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Semantic Axioms in Electronic Health Records, as Instantiated by the TURBO Cohort Pipeline in PennTURBO

Introduction

“PennTURBO” refers to a solution for the semantic modeling of biomedical information, especially electronic healthcare records. This initiative takes its name from the underlying principle: Transforming and Unifying Research with Biomedical Ontologies. The same name is used for the supporting ontology itself: turbo_merged.owl. The TURBO ontology, written in the OWL2 language, follows the principles of the Open Biological and Biomedical Ontology Foundry including the use of BFO as an upper ontology, and therefore adherence to ontological realism. In addition to terms that were developed for the TURBO ontology per se, many other classes (like healthcare encounter) and properties (like has specified output) were imported from other OBO foundry ontologies, using tools like OntoFox, OntoDog, and/or ROBOT. The TURBO ontology has a GitHub repository.

This whitepaper describes the axiom patterns (or types of semantic triples) that the TURBO Cohort pipeline generates to populate the TURBO Semantic repository, an RDF triplestore, specifically:

The TURBO Cohort pipeline is described, and a distinction is drawn between shortcut semantics and expanded (or reality-based) semantics.

These topic will be illustrated with a minimal synthetic dataset about patient demographics:

Enterprise_Master_Patient_ID Gender_code Birth_Date Race_code
1 M 1/15/1986 WHITE
2 F 11/28/1935 BLACK

Background and Types of Data Ingested by the TURBO Cohort pipeline

PennTURBO uses multiple computational technologies to transform data into realism-based RDF triples. The TURBO team envisions supporting multiple data sources with various levels of structure, but there is currently one predominant use case. It’s expected that most of what is found in the TURBO Semantic repository will come from a clinical data warehouse, presumably implemented as a relational database. The TURBO Cohort pipeline starts with the TURBO Carnival server (employing the Carnival system built for the Penn Medicine BioBank), moving data from a clinical data warehouse (and related systems) into a shallow property graph. Related systems include RedCap (e.g. biobank records, like case report forms) and CSV files (e.g. loss-of-function calls based on whole exome sequencing).

Steps involved in transforming relational EHR data into realism-based axioms

Step 1: From the Penn Data Store to the TURBO Carnival server.

Carnival is a data aggregation and unification technology stack, written in Groovy, and using a Neo4J property graph back-end. Among other things, it integrates and further normalizes data from sources like thse described above. Carnival implements vines that tunnel data from the tabular or relational sources into a consistent and intuitive model. Convenience features include chunking of large SQL queries, resumption of failed queries, local caching of query results, and more.

A Carnival command line interface is available for users who do not wish to interact directly with the Neo4J graph. This interface uses the TURBO API server to identify patients with user-specified characteristics, by comparing data values form the EHR against semantic resources like the Drug Ontology, ChEBI, RxNORM and the Monarch Disease Ontology. The TURBO Carnival server also uses set arithmetic to assemble the patients into stratified test/control cohorts.

Future plans for the TURBO Carnival server:

A Carnival Vine into a Clinical Data Warehouse

The TURBO Carnival server uses SQL queries to gather data from a clinical data warehouse and populate the property graph. Portions of reality already modeled by Carnival and PennTURBO include demographic and anthropometric data about patients, medication orders, and assigned diagnosis codes. The table in the introduction of this paper illustrates representative patient demographics.

Once loaded into TURBO Carnival’s property graph, the data are modeled as two patient nodes, with an is_member_of relationship to a patient group node, an is_identified_by relationship with an identifier node, and a has_demographics_summary relationship with a demographics summary node. The demographic values themselves are implemented as properties of each demographics summary.

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Step 2: From the TURBO Carnival server to Shortcut Triples in the TURBO Semantic repository

Clinical data warehouses and the TURBO Carnival server are key to the TURBO Cohort pipeline. Nonetheless, the TURBO Cohort pipeline has been designed to ingest data from other sources and in other forms. If a system can write terse shortcut triples using classes and predicates form the TURBO ontology, then a Scala application in the TURBO Cohort pipeline will expand those shortcuts into statements about reality. The expanded statements can even include rule-based conclusions. Furthermore, if the data (like “1” and “WHITE”) come from a trusted source like the TURBO Carnival server, then the TURBO Cohort pipeline will even write the shortcut triples.

The TURBO Cohort pipeline uses the SPARQL language, plus methods from the RDF4J library to write and expand shortcuts in a triplestore like Ontotext GraphDB.

The TURBO Semantic repository component of the TURBO Cohort pipeline was previously referred to as Drivetrain GitHUb repository.

Shortcut Relations in the TURBO Ontology

TURBO shortcuts enable statements that have weak semantics and only imply some portion of reality. For example turbo:TURBO_0000607 is a shortcut from a patient to a registry of patient identifiers, like MRNs or EMPIs. The presence of this shortcut implies that

In other words, the relationship isn’t really between the patient and the registry. The TURBO Cohort pipeline uses shortcuts to lessen the semantic burden on cooperating systems and teams.

In contrast with OWL2 object property chains, the current generation of TURBO shortcuts are implicit chains of object properties between two or more things, terminating in a data property. When a shortcut needs to connect one (subject) entity to another (object) entity, the URI for the object is wrapped in a string, like "http://transformunify.org/ontologies/TURBO_0000440"^^xsd:anyURI. Without this design, it would be difficult or impossible to assert that the identifier itself has a value of 1.

A separate branch of pure property-chain shortcuts is under development.

Shortcuts Written by the TURBO Cohort pipeline

The TURBO Cohort pipeline vine pulls data out of the TURBO Carnival property graph and re-writes it with class and property terms from the TURBO ontology. As a collection of shortcut triples, the two-patient demographic dataset would look like this:

prefix xsd:                             <http://www.w3.org/2001/XMLSchema#> 
prefix pmbb:                            <http://www.itmat.upenn.edu/biobank/>
prefix human:                           <http://purl.obolibrary.org/obo/NCBITaxon_9606> 
prefix patient2DOB-text_sc:             <http://transformunify.org/ontologies/TURBO_0000604> 
prefix patient2DOB-xsd_sc:              <http://transformunify.org/ontologies/TURBO_0000605> 
prefix patient2GID-text_sc:             <http://transformunify.org/ontologies/TURBO_0000606> 
prefix patient2GID-URI_sc:              <http://transformunify.org/ontologies/TURBO_0000607> 
prefix patient2RID-URI_sc:              <http://transformunify.org/ontologies/TURBO_0000614> 
prefix patient2RID-text_sc:             <http://transformunify.org/ontologies/TURBO_0000615> 
prefix centrally-registered_patient-id: <http://transformunify.org/ontologies/TURBO_0000503> 
prefix denotes:                         <http://purl.obolibrary.org/obo/IAO_0000219> 
prefix patient2dataset-title_sc:        <http://transformunify.org/ontologies/TURBO_0003603> 
prefix patient2patient-id-text_sc:      <http://transformunify.org/ontologies/TURBO_0003608> 
prefix patient2patient-registry-URI_sc: <http://transformunify.org/ontologies/TURBO_0003610> 


