Class descriptions added manually. Class restrictions added manually. Data ranges modified manually for a better performance. Integrated with other ontologies. 3.1 LEFT RIGHT LATERO_LATERAL TERMINO_LATERAL TERMINO_TERMINAL LEFT RIGHT ABSENT PRESENT INFERIOR_LIP SUPERIOR_LIP VESTIBULE HYOID_BONE SOVRAHYOID_REGION SUBLINGUAL_GLAND SUBMANDIBULAR_GLAND ANTERIOR_PALATINE_PILLAR TONSILLAR_FOSSA EMI_MAXILLARY_ALVEOLAR_RIDGE INCISAL MOLAR PREMOLAR' LEFT RIGHT IA IB IIA IIB III IV VA VB VI Absent Present Probable VeryProbable 180 200 Absent Present Probable VeryProbable LEFT RIGHT LEFT RIGHT LEFT RIGHT IA IB IIA IIB III IV VA VB VI LIQUID_DIET NORMAL PEG PERMANENT_TRACHEOSTOMY SEMILIQUID_DIET SNG HIGH MILD MODERATE NONE 60 64 70 60 64 70 HEAVY_DRINKER MODERATE_DRINKER NORMAL NOT_NORMAL LEFT RIGHT C00.0 External upper lip C00.1 External lower lip C00.2 External lip-NOS C00.3 Mucosa of upper lip C00.4 Mucosa of lower lip C00.5 Mucosa of lip-NOS C00.6 Commissure of lip C00.8 Overlapping lesion of lip C00.9 Lip-NOS','C01 Base of tongue C02.0 Dorsal surface of tongue-NOS C02.1 Border of tongue C02.2 Ventral surface of tongue-NOS C02.3 Anterior two-thirds of tongue-NOS C02.4 Lingual tonsil C02.8 Overlapping lesion of tongue C02.9 Tongue-NOS C03.0 Upper gum C03.1 Lower gum C03.9 Gum-NOS C04.0 Anterior floor of the mouth C04.1 Lateral floor of the mouth C04.8 Overlapping lesion of floor of mouth C04.9 Floor of mouth-NOS C05.0 Hard palate C05.1 Soft palate C05.2 Uvula C05.8 Overlapping lesion of palate C05.9 Palate-NOS C06.0 Cheek mucosa C06.1 Vestibule of mouth C06.2 Retromolar area C06.8 Overlapping lesion of other and unspecified parts of mouth C06.9 Mouth-NOS C07 Parotid gland C08.0 Submandibular gland C08.1 Sublingual gland C08.8 Overlapping lesion of major salivary glands C08.9 Major salivary gland-NOS C09.0 Tonsillar fossa C09.1 Tonsillar pillar C09.8 Overlapping lesion of tonsil C09.9 Tonsil-NOS C10.0 Vallecula C10.1 Anterior surface of epiglottis C10.2 Lateral wall of oropharynx C10.3 Posterior wall of oropharynx C10.4 Branchial cleft C10.8 Overlapping lesion of oropharynx C10.9 Oropharynx-NOS C11.0 Superior wall of nasopharynx C11.1 Posterior wall of nasopharynx C11.2 Lateral wall of nasopharynx C11.3 Anterior wall of nasopharynx C11.8 Overlapping lesion of nasopharynx C11.9 Nasopharynx-NOS C12 Piriform sinus C13.0 Postcricoid region C13.1 Aryepiglottic fold - hypopharyngeal aspect C13.2 Posterior wall of hypopharynx C13.8 Overlapping lesion of hypopharynx C13.9 Hypopharynx-NOS C14.0 Pharynx-NOS C14.2 Waldeyers ring C14.8 Overlapping lesion of lip - oral cavity and pharynx LEFT RIGHT LEFT RIGHT LEFT RIGHT LEFT RIGHT PARTIAL TOTAL LEFT RIGHT MASTICATION PHONATION SWALLOWING ABSENT PRESENT EXTRINSIC_TONGUE_MUSCLES HYOID_BONE