From 21d7319eea02d80f4ccf5bd49781e66720b8f9e0 Mon Sep 17 00:00:00 2001 From: Ming Ying Date: Wed, 11 Jan 2023 14:37:14 -0500 Subject: [PATCH] Added example dataset --- examples/icdc/data-model/icdc-model-props.yml | 1912 +++++++++++++++++ examples/icdc/data-model/icdc-model.yml | 734 +++++++ examples/icdc/dataset/CMCP-program.txt | 2 + examples/icdc/dataset/OSA01-case.txt | 61 + examples/icdc/dataset/OSA01-demographic.txt | 61 + examples/icdc/dataset/OSA01-diagnosis.txt | 61 + examples/icdc/dataset/OSA01-enrollment.txt | 61 + .../dataset/OSA01-principal_investigator.txt | 3 + examples/icdc/dataset/OSA01-publication.txt | 2 + examples/icdc/dataset/OSA01-registration.txt | 86 + examples/icdc/dataset/OSA01-sample.txt | 140 ++ ...Unrestricted with new description text.txt | 2 + examples/icdc/icdc-local.yml | 47 + 13 files changed, 3172 insertions(+) create mode 100644 examples/icdc/data-model/icdc-model-props.yml create mode 100644 examples/icdc/data-model/icdc-model.yml create mode 100644 examples/icdc/dataset/CMCP-program.txt create mode 100644 examples/icdc/dataset/OSA01-case.txt create mode 100644 examples/icdc/dataset/OSA01-demographic.txt create mode 100644 examples/icdc/dataset/OSA01-diagnosis.txt create mode 100644 examples/icdc/dataset/OSA01-enrollment.txt create mode 100644 examples/icdc/dataset/OSA01-principal_investigator.txt create mode 100644 examples/icdc/dataset/OSA01-publication.txt create mode 100644 examples/icdc/dataset/OSA01-registration.txt create mode 100644 examples/icdc/dataset/OSA01-sample.txt create mode 100644 examples/icdc/dataset/OSA01-study 000006 Unrestricted with new description text.txt create mode 100644 examples/icdc/icdc-local.yml diff --git a/examples/icdc/data-model/icdc-model-props.yml b/examples/icdc/data-model/icdc-model-props.yml new file mode 100644 index 00000000..02a4a4dd --- /dev/null +++ b/examples/icdc/data-model/icdc-model-props.yml @@ -0,0 +1,1912 @@ +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 and/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: + - 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 + 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 defined by as defined by the Veterinary Comparative Oncology Group's Common Terminology Criteria for Adverse Events (VCOG-CTCAE). This may not be needed, because enumerated grades are standard adverse_event reporting terms, although the narrative terms will be useful to users not already familiar with adverse event grading. + Src: Data Owner(s) + Enum: + - Mild + - Moderate + - Severe + - Life-threatening + - Death + 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: + - http://localhost/terms/domain/agent_name + Req: 'Yes' + 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: + units: + - mg/kg # there's no way we can specify all of the possible dosage rates - they vary wildly + value_type: number + Req: 'Yes' + 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 not 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 + 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 + Req: 'Yes' + attribution_to_commercial: + Desc: A qualitative indication as to whether any given adverse event is likely, possibly, probably or definitely caused by NEED INPUT ON THIS, 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 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 + 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' + 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' + 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: + 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.
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.
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 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 + - 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: 'No' + 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 + # 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' + 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' + 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 + # 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 + - T1N0M0 + - T1NXM0 + - T2N0M0 + - T2N0M1 + - T2N1M0 + - T2N1M1 + - 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' + 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.
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 + Req: 'Yes' + program_sort_order: + Desc: An arbitrarily-assigned value used to dictate the order in which programs are displayed within the application's UI. + Src: Internally-curated + Type: integer + Req: 'No' + # publication props + publication_title: + Desc: The full title of the publication stated exactly as it appears on the published work.
This property is used as the key via which to identify the correct records during data updates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true + authorship: + Desc: A list of authors for the cited work. More specifically, for publications with no more than three authors, authorship quoted in full; for publications with more than three authors, authorship abbreviated to first author et al. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Tags: + Labeled: Authorship + year_of_publication: + Desc: The year in which the cited work was published. + Src: Data Owner(s) + Type: number + Req: 'Yes' + Tags: + Labeled: Year of Publication + journal_citation: + Desc: The name of the journal in which the cited work was published, inclusive of the citation itself in terms of journal volume number, part number where applicable, and page numbers. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Tags: + Labeled: Journal + digital_object_id: + Desc: Where applicable, the digital object identifier for the cited work, by which it can be permanently identified, and linked to via the internet. + Src: Data Owner(s) + Type: string + Req: Preferred + Tags: + Labeled: DOI + pubmed_id: + Desc: Where applicable, the unique numerical identifier assigned to the cited work by PubMed, by which it can be linked to via the internet. + Src: Data Owner(s) + Type: number + Req: Preferred + Tags: + Labeled: PubMed ID + # registration props + registration_origin: + Desc: The entity with which each registration ID is directly associated, for example, an ICDC study, as denoted by the appropriate study code, or the biobank or tissue repository from which samples for a study/trial participant were acquired, as denoted by the appropriate acronym. + Src: Data Owner(s) + Type: string + Req: 'Yes' + registration_id: + Desc: Any ID used by a data submitter to identify a patient/subject/donor, either locally or globally. + Src: Data Owner(s) + Type: string + Req: 'Yes' + #is_primary_id: + #Desc: Indicator as to whether the ID in question was also independently captured as patient_id and therefore used to create case_id; for each study/trial participant subject, one, and only one, registration ID must be flagged as being a primary ID + #Type: + # - 'Yes' + # - 'No' + #Req: 'Yes' + # sample props + # comment: also included in sample node, defined elsewhere + # Desc: generic comment concerning the preparation and/or annotation of the sample + # Type: string + date_of_sample_collection: + Desc: The date upon which the sample was acquired from the patient/subject/donor. + Src: Data Owner(s) + Type: datetime + Req: 'No' + general_sample_pathology: + Desc: An indication as to whether a sample represents normal tissue versus representing diseased or tumor tissue. + Src: Data Owner(s) + Enum: + - Normal + - Malignant + - Benign + - Hyperplastic + - Diseased + - Not Applicable # included to accommodate the inevitable ambiguity in assigning a general sample pathology to certain sample types, e.g. blood + Req: 'Yes' + Tags: + Labeled: General Sample Pathology + length_of_tumor: + Desc: The length of the tumor from which a tumor sample was derived, as measured in mm. + Src: Data Owner(s) + Type: + units: + - mm + value_type: number + Req: 'No' + molecular_subtype: + Desc: Where applicable, the molecular subtype of the tumor sample in question, for example, the tumor being basal versus lumnial in nature. + Src: Data Owner(s) + Type: string + Req: 'No' + necropsy_sample: + Desc: An indication as to whether a sample was acquired as a result of a necropsy examination. + Src: Data Owner(s) + Enum: + - 'Yes' + - 'No' + - Unknown + - Not Applicable # included to accommodate cell line samples + Req: 'Yes' + Tags: + Labeled: Necropsy Sample + percentage_tumor: + Desc: The purity of a sample of tumor tissue in terms of the percentage of the sample that is represnted by tumor cells, expressed either as a discrete percentage or as a percentage range. + Src: Data Owner(s) + Type: string #changed to string in order to accommodate values being quoted in ranges, as greater or less than, or as Unknown + Req: Preferred + Tags: + Labeled: Percentage Tumor + sample_chronology: + Desc: An indication as to when a sample was acquired relative to any therapeutic intervention and/or key disease outcome observations. + Src: Data Owner(s) + Enum: + - Before Treatment + - During Treatment + - After Treatment + - Upon Progression + - Upon Relapse + - Upon Death + - Not Applicable # included to accommodate samples being acquired via a study which did not assess the effects of any therapeutic intervention + - Unknown # included to accommodate the inevitable ambiguity about the correct value for a required field + Req: 'Yes' + Tags: + Labeled: Sample Chronology + sample_id: + Desc: The globally unique ID by which any given sample can be unambiguously identified and displayed across studies/trials; specifically the preferred value of the sample identifier used by the data submitter, prefixed with the appropriate ICDC study code during data transformation.
This property is used as the key via which child records, e.g. file records, can be associated with the appropriate sample during data loading, and to identify the correct records during data updates. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Key: true + Tags: + Labeled: Sample ID + sample_preservation: + Desc: The method by which a sample was preserved. + Src: Data Owner(s) + Enum: + - EDTA + - FFPE + - Snap Frozen # list of acceptable values will gradually be expanded as data submission requirements solidify + - Not Applicable # included to accommodate cell line samples, which will generally be processed absent interim preservation and storage + - Unknown # included to accommodate the inevitable ambiguity about the correct value for a required field + Req: 'Yes' + Tags: + Labeled: Sample Preservation + sample_site: + Desc: The specific anatomical location from which any given sample was acquired. + Src: Data Owner(s) + Enum: #string # temporarily, to facilitate data loading with validation on, until STS is in place + #- http://localhost/terms/domain/anatomical_location + - Bladder + - Bladder Apex + - Bladder Apex-Mid + - Bladder Mid + - Bladder Mid-Trigone + - Bladder Mucosa + - Bladder Trigone + - Bladder Trigone-Urethra + - Blood + - Bone + - Bone Marrow + - Brain + - Carpus + - Cerebellar + - Cutis + - Distal Urethra + - Femur + - Hemispheric + - Humerus + - Kidney + - Liver + - Liver, Spleen, Heart + - Lung + - Lung, Caudal Aspect of Left Caudal Lobe + - Lung, Caudal Right Lobe + - Lung, Cranial Left Lobe + - Lymph Node + - Lymph Node, Popliteal + - Mammary Gland + - Mandible, Mucosa + - Midline + - Mouth + - Mouth, Lingual + - Mouth, Mandible, Mucosa + - Mouth, Maxilla, Mucosa + - Muscle + - Pleural Effusion + - Radius + - Skin + - Spleen + - Subcutaneous Tissue + - Thyroid Gland + - Tibia + - Unknown + - Urethra + - Urethra Mid-distal + # these represent the de facto acceptable values, i.e. the values that our data submitters have used thus far + Req: 'Yes' + Tags: + Labeled: Sample Site + physical_sample_type: + Desc: An indication as to the physical nature of any given sample. + Src: Data Owner(s) + Enum: + - Tissue + - Blood + - Cell Line # required for the CCL01 and OSA01 studies + - Whole Blood + # list of acceptable values will gradually be expanded as data submission requirements solidify + Req: 'Yes' + Tags: + Labeled: Physical Sample Type + specific_sample_pathology: + Desc: The specific histology and/or pathology associated with a sample. + Src: Data Owner(s) + Enum: + - Astrocytoma + - B Cell Lymphoma + - Carcinoma + - Carcinoma With Simple And Complex Components + - Chondroblastic Osteosarcoma + - Complex Carcinoma + - Fibroblastic Osteosarcoma + - Giant Cell Osteosarcoma + - Hemangiosarcoma + - Histiocytic Sarcoma + - Lymphoma + - Mast Cell Tumor + - Melanoma + - Not Applicable + - Oligodendroglioma + - Osteoblastic Osteosarcoma + - Osteoblastic and Chrondroblastic Osteosarcoma + - Osteosarcoma + - Osteosarcoma; Combined Type + - Primitive T-Cell Leukemia + - Pulmonary Adenocarcinoma + - Pulmonary Carcinoma + - Simple Carcinoma + - Simple Carcinoma,  Ductular, Vascular Invasive + - Simple Carcinoma, Ductal + - Simple Carcinoma, Ductular + - Simple Carcinoma, Inflammatory + - Simple Carcinoma, Invasive, Ductal + - Soft Tissue Sarcoma + - T Cell Lymphoma + - Undefined + - 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: Pathology/Morphology + summarized_sample_type: + Desc: A summarized representation of a sample's physical nature, normality, and derivation from a primary versus a metastatic tumor, based upon the combination of values in the three independent properties of physical_sample_type, general_sample_pathology and tumor_sample_origin. + Src: Data Owner(s) + Enum: #string # will be superseded by an enumerated list of acceptable values as data submission requirements solidify + - Metastatic Tumor Tissue + - Normal Cell Line + - Normal Tissue + - Primary Malignant Tumor Tissue + - Tumor Cell Line + - Tumor Cell Line (metastasis-derived) + - Whole Blood + # these represent the de facto acceptable values, i.e. the values to which we have thus far aligned submitted data + Req: 'Yes' + Tags: + Labeled: Sample Type + tumor_grade: + Desc: The grade of the tumor from which the sample was acquired, i.e. the degree of cellular differentiation within the tumor in question, as determined by a pathologist's evaluation. + Src: Data Owner(s) + Enum: + - "1" + - "2" + - "3" + - "4" + - High + - Medium + - Low + - Unknown + - Not Applicable + Req: Preferred + Tags: + Labeled: Tumor Grade + tumor_sample_origin: + Desc: An indication as to whether a tumor sample was derived from a primary versus a metastatic tumor. + Src: Data Owner(s) + Enum: + - Primary + - Metastatic + - Not Applicable # included to accommodate samples not derived from tumors + - Unknown # included to accommodate the almost inevitable case where the origin of a tumor sample is uncertain + Req: 'Yes' + Tags: + Labeled: Tumor Sample Origin + volume_of_tumor: + Desc: The volume of the tumor from which a tumor sample was derived, as measured in cubic centimeters. + Src: Data Owner(s) + Type: + units: + - cm3 + value_type: number + Req: 'No' + width_of_tumor: + Desc: The width of the tumor from which a tumor sample was derived, as measured in mm. + Src: Data Owner(s) + Type: + units: + - mm + value_type: number + Req: 'No' + # study props + clinical_study_description: + Desc: A multiple sentence summary of what the study/trial was intended to determine and how it was conducted. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Tags: + Labeled: Description + clinical_study_designation: + Desc: A unique, human-friendly, alpha-numeric identifier by which the study/trial will be identified within the UI.