pmbb:patient1 a human: ;
	patient2DOB-text_sc: "01/15/1986";
	patient2DOB-xsd_sc:  "1986-01-15"^^xsd:Date;
	patient2GID-text_sc: "M";
	patient2GID-URI_sc:  "http://purl.obolibrary.org/obo/OMRSE_00000141"^^xsd:anyURI;
	patient2RID-URI_sc:  "http://purl.obolibrary.org/obo/OMRSE_00000184"^^xsd:anyURI;
	patient2RID-text_sc: "WHITE" .
pmbb:patientCrid1 a centrally-registered_patient-id: ;
	denotes: pmbb:patient1;
	patient2dataset-title_sc:        "carnival_dataset_20190306";
	patient2patient-id-text_sc:      "1";
	patient2patient-registry-URI_sc: "http://transformunify.org/ontologies/TURBO_0000402"^^xsd:anyURI .
pmbb:patient2 a human: ;
	patient2DOB-text_sc: "11/28/1935";
	patient2DOB-xsd_sc:  "1935-11-28"^^xsd:Date;
	patient2GID-text_sc: "F";
	patient2GID-URI_sc:  "http://purl.obolibrary.org/obo/OMRSE_00000138"^^xsd:anyURI;
	patient2RID-URI_sc:  "http://purl.obolibrary.org/obo/OMRSE_00000182"^^xsd:anyURI;
	patient2RID-text_sc: "BLACK" .
pmbb:patientCrid2 a centrally-registered_patient-id: ;
	denotes: pmbb:patient2;
	patient2dataset-title_sc:        "carnival_dataset_20190306";
	patient2patient-id-text_sc:      "2";
	patient2patient-registry-URI_sc: "http://transformunify.org/ontologies/TURBO_0000402"^^xsd:anyURI .

Here, Turtle prefixes have been used not just to abbreviate the base portion of terms:

prefix xsd: <http://www.w3.org/2001/XMLSchema#>

but also to provide human-readable substitutes for terms in their entirety:

prefix human: <http://purl.obolibrary.org/obo/NCBITaxon_9606>

Therefore, readers who aren’t interested in the URI representation of TURBO terms can ignore the entire prefix block

abbreviation meaning
DOB date of birth datum (as opposed to the actual day on which someone was born)
GID gender identity datum
RID racial identity datum

These shortcut triples illustrate that the TURBO Cohort pipeline doesn’t just rewrite the tabular data in a different format. It also starts the process of asserting what entities the data are about, even though that might be done in an indirect fashion. For example, a date of birth datum can only exist (in good faith) if it is about some human or other organism that exists (or existed) in reality. Furthermore, the TURBO Cohort pipeline recodes data values that have a discrete but implicit meaning into explicit and discrete ontology terms. In order to do this, the TURBO Cohort pipeline must must be configured with some basic source- and domain-specific knowledge. For example Race_code column values of BLACK and WHITE are retained for provenance, but also represented with string-wrapped semantic terms from the Ontology for Medically Relevant Social Entities: http://purl.obolibrary.org/obo/OMRSE_00000182 for a “black or African American identity datum” and http://purl.obolibrary.org/obo/OMRSE_00000184 for a “white identity datum.” The gender identity “datums” are processed in a similar manner.

The TURBO Cohort pipeline has also asserted the registry which assigned the two identifiers that denote the two patients: http://transformunify.org/ontologies/TURBO_0000402 or ‘PDS EMPI patient identifier registry’. This was driven by an understanding of the source of the file and the column header (Enterprise_Master_Patient_ID), not by values present in the database.

Finally, the TURBO Cohort pipeline understands that different sources my express dates in different formats, like MM/DD/YYYY, MM/DD/YY, YYYY-MM-DD etc. Therefore, the TURBO Cohort pipeline retains the original textual representations of dates but also rewrites them, based on knowledge of the sources.

In summary, this step has instantiated two individuals each from the classes for Homo sapiens and patient identifier. Upon loading the TURBO ontology, the labels, superclass assertions and other reality-oriented axiomatic knowledge about humans and patient identifiers will be accessible. The fact that the identifiers denote the humans has been stated explicitly with ad object property, but all additional knowledge about the humans the identifiers is still in a shortcutted, data-only realm, using data properties.

Once inserted into the TURBO Semnatic repository, a visualization like the following can be easily generated. Note that the textual panels next to each entity are not intrinsic parts of the visualization. They have to be opened one at a time in a right-hand panel by clicking on the entity of interest and further clicking on a nearby “i” icon.

image failed to load

Step 3: : Reality-Based Expansion of Shortcut Triples, via Drivetrain

The TURBO Cohort pipeline expands shortcut patterns like these into BFO-compliant statements about reality. The rules for the expansions currently consist of parameterized SPARQL, hard coded into the the TURBO Cohort pipeline source code. Opportunities for expressing the rules in some kind of graph structure (in Neo4J, raw RDF, or as part of the TURBO ontology itself) are under evaluation.

Expanded Triples about Patient1 and Patient2

@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix dc11: <http://purl.org/dc/elements/1.1/> .
@prefix ns0: <http://purl.obolibrary.org/obo/> .
@prefix ns1: <http://transformunify.org/ontologies/> .

<http://example.org/hand_expanded#dob1>
  a <http://www.ebi.ac.uk/efo/EFO_0004950> ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#dataset1> ;
  ns0:IAO_0000136 <http://example.org/hand_expanded#neoStart1> ;
  ns1:TURBO_0010095 "01/15/1986" ;
  ns1:TURBO_0010096 "1986-01-15" .

<http://example.org/hand_expanded#dob2>
  a <http://www.ebi.ac.uk/efo/EFO_0004950> ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#dataset1> ;
  ns0:IAO_0000136 <http://example.org/hand_expanded#neoStart2> ;
  ns1:TURBO_0010095 "11/28/1935" ;
  ns1:TURBO_0010096 "1935-11-28" .

<http://example.org/hand_expanded#gid1>
  a ns0:OMRSE_00000141 ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#dataset1> ;
  ns0:IAO_0000136 <http://example.org/hand_expanded#patient1> ;
  ns1:TURBO_0010095 "M" .

<http://example.org/hand_expanded#gid2>
  a ns0:OMRSE_00000138 ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#dataset1> ;
  ns0:IAO_0000136 <http://example.org/hand_expanded#patient2> ;
  ns1:TURBO_0010095 "F" .

<http://example.org/hand_expanded#neoStart1> a ns0:UBERON_0035946 .
<http://example.org/hand_expanded#neoStart2> a ns0:UBERON_0035946 .
<http://example.org/hand_expanded#patCridSymb1>
  a ns1:TURBO_0010093 ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#patientCrid1> ;
  ns1:TURBO_0010094 "1" .

<http://example.org/hand_expanded#patCridSymb2>
  a ns1:TURBO_0010093 ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#patientCrid2> ;
  ns1:TURBO_0010094 "2" .

<http://example.org/hand_expanded#patRegDen1>
  a ns1:TURBO_0000505 ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#patientCrid1> ;
  ns0:IAO_0000219 ns1:TURBO_0000402 .

