mdf-reader

PropDefinitions: # adverse_event props day_in_cycle: Desc: Numerically, the day in the treatment cycle upon which any given adverse event was first observed, where Day 1 is the first day of the treatment cycle within which the adverse event was observed. Some patients/subjects may undergo multiple treatment cycles, such that two or more adverse events may be observed on the same day in cycle, but actually be observed on different dates, because they occur in different treatment cycles. Src: Data Owner(s) Type: integer Req: Preferred date_of_onset: Desc: The date upon which any given adverse event was first observed. Src: Data Owner(s) Type: datetime Req: Preferred # per Jim's input, gaps in the data are inevitable, meaning that this can't be required existing_adverse_event: Desc: An indication as to whether any given adverse event occurred prior to the enrollment of a patient/subject into the clinical trial in question, and/or was ongoing at the time of trial enrollment. Src: Data Owner(s) Enum: - 'Yes' - 'No' Req: Preferred # this can't be required, because there will only be data values when adverse events occur prior to the trial or are ongoing date_of_resolution: Desc: The date upon which any given adverse event resolved. If an adverse event was ongong at the time of death, the date of death should be used as the value date_of_resolution. Src: Data Owner(s) Type: string Req: Preferred # per Jim's input, gaps in the data are inevitable, meaning that this can't be required ongoing_adverse_event: Desc: An indication as to whether any given adverse event was ongoing as of the end of a treatment cycle, the end of the clinical trial itself, or the patient/subject being taken off study. Src: Data Owner(s) Enum: - 'Yes' - 'No' Req: Preferred # this can't be required, because there will only be data values when adverse events are unresolved and therefore ongoing as of the end of the trial or the patient going off study adverse_event_term: Desc: The specific controlled vocabulary term for any given adverse event, as defined by the Veterinary Comparative Oncology Group's Common Terminology Criteria for Adverse Events (VCOG-CTCAE). Src: Data Owner(s) Type: string # changing this to string at least temporarily #- http://localhost/terms/domain/adverse_events Req: 'Yes' adverse_event_description: Desc: A narrative description of any given adverse event which provides extra details as to its associated clinical, physical and behavioral observations, and/or mitigations for the adverse event. Src: Data Owner(s) Type: string Req: Preferred adverse_event_grade: Desc: The grade of any given adverse event, reported as an enumerated value corresponding to one of the five distinct grades as defined by the Veterinary Comparative Oncology Group's Common Terminology Criteria for Adverse Events (VCOG-CTCAE). Src: Data Owner(s) Enum: - "1" # Mild - "2" # Moderate - "3" # Severe - "4" # Life-threatening - "5" # Death - Unknown # accommodates situations where an adverse event is described in detail but somehow not assigned any grade Req: 'Yes' adverse_event_grade_description: Desc: The grade of any given adverse event, reported in the form of a single descriptive term corresponding to one of the five enumerated grades as defined by the Veterinary Comparative Oncology Group's Common Terminology Criteria for Adverse Events (VCOG-CTCAE). Although numerical values for grade are standard terms for the reporting of adverse events, the narrative form of adverse event grades will be useful to users not already familiar with adverse event grading. Src: Data Owner(s) Enum: - Mild - Moderate - Severe - Life-threatening - Death - Unknown # accommodates situations where an adverse event is described in detail but somehow not assigned any grade Req: Preferred adverse_event_agent_name: Desc: The name of any investigational new drug being administered at the time of any given adverse event being observed. Src: Data Owner(s) Type: string # changing this to string at least temporarily #- http://localhost/terms/domain/agent_name Req: 'No' adverse_event_agent_dose: Desc: The corresponding dose of any investigational new drug being administered at the time of any given adverse event being observed. Src: Data Owner(s) Type: string # changing this to string in order to accomodate the wide range of dosing units that we will be encountering #units: #- mg/kg # there's no way we can specify all of the possible dosage rates - they vary wildly #value_type: number Req: 'No' attribution_to_research: Desc: A qualitative indication as to whether any given adverse event is likely, possibly, probably or definitely caused by the clinical trial/research environment in general, or is unrelated to it. Src: Data Owner(s) Enum: - Unrelated # the adverse event is clearly not related to the research/clinical enviroment - Unlikely # the adverse event is doubtfully related to the research/clinical enviroment - Possible # the adverse event may be related to the research/clinical enviroment - Probable # the adverse event is likely related to the research/clinical enviroment - Definite # the adverse event is clearly related to the research/clinical enviroment - Undefined # the adverse event cannot be assigned any of the five definitive attribution probabilities with sufficient confidence Req: 'Yes' attribution_to_ind: Desc: A qualitative indication as to whether any given adverse event is