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GSCID/BRC Project and Sample Application Standard: Core Sample


v1.3
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.
Data Category: Host Characterization
Allowed Values: Free text
Syntax: Free text
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.
BioSample Definition: a unique identifier by which each subject can be referred to, de-identified
Other Synonyms: MIxS: host_subject_id; BioSample: host-subject-id; 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".
Data Category: Pathogen Detection
Allowed Values: "Clinical/host-associated pathogen" or "environmental/food/other pathogen”
Syntax: Pick list is recommended for values column.
Example Values: clinical or host-associated pathogen
Data Source: Sample Provider
Comments: BioSample: value provided in this field drives validation of other fields. Allowed values for pathogen submissions are ʺPathogen.clʺ (for clinical or host-associated pathogen) or ʺPathogen.envʺ (for environmental, food or other pathogen).
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.
BioSample Definition: Specify the attribute package
Other Synonyms: BioSample: sample category*; 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.
Data Category: Host Characterization
Allowed Values: NCBI taxonomy, except Avibase for avian (http://www.bsc-eoc.org/avibase/avibase.jsp). ‘Experimental’, ‘Unknown’ or ‘Not applicable’ can be used as acceptable values.
Syntax: Free text but only from controlled vocabulary as in allowed values column.
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. BioSample: Required for 'Pathogen.cl' attribute package. If taxonomic name is unknown, enter Species Source Common Name or 'Not collected', 'Not applicable' or 'Missing'
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.
BioSample Definition: Taxid or organism name of host
Other Synonyms: BioSample: specific_host*; MIxS: host_taxid; 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.
Data Category: Host Characterization
Allowed Values: Free text of Source species (common name), 'Not collected', 'Not applicable', 'Missing' or ‘unknown’ can be used as acceptable values.
Syntax: Free text. Source species (common name)
Example Values: mallard; human; mosquito
Data Source: Sample Provider
Comments: BioSample: ʺRequired if Specimen Source Species is empty.ʺ
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.
BioSample Definition: Taxid or organism name of host
Other Synonyms: BioSample: host-common-name; MIxS: host_common_name; 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.
Data Category: Host Characterization
Allowed Values: –‘male’, ‘female’, ‘Unknown’ or ‘Not applicable’ can be used as acceptable values.
Syntax: Free text but only from controlled vocabulary. Pick list is recommend.
Example Values: male
Data Source: Sample Provider
Comments: Required field.
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.
BioSample Definition: Gender or physical sex of the host
Other Synonyms: BioSample: host-sex; MIxS:sex; 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.
Data Category: Host Characterization
Allowed Values: floating number. ‘Unknown’ or ‘Not applicable’ can be used as acceptable values.
Syntax: floating number
Example Values: 18
Data Source: Sample Provider
Comments: Required field. BioSample: Combined w/ Specimen Source Age – Unit.
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
BioSample Definition: Age of host at the time of sampling
Other Synonyms: BioSample: host-age; MIxS: age; 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.
Data Category: Host Characterization
Allowed Values: days, weeks, months, years
Syntax: Pick list or check box for controlled vocabulary
Example Values: years
Data Source: Sample Provider
Comments: BioSample: Combined w/ Specimen Source Age - Value
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.
BioSample Definition: Age of host at the time of sampling
Other Synonyms: BioSample: host-age;

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.
Data Category: Host Characterization
Allowed Values: healthy, sick or deceased. ‘Unknown’ or ‘Not applicable’ can be used as acceptable values.
Syntax: Pick list of allowed values is recommended.
Example Values: healthy
Data Source: Sample Provider
Comments: OBI mapping comment: should be PATO:quality, 'manifestation of a disease' (http://purl.obolibrary.org/obo/OGMS_0000022) and 'viability' (http://purl.obolibrary.org/obo/PATO_0000169
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.
BioSample Definition: Information regarding health state of the individual sampled at the time of sampling
Other Synonyms: BioSample: host-health-state; MIxS: health_disease stat

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.
Data Category: Host Characterization
Allowed Values: Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://www.ncbi.nlm.nih.gov/mesh. ‘Unknown’, ‘Not applicable’, ‘Missing’ or ‘Withheld’ can be used as acceptable values.
Syntax: Free text but only from controlled vocabulary
Example Values: Salmonella gastroenteritis
Data Source: Sample Provider
Comments: BioSample: Required for 'Pathogen.cl' attribute package. If unknown, enter 'Not collected', 'Not applicable' or 'Missing’
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.
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
Other Synonyms: BioSample: host-disease*; MIxS: disease status