<http://example.org/hand_expanded#patRegDen2>
  a ns1:TURBO_0000505 ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#patientCrid2> ;
  ns0:IAO_0000219 ns1:TURBO_0000402 .

<http://example.org/hand_expanded#patient1>
  a ns0:NCBITaxon_9606 ;
  ns1:TURBO_0000303 <http://example.org/hand_expanded#neoStart1> .

<http://example.org/hand_expanded#patient2>
  a ns0:NCBITaxon_9606 ;
  ns1:TURBO_0000303 <http://example.org/hand_expanded#neoStart2> .

<http://example.org/hand_expanded#patientCrid1>
  a ns1:TURBO_0010092 ;
  ns0:IAO_0000219 <http://example.org/hand_expanded#patient1> .

<http://example.org/hand_expanded#patientCrid2>
  a ns1:TURBO_0010092 ;
  ns0:IAO_0000219 <http://example.org/hand_expanded#patient2> .

<http://example.org/hand_expanded#rid1>
  a ns0:OMRSE_00000184 ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#dataset1> ;
  ns0:IAO_0000136 <http://example.org/hand_expanded#patient1> ;
  ns1:TURBO_0010095 "WHITE" .

<http://example.org/hand_expanded#rid2>
  a ns0:OMRSE_00000182 ;
  ns0:BFO_0000050 <http://example.org/hand_expanded#dataset1> ;
  ns0:IAO_0000136 <http://example.org/hand_expanded#patient2> .

Expanded Visualization of Patient1 and Patient2

image failed to load

Appendices

Accounting of instances appearing in a production TURBO Semantic repository

The visualization above shows a general pattern for describing some patient knowledge from a realism perspective. However, it omits several other important patterns, and it doesn’t provide any quantitative information.

The following tables provide counts, not for the two-patient, demographics-only case, but for roughly 11,300 patients and additional data types like loss-of-function predictions, prescriptions, diagnoses and more.

Textual and axiomatic definitions for most of these terms can be found in the TURBO ontology.

These counts are specifically from the graph pmbb:expanded in GraphDB repository turbo_20181214_carnivalShortcuts in mid March, 2019.

For example, there are 5,515,042 instances of class efo:OBI_0001352 (“allele information”) in this graph. That’s because this graph models roughly 11,300 patients, each of which have predicted loss of function in an average of 500 genes.

subjType subjTypeLab triplesCount
efo:OBI_0001352 allele information 5515042
efo:OGMS_0000073 diagnosis 274741
efo:PDRO_0000001 health care prescription; prescription de santé 202011
efo:TURBO_0000561 prescription crid 202011
efo:TURBO_0000562 prescription crid symbol 202011
efo:OBI_0000097 participant under investigation role 121693
efo:OGMS_0000097 health care encounter 107293
efo:TURBO_0000508 health care encounter crid 107293
efo:TURBO_0000509 health care encounter crid symbol 107293
efo:TURBO_0000510 health care encounter registry denoter 107293
efo:TURBO_0000511 health care encounter start 107293
efo:TURBO_0000512 health care encounter start date 107293
efo:TURBO_0000907 retired placeholder for health care encounter 107293
efo:TURBO_0000908 retired placeholder for health care encounter crid 107293
efo:TURBO_0000909 retired placeholder for health care encounter symbol 107293
efo:TURBO_0000910 retired placeholder for health care encounter registry denoter 107293
efo:TURBO_0000911 retired placeholder for health care encounter start 107293
efo:TURBO_0000912 retired placeholder for health care encounter start date 107293
efo:OBI_0001931 scalar value specification 53926
efo:IAO_0000414 mass measurement datum 27165
efo:OBI_0000445 mass measurement assay 27165
efo:IAO_0000408 length measurement datum 26761
efo:TURBO_0001511 length measurement assay 26761
efo:OBI_0001933 value specification 26573
efo:TURBO_0001903 retired placeholder for bmi datum 26573
efo:TURBO_0001904 retired placeholder for value specification 26573
efo:EFO_0004340 body mass index 26573
efo:TURBO_0000527 biobank encounter 14400
efo:TURBO_0000531 biobank encounter start 14400
efo:TURBO_0000532 biobank encounter start date 14400
efo:TURBO_0000533 biobank encounter crid 14400
efo:TURBO_0000534 biobank encounter crid symbol 14400
efo:TURBO_0000535 biobank encounter registry denoter 14400
efo:TURBO_0000927 retired placeholder for biobank encounter 14400
efo:TURBO_0000931 retired placeholder for biobank encounter start 14400
efo:TURBO_0000932 retired placeholder for biobank encounter start date 14400
efo:TURBO_0000933 retired placeholder for biobank encounter crid 14400
efo:TURBO_0000934 retired placeholder for biobank encounter symbol 14400
efo:TURBO_0000935 retired placeholder for biobank encounter registry denoter 14400
efo:OMRSE_00000099 racial identification process 11084
efo:PATO_0000047 biological sex 11084
efo:PATO_0000119 height 11084
efo:PATO_0000128 weight 11084
efo:UBERON_0001013 adipose tissue 11084
efo:UBERON_0035946 start of neonate stage 11084
efo:TURBO_0000502 biobank consenter 11084
efo:TURBO_0000503 biobank consenter crid 11084
efo:TURBO_0000504 biobank consenter crid symbol 11084
efo:TURBO_0000505 patient registry denoter 11084
efo:TURBO_0000902 retired placeholder for biobank consenter 11084
efo:TURBO_0000903 retired placeholder for biobank consenter crid 11084
efo:TURBO_0000904 retired placeholder for biobank consenter symbol 11084
efo:TURBO_0000905 retired placeholder for biobank consenter registry denoter 11084
efo:TURBO_0001901 retired placeholder for adipose tissue 11084
efo:TURBO_0001902 retired placeholder for biological sex 11084
efo:TURBO_0001905 retired placeholder for height quality 11084
efo:TURBO_0001906 retired placeholder for process boundary 11084
efo:TURBO_0001908 retired placeholder for weight quality 11084
efo:EFO_0004950 date of birth 11084
efo:OBI_0000257 dna extraction 10950
efo:OBI_0001051 dna extract 10950
efo:OBI_0001479 specimen from organism 10950
efo:OBI_0001573 dna sequence data 10950
efo:OBI_0002118 exome sequencing assay 10950
efo:OBI_0200000 data transformation 10950
efo:OBI_0600005 collecting specimen from organism 10950
efo:TURBO_0000566 genotype crid 10950
efo:TURBO_0000567 genotype identifier registry denoter 10950
efo:TURBO_0000568 genotype crid symbol 10950
efo:OBI_0001868 genetic material 10868
efo:OMRSE_00000184 white identity datum 8054
efo:OMRSE_00000141 male gender identity datum 6568
efo:OMRSE_00000138 female gender identity datum 4516
efo:OMRSE_00000182 black or african american identity datum 2060
efo:OBI_0000852 record of missing knowledge 428
efo:OMRSE_00000098 racial identity datum 391
efo:OMRSE_00000181 asian identity datum 141
efo:OMRSE_00000183 native hawaiian or other pacific islander identity datum 8
efo:IAO_0000100 data set 6
efo:TURBO_0000543 biobank encounter identifier registry 3
efo:OMRSE_00000180 american indian or alaska native identity datum 2
efo:TURBO_0000571 zygosity value specification 2
efo:TURBO_0000506 patient identifier registry 1
efo:TURBO_0000513 health care encounter identifier registry 1
efo:TURBO_0000522 r2r instantiation 1

Frequency of object-property statement styles in the pmbb:expanded graph

There are 5,515,042 triples in which an instance of class obo:OBI_0001352 (“allele information”) is asserted to have a particular zygosty level: heterozygous, or homozygous LOF. The zygosity level is represented with an instance of class turbo:TURBO_0000571, (“zygosity value specification.)