likely, possibly, probably or definitely caused by any investigational new drugs being administered as part of the clinical trial, or is unrelated to it. Src: Data Owner(s) Enum: - Unrelated - Unlikely - Possible - Probable - Definite - Not Applicable # needed to accommodate clinical trials which don't assess the effects of an investigational new drug Req: 'Yes' attribution_to_disease: Desc: A qualitative indication as to whether any given adverse event is likely, possibly, probably or definitely caused by the disease for which the patient/subject is being treated, or is unrelated to it. Src: Data Owner(s) Enum: - Unrelated - Unlikely - Possible - Probable - Definite - Undefined # the adverse event cannot be assigned any of the five definitive attribution probabilities with sufficient confidence Req: 'Yes' attribution_to_commercial: Desc: A qualitative indication as to whether any given adverse event is likely, possibly, probably or definitely caused by a commercially-available, FDA-approved therapeutic agent, used within the confines of the clinical trial either for its FDA-approved indication or in an off-label manner, but not as the investigational new drug or part of the investigational new therapy, versus the adverse event in question being unrelated to it. Src: Data Owner(s) Enum: - Unrelated - Unlikely - Possible - Probable - Definite - Not Applicable # needed to accommodate clinical trials which don't directly assess the effects of any commercially available therapeutic agent or use such agents as part of the therapy Req: 'Yes' attribution_to_other: Desc: A qualitative indication as to whether any given adverse event is likely, possibly, probably or definitely caused by some other factor(s), as described by the other_attribution_description property, or is unrelated to such other factors. Src: Data Owner(s) Enum: - Unrelated - Unlikely - Possible - Probable - Definite - Undefined # the adverse event cannot be assigned any of the five definitive attribution probabilities with sufficient confidence Req: 'Yes' other_attribution_description: Desc: A description of any other factor or factors to which any given adverse event has been attributed. Where an adverse event is attributed to factors other than the standard factors of research, disease, IND or commercial, a description of the other factor(s) to which the adverse event was attributed is required. Src: Data Owner(s) Type: string Req: 'No' # although not strictly required, if attribution_to_other is anything other than unlikely, the other attribution must be stated dose_limiting_toxicity: Desc: An indication as to whether any given adverse event observed during the clinical trial is indicative of the dose of the therapeutic agent under test being limiting in terms of its toxicity. Src: Data Owner(s) Enum: - 'Yes' - 'No' - Not Applicable # accommodates situations where an adverse event is not attributed to any therapeutic agent and cannot therefore be limiting in terms of dosage Req: 'Yes' unexpected_adverse_event: Desc: An indication as to whether any given adverse event observed during the clinical trial is completely unanticipated and therefore considered novel. Src: Data Owner(s) Enum: - 'Yes' - 'No' - Undefined # accommodates situations where there is any ambiguity in terms of an adverse event being expected or not Req: 'Yes' # agent props document_number: Desc: S/N of the executed CRF Src: ALL Type: pattern: "^R[0-9]+$\n" medication: Src: STUDY_MED_ADMIN/SDAD/1 Type: - http://localhost/terms/domain/medication # agent_administration props comment: Desc: generic comment Type: string date_of_missed_dose: Src: STUDY_MED_ADMIN/SDAD/1 Type: datetime # document_number also included in agent_administration dose_level: Src: STUDY_MED_ADMIN/SDAD/1 Type: units: - mg/kg value_type: number dose_units_of_measure: Deprecated: true Src: STUDY_MED_ADMIN/SDAD/1 Type: string # medication also included in agent_administration medication_actual_dose: Src: STUDY_MED_ADMIN/SDAD/1 Type: units: - mg/kg value_type: number medication_actual_units_of_measure: Deprecated: true Src: STUDY_MED_ADMIN/SDAD/1 Type: string medication_course_number: Src: STUDY_MED_ADMIN/SDAD/1 Type: string medication_duration: Src: STUDY_MED_ADMIN/SDAD/1 Type: units: - days - hr - min value_type: number medication_lot_number: Src: STUDY_MED_ADMIN/SDAD/1 Type: string medication_missed_dose: Desc: Q.- form has "medication" Src: STUDY_MED_ADMIN/SDAD/1 Type: - http://localhost/terms/domain/agent_name medication_units_of_measure: Deprecated: true Src: STUDY_MED_ADMIN/SDAD/1 Type: string medication_vial_id: Src: STUDY_MED_ADMIN/SDAD/1 Type: string missed_dose_amount: Src: STUDY_MED_ADMIN/SDAD/1 Type: units: - mg/kg value_type: number missed_dose_units_of_measure: Deprecated: true Desc: Q.- form has "dose uom_ful" Src: STUDY_MED_ADMIN/SDAD/1 Type: string phase_not_present_in_propdefs: Desc: Where should this live?