SOVRAHYOID_REGION MANDIBULAR_BODY EMITONGUE MIDLINE TONGUE_MARGIN ARYEPIGLOTTIC_FOLDS EPIGLOTTIC LARYNX TONGUE_BASE ORAL_TONGUE ANTERIOR LEFT RIGHT ANCHILOGLOSSIA FISTULA LOSS_OF_TASTE MOUNTH_BLEEDING/HAEMORRHAGE NASAL_FOSSA_OBSTRUCTION OTODINIA PAIN PARALYSIS RECURRENT_SINUSITIS SUBMANDIBOLAR_SIALOADENITIS TRISMUS ULCERATIONS LEFT RIGHT LEFT RIGHT ACUTE_RESPIRATORY_INSUFFICIENCY HEPATIC_INSUFFICIENCY ILEO IRA MYOCARDIAL_ISCHEMIA PULMUNAR_DISEASE SEPSIS STROKE THROMBOSIS 1_G1 2_G2 3_G3 ABSENT PRESENT JAW_BONE MIDLINE_CROSSED MIDLINE_NOT_CROSSED SOFT_PALATE NASAL_FOSSA LEFT RIGHT WITH_CRICOIDOEPIGLOTTOPESSY WITH_CRICOIDOPESSY LEFT RIGHT ABSENT PRESENT BUCCAL_MUCOSA EMI_MANDIBULAR_ALVEOLAR_RIDGE INCISAL_ALVEOLAR_RIDGE INFERIOR_LIP PREMOLAR_ALVEOLAR_RIDGE VESTIBULE HYOID_BONE SOVRAHYOID_REGION SUBLINGUAL_GLAND SUBMANDIBOLAR_REGION SUBMANDIBULAR_GLAND BUCCAL_MUCOSA EMI_MANDIBULAR_ALVEOLAR_RIDGE INFERIOR_LIP PREMOLAR_ALVEOLAR_RIDGE VESTIBULE FOM MIDLINE_CROSSED MIDLINE_NOT_CROSSED ORAL_TONGUE TONGUE_BASE FOM MOLAR_ALVEOLAR_RIDGE ORAL_TONGUE RETROMOLAR_TRIGONE INFERIOR_INCISORS INFERIOR_MOLAR INFERIOR_PREMOLAR LEFT RIGHT CT CT + contrast T1 SE Fat Saturated + contrast axial T1 SE Fat Saturated + contrast coronal T1 SE Fat Saturated + contrast sagittal T1 TSE axial T2 TSE Fat Saturated Coronal T2 TSE axial AUTOIMMUNE_DISEASE CHEMOTHERAPY CORTICOSTEROIDS TRANSPLANTATION Absent Present Probable VeryProbable N0 N1 N2A N2B N2C N3 NX T1 T2 T3 T4A T4B LEFT RIGHT LOWER UPPER LEFT RIGHT LAMINA_PROPIA MICROINVASION MUSCLE SUBMUCOSA LEFT RIGHT LEFT RIGHT LOWER UPPER ABSCESS DEHISCENCE FISTULA FLAP_FAILURE FLAP_REVISION FLAP_THROMBOSIS HAEMATOMA HAEMORRAGE LYMPHATIC_FISTULA ABBE BOZOLA_LEFT BOZOLA_RIGHT FAMM_LEFT FAMM_RIGHT MARKED MILD MODERATE NONE 0_M0 1_M1 X_MX LEFT RIGHT Absent Present Probable VeryProbable LEFT RIGHT INFERIOR_AND_SUPERIOR NFERIOR SUPERIOR ABSENT PRESENT BILATERAL CONTRALATERAL OMOLATERAL 0_N0 1_N1 2A_N2A 2B_N2B 2C_N2C 3_N3 X_NX LEFT RIGHT FUNCTIONAL RADICAL SELECTIVE SENTINEL_NODE_BIOPSY SINGLE_NODE_BIOBSY HYPOGLOSS INFERIOR_ALVEOLAR_NERVE INFRAORBITAL_NERVE LINGUAL OPTIC_NERVE SPINAL_NERVE VAGUS GENERAL_STATUS INOPERABLE PATIENT_S_REFUSE HARD_LIGNEOUS STRAINED_ELASTIC ABSENT PRESENT 3-6CM LESS_THEN_3CM MORE_THEN_6CM ELONGATED ROUND ABSENT EVOCABLE SPONTANEOUS MULTIPLE SINGLE EXTREME MARKED MILD MODERATE NONE ABSENT PRESENT HYOID_BONE SOVRAHYOID_MUSCLES STYLOID_MUSCLES SUBLINGUAL_MUSCLES LATERAL_FOM MANDIBULAR_BODY ARYEPIGLOTTIC_FOLDS EPIGLOTTIC LARYNX TONGUE_BASE AMIGDALO_GLOSSUS_SULCUS ANTERIOR_PALATINE_PILLAR SOFT_PALATE AP_TIP_ANTERIOR_1_3 AP_TIP_MEDIAN_1_3 AP_TIP_POSTERIOR_1_3 LEFT LL_LATERAL_1_3 LL_MEDIAN_1_3 LL_MIDDLE_1_3 RIGHT WHOLE_TONGUE IA IB IIA IIB III IV VA VB VI ADEQUATE NOT_ADEQUATE INFERIOR