In this graph, assertions about homozygous wild-type genes have not been made.

subjType subjTypeLab predicate predLab objType objTypeLab triplesCount
obo:OBI_0001352 allele information obo:OBI_0001938 has value specification turbo:TURBO_0000571 zygosity value specification 5515042
obo:OBI_0001352 allele information obo:IAO_0000136 is about obo:OBI_0001868 genetic material 5515042
obo:OBI_0001352 allele information obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 5515042
obo:OGMS_0000073 diagnosis obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 274741
obo:PDRO_0000001 health care prescription; prescription de santé obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 202011
turbo:TURBO_0000561 prescription crid obo:IAO_0000219 denotes obo:PDRO_0000001 health care prescription; prescription de santé 202011
turbo:TURBO_0000561 prescription crid obo:BFO_0000051 has part; has_part turbo:TURBO_0000562 prescription crid symbol 202011
turbo:TURBO_0000562 prescription crid symbol obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 202011
turbo:TURBO_0000562 prescription crid symbol obo:BFO_0000050 is part of; part of turbo:TURBO_0000561 prescription crid 202011
turbo:TURBO_0000508 health care encounter crid obo:IAO_0000219 denotes obo:OGMS_0000097 health care encounter 107293
turbo:TURBO_0000508 health care encounter crid obo:BFO_0000051 has part; has_part turbo:TURBO_0000509 health care encounter crid symbol 107293
turbo:TURBO_0000508 health care encounter crid obo:BFO_0000051 has part; has_part turbo:TURBO_0000510 health care encounter registry denoter 107293
turbo:TURBO_0000508 health care encounter crid turbo:TURBO_0000302 linked in dataset with turbo:TURBO_0000503 biobank consenter crid 107293
turbo:TURBO_0000509 health care encounter crid symbol obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 107293
turbo:TURBO_0000509 health care encounter crid symbol obo:BFO_0000050 is part of; part of turbo:TURBO_0000508 health care encounter crid 107293
turbo:TURBO_0000510 health care encounter registry denoter obo:IAO_0000219 denotes turbo:TURBO_0000513 health care encounter identifier registry 107293
turbo:TURBO_0000510 health care encounter registry denoter obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 107293
turbo:TURBO_0000510 health care encounter registry denoter obo:BFO_0000050 is part of; part of turbo:TURBO_0000508 health care encounter crid 107293
turbo:TURBO_0000511 health care encounter start obo:RO_0002223 starts obo:OGMS_0000097 health care encounter 107293
turbo:TURBO_0000512 health care encounter start date obo:IAO_0000136 is about turbo:TURBO_0000511 health care encounter start 107293
turbo:TURBO_0000512 health care encounter start date obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 107293
obo:OBI_0000097 participant under investigation role obo:BFO_0000054 realized in obo:OGMS_0000097 health care encounter 107293
turbo:TURBO_0000907 retired placeholder for health care encounter turbo:TURBO_0001700 replaced with iui obo:OGMS_0000097 health care encounter 107293
turbo:TURBO_0000908 retired placeholder for health care encounter crid turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000508 health care encounter crid 107293
turbo:TURBO_0000910 retired placeholder for health care encounter registry denoter turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000510 health care encounter registry denoter 107293
turbo:TURBO_0000911 retired placeholder for health care encounter start turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000511 health care encounter start 107293
turbo:TURBO_0000912 retired placeholder for health care encounter start date turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000512 health care encounter start date 107293
turbo:TURBO_0000909 retired placeholder for health care encounter symbol turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000509 health care encounter crid symbol 107293
obo:OGMS_0000097 health care encounter obo:RO_0002234 has output obo:OGMS_0000073 diagnosis 67137
obo:OBI_0000445 mass measurement assay obo:OBI_0000293 has_specified_input turbo:TURBO_0000502 biobank consenter 27165
obo:OBI_0000445 mass measurement assay obo:OBI_0000299 has_specified_output obo:IAO_0000414 mass measurement datum 27165
obo:IAO_0000414 mass measurement datum obo:OBI_0001938 has value specification obo:OBI_0001931 scalar value specification 27165
obo:IAO_0000414 mass measurement datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 27165
obo:IAO_0000414 mass measurement datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 27165
obo:IAO_0000414 mass measurement datum obo:IAO_0000221 is quality measurement of obo:PATO_0000128 weight 27165
turbo:TURBO_0001511 length measurement assay obo:OBI_0000293 has_specified_input turbo:TURBO_0000502 biobank consenter 26761
turbo:TURBO_0001511 length measurement assay obo:OBI_0000299 has_specified_output obo:IAO_0000408 length measurement datum 26761
obo:IAO_0000408 length measurement datum obo:OBI_0001938 has value specification obo:OBI_0001931 scalar value specification 26761
obo:IAO_0000408 length measurement datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 26761
obo:IAO_0000408 length measurement datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 26761
obo:IAO_0000408 length measurement datum obo:IAO_0000221 is quality measurement of obo:PATO_0000119 height 26761
efo:EFO_0004340 body mass index obo:OBI_0001938 has value specification obo:OBI_0001933 value specification 26573
efo:EFO_0004340 body mass index obo:IAO_0000136 is about obo:UBERON_0001013 adipose tissue 26573
efo:EFO_0004340 body mass index obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 26573
turbo:TURBO_0001903 retired placeholder for bmi datum turbo:TURBO_0001700 replaced with iui efo:EFO_0004340 body mass index 26573
turbo:TURBO_0001904 retired placeholder for value specification turbo:TURBO_0001700 replaced with iui obo:OBI_0001933 value specification 26573
turbo:TURBO_0000533 biobank encounter crid obo:IAO_0000219 denotes turbo:TURBO_0000527 biobank encounter 14400
turbo:TURBO_0000533 biobank encounter crid obo:BFO_0000051 has part; has_part turbo:TURBO_0000534 biobank encounter crid symbol 14400
turbo:TURBO_0000533 biobank encounter crid obo:BFO_0000051 has part; has_part turbo:TURBO_0000535 biobank encounter registry denoter 14400
turbo:TURBO_0000533 biobank encounter crid turbo:TURBO_0000302 linked in dataset with turbo:TURBO_0000503 biobank consenter crid 14400
turbo:TURBO_0000534 biobank encounter crid symbol obo:BFO_0000050 is part of; part of turbo:TURBO_0000533 biobank encounter crid 14400
turbo:TURBO_0000534 biobank encounter crid symbol obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 14400
turbo:TURBO_0000535 biobank encounter registry denoter obo:IAO_0000219 denotes turbo:TURBO_0000543 biobank encounter identifier registry 14400
turbo:TURBO_0000535 biobank encounter registry denoter obo:BFO_0000050 is part of; part of turbo:TURBO_0000533 biobank encounter crid 14400
turbo:TURBO_0000535 biobank encounter registry denoter obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 14400
