diff --git a/.gitignore b/.gitignore index b6e4761..75cb1b3 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ +.DS_Store +.idea + # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] diff --git a/Diagnosis.yaml b/Diagnosis.yaml new file mode 100644 index 0000000..c56abed --- /dev/null +++ b/Diagnosis.yaml @@ -0,0 +1,23 @@ +stage: +- method_type: + - coding: + - code: C125738 + system: http://ncithesaurus.nci.nih.gov/ + label: FIGO Stage + tag: + - harmonized + observations: + - observation_type: + coding: + - code: C25605 + system: http://ncithesaurus.nci.nih.gov/ + label: Overall + tag: + - harmonized + value_codeable_concept: + coding: + - code: C96258 + system: http://ncithesaurus.nci.nih.gov/ + label: FIGO Stage IIIC + tag: + - harmonized diff --git a/Diagnosis_id.yaml b/Diagnosis_id.yaml new file mode 100644 index 0000000..5005762 --- /dev/null +++ b/Diagnosis_id.yaml @@ -0,0 +1,59 @@ +id: "pdc-diagnosis:ff2f0efb-70ca-11e8-bcf1-0a2705229b82" +#identifier: # type = Identifier +# - value: "tcga:TCGA-13-1409-DX" +age_at_diagnosis: # type = Quantity + value_decimal: 26836 + unit: # type = CodeableConcept + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized +morphology: # type = CodeableConcept + coding: # type = Coding + - code: C3778 + label: Serous Cystadenocarcinoma + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized +condition: # type = CodeableConcept + coding: # type = Coding + - code: C3778 + label: Serous Cystadenocarcinoma + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized +#primary_site: # type = BodySite +# - site: # type = CodeableConcept +# coding: # type = Coding +# - code: C12404 +# label: Ovary +# system: https://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +stage: # type = CancerStageObservationSet + - method_type: # type = CodeableConcept + - coding: # type = Coding + - code: C125738 + label: FIGO Stage + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized +# - observations: # type = CancerStageObservation +# - observation_type: # type = CodeableConcept +# coding: # type = Coding +# - code: C25605 +# label: Overall +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# value_codeable_concept: # type = CodeableConcept +# coding: # type = Coding +# - code: C96258 +# label: FIGO Stage IIIC +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +#diagnosis_date: +# date_time: 2008 diff --git a/GDC to CCDH conversion.ipynb b/GDC to CCDH conversion.ipynb index 13e8d8b..3c6d57b 100644 --- a/GDC to CCDH conversion.ipynb +++ b/GDC to CCDH conversion.ipynb @@ -38,7 +38,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 1, "id": "0b848016", "metadata": {}, "outputs": [], @@ -72,7 +72,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 2, "id": "8e146c12", "metadata": { "scrolled": false @@ -591,7 +591,7 @@ "[560 rows x 25 columns]" ] }, - "execution_count": 3, + "execution_count": 2, "metadata": {}, "output_type": "execute_result" } @@ -620,7 +620,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "id": "a16e6db1", "metadata": { "scrolled": false @@ -634,6 +634,36 @@ " Any material taken as a sample from a biological entity (living or dead), or from a physical object or the\n", " environment. Specimens are usually collected as an example of their kind, often for use in some investigation.\n", " \n", + "Documentation for BodySite: \n", + " A site in the body of an organism, typically described in terms of an anatomical location and optional qualifiers\n", + " (e.g. left/right, upper/lower). But body sites as defined here may include 'non-anatomic' sites, such as the\n", + " location of an implanted medical device.\n", + " \n" + ] + } + ], + "source": [ + "# from ccdh import ccdhmodel as ccdh\n", + "import crdch_model as ccdh\n", + "\n", + "# Documentation for an entity.\n", + "print(f\"Documentation for Specimen: {ccdh.Specimen.__doc__}\")\n", + "\n", + "\n", + "# Documentation for an entity.\n", + "print(f\"Documentation for BodySite: {ccdh.BodySite.__doc__}\")\n" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "df14d2c6", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ "Documentation for Specimen.specimen_type: \n", " A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original\n", " sample extracted from a source).\n", @@ -643,22 +673,20 @@ " - Value \"aliquot\": A specimen that results from the division of some parent specimen into equal amounts for downstream analysis.\n", " - Value \"analyte\": A specimen generated through the extraction of a specified class of substance/chemical (e.g. DNA, RNA, protein) from a parent specimen, which is stored in solution as an analyte.\n", " - Value \"slide\": A specimen that is mounted on a slide or coverslip for microscopic analysis.\n", - " - Value \"initial sample\": A specimen representing the material that was directly collected from a subject (i.e. not generated through portioning, aliquoting, or analyte extraction from an existing specimen).\n" + " - Value \"Fresh Specimen\": A specimen representing the material that was directly collected from a subject (i.e. not generated through portioning, aliquoting, or analyte extraction from an existing specimen).\n" ] } ], "source": [ - "from ccdh import ccdhmodel as ccdh\n", - "\n", - "# Documentation for an entity.\n", - "print(f\"Documentation for Specimen: {ccdh.Specimen.__doc__}\")\n", - "\n", "# Documentation for an enumeration.\n", - "print(f\"Documentation for Specimen.specimen_type: {ccdh.EnumCCDHSpecimenSpecimenType.__doc__}\")\n", + "# print(f\"Documentation for Specimen.specimen_type: {ccdh.EnumCCDHSpecimenSpecimenType.__doc__}\")\n", + "print(f\"Documentation for Specimen.specimen_type: {ccdh.EnumCRDCHSpecimenSpecimenType.__doc__}\")\n", "\n", "# List of permissible values for Specimen.specimen_type\n", + "# wiht move to codeable concepts,this may be of limited usefulness now\n", "print(\"Permissible values in enumeration Specimen.specimen_type:\")\n", - "pvalues = [pv for key, pv in ccdh.EnumCCDHSpecimenSpecimenType.__dict__.items() if isinstance(pv, ccdh.PermissibleValue)]\n", + "# pvalues = [pv for key, pv in ccdh.EnumCCDHSpecimenSpecimenType.__dict__.items() if isinstance(pv, ccdh.PermissibleValue)]\n", + "pvalues = [pv for key, pv in ccdh.EnumCRDCHSpecimenSpecimenType.__dict__.items() if isinstance(pv, ccdh.PermissibleValue)]\n", "for pv in pvalues:\n", " print(f' - Value \"{pv.text}\": {pv.description}')" ] @@ -683,56 +711,176 @@ "execution_count": 5, "id": "76578a61", "metadata": {}, + "outputs": [], + "source": [ + "import requests\n", + "import pandas as pd\n", + "import difflib\n", + "\n", + "# use terminology.ccdh.io to drive mapping strings to codable concepts\n", + "# paramterize the URL below\n", + "response = requests.get(\n", + " \"https://terminology.ccdh.io/models/CRDC-H/entities/BodySite/attributes/site\"\n", + ")\n", + "resp_struct = response.json()\n", + "BodyPart_frame = pd.DataFrame(resp_struct[\"concept_references\"])\n", + "\n", + "# could also use\n", + "# https://terminology.ccdh.io/enumerations/CRDC-H.BodySite.site\n", + "\n", + "\n", + "def create_body_site(site_name):\n", + " \"\"\"Create a CCDH BodySite based on the name of a site in the human body.\"\"\"\n", + "\n", + " # Accept 'None'.\n", + " if site_name is None:\n", + " return None\n", + " #\n", + " # # Some body sites are not currently included in the CCDH model. We will need to translate these sites\n", + " # # into values that *are* included in the CCDH model.\n", + " # # site_mappings = {\n", + " # # 'Larynx, NOS': ccdh.EnumCCDHBodySiteSite.Larynx\n", + " # # }\n", + " # site_mappings = {\n", + " # 'Larynx, NOS': ccdh.CodeableConcept(coding=[ccdh.Coding(code=\"UBERON:0001737\", system=\"http://purl.obolibrary.org/obo/uberon.owl\", label=\"larynx\")])\n", + " # }\n", + " #\n", + " # # previously: Map values if needed. Otherwise, pass them through unmapped.\n", + " # # now: can't pass through text because the site has to be a codable concept.\n", + " # # should the mapping be done here in the application, via the CCDH terminology serivce?