/What is? Src: COURSE INIT/CINIT/1 Type: TBD route_of_administration: Src: STUDY_MED_ADMIN/SDAD/1 Type: - http://localhost/terms/domain/route_of_administration start_time: Src: STUDY_MED_ADMIN/SDAD/1 Type: datetime stop_time: Src: STUDY_MED_ADMIN/SDAD/1 Type: datetime # biospecimen_source props biospecimen_repository_acronym: Desc: The name of the biobank or tissue repository from which or to which samples for any given patient/subject/donor were acquired or submitted, expressed in the form of an acronym. Src: Internally-curated Type: string Req: 'Yes' Tags: Labeled: Biobank biospecimen_repository_full_name: Desc: The name of the biobank or tissue repository from which or to which samples for any given patient/subject/donor were acquired or submitted, expressed in full text form. Src: Internally-curated Type: string Req: 'Yes' # canine individual props canine_individual_id: Desc: A unique numerical ID, which, based upon the existence of registration-based matches between two or more study-specific cases, is auto-generated by the data loader, and which thereby tethers matching cases to the single underlying multi-study participant. Src: Loader-generated Auto: true Type: string Req: 'Yes' Key: true Tags: Labeled: Canine ID # case props case_id: Desc: The globally unique ID by which any given patient/subject/donor can be unambiguously identified and displayed across studies/trials; specifically the value of patient_id as supplied by the data submitter, prefixed with the appropriate ICDC study code during data alignment and/or transformation. <br>This property is used as the key via which child records, e.g. sample records, can be associated with the appropriate case during data loading, and to identify the correct records during data updates. Src: Internally-generated Type: string Req: 'Yes' Key: true Tags: Labeled: Case ID patient_first_name: Desc: Where available, the given name of the patient/subject/donor. Src: Data Owner(s) Type: string Req: Preferred Tags: Labeled: Case Name patient_id: Desc: The preferred ID by which the data submitter uniquely identifies any given patient/subject/donor, at least within a single study/trial, recorded exactly as provided by the data submitter. Once prefixed with the appropriate ICDC study code during data alignment and/or transformation, values of Patient ID become values of Case ID. Src: Data Owner(s) Type: string Req: 'Yes' # cohort props cohort_description: Desc: Where applicable, the nature of each cohort into which the study/trial has been divided, e.g. in studies examining the effects of multiple doses of a therapeutic agent, the name and dose of the therapeutic agent used in any given cohort. Src: Internally-curated Type: string Req: 'Yes' Tags: Labeled: Cohort, Assigned to Cohort cohort_dose: Desc: The intended or protocol dose of the therapeutic agent used in any given cohort. Src: Internally-curated Type: string # setting this as string so as to accommodate a lack of consistency in the way in which dosing is quoted within the COTC007B study, which will otherwise confound data loading for MVP Req: 'No' Tags: Labeled: Cohorts cohort_id: Desc: A unique identifier via which cohorts can be differentiated from one another across studies/trials. <br>This property is used as the key via which cases can be associated with the appropriate cohort during data loading, and to identify the correct records during data updates. Src: Internally-curated Type: string Req: 'Yes' Key: true # cycle props cycle_number: Desc: For a patient/subject/donor enrolled in a clinical trial evaluating the effects of therapy administered in multiple cycles, the number of the treatment cycle during which visits occurred such that therapy could be administered and/or clinical observations could be made, with cycles numbered according to their chronological order. Src: Data Owner(s) Type: integer Req: 'Yes' date_of_cycle_end: Desc: The date upon which the treatent cycle in question ended. Src: Data Owner(s) Type: datetime date_of_cycle_start: Desc: The date upon which the treament cycle in question began. Src: Data Owner(s) Type: datetime # demographic props additional_breed_detail: Desc: For patients/subjects/donors formally designated as either Mixed Breed or Other, any available detail as to the breeds contributing to the overall mix of breeds or clarification of the nature of the Other breed. Values for this field are therefore not relevant to pure-bred patients/subjects/donors, but for those of mixed breed or other origins, values are definitely preferred wherever available. Src: Data Owner(s) Type: string Req: Preferred breed: Desc: The specific breed of the canine patient/subject/donor, per the list of breeds officially recognized by the American Kennel Club. Src: Data Owner(s) Enum: # temporarily, to facilitate data loading with validation on, until STS is in place at https://sts.ctos-data-team.org/v1/model/ICDC/node/demographic/property/breed/terms - Affenpinscher - Afghan Hound - Airedale Terrier - Akita - Alaskan Klee Kai - Alaskan Malamute - American Bulldog - American English Coonhound - American Eskimo Dog - American Foxhound - American Hairless Terrier - American Leopard Hound - American Staffordshire Terrier - American Water Spaniel - Anatolian Shepherd Dog - Appenzeller Sennenhunde - Australian Cattle Dog - Australian Kelpie - Australian Shepherd - Australian Stumpy Tail Cattle Dog - Australian Terrier - Azawakh - Barbado da Terceira - Barbet - Basenji - Basset Fauve de Bretagne - Basset Hound - Bavarian Mountain Scent Hound - Beagle - Bearded Collie - Beauceron - Bedlington Terrier - Belgian Laekenois - Belgian Malinois - Belgian Sheepdog - Belgian Tervuren - Bergamasco Sheepdog - Berger Picard - Bernese Mountain Dog - Bichon Frise - Biewer Terrier - Black Russian Terrier - Black and Tan Coonhound - Bloodhound - Bluetick Coonhound - Boerboel - Bohemian Shepherd - Bolognese - Border Collie - Border Terrier - Borzoi - Boston Terrier - Bouvier