turbo:TURBO_0000531 biobank encounter start obo:RO_0002223 starts turbo:TURBO_0000527 biobank encounter 14400
turbo:TURBO_0000532 biobank encounter start date obo:IAO_0000136 is about turbo:TURBO_0000531 biobank encounter start 14400
obo:OBI_0000097 participant under investigation role obo:BFO_0000054 realized in turbo:TURBO_0000527 biobank encounter 14400
turbo:TURBO_0000927 retired placeholder for biobank encounter turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000527 biobank encounter 14400
turbo:TURBO_0000933 retired placeholder for biobank encounter crid turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000533 biobank encounter crid 14400
turbo:TURBO_0000935 retired placeholder for biobank encounter registry denoter turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000535 biobank encounter registry denoter 14400
turbo:TURBO_0000931 retired placeholder for biobank encounter start turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000531 biobank encounter start 14400
turbo:TURBO_0000932 retired placeholder for biobank encounter start date turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000532 biobank encounter start date 14400
turbo:TURBO_0000934 retired placeholder for biobank encounter symbol turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000534 biobank encounter crid symbol 14400
turbo:TURBO_0000532 biobank encounter start date obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 14294
obo:OGMS_0000097 health care encounter obo:BFO_0000051 has part; has_part obo:OBI_0000445 mass measurement assay 14171
obo:OBI_0000445 mass measurement assay obo:BFO_0000050 is part of; part of obo:OGMS_0000097 health care encounter 14171
obo:OGMS_0000097 health care encounter obo:BFO_0000051 has part; has_part turbo:TURBO_0001511 length measurement assay 13809
turbo:TURBO_0001511 length measurement assay obo:BFO_0000050 is part of; part of obo:OGMS_0000097 health care encounter 13809
efo:EFO_0004340 body mass index obo:IAO_0000581 has time stamp turbo:TURBO_0000512 health care encounter start date 13640
obo:OGMS_0000097 health care encounter obo:RO_0002234 has output efo:EFO_0004340 body mass index 13640
turbo:TURBO_0000527 biobank encounter obo:BFO_0000051 has part; has_part obo:OBI_0000445 mass measurement assay 12994
obo:OBI_0000445 mass measurement assay obo:BFO_0000050 is part of; part of turbo:TURBO_0000527 biobank encounter 12994
turbo:TURBO_0000527 biobank encounter obo:BFO_0000051 has part; has_part turbo:TURBO_0001511 length measurement assay 12952
turbo:TURBO_0001511 length measurement assay obo:BFO_0000050 is part of; part of turbo:TURBO_0000527 biobank encounter 12952
turbo:TURBO_0000527 biobank encounter obo:OBI_0000299 has_specified_output efo:EFO_0004340 body mass index 12933
efo:EFO_0004340 body mass index obo:IAO_0000581 has time stamp turbo:TURBO_0000532 biobank encounter start date 12933
obo:OGMS_0000097 health care encounter obo:RO_0002234 has output obo:PDRO_0000001 health care prescription; prescription de santé 12721
obo:UBERON_0001013 adipose tissue obo:BFO_0000050 is part of; part of turbo:TURBO_0000502 biobank consenter 11084
turbo:TURBO_0000502 biobank consenter turbo:TURBO_0000303 born at obo:UBERON_0035946 start of neonate stage 11084
turbo:TURBO_0000502 biobank consenter obo:BFO_0000051 has part; has_part obo:UBERON_0001013 adipose tissue 11084
turbo:TURBO_0000502 biobank consenter obo:RO_0000086 has quality obo:PATO_0000047 biological sex 11084
turbo:TURBO_0000502 biobank consenter obo:RO_0000086 has quality obo:PATO_0000119 height 11084
turbo:TURBO_0000502 biobank consenter obo:RO_0000086 has quality obo:PATO_0000128 weight 11084
turbo:TURBO_0000502 biobank consenter obo:RO_0000087 has role obo:OBI_0000097 participant under investigation role 11084
turbo:TURBO_0000502 biobank consenter obo:RO_0000056 participates in turbo:TURBO_0000527 biobank encounter 11084
turbo:TURBO_0000503 biobank consenter crid obo:IAO_0000219 denotes turbo:TURBO_0000502 biobank consenter 11084
turbo:TURBO_0000503 biobank consenter crid obo:BFO_0000051 has part; has_part turbo:TURBO_0000504 biobank consenter crid symbol 11084
turbo:TURBO_0000503 biobank consenter crid obo:BFO_0000051 has part; has_part turbo:TURBO_0000505 patient registry denoter 11084
turbo:TURBO_0000503 biobank consenter crid turbo:TURBO_0000302 linked in dataset with turbo:TURBO_0000533 biobank encounter crid 11084
turbo:TURBO_0000504 biobank consenter crid symbol obo:BFO_0000050 is part of; part of turbo:TURBO_0000503 biobank consenter crid 11084
turbo:TURBO_0000504 biobank consenter crid symbol obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 11084
efo:EFO_0004950 date of birth obo:IAO_0000136 is about obo:UBERON_0035946 start of neonate stage 11084
efo:EFO_0004950 date of birth obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 11084
turbo:TURBO_0000505 patient registry denoter obo:IAO_0000219 denotes turbo:TURBO_0000506 patient identifier registry 11084
turbo:TURBO_0000505 patient registry denoter obo:BFO_0000050 is part of; part of turbo:TURBO_0000503 biobank consenter crid 11084
turbo:TURBO_0000505 patient registry denoter obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 11084
turbo:TURBO_0001901 retired placeholder for adipose tissue turbo:TURBO_0001700 replaced with iui obo:UBERON_0001013 adipose tissue 11084
turbo:TURBO_0000902 retired placeholder for biobank consenter turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000502 biobank consenter 11084
turbo:TURBO_0000903 retired placeholder for biobank consenter crid turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000503 biobank consenter crid 11084
turbo:TURBO_0000905 retired placeholder for biobank consenter registry denoter turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000505 patient registry denoter 11084
turbo:TURBO_0000904 retired placeholder for biobank consenter symbol turbo:TURBO_0001700 replaced with iui turbo:TURBO_0000504 biobank consenter crid symbol 11084
turbo:TURBO_0001902 retired placeholder for biological sex turbo:TURBO_0001700 replaced with iui obo:PATO_0000047 biological sex 11084
turbo:TURBO_0001905 retired placeholder for height quality turbo:TURBO_0001700 replaced with iui obo:PATO_0000119 height 11084
turbo:TURBO_0001906 retired placeholder for process boundary turbo:TURBO_0001700 replaced with iui obo:UBERON_0035946 start of neonate stage 11084
turbo:TURBO_0001908 retired placeholder for weight quality turbo:TURBO_0001700 replaced with iui obo:PATO_0000128 weight 11084
obo:OBI_0600005 collecting specimen from organism obo:OBI_0000293 has_specified_input turbo:TURBO_0000502 biobank consenter 10950
obo:OBI_0600005 collecting specimen from organism obo:OBI_0000299 has_specified_output obo:OBI_0001479 specimen from organism 10950
obo:OBI_0600005 collecting specimen from organism obo:BFO_0000050 is part of; part of turbo:TURBO_0000527 biobank encounter 10950
obo:OBI_0200000 data transformation obo:OBI_0000293 has_specified_input obo:OBI_0001573 dna sequence data 10950
obo:OBI_0200000 data transformation obo:OBI_0000299 has_specified_output obo:OBI_0001352 allele information 10950
obo:OBI_0000257 dna extraction obo:OBI_0000293 has_specified_input obo:OBI_0001479 specimen from organism 10950