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.
Data Category: Specimen Isolation
Allowed Values: A valid date. ‘Unknown’, ‘Not applicable’, ‘Not available’ or ‘Available upon request’ can be used as acceptable values.
Syntax: dd-first 3 letters of month-yyyy
Example Values: 14-Sep-2011
Data Source: Sample Provider
Comments: Required field Human subject participant confidentiality will need to be addressed. BioSample: if unknown, enter 'Not collected'. 'Not applicable' or 'Missing'
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
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)
Other Synonyms: BioSample: collection_date*; MIxS: collection date; 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.
Data Category: Specimen Isolation
Allowed Values: ISO 6709. ‘Unknown’, ‘Not applicable’, ‘Not collected’, ‘Available on request’, ‘Missing’ or ‘Censored’ can be used as acceptable values. Values should be stored in signed decimal degrees format based on the WGS84 geodetic reference system. Multiple value pairs (delimited by ";") may be entered if the site is not a point.
Syntax: ISO 6709 Syntax is acceptable,
Example Values: 15.871732; 37.2556 N; unknown; censored
Data Source: Sample Provider
Comments: Required field. 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. BioSample: If unknown, enter 'Not collected'. 'Not applicable' or 'Missing'. (Combined w/Longitude).
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.
BioSample Definition: Report values in decimal degrees and in WGS84 system
Other Synonyms: BioSample: lat_lon*; MIxS: geographic location (latitude and longitude); 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.
Data Category: Specimen Isolation
Allowed Values: ISO 6709. ‘Unknown’, ‘Not applicable’, ‘Not collected’, ‘Available on request’, ‘Missing’ or ‘Censored’ can be used as acceptable values. Values should be stored in signed decimal degrees format based on the WGS84 geodetic reference system. Multiple value pairs (delimited by ";") may be entered if the site is not a point.
Syntax: ISO 6709 Syntax is acceptable.
Example Values: 100.279899; 80.4290 W; Unknown; Censored
Data Source: Sample Provider
Comments: Required field. 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. BioSample: If unknown, enter ‘Unknown’, 'Not collected', 'Not applicable' or 'Missing' (Combined w/ Specimen Collection Location - Latitude)"
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.
BioSample Definition: Report values in decimal degrees and in WGS84 system
Other Synonyms: BioSample: lat_lon*; MIxS: geographic location (latitude and longitude); 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.
Data Category: Specimen Isolation
Allowed Values: GAZ Ontology. ‘Not collected’, ‘Unknown’ or ‘Not applicable’ can be used as acceptable values.
Syntax: Free text but only from controlled vocabulary
Example Values: GAZ:00003953 (Haiti)
Data Source: Sample Provider
Comments: Recommend the use of GAZ because it allows inference of higher level location information. BioSample: if unknown, enter 'Not collected', 'Not applicable' or 'Missing' (Combined w/ Specimen Collection Location - Country)
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.
BioSample Definition: Geographical origin of the sample
Other Synonyms: BioSample: geo_loc_name*. 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.
Data Category: Specimen Isolation
Allowed Values: ISO 3166 standard abbreviation (2-alpha), www.iso.org/iso/iso-3166-1_decoding_table or NCBI country list. 'Not collected', 'Not applicable' or 'Missing' can be used as acceptable values.
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. BioSample: If unknown, enter 'Not collected’, 'Not applicable' or 'Missing' (Combined w/ Specimen Collection Location - Location)"
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.
BioSample Definition: Geographical origin of the sample
Other Synonyms: BioSample: geo_loc_name*; MIxS:geographic location (country and/or sea,region); 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.
Data Category: Specimen Isolation
Allowed Values: Free text
Syntax:
Example Values: CRIP1123455
Data Source: Sample Provider
Comments: BioSample: Must be unique within a submitter name space. 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.
BioSample Definition: Submitter-supplied Sample Name or identifier.
Other Synonyms: BioSample: sample name*