des Flandres - Boxer - Boykin Spaniel - Bracco Italiano - Braque Francais Pyrenean - Braque du Bourbonnais - Briard - Brittany - Broholmer - Brussels Griffon - Bull Terrier - Bulldog - Bullmastiff - Cairn Terrier - Canaan Dog - Cane Corso - Cardigan Welsh Corgi - Carolina Dog - Catahoula Hound - Catahoula Leopard Dog - Caucasian Shepherd Dog - Cavalier King Charles Spaniel - Central Asian Shepherd Dog - Cesky Terrier - Chesapeake Bay Retriever - Chihuahua - Chinese Crested - Chinese Shar-Pei - Chinook - Chow Chow - Cirneco dell'Etna - Clumber Spaniel - Cocker Spaniel - Collie - Coton de Tulear - Croatian Sheepdog - Curly-Coated Retriever - Czechoslovakian Vlcak - Dachshund - Dalmatian - Dandie Dinmont Terrier - Danish-Swedish Farmdog - Deutscher Wachtelhund - Doberman Pinscher - Dogo Argentino - Dogue de Bordeaux - Drentsche Patrijshond - Drever - Dutch Shepherd - English Cocker Spaniel - English Foxhound - English Setter - English Springer Spaniel - English Toy Spaniel - Entlebucher Mountain Dog - Estrela Mountain Dog - Eurasier - Field Spaniel - Finnish Lapphund - Finnish Spitz - Flat-Coated Retriever - French Bulldog - French Spaniel - German Longhaired Pointer - German Pinscher - German Shepherd Dog - German Shorthaired Pointer - German Spitz - German Wirehaired Pointer - Giant Schnauzer - Glen of Imaal Terrier - Golden Retriever - Gordon Setter - Grand Basset Griffon Vendeen - Great Dane - Great Pyrenees - Greater Swiss Mountain Dog - Greyhound - Hamiltonstovare - Hanoverian Scenthound - Harrier - Havanese - Hokkaido - Hovawart - Ibizan Hound - Icelandic Sheepdog - Irish Red and White Setter - Irish Setter - Irish Terrier - Irish Water Spaniel - Irish Wolfhound - Italian Greyhound - Jagdterrier - Japanese Akitainu - Japanese Chin - Japanese Spitz - Japanese Terrier - Jindo - Kai Ken - Karelian Bear Dog - Keeshond - Kerry Blue Terrier - Kishu Ken - Komondor - Kromfohrlander - Kuvasz - Labrador Retriever - Lagotto Romagnolo - Lakeland Terrier - Lancashire Heeler - Lapponian Herder - Leonberger - Lhasa Apso - Lowchen - Maltese - Manchester Terrier - Mastiff - Miniature American Shepherd - Miniature Bull Terrier - Miniature Dachshund - Miniature Pinscher - Miniature Schnauzer - Mixed Breed - Mountain Cur - Mudi - Neapolitan Mastiff - Nederlandse Kooikerhondje - Newfoundland - Norfolk Terrier - Norrbottenspets - Norwegian Buhund - Norwegian Elkhound - Norwegian Lundehund - Norwich Terrier - Nova Scotia Duck Tolling Retriever - Old English Sheepdog - Other - Otterhound - Papillon - Parson Russell Terrier - Pekingese - Pembroke Welsh Corgi - Perro de Presa Canario - Peruvian Inca Orchid - Petit Basset Griffon Vendeen - Pharaoh Hound - Plott Hound - Pointer - Polish Lowland Sheepdog - Pomeranian - Poodle - Porcelaine - Portuguese Podengo - Portuguese Podengo Pequeno - Portuguese Pointer - Portuguese Sheepdog - Portuguese Water Dog - Pudelpointer - Pug - Puli - Pumi - Pyrenean Mastiff - Pyrenean Shepherd - Rafeiro do Alentejo - Rat Terrier - Redbone Coonhound - Rhodesian Ridgeback - Romanian Mioritic Shepherd Dog - Rottweiler - Russell Terrier - Russian Toy - Russian Tsvetnaya Bolonka - Saint Bernard - Saluki - Samoyed - Schapendoes - Schipperke - Scottish Deerhound - Scottish Terrier - Sealyham Terrier - Segugio Italiano - Shetland Sheepdog - Shiba Inu - Shih Tzu - Shikoku - Siberian Husky - Silky Terrier - Skye Terrier - Sloughi - Slovakian Wirehaired Pointer - Slovensky Cuvac - Slovensky Kopov - Small Munsterlander Pointer - Smooth Fox Terrier - Soft Coated Wheaten Terrier - Spanish Mastiff - Spanish Water Dog - Spinone Italiano - Stabyhoun - Staffordshire Bull Terrier - Standard Schnauzer - Sussex Spaniel - Swedish Lapphund - Swedish Vallhund - Taiwan Dog - Teddy Roosevelt Terrier - Thai Ridgeback - Tibetan Mastiff - Tibetan Spaniel - Tibetan Terrier - Tornjak - Tosa - Toy Fox Terrier - Toy Poodle - Transylvanian Hound - Treeing Tennessee Brindle Coonhound - Treeing Walker Coonhound - Unknown - Vizsla - Weimaraner - Welsh Springer Spaniel - Welsh Terrier - West Highland White Terrier - Wetterhoun - Whippet - Wire Fox Terrier - Wirehaired Pointing Griffon - Wirehaired Vizsla - Working Kelpie - Xoloitzcuintli - Yakutian Laika - Yorkshire Terrier Req: 'Yes' Tags: Labeled: Breed date_of_birth: Desc: The date of birth of the canine patient/subject/donor. Src: Data Owner(s) Type: datetime Req: 'No' demographic_id: Desc: A unique identifier of each demographic record, used to identify the correct demographic records during data updates. The value of this property will generally be the same as the value of the case_id property. Src: Data Owner(s) Type: string Req: 'Yes' Key: true neutered_indicator: Desc: Indicator as to whether the patient/subject/donor has been either spayed (female subjects) or neutered (male subjects). Src: Data Owner(s) Enum: - 'Yes' - 'No' - Unknown Req: 'Yes' Tags: Labeled: Neutered Status patient_age_at_enrollment: Desc: The age of the canine patient/subject/donor as of study/trial enrollment, expressed in standard human years, as opposed to dog years. Src: Data Owner(s) Type: units: - years value_type: number Req: Preferred Tags: Labeled: Age, Age at Enrollment sex: Desc: The biological sex of the patient/subject/donor. Src: Data Owner(s) Enum: - Male - Female - Unknown Req: 'Yes' Tags: Labeled: Sex weight: Desc: The weight of the patient/subject/donor at the time of study/trial enrollment and/or biospecimens being