Constants

The phenopacket-tools library offers a selection of recommended and predefined OntologyClass objects for commonly used concepts. For instance, this is the code one would need to write using the native Protobuf framework to get an OntologyClass instance that represents the modifier Left:

OntologyClass left = OntologyClass.newBuilder()
  .setId("HP:0012835")
  .setLabel("Left")
  .build();

In contrast, this is the code required with phenopacket-tools (omitting import statements in both cases):

OntologyClass left = left();

The following tables present the available static functions with predefined concepts.

AdministrationRoute

Terms from the NCI Thesaurus to represent the way in which a medicinal product is introduced into the body.

id	label	function name
NCIT:C38276	Intravenous Route of Administration	intravenous()
NCIT:C38222	Intraarterial Route of Administration	intraarterial()
NCIT:C183503	Administration via Wound Irrigation	woundIrrigation()
NCIT:C149695	Nebulizer Route of Administration	nebulizer()
NCIT:C38288	Oral Route of Administration	oral()
NCIT:C38267	Intrathecal Route of Administration	intrathecal()
NCIT:C38677	Peridural Route of Administration	peridural()
NCIT:C38304	Topical Route of Administration	topical()
NCIT:C38305	Transdermal Route of Administration	transdermal()

AllelicState

Terms from the GENE ontology are used to describe the allelic state of variants.

id	label	function name
GENO:0000135	heterozygous	heterozygous()
GENO:0000136	homozygous	homozygous()
GENO:0000134	hemizygous	hemizygous()
GENO:0000137	unspecified zygosity	unspecifiedZygosity()

BiospecimenType

Terms from the NCI Thesaurus are used to denote the source of a biospecimen.

id	label	function name
NCIT:C133261	Bone Marrow Aspirate	boneMarrowAspirate()
NCIT:C158416	Blood DNA	bloodDNA()
NCIT:C185194	Cerebrospinal Fluid Sample	cerebrospinalFluidSample()
NCIT:C156435	Formalin-Fixed Paraffin-Embedded DNA	formalinFixedParaffinEmbeddedDNA()
NCIT:C13195	Bronchoalveolar Lavage Fluid	bronchoalveolarLavageFluid()
NCIT:C187062	Pericardial Fluid Specimen	pericardialFluidSpecimen()
NCIT:C185197	Peritoneal Fluid Sample	peritonealFluidSample()
NCIT:C163995	Total RNA	totalRNA()
NCIT:C18009	Tumor Tissue	tumorTissue()

DiseaseGrade

Terms from the NCI Thesaurus to represent the tumor grade.

id	label	function name
NCIT:C28077	Grade 1	grade1()
NCIT:C28078	Grade 2	grade2()
NCIT:C28079	Grade 3	grade3()
NCIT:C28080	Grade 3a	grade3a()
NCIT:C28081	Grade 3b	grade3b()
NCIT:C28082	Grade 4	grade4()

DiseaseStage

These codes from NCI Thesaurus can be used to denote that clinical stage of cancer or heart failure. Other codes should be used for specific diseases with their own clinical stage systems.

id	label	function name
NCIT:C28051	Stage 0	stage0()
NCIT:C27966	Stage I	stageI()
NCIT:C28054	Stage II	stageII()
NCIT:C27970	Stage III	stageIII()
NCIT:C27971	Stage IV	stageIV()
NCIT:C66904	New York Heart Association Class I	nyhaClassI()
NCIT:C66905	New York Heart Association Class II	nyhaClassII()
NCIT:C66907	New York Heart Association Class III	nyhaClassIII()
NCIT:C7922	New York Heart Association Class III/IV	nyhaClassIII_or_IV()
NCIT:C66908	New York Heart Association Class IV	nyhaClassIV()

Evidence

Terms from the Evidence and Con clusion Ontology <https://evidenceontology.org/browse/#ECO_SN> are used to specify evidence categories.

id	label	function name
ECO:0006016	author statement from published clinical study	authorStatementFromPublishedClinicalStudy()
ECO:0007539	author statement from published clinical study used in automatic assertion	authorStatementFromPublishedClinicalStudyAutomaticAssertion()
ECO:0006017	author statement from published clinical study used in manual assertion	authorStatementFromPublishedClinicalStudyManualAssertion()
ECO:0000033	author statement supported by traceable reference	authorStatementSupportedByTraceableReference()
ECO:0006154	self-reported patient statement evidence	selfReportedPatientStatementEvidence()

