.. _rstconstants:

..
  DO NOT EDIT MANUALLY!
  The document is generated by the `phenopacket-tools/constants/create_rtd.py` script.

=========
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``:

.. code-block:: java

   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):

.. code-block:: java

   OntologyClass left = left();


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


AdministrationRoute
^^^^^^^^^^^^^^^^^^^

Terms from the `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ to represent the way in which a medicinal product is introduced into the body.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://www.ebi.ac.uk/ols/ontologies/geno>`_ are used to describe the allelic state of variants.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "GENO:0000135", "heterozygous", "heterozygous()"
   "GENO:0000136", "homozygous", "homozygous()"
   "GENO:0000134", "hemizygous", "hemizygous()"
   "GENO:0000137", "unspecified zygosity", "unspecifiedZygosity()"


BiospecimenType
^^^^^^^^^^^^^^^

Terms from the `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ are used to denote the source of a biospecimen.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ to represent the tumor grade.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ 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.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://loinc.org/>`_ codes should be used to specify self-reported gender.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://hpo.jax.org/app/>`_ are used to describe laterality.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "HP:0012834", "Right", "right()"
   "HP:0012835", "Left", "left()"
   "HP:0012833", "Unilateral", "unilateral()"
   "HP:0012832", "Bilateral", "bilateral()"


MaterialSample
^^^^^^^^^^^^^^

Terms from the `EFO <https://www.ebi.ac.uk/ols/ontologies/efo>`_ to specify the status of the sample.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "EFO:0009655", "abnormal sample", "abnormalSample()"
   "EFO:0009654", "reference sample", "referenceSample()"


MedicalActions
^^^^^^^^^^^^^^

Terms from the `NCI Thesaurus <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ are used for components of medical action messages.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://hpo.jax.org/app/>`_ are used to describe age of onset or diseases or specific phenotypic features.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://www.ebi.ac.uk/ols/ontologies/uberon>`_ are used to describe organs.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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).

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ 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.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://hpo.jax.org/app/>`_ are used to describe the severity, defined as the intensity or degree of a manifestation.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://hpo.jax.org/app/>`_ are used to describe spatial patterns of phenotypic abnormalities.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ to represent the reason that the treatment was completed or stopped early.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://www.ebi.ac.uk/ols/ontologies/ncit>`_ are used to indicate if a specimen is from the primary tumor, a metastasis or a recurrence.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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 <https://units-of-measurement.org/>`_ are used to denote units.

.. csv-table:: 
   :header: "id", "label", "function name"
   :widths: 30, 200, 200

   "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()"