\n", + " # # mock up for now with some other lookup service?\n", + " # if site_name in site_mappings:\n", + " # return ccdh.BodySite(site=(site_mappings[site_name]))\n", + " # else:\n", + " # return None\n", + " #\n", + " # # return ccdh.BodySite(site=site_name)\n", + " \n", + " # blindly get closest match\n", + " closest_BodyPart_label = difflib.get_close_matches(\n", + " site_name, list(BodyPart_frame[\"designation\"])\n", + " )[0]\n", + " # send to logger or wrap as an optional debug mode\n", + " print(\"input site: \" + site_name)\n", + " print(\"closest match: \" + closest_BodyPart_label)\n", + " closest_BodyPart = BodyPart_frame.loc[\n", + " BodyPart_frame[\"designation\"] == closest_BodyPart_label\n", + " ]\n", + " closest_BodyPart = closest_BodyPart.to_dict(orient=\"records\")[0]\n", + " print(closest_BodyPart)\n", + " # this doesn't really say what the \"system\" should be\n", + " mapped = ccdh.BodySite(\n", + " site=ccdh.CodeableConcept(\n", + " coding=[\n", + " ccdh.Coding(\n", + " code=closest_BodyPart[\"code\"],\n", + " system=\"https://terminology.ccdh.io/models/CRDC-H/entities/BodySite/attributes/site\",\n", + " label=closest_BodyPart[\"designation\"]\n", + " )\n", + " ], text = site_name\n", + " )\n", + " )\n", + " return mapped\n" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "56ff4218", + "metadata": {}, + "outputs": [], + "source": [ + "# # Try to create a body site for a site name not currently included in the CCDH model.\n", + "# try:\n", + "# created = create_body_site('Laryn') # Note misspelling.\n", + "# except ValueError as v:\n", + "# print(f'Could not create BodySite: {v}')\n", + "# print(created)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "9b6d02c5", + "metadata": {}, + "outputs": [], + "source": [ + "# # Using a valid name generates no errors.\n", + "# create_body_site('Larynx') \n", + "\n", + "# # Using a mapped name generates no errors, as it is mapped to a valid name.\n", + "# create_body_site('Larynx, NOS')" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "7db02802", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "PermissibleValue(text='Larynx', description='Larynx', meaning=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None)" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# how is this still useful? why is it still in the model?\n", + "ccdh.EnumCRDCHBodySiteSite.Larynx" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "b0b9747b", + "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Could not create BodySite: Unknown EnumCCDHBodySiteSite enumeration code: Laryn\n" + "input site: Laryn\n", + "closest match: Larynx\n", + "{'code': 'C12420', 'uri': 'http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12420', 'designation': 'Larynx', 'definition': 'The cartilaginous structure of the respiratory tract between the pharynx and the trachea. It contains elastic vocal cords required for sound production.', 'reference': 'https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI%20Thesaurus&code=C12420'}\n" ] - }, + } + ], + "source": [ + "created_body_site = create_body_site(\"Laryn\")" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "41ef6178", + "metadata": {}, + "outputs": [ { "data": { "text/plain": [ - "BodySite(site=(text='Larynx', description='Larynx'), qualifier=[])" + "BodySite(site=CodeableConcept(coding=[Coding(code='C12420', system='https://terminology.ccdh.io/models/CRDC-H/entities/BodySite/attributes/site', label='Larynx', system_version=None, value_set=None, value_set_version=None, tag=[])], text='Laryn'), qualifier=[])" ] }, - "execution_count": 5, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "def create_body_site(site_name):\n", - " \"\"\" Create a CCDH BodySite based on the name of a site in the human body.\"\"\"\n", - " \n", - " # Accept 'None'.\n", - " if site_name is None:\n", - " return None\n", - " \n", - " # Some body sites are not currently included in the CCDH model. We will need to translate these sites\n", - " # into values that *are* included in the CCDH model.\n", - " site_mappings = {\n", - " 'Larynx, NOS': ccdh.EnumCCDHBodySiteSite.Larynx\n", - " }\n", - " \n", - " # Map values if needed. Otherwise, pass them through unmapped.\n", - " if site_name in site_mappings:\n", - " return ccdh.BodySite(site=(site_mappings[site_name]))\n", - " \n", - " return ccdh.BodySite(site=site_name)\n", - "\n", - "# Try to create a body site for a site name not currently included in the CCDH model.\n", - "try:\n", - " create_body_site('Laryn') # Note misspelling.\n", - "except ValueError as v:\n", - " print(f'Could not create BodySite: {v}')\n", - "\n", - "# Using a valid name generates no errors.\n", - "create_body_site('Larynx') \n", - "\n", - "# Using a mapped name generates no errors, as it is mapped to a valid name.\n", - "create_body_site('Larynx, NOS')" + "created_body_site" + ] + }, + { + "cell_type": "markdown", + "id": "83a7dfe9", + "metadata": {}, + "source": [ + "---" ] }, { @@ -743,25 +891,620 @@ "We need a more sophisticated transformation method for transforming the GDC cancer stage information into [CCDH Cancer Stage Observation Set](https://cancerdhc.github.io/ccdhmodel/latest/CancerStageObservationSet/). Each observation set is made up of a number of [CCDH Cancer Stage Observations](https://cancerdhc.github.io/ccdhmodel/latest/CancerStageObservation/), each of which represents a different type of observation." ] }, + { + "cell_type": "markdown", + "id": "66a25c65", + "metadata": {}, + "source": [ + "https://terminology.ccdh.io/models/CRDC-H/entities/CancerStageObservation/attributes\n", + "\n", + "```\n", + "[\n", + " {\n", + " \"name\": \"category\"\n", + " },\n", + " {\n", + " \"name\": \"observation_type\"\n", + " },\n", + " {\n", + " \"name\": \"method_type\"\n", + " },\n", + " {\n", + " \"name\": \"valueCodeableConcept\"\n", + " },\n", + " {\n", + " \"name\": \"id\"\n", + " },\n", + " {\n", + " \"name\": \"focus\"\n", + " },\n", + " {\n", + " \"name\": \"subject\"\n", + " },\n", + " {\n", + " \"name\": \"performed_by\"\n", + " },\n", + " {\n", + " \"name\": \"valueEntity\"\n", + " }\n", + "]\n", + "```\n", + "\n", + "`enum_CRDCH_CancerStageObservation_observation_type` still has `permissible_values` but I don't see a codeable concept endpoint for these like I showed for the BodySites above." + ] + }, { "cell_type": "code", - "execution_count": 6, - "id": "2d661175", - "metadata": { - "scrolled": true - }, + "execution_count": 11, + "id": "4dec653c", + "metadata": {}, + "outputs": [], + "source": [ + "# pvalues = [pv for key, pv in ccdh.EnumCRDCHCancerStageObservationObservationType.__dict__.items() if isinstance(pv, ccdh.PermissibleValue)]\n", + "# csoot_list = []\n", + "# for pv in pvalues:\n", + "# csoot_list.append(pv.text)\n", + "# csoot_list.sort()\n", + "# csoot_list\n" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "c08d80b5", + "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "CancerStageObservationSet(id=None, category=None, focus=[], subject=None, method_type=[(text='AJCC staging system 7th edition', description='The 7th edition of the criteria developed by the American Joint Committee on Cancer (AJCC) in 2010, used for the classification and staging of neoplastic diseases.')], performed_by=None, observations=[CancerStageObservation(observation_type=(text='Overall', description='The overall stage of the disease'), valueCodeableConcept=(text='Stage IVC', description='Stage IVC'), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, valueEntity=None), CancerStageObservation(observation_type=(text='Clinical Overall', description='The overall stage of the disease; clinical stage is determined from evidence acquired before treatment (including clinical examination, imaging, endoscopy, biopsy, surgical exploration)'), valueCodeableConcept=(text='Stage IVC', description='Stage IVC'), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, valueEntity=None), CancerStageObservation(observation_type=(text='Clinical