Gender

LOINC codes should be used to specify self-reported gender.

id	label	function name
LOINC:LA22878-5	Identifies as male	identifiesAsMale()
LOINC:LA22879-3	Identifies as female	identifiesAsFemale()
LOINC:LA22880-1	Female-to-male transsexual	femaleToMaleTranssexual()
LOINC:LA22881-9	Male-to-female transsexual	maleToFemaleTranssexual()
LOINC:LA22882-7	Identifies as non-conforming	identifiesAsNonConforming()
LOINC:LA46-8	other	otherGender()
LOINC:LA20384-6	Asked but unknown	askedButUnknown()

Laterality

Modifier terms from the HPO are used to describe laterality.

id	label	function name
HP:0012834	Right	right()
HP:0012835	Left	left()
HP:0012833	Unilateral	unilateral()
HP:0012832	Bilateral	bilateral()

MaterialSample

Terms from the EFO to specify the status of the sample.

id	label	function name
EFO:0009655	abnormal sample	abnormalSample()
EFO:0009654	reference sample	referenceSample()

MedicalActions

Terms from the NCI Thesaurus are used for components of medical action messages.

id	label	function name
NCIT:C41331	Adverse Event	adverseEvent()
NCIT:C64530	Four Times Daily	fourTimesDaily()
NCIT:C38222	Intraarterial Route of Administration	intraArterialAdministration()
NCIT:C38276	Intravenous Route of Administration	intravenousAdministration()
NCIT:C38288	Oral Route of Administration	oralAdministration()
NCIT:C64576	Once	once()
NCIT:C125004	Once Daily	onceDaily()
NCIT:C64527	Three Times Daily	threeTimesDaily()
NCIT:C64496	Twice Daily	twiceDaily()

Onset

Terms from the HPO are used to describe age of onset or diseases or specific phenotypic features.

id	label	function name
HP:0030674	Antenatal onset	antenatalOnset()
HP:0011460	Embryonal onset	embryonalOnset()
HP:0011461	Fetal onset	fetalOnset()
HP:0034199	Late first trimester onset	lateFirstTrimesterOnset()
HP:0034198	Second trimester onset	secondTrimesterOnset()
HP:0034197	Third trimester onset	thirdTrimesterOnset()
HP:0003577	Congenital onset	congenitalOnset()
HP:0003623	Neonatal onset	neonatalOnset()
HP:0003593	Infantile onset	infantileOnset()
HP:0011463	Childhood onset	childhoodOnset()
HP:0003621	Juvenile onset	juvenileOnset()
HP:0003581	Adult onset	adultOnset()
HP:0011462	Young adult onset	youngAdultOnset()
HP:0025708	Early young adult onset	earlyYoungAdultOnset()
HP:0025709	Intermediate young adult onset	intermediateYoungAdultOnset()
HP:0025710	Late young adult onset	lateYoungAdultOnset()
HP:0003596	Middle age onset	middleAgeOnset()
HP:0003584	Late onset	lateOnset()

Organ

Terms from the UBERON ontology are used to describe organs.

id	label	function name
UBERON:0000955	brain	brain()
UBERON:0002037	cerebellum	cerebellum()
UBERON:0001690	ear	ear()
UBERON:0000970	eye	eye()
UBERON:0002107	heart	heart()
UBERON:0002113	kidney	kidney()
UBERON:0000059	large intestine	largeIntestine()
UBERON:0002107	liver	liver()
UBERON:0002048	lung	lung()
UBERON:0000004	nose	nose()
UBERON:0002108	small intestine	smallIntestine()
UBERON:0002240	spinal cord	spinalCord()
UBERON:0002106	spleen	spleen()
UBERON:0001723	tongue	tongue()
UBERON:0002370	thymus	thymus()

PathologicalTnm

TNM staging performed as part of pathologic specimen (based on surgical specimens including sentinel lymph node biopsy specimens).

