(s) found in the initial specimen based on submitter assay(s)/determination(s).
Privacy Risks: No
Data Categories: Pathogen Detection
Allowed Values: NCBI taxonomy
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: No
Syntax:  
Example Values: Influenza A virus
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: infectious agent
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0000925
OBO Foundry Definition: Is a material entity bearing the disposition to infect an organism.
OBI Mapping Comments: should consider rank of NCBITaxon (rank: species)
BioSample Synonym: organism*
BioSample Definition: The most descriptive organism name for this sample (to the species, if relevant; to the strain for bacteria)
BioSample Comments: Will be validated against NCBI taxonomy database
MIxS Synonym:  
Other Synonyms: Suspected Pathogen in Specimen
18.  Suspected Organism(s) in Specimen - Subclassification
Core Sample Field ID: CS18
Field Name: Suspected Organism(s) in Specimen - Subclassification
Description: Anticipated subclassification of the organism(s) (e.g. genotype, serotype) found in the initial specimen based on submitter assay(s)/determination(s)
Privacy Risks: No
Data Categories: Pathogen Detection
Allowed Values: free text
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable
Syntax:  
Example Values: H5N1
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: infectious agent
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0000925
OBO Foundry Definition: is a material entity bearing the disposition to infect an organism
OBI Mapping Comments: should consider rank of NCBITaxon (rank: subclassification of species)
BioSample Synonym: strain
BioSample Definition: N/A
BioSample Comments: strain and/or isolate must be provided
MIxS Synonym: subspecific genetic lineage
Other Synonyms:  
19.  Human Pathogenicity of Suspected Organism(s) in Specimen
Core Sample Field ID: CS19
Field Name: Human Pathogenicity of Suspected Organism(s) in Specimen
Description: Anticipated pathogenicity of the organism(s) found in the initial specimen based on submitter assay(s)/determination(s) in the human host
Privacy Risks: No
Data Categories: Pathogen Characteristic
Allowed Values: free text
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable
Syntax:  
Example Values: pathogenic in human; not pathogenic in human
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: human pathogenicity disposition
OBO Foundry Purl: http://purl.obolibrary.org/obo/IDO_0000666
OBO Foundry Definition: A disposition to initiate processes that result in a disorder in a human organism.
OBO Mapping Concepts I think it may be subclass of IDO:'pathogenic disposition' or 'pathogen role', human pathogenic disposition (role), or non-human pathogenic disposition (role)
Both terms are not in OBI yet.
BioSample Synonym: pathogenicity
BioSample Definition: To what is the entity pathogenic
BioSample Comments: will be included as custom attribute
MIxS Synonym: phenotype
Other Synonyms:  
20.  Environmental Material
Core Sample Field ID: CS20
Field Name: Environmental Material
Description: Describes the matter that was displaced by the sample, prior to the sampling event. Examples include: air, soil, or water.
Privacy Risks: No
Data Categories: Specimen Isolation
Allowed Values: EnvO (v1.53) terms listed under environmental matter can be found from the link: http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00010483
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Not applicable
Syntax:  
Example Values: pond water; feces; not applicable
Data Source: Sample Provider
Comments: This field would be used only when the specimen source is not an organism; required with not applicable as an allowed values
OBO Foundry Synonym: environmental material
OBO Foundry Purl: http://purl.obolibrary.org/obo/ENVO_00010483
OBO Foundry Definition: Material in or on which organisms may live.
OBI Mapping Comments:  
BioSample Synonym: isolation-source*
BioSample Definition: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.
BioSample Comments: If unknown, enter 'Not collected'. 'Not applicable' or 'Missing'
MIxS Synonym: environment (material)
Other Synonyms:  
21.  Organism Detection Method
Core Sample Field ID: CS21
Field Name: Organism Detection Method
Description: Experimental technique used to identify the organism species in the specimen sample.
Privacy Risks: No
Data Categories: Pathogen Detection
Allowed Values: OBI, http://bioportal.bioontology.org/ontologies/40832
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable
Syntax: Need "Unknown" as an acceptable value
Example Values: real time reverse-transcription polymerase chain reaction assay - obo:OBI_0000911
Data Source: Sample Provider
Comments: required with not applicable as an allowed values
OBO Foundry Synonym: organism identification assay
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001624
OBO Foundry Definition: An assay that identifies the organism species in a specimen.