Tumor (T)', description='T classifies the size or direct extent of the primary tumor; clinical stage is determined from evidence acquired before treatment (including clinical examination, imaging, endoscopy, biopsy, surgical exploration)'), valueCodeableConcept=(text='T3', description='T3 Stage Finding'), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, valueEntity=None), CancerStageObservation(observation_type=(text='Clinical Node (N)', description='N classifies the degree of spread to regional lymph nodes; clinical stage is determined from evidence acquired before treatment (including clinical examination, imaging, endoscopy, biopsy, surgical exploration)'), valueCodeableConcept=(text='N1', description='N1 Stage Finding'), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, valueEntity=None), CancerStageObservation(observation_type=(text='Clinical Metastasis (M)', description='M classifies the presence of distant metastasis; clinical stage is determined from evidence acquired before treatment (including clinical examination, imaging, endoscopy, biopsy, surgical exploration)'), valueCodeableConcept=(text='M1', description='M1 Stage Finding'), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, valueEntity=None), CancerStageObservation(observation_type=(text='Pathological Overall', description='The overall stage of the disease; stage given by histopathologic examination of a surgical specimen'), valueCodeableConcept=(text='Stage IVC', description='Stage IVC'), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, valueEntity=None), CancerStageObservation(observation_type=(text='Pathological Tumor (T)', description='T classifies the size or direct extent of the primary tumor; stage given by histopathologic examination of a surgical specimen'), valueCodeableConcept=(text='T3', description='T3 Stage Finding'), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, valueEntity=None), CancerStageObservation(observation_type=(text='Pathological Node (N)', description='N classifies the degree of spread to regional lymph nodes; stage given by histopathologic examination of a surgical specimen'), valueCodeableConcept=(text='N1', description='N1 Stage Finding'), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, valueEntity=None), CancerStageObservation(observation_type=(text='Pathological Metastasis (M)', description='M classifies the presence of distant metastasis; stage given by histopathologic examination of a surgical specimen'), valueCodeableConcept=(text='M1', description='M1 Stage Finding'), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, valueEntity=None)])" + "'M classifies the presence of distant metastasis; stage given by histopathologic examination of a surgical specimen'" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pvalues = [pv for key, pv in ccdh.EnumCRDCHCancerStageObservationObservationType.__dict__.items() if isinstance(pv, ccdh.PermissibleValue)]\n", + "# pvalues\n", + "ccdh.EnumCRDCHCancerStageObservationObservationType['Pathological Metastasis (M)'].description" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "e10411e7", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "age_at_diagnosis\n", + " 22107\n", + "ajcc_clinical_m\n", + " M1\n", + "ajcc_clinical_n\n", + " N1\n", + "ajcc_clinical_stage\n", + " Stage IVC\n", + "ajcc_clinical_t\n", + " T3\n", + "ajcc_pathologic_m\n", + " M1\n", + "ajcc_pathologic_n\n", + " N1\n", + "ajcc_pathologic_stage\n", + " Stage IVC\n", + "ajcc_pathologic_t\n", + " T3\n", + "ajcc_staging_system_edition\n", + " 7th\n", + "classification_of_tumor\n", + " not reported\n", + "created_datetime\n", + " None\n", + "days_to_diagnosis\n", + " 0\n", + "days_to_last_follow_up\n", + " None\n", + "days_to_last_known_disease_status\n", + " None\n", + "days_to_recurrence\n", + " None\n", + "diagnosis_id\n", + " 9e30aa6c-91e6-5dd3-9512-75c162a89913\n", + "icd_10_code\n", + " C32.9\n", + "last_known_disease_status\n", + " not reported\n", + "morphology\n", + " 8070/3\n", + "primary_diagnosis\n", + " Squamous cell carcinoma, NOS\n", + "prior_malignancy\n", + " no\n", + "prior_treatment\n", + " No\n", + "progression_or_recurrence\n", + " not reported\n", + "site_of_resection_or_biopsy\n", + " Larynx, NOS\n", + "state\n", + " released\n", + "submitter_id\n", + " TCGA-QK-A8Z8_diagnosis\n", + "synchronous_malignancy\n", + " No\n", + "tissue_or_organ_of_origin\n", + " Larynx, NOS\n", + "tumor_grade\n", + " not reported\n", + "tumor_stage\n", + " stage ivc\n", + "updated_datetime\n", + " 2019-08-08T16:48:06.888156-05:00\n", + "year_of_diagnosis\n", + " 2013\n" + ] + } + ], + "source": [ + "\n", + "temp = gdc_head_and_mouth[131]['diagnoses'][0]\n", + "for k,v in temp.items():\n", + " print(k)\n", + " print(\" \" + str(v))" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "4dc921d7", + "metadata": {}, + "outputs": [], + "source": [ + "gdc_to_crdch_csoot_dict = [\n", + " {\"GDC\": \"ajcc_clinical_m\", \"CRDC-H\": \"Clinical Metastasis (M)\"},\n", + " {\"GDC\": \"ajcc_clinical_n\", \"CRDC-H\": \"Clinical Node (N)\"},\n", + " {\"GDC\": \"ajcc_clinical_stage\", \"CRDC-H\": \"Clinical Overall\"},\n", + " {\"GDC\": \"ajcc_clinical_t\", \"CRDC-H\": \"Clinical Tumor (T)\"},\n", + " {\"GDC\": \"tumor_stage\", \"CRDC-H\": \"Overall\"},\n", + " {\"GDC\": \"ajcc_pathologic_m\", \"CRDC-H\": \"Pathological Metastasis (M)\"},\n", + " {\"GDC\": \"ajcc_pathologic_n\", \"CRDC-H\": \"Pathological Node (N)\"},\n", + " {\"GDC\": \"ajcc_pathologic_stage\", \"CRDC-H\": \"Pathological Overall\"},\n", + " {\"GDC\": \"ajcc_pathologic_t\", \"CRDC-H\": \"Pathological Tumor (T)\"},\n", + " {\"GDC\": \"age_at_diagnosis\", \"CRDC-H\": None},\n", + " {\"GDC\": \"ajcc_staging_system_edition\", \"CRDC-H\": None},\n", + " {\"GDC\": \"classification_of_tumor\", \"CRDC-H\": None},\n", + " {\"GDC\": \"created_datetime\", \"CRDC-H\": None},\n", + " {\"GDC\": \"days_to_diagnosis\", \"CRDC-H\": None},\n", + " {\"GDC\": \"days_to_last_follow_up\", \"CRDC-H\": None},\n", + " {\"GDC\": \"days_to_last_known_disease_status\", \"CRDC-H\": None},\n", + " {\"GDC\": \"days_to_recurrence\", \"CRDC-H\": None},\n", + " {\"GDC\": \"diagnosis_id\", \"CRDC-H\": None},\n", + " {\"GDC\": \"icd_10_code\", \"CRDC-H\": None},\n", + " {\"GDC\": \"last_known_disease_status\", \"CRDC-H\": None},\n", + " {\"GDC\": \"morphology\", \"CRDC-H\": None},\n", + " {\"GDC\": \"primary_diagnosis\", \"CRDC-H\": None},\n", + " {\"GDC\": \"prior_malignancy\", \"CRDC-H\": None},\n", + " {\"GDC\": \"prior_treatment\", \"CRDC-H\": None},\n", + " {\"GDC\": \"progression_or_recurrence\", \"CRDC-H\": None},\n", + " {\"GDC\": \"site_of_resection_or_biopsy\", \"CRDC-H\": None},\n", + " {\"GDC\": \"state\", \"CRDC-H\": None},\n", + " {\"GDC\": \"submitter_id\", \"CRDC-H\": None},\n", + " {\"GDC\": \"synchronous_malignancy\", \"CRDC-H\": None},\n", + " {\"GDC\": \"tissue_or_organ_of_origin\", \"CRDC-H\": None},\n", + " {\"GDC\": \"tumor_grade\", \"CRDC-H\": None},\n", + " {\"GDC\": \"updated_datetime\", \"CRDC-H\": None},\n", + " {\"GDC\": \"year_of_diagnosis\", \"CRDC-H\": None},\n", + "]\n" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "0748f138", + "metadata": {}, + "outputs": [], + "source": [ + "gdc_to_crdch_csoot_frame = pd.DataFrame(gdc_to_crdch_csoot_dict)" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "b11fc7cd", + "metadata": {}, + "outputs": [], + "source": [ + "gdc_to_crdch_csoot_frame_complete = gdc_to_crdch_csoot_frame.loc[ ~ gdc_to_crdch_csoot_frame['CRDC-H'].isnull()]" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "cddb36a5", + "metadata": {}, + "outputs": [ + { + "data": { + 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GDCCRDC-H
0ajcc_clinical_mClinical Metastasis (M)
1ajcc_clinical_nClinical Node (N)
2ajcc_clinical_stageClinical Overall
3ajcc_clinical_tClinical Tumor (T)
4tumor_stageOverall
5ajcc_pathologic_mPathological Metastasis (M)
6ajcc_pathologic_nPathological Node (N)
7ajcc_pathologic_stagePathological Overall
