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 Sex | ||
| Core Sample Field ID: | CS5 | |
| Field Name: | Specimen Source Sex | |
| 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: | Sex of the host | |
| BioSample Comments: | ||
| MIxS Synonym: | sex | |
| Other Synonyms: | Specimen Source Biological Sex; Host Sex; Primary Sample Source 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 | OBI Mapping Comments: | 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 | |