LEFT RIGHT SUPERIOR Absent Present Probable VeryProbable BANDS CORDS ISLANDS PUSHING SINGLE_CELLS LEFT RIGHT ANTERIOR LATERAL_LEFT LATERAL_RIGHT Absent Present Probable VeryProbable Absent Present Probable VeryProbable Axial Coroal Sagittal FOLLOWING_HOSPITALIZATION IMMEDIATE_POST_TREATMENT ERYTHROPLAKIA LEUKOPLAKIA LICHEN_RUBEN_PLANUS NO ORAL_SUBMUCOSUS_FIBROSIS C01 Base of tongue C02.0 Dorsal surface of tongue-NOS C02.1 Border of tongue C02.2 Ventral surface of tongue-NOS C02.3 Anterior two-thirds of tongue-NOS C02.4 Lingual tonsil C02.8 Overlapping lesion of tongue C02.9 Tongue-NOS C03.0 Upper gum C03.1 Lower gum C03.9 Gum-NOS C04.0 Anterior floor of the mouth C04.1 Lateral floor of the mouth C04.8 Overlapping lesion of floor of mouth C04.9 Floor of mouth-NOS C05.0 Hard palate C05.1 Soft palate C05.2 Uvula C05.8 Overlapping lesion of palate C05.9 Palate-NOS C06.0 Cheek mucosa C06.1 Vestibule of mouth C06.2 Retromolar area C06.8 Overlapping lesion of other and unspecified parts of mouth C06.9 Mouth-NOS C09.8 Overlapping lesion of tonsil C10.0 Vallecula C10.1 Anterior surface of epiglottis C10.2 Lateral wall of oropharynx C10.3 Posterior wall of oropharynx C10.4 Branchial cleft C10.8 Overlapping lesion of oropharynx C10.9 Oropharynx-NOS ABSENT PRESENT BUCCAL_MUCOSA FOM ORAL_TONGUE TONGUE_BASE ANTERIOR_PALATINE_PILLAR OROPHARYNGEAL_TONSIL POSTERIOR_PALATINE_PILLAR MANDIBULAR_BODY MANDIBULAR_RAMUS MEDIAN_PTERYGOID_MUSCLE HARD_PALATE SOFT_PALATE TUBER_MAXILLAE LEFT RIGHT 2D_RT 3D_RT IM_RT TYPE_1 TYPE_2 TYPE_3 LEFT RIGHT MEDICAL_TREATMENT_FOR_AEDEMA NORMAL PERMANENT_TRACHEOSTOMY TRACHEOSTOMY_AEDEMA TRACHEOSTOMY_FOR_DEGLUTITION ABSENT PRESENT BUCCAL_MUCOSA INCISAL_ALVEOLAR_RIDGE PREMOLAR_ALVEOLAR_RIDGE SUPERIOR_LIP VESTIBULE BUCCAL_MUCOSA EMI_MAXILLARY_ALVEOLAR_RIDGE PREMOLAR_ALVEOLAR_RIDGE SUPERIOR_LIP VESTIBULE HARD_PALATE MIDLINE_CROSSED MIDLINE_NOT_CROSSED ANTERIOR_PALATINE_PILLAR EMI_MAXILLARY_ALVEORLAR_RIDGE HARD_PALATE MOLAR_ALVEOLAR_RIDGE RETROMOLAR_TRIGONE TUBER_MAXILLAE MAXILLARY_SINUS NASAL_FOSSA SUPERIOR_INCISORS SUPERIOR_MOLAR SUPERIOR_PREMOLAR HARD_PALATE JAW_BONE ANTERIOR_PALATINE_PILLAR OROPHARYNGEAL_TONSIL POSTERIOR_PALATINE_PILLAR MIDLINE_CROSSED MIDLINE_NOT_CROSSED NASAL_FOSSA NASOPHARYNX LEFT RIGHT B C R S HIGH LOW MIDDLE B C R S ENUCLEORESECTION PAROTIDECTOMY SUBLINGUAL_GLAND_RESECTION SUBMANDIBULAR_GLAND_RESECTION SUPERFICIAL TOTAL LEFT RIGHT LEFT RIGHT Bilateral Contralateral Ipsilateral 2-4CM LESS_THEN_2CM MORE_THEN_4CM CHEEK CHIN NECK 'CIGAR_AND_PIPES BETEL_QUID CIGARETTES SMOKELESS_TOBACCO ENTERS_FAMILY_LIFE ENTERS_SOCIAL_LIFE ISOLATED LEFT RIGHT GOOD INTELLIGIBLE INTELLIGIBLE_WITH_EFFORT PERMANENT_TRACHEOSTOMY UNINTELLIGIBLE Stage0 StageI StageII StageIII StageIVA StageIVB StageIVC LEFT