8ajcc_pathologic_tPathological Tumor (T)
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" + ], + "text/plain": [ + " GDC CRDC-H\n", + "0 ajcc_clinical_m Clinical Metastasis (M)\n", + "1 ajcc_clinical_n Clinical Node (N)\n", + "2 ajcc_clinical_stage Clinical Overall\n", + "3 ajcc_clinical_t Clinical Tumor (T)\n", + "4 tumor_stage Overall\n", + "5 ajcc_pathologic_m Pathological Metastasis (M)\n", + "6 ajcc_pathologic_n Pathological Node (N)\n", + "7 ajcc_pathologic_stage Pathological Overall\n", + "8 ajcc_pathologic_t Pathological Tumor (T)" ] }, - "execution_count": 6, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } ], + "source": [ + "gdc_to_crdch_csoot_frame_complete" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "c7c33259", + "metadata": {}, + "outputs": [], + "source": [ + "from linkml_runtime.dumpers import yaml_dumper\n", + "\n", + "cancer_stage_method_type = None\n", + "# if diagnosis.get('ajcc_staging_system_edition') == '7th':\n", + "# cancer_stage_method_type = 'AJCC staging system 7th edition'\n", + "\n", + "# Create an observation set\n", + "obs = ccdh.CancerStageObservationSet(method_type=cancer_stage_method_type)\n", + "\n", + "\n", + "def diag_cc_mapper(diag_info_type, diag_info_val):\n", + " if diag_info_val is not None:\n", + " crdch_diag_info_type = gdc_to_crdch_csoot_frame_complete[\"CRDC-H\"].loc[\n", + " gdc_to_crdch_csoot_frame_complete[\"GDC\"] == diag_info_type\n", + " ]\n", + " crdch_diag_info_type = list(crdch_diag_info_type)\n", + " if len(crdch_diag_info_type) == 1:\n", + " crdch_diag_info_type = crdch_diag_info_type[0]\n", + " # we could look up the sescription for the mapped type enum\n", + " # but where would we put it in the obs structure?\n", + " crdch_diag_info_type_desc = (\n", + " ccdh.EnumCRDCHCancerStageObservationObservationType[\n", + " crdch_diag_info_type\n", + " ].description\n", + " )\n", + " current_observation = ccdh.CancerStageObservation(\n", + " observation_type=ccdh.CodeableConcept(\n", + " coding=[\n", + " ccdh.Coding(\n", + " code=crdch_diag_info_type,\n", + " system=\"crdch-model 1.1.5 legacy enums\",\n", + " )\n", + " ],\n", + " text=diag_info_type,\n", + " ),\n", + " # valueCodeableConcept ?\n", + " value_codeable_concept=ccdh.CodeableConcept(\n", + " coding=[\n", + " ccdh.Coding(\n", + " code=diag_info_val, system=\"crdch-model 1.1.5 legacy enums\"\n", + " )\n", + " ]\n", + " ),\n", + " )\n", + " obs.observations.append(current_observation)\n", + "\n", + "\n", + "diagnosis_dict = gdc_head_and_mouth[131][\"diagnoses\"][0]\n", + "for k, v in diagnosis_dict.items():\n", + " diag_cc_mapper(k, v)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "id": "9c531670", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "CancerStageObservation(observation_type=CodeableConcept(coding=[Coding(code='Clinical Metastasis (M)', system='crdch-model 1.1.5 legacy enums', label=None, system_version=None, value_set=None, value_set_version=None, tag=[])], text='ajcc_clinical_m'), value_codeable_concept=CodeableConcept(coding=[Coding(code='M1', system='crdch-model 1.1.5 legacy enums', label=None, system_version=None, value_set=None, value_set_version=None, tag=[])], text=None), id=None, category=None, method_type=None, focus=None, subject=None, performed_by=None, value_entity=None)\n" + ] + } + ], + "source": [ + "print(obs.observations[0])" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "482376b6", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "observations:\n", + "- observation_type:\n", + " coding:\n", + " - code: Clinical Metastasis (M)\n", + " system: crdch-model 1.1.5 legacy enums\n", + " text: ajcc_clinical_m\n", + " value_codeable_concept:\n", + " coding:\n", + " - code: M1\n", + " system: crdch-model 1.1.5 legacy enums\n", + "- observation_type:\n", + " coding:\n", + " - code: Clinical Node (N)\n", + " system: crdch-model 1.1.5 legacy enums\n", + " text: ajcc_clinical_n\n", + " value_codeable_concept:\n", + " coding:\n", + " - code: N1\n", + " system: crdch-model 1.1.5 legacy enums\n", + "- observation_type:\n", + " coding:\n", + " - code: Clinical Overall\n", + " system: crdch-model 1.1.5 legacy enums\n", + " text: ajcc_clinical_stage\n", + " value_codeable_concept:\n", + " coding:\n", + " - code: Stage IVC\n", + " system: crdch-model 1.1.5 legacy enums\n", + "- observation_type:\n", + " coding:\n", + " - code: Clinical Tumor (T)\n", + " system: crdch-model 1.1.5 legacy enums\n", + " text: ajcc_clinical_t\n", + " value_codeable_concept:\n", + " coding:\n", + " - code: T3\n", + " system: crdch-model 1.1.5 legacy enums\n", + "- observation_type:\n", + " coding:\n", + " - code: Pathological Metastasis (M)\n", + " system: crdch-model 1.1.5 legacy enums\n", + " text: ajcc_pathologic_m\n", + " value_codeable_concept:\n", + " coding:\n", + " - code: M1\n", + " system: crdch-model 1.1.5 legacy enums\n", + "- observation_type:\n", + " coding:\n", + " - code: Pathological Node (N)\n", + " system: crdch-model 1.1.5 legacy enums\n", + " text: ajcc_pathologic_n\n", + " value_codeable_concept:\n", + " coding:\n", + " - code: N1\n", + " system: crdch-model 1.1.5 legacy enums\n", + "- observation_type:\n", + " coding:\n", + " - code: Pathological Overall\n", + " system: crdch-model 1.1.5 legacy enums\n", + " text: ajcc_pathologic_stage\n", + " value_codeable_concept:\n", + " coding:\n", + " - code: Stage IVC\n", + " system: crdch-model 1.1.5 legacy enums\n", + "- observation_type:\n", + " coding:\n", + " - code: Pathological Tumor (T)\n", + " system: crdch-model 1.1.5 legacy enums\n", + " text: ajcc_pathologic_t\n", + " value_codeable_concept:\n", + " coding:\n", + " - code: T3\n", + " system: crdch-model 1.1.5 legacy enums\n", + "- observation_type:\n", + " coding:\n", + " - code: Overall\n", + " system: crdch-model 1.1.5 legacy enums\n", + " text: tumor_stage\n", + " value_codeable_concept:\n", + " coding:\n", + " - code: stage ivc\n", + " system: crdch-model 1.1.5 legacy enums\n", + "\n" + ] + } + ], + "source": [ + "print(yaml_dumper.dumps(obs))" + ] + }, + { + "cell_type": "markdown", + "id": "104a932f", + "metadata": {}, + "source": [ + "## Expecting something like this:\n", + "\n", + "```\n", + "observations:\n", + "- observation_type:\n", + " text: Overall\n", + " description: The overall stage of the disease\n", + " valueCodeableConcept:\n", + " text: Stage IVC\n", + " description: Stage IVC\n", + "- observation_type:\n", + " text: Clinical Overall\n", + " description: The overall stage of the disease; clinical stage is determined from\n", + " evidence acquired before treatment (including clinical examination, imaging,\n", + " endoscopy, biopsy, surgical exploration)\n", + " valueCodeableConcept:\n", + " text: Stage IVC\n", + " description: Stage IVC\n", + "- observation_type:\n", + " text: Clinical Tumor (T)\n", + " description: T classifies the size or direct extent of the primary tumor; clinical\n", + " stage is determined from evidence acquired before treatment (including clinical\n", + " examination, imaging, endoscopy, biopsy, surgical exploration)\n", + " valueCodeableConcept:\n", + " text: T3\n", + " description: T3 Stage Finding\n", + "- observation_type:\n", + " text: Clinical Node (N)\n", + " description: N classifies the degree of spread to regional lymph nodes; clinical\n", + " stage is determined from evidence acquired before treatment (including clinical\n", + " examination, imaging, endoscopy, biopsy, surgical exploration)\n", + " valueCodeableConcept:\n", + " text: N1\n", + " description: N1 Stage Finding\n", + "- observation_type:\n", + " text: Clinical Metastasis (M)\n", + " description: M classifies the presence of distant metastasis; clinical stage is\n", + " determined from evidence acquired before treatment (including clinical examination,\n", + " imaging, endoscopy, biopsy, surgical exploration)\n", + " valueCodeableConcept:\n", + " text: M1\n", + " description: M1 Stage Finding\n", + "- observation_type:\n", + " text: Pathological Overall\n", + " description: The