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| Property | Expected Type | Description |
|---|---|---|
| Properties from AnalysisSample | ||
abstract | Text | An abstract is a short description that summarizes an AnalysisSample |
accessibilityHazard | Text | A characteristic of the described resource that is physiologically dangerous to some users. Related to WCAG 2.0 guideline 2.3 (WebSchemas wiki lists possible values). |
aliquoter | Person | Specifies the Person or Thing performing the aliquoting action when the AnalysisSample was drawn or created from a previous AnalysisSample |
aligquotingTime | DateTime | Specifies the date and time when the aliquoting event that filled the storageContainer with the AnalysisSample occurred |
concentrationFactor | QuantitativeValue | A numeric value that reflects the dilution or concentration factor in the AnalysisSample. Undiluted, raw samples have a value of 1. A sample that has been concentrated for analysis one-thousand fold, for example 1 L being concentrated down to 1 mL, would have a value of 1000. A sample that has been diluted 1:10 has a value of 0.1. |
constituent | AnalysisSample | In the event of sample pooling, the individual constituent samples can be referenced. Pooling events should imply a concentrationFactor value less than 1. |
custodyEvent | CustodyEvent | Extends Event. Refers to the time, place and condtions when custody of an AnalysisSample took place |
encoding | MediaObject | A media object that encodes this AnalysisSample. This property is a synonym for associatedMedia. Supersedes encodings. |
encodingFormat | Text or URL | Media type typically expressed using a MIME format (see IANA site and MDN reference) e.g. application/zip for a SoftwareApplication binary, audio/mpeg for .mp3 etc.). In cases where a AnalysisSample has several media type representations, encoding can be used to indicate each MediaObject alongside particular encodingFormat information. Unregistered or niche encoding and file formats can be indicated instead via the most appropriate URL, e.g. defining Web page or a Wikipedia/Wikidata entry. Supersedes fileFormat. |
expires | DateTime | Date the AnalysisSample expires and is no longer useful or available due to the expected methodology of analysis or expected degradation of the sample from a usable or analytically representative state. |
funder | Organization or Person | A person or organization that supports (sponsors) the collection, submission, or and/or analysis of the AnalysisSample through some kind of financial contribution. |
hasPart | AnalysisSample | Specifies a child AnalysisSample instance created duing an aliquoting. This is to represent the disposition of splits when the original AnalysisSample is broken apart into individual containers, reducing the amount of the parent AnalysisSample. |
isPartOf | AnalysisSample | Specifies a parent AnalysisSample instance from which the AnalysisSample was aliquoted |
keywords | DefinedTerm or Text or URL | Keywords or tags used to describe this AnalysisSample. Multiple entries in a keywords list are typically delimited by commas. |
measuredParameter | MeasuredParameter | Specifies a parameter tested for. Can be an analyte (i.e. Benzene, SARS-Cov-2 RNA) or measurment of a property (pH, alkalinity, viscosity) |
parameterOfInterest | ParameterOfInterest | Specifies a parameter desired to or intended to be tested for. Can be an analyte (i.e. Benzene, SARS-Cov-2 RNA) or measurment of a property (pH, alkalinity, viscosity) |
role | DefinedTerm or Text or URL | Specifies the purpose of the samle in a sampling or analysis batch (Diagnostic, Study, Calibrant, Blank, Spike, Check, etc) |
sampledBodySite | DefinedTerm | The location on a body or organism that's part of an anatomy vocabulary |
sampledPerson |
Patient or
Person
or PropertyValue or Text or URL | Specifies a Person or unique identifier when the Person's identity is protected for legal or clinical purposes. Can reference a URL that is specific to the individual. |
sampledOrganism | Text | Specifies an name of or identifier code for a human or non-human organism from which a sample was taken |
samplingAltitude | QuantitativeValue or Text | Specifies the height in altitude when the sample is taken from an air column above a location or the altitude of a location from which a sample was drawn |
samplingDepth | Text | The depth from which a sample was taken when the sample was derived from a subsurface location. This can apply to both water and soil samples (i.e '6ft beneath water surface', 'surface', or '3 inches' |
samplingDevice | Product or Text | Specifies the device used to gather a sample material or amount from the sample source. |
samplingLocation | PostalAddress or GeoCoordinates or GeoShape or Organization or Person or Place | A mailing address in the case where the value is a PostalAddress. Where there is no Postal Address or a PostalAddress is insufficent to be precise enough to represent the location of the AnalysisSample origin. An Organizaiton, Person or Place value may be the limit of the precision available. |
samplingMethod |
CreativeWork or Text | A citation or reference to another creative work, such as another publication, web page, scholarly article, etc. where the CreativeWork references a sampling methodolgy. |
samplingSubSite | Text | A specific sub-site designation that's part of a named samplingLocation (i.e. bathroom sink, Well #1, soil pile on north side of structure) |
samplingTime | DateTime | Specifies the date and time when an AnalysisSample was taken from the original source.. |
sampler |
Person or Text | Specifies the Person or Thing performing the aliquoting action when the AnalysisSample was drawn or created from its original source. |