obo:OBI_0000257 dna extraction obo:OBI_0000299 has_specified_output obo:OBI_0001051 dna extract 10950
obo:OBI_0002118 exome sequencing assay obo:OBI_0000293 has_specified_input obo:OBI_0001051 dna extract 10950
obo:OBI_0002118 exome sequencing assay obo:OBI_0000299 has_specified_output obo:OBI_0001573 dna sequence data 10950
turbo:TURBO_0000566 genotype crid obo:IAO_0000219 denotes obo:OBI_0001479 specimen from organism 10950
turbo:TURBO_0000566 genotype crid obo:BFO_0000051 has part; has_part turbo:TURBO_0000568 genotype crid symbol 10950
turbo:TURBO_0000566 genotype crid obo:BFO_0000051 has part; has_part turbo:TURBO_0000567 genotype identifier registry denoter 10950
turbo:TURBO_0000568 genotype crid symbol obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 10950
turbo:TURBO_0000568 genotype crid symbol obo:BFO_0000050 is part of; part of turbo:TURBO_0000566 genotype crid 10950
turbo:TURBO_0000567 genotype identifier registry denoter obo:BFO_0000050 is part of; part of turbo:TURBO_0000566 genotype crid 10950
turbo:TURBO_0000527 biobank encounter obo:BFO_0000051 has part; has_part obo:OBI_0600005 collecting specimen from organism 10949
obo:OBI_0001868 genetic material obo:OBI_0000643 has grain obo:OBI_0001051 dna extract 10868
obo:OBI_0001868 genetic material obo:OGG_0000000014 is genome of organism turbo:TURBO_0000502 biobank consenter 10868
turbo:TURBO_0000502 biobank consenter obo:RO_0000056 participates in obo:OGMS_0000097 health care encounter 8132
turbo:TURBO_0000503 biobank consenter crid turbo:TURBO_0000302 linked in dataset with turbo:TURBO_0000508 health care encounter crid 8132
obo:OMRSE_00000099 racial identification process obo:OBI_0000299 has_specified_output obo:OMRSE_00000184 white identity datum 8054
obo:OMRSE_00000184 white identity datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 8054
obo:OMRSE_00000184 white identity datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 8054
obo:OMRSE_00000141 male gender identity datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 6568
obo:OMRSE_00000141 male gender identity datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 6568
obo:OMRSE_00000138 female gender identity datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 4516
obo:OMRSE_00000138 female gender identity datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 4516
obo:OMRSE_00000182 black or african american identity datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 2060
obo:OMRSE_00000182 black or african american identity datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 2060
obo:OMRSE_00000099 racial identification process obo:OBI_0000299 has_specified_output obo:OMRSE_00000182 black or african american identity datum 2060
obo:OMRSE_00000099 racial identification process obo:OBI_0000299 has_specified_output obo:OBI_0000852 record of missing knowledge 428
obo:OBI_0000852 record of missing knowledge obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 428
obo:OBI_0000852 record of missing knowledge obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 428
obo:OMRSE_00000099 racial identification process obo:OBI_0000299 has_specified_output obo:OMRSE_00000098 racial identity datum 391
obo:OMRSE_00000098 racial identity datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 391
obo:OMRSE_00000098 racial identity datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 391
obo:OMRSE_00000181 asian identity datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 141
obo:OMRSE_00000181 asian identity datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 141
obo:OMRSE_00000099 racial identification process obo:OBI_0000299 has_specified_output obo:OMRSE_00000181 asian identity datum 141
obo:OMRSE_00000183 native hawaiian or other pacific islander identity datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 8
obo:OMRSE_00000183 native hawaiian or other pacific islander identity datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 8
obo:OMRSE_00000099 racial identification process obo:OBI_0000299 has_specified_output obo:OMRSE_00000183 native hawaiian or other pacific islander identity datum 8
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000509 health care encounter crid symbol 3
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000510 health care encounter registry denoter 3
obo:OMRSE_00000180 american indian or alaska native identity datum obo:IAO_0000136 is about turbo:TURBO_0000502 biobank consenter 2
obo:OMRSE_00000180 american indian or alaska native identity datum obo:BFO_0000050 is part of; part of obo:IAO_0000100 data set 2
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000534 biobank encounter crid symbol 2
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part efo:EFO_0004340 body mass index 2
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:IAO_0000408 length measurement datum 2
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:IAO_0000414 mass measurement datum 2
obo:OMRSE_00000099 racial identification process obo:OBI_0000299 has_specified_output obo:OMRSE_00000180 american indian or alaska native identity datum 2
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OBI_0001352 allele information 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OMRSE_00000180 american indian or alaska native identity datum 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OMRSE_00000181 asian identity datum 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000504 biobank consenter crid symbol 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000535 biobank encounter registry denoter 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000532 biobank encounter start date 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OMRSE_00000182 black or african american identity datum 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part efo:EFO_0004950 date of birth 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OGMS_0000073 diagnosis 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OMRSE_00000138 female gender identity datum 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000568 genotype crid symbol 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000512 health care encounter start date 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:PDRO_0000001 health care prescription; prescription de santé 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OMRSE_00000141 male gender identity datum 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OMRSE_00000183 native hawaiian or other pacific islander identity datum 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000505 patient registry denoter 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part turbo:TURBO_0000562 prescription crid symbol 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OMRSE_00000098 racial identity datum 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OBI_0000852 record of missing knowledge 1
obo:IAO_0000100 data set obo:BFO_0000051 has part; has_part obo:OMRSE_00000184 white identity datum 1
turbo:TURBO_0000522 r2r instantiation obo:OBI_0000293 has_specified_input obo:IAO_0000100 data set 1