id	label	function name
NCIT:C48740	pM0 Stage Finding	pM0StageFinding()
NCIT:C48741	pM1 Stage Finding	pM1StageFinding()
NCIT:C48742	pM1a Stage Finding	pM1aStageFinding()
NCIT:C48743	pM1b Stage Finding	pM1bStageFinding()
NCIT:C48744	pM1c Stage Finding	pM1cStageFinding()
NCIT:C48745	pN0 Stage Finding	pN0StageFinding()
NCIT:C48746	pN1 Stage Finding	pN1StageFinding()
NCIT:C48747	pN1a Stage Finding	pN1aStageFinding()
NCIT:C48748	pN1b Stage Finding	pN1bStageFinding()
NCIT:C48749	pN1c Stage Finding	pN1cStageFinding()
NCIT:C48750	pN2 Stage Finding	pN2StageFinding()
NCIT:C48751	pN2a Stage Finding	pN2aStageFinding()
NCIT:C48752	pN2b Stage Finding	pN2bStageFinding()
NCIT:C48753	pN2c Stage Finding	pN2cStageFinding()
NCIT:C48754	pN3 Stage Finding	pN3StageFinding()
NCIT:C48755	pN3a Stage Finding	pN3aStageFinding()
NCIT:C48756	pN3b Stage Finding	pN3bStageFinding()
NCIT:C48757	pN3c Stage Finding	pN3cStageFinding()
NCIT:C48758	pT0 Stage Finding	pT0StageFinding()
NCIT:C48759	pT1 Stage Finding	pT1StageFinding()
NCIT:C48760	pT1a Stage Finding	pT1aStageFinding()
NCIT:C48761	pT1b Stage Finding	pT1bStageFinding()
NCIT:C48763	pT1c Stage Finding	pT1cStageFinding()
NCIT:C48764	pT2 Stage Finding	pT2StageFinding()
NCIT:C48765	pT2a Stage Finding	pT2aStageFinding()
NCIT:C48766	pT2b Stage Finding	pT2bStageFinding()
NCIT:C48767	pT2c Stage Finding	pT2cStageFinding()
NCIT:C48768	pT3 Stage Finding	pT3StageFinding()
NCIT:C48769	pT3a Stage Finding	pT3aStageFinding()
NCIT:C48770	pT3b Stage Finding	pT3bStageFinding()
NCIT:C48771	pT3c Stage Finding	pT3cStageFinding()
NCIT:C48772	pT4 Stage Finding	pT4StageFinding()
NCIT:C48773	pT4a Stage Finding	pT4aStageFinding()
NCIT:C48774	pT4b Stage Finding	pT4bStageFinding()
NCIT:C48775	pT4c Stage Finding	pT4cStageFinding()
NCIT:C48776	pT4d Stage Finding	pT4dStageFinding()

Response

These codes from NCI Thesaurus can be used to code the overall response of a patient to treatment. Favorable and Unfavorble can be used for general purposes and the remaining codes are intended to be used for oncology.

id	label	function name
NCIT:C123584	Favorable Response	favorableResponse()
NCIT:C123617	Unfavorable Response	unfavorableResponse()
NCIT:C123600	No Response	noResponse()
NCIT:C123614	Stringent Complete Response	stringentCompleteResponse()
NCIT:C123598	Minimal Response	minimalResponse()
NCIT:C4870	Complete Remission	completeRemission()
NCIT:C18058	Partial Remission	partialRemission()
NCIT:C70604	Primary Refractory	primaryRefractory()
NCIT:C142357	iRECIST Complete Response	iRECISTCompleteResponse()
NCIT:C142356	iRECIST Confirmed Progressive Disease	iRECISTConfirmedProgressiveDisease()
NCIT:C142358	iRECIST Partial Response	iRECISTPartialResponse()
NCIT:C142359	iRECIST Stable Disease	iRECISTStableDisease()
NCIT:C142360	iRECIST Unconfirmed Progressive Disease	iRECISTUnconfirmedProgressiveDisease()

Severity

Terms from the HPO are used to describe the severity, defined as the intensity or degree of a manifestation.

id	label	function name
HP:0012827	Borderline	borderline()
HP:0012825	Mild	mild()
HP:0012826	Moderate	moderate()
HP:0012828	Severe	severe()
HP:0012829	Profound	profound()