This property is used as the key via which child records, e.g. case records, can be associated with the appropriate study during data loading, and to identify the correct records during data updates. + Src: Internally-generated + Type: string + Req: 'Yes' + Key: true + Tags: + Labeled: Study Code, Assigned to Study + clinical_study_id: + Desc: Where applicable, the ID for the study/trial as generated by the source database. + Src: Data Owner(s) + Type: string + Req: 'No' + clinical_study_name: + Desc: A succinct, narrative title for the study/trial, exactly as it should be displayed within the application's UI. + Src: Data Owner(s) + Type: string + Req: 'Yes' + Tags: + Labeled: Study Name + clinical_study_type: + Desc: An arbitrary designation of the study/trial to indicate its underlying. + nature, e.g. Clinical Trial, Transcriptomics, Genomics. + Src: Internally-curated + Type: string + Req: 'Yes' + Tags: + Labeled: Study Type + date_of_iacuc_approval: + Desc: Where applicable, the date upon which the study/trial was approved by the IACUC. + Src: Data Owner(s) + Type: datetime + Req: 'No' + Tags: + Labeled: Date of IACUC Approval + dates_of_conduct: + Desc: An indication of the general time period during which the study/trial was active, e.g. (from) month and year (to) month and year. + Src: Data Owner(s) + Type: string + Req: Preferred + Tags: + Labeled: Conducted + accession_id: + Desc: A unique, alpha-numeric identifier, in the format of six digits, which is assigned to the study/trial as of it being on-boarded, and which can be resolved by identifiers.org when prefixed with "icdc:" to create a compact identifier in the format icdc:xxxxxx. + Src: Internally-curated + Type: string + Req: 'Yes' + Tags: + Labeled: Accession ID + study_disposition: + Desc: An arbitrarily-assigned value used to dictate how the study/trial is displayed via the ICDC Production environment, based upon the degree to which the data has been on-boarded and/or whether the data is subject to any temporary embargo which prevents its public release. + Src: Internally-curated + Enum: + - Unrestricted + - Pending + - Under Embargo + Req: 'Yes' + # study_arm props + arm: + Desc: Where applicable, the nature of each arm into which the study/trial has been divided. For example, in multiple agent clinical trials, the name of the therapeutic agent used in any given study arm. + Src: Internally-curated + Type: string + Req: Preferred + Tags: + Labeled: Arm, Assigned to Arm + arm_description: + Desc: A short description of the study arm. + Src: Internally-curated + Type: string + Req: Preferred + ctep_treatment_assignment_code: + Desc: TBD + Src: Internally-curated + Type: + pattern: "^.+$\n" + Req: 'No' + arm_id: + Desc: A unique identifier via which study arms can be differentiated from one another across studies/trials.
This property is used as the key via which child records, e.g. cohort records, can be associated with the appropriate study arm during data loading, and to identify the correct records during data updates. + Src: Internally-curated + Type: string + Req: 'Yes' + Key: true + # study_site props + registering_institution: + Desc: Pending + Src: Data Owner(s) + Type: string + Req: 'No' + site_short_name: + Desc: The widely-accepted acronym for the institution at which the patient/subject/donor was enrolled into the study/trial, and then treated under the appropriate veterinary medicine program. + Src: Data Owner(s) + Type: string + Req: 'No' + Tags: + Labeled: Study Site + veterinary_medical_center: + Desc: The full name of the insitution at which the patient/subject/donor was enrolled into the study/trial, and then treated under the appropriate veterinary medicine program, together with the site's city and state. + Src: Data Owner(s) + Type: string + Req: 'No' + # visit props + visit_date: + Desc: The date upon which the visit occurred. + Src: Data-derived + Type: datetime + Req: 'No' + visit_id: + Desc: A globally unique identifier of each visit record; specifically the value of case_id concatenated with the value of visit_date, the date upon which the visit occurred.
This property is used as the key via which child records, e.g. physical examination records, can be associated with the appropriate visit, and to identify the correct visit records during data updates. + Src: Data-derived + Type: string + Req: 'Yes' + Key: true + visit_number: + Desc: The number of the visit during which therapy was administered and/or clinical observations were made, with visits numbered according to their chronological order. + Src: Data-deived + Type: Integer + # vital_signs props + # assessment_timepoint: also included in vital_signs node, defined elsewhere + # Src: PHYSICAL_EXAM/PE/1 + # Type: integer + body_surface_area: + Desc: The body surface area of the patient/subject/donor at the time of the vital signs evaluation, expressed in square meters. + Src: Data Owner(s) + Type: + units: + - sq meters + value_type: number + body_temperature: + Desc: The temperature of the patient/subject/donor at the time of the vital signs evaluation. + Src: Data Owner(s) + Type: + units: + - degrees F + - degrees C + value_type: number + date_of_vital_signs: + Desc: The date upon which the vital signs evaluation in question was conducted. + Src: Data Owner(s) + Type: datetime + ecg: + Desc: Indication as to the normality of the electrocardiogram conducted during the vital signs evaluation. + Src: Data Owner(s) + Type: TBD + modified_ecog: + Desc: The Eastern Cooperative Oncology Group (ECOG) performance status of the patient/subject/donor at the time of the vital signs evaluation. The value of this metric indicates the overall function of the patient/subject/donor and his/her ability to tolerate therapy. + Src: Data Owner(s) + Type: + - http://localhost/terms/domain/modified_ecog + patient_weight: + Desc: The weight of the patient/subject/donor at the time of the vital signs evaluation, measured in kilograms. + Src: Data Owner(s) + Type: + units: + - kg + value_type: number + # phase: + # Desc: Where should this live?/What is? + # Src: COURSE INIT/CINIT/1 + # Type: TBD + pulse: + Desc: The heart rate of the patient/subject/donor at the time of the vital signs evaluation, measured in beats per minute. + Src: Data Owner(s) + Type: + units: + - bpm + value_type: integer + pulse_ox: + Desc: The level of oxygen saturation in the blood of the patient/subject/donor at the time of the vital signs evaluation, expressed in terms of the percentage saturation. + Src: Data Owner(s) + Type: + units: + - '%' + value_type: number + respiration_pattern: + Desc: An indication as to the normality of the breathing pattern of the patient/subject/donor at the time of the vital signs evaluation. + Src: Data Owner(s) + Type: + - http://localhost/terms/domain/respiration_pattern + respiration_rate: + Desc: The rate of respiration of the patient/subject/donor at the time of the vital signs evaluation, measured in the number of breaths taken per minute. + Src: Data Owner(s) + Type: + units: + - breaths/min + value_type: integer + systolic_bp: + Desc: The systolic blood pressure of the patient/subject/donor at the time of the vital signs evaluation, measured in mm of mercury. + Src: Data Owner(s) + Type: + units: + - mm Hg + value_type: integer diff --git a/examples/icdc/data-model/icdc-model.yml b/examples/icdc/data-model/icdc-model.yml new file mode 100644 index 00000000..b9819b70 --- /dev/null +++ b/examples/icdc/data-model/icdc-model.yml @@ -0,0 +1,734 @@ +# ICDC model nodes and relns +# Title case names are "reserved" (meaningful to the parser) +# Lower case names are labels for the entities +# document number - really a property of properties (where did this question appear) + +Nodes: + program: + Desc: Within the Integrated Canine Data Commons, studies are grouped into discrete programs, based upon the origins and/or scientific nature of each study/trial. These programs may or may not directly relate to any official, e.g. NCI, funding program. The Program node contains the properties required to appropriately characterize any given ICDC program. + Tags: + Category: administrative + Assignment: core + Class: primary + Template: 'Yes' + Color: black + Props: + - program_name + - program_acronym + - program_short_description + - program_full_description + - program_external_url + - program_sort_order + study: + Desc: The Study node contains properties required to characterize each study/trial in terms of a title, how and why the study/trial was conducted, and the results that were generated. + Tags: + Category: study + Assignment: core + Class: primary + Template: 'Yes' + Color: black + Props: + - clinical_study_id + - clinical_study_designation + - clinical_study_name + - clinical_study_description + - clinical_study_type + - date_of_iacuc_approval + - dates_of_conduct + - accession_id + - study_disposition + study_site: + Desc: The Study Site node contains properties which identify the various sites at which any given study/trial was conducted, either in terms of where clinical trial patients were assessed and treated, or in terms of the geographical sites at which biospecimens were acquired from patients/subjects/donors for subsequent analysis. + Tags: + Category: study + Assignment: core + Class: secondary + Template: 'Yes' + Color: black + Props: + - site_short_name + - veterinary_medical_center + - registering_institution + study_arm: + Desc: The Study Arm node contains properties required to describe the arms into which any given study/trial was divided. Division of a study/trial into multiple arms is optional and is at the discretion of the data owners, based upon the way in which the study/trial in question was structured, and how best that structure can be represented within the ICDC. Where applicable, the appropriate study arms are defined during the study on-boarding process and then created via a specific data loading file. + Tags: + Category: study + Assignment: core + Class: secondary + Template: 'Yes' + Color: black + Props: + - arm + - ctep_treatment_assignment_code + # arm has no example in the data, putting cohort_description in here + # to help define study_arm + - arm_description + - arm_id # potentially needed to differentiate between arms having the same name, but which actually belong to different studies. Proactively including sooner rather than later. + agent: + Desc: The Agent node documents the name of each therapeutic agent being administered during a clinical trial. In this way, in clinical trials which assess the efficacy of combination therapies, adverse events observed during the trial can be attributed specifically to one or more of the medications being used. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'No' + Color: black + Props: + - medication + # d/n from STUDY_MED_ADMIN/SDAD/1 + - document_number + cohort: + Desc: The Cohort node contains properties required to describe the cohorts into which any given study/trial was divided. Division of a study/trial into multiple cohorts is optional and is at the discretion of the data owners, based upon the way in which the study/trial in question was structured, and how best that structure can be represented within the ICDC. Where applicable, the appropriate cohorts are defined during the study on-boarding process and then created via a specific data loading file. + Tags: + Category: study + Assignment: core + Class: secondary + Template: 'Yes' + Color: black + Props: + - cohort_description + # the intended or protocol dose + - cohort_dose + - cohort_id # needed to differentiate between cohorts that share values for cohort description, but which actually belong to different studies + case: + Desc: The Case node contains properties required to unambiguously identify each patient/subject/donor, either based upon the data submitter's original ID, or upon a study-specific Case ID derived from it during data transformation, which prefixes each original ID with a short, study-specific code. + Tags: + Category: case + Assignment: core + Class: primary + Template: 'Yes' + Color: black + Props: + - case_id + - patient_id + - patient_first_name + registration: + Desc: The Registration node functions to capture multiple IDs that may be associated with any single patient/subject/donor. Specifically, it captures multiple IDs in the form of Key:Value pairs, which represent each alternate ID and the specific source from which that alternate ID originates. These registrations can then be used to identify multi-study participants, i.e. canine individuals enrolled in two or more ICDC studies as study-specific cases, but which nonetheless represent the same underlying patient/subject/donor. + Tags: + Category: case + Assignment: core + Class: secondary + Template: 'Yes' + Color: black + Props: + - registration_origin + - registration_id + #- is_primary_id + biospecimen_source: + Desc: The Biospecimen Source node functions essentially as a look-up table used by the front-end of the application to convert the names of biobanks and tissue repositories represented in the form of acronyms into human-readable, full text names. + Tags: + Category: biospecimen + Assignment: core + Class: secondary + Template: 'No' + Color: black + Props: + - biospecimen_repository_acronym + - biospecimen_repository_full_name + canine_individual: + Desc: The Canine Individual node contains only a single property, i.e. canine_individual_id, a loader-generated ID which identifies each underlying canine subject represented by two or more study-specific ICDC cases. This ID functions to map data sets ultimately derived from the same underlying patient/subject/donor, but generated from discrete cases in separate studies, to the underlying canine individual, such that all data sets derived from any given canine individual can be identified within the application’s user interface and combined. + Tags: + Category: case + Assignment: core + Class: secondary + Template: 'No' + Color: black + Props: + - canine_individual_id + demographic: + Desc: The Demographic node is comprised of properties which describe the key characteristics of each patient/subject/donor, such as breed, sex and neutered status. + Tags: + Category: case + Assignment: core + Class: primary + Template: 'Yes' + Color: black + Props: + - demographic_id + - breed + - additional_breed_detail + - patient_age_at_enrollment + - date_of_birth + - sex + - weight + - neutered_indicator + cycle: + Desc: In clinical trials where therapeutic agents are administered in multiple discrete treatment cycles, the properties within the Cycle node serve to capture the dates upon which each cycle started and ended, providing a detailed timeframe for the therapeutic intervention(s) in question. Adverse events can then be associated with the correct cycle based upon when they were observed. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + - cycle_number + - date_of_cycle_start + - date_of_cycle_end + visit: + Desc: Clinical trials typically require the patient to make multiple visits to the study site for clinical evaluation and/or the administration of additional medication(s). Properties within the Visit node serve to capture the date upon which each visit occurs. Adverse events and various clinical assessments can then be associated with the correct visit based upon date. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + - visit_date + - visit_number + - visit_id + principal_investigator: + Desc: The Principal Investigator node contains properties which identify the principal investigator(s) responsible for any given study/trial. A study/trial may have one or more principal investigators, and any given individual may be listed as a principal investigator on more than one study/trial. + Tags: + Category: study + Assignment: core + Class: primary + Template: 'Yes' + Color: black + Props: + - pi_first_name + - pi_last_name + - pi_middle_initial + diagnosis: + Desc: The Diagnosis node contains numerous properties which fully characterize the type of cancer with which any given patient/subject/donor was diagnosed, inclusive of stage. This node also contains properties pertaining to comorbidities, and the availability of pathology reports, treatment data and follow-up data. + Tags: + Category: clinical + Assignment: core + Class: primary + Template: 'Yes' + Color: black + Props: + - diagnosis_id + - disease_term + - primary_disease_site + - stage_of_disease + - date_of_diagnosis + - histology_cytopathology + - date_of_histology_confirmation + - histological_grade + - best_response + - pathology_report + - treatment_data + - follow_up_data + - concurrent_disease + - concurrent_disease_type + enrollment: + Desc: The Enrollment node is comprised of properties which document when and where a patient/subject/donor was enrolled onto a study/trial. + Tags: + Category: case + Assignment: core + Class: primary + Template: 'Yes' + Color: black + Props: + - enrollment_id + - date_of_registration + - registering_institution + - initials + - date_of_informed_consent + - site_short_name + - veterinary_medical_center + #- cohort_description + - patient_subgroup + prior_therapy: + Desc: Properties within the Prior Therapy node detail therapies received by the patient/subject/donor prior to being enrolled in the study/trial in question. Clinical trials will typically capture more of this information than will cross-sectional and/or mechanistic studies. + Tags: + Category: clinical + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + - date_of_first_dose + - date_of_last_dose + - agent_name + - dose_schedule + - total_dose + - agent_units_of_measure + - best_response_to_prior_therapy + - nonresponse_therapy_type + - prior_therapy_type + - prior_steroid_exposure + - number_of_prior_regimens_steroid + - total_number_of_doses_steroid + - date_of_last_dose_steroid + - prior_nsaid_exposure + - number_of_prior_regimens_nsaid + - total_number_of_doses_nsaid + - date_of_last_dose_nsaid + - tx_loc_geo_loc_ind_nsaid + - min_rsdl_dz_tx_ind_nsaids_treatment_pe + - therapy_type + - any_therapy + - number_of_prior_regimens_any_therapy + - total_number_of_doses_any_therapy + - date_of_last_dose_any_therapy + - treatment_performed_at_site + - treatment_performed_in_minimal_residual + prior_surgery: + Desc: Properties within the Prior Surgery node detail surgical procedures that the patient/subject/donor underwent prior to being enrolled in the study/trial in question. Clinical trials will typically capture more of this information than will cross-sectional and/or mechanistic studies. + Tags: + Category: clinical + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + - date_of_surgery + - procedure + - anatomical_site_of_surgery + - surgical_finding + - residual_disease + - therapeutic_indicator + agent_administration: + Desc: Properties within the Agent Administration node detail the dosing of the therapeutic agent(s) being studied, alongside the specifics of how and when such agents were administered. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + # d/n from STUDY_MED_ADMIN/SDAD/1 + - document_number + - medication + - route_of_administration + - medication_lot_number + - medication_vial_id + - medication_actual_units_of_measure + - medication_duration + - medication_units_of_measure + - medication_actual_dose + # what is phase? + - phase + - start_time + - stop_time + - dose_level + - dose_units_of_measure + - date_of_missed_dose + - medication_missed_dose + - missed_dose_amount + - missed_dose_units_of_measure + - medication_course_number + - comment + sample: + Desc: The Sample node contains numerous properties which provide an in-depth characterization of the types of samples which were collected from any given patient/subject/donor and subsequently analyzed. Many of these sample annotations are required. + Tags: + Category: biospecimen + Assignment: core + Class: primary + Template: 'Yes' + Color: black + Props: + - sample_id + - sample_site + - physical_sample_type # formerly just sample_type + - general_sample_pathology + - tumor_sample_origin + - summarized_sample_type # value is generated during data transformation based upon the combination of the preceding three properties + - molecular_subtype + - specific_sample_pathology + - date_of_sample_collection + - sample_chronology + - necropsy_sample + - tumor_grade + - length_of_tumor + - width_of_tumor + - volume_of_tumor + - percentage_tumor + - sample_preservation + - comment + assay: + Desc: The Assay node does not yet have any properties associated with it and is not currently used. + Tags: + Category: analysis + Assignment: extended + Class: secondary + Template: 'No' + Color: black + Props: null + file: + Desc: Files can be associated with ICDC study, case, diagnosis and sample records, but are not themselves stored within the application. Instead, the application stores records as to the existence and nature of such files. The File node is comprised of properties which characterize these files in terms of their size, format and content, such that they can be appropriately represented within the application’s UI, and in terms of their storage location, such that they can be retrieved for analysis. + Tags: + Category: data_file + Assignment: core + Class: primary + Template: 'Yes' + Color: black + Props: + - file_name + - file_type + - file_description + - file_format + - file_size + - md5sum + - file_status + - uuid + - file_location + image: + Desc: The Image node does not yet have any properties associated with it and is not currently used. + Tags: + Category: data_file + Assignment: core + Class: secondary + Template: 'No' + Color: black + Props: null + image_collection: + Desc: The Image Collection node is comprised of properties which describe collections of images that are associated with any given study/trial. These properties characterize such image collections in terms of the types of images they contain, where the collections are hosted, and how they can be accessed. + Tags: + Category: study + Assignment: core + Class: secondary + Template: 'Yes' + Color: black + Props: + - image_collection_name + - image_type_included + - image_collection_url + - repository_name + - collection_access + physical_exam: + Desc: Properties within the Physical Exam node detail observations around the status of multiple body systems as of a patient enrolled in a clinical trial, as of that patient being examined by a veterinarian during a scheduled visit to the appropriate study site. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + - date_of_examination + - day_in_cycle + - body_system + - pe_finding + - pe_comment + - phase_pe + - assessment_timepoint + publication: + Desc: The Publication node is comprised of properties which describe publications that are directly associated with any given study/trial of interest, inclusive of the location(s) at which publications can be viewed in electronic form. + Tags: + Category: study + Assignment: core + Class: secondary + Template: 'Yes' + Color: black + Props: + - publication_title + - authorship + - year_of_publication + - journal_citation + - digital_object_id + - pubmed_id + vital_signs: + Desc: Properties within the Vital Signs node detail observations around the key indicators of the bodily functions of a patient enrolled in a clinical trial, as of that patient being examined by a veterinarian during a scheduled visit to the appropriate study site. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + - date_of_vital_signs + - body_temperature + - pulse + - respiration_rate + - respiration_pattern + - systolic_bp + - pulse_ox + - patient_weight + - body_surface_area + - modified_ecog + - ecg + - assessment_timepoint + - phase + lab_exam: + Desc: The Lab Exam node does not yet have any properties associated with it and is not currently used. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'No' + Color: black + Props: null + adverse_event: + # how to link? To case and agent? Also to visit/followup? + Desc: Properties within the Adverse Event node detail unexpected medical, physical and behavioral problems occurring during therapy, in terms of what issues are observed, their severity, and what is considered to be their root cause. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + - day_in_cycle + - date_of_onset + - existing_adverse_event + - date_of_resolution + - ongoing_adverse_event + - adverse_event_term + - adverse_event_description + - adverse_event_grade + - adverse_event_grade_description + - adverse_event_agent_name + - adverse_event_agent_dose + - attribution_to_research + - attribution_to_ind + - attribution_to_disease + - attribution_to_commercial + - attribution_to_other + - other_attribution_description + - dose_limiting_toxicity + - unexpected_adverse_event + disease_extent: + Desc: Properties within the Disease Extent node detail the extent to which the disease for which the patient is being treated has either responded to treatment or progressed, based upon observations of one or more specific lesions. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + - lesion_number + - lesion_site + - lesion_description + - previously_irradiated + - previously_treated + - measurable_lesion + - target_lesion + - date_of_evaluation + - measured_how + - longest_measurement + - evaluation_number + - evaluation_code + follow_up: + Desc: The Follow-up node is comprised of properties which document when a follow-up evaluation was performed, and what observations were made at each follow-up evaluation. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + # d/n from FOLLOW_UP/FLWU/1 + - document_number + - date_of_last_contact + - patient_status + - explain_unknown_status + - contact_type + - treatment_since_last_contact + - physical_exam_performed + - physical_exam_changes + off_study: + # off_study, off_treatment -- how related? should be a dependency and normalize properties? + Desc: Properties within the Off Study node detail when a patient was removed from a clinical trial relative to other key dates, and the reason(s) for the patient being removed. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + # d/n from OFF_STUDY/OSSM/1 + - document_number + - date_off_study + - reason_off_study + - date_of_disease_progression + - date_off_treatment + - best_resp_vet_tx_tp_secondary_response + - date_last_medication_administration + - best_resp_vet_tx_tp_best_response + - date_of_best_response + off_treatment: + Desc: Properties within the Off Treatment node detail when a clinical trial patient's treatment was curtailed relative to other key dates. Properties also detail the best response to treatment observed to that point, and the reason(s) for treatment being curtailed. + Tags: + Category: clinical_trial + Assignment: extended + Class: secondary + Template: 'Yes' + Color: black + Props: + # d/n from OFF_TREATMENT/OTSM/1 + - document_number + - date_off_treatment + - reason_off_treatment + - date_of_disease_progression + - best_resp_vet_tx_tp_secondary_response + - date_last_medication_administration + - best_resp_vet_tx_tp_best_response + - date_of_best_response +Relationships: + member_of: + Mul: many_to_one + Ends: + - Src: case + Dst: cohort + - Src: cohort + Dst: study_arm + - Src: study_arm + Dst: study + - Src: study + Dst: program + - Src: case + Dst: study + # to accommodate Cases not mapped to any Cohort, either due to error or by design + - Src: cohort + Dst: study + # to accommodate a Study having Cases that should be grouped into Cohorts, but where Study Arms do not apply + Props: null + of_case: + Mul: many_to_one + Ends: + - Src: enrollment + Dst: case + Mul: one_to_one + - Src: demographic + Dst: case + Mul: one_to_one + - Src: diagnosis + Dst: case + - Src: cycle + Dst: case + - Src: follow_up + Dst: case + - Src: sample + Dst: case + # to accommodate a Sample being directly associated with a Case, rather than being only indirectly associated with a Case through a Visit, etc. + - Src: file + Dst: case + # to accommodate a File being directly associated with a Case, rather than being only indirectly associated with a Case through a Sample or Diagnosis + - Src: visit + Dst: case + # to accommodate situations in which a Visit cannot be unambiguously associated with a treatment Cycle + - Src: adverse_event + Dst: case + # required because adverse event observations are tied to date of onset rather than being tied to the date of the visit at which they were reported + - Src: registration + Dst: case + Mul: many_to_many + Props: null + of_study_arm: + Mul: many_to_many + Ends: + - Src: agent + Dst: study_arm + - Src: case + Dst: study_arm + Mul: many_to_one + Props: null + of_study: + Mul: many_to_many + Ends: + - Src: study_site + Dst: study + - Src: principal_investigator + Dst: study + - Src: file + Dst: study + Mul: many_to_one + - Src: image_collection + Dst: study + Mul: many_to_one + - Src: publication + Dst: study + Mul: many_to_one + Props: null + of_agent: + Mul: many_to_one + Ends: + - Src: agent_administration + Dst: agent + - Src: adverse_event + Dst: agent + Props: null + had_adverse_event: + Mul: many_to_one + Ends: + - Src: case + Dst: adverse_event + Props: null + at_enrollment: + Mul: many_to_one + Ends: + - Src: prior_therapy + Dst: enrollment + - Src: prior_surgery + Dst: enrollment + - Src: physical_exam + Dst: enrollment + Props: null + of_cycle: + Mul: many_to_one + Ends: + - Src: visit + Dst: cycle + Props: null + on_visit: + Mul: many_to_one + Ends: + - Src: agent_administration + Dst: visit + - Src: sample + Dst: visit + - Src: physical_exam + Dst: visit + - Src: lab_exam + Dst: visit + # removed relationship between adverse event and visit because adverse events are tied to date of onset rather than being tied to the date of the visit at which they were reported + - Src: disease_extent + Dst: visit + - Src: vital_signs + Dst: visit + Props: null + of_sample: + Mul: many_to_one + Ends: + - Src: assay + Dst: sample + - Src: file + Dst: sample + # added primarily to support direct association of sequence files with the primary samples to which they relate, when we have no data around the processing intermediates + Props: null + of_assay: + Mul: many_to_one + Ends: + - Src: file + Dst: assay + - Src: image + Dst: assay + Props: null + from_diagnosis: + Mul: many_to_one + Ends: + - Src: file + Dst: diagnosis + Props: null + went_off_study: + Mul: one_to_one + Ends: + - Src: case + Dst: off_study + Props: null + went_off_treatment: + Mul: one_to_one + Ends: + - Src: case + Dst: off_treatment + Props: null + next: + Mul: one_to_one + Ends: + - Src: visit + Dst: visit + - Src: sample + Dst: sample + - Src: prior_therapy + Dst: prior_therapy + - Src: prior_surgery + Dst: prior_surgery + - Src: adverse_event + Dst: adverse_event + Props: null + represents: + Mul: many_to_one + Ends: + - Src: case + Dst: canine_individual + Props: null diff --git a/examples/icdc/dataset/CMCP-program.txt b/examples/icdc/dataset/CMCP-program.txt new file mode 100644 index 00000000..150cb715 --- /dev/null +++ b/examples/icdc/dataset/CMCP-program.txt @@ -0,0 +1,2 @@ +type program_name program_acronym program_short_description program_full_description program_external_url program_sort_order +program Comparative Molecular Characterization Program CMCP "The Comparative Molecular Characterization Program serves as an umbrella program under which studies lacking any pre-designated program affiliation, but generating multi-omics and molecular data focused upon comparative study of canine cancers, can be grouped." "The Comparative Molecular Characterization Program serves as an umbrella program under which studies lacking any pre-designated program affiliation, but generating multi-omics and molecular data focused upon comparative study of canine cancers, can be grouped." 