overall stage of the disease; stage given by histopathologic\n", + " examination of a surgical specimen\n", + " valueCodeableConcept:\n", + " text: Stage IVC\n", + " description: Stage IVC\n", + "- observation_type:\n", + " text: Pathological Tumor (T)\n", + " description: T classifies the size or direct extent of the primary tumor; stage\n", + " given by histopathologic examination of a surgical specimen\n", + " valueCodeableConcept:\n", + " text: T3\n", + " description: T3 Stage Finding\n", + "- observation_type:\n", + " text: Pathological Node (N)\n", + " description: N classifies the degree of spread to regional lymph nodes; stage\n", + " given by histopathologic examination of a surgical specimen\n", + " valueCodeableConcept:\n", + " text: N1\n", + " description: N1 Stage Finding\n", + "- observation_type:\n", + " text: Pathological Metastasis (M)\n", + " description: M classifies the presence of distant metastasis; stage given by histopathologic\n", + " examination of a surgical specimen\n", + " valueCodeableConcept:\n", + " text: M1\n", + " description: M1 Stage Finding\n", + "\n", + "```" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "id": "2d661175", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "ename": "TypeError", + "evalue": "type object argument after ** must be a mapping, not str", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m/tmp/ipykernel_338501/868770706.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 68\u001b[0m \u001b[0;31m# Note that the resulting CancerStageObservationSet contains descriptions for the concepts included in it.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 69\u001b[0m \u001b[0;31m# example_observation_set = create_stage_from_gdc(gdc_head_and_mouth[131]['diagnoses'][0], ccdh.Subject(id='1234'))\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 70\u001b[0;31m \u001b[0mexample_observation_set\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcreate_stage_from_gdc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgdc_head_and_mouth\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m131\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'diagnoses'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 71\u001b[0m \u001b[0mexample_observation_set\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m/tmp/ipykernel_338501/868770706.py\u001b[0m in \u001b[0;36mcreate_stage_from_gdc\u001b[0;34m(diagnosis)\u001b[0m\n\u001b[1;32m 31\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 32\u001b[0m \u001b[0;31m# Create an observation set\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 33\u001b[0;31m obs = ccdh.CancerStageObservationSet(\n\u001b[0m\u001b[1;32m 34\u001b[0m \u001b[0mmethod_type\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcancer_stage_method_type\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 35\u001b[0m )\n", + "\u001b[0;32m~/.local/share/virtualenvs/example-data-8chtNU61/lib/python3.8/site-packages/crdch_model.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, id, category, focus, subject, method_type, performed_by, observations, **kwargs)\u001b[0m\n", + "\u001b[0;32m~/.local/share/virtualenvs/example-data-8chtNU61/lib/python3.8/site-packages/crdch_model.py\u001b[0m in \u001b[0;36m__post_init__\u001b[0;34m(self, *_, **kwargs)\u001b[0m\n\u001b[1;32m 436\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 437\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 438\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mv\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mv\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mCodeableConcept\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0mCodeableConcept\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mas_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mv\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mv\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 439\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 440\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mperformed_by\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mperformed_by\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mOrganization\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m~/.local/share/virtualenvs/example-data-8chtNU61/lib/python3.8/site-packages/crdch_model.py\u001b[0m in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 436\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 437\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 438\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mv\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mv\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mCodeableConcept\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0mCodeableConcept\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mas_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mv\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mv\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmethod_type\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 439\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 440\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mperformed_by\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mperformed_by\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mOrganization\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mTypeError\u001b[0m: type object argument after ** must be a mapping, not str" + ] + } + ], "source": [ "def create_stage_observation(type, value):\n", " \"\"\" Create a CCDHCancerStageObservation from a type of observation and a codeable concept.\"\"\"\n", @@ -846,91 +1589,24 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "id": "14d23f3f", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "observations:\n", - "- observation_type:\n", - " text: Overall\n", - " description: The overall stage of the disease\n", - " valueCodeableConcept:\n", - " text: Stage IVC\n", - " description: Stage IVC\n", - "- observation_type:\n", - " text: Clinical Overall\n", - " description: The overall stage of the disease; clinical stage is determined from\n", - " evidence acquired before treatment (including clinical examination, imaging,\n", - " endoscopy, biopsy, surgical exploration)\n", - " valueCodeableConcept:\n", - " text: Stage IVC\n", - " description: Stage IVC\n", - "- observation_type:\n", - " text: Clinical Tumor (T)\n", - " description: T classifies the size or direct extent of the primary tumor; clinical\n", - " stage is determined from evidence acquired before treatment (including clinical\n", - " examination, imaging, endoscopy, biopsy, surgical exploration)\n", - " valueCodeableConcept:\n", - " text: T3\n", - " description: T3 Stage Finding\n", - "- observation_type:\n", - " text: Clinical Node (N)\n", - " description: N classifies the degree of spread to regional lymph nodes; clinical\n", - " stage is determined from evidence acquired before treatment (including clinical\n", - " examination, imaging, endoscopy, biopsy, surgical exploration)\n", - " valueCodeableConcept:\n", - " text: N1\n", - " description: N1 Stage Finding\n", - "- observation_type:\n", - " text: Clinical Metastasis (M)\n", - " description: M classifies the presence of distant metastasis; clinical stage is\n", - " determined from evidence acquired before treatment (including clinical examination,\n", - " imaging, endoscopy, biopsy, surgical exploration)\n", - " valueCodeableConcept:\n", - " text: M1\n", - " description: M1 Stage Finding\n", - "- observation_type:\n", - " text: Pathological Overall\n", - " description: The overall stage of the disease; stage given by histopathologic\n", - " examination of a surgical specimen\n", - " valueCodeableConcept:\n", - " text: Stage IVC\n", - " description: Stage IVC\n", - "- observation_type:\n", - " text: Pathological Tumor (T)\n", - " description: T classifies the size or direct extent of the primary tumor; stage\n", - " given by histopathologic examination of a surgical