RIGHT ANILINA NO PHENOLS CERVICOTOMY CRANIO_FACIAL ENDORAL LABIOTOMY MANDIBOLOTOMY OLLIER OTHER PULL_TROUGH WEBER_FERGUSON HYOID_BONE ORAL_TONGUE SOVRAHYOID_REGION SUBLINGUAL_MUSCLES DEEP_FASCIAL_SPACES_OF_UPPER_NECK NEUROVASCULAR_BUNDLE ARYEPIGLOTTIC_FOLDS EPIGLOTTIC LARYNX ANTERIOR_PALATINE_PILLAR OROPHARYNGEAL_TONSIL POSTERIOR_PALATINE_PILLAR SOFT_PALATE PHARYNGEAL_WALL EMI_BASE LEFT RIGHT WHOLE_BASE 'SOFT HARD_LIGNEOUS STRAINED_ELASTIC EPIGLOTTIC THYROID_CARTILAGE TONGUE_BASE OROPHARYNX HARD_PALATE SKULL_BASE SOFT_PALATE LEFT RIGHT 'EXOPHYTIC_PAPILLARY EDOPHYTIC_BURROWING ENDOPHYTIC_INVASIVE' ENDOPHYTIC_ULCERATED ERITHROLEUKOPLACIK ERYTHROPLACIK EXOPHYTIC_FUNGATING EXOPHYTIC_VERRUCOCIFORM LEUKOPLASIC M0 M1 N0 N1 N2A N2B N2C N3 T1 T2 T3 T4A T4B T4C TIS 0_T0 1S_T1S 1_T1 2_T2 3_T3 4A_T4A 4B_T4B X_TX LEFT RIGHT HEMITHYROIDECTOMY TOTAL_THYROIDECTOMY LEFT RIGHT LEFT RIGHT TOTAL_CIRCULAR_PHARANGOLARYNGECTOMY TOTAL_EMIPHARYNGOLARYNGECTOMY LEFT RIGHT LEFT RIGHT JUGULAR_TURGOR_PRESENT NECK_MOBILITY_LIMITATION SKIN_ULCERATION SPINAL_ACCESSORY_NERVE CANDIDA HIV PAPILLOMAVIRUSES_16 PAPILLOMAVIRUSES_18 PAPILLOMAVIRUSES_33 HEAT UV X-RAYS LEFT RIGHT LATERO_LATERAL TERMINO_LATERAL TERMINO_TERMINAL III-MiddleJugularNode IIa-AnteriorHighJugularNode IIb-PosteriorHighJugularNode IV-LowJugularNode Ia-SubmentalNode Ib-SubmandibularNode V-SovraclavearNodeAndPosteriorTriangle' VI-AnteriorNode III-MiddleJugularNode IIa-AnteriorHighJugularNode IIb-PosteriorHighJugularNode IV-LowJugularNode Ia-SubmentalNode Ib-SubmandibularNode V-SovraclavearNodeAndPosteriorTriangle VI-AnteriorNode Metastasis PrimaryTumorSite RegionalNode RemoteNode Undefined 12M 15M 18M 21M 24M 3M 6M 9M M0 M1 MX N0 N1 N2A N2B N2C N3 NX T1 T2 T3 T4A T4B 1 ontologies:ClinicalData Data obtained from clinical examination. Clinical Data ontologies:ClinicalReoccurrence Reoccurrence based on clinical data. Clinical Reoccurrence ontologies:Countries Country of residence of the patient. Country 1 It should not be this way 1 1 1 1 ontologies:DiseaseInstance Description of the first visit of the patient. The originalVisitID is the identifier to be used in the following visits. Disease Instance 1 ontologies:DistantPedicledFlap Flap taken from distant site with no interruption of the vascular pedicle that maintains connection with the donor site. Distant Pedicled Flap 1 1 1 1 1 1 1 1 ontologies:Evaluations The physician’s opinion on examinations and diagnostic tests performed to the patient. Evaluation 1 1 1 ontologies:FollowUpVisits The visit performed after the treatment to check the status of the patient and the maintenance of the patient remission status. Follow Up Visit 1 ontologies:FreeFlap Flap taken from distant site with vascular pedicle directly anostomized with head and neck