Frequency of data-property statement styles in the pmbb:expanded graph

There are 5,515,042 triples in which a instance of class obo:OBI_0001352 (“allele information”) is asserted to have some string as it textual value (via property turbo:TURBO_0006512.) The textual values are taken verbatim form the source. For example: “gene:SETBP1(ENSG00000152217);zygosity:2” mean that some patient is predicted to be homozygous LOF for SET Binding Protein 1.

subjType subjTypeLab predicate predLab dataType triplesCount
obo:OBI_0001352 allele information turbo:TURBO_0006512 has textual value xsd:string 5515042
obo:OGMS_0000073 diagnosis turbo:TURBO_0006512 has textual value xsd:string 274741
obo:OGMS_0000073 diagnosis turbo:TURBO_0006515 has namespace textual value xsd:string 274741
obo:OGMS_0000073 diagnosis turbo:TURBO_0010013 primary diagnoisis xsd:boolean 274691
obo:OGMS_0000073 diagnosis turbo:TURBO_0010014 order in diagnosis sequence xsd:integer 269645
turbo:TURBO_0000562 prescription crid symbol turbo:TURBO_0006510 has literal value xsd:string 202011
obo:PDRO_0000001 health care prescription; prescription de santé turbo:TURBO_0006512 has textual value xsd:string 201978
obo:OGMS_0000097 health care encounter turbo:TURBO_0006500 referent tracked? xsd:boolean 107293
turbo:TURBO_0000508 health care encounter crid turbo:TURBO_0006500 referent tracked? xsd:boolean 107293
turbo:TURBO_0000509 health care encounter crid symbol turbo:TURBO_0006500 referent tracked? xsd:boolean 107293
turbo:TURBO_0000510 health care encounter registry denoter turbo:TURBO_0006500 referent tracked? xsd:boolean 107293
turbo:TURBO_0000511 health care encounter start turbo:TURBO_0006500 referent tracked? xsd:boolean 107293
turbo:TURBO_0000512 health care encounter start date turbo:TURBO_0006500 referent tracked? xsd:boolean 107293
turbo:TURBO_0000512 health care encounter start date turbo:TURBO_0006511 has date value xsd:date 107293
turbo:TURBO_0000509 health care encounter crid symbol turbo:TURBO_0006510 has literal value xsd:string 107293
turbo:TURBO_0000512 health care encounter start date turbo:TURBO_0006512 has textual value xsd:string 107293
obo:OGMS_0000097 health care encounter turbo:TURBO_0006601 pre-expansion uri text xsd:string 107293
obo:OGMS_0000097 health care encounter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000508 health care encounter crid turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000509 health care encounter crid symbol turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000510 health care encounter registry denoter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000511 health care encounter start turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000512 health care encounter start date turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000907 retired placeholder for health care encounter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000908 retired placeholder for health care encounter crid turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000909 retired placeholder for health care encounter symbol turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000910 retired placeholder for health care encounter registry denoter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000911 retired placeholder for health care encounter start turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
turbo:TURBO_0000912 retired placeholder for health care encounter start date turbo:TURBO_0006602 pre-reftracking uri text xsd:string 107293
obo:OBI_0001931 scalar value specification obo:OBI_0002135 has specified value xsd:string 27980
obo:OBI_0001933 value specification turbo:TURBO_0006500 referent tracked? xsd:boolean 26573
efo:EFO_0004340 body mass index turbo:TURBO_0006500 referent tracked? xsd:boolean 26573
obo:OBI_0001933 value specification turbo:TURBO_0006602 pre-reftracking uri text xsd:string 26573
turbo:TURBO_0001903 retired placeholder for bmi datum turbo:TURBO_0006602 pre-reftracking uri text xsd:string 26573
turbo:TURBO_0001904 retired placeholder for value specification turbo:TURBO_0006602 pre-reftracking uri text xsd:string 26573
efo:EFO_0004340 body mass index turbo:TURBO_0006602 pre-reftracking uri text xsd:string 26573
turbo:TURBO_0000527 biobank encounter turbo:TURBO_0006500 referent tracked? xsd:boolean 14400
turbo:TURBO_0000531 biobank encounter start turbo:TURBO_0006500 referent tracked? xsd:boolean 14400
turbo:TURBO_0000532 biobank encounter start date turbo:TURBO_0006500 referent tracked? xsd:boolean 14400
turbo:TURBO_0000533 biobank encounter crid turbo:TURBO_0006500 referent tracked? xsd:boolean 14400
turbo:TURBO_0000534 biobank encounter crid symbol turbo:TURBO_0006500 referent tracked? xsd:boolean 14400
turbo:TURBO_0000535 biobank encounter registry denoter turbo:TURBO_0006500 referent tracked? xsd:boolean 14400
turbo:TURBO_0000534 biobank encounter crid symbol turbo:TURBO_0006510 has literal value xsd:string 14400
turbo:TURBO_0000527 biobank encounter turbo:TURBO_0006601 pre-expansion uri text xsd:string 14400
turbo:TURBO_0000527 biobank encounter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000531 biobank encounter start turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000532 biobank encounter start date turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000533 biobank encounter crid turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000534 biobank encounter crid symbol turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000535 biobank encounter registry denoter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000927 retired placeholder for biobank encounter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000931 retired placeholder for biobank encounter start turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000932 retired placeholder for biobank encounter start date turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000933 retired placeholder for biobank encounter crid turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000934 retired placeholder for biobank encounter symbol turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000935 retired placeholder for biobank encounter registry denoter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 14400
turbo:TURBO_0000532 biobank encounter start date turbo:TURBO_0006511 has date value xsd:date 14294
turbo:TURBO_0000532 biobank encounter start date turbo:TURBO_0006512 has textual value xsd:string 14294
obo:OBI_0001933 value specification obo:OBI_0002135 has specified value xsd:string 13640
obo:OBI_0001931 scalar value specification obo:OBI_0002135 has specified value xsd:float 13033
obo:OBI_0001933 value specification obo:OBI_0002135 has specified value xsd:double 12933
obo:OBI_0001931 scalar value specification obo:OBI_0002135 has specified value xsd:double 12913
obo:PATO_0000047 biological sex turbo:TURBO_0006500 referent tracked? xsd:boolean 11084
obo:PATO_0000119 height turbo:TURBO_0006500 referent tracked? xsd:boolean 11084
obo:PATO_0000128 weight turbo:TURBO_0006500 referent tracked? xsd:boolean 11084
obo:UBERON_0001013 adipose tissue turbo:TURBO_0006500 referent tracked? xsd:boolean 11084
obo:UBERON_0035946 start of neonate stage turbo:TURBO_0006500 referent tracked? xsd:boolean 11084
turbo:TURBO_0000502 biobank consenter turbo:TURBO_0006500 referent tracked? xsd:boolean 11084
turbo:TURBO_0000503 biobank consenter crid turbo:TURBO_0006500 referent tracked? xsd:boolean 11084
turbo:TURBO_0000504 biobank consenter crid symbol turbo:TURBO_0006500 referent tracked? xsd:boolean 11084
turbo:TURBO_0000505 patient registry denoter turbo:TURBO_0006500 referent tracked? xsd:boolean 11084
efo:EFO_0004950 date of birth turbo:TURBO_0006511 has date value xsd:date 11084
turbo:TURBO_0000504 biobank consenter crid symbol turbo:TURBO_0006510 has literal value xsd:string 11084
efo:EFO_0004950 date of birth turbo:TURBO_0006510 has literal value xsd:string 11084
turbo:TURBO_0000502 biobank consenter turbo:TURBO_0006601 pre-expansion uri text xsd:string 11084
obo:PATO_0000047 biological sex turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
obo:PATO_0000119 height turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
obo:PATO_0000128 weight turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
obo:UBERON_0001013 adipose tissue turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
obo:UBERON_0035946 start of neonate stage turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0000502 biobank consenter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0000503 biobank consenter crid turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0000504 biobank consenter crid symbol turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0000505 patient registry denoter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0000902 retired placeholder for biobank consenter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0000903 retired placeholder for biobank consenter crid turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0000904 retired placeholder for biobank consenter symbol turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0000905 retired placeholder for biobank consenter registry denoter turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0001901 retired placeholder for adipose tissue turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0001902 retired placeholder for biological sex turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0001905 retired placeholder for height quality turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0001906 retired placeholder for process boundary turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0001908 retired placeholder for weight quality turbo:TURBO_0006602 pre-reftracking uri text xsd:string 11084
turbo:TURBO_0000568 genotype crid symbol turbo:TURBO_0006510 has literal value xsd:string 10950
obo:OMRSE_00000184 white identity datum turbo:TURBO_0006512 has textual value xsd:string 8054
obo:OMRSE_00000141 male gender identity datum turbo:TURBO_0006510 has literal value xsd:string 6568
obo:OMRSE_00000138 female gender identity datum turbo:TURBO_0006510 has literal value xsd:string 4516
obo:OMRSE_00000182 black or african american identity datum turbo:TURBO_0006512 has textual value xsd:string 2060
obo:OBI_0000852 record of missing knowledge turbo:TURBO_0006512 has textual value xsd:string 428
obo:OMRSE_00000098 racial identity datum turbo:TURBO_0006512 has textual value xsd:string 391
obo:OMRSE_00000181 asian identity datum turbo:TURBO_0006512 has textual value xsd:string 141
obo:OMRSE_00000183 native hawaiian or other pacific islander identity datum turbo:TURBO_0006512 has textual value xsd:string 8
obo:IAO_0000100 data set http://purl.org/dc/elements/1.1/title title xsd:string 6
obo:OMRSE_00000180 american indian or alaska native identity datum turbo:TURBO_0006512 has textual value xsd:string 2