acquired, at least in the case of studies that are not longitudinal in nature. Src: Data Owner(s) Type: units: - kg value_type: number Req: Preferred Tags: Labeled: Weight (kg) # diagnosis props best_response: Desc: Where applicable, an indication as to the best overall response to therapeutic intervention observed within an individual patient/subject/donor. Src: Data Owner(s) Enum: - Complete Response - Partial Response - Stable Disease - Progressive Disease - Not Determined # included to accommodate situations either where the study in question does not assess the effects of any therapeutic intervention, or where the response to therapeutic intervention could not be determined - Not Applicable # included to accommodate situations in which healthy control subjects are included within a study that does assess the effects of a therapeutic intervention - Unknown # included to accommodate situations where a value for stage of disease simply isn't available Req: 'Yes' Tags: Labeled: Response to Treatment concurrent_disease: Desc: An indication as to whether the patient/subject/donor suffers from any significant secondary disease condition(s). Src: Data Owner(s) Enum: - 'Yes' - 'No' - Unknown Req: Preferred Tags: Labeled: Concurrent Disease(s) concurrent_disease_type: Desc: The specifics of any notable secondary disease condition(s) observed within the patient/subject/donor. Src: Data Owner(s) Type: string Req: Preferred Tags: Labeled: Concurrent Disease Specifics date_of_diagnosis: Desc: The date upon which the patient/subject/donor was diagnosed with the primary disease in question. Src: Data Owner(s) Type: datetime Req: 'No' Tags: Labeled: Date of Diagnosis date_of_histology_confirmation: Desc: The date upon which the results of a histological evaluation of a sample from the patient/subject/donor were confirmed. Src: Data Owner(s) Type: datetime Req: 'No' diagnosis_id: Desc: A unique identifier of each diagnosis record, used to associate child records, e.g. pathology reports, with the appropriate parent, and to identify the correct diagnosis records during data updates. The value of this property will generally be the same as the value of the case_id property. Src: Data Owner(s) Type: string Req: 'Yes' Key: true disease_term: Desc: The primary disease condition with which the patient/subject/donor was diagnosed. Src: Data Owner(s) Enum: #- http://localhost/terms/domain/disease_term - B Cell Lymphoma - Bladder Cancer - Fibrolipoma - Glioma - Healthy Control - Hemangiosarcoma - Histiocytic Sarcoma - Lipoma - Lymphoma - Mammary Cancer - Mast Cell Tumor - Melanoma - Osteosarcoma - Pulmonary Neoplasms - Soft Tissue Sarcoma - Splenic Hematoma - Splenic Hyperplasia - T Cell Leukemia - T Cell Lymphoma - Thyroid Cancer - Unknown - Urothelial Carcinoma # these represent the de facto acceptable values, i.e. the values that our data submitters have used thus far Req: 'Yes' Tags: Labeled: Diagnosis, Disease follow_up_data: Desc: An indication as to the existence of any follow-up data for the patient/subject/donor, typically in the form of a study-level supplemental data file. Src: Data Owner(s) Enum: - 'Yes' - 'No' - Not Applicable # to accommodate situations where the subject is a healthy control Req: Preferred Tags: Labeled: Follow Up Data Available histological_grade: Desc: The histological grading of the tumor(s) present in the patient/subject/donor, based upon microscopic evaluation(s), and recorded at the subject level; grading of specific tumor samples subject to downstream analysis is recorded at the sample level. Src: Data Owner(s) Type: string # temporarily, to facilitate data loading with validation on, until STS is in place #- http://localhost/terms/domain/histological_grade Req: 'No' Tags: Labeled: Histological Grade histology_cytopathology: Desc: A narrative summary of the primary observations from the the evaluation of a tumor sample from a patient/subject/donor, in terms of its histology and/or cytopathology. Src: Data Owner(s) Type: string Req: 'No' Tags: Labeled: Histology/Cytology, Histology/Cytopathology pathology_report: Desc: An indication as to the existence of any detailed pathology evaluation upon which the primary diagnosis was based, either in the form of a formal, subject-specific pathology report, or as detailed in a study-level supplemental data file. Src: Data Owner(s) Enum: - 'Yes' - 'No' - Not Applicable # to accommodate situations where the subject is a healthy control Req: Preferred Tags: Labeled: Detailed Pathology Evaluation Available primary_disease_site: Desc: The anatomical location at which the primary disease originated, recorded in relatively general terms at the subject level; the anatomical locations from which tumor samples subject to downstream analysis were acquired is recorded in more detailed terms at the sample level. Src: Data Owner(s) Enum: #- http://localhost/terms/domain/primary_disease_site - Bladder - Bladder, Prostate - Bladder, Urethra - Bladder, Urethra, Prostate - Bladder, Urethra, Vagina - Bone - Bone (Appendicular) - Bone (Axial) - Bone Marrow - Brain - Carpus - Chest Wall - Distal Urethra - Kidney - Lung - Lymph Node - Mammary Gland - Mouth - Not Applicable - Pleural Cavity - Shoulder - Skin - Spleen - Subcutis - Thyroid Gland - Unknown - Urethra, Prostate - Urinary Tract - Urogenital Tract # these represent the de facto acceptable values, i.e. the values that our data submitters have used