2 diff --git a/examples/icdc/dataset/OSA01-case.txt b/examples/icdc/dataset/OSA01-case.txt new file mode 100644 index 00000000..b1666868 --- /dev/null +++ b/examples/icdc/dataset/OSA01-case.txt @@ -0,0 +1,61 @@ +type study.clinical_study_designation case_id patient_id +case OSA01 OSA01-WLOS_0001 WLOS_0001 +case OSA01 OSA01-WLOS_0002 WLOS_0002 +case OSA01 OSA01-WLOS_0003 WLOS_0003 +case OSA01 OSA01-WLOS_0004 WLOS_0004 +case OSA01 OSA01-WLOS_0005 WLOS_0005 +case OSA01 OSA01-WLOS_0006 WLOS_0006 +case OSA01 OSA01-WLOS_0007 WLOS_0007 +case OSA01 OSA01-WLOS_0008 WLOS_0008 +case OSA01 OSA01-WLOS_0009 WLOS_0009 +case OSA01 OSA01-WLOS_0010 WLOS_0010 +case OSA01 OSA01-WLOS_0011 WLOS_0011 +case OSA01 OSA01-WLOS_0012 WLOS_0012 +case OSA01 OSA01-WLOS_0013 WLOS_0013 +case OSA01 OSA01-WLOS_0014 WLOS_0014 +case OSA01 OSA01-WLOS_0015 WLOS_0015 +case OSA01 OSA01-WLOS_0016 WLOS_0016 +case OSA01 OSA01-WLOS_0017 WLOS_0017 +case OSA01 OSA01-WLOS_0018 WLOS_0018 +case OSA01 OSA01-WLOS_0019 WLOS_0019 +case OSA01 OSA01-WLOS_0020 WLOS_0020 +case OSA01 OSA01-WLOS_0021 WLOS_0021 +case OSA01 OSA01-WLOS_0022 WLOS_0022 +case OSA01 OSA01-WLOS_0023 WLOS_0023 +case OSA01 OSA01-WLOS_0024 WLOS_0024 +case OSA01 OSA01-WLJ_001 WLJ_001 +case OSA01 OSA01-WLJ_002 WLJ_002 +case OSA01 OSA01-WLJ_007 WLJ_007 +case OSA01 OSA01-WLJ_008 WLJ_008 +case OSA01 OSA01-WLJ_0010 WLJ_0010 +case OSA01 OSA01-WLJ_0013 WLJ_0013 +case OSA01 OSA01-WLJ_015 WLJ_015 +case OSA01 OSA01-WLJ_026 WLJ_026 +case OSA01 OSA01-WLJ_027 WLJ_027 +case OSA01 OSA01-WLJ_029 WLJ_029 +case OSA01 OSA01-WLJ_030 WLJ_030 +case OSA01 OSA01-WLJ_047 WLJ_047 +case OSA01 OSA01-WLJ_050 WLJ_050 +case OSA01 OSA01-WLJ_054 WLJ_054 +case OSA01 OSA01-WLJ_055 WLJ_055 +case OSA01 OSA01-WLJ_056 WLJ_056 +case OSA01 OSA01-WLJ_059 WLJ_059 +case OSA01 OSA01-WLJ_106 WLJ_106 +case OSA01 OSA01-E1 E1 +case OSA01 OSA01-E2 E2 +case OSA01 OSA01-E3 E3 +case OSA01 OSA01-E4 E4 +case OSA01 OSA01-E5 E5 +case OSA01 OSA01-E6 E6 +case OSA01 OSA01-E8 E8 +case OSA01 OSA01-E12 E12 +case OSA01 OSA01-E13 E13 +case OSA01 OSA01-E14 E14 +case OSA01 OSA01-E41 E41 +case OSA01 OSA01-E44 E44 +case OSA01 OSA01-E45 E45 +case OSA01 OSA01-E51 E51 +case OSA01 OSA01-E52 E52 +case OSA01 OSA01-E53 E53 +case OSA01 OSA01-E54 E54 +case OSA01 OSA01-K9Ob K9Ob diff --git a/examples/icdc/dataset/OSA01-demographic.txt b/examples/icdc/dataset/OSA01-demographic.txt new file mode 100644 index 00000000..e51d0441 --- /dev/null +++ b/examples/icdc/dataset/OSA01-demographic.txt @@ -0,0 +1,61 @@ +type case.case_id breed patient_age_at_enrollment date_of_birth sex neutered_indicator weight +demographic OSA01-WLOS_0001 Great Pyrenees 9 Male Yes +demographic OSA01-WLOS_0002 Great Dane 7 Female Yes +demographic OSA01-WLOS_0003 Labrador Retriever 6 Male Yes +demographic OSA01-WLOS_0004 Great Dane 5.5 Female Yes +demographic OSA01-WLOS_0005 Mixed Breed 7 Male Yes +demographic OSA01-WLOS_0006 Great Dane 4 Female Yes +demographic OSA01-WLOS_0007 Old English Sheepdog 8 Male Yes +demographic OSA01-WLOS_0008 Mixed Breed 9 Male Yes +demographic OSA01-WLOS_0009 Great Dane 6 Male Yes +demographic OSA01-WLOS_0010 Mixed Breed 10 Male Yes +demographic OSA01-WLOS_0011 Golden Retriever 8 Female Yes +demographic OSA01-WLOS_0012 Mixed Breed 11 Female Yes +demographic OSA01-WLOS_0013 Mastiff 6 Female Yes +demographic OSA01-WLOS_0014 Labrador Retriever 11.5 Male Yes +demographic OSA01-WLOS_0015 Greyhound 12 Female Yes +demographic OSA01-WLOS_0016 Old English Sheepdog 9 Female Yes +demographic OSA01-WLOS_0017 Mixed Breed 9 Male No +demographic OSA01-WLOS_0018 Golden Retriever 6 Male Yes +demographic OSA01-WLOS_0019 Bullmastiff 6 Female Yes +demographic OSA01-WLOS_0020 Newfoundland 6 Male Yes +demographic OSA01-WLOS_0021 Doberman Pinscher 6 Male Yes +demographic OSA01-WLOS_0022 Golden Retriever 11 Male Yes +demographic OSA01-WLOS_0023 Saint Bernard 5.5 Female Yes +demographic OSA01-WLOS_0024 Rottweiler 9 Male Yes +demographic OSA01-WLJ_001 Greyhound 7 Male Yes +demographic OSA01-WLJ_002 Greyhound 7 Male Yes +demographic OSA01-WLJ_007 Golden Retriever 1 Female No +demographic OSA01-WLJ_008 Greyhound 6 Male Yes +demographic OSA01-WLJ_0010 Great Pyrenees 8 Male Yes +demographic OSA01-WLJ_0013 Labrador Retriever 10 Female Yes +demographic OSA01-WLJ_015 Golden Retriever 6 Female Yes +demographic OSA01-WLJ_026 Labrador Retriever 7 Male Yes +demographic OSA01-WLJ_027 German Shepherd Dog 5 Female No +demographic OSA01-WLJ_029 Newfoundland 5 Female Yes +demographic OSA01-WLJ_030 Great Dane 7 Male Yes +demographic OSA01-WLJ_047 Doberman Pinscher 6.5 Male Yes +demographic OSA01-WLJ_050 German Shepherd Dog 8 Female Yes +demographic OSA01-WLJ_054 Mixed Breed 12 Male Yes +demographic OSA01-WLJ_055 Mixed Breed 10 Female Yes +demographic OSA01-WLJ_056 Rottweiler 8 Female Yes +demographic OSA01-WLJ_059 Rottweiler 10 Female Yes +demographic OSA01-WLJ_106 Great Pyrenees 10 Male Yes +demographic OSA01-E1 Golden Retriever 8.2 Female Yes +demographic OSA01-E2 Greyhound 9.8 Male Yes +demographic OSA01-E3 Golden Retriever 10.4 Male Yes +demographic OSA01-E4 Mixed Breed 9 Male Yes +demographic OSA01-E5 Greyhound 7 Male Yes +demographic OSA01-E6 Old English Sheepdog 6.5 Male No +demographic OSA01-E8 Labrador Retriever 8.9 Male Yes +demographic OSA01-E12 Great Pyrenees 7.7 Female Yes +demographic OSA01-E13 Golden Retriever 9 Male Yes +demographic OSA01-E14 Mixed Breed 9.7 Female Yes +demographic OSA01-E41 Mixed Breed 3 Female Yes +demographic OSA01-E44 Greyhound 7 Female Yes +demographic OSA01-E45 Rottweiler 7 Male Yes +demographic OSA01-E51 Great Pyrenees 2 Female No +demographic OSA01-E52 Great Pyrenees 8 Female Yes +demographic OSA01-E53 Greyhound 6 Female Yes +demographic OSA01-E54 Greyhound 7 Female Yes +demographic OSA01-K9Ob Unknown Unknown Unknown diff --git a/examples/icdc/dataset/OSA01-diagnosis.txt b/examples/icdc/dataset/OSA01-diagnosis.txt new file mode 100644 index 00000000..170512da --- /dev/null +++ b/examples/icdc/dataset/OSA01-diagnosis.txt @@ -0,0 +1,61 @@ +type case.case_id diagnosis_id disease_term primary_disease_site stage_of_disease date_of_diagnosis best_response treatment_data follow_up_data pathology_report concurrent_disease concurrent_disease_type +diagnosis OSA01-WLOS_0001 OSA01-WLOS_0001 Osteosarcoma Bone (Appendicular) II 2009-09-01 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0002 OSA01-WLOS_0002 Osteosarcoma Bone (Appendicular) II 2013-03-07 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0003 OSA01-WLOS_0003 Osteosarcoma Bone (Appendicular) II 2010-04-14 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0004 OSA01-WLOS_0004 Osteosarcoma Bone (Appendicular) II 2010-08-26 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0005 OSA01-WLOS_0005 Osteosarcoma Bone (Appendicular) II 2014-09-08 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0006 OSA01-WLOS_0006 Osteosarcoma Bone (Appendicular) II 2015-02-03 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0007 OSA01-WLOS_0007 Osteosarcoma Bone (Appendicular) II 2011-04-28 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0008 OSA01-WLOS_0008 Osteosarcoma Bone (Appendicular) II 2011-06-14 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0009 OSA01-WLOS_0009 Osteosarcoma Bone (Appendicular) II 2011-07-21 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0010 OSA01-WLOS_0010 Osteosarcoma Bone (Appendicular) II 2011-08-18 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0011 OSA01-WLOS_0011 Osteosarcoma Bone (Appendicular) II 2012-02-27 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0012 OSA01-WLOS_0012 Osteosarcoma Bone (Appendicular) II 2012-05-30 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0013 OSA01-WLOS_0013 Osteosarcoma Bone (Appendicular) II 2012-05-31 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0014 OSA01-WLOS_0014 Osteosarcoma Bone (Appendicular) II 2013-08-28 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0015 OSA01-WLOS_0015 Osteosarcoma Bone (Appendicular) II 2014-01-06 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0016 OSA01-WLOS_0016 Osteosarcoma Bone (Appendicular) II 2014-10-02 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0017 OSA01-WLOS_0017 Osteosarcoma Bone (Appendicular) II 2015-03-20 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0018 OSA01-WLOS_0018 Osteosarcoma Bone (Appendicular) II 2015-07-02 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0019 OSA01-WLOS_0019 Osteosarcoma Bone (Appendicular) II 2015-10-07 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0020 OSA01-WLOS_0020 Osteosarcoma Bone (Appendicular) II 2015-12-30 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0021 OSA01-WLOS_0021 Osteosarcoma Bone (Appendicular) II 2016-01-04 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0022 OSA01-WLOS_0022 Osteosarcoma Bone (Appendicular) II 2016-02-18 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0023 OSA01-WLOS_0023 Osteosarcoma Bone (Appendicular) II 2016-04-19 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-WLOS_0024 OSA01-WLOS_0024 Osteosarcoma Bone (Appendicular) II 2016-08-15 Not Determined No Yes Yes Unknown +diagnosis OSA01-WLJ_001 OSA01-WLJ_001 Osteosarcoma Bone (Appendicular) II 2006-12-14 Not Determined No No No Unknown +diagnosis OSA01-WLJ_002 OSA01-WLJ_002 Osteosarcoma Bone (Appendicular) II 2006-12-28 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_007 OSA01-WLJ_007 Osteosarcoma Bone (Appendicular) II 2006-10-26 Not Determined No No No Unknown +diagnosis OSA01-WLJ_008 OSA01-WLJ_008 Osteosarcoma Bone (Appendicular) II 2007-01-03 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_0010 OSA01-WLJ_0010 Osteosarcoma Bone (Appendicular) II 2006-11-02 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_0013 OSA01-WLJ_0013 Osteosarcoma Bone (Appendicular) II 2007-02-14 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_015 OSA01-WLJ_015 Osteosarcoma Bone (Appendicular) II 2006-08-30 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_026 OSA01-WLJ_026 Osteosarcoma Bone (Appendicular) II 2006-03-07 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_027 OSA01-WLJ_027 Osteosarcoma Bone (Appendicular) II 2004-08-18 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_029 OSA01-WLJ_029 Osteosarcoma Bone (Appendicular) II 2006-06-20 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_030 OSA01-WLJ_030 Osteosarcoma Bone (Appendicular) II 2005-11-29 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_047 OSA01-WLJ_047 Osteosarcoma Bone (Appendicular) II 2007-10-03 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_050 OSA01-WLJ_050 Osteosarcoma Bone (Appendicular) II 2008-02-22 Not Determined No No No Unknown +diagnosis OSA01-WLJ_054 OSA01-WLJ_054 Osteosarcoma Bone (Appendicular) II 2007-11-01 Not Determined No No No Unknown +diagnosis OSA01-WLJ_055 OSA01-WLJ_055 Osteosarcoma Bone (Appendicular) II 2007-12-20 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_056 OSA01-WLJ_056 Osteosarcoma Bone (Appendicular) II 2007-11-16 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_059 OSA01-WLJ_059 Osteosarcoma Bone (Appendicular) III 2008-03-04 Not Determined No Yes No Unknown +diagnosis OSA01-WLJ_106 OSA01-WLJ_106 Osteosarcoma Bone (Appendicular) II 2006-11-22 Not Determined No Yes No Unknown +diagnosis OSA01-E1 OSA01-E1 Osteosarcoma Bone (Appendicular) II 2008-12-18 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E2 OSA01-E2 Osteosarcoma Bone (Appendicular) II 2011-02-23 