specimen\n", - " valueCodeableConcept:\n", - " text: T3\n", - " description: T3 Stage Finding\n", - "- observation_type:\n", - " text: Pathological Node (N)\n", - " description: N classifies the degree of spread to regional lymph nodes; stage\n", - " given by histopathologic examination of a surgical specimen\n", - " valueCodeableConcept:\n", - " text: N1\n", - " description: N1 Stage Finding\n", - "- observation_type:\n", - " text: Pathological Metastasis (M)\n", - " description: M classifies the presence of distant metastasis; stage given by histopathologic\n", - " examination of a surgical specimen\n", - " valueCodeableConcept:\n", - " text: M1\n", - " description: M1 Stage Finding\n", - "\n" - ] - } - ], + "outputs": [], "source": [ "from linkml_runtime.dumpers import yaml_dumper\n", "\n", "print(yaml_dumper.dumps(example_observation_set))" ] }, + { + "cell_type": "markdown", + "id": "adfafac7", + "metadata": {}, + "source": [ + "## Trying to replicate up to this ^ point today" + ] + }, { "cell_type": "markdown", "id": "7d65dc11", @@ -941,21 +1617,10 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "id": "d5e41d21", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "Specimen(id='69a89590-eb61-41d5-b33e-e7bc5adb92bf', identifier=[], description=None, specimen_type=None, analyte_type=None, associated_project=None, data_provider=None, source_material_type='Solid Tissue Normal', parent_specimen=[], source_subject=None, tumor_status_at_collection=None, creation_activity=SpecimenCreationActivity(activity_type=None, date_started=None, date_ended=TimePoint(id=None, dateTime=None, indexTimePoint=None, offsetFromIndex=None, eventType=[]), performed_by=None, collection_method_type=None, derivation_method_type=None, additive=[], collection_site=None, quantity_collected=None, execution_time_observation=[], execution_condition_observation=[], specimen_order=None), processing_activity=[], storage_activity=[], transport_activity=[], contained_in=None, dimensional_measures=None, quantity_measure=[], quality_measure=[], cellular_composition_type=None, histological_composition_measures=[], general_tissue_morphology='Not Reported', specific_tissue_morphology=None, preinvasive_tissue_morphology=None, morphology_pathologically_confirmed=None, morphology_assessor_role=None, morphlogy_assessment_method=None, degree_of_dysplasia=None, dysplasia_fraction=None, related_document=[], section_location=None, derived_product=[], distance_from_paired_specimen=None)" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "def transform_sample_to_specimen(sample):\n", " \"\"\"\n", @@ -988,112 +1653,10 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "id": "bf62937c", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "id: 9e30aa6c-91e6-5dd3-9512-75c162a89913\n", - "identifier:\n", - "- value: TCGA-QK-A8Z8_diagnosis\n", - " system: GDC-submitter-id\n", - "year_at_diagnosis: 2013\n", - "condition:\n", - " text: Squamous cell carcinoma, NOS\n", - "metastatic_site:\n", - "- site:\n", - " text: Larynx\n", - " description: Larynx\n", - "stage:\n", - "- observations:\n", - " - observation_type:\n", - " text: Overall\n", - " description: The overall stage of the disease\n", - " valueCodeableConcept:\n", - " text: Stage IVC\n", - " description: Stage IVC\n", - " - observation_type:\n", - " text: Clinical Overall\n", - " description: The overall stage of the disease; clinical stage is determined\n", - " from evidence acquired before treatment (including clinical examination, imaging,\n", - " endoscopy, biopsy, surgical exploration)\n", - " valueCodeableConcept:\n", - " text: Stage IVC\n", - " description: Stage IVC\n", - " - observation_type:\n", - " text: Clinical Tumor (T)\n", - " description: T classifies the size or direct extent of the primary tumor; clinical\n", - " stage is determined from evidence acquired before treatment (including clinical\n", - " examination, imaging, endoscopy, biopsy, surgical exploration)\n", - " valueCodeableConcept:\n", - " text: T3\n", - " description: T3 Stage Finding\n", - " - observation_type:\n", - " text: Clinical Node (N)\n", - " description: N classifies the degree of spread to regional lymph nodes; clinical\n", - " stage is determined from evidence acquired before treatment (including clinical\n", - " examination, imaging, endoscopy, biopsy, surgical exploration)\n", - " valueCodeableConcept:\n", - " text: N1\n", - " description: N1 Stage Finding\n", - " - observation_type:\n", - " text: Clinical Metastasis (M)\n", - " description: M classifies the presence of distant metastasis; clinical stage\n", - " is determined from evidence acquired before treatment (including clinical\n", - " examination, imaging, endoscopy, biopsy, surgical exploration)\n", - " valueCodeableConcept:\n", - " text: M1\n", - " description: M1 Stage Finding\n", - " - observation_type:\n", - " text: Pathological Overall\n", - " description: The overall stage of the disease; stage given by histopathologic\n", - " examination of a surgical specimen\n", - " valueCodeableConcept:\n", - " text: Stage IVC\n", - " description: Stage IVC\n", - " - observation_type:\n", - " text: Pathological Tumor (T)\n", - " description: T classifies the size or direct extent of the primary tumor; stage\n", - " given by histopathologic examination of a surgical specimen\n", - " valueCodeableConcept:\n", - " text: T3\n", - " description: T3 Stage Finding\n", - " - observation_type:\n", - " text: Pathological Node (N)\n", - " description: N classifies the degree of spread to regional lymph nodes; stage\n", - " given by histopathologic examination of a surgical specimen\n", - " valueCodeableConcept:\n", - " text: N1\n", - " description: N1 Stage Finding\n", - " - observation_type:\n", - " text: Pathological Metastasis (M)\n", - " description: M classifies the presence of distant metastasis; stage given by\n", - " histopathologic examination of a surgical specimen\n", - " valueCodeableConcept:\n", - " text: M1\n", - " description: M1 Stage Finding\n", - "morphology:\n", - " text: 8070/3\n", - "related_specimen:\n", - "- id: a118da56-784d-4b67-aade-d9a7a8b49f18\n", - " source_material_type: Primary Tumor\n", - " general_tissue_morphology: Not Reported\n", - "- id: cff6967e-e8f7-4a25-aa31-9328e4b42816\n", - " source_material_type: Primary Tumor\n", - " creation_activity:\n", - " date_ended:\n", - " dateTime: '2018-05-17T12:19:46.292188-05:00'\n", - " general_tissue_morphology: Not Reported\n", - "- id: 1efb2d28-ac51-4d70-a24d-667a2b53467a\n", - " source_material_type: Blood Derived Normal\n", - " general_tissue_morphology: Not Reported\n", - "\n" - ] - } - ], + "outputs": [], "source": [ "def transform_diagnosis(diagnosis, case):\n", " ccdh_diagnosis = ccdh.Diagnosis(\n", @@ -1139,816 +1702,12 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "id": "c9d31519", "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"id\": \"9e30aa6c-91e6-5dd3-9512-75c162a89913\",\n", - " \"identifier\": [\n", - " {\n", - " \"value\": \"TCGA-QK-A8Z8_diagnosis\",\n", - " \"system\": \"GDC-submitter-id\"\n", - " }\n", - " ],\n", - " \"year_at_diagnosis\": 2013,\n", - " \"condition\": {\n", - " \"text\": \"Squamous cell carcinoma, NOS\"\n", - " },\n", - " \"metastatic_site\": [\n", - " {\n", - " \"site\": {\n", - " \"text\": \"Larynx\",\n", - " \"description\": \"Larynx\"\n", - " }\n", - " }\n", - " ],\n", - " \"stage\": [\n", - " {\n", - " \"observations\": [\n", - " {\n", - " \"observation_type\": {\n", - " \"text\": \"Overall\",\n", - " \"description\": \"The overall stage of the disease\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"text\": \"Stage IVC\",\n", - " \"description\": \"Stage IVC\"\n", - " }\n", - " },\n", - " {\n", - " \"observation_type\": {\n", - " \"text\": \"Clinical Overall\",\n", - " \"description\": \"The overall stage of the disease; clinical stage is determined from evidence acquired before treatment (including clinical examination, imaging, endoscopy, biopsy, surgical