thus far Req: 'Yes' Tags: Labeled: Primary Disease Site, Disease Site, Primary Site stage_of_disease: Desc: The formal assessment of the extent to which the primary cancer with which the patient/subject/donor was diagnosed has progressed, according to the TNM staging or cancer stage grouping criteria. Src: Data Owner(s) Enum: - I - Ia - Ib - II - IIa - IIb - III - IIIa - IIIb - IV - IVa - IVb - V - Va - Vb - TisN0M0 - TisN1M1 #added per ORGANOIDS01 - T1N0M0 - T1NXM0 - T2N0M0 - T2N0M1 - T2N1M0 - T2N1M1 #added per ORGANOIDS01 - T2N2M1 - T3N0M0 - T3N0M1 - T3N1M0 - T3N1M1 - T3NXM1 - TXN0M0 - Not Applicable # to accommodate situations where the subject is a healthy control - Not Determined # to accommodate situations where stage of disease was deliberately not assessed - Unknown # to accommodate situations where a value for stage of disease simply isn't available Req: 'Yes' Tags: Labeled: Stage of Disease treatment_data: Desc: An indication as to the existence of any treatment data for the patient/subject/donor, typically in the form of a study-level supplemental data file. Src: Data Owner(s) Enum: - 'Yes' - 'No' - Not Applicable # to accommodate situations where the subject is a healthy control Req: Preferred Tags: Labeled: Treatment Data Available # disease_extent props date_of_evaluation: Desc: The date upon which the extent of disease evaluation was conducted. Src: Data Owner(s) Type: datetime Req: 'No' evaluation_code: Desc: An indication as to the status of any given lesion being evaluated, in terms of the evaluation establishing a baseline for the lesion, versus the lesion subject to evaluation being new, being stable in size, decreasing in size, increasing in size or having resolved. Src: Data Owner(s) Type: string Req: 'No' evaluation_number: Desc: The number of the evaluation durinhg which any given lesion was examined, with evaluations numbered according to their chronological order. Src: Data Owner(s) Type: Integer Req: 'No' lesion_description: Desc: Additional detail as to the specific location of the lesion subject to evaluation. For example, in the case of a lymph node lesion, the specific lymph node in which the lesion is located. Src: Data Owner(s) Type: string Req: 'No' lesion_number: Desc: An arbitrary numerical designation for each lesion subject to evaluation, by which that lesion can be unambiguously identified. Src: Data Owner(s) Type: Integer Req: 'No' lesion_site: Desc: The overall anatomical location of the lesion being assessed in terms of the organ or organ system in which it is located. For example, lung, lymph node, etc. Src: Data Owner(s) Type: string Req: 'No' longest_measurement: Desc: The longest dimension of the lesion subject to evaluation, as measured in (units TBD) Src: Data Owner(s) Type: units: - TBD value_type: number Req: 'No' measurable_lesion: Desc: Pending #An indication as to whether any given lesion is large enough for its size to be determined with any accuracy. Src: Data Owner(s) Type: TBD Req: 'No' measured_how: Desc: The method by which the size of any given lesion was determined. Src: Data Owner(s) Type: string Req: 'No' previously_irradiated: Desc: Pending Src: Data Owner(s) Type: TBD Req: 'No' previously_treated: Desc: Pending Src: Data Owner(s) Type: TBD Req: 'No' target_lesion: Desc: Pending Src: Data Owner(s) Type: TBD Req: 'No' # enrollment props # cohort_description: also included in enrollment node, defined elsewhere in this document # Desc: essentially, the name of the agent under test and the dose at which it is being used # Src: ENROLLMENT/ENROLL/1 # Type: string date_of_informed_consent: Desc: The date upon which the owner of the patient/subject/donor signed an informed consent on behalf of the subject. Src: Data Owner(s) Type: datetime Req: 'No' Tags: Labeled: Date of Informed Consent date_of_registration: Desc: The date upon which the patient/subject/donor was enrolled in the study/trial. Src: Data Owner(s) Type: datetime Req: 'No' Tags: Labeled: Date of Registration enrollment_id: Desc: A unique identifier of each enrollment record, used to associate child records, e.g. prior surgery records, with the appropriate parent, and to identify the correct enrollment records during data updates. The value of this property will generally be the same as the value of the case_id property. Src: Data Owner(s) Type: string Req: 'Yes' Key: true initials: Desc: The initials of the patient/subject/donor based upon the subject's first or given name, and the last or family name of the subject's owner. Src: Data Owner(s) Type: string Req: Preferred Tags: Labeled: Initials patient_subgroup: Desc: A short description as to the reason for the patient/subject/donor being enrolled in any given study/trial arm or cohort, for example, a clinical trial patient having been enrolled in a dose escalation cohort. Src: Data Owner(s) Type: string Req: 'No' Tags: Labeled: Patient Subgroup # registering_institution: also included in enrollment node, defined elsewhere # Src: ENROLLMENT/ENROLL/1 # Type: string # site_short_name: also included in enrollment node, defined elsewhere # Desc: widely accepted acronym for the university at which the patient was enrolled into the study/trial, and then treated under the appropriate veterinary medicine program # Src: ENROLLMENT/ENROLL/1 # Type: string # veterinary_medical_center: also included in enrollment node, defined elsewhere # Desc: full name of the university at which