SpatialPattern

Modifier terms from the HPO are used to describe spatial patterns of phenotypic abnormalities.

id	label	function name
HP:0032544	Predominant small joint localization	predominantSmallJointLocalization()
HP:0031450	Polycyclic	polycyclic()
HP:0025287	Axial	axial()
HP:0033813	Perilobular	perilobular()
HP:0033814	Paraseptal	paraseptal()
HP:0033815	Bronchocentric	bronchocentric()
HP:0033816	Centrilobular	centrilobular()
HP:0033817	Miliary	miliary()
HP:0012837	Generalized	generalized()
HP:0033819	Perilymphatic	perilymphatic()
HP:0012838	Localized	localized()
HP:0033818	Reticular	reticular()
HP:0012839	Distal	distal()
HP:0030645	Central	central()
HP:0025290	Upper-body predominance	upperBodyPredominance()
HP:0032539	Joint extensor surface localization	jointExtensorSurfaceLocalization()
HP:0025295	Herpetiform	herpetiform()
HP:0025296	Morbilliform	morbilliform()
HP:0030649	Pericentral	pericentral()
HP:0025294	Dermatomal	dermatomal()
HP:0030648	Midperipheral	midperipheral()
HP:0025293	Distributed along Blaschko lines	distributedAlongBlaschkoLines()
HP:0025292	Acral	acral()
HP:0030647	Paracentral	paracentral()
HP:0025275	Lateral	lateral()
HP:0030646	Peripheral	peripheral()
HP:0025291	Lower-body predominance	lowerBodyPredominance()
HP:0020034	Diffuse	diffuse()
HP:0012840	Proximal	proximal()
HP:0033820	Apical	apical()
HP:0030650	Focal	focal()
HP:0030651	Multifocal	multifocal()
HP:0032540	Joint flexor surface localization	jointFlexorSurfaceLocalization()

TreatmentTermination

Terms from the NCI Thesaurus to represent the reason that the treatment was completed or stopped early.

id	label	function name
NCIT:C105740	Treatment Completed as Prescribed	treatmentCompletedAsPrescribed()
NCIT:C105741	Treatment Terminated Due to Toxicity	treatmentTerminatedDueToToxicity()
NCIT:C106470	Treatment on Hold	treatmentOnHold()
NCIT:C41331	Adverse Event	adverseEvent()

TumorProgression

Terms from the NCI Thesaurus are used to indicate if a specimen is from the primary tumor, a metastasis or a recurrence.

id	label	function name
NCIT:C8509	Primary Neoplasm	primaryNeoplasm()
NCIT:C3261	Metastatic Neoplasm	metastaticNeoplasm()
NCIT:C4798	Recurrent Neoplasm	recurrentNeoplasm()

Unit

With some exceptions, terms from the The Unified Code for Units of Measure are used to denote units.

id	label	function name
UCUM:degree	degree (plane angle)	degreeOfAngle()
UCUM:[diop]	diopter	diopter()
UCUM:g	gram	gram()
UCUM:g.kg-1	gram per kilogram	gramPerKilogram()
UCUM:kg	kilogram	kilogram()
UCUM:L	liter	liter()
UCUM:m	meter	meter()
UCUM:ug	microgram	microgram()
UCUM:ug.dL-1	microgram per deciliter	microgramPerDeciliter()
UCUM:ug.L-1	microgram per liter	microgramPerLiter()
UCUM:uL	microliter	microliter()
UCUM:um	micrometer	micrometer()
UCUM:mg	milligram	milligram()
UCUM:mg.d-1	milligram per day	milligramPerDay()
UCUM:mg.dL-1	milligram per deciliter	milligramPerDeciliter()
UCUM:mg.kg-1	milligram per kilogram	mgPerKg()
UCUM:mL	milliliter	milliliter()
UCUM:mm	millimeter	millimeter()
UCUM:mm[Hg]	millimetres of mercury	mmHg()
UCUM:mmol	millimole	millimole()
UCUM:mol	mole	mole()
UCUM:mol.L-1	mole per liter	molePerLiter()
UCUM:mol.mL-1	mole per milliliter	molePerMilliliter()
UCUM:U.L-1	enzyme unit per liter	enzymeUnitPerLiter()