OBI Mapping Comments:  
BioSample Synonym: organism-detection-method
BioSample Definition:  
BioSample Comments: will be included as custom attribute
MIxS Synonym: sample collection device or method
Other Synonyms:  
22.  Specimen Repository
Core Sample Field ID: CS22
Field Name: Specimen Repository
Description: Name of repository where a specimen sample has been deposited.
Privacy Risks: No
Data Categories: Specimen Processing
Allowed Values: free text
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable
Syntax:  
Example Values: BEI Resources
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: specimen repository organization
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001885
OBO Foundry Definition:  
OBI Mapping Comments:  
BioSample Synonym: culture-collection
BioSample Definition: Name of source institute and unique culture identifier.
BioSample Comments:  
MIxS Synonym: source material identifiers
Other Synonyms: Sample Repository Name
23.  Specimen Repository Sample ID
Core Sample Field ID: CS23
Field Name: Specimen Repository Sample ID
Description: Unique identifier assigned by sample repository to identity the specimen sample.
Privacy Risks: No
Data Categories: Specimen Processing
Allowed Values: Valid repository assigned identifier of sample
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable
Syntax:  
Example Values: ATCC BAA-1343
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: specimen identifier assigned by specimen repository
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001900
OBO Foundry Definition: An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
OBI Mapping Comments: update with adding OBI:specimen identifier
BioSample Synonym: culture-collection
BioSample Definition: Name of source institute and unique culture identifier.
BioSample Comments:  
MIxS Synonym: source material identifiers
Other Synonyms: Repository Sample ID
24.  Comments
Core Sample Field ID: CS24
Field Name: Comments
Description: Any additional information about the initial specimen collection event, the sample preparation process, or any other aspect of the project worth noting.
Privacy Risks: No
Data Categories: Specimen Comments
Allowed Values: free text
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Not applicable
Syntax: free text
Example Values: host was found dead at location
Data Source: Sample Provider and/or GSCID
Comments: Need to have a free text box for any Comments, but this could be for the entire sample collection/sequencing process
OBO Foundry Synonym: comment on investigation
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001898
OBO Foundry Definition: A textual entity that is about any of the aspects of an investigation worth noting
OBI Mapping Comments:  
BioSample Synonym:  
BioSample Definition:  
BioSample Comments:  
MIxS Synonym:  
Other Synonyms:  
25.  Specimen Collector Name
Core Sample Field ID: CS25
Field Name: Specimen Collector Name
Description: Name of the person collecting the specimen and specimen collection metadata
Privacy Risks: No
Data Categories: Specimen Isolation
Allowed Values: free text
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable/censored
Syntax: free text
Example Values: Will Birder
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: specimen collector
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001895
OBO Foundry Definition: A person who collects the specimen
OBI Mapping Comments:  
BioSample Synonym: collected-by*
BioSample Definition:  
BioSample Comments:  
MIxS Synonym:  
Other Synonyms: Sample Collector Name
26.  Specimen Collector's Institution
Core Sample Field ID: CS26
Field Name: Specimen Collector's Institution
Description: Institutional affiliation of the person collecting the specimen and specimen collection metadata
Privacy Risks: No
Data Categories: Specimen Isolation
Allowed Values: free text
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable/censored
Syntax: free text
Example Values: International Ornithology Institute
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: organization of specimen collector
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001893
OBO Foundry Definition: An organization that is the affiliation of the person collecting the specimen
OBI Mapping Comments:  
BioSample Synonym: specimen-collector's-institution
BioSample Definition:  
BioSample Comments: will be included as custom attribute
MIxS Synonym:  
Other Synonyms: Sample Collector's Institution
27.  Specimen Collector's email
Core Sample Field ID: CS27
Field Name: Specimen Collector's email
Description: Preferred email address of the person collecting the specimen and specimen collection metadata
Privacy Risks: No
Data Categories: Specimen Isolation
Allowed Values: free text
Alternate Allowed Values:  
Unknown/Not Applicable/Censored Allowed: Unknown/not applicable/censored
Syntax: free text
Example Values: will.birder@ioi.org
Data Source: Sample Provider
Comments:  
OBO Foundry Synonym: email address of specimen collector
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001890
OBO Foundry Definition: An email address of the person collecting the specimen
OBI Mapping Comments:  
BioSample Synonym: specimen-collector's-institution
BioSample Definition:  
BioSample Comments: will be included as custom attribute
MIxS Synonym:  
Other Synonyms: Sample Collector's email