exploration)\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"text\": \"Stage IVC\",\n", - " \"description\": \"Stage IVC\"\n", - " }\n", - " },\n", - " {\n", - " \"observation_type\": {\n", - " \"text\": \"Clinical Tumor (T)\",\n", - " \"description\": \"T classifies the size or direct extent of the primary tumor; clinical stage is determined from evidence acquired before treatment (including clinical examination, imaging, endoscopy, biopsy, surgical exploration)\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"text\": \"T3\",\n", - " \"description\": \"T3 Stage Finding\"\n", - " }\n", - " },\n", - " {\n", - " \"observation_type\": {\n", - " \"text\": \"Clinical Node (N)\",\n", - " \"description\": \"N classifies the degree of spread to regional lymph nodes; clinical stage is determined from evidence acquired before treatment (including clinical examination, imaging, endoscopy, biopsy, surgical exploration)\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"text\": \"N1\",\n", - " \"description\": \"N1 Stage Finding\"\n", - " }\n", - " },\n", - " {\n", - " \"observation_type\": {\n", - " \"text\": \"Clinical Metastasis (M)\",\n", - " \"description\": \"M classifies the presence of distant metastasis; clinical stage is determined from evidence acquired before treatment (including clinical examination, imaging, endoscopy, biopsy, surgical exploration)\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"text\": \"M1\",\n", - " \"description\": \"M1 Stage Finding\"\n", - " }\n", - " },\n", - " {\n", - " \"observation_type\": {\n", - " \"text\": \"Pathological Overall\",\n", - " \"description\": \"The overall stage of the disease; stage given by histopathologic examination of a surgical specimen\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"text\": \"Stage IVC\",\n", - " \"description\": \"Stage IVC\"\n", - " }\n", - " },\n", - " {\n", - " \"observation_type\": {\n", - " \"text\": \"Pathological Tumor (T)\",\n", - " \"description\": \"T classifies the size or direct extent of the primary tumor; stage given by histopathologic examination of a surgical specimen\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"text\": \"T3\",\n", - " \"description\": \"T3 Stage Finding\"\n", - " }\n", - " },\n", - " {\n", - " \"observation_type\": {\n", - " \"text\": \"Pathological Node (N)\",\n", - " \"description\": \"N classifies the degree of spread to regional lymph nodes; stage given by histopathologic examination of a surgical specimen\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"text\": \"N1\",\n", - " \"description\": \"N1 Stage Finding\"\n", - " }\n", - " },\n", - " {\n", - " \"observation_type\": {\n", - " \"text\": \"Pathological Metastasis (M)\",\n", - " \"description\": \"M classifies the presence of distant metastasis; stage given by histopathologic examination of a surgical specimen\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"text\": \"M1\",\n", - " \"description\": \"M1 Stage Finding\"\n", - " }\n", - " }\n", - " ]\n", - " }\n", - " ],\n", - " \"morphology\": {\n", - " \"text\": \"8070/3\"\n", - " },\n", - " \"related_specimen\": [\n", - " {\n", - " \"id\": \"a118da56-784d-4b67-aade-d9a7a8b49f18\",\n", - " \"source_material_type\": \"Primary Tumor\",\n", - " \"general_tissue_morphology\": \"Not Reported\"\n", - " },\n", - " {\n", - " \"id\": \"cff6967e-e8f7-4a25-aa31-9328e4b42816\",\n", - " \"source_material_type\": \"Primary Tumor\",\n", - " \"creation_activity\": {\n", - " \"date_ended\": {\n", - " \"dateTime\": \"2018-05-17T12:19:46.292188-05:00\"\n", - " }\n", - " },\n", - " \"general_tissue_morphology\": \"Not Reported\"\n", - " },\n", - " {\n", - " \"id\": \"1efb2d28-ac51-4d70-a24d-667a2b53467a\",\n", - " \"source_material_type\": \"Blood Derived Normal\",\n", - " \"general_tissue_morphology\": \"Not Reported\"\n", - " }\n", - " ],\n", - " \"@type\": \"Diagnosis\",\n", - " \"@context\": {\n", - " \"GDC\": \"http://example.org/gdc/\",\n", - " \"HTAN\": \"http://example.org/htan/\",\n", - " \"ICDC\": \"http://example.org/icdc/\",\n", - " \"NCIT\": {\n", - " \"@id\": \"http://purl.obolibrary.org/obo/NCIT_\",\n", - " \"@prefix\": true\n", - " },\n", - " \"PDC\": \"http://example.org/pdc/\",\n", - " \"ccdh\": \"https://example.org/ccdh/\",\n", - " \"linkml\": \"https://w3id.org/linkml/\",\n", - " \"skos\": \"http://www.w3.org/2004/02/skos/core#\",\n", - " \"@vocab\": \"https://example.org/ccdh/\",\n", - " \"category\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"focus\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"method_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"observation_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"performed_by\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"subject\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"valueCodeableConcept\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"valueInteger\": {\n", - " \"@type\": \"xsd:integer\"\n", - " },\n", - " \"identifier\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"passage_number\": {\n", - " \"@type\": \"xsd:integer\"\n", - " },\n", - " \"product_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"qualifier\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"site\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"observations\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"valueEntity\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"coding\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"age_at_diagnosis\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"condition\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"disease_status\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"grade\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"metastatic_site\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"method_of_diagnosis\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"morphology\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"primary_site\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"primary_tumor_dimensional_measures\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"prior_diagnosis\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"related_specimen\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"stage\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"supporting_observation\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"year_at_diagnosis\": {\n", - " \"@type\": \"xsd:integer\"\n", - " },\n", - " \"valueQuantity\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"document_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"alcohol_exposure\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"environmental_exposure\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"tobacco_exposure\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"valueBoolean\": {\n", - " \"@type\": \"xsd:boolean\"\n", - " },\n", - " \"valueDateTime\": {\n", - " \"@type\": \"xsd:dateTime\"\n", - " },\n", - " \"valueDecimal\": {\n", - " \"@type\": \"xsd:decimal\"\n", - " },\n", - " \"unit\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"associated_timepoint\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"date_ended\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"date_started\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"part_of\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"primary_anatomic_site\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"research_project_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"age_at_enrollment\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"associated_subject\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"comorbid_diagnosis\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"index_timepoint\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"member_of_research_project\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"originating_site\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"primary_diagnosis\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"primary