sampleMatrix | DefinedTerm | Specifies a matrix. For example, blood, tissue, drinking water, absorption cartridge, soil etc. |
spikedAmount | MeasuredParameter | Specifies known amounts of measured parameters purposefully added to a sample as a calibrant or check sample for quality control purposes. |
storageCondition | MeasuredParameter | Specifies a request for conditions of storage at a specific time relating to a AnalysisSample. |
storageContainer | StorageContainer | Specifies the exact StorageContainer identity and properties that is used to hold and store the AnalysisSample |
sdPublisher |
Organization or Person | Indicates the party responsible for generating and publishing the current structured data markup, typically in cases where the structured data is derived automatically from existing published content but published on a different site. For example, student projects and open data initiatives often re-publish existing content with more explicitly structured metadata. The sdPublisher property helps make such practices more explicit. |
text | Text | The textual content of this AnalysisSample. |
thumbnailUrl | URL | A thumbnail image relevant to theAnalysisSample |
video |
Clip or VideoObject | An video object that bears record of the presence or nature of the AnalysisSample |
| Properties from Thing | ||
additionalType | URL | An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally. |
alternateName | Text | An alias for the item. |
description | Text | A description of the item. |
disambiguatingDescription | Text | A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation. |
identifier |
PropertyValue or Text or URL | The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details. |
image |
ImageObject or URL | An image of the item. This can be a URL or a fully described ImageObject. |
mainEntityOfPage |
CreativeWork or URL | Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details. Inverse property: mainEntity. |
name | Text | The name of the item. |
url | URL | URL of the item. |
Examples:
A field testing lab set up at Harding Community College, 1645 7th Ave SE, run by an organization called BioCorpoZon, located at 3400 S. Lulu Ave, St. Paul, Dakota County, Minnesota 55124
A Covid-19 Molecular test was requested by a patient whose name was Taylor Chayton. She lives at 452 E. Cochise Ave in St. Paul, Zip Code 55124. Her appointment was set at 3:30PM on August 19, 2020. It took 20 minutes to process her paperwork before the sampling occurred.
A swab was used to collect a nasopharyngeal (NP) specimen. This swab was produced by Puritan Medical Products in Guilford Maine located at 31 School St., Zip Code 04443 ( SKU#: 25-3320-U EMB 80MM it had a Lot # of 053928-A ) The swab containing the sample material from the rear of the patient’s nasal cavity was placed in a UTM Tube (part # 331C) produced by Copan Diagnostics, 26055 Jefferson Ave, Murietta CA, 92562. The lot number of the tubes used was 0045-2093-37. The sample’s paperwork had a pre-printed SNOWMED code on it of 840533007 (indicating the presence of SARS-CoV-2)
It was collected and stored as per LabCorp published Guidelines
https://www.labcorp.com/assets-media/2333
The UTM Tube containing the swab was placed in a freezer on-site by a Nurse Practioner, the same person who performed the test, named Annabelle Ling. She recorded the time the sample was placed in the freezer as 4:05pm. The freezer temperature recorded was -18 deg C. The sample’s was picked up at at 7:10 PM by a field sampling driver named Howard DeClerc. He placed it in his van’s freezer compartment at 7:20. The temperature of the freezer compartment was recorded to be -12 C at that time. He drove it to a local LabCorp facility located at 402 County Rd. D West, St. Paul, MN 55112, and signed off on it at 8:55pm. The sample was logged in by a person, Nancy Windstead, working at the front desk. At 9:02pm It was assigned a LIMS generated lab control number of 08192203. The sample container was labeled 08192203-A. Ms. Windstead used a batch entry macro that simultaneously requested test 139900–Covid019 to be performed on that sample. She took an image with a lab assigned cell phone and uploaded the image into her LIMS at 9:27pm. She put the sample container in a storage freezer, labeled F-29UC, at the facility at 9:31pm. She did not make note of the freezer temperature.
The next morning, at 10:45am of August 20th, a level 4 medical technician named Donnie Blum took possession of the sample from the freezer F-29UC and immediately tested the sample using PCR cycling. The LOINC Code for the test being performed was 94500-6. He followed the FDA EUA methodology here:
https://www.fda.gov/media/136151/download
He failed to detect the target RNA sequences N1, N2 and N3 after RNA amplification and fluorescent marker spectroscopy. The device he used to obtain the result was an Applied Biosystems QuantStudio(TM) 5 Real Time PCR instrument. The lab has 14 of these test devices and this particular one the test was performed on is uniquely called, by that laboratory’s technicians, “Baldur” after a Norse mythological character. He obtained the result at 2:30pm the same day. He logged the result into the LIMS system manually as “NEG”. As the sample was entirely consumed by the test, there was nothing left to store afterwards so the swab and UTM container were disposed of.
On the report generated by the LIMS system, delivered back to the clinical pathologists at BioCorpoZon, the Negative test result for the sample was communicated labeled “SARS-CoV-2” and had an accompanying LOINC Result Code of 139975.