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E3 OSA01-E3 Osteosarcoma Bone (Appendicular) III 2012-04-10 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E4 OSA01-E4 Osteosarcoma Bone (Appendicular) II 2014-06-25 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E5 OSA01-E5 Osteosarcoma Bone (Appendicular) II 2015-09-03 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E6 OSA01-E6 Osteosarcoma Bone (Appendicular) II 2008-05-20 Not Determined Yes Yes No Unknown +diagnosis OSA01-E8 OSA01-E8 Osteosarcoma Bone (Appendicular) II 2006-12-22 Not Determined Yes Yes No Unknown +diagnosis OSA01-E12 OSA01-E12 Osteosarcoma Bone (Appendicular) II 2016-07-19 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E13 OSA01-E13 Osteosarcoma Bone (Appendicular) II 2009-11-09 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E14 OSA01-E14 Osteosarcoma Bone (Appendicular) II 2009-09-22 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E41 OSA01-E41 Osteosarcoma Bone (Appendicular) II 2011-01-19 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E44 OSA01-E44 Osteosarcoma Bone (Appendicular) II 2010-06-03 Not Determined Yes Yes Yes Unknown +diagnosis OSA01-E45 OSA01-E45 Osteosarcoma Bone (Appendicular) II 2011-09-06 Not Determined No No No Unknown +diagnosis OSA01-E51 OSA01-E51 Osteosarcoma Bone (Appendicular) Unknown 2009-12-17 Not Determined No No Yes Unknown +diagnosis OSA01-E52 OSA01-E52 Osteosarcoma Bone (Appendicular) Unknown 2011-07-12 Not Determined No No Yes Unknown +diagnosis OSA01-E53 OSA01-E53 Osteosarcoma Bone (Appendicular) Unknown 2009-04-24 Not Determined No No Yes Unknown +diagnosis OSA01-E54 OSA01-E54 Osteosarcoma Bone (Appendicular) Unknown 2009-10-22 Not Determined No No Yes Unknown +diagnosis OSA01-K9Ob OSA01-K9Ob Unknown Unknown Unknown Not Determined No No No Unknown diff --git a/examples/icdc/dataset/OSA01-enrollment.txt b/examples/icdc/dataset/OSA01-enrollment.txt new file mode 100644 index 00000000..6ffeef7f --- /dev/null +++ b/examples/icdc/dataset/OSA01-enrollment.txt @@ -0,0 +1,61 @@ +type case.case_id enrollment_id site_short_name +enrollment OSA01-WLOS_0001 OSA01-WLOS_0001 210 +enrollment OSA01-WLOS_0002 OSA01-WLOS_0002 210 +enrollment OSA01-WLOS_0003 OSA01-WLOS_0003 210 +enrollment OSA01-WLOS_0004 OSA01-WLOS_0004 210 +enrollment OSA01-WLOS_0005 OSA01-WLOS_0005 210 +enrollment OSA01-WLOS_0006 OSA01-WLOS_0006 210 +enrollment OSA01-WLOS_0007 OSA01-WLOS_0007 210 +enrollment OSA01-WLOS_0008 OSA01-WLOS_0008 210 +enrollment OSA01-WLOS_0009 OSA01-WLOS_0009 210 +enrollment OSA01-WLOS_0010 OSA01-WLOS_0010 210 +enrollment OSA01-WLOS_0011 OSA01-WLOS_0011 210 +enrollment OSA01-WLOS_0012 OSA01-WLOS_0012 210 +enrollment OSA01-WLOS_0013 OSA01-WLOS_0013 210 +enrollment OSA01-WLOS_0014 OSA01-WLOS_0014 210 +enrollment OSA01-WLOS_0015 OSA01-WLOS_0015 210 +enrollment OSA01-WLOS_0016 OSA01-WLOS_0016 210 +enrollment OSA01-WLOS_0017 OSA01-WLOS_0017 210 +enrollment OSA01-WLOS_0018 OSA01-WLOS_0018 210 +enrollment OSA01-WLOS_0019 OSA01-WLOS_0019 210 +enrollment OSA01-WLOS_0020 OSA01-WLOS_0020 210 +enrollment OSA01-WLOS_0021 OSA01-WLOS_0021 210 +enrollment OSA01-WLOS_0022 OSA01-WLOS_0022 210 +enrollment OSA01-WLOS_0023 OSA01-WLOS_0023 210 +enrollment OSA01-WLOS_0024 OSA01-WLOS_0024 210 +enrollment OSA01-WLJ_001 OSA01-WLJ_001 210 +enrollment OSA01-WLJ_002 OSA01-WLJ_002 210 +enrollment OSA01-WLJ_007 OSA01-WLJ_007 210 +enrollment OSA01-WLJ_008 OSA01-WLJ_008 210 +enrollment OSA01-WLJ_0010 OSA01-WLJ_0010 210 +enrollment OSA01-WLJ_0013 OSA01-WLJ_0013 210 +enrollment OSA01-WLJ_015 OSA01-WLJ_015 210 +enrollment OSA01-WLJ_026 OSA01-WLJ_026 210 +enrollment OSA01-WLJ_027 OSA01-WLJ_027 210 +enrollment OSA01-WLJ_029 OSA01-WLJ_029 210 +enrollment OSA01-WLJ_030 OSA01-WLJ_030 210 +enrollment OSA01-WLJ_047 OSA01-WLJ_047 210 +enrollment OSA01-WLJ_050 OSA01-WLJ_050 210 +enrollment OSA01-WLJ_054 OSA01-WLJ_054 210 +enrollment OSA01-WLJ_055 OSA01-WLJ_055 210 +enrollment OSA01-WLJ_056 OSA01-WLJ_056 210 +enrollment OSA01-WLJ_059 OSA01-WLJ_059 210 +enrollment OSA01-WLJ_106 OSA01-WLJ_106 210 +enrollment OSA01-E1 OSA01-E1 210 +enrollment OSA01-E2 OSA01-E2 210 +enrollment OSA01-E3 OSA01-E3 210 +enrollment OSA01-E4 OSA01-E4 210 +enrollment OSA01-E5 OSA01-E5 210 +enrollment OSA01-E6 OSA01-E6 523 +enrollment OSA01-E8 OSA01-E8 523 +enrollment OSA01-E12 OSA01-E12 210 +enrollment OSA01-E13 OSA01-E13 210 +enrollment OSA01-E14 OSA01-E14 210 +enrollment OSA01-E41 OSA01-E41 210 +enrollment OSA01-E44 OSA01-E44 210 +enrollment OSA01-E45 OSA01-E45 210 +enrollment OSA01-E51 OSA01-E51 523 +enrollment OSA01-E52 OSA01-E52 706 +enrollment OSA01-E53 OSA01-E53 210 +enrollment OSA01-E54 OSA01-E54 210 +enrollment OSA01-K9Ob OSA01-K9Ob diff --git a/examples/icdc/dataset/OSA01-principal_investigator.txt b/examples/icdc/dataset/OSA01-principal_investigator.txt new file mode 100644 index 00000000..51e1e9d5 --- /dev/null +++ b/examples/icdc/dataset/OSA01-principal_investigator.txt @@ -0,0 +1,3 @@ +type study.clinical_study_designation pi_first_name pi_last_name pi_middle_initial +principal_investigator OSA01 William Hendricks P.D. +principal_investigator OSA01 Heather Gardner L. \ No newline at end of file diff --git a/examples/icdc/dataset/OSA01-publication.txt b/examples/icdc/dataset/OSA01-publication.txt new file mode 100644 index 00000000..d4400d8b --- /dev/null +++ b/examples/icdc/dataset/OSA01-publication.txt @@ -0,0 +1,2 @@ +type study.clinical_study_designation publication_title authorship year_of_publication journal_citation digital_object_id pubmed_id +publication OSA01 Canine osteosarcoma genome sequencing identifies recurrent mutations in DMD and the histone methyltransferase gene SETD2 Heather L. Gardner et al 2019 Commun Biol 2:266 10.1038/s42003-019-0487-2 31341965 \ No newline at end of file diff --git a/examples/icdc/dataset/OSA01-registration.txt b/examples/icdc/dataset/OSA01-registration.txt new file mode 100644 index 00000000..1db161a9 --- /dev/null +++ b/examples/icdc/dataset/OSA01-registration.txt @@ -0,0 +1,86 @@ +type case.case_id registration_origin registration_id +registration OSA01-WLOS_0001 OSA01 WLOS_0001 +registration OSA01-WLOS_0002 OSA01 WLOS_0002 +registration OSA01-WLOS_0003 OSA01 WLOS_0003 +registration OSA01-WLOS_0004 OSA01 WLOS_0004 +registration OSA01-WLOS_0005 OSA01 WLOS_0005 +registration OSA01-WLOS_0006 OSA01 WLOS_0006 +registration OSA01-WLOS_0007 OSA01 WLOS_0007 +registration OSA01-WLOS_0008 OSA01 WLOS_0008 +registration OSA01-WLOS_0009 OSA01 WLOS_0009 +registration OSA01-WLOS_0010 OSA01 WLOS_0010 +registration OSA01-WLOS_0011 OSA01 WLOS_0011 +registration OSA01-WLOS_0012 OSA01 WLOS_0012 +registration OSA01-WLOS_0013 OSA01 WLOS_0013 +registration OSA01-WLOS_0014 OSA01 WLOS_0014 +registration OSA01-WLOS_0015 OSA01 WLOS_0015 +registration OSA01-WLOS_0016 OSA01 WLOS_0016 +registration OSA01-WLOS_0017 OSA01 WLOS_0017 +registration OSA01-WLOS_0018 OSA01 WLOS_0018 +registration OSA01-WLOS_0019 OSA01 WLOS_0019 +registration OSA01-WLOS_0020 OSA01 WLOS_0020 +registration OSA01-WLOS_0021 OSA01 WLOS_0021 +registration OSA01-WLOS_0022 OSA01 WLOS_0022 +registration OSA01-WLOS_0023 OSA01 WLOS_0023 +registration OSA01-WLOS_0024 OSA01 WLOS_0024 +registration OSA01-WLJ_001 OSA01 WLJ_001 +registration OSA01-WLJ_002 OSA01 WLJ_002 +registration OSA01-WLJ_007 OSA01 WLJ_007 +registration OSA01-WLJ_008 OSA01 WLJ_008 +registration OSA01-WLJ_0010 OSA01 WLJ_0010 +registration OSA01-WLJ_0013 OSA01 WLJ_0013 +registration OSA01-WLJ_015 OSA01 WLJ_015 +registration OSA01-WLJ_026 OSA01 WLJ_026 +registration OSA01-WLJ_027 OSA01 WLJ_027 +registration OSA01-WLJ_029 OSA01 WLJ_029 +registration OSA01-WLJ_030 OSA01 WLJ_030 +registration OSA01-WLJ_047 OSA01 WLJ_047 +registration OSA01-WLJ_050 OSA01 WLJ_050 +registration OSA01-WLJ_054 OSA01 WLJ_054 +registration OSA01-WLJ_055 OSA01 WLJ_055 +registration OSA01-WLJ_056 OSA01 WLJ_056 +registration OSA01-WLJ_059 OSA01 WLJ_059 +registration OSA01-WLJ_106 OSA01 WLJ_106 +registration OSA01-E1 OSA01 E1 +registration OSA01-E2 OSA01 E2 +registration OSA01-E3 OSA01 E3 +registration OSA01-E4 OSA01 E4 +registration OSA01-E5 OSA01 E5 +registration OSA01-E6 OSA01 E6 +registration OSA01-E8 OSA01 E8 +registration OSA01-E12 OSA01 E12 +registration OSA01-E13 OSA01 E13 +registration OSA01-E14 OSA01 E14 +registration OSA01-E41 OSA01 E41 +registration OSA01-E44 OSA01 E44 +registration OSA01-E45 OSA01 E45 +registration OSA01-E51 OSA01 E51 +registration OSA01-E52 OSA01 E52 +registration OSA01-E53 OSA01 E53 +registration OSA01-E54 OSA01 E54 +registration OSA01-K9Ob OSA01 K9Ob +registration OSA01-WLOS_0001 CCOGC CCB020141 +registration OSA01-WLOS_0003 CCOGC CCB020180 +registration OSA01-WLOS_0007 CCOGC CCB020265 +registration OSA01-WLOS_0008 CCOGC CCB020270 +registration OSA01-WLOS_0009 CCOGC CCB020273 +registration OSA01-WLOS_0010 CCOGC CCB020281 +registration OSA01-WLJ_047 CCOGC CCB020010 +registration OSA01-WLJ_050 CCOGC CCB020027 +registration OSA01-WLJ_054 CCOGC CCB020018 +registration OSA01-WLJ_055 CCOGC CCB020020 +registration OSA01-WLJ_056 CCOGC CCB020022 +registration OSA01-WLJ_059 CCOGC CCB020029 +registration OSA01-WLJ_106 CCOGC CCB020093 +registration OSA01-E1 CCOGC CCB020081 +registration OSA01-E2 CCOGC CCB020248 +registration OSA01-E6 CCOGC CCB010068 +registration OSA01-E13 CCOGC CCB020156 +registration OSA01-E14 CCOGC CCB020146 +registration OSA01-E41 CCOGC CCB020189 +registration OSA01-E44 CCOGC CCB040464 +registration OSA01-E45 CCOGC CCB020240 +registration OSA01-E51 CCOGC CCB010222 +registration OSA01-E52 CCOGC CCB030081 +registration OSA01-E53 CCOGC CCB020108 +registration OSA01-E54 CCOGC CCB020151 diff --git a/examples/icdc/dataset/OSA01-sample.txt b/examples/icdc/dataset/OSA01-sample.txt new file mode 100644 index 00000000..62cfd828 --- /dev/null +++ b/examples/icdc/dataset/OSA01-sample.txt @@ -0,0 +1,140 @@ +type case.case_id sample_id physical_sample_type general_sample_pathology tumor_sample_origin summarized_sample_type sample_site sample_chronology specific_sample_pathology tumor_grade date_of_sample_collection sample_preservation necropsy_sample percentage_tumor comment length_of_tumor width_of_tumor volume_of_tumor +sample OSA01-WLOS_0001 OSA01-WLOS_0001_MR376519_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 100 +sample OSA01-WLOS_0001 OSA01-WLOS_0001_MR376519_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 100 +sample OSA01-WLOS_0001 OSA01-WLOS_0001_MR376519_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0002 OSA01-WLOS_0002_MR407424_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining tissue is some pre-exisiting bone and bone marrow +sample OSA01-WLOS_0002 OSA01-WLOS_0002_MR407424_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining tissue is some pre-exisiting bone and bone marrow +sample OSA01-WLOS_0002 OSA01-WLOS_0002_MR407424_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0003 