major vessels. Free Flap 1 ontologies:GeneralImagingData Set of the most significant features extracted from the imaging processing. General Imaging Data ontologies:GenomicReoccurrence Reoccurrence based on genomic data. Genomic Reoccurrence 1 1 ontologies:GeometricData Geometric Information associated with a Lymphnode or a tumor. Geometric Data 1 ontologies:Image A picture of the tumor. Image 1 ontologies:ImagePreview to show to the doctor because of its significance. Image Preview ontologies:ImagingReoccurrence Reoccurrence based on imaging data. Imaging Reoccurrence 1 ontologies:LocalFlaps Flap taken from a local site with vascular pedicle maintained. Local Flap 1 ontologies:LocoRegional Flap taken from loco-regional tissue in head and neck area. Loco Regional Flap 1 1 1 1 ontologies:LymphNode A small circular ball shape organ of the immune system. Lymph Node 1 ontologies:LymphNodeImagingData The radiological feature of the lymph node performed by RNA, magnetic resonance imaging or CTscanner. Lymph Node Imaging Data 1 ontologies:MicroArrayData Information extracted from each row of the feature extractor. MicroArray Data 1 ontologies:MicroArrayGroupData Contains the gene ontology term id, description and the associated enrichment value of the analyzed FE data. MicroArray Group Data 1 1 ontologies:MicroArrayGroupList Collection of information provided by gene ontology analyses of FE data based on Gorilla approach (http://cbl-gorilla.cs.technion.ac.il/). MicroArray Group List 1 1 1 ontologies:MicroArrayInfo Collection of all the information related to the micro array. MicroArray Info 1 1 ontologies:MicroArrayList Collection of the information provided by the feature extractor. MicroArray List 1 ontologies:NClinicalAspects Clinical characteristic features of the neck lymph node. N Clinical Aspects 1 ontologies:NSurgicalProcedure Description of the surgical treatment for the lymph node performed by the surgeon. N Surgical Procedure 1 ontologies:OtherTreatments Description of other kind of treatment but not surgical or none treatment. Other Treatment 1 ontologies:PathologicalData Data extracted from pathology with the use of microscope, immunohistochemical analysis and INNO-LiPA HPV genotyping system based on PCR and hybridization. Pathological Data 1 1 1 1 1 ontologies:Patient The person who receives medical attention with oral or oropharynx squamous cell carcicomas detected. Patient 1 ontologies:PcrData Information provided by the Real Time PCR. PCR Data 1 ontologies:PostTreatment After treatment (after surgery, after chemo/radiotherapy). It applies to clinical actions, patient’s status and follow-up. Post Treatment 1 ontologies:QualityOfLife The status of the patient after every follow up visit. Quality Of Life 