_diagnosis_condition\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"primary_diagnosis_site\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"analyte_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"associated_project\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"cellular_composition_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"contained_in\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"creation_activity\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"data_provider\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"degree_of_dysplasia\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"derived_product\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"dimensional_measures\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"distance_from_paired_specimen\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"general_tissue_morphology\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"histological_composition_measures\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"morphlogy_assessment_method\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"morphology_assessor_role\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"morphology_pathologically_confirmed\": {\n", - " \"@type\": \"xsd:boolean\"\n", - " },\n", - " \"parent_specimen\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"preinvasive_tissue_morphology\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"processing_activity\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"quality_measure\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"quantity_measure\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"related_document\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"section_location\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"source_material_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"source_subject\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"specific_tissue_morphology\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"specimen_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"storage_activity\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"transport_activity\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"tumor_status_at_collection\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"additive\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"container_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"parent_container\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"activity_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"collection_method_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"collection_site\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"derivation_method_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"execution_condition_observation\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"execution_time_observation\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"quantity_collected\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"specimen_order\": {\n", - " \"@type\": \"xsd:integer\"\n", - " },\n", - " \"duration\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"container\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"transport_destination\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"transport_origin\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"age_at_death\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"breed\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"cause_of_death\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"ethnicity\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"race\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"sex\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"species\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"vital_status\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"year_of_birth\": {\n", - " \"@type\": \"xsd:integer\"\n", - " },\n", - " \"year_of_death\": {\n", - " \"@type\": \"xsd:integer\"\n", - " },\n", - " \"role\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"substance_quantity\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"substance_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"periodEnd_end\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"periodStart_start\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"dateTime\": {\n", - " \"@type\": \"xsd:dateTime\"\n", - " },\n", - " \"eventType\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"indexTimePoint\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"offsetFromIndex\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"concurrent_treatment\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"number_of_cycles\": {\n", - " \"@type\": \"xsd:integer\"\n", - " },\n", - " \"regimen\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"therapeutic_agent\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"treatment_anatomic_site\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"treatment_effect\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"treatment_end_reason\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"treatment_for_diagnosis\": {\n", - " \"@type\": \"@id\"\n", - " },\n", - " \"treatment_frequency\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"treatment_intent\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"treatment_outcome\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " },\n", - " \"treatment_type\": {\n", - " \"@context\": {\n", - " \"@vocab\": \"@null\",\n", - " \"text\": \"skos:notation\",\n", - " \"description\": \"skos:prefLabel\",\n", - " \"meaning\": \"@id\"\n", - " }\n", - " }\n", - " }\n", - "}\n" - ] - } - ], + "outputs": [], "source": [ "from linkml.generators.jsonldcontextgen import ContextGenerator\n", "from linkml_runtime.dumpers import json_dumper\n", @@ -1970,7 +1729,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "id": "1aa40681", "metadata": {}, "outputs": [], @@ -2002,34 +1761,10 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "id": "3300fabd", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "@prefix : .\n", - "@prefix ccdh: .\n", - "\n", - "[] ccdh:condition [ ccdh:text \"Squamous cell carcinoma, NOS\" ] ;\n", - " ccdh:id \"4dbbefaa-8e8e-4a44-943b-48687f123673\" ;\n", - " ccdh:identifier [ ccdh:system \"GDC-submitter-id\" ;\n", - " ccdh:value \"GENIE-MSK-P-0010088-T01-IM5_diagnosis\" ] ;\n", - " ccdh:metastatic_site [ ccdh:site [ ccdh:description \"Oropharynx\" ;\n", - " ccdh:text \"Oropharynx\" ] ] ;\n", - " ccdh:morphology [ ccdh:text \"8070/3\" ] ;\n", - " ccdh:related_specimen [ ccdh:creation_activity [ ccdh:date_ended [ ccdh:dateTime \"2018-10-03T04:13:38.880466-05:00\"^^ ] ] ;\n", - " ccdh:general_tissue_morphology \"Not Reported\" ;\n", - " ccdh:id \"b5da1115-1fe3-49a4-892b-ef43e64dbee4\" ;\n", - " ccdh:source_material_type \"Metastatic\" ] ;\n", - " ccdh:stage [ ccdh:observations [ ccdh:observation_type [ ccdh:description \"The overall stage of the disease\" ;\n", - " ccdh:text \"Overall\" ] ;\n", - " ccdh:\n" - ] - } - ], + "outputs": [], "source": [ "# We can read this JSON-LD in Turtle.\n", "from rdflib import Graph\n", @@ -2041,6 +1776,96 @@ "with open('head-and-mouth/diagnoses.ttl', 'w') as file:\n", " file.write(rdfAsTurtle)" ] + }, + { + "cell_type": "markdown", + "id": "372dbf27", + "metadata": {}, + "source": [ + "---" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f7a21993", + "metadata": {}, + "outputs": [], + "source": [ + "# maybe not that helpful\n", + "# ccdh.BodySite.__dict__\n", + "# see also https://cancerdhc.github.io/ccdhmodel/v1.1/BodySite/\n", + "# takes a CodeableConcept in the mandatory site and optional qualifier 0 slots\n", + "# CodeableConcept takes the following slots\n", + "# \n", + "# coding 0..*\n", + "# Description: A reference to a code defined by a terminology system\n", + "# Range: Coding\n", + "# text 0..1\n", + "# Description: A human language representation of the concept represented by