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.
Data Category: Specimen Isolation
Allowed Values: blood, X tissue, CSF, nasal swab, BAL, feather, hair, fur, nasal secretion, Whole Blood, Serum, Plasma, PBMC, Cell Supernatant or Tissue. Term of organism appropriate anatomy ontology, e.g. Foundational Model of Anatomy Ontology or Mosquito Gross Anatomy Ontology.
Syntax: Pick list or search box for allowed values.
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).
BioSample Definition: Type of tissue the initial sample was taken from. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1005)
Other Synonyms: BioSample: host-tissue-sampled; MIxS: body habitat, body site, body product; 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).
Data Category: Pathogen Detection
Allowed Values: NCBI taxonomy
Syntax: Free text but only from controlled vocabulary
Example Values: Influenza A virus
Data Source: Sample Provider
Comments: OBI mapping comment: should consider rank of NCBITaxon (rank: species); BioSample: Will be validated against NCBI taxonomy database. 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.
BioSample Definition: The most descriptive organism name for this sample (to the species, if relevant; to the strain for bacteria)
Other Synonyms: BioSample: organism*; 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)
Data Category: Pathogen Detection
Allowed Values: Free text
Syntax:
Example Values: H5N1
Data Source: Sample Provider
Comments: OBI mapping comment: should consider rank of NCBITaxon (rank: subclassification of species). BioSample: strain and/or isolate must be provided.
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
BioSample Definition: N/A
Other Synonyms: BioSample: strain; MIxS: subspecific genetic lineage

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
Data Category: Pathogen Characteristic
Allowed Values: Free text
Syntax:
Example Values: pathogenic in human; not pathogenic in human
Data Source: Sample Provider
Comments: OBI mapping comment: may be subclass of IDO:'pathogenic disposition' or 'pathogen role', human pathogenic disposition (role), or non-human pathogenic disposition (role); BioSample: will be included as custom attribute.
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.
BioSample Definition: To what is the entity pathogenic
Other Synonyms: BioSample: pathogenicity; MIxS:phenotype

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.
Data Category: 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. ‘Not applicable’, ‘Not collected’ or ‘Missing’ can be used as acceptable values.
Syntax: Free text but only from controlled vocabulary
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 field.
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.
BioSample Definition: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.
Other Synonyms: BioSample: isolation-source*; MIxS: environment (material)

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.
Data Category: Pathogen Detection
Allowed Values: OBI, http://bioportal.bioontology.org/ontologies/40832. ‘Unknown’ or ‘Not applicable’ can be used as acceptable values.
Syntax: Free text but only from controlled vocabulary
Example Values: real time reverse-transcription polymerase chain reaction assay - obo:OBI_0000911
Data Source: Sample Provider
Comments: Required field. BioSample: will be included as custom attribute.
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.
BioSample Definition:
Other Synonyms: BioSample: organism-detection-method; MIxS:sample collection device or method

22. Specimen Repository
Core Sample Field ID: CS22
Field Name: Specimen Repository
Description: Name of repository where a specimen sample has been deposited.
Data Category: Specimen Processing
Allowed Values: Free text. ‘Unknown’ or ‘Not applicable’ can be used as acceptable values.
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:
BioSample Definition: Name of source institute and unique culture identifier.
Other Synonyms: BioSample: culture-collection; MIxS: source material identifiers . 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.
Data Category: Specimen Processing
Allowed Values: Valid repository assigned identifier of sample. ‘Unknown’ or ‘Not applicable’ can be used as acceptable values.
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.
BioSample Definition: Name of source institute and unique culture identifier.
Other Synonyms: BioSample: culture-collection; MIxS: source material identifiers. 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.
Data Category: Specimen Comments
Allowed Values: Free text
Syntax: Free text
Example Values: host was found dead at location
Data Source: Sample Provider and/or GSCID
Comments:
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
BioSample Definition:
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
Data Category: Specimen Isolation
Allowed Values: Free text
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
BioSample Definition:
Other Synonyms: BioSample: collected-by*; 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
Data Category: Specimen Isolation
Allowed Values: Free text
Syntax: Free text
Example Values: International Ornithology Institute
Data Source: Sample Provider
Comments: BioSample: will be included as custom attribute
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
BioSample Definition:
Other Synonyms: BioSample: specimen-collector's-institution; 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
Data Category: Specimen Isolation
Allowed Values: Free text
Syntax: Free text
Example Values: will.birder@ioi.org
Data Source: Sample Provider
Comments: BioSample: will be included as custom attribute
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
BioSample Definition:
Other Synonyms: BioSample: specimen-collector's-institution; Sample Collector's email

Last Updated January 07, 2014