the patient was enrolled into the study/trial, and then treated under the appropriate veterinary medicine program, together with the site's city and state # Src: ENROLLMENT/ENROLL/1 # Type: string # removed residual evaluation props from here # file props file_name: Desc: The name of the file, maintained exactly as provided by the data submitter. Src: Data Owner(s) Type: string Req: 'Yes' Tags: Labeled: File Name file_type: Desc: An indication as to the nature of the file in terms of its content, i.e. what type of information the file contains, as opposed to the file's format. Src: Data Owner(s) Enum: - Study Protocol - Supplemental Data File - Pathology Report - Image File - RNA Sequence File - Whole Genome Sequence File - Whole Exome Sequence File - DNA Methylation Analysis File - Index File - Array CGH Analysis File # required for the MGT01 study - Variant Call File # for raw .vcf files - Mutation Annotation File # for annotated .maf files - Variant Report # for reports detailing validated variants - Data Analysis Whitepaper # for any document detailing a data analysis pipeline and/or methodology - Affymetrix GeneChip Analysis File Req: 'Yes' Tags: Labeled: File Type file_description: Desc: An optional description of the file and/or its content, as provided by the data submitter, preferably limited to no more than 60 characters in length. Src: Data Owner(s) Type: string Req: Preferred Tags: Labeled: Description file_format: Desc: The specific format of the file as determined by the data loader. Src: Loader-derived Type: string Req: 'Yes' Tags: Labeled: Format file_size: Desc: The exact size of the file in bytes. Src: Loader-derived Type: number Req: 'Yes' Tags: Labeled: Size md5sum: Desc: The 32-character hexadecimal md5 checksum value of the file, used to confirm the integrity of files submitted to the ICDC. Src: Loader-derived Type: string Req: 'Yes' Tags: Labeled: Md5sum file_status: Desc: An enumerated representation of the status of any given file. Src: Loader-derived Enum: - uploading - uploaded - md5summing - md5summed - validating - error - invalid - suppressed - redacted - live - validated - submitted - released # let's talk about this one /maj Req: 'Yes' uuid: Desc: The universally unique alpha-numeric identifier assigned to each file. Src: Loader-derived Type: string Req: 'Yes' Key: true Tags: Labeled: File UUID, File ID file_location: Desc: The specific location within the ICDC S3 storage bucket at which the file is stored, expressed in terms of a unique url. Src: Loader-derived Type: string Req: 'Yes' # follow_up props contact_type: Desc: need vocab Src: FOLLOW_UP/FLWU/1 Type: string date_of_last_contact: Src: FOLLOW_UP/FLWU/1 Type: datetime # document_number: also included in follow_up node, defined elsewhere in this document # Desc: S/N of the executed CRF # Src: ALL # Type: # pattern: "^R[0-9]+$\n" explain_unknown_status: Desc: free text? Src: FOLLOW_UP/FLWU/1 Type: string patient_status: Desc: need vocab Src: FOLLOW_UP/FLWU/1 Type: string physical_exam_changes: Desc: How described? Relative to data already stored in "physical_exam" node? Src: FOLLOW_UP/FLWU/1 Type: TBD physical_exam_performed: Desc: y/n Src: FOLLOW_UP/FLWU/1 Type: boolean treatment_since_last_contact: Desc: y/n Src: FOLLOW_UP/FLWU/1 Type: boolean # image collection props image_collection_name: Desc: The name of the image collection exactly as it appears at the location where the collection can be viewed and/or accessed. Src: Internally-curated Type: string Req: 'Yes' Tags: Labeled: Collection image_type_included: Desc: A list of the image types included in the image collection, drawn from a list of acceptable values. Src: Internally-curated Type: value_type: list Enum: - CT - Histopathology - MRI - PET - X-ray - Optical - Ultrasound Req: 'Yes' Tags: Labeled: Image Types image_collection_url: Desc: The external url via which the image collection can be viewed and/or accessed. Src: Internally-curated Type: string Req: 'Yes' repository_name: Desc: The name of the image repository within which the image collection can be found, stated in the form of the appropriate acronym. Src: Internally-curated Type: string Req: 'Yes' collection_access: Desc: Indicator as to whether the image collection can be accessed via download versus being accessible only via the cloud. Src: Internally-curated Enum: - Download - Cloud Req: 'Yes' # off_study props and # off_treatment props best_resp_vet_tx_tp_best_response: Src: OFF_STUDY/OSSM/1 Type: TBD best_resp_vet_tx_tp_secondary_response: Src: OFF_STUDY/OSSM/1 Type: TBD date_last_medication_administration: Src: OFF_STUDY/OSSM/1 Type: datetime date_of_best_response: Src: OFF_STUDY/OSSM/1 Type: datetime date_of_disease_progression: Src: OFF_STUDY/OSSM/1 Type: datetime date_off_study: Src: OFF_STUDY/OSSM/1 Type: datetime date_off_treatment: Src: OFF_STUDY/OSSM/1 Type: datetime # document_number: also included in off_study node, defined elsewhere in this document # Desc: S/N of the executed CRF # Src: ALL # Type: # pattern: "^R[0-9]+$\n" reason_off_study: Src: OFF_STUDY/OSSM/1 Type: string reason_off_treatment: Src: OFF_STUDY/OSSM/1 Type: string # physical_exam props assessment_timepoint: Desc: Pending Src: Data Owner(s) Type: integer body_system: Desc: Major organ system or physiological characteristic assessed during the examination of the patient/subject/donor during a follow-up visit. Observations are reported independently on