1 ontologies:RiskFactors Factors from clinical literature associated with the development of the cancer. Risk Factors 1 ontologies:SurgicalReconstruction Procedure of the reconstruction of the surgical defect. Surgical Reconstruction 1 ontologies:TClinicalAspects Clinical features of the tumor. Evidences of the tumor drawn by means of a clinical evaluation. T Clinical Aspects 1 ontologies:TLocalization Area of the oral cavity of pharynx in which the tumor is growing. T Localization 1 ontologies:TSurgicalProcedure Description of the surgical treatment for the tumor performed by the surgeon. T Surgical Procedure 1 1 ontologies:Treatment The therapy performed by the patient. Treatment 1 1 1 1 1 1 1 ontologies:Tumor New abnormal growth of tissue. Tumor 1 ontologies:TumorImagingData The radiological feature of the tumor performed by RNA, magnetic resonance imaging or CTscanner. Tumor Imaging Data neomark:BiologicalProcess Biological process associated to a gene analyzed by the PCR. Biological Process neomark:BiologicalProcessReference Reference to a biological process of the Gene Ontology. Biological Process Reference neomark:BiologicalRegulation Biological regulation process associated to a gene analyzed by the PCR. Biological Regulation Process neomark:CellKilling Cell killing process associated to a gene analyzed by the PCR. Cell Killing Process neomark:CellularComponent Cellular component associated to a gene analyzed by the PCR. Cellular Component neomark:Death Death process associated to a gene analyzed by the PCR. Death Process neomark:ExternalReference Reference to a class of other ontology. External Reference neomark:ExtracellularRegion Extracellular region associated to a gene analyzed by the PCR. ExtraCellular Region neomark:ExtracellularRegionPart Extracellular region part associated to a gene analyzed by the PCR. ExtraCellular Region Part neomark:Gene Gene evaluated by the PCR. Gene neomark:GeneOntologyReference Reference to a Gene Ontology class. Gene Ontology Reference neomark:ImmuneSystemProcess Immune system process associated to a gene analyzed by the PCR. Immune System Process neomark:MacromollecularComplex Macromollecular complex associated to a gene analyzed by the PCR. Macromollecular Complex 1 neomark:Reoccurrence The visit performed after the treatment to check the status of the patient and the maintenance of the patient remission status. Reoccurrence neomark:Signaling Signaling associated to a gene analyzed by the PCR. Signaling neomark:SignalingProcess Signaling process associated to a gene analyzed by the PCR. Signaling Process 3.1 Class descriptions added manually. Class restrictions added manually. Data ranges modified manually for a better performance. Integrated with other ontologies. 3.1