Philips ISPM Specimen

The table onc_philips_mtb_specimen_data includes specimen-related information from the Philips IntelliSpace Precision Medicine (ISPM) genomics database at Stanford. The fields in this table are related to specimen details, including accession numbers and collection information.

Table Columns

column name	type	phi	phi-scrubbing operation
accession_number	STRING	Yes	Hash
collection_collected_datetime	STRING		Jitter
created	DATETIME	Yes	Jitter
isprimary	STRING
person_id		Yes	Stable Between Data Refreshes
sampleid	STRING	Yes	Nullified
sampletype	STRING
specimen_identifier	STRING		Nullified
stanford_patient_uid	STRING	Yes	Del
tumorpercentage	STRING

Columns Description

accession_number

Identifier for the specimen. This field can be used to link to the pat_diag_orders table. Note that there can be multiple records with the same accession number.

collection_collected_datetime

Datetime for specimen collection. Entirely null field.

created

Timestamp of specimen creation. The combination of created and accession_number is the Primary Key for specimen_data table

isprimary

This is a field indicating if the specimen is from the primary tumor site.

person_id

Person_id as corresponds to the OMOP dataset

sampleid

Free-text field containing a mix of information, such as testing sites and/or accession numbers etc. Nullify for now but we will explore further in the future

sampletype

No description available

specimen_identifier

Entirely null field

stanford_patient_uid

Internal Stanford tracking ID (this is the patient’s MRN | DOB)

tumorpercentage

Refers to percentage of tumor cells compared to whole sample present in the sample selected, for performing next-generation sequencing (NGS) test.