each organ system or physiological characteristic. Src: Data Owner(s) Enum: - Attitude - Eyes, Ears, Nose and Throat - Respiratory - Cardiovascular - Gastrointestinal - Musculoskeletal - Integumentary - Lymphatic - Endocrine - Genitourinary - Neurologic - Other date_of_examination: Desc: The date upon which the physical examination in question was conducted. Src: Data Owner(s) Type: datetime # day_in_cycle: also included in physical_exam node, defined elsewhere in this document pe_comment: Desc: Narrative comment describing any notable observations concerning any given major organ system or physiological status assessed. Src: Data Owner(s) Type: string pe_finding: Desc: Indication as to the normal versus abnormal function of the major organ system or physiological characteristic assessed. Src: Data Owner(s) Enum: - Normal - Abnormal - Not examined phase_pe: Desc: Pending Src: Data Owner(s) Type: TBD # principal_investigator props pi_first_name: Desc: The first or given name of each principal investigator of the study/trial. Src: Data Owner(s) Type: string Req: 'Yes' Tags: Labeled: Principal Investigators pi_last_name: Desc: The last or family name of each principal investigator of the study/trial. Src: Data Owner(s) Type: string Req: 'Yes' Tags: Labeled: Principal Investigators pi_middle_initial: Desc: Where applicable, the middle initial(s) of each principal investigator of the study/trial. Src: Data Owner(s) Type: string Req: 'No' Tags: Labeled: Principal Investigators # prior_surgery props anatomical_site_of_surgery: Desc: The anatomical location at which the prior surgery in question occurred. Src: Data Owner(s) Type: - https://localhost/term/domain/anatomical_site Req: 'Yes' date_of_surgery: Desc: The date upon which the prior surgery in question occurred. Src: Data Owner(s) Type: datetime Req: Preferred procedure: Desc: The type of procedure performed during the prior surgery in question. Src: Data Owner(s) Type: - https://localhost/term/domain/procedure Req: 'Yes' residual_disease: Desc: TBD Src: Data Owner(s) Type: TBD surgical_finding: Desc: A narrative description of any notable observations made during the prior surgery in question. Src: Data Owner(s) Type: string Req: Preferred therapeutic_indicator: Desc: TBD Src: Data Owner(s) Type: TBD Req: 'No' # prior_therapy props agent_name: Src: PRIOR_THRPY_SUPP/PTHR/1 Type: - http://localhost/terms/domain/agent_name agent_units_of_measure: Deprecated: true Desc: Agent UOM_FUL in form Src: PRIOR_THRPY_SUPP/PTHR/1 Type: string any_therapy: Src: PRIOR_TREAT_SUMM/PTX/1 Type: boolean best_response_to_prior_therapy: Src: PRIOR_THRPY_SUPP/PTHR/1 Type: string date_of_first_dose: Src: PRIOR_THRPY_SUPP/PTHR/1 Type: datetime date_of_last_dose: Src: PRIOR_THRPY_SUPP/PTHR/1 Type: datetime date_of_last_dose_any_therapy: Src: PRIOR_TREAT_SUMM/PTX/1 Type: datetime date_of_last_dose_nsaid: Src: PRIOR_TREAT_SUMM/PTX/1 Type: datetime date_of_last_dose_steroid: Src: PRIOR_TREAT_SUMM/PTX/1 Type: datetime dose_schedule: Desc: Schedule_FUL in form Src: PRIOR_THRPY_SUPP/PTHR/1 Type: TBD min_rsdl_dz_tx_ind_nsaids_treatment_pe: Src: PRIOR_TREAT_SUMM/PTX/1 Type: TBD nonresponse_therapy_type: Src: PRIOR_THRPY_SUPP/PTHR/1 Type: string number_of_prior_regimens_any_therapy: Src: PRIOR_TREAT_SUMM/PTX/1 Type: integer number_of_prior_regimens_nsaid: Src: PRIOR_TREAT_SUMM/PTX/1 Type: integer number_of_prior_regimens_steroid: Src: PRIOR_TREAT_SUMM/PTX/1 Type: integer prior_nsaid_exposure: Desc: Has the patient ever been on NSAIDS? in form Src: PRIOR_TREAT_SUMM/PTX/1 Type: boolean prior_steroid_exposure: Desc: Has the patient ever been on steroids? in form Src: PRIOR_TREAT_SUMM/PTX/1 Type: boolean prior_therapy_type: Src: PRIOR_THRPY_SUPP/PTHR/1 Type: string therapy_type: Src: PRIOR_TREAT_SUMM/PTX/1 Type: string total_dose: Src: PRIOR_THRPY_SUPP/PTHR/1 Type: units: - mg value_type: number total_number_of_doses_any_therapy: Src: PRIOR_TREAT_SUMM/PTX/1 Type: integer total_number_of_doses_nsaid: Src: PRIOR_TREAT_SUMM/PTX/1 Type: integer total_number_of_doses_steroid: Src: PRIOR_TREAT_SUMM/PTX/1 Type: integer treatment_performed_at_site: Src: PRIOR_TREAT_SUMM/PTX/1 Type: boolean treatment_performed_in_minimal_residual: Src: PRIOR_TREAT_SUMM/PTX/1 Type: boolean tx_loc_geo_loc_ind_nsaid: Src: PRIOR_TREAT_SUMM/PTX/1 Type: TBD # program props program_acronym: Desc: The name of the program under which related studies will be grouped, expressed in the form of the acronym by which it will identified within the UI. <br>This property is used as the key via which study records can be associated with the appropriate program during data loading, and to identify the correct records during data updates. Src: Internally-curated Type: string Req: 'Yes' Key: true Tags: Labeled: Program program_external_url: Desc: The external url to which users should be directed in order to learn more about the program. Src: Internally-curated Type: string Req: Preferred program_full_description: Desc: A more detailed, multiple sentence description of the program. Src: Internally-curated Type: string Req: 'Yes' program_name: Desc: The name of the program under which related studies will be grouped, in full text and unabbreviated form, exactly as it will be displayed within the UI. Src: Internally-curated Type: string Req: 'Yes' program_short_description: Desc: An abbreviated, single sentence description of the program. Src: Internally-curated Type: string