Styles of statements appearing in the pmbb:expanded graph, where the object is classified in some other graph, eg. pmbb:ontology

See also notes below.

subjType subjTypeLab predicate predLab triplesCount
obo:OGMS_0000073 diagnosis turbo:TURBO_0000306 has matching icd term 274741
obo:OGMS_0000073 diagnosis turbo:TURBO_0000703 has namespace 274741
turbo:TURBO_0000907 retired placeholder for health care encounter obo:IAO_0000225 obsolescence reason specification 107293
turbo:TURBO_0000908 retired placeholder for health care encounter crid obo:IAO_0000225 obsolescence reason specification 107293
turbo:TURBO_0000909 retired placeholder for health care encounter symbol obo:IAO_0000225 obsolescence reason specification 107293
turbo:TURBO_0000910 retired placeholder for health care encounter registry denoter obo:IAO_0000225 obsolescence reason specification 107293
turbo:TURBO_0000911 retired placeholder for health care encounter start obo:IAO_0000225 obsolescence reason specification 107293
turbo:TURBO_0000912 retired placeholder for health care encounter start date obo:IAO_0000225 obsolescence reason specification 107293
obo:OBI_0001931 scalar value specification obo:IAO_0000039 has measurement unit label 53926
turbo:TURBO_0001903 retired placeholder for bmi datum obo:IAO_0000225 obsolescence reason specification 26573
turbo:TURBO_0001904 retired placeholder for value specification obo:IAO_0000225 obsolescence reason specification 26573
turbo:TURBO_0000927 retired placeholder for biobank encounter obo:IAO_0000225 obsolescence reason specification 14400
turbo:TURBO_0000931 retired placeholder for biobank encounter start obo:IAO_0000225 obsolescence reason specification 14400
turbo:TURBO_0000932 retired placeholder for biobank encounter start date obo:IAO_0000225 obsolescence reason specification 14400
turbo:TURBO_0000933 retired placeholder for biobank encounter crid obo:IAO_0000225 obsolescence reason specification 14400
turbo:TURBO_0000934 retired placeholder for biobank encounter symbol obo:IAO_0000225 obsolescence reason specification 14400
turbo:TURBO_0000935 retired placeholder for biobank encounter registry denoter obo:IAO_0000225 obsolescence reason specification 14400
turbo:TURBO_0000902 retired placeholder for biobank consenter obo:IAO_0000225 obsolescence reason specification 11084
turbo:TURBO_0000903 retired placeholder for biobank consenter crid obo:IAO_0000225 obsolescence reason specification 11084
turbo:TURBO_0000904 retired placeholder for biobank consenter symbol obo:IAO_0000225 obsolescence reason specification 11084
turbo:TURBO_0000905 retired placeholder for biobank consenter registry denoter obo:IAO_0000225 obsolescence reason specification 11084
turbo:TURBO_0001901 retired placeholder for adipose tissue obo:IAO_0000225 obsolescence reason specification 11084
turbo:TURBO_0001902 retired placeholder for biological sex obo:IAO_0000225 obsolescence reason specification 11084
turbo:TURBO_0001905 retired placeholder for height quality obo:IAO_0000225 obsolescence reason specification 11084
turbo:TURBO_0001906 retired placeholder for process boundary obo:IAO_0000225 obsolescence reason specification 11084
turbo:TURBO_0001908 retired placeholder for weight quality obo:IAO_0000225 obsolescence reason specification 11084
turbo:TURBO_0000567 genotype identifier registry denoter obo:IAO_0000219 denotes 10950

Notes about objects that are classified in the TURBO ontology, not pmbb:expanded

predicate predLab Typical statement objects, defined in pmbb:ontology
obo:IAO_0000039 has measurement unit label Measurement unit labels like obo:UO_0000015 and obo:UO_0000009
obo:IAO_0000219 denotes some registry patient registry
obo:IAO_0000231 has obsolescence reason Obsolescence reason specifications (instances of class obo:IAO_0000225)
turbo:TURBO_0000306 has matching icd term the diagnosis outputs of encounters can have matching ICD terms, which would be defined in the ICD9 or ICD10 graphs.
turbo:TURBO_0000703 has namespace the diagnosis outputs of encounters can clarify the namespace from to which a code belongs (NCIT 71890 or 71890, for ICD9CM and ICD10CM)