OSA01-WLOS_0003_MR407819_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 50 Remaining tissue is connective tissue +sample OSA01-WLOS_0003 OSA01-WLOS_0003_MR407819_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 50 Remaining tissue is connective tissue +sample OSA01-WLOS_0003 OSA01-WLOS_0003_MR407819_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0004 OSA01-WLOS_0004_MR410976_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 30 Vast majority is chondroid cells, There is one small island of neoplastic osteoblasts. Remaining tissue is connective tissue and lymphoid nodules +sample OSA01-WLOS_0004 OSA01-WLOS_0004_MR410976_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 30 Vast majority is chondroid cells, There is one small island of neoplastic osteoblasts. Remaining tissue is connective tissue and lymphoid nodules +sample OSA01-WLOS_0004 OSA01-WLOS_0004_MR410976_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0005 OSA01-WLOS_0005_MR411336_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 40 Remaining tissue is pre-exisiting bone and connective tissue +sample OSA01-WLOS_0005 OSA01-WLOS_0005_MR411336_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 40 Remaining tissue is pre-exisiting bone and connective tissue +sample OSA01-WLOS_0005 OSA01-WLOS_0005_MR411336_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0006 OSA01-WLOS_0006_MR414747_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 80 Remaining tissue is nerve and connective tissue +sample OSA01-WLOS_0006 OSA01-WLOS_0006_MR414747_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 80 Remaining tissue is nerve and connective tissue +sample OSA01-WLOS_0006 OSA01-WLOS_0006_MR414747_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0007 OSA01-WLOS_0007_MR415976_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 60 There is approximately 10% of the tumor that is necrotic. Remaining tissue is pre-exisiting bone and connective tissue +sample OSA01-WLOS_0007 OSA01-WLOS_0007_MR415976_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 60 There is approximately 10% of the tumor that is necrotic. Remaining tissue is pre-exisiting bone and connective tissue +sample OSA01-WLOS_0007 OSA01-WLOS_0007_MR415976_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0008 OSA01-WLOS_0008_MR416666_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 100 There are pockets of neutrophils scattered across the tumor +sample OSA01-WLOS_0008 OSA01-WLOS_0008_MR416666_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 100 There are pockets of neutrophils scattered across the tumor +sample OSA01-WLOS_0008 OSA01-WLOS_0008_MR416666_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0009 OSA01-WLOS_0009_MR417471_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 70 40% of tumor is necrotic. Remaining tissue is pre-exisiting bone with some connective tissue +sample OSA01-WLOS_0009 OSA01-WLOS_0009_MR417471_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 70 40% of tumor is necrotic. Remaining tissue is pre-exisiting bone with some connective tissue +sample OSA01-WLOS_0009 OSA01-WLOS_0009_MR417471_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0010 OSA01-WLOS_0010_MR418029_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 100 10% of the tumor is necrotic +sample OSA01-WLOS_0010 OSA01-WLOS_0010_MR418029_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 100 10% of the tumor is necrotic +sample OSA01-WLOS_0010 OSA01-WLOS_0010_MR418029_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0011 OSA01-WLOS_0011_MR421928_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 100 50% of the tumor is necrotic +sample OSA01-WLOS_0011 OSA01-WLOS_0011_MR421928_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 100 50% of the tumor is necrotic +sample OSA01-WLOS_0011 OSA01-WLOS_0011_MR421928_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0012 OSA01-WLOS_0012_MR424011_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining tissue is pre-exisiting bone +sample OSA01-WLOS_0012 OSA01-WLOS_0012_MR424011_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining tissue is pre-exisiting bone +sample OSA01-WLOS_0012 OSA01-WLOS_0012_MR424011_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0013 OSA01-WLOS_0013_MR424015_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining area is connective tissue and pre-exisiting bone. Approximately 35% of tumor is necrotic. +sample OSA01-WLOS_0013 OSA01-WLOS_0013_MR424015_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining area is connective tissue and pre-exisiting bone. Approximately 35% of tumor is necrotic. +sample OSA01-WLOS_0013 OSA01-WLOS_0013_MR424015_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0014 OSA01-WLOS_0014_MR433678_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 85 50% of tumor area is necrotic. Remaining tissue is connective tissue. +sample OSA01-WLOS_0014 OSA01-WLOS_0014_MR433678_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 85 50% of tumor area is necrotic. Remaining tissue is connective tissue. +sample OSA01-WLOS_0014 OSA01-WLOS_0014_MR433678_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0015 OSA01-WLOS_0015_MR436258_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 80 Remaining tissue is muscle and connective tissue. Tumor is almost entirely chondroid, 1 small island of suspect neoplastic osteosarcoma cells. +sample OSA01-WLOS_0015 OSA01-WLOS_0015_MR436258_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 80 Remaining tissue is muscle and connective tissue. Tumor is almost entirely chondroid, 1 small island of suspect neoplastic osteosarcoma cells. +sample OSA01-WLOS_0015 OSA01-WLOS_0015_MR436258_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0016 OSA01-WLOS_0016_MR442248_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 40 Remaining area is necrotic tumor +sample OSA01-WLOS_0016 OSA01-WLOS_0016_MR442248_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 40 Remaining area is necrotic tumor +sample OSA01-WLOS_0016 OSA01-WLOS_0016_MR442248_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0017 OSA01-WLOS_0017_MR446007_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 85 Element of inflammation with neutrophils (less than 5%). Small percent of other tissue is adipose. +sample OSA01-WLOS_0017 OSA01-WLOS_0017_MR446007_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 85 Element of inflammation with neutrophils (less than 5%). Small percent of other tissue is adipose. +sample OSA01-WLOS_0017 OSA01-WLOS_0017_MR446007_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0018 OSA01-WLOS_0018_MR448467_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 95 +sample OSA01-WLOS_0018 OSA01-WLOS_0018_MR448467_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 95 +sample OSA01-WLOS_0018 OSA01-WLOS_0018_MR448467_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0019 OSA01-WLOS_0019_MR450922_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 100 +sample OSA01-WLOS_0019 OSA01-WLOS_0019_MR450922_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 100 +sample OSA01-WLOS_0019 OSA01-WLOS_0019_MR450922_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0020 OSA01-WLOS_0020_MR452859_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining tissue is mature collagen +sample OSA01-WLOS_0020 OSA01-WLOS_0020_MR452859_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining tissue is mature collagen +sample OSA01-WLOS_0020 OSA01-WLOS_0020_MR452859_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0021 OSA01-WLOS_0021_MR452979_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 50% of tumor area is necrosis, 10% of total area is pre-exisiting bone and connective tissue. There is a hint of chondroid change in small number of tumor cells +sample OSA01-WLOS_0021 OSA01-WLOS_0021_MR452979_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 50% of tumor area is necrosis, 10% of total area is pre-exisiting bone and connective tissue. There is a hint of chondroid change in small number of tumor cells +sample OSA01-WLOS_0021 OSA01-WLOS_0021_MR452979_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0022 OSA01-WLOS_0022_MR454062_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining tissue was normal tissue +sample OSA01-WLOS_0022 OSA01-WLOS_0022_MR454062_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 90 Remaining tissue was normal tissue +sample OSA01-WLOS_0022 OSA01-WLOS_0022_MR454062_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0023 OSA01-WLOS_0023_MR456397_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 70 Remaining tissue was necrotic +sample OSA01-WLOS_0023 OSA01-WLOS_0023_MR456397_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 70 Remaining tissue was necrotic +sample OSA01-WLOS_0023 OSA01-WLOS_0023_MR456397_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-WLOS_0024 OSA01-WLOS_0024_MR458906_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 40 Remaining tissue was necrotic +sample OSA01-WLOS_0024 OSA01-WLOS_0024_MR458906_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 40 Remaining tissue was necrotic +sample OSA01-WLOS_0024 OSA01-WLOS_0024_MR458906_C2 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-K9Ob OSA01-WLOS_CONSRNA_K09OB_C2 Cell Line Normal Not Applicable Normal Cell Line Bone Not Applicable Not Applicable Not Applicable Snap Frozen Not Applicable Not Applicable +sample OSA01-WLJ_001 OSA01-WLJ_001_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_002 OSA01-WLJ_002_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_007 OSA01-WLJ_007_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_008 OSA01-WLJ_008_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_0010 OSA01-WLJ_0010_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_0013 OSA01-WLJ_0013_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_015 OSA01-WLJ_015_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_026 OSA01-WLJ_026_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_027 OSA01-WLJ_027_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_029 OSA01-WLJ_029_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_030 OSA01-WLJ_030_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Giant Cell Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_047 OSA01-WLJ_047_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_050 OSA01-WLJ_050_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_054 OSA01-WLJ_054_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_055 OSA01-WLJ_055_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_056 OSA01-WLJ_056_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_059 OSA01-WLJ_059_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteoblastic and Chrondroblastic Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-WLJ_106 OSA01-WLJ_106_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-E1 OSA01-HPCI_0001_1_BN_Whole_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteosarcoma; Combined Type Unknown Snap Frozen No 70 There is peripheral connective tissue around the outside of the tumor. There are fibroblastic and chondroid matrices present in the tumor along with small amounts of osteoid suggesting combined type is most appropriate +sample OSA01-E1 OSA01-HPCI_0001_1_BN_Whole_T4 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteosarcoma; Combined Type Unknown Snap Frozen No 70 There is peripheral connective tissue around the outside of the tumor. There are fibroblastic and chondroid matrices present in the tumor along with small amounts of osteoid suggesting combined type is most appropriate +sample OSA01-E1 OSA01-HPCI_0001_1_BN_Whole_T6 Tissue Malignant Metastatic Metastatic Tumor Tissue Muscle After Treatment Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E1 OSA01-HPCI_0001_1_BN_Whole_C5 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E2 OSA01-HPCI_0002_1_PB_Whole_C5 Blood Normal Not Applicable Whole Blood Blood Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E2 OSA01-HPCI_0002_1_BN_Whole_T3 Tissue Malignant Metastatic Metastatic Tumor Tissue Lung Not Applicable Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E2 OSA01-HPCI_0002_1_BN_Whole_T4 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Fibroblastic Osteosarcoma Unknown Snap Frozen No 90 90% of the tumor is necrotic +sample OSA01-E2 OSA01-HPCI_0002_1_BN_Whole_T2 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Fibroblastic Osteosarcoma Unknown Snap Frozen No 90 90% of the tumor is necrotic +sample OSA01-E3 OSA01-HPCI_0003_1_PB_Whole_C5 Blood Normal Not Applicable Whole Blood Blood Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E3 OSA01-HPCI_0003_1_BN_Whole_T3 Tissue Malignant Metastatic Metastatic Tumor Tissue Lung Before Treatment Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E3 OSA01-HPCI_0003_1_BN_Whole_T4 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen Unknown 100 40% of the tumor is necrotic +sample OSA01-E3 OSA01-HPCI_0003_1_BN_Whole_T2 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen Unknown 100 40% of the tumor is necrotic +sample OSA01-E4 OSA01-HPCI_0004_1_BN_Whole_C4 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E4 OSA01-HPCI_0004_1_BN_Whole_T3 Tissue Malignant Metastatic Metastatic Tumor Tissue Lung After Treatment Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E4 OSA01-HPCI_0004_1_BN_Whole_T5 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 100 Many small seams of osteoid. +sample OSA01-E5 OSA01-HPCI_0005_1_PB_Whole_C4 Blood Normal Not Applicable Whole Blood Blood Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E5 OSA01-HPCI_0005_1_BN_Whole_T2 Tissue Malignant Metastatic Metastatic Tumor Tissue Lung After Treatment Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E5 OSA01-HPCI_0005_1_BN_Whole_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 100 70% of the tumor is necrotic with mutiple regions of neutrophil infiltration +sample OSA01-E5 OSA01-HPCI_0005_1_BN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 101 70% of the tumor is necrotic with mutiple regions of neutrophil infiltration +sample OSA01-E6 OSA01-HPCI_0006_1_BN_Whole_C3 Tissue Normal Not Applicable Normal Tissue Unknown Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E6 OSA01-HPCI_0006_1_BN_Whole_T2 Tissue Malignant Metastatic Metastatic Tumor Tissue Lung After Treatment Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E6 OSA01-HPCI_0007_1_BN_Whole_T2 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-E6 OSA01-HPCI_0007_1_BN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-E8 OSA01-HPCI_0008_1_BN_Whole_C3 Tissue Normal Not Applicable Normal Tissue Lung Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E8 OSA01-HPCI_0008_1_BN_Whole_T2 Tissue Malignant Metastatic Metastatic Tumor Tissue Lung After Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E8 OSA01-HPCI_0009_1_BN_Whole_T2 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-E8 OSA01-HPCI_0009_1_BN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-E12 OSA01-HPCI_0012_1_PB_Whole_C4 Blood Normal Not Applicable Whole Blood Blood Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E12 OSA01-HPCI_0012_1_BN_Whole_T3 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 100 Lots of artifact from more mineralized areas and ossified regions cutting poorly, soft areas of tumor has small regions of osteoid. +sample OSA01-E12 OSA01-HPCI_0012_1_BN_Whole_T5 Tissue Malignant Metastatic Metastatic Tumor Tissue Subcutaneous Tissue After Treatment Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E13 OSA01-HPCI_0013_1_PB_Whole_C3 Blood Normal Not Applicable Whole Blood Blood Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E13 OSA01-HPCI_0013_1_BN_Whole_T2 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Fibroblastic Osteosarcoma Unknown Snap Frozen No 100 Large amount of collagenous matrix with smaller amount of osteoid. Small areas of necrosos (5%) with netruophil infiltration +sample OSA01-E13 OSA01-HPCI_0013_1_BN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Fibroblastic Osteosarcoma Unknown Snap Frozen No 100 Large amount of collagenous matrix with smaller amount of osteoid. Small areas of necrosos (5%) with netruophil infiltration +sample OSA01-E14 OSA01-HPCI_0042_1_PB_Whole_C1 Blood Normal Not Applicable Whole Blood Blood Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E14 OSA01-HPCI_0014_1_BN_Whole_T2 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 50 50% of the section is undecalcified bone that didn't section properly, other areas are collagenous matrix +sample OSA01-E14 OSA01-HPCI_0014_1_BN_Whole_T4 Tissue Malignant Metastatic Metastatic Tumor Tissue Lung After Treatment Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E14 OSA01-HPCI_0014_1_BN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Chondroblastic Osteosarcoma Unknown Snap Frozen No 50 50% of the section is undecalcified bone that didn't section properly, other areas are collagenous matrix +sample OSA01-E41 OSA01-HPCI_0041_1_PB_Whole_C3 Blood Normal Not Applicable Whole Blood Blood Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E41 OSA01-HPCI_0041_1_BN_Whole_T2 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 90 Significant artifact from presxisting trabecular bone folding during slide cutting, 10% of tumor is necrotic +sample OSA01-E41 OSA01-HPCI_0041_1_BN_Whole_T1 Tissue Malignant Metastatic Metastatic Tumor Tissue Lung After Treatment Osteosarcoma Unknown Snap Frozen Unknown Unknown +sample OSA01-E44 OSA01-HPCI_0044_1_PB_Whole_C2 Blood Normal Not Applicable Whole Blood Blood Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E44 OSA01-HPCI_0044_1_BN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteoblastic Osteosarcoma Unknown Snap Frozen No 85 Small amount of prexcisting trabecular bone +sample OSA01-E45 OSA01-HPCI_0045_1_BN_Whole_C1 Tissue Normal Not Applicable Normal Tissue Muscle Before Treatment Not Applicable Not Applicable Snap Frozen No Not Applicable +sample OSA01-E45 OSA01-HPCI_0045_1_BN_Whole_T2 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Before Treatment Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-E51 OSA01-HPCI_0051_1_MN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-E52 OSA01-HPCI_0052_1_BN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-E53 OSA01-HPCI_0053_1_BN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteosarcoma Unknown Snap Frozen No Unknown +sample OSA01-E54 OSA01-HPCI_0054_1_BN_Whole_T1 Tissue Malignant Primary Primary Malignant Tumor Tissue Bone Not Applicable Osteosarcoma Unknown Snap Frozen No Unknown diff --git a/examples/icdc/dataset/OSA01-study 000006 Unrestricted with new description text.txt b/examples/icdc/dataset/OSA01-study 000006 Unrestricted with new description text.txt new file mode 100644 index 00000000..8dc129b3 --- /dev/null +++ b/examples/icdc/dataset/OSA01-study 000006 Unrestricted with new description text.txt @@ -0,0 +1,2 @@ +type program.program_acronym clinical_study_designation clinical_study_id clinical_study_name clinical_study_description clinical_study_type date_of_iacuc_approval dates_of_conduct accession_id study_disposition +study CMCP OSA01 A Multi-Platform Sequencing Analysis of Canine Appendicular Osteosarcoma. In order to facilitate comparative studies of canine and human osteosarcoma, this study characterized the genomic landscape of primary and metastatic canine appendicular osteosarcoma through multi-platform analysis of a retrospective cohort of tumors from 59 dogs. Sequencing analyses included whole genome and whole exome sequencing of matched tumor and normal tissue from 24 and 13 dogs, respectively. Of the 13 dogs subject to exome sequencing, 10 have sequencing data from matched primary tumor tissue, metastatic tumor tissue and normal tissue. RNA sequencing analysis is available from 54 primary tumors. Here we provide these multi-omics data not only to expand our genomic understanding of canine and human osteosarcoma, but also to further enable comparisons of genomic techniques (exome, genome, RNA) as well as primary versus metastatic tumors from the same dog. Genomics 2018-03-22 January 2016 – September 2019 000006 Unrestricted \ No newline at end of file diff --git a/examples/icdc/icdc-local.yml b/examples/icdc/icdc-local.yml new file mode 100644 index 00000000..83b2b268 --- /dev/null +++ b/examples/icdc/icdc-local.yml @@ -0,0 +1,47 @@ +Config: + temp_folder: tmp + backup_folder: /tmp/data-loader-backups + + neo4j: + # Location of Neo4j server, e.g., bolt://127.0.0.1:7687 + uri: bolt://127.0.0.1:7687 + # Neo4j username + user: neo4j + # Neo4j password + password: + + # Schema files' locations + schema: + - examples/icdc/data-model/icdc-model.yml + - examples/icdc/data-model/icdc-model-props.yml + + plugins: + - module: loader_plugins.visit_creator + class: VisitCreator + - module: loader_plugins.individual_creator + class: IndividualCreator + + #Property file location + prop_file: config/props-icdc-pmvp.yml + + # Skip validations, aka. Cheat Mode + cheat_mode: false + # Validations only, skip loading + dry_run: false + # Wipe out database before loading, you'll lose all data! + wipe_db: false + # Skip backup step + no_backup: true + # Automatically confirm deletion and database wiping (without asking user to confirm) + no_confirmation: false + # Max violations to display, default is 10 + max_violations: 10 + + # S3 bucket name, if you are loading from an S3 bucket + s3_bucket: + # S3 folder for dataset + s3_folder: + # Loading mode, can be UPSERT_MODE, NEW_MODE or DELETE_MODE, default is UPSERT_MODE + loading_mode: UPSERT_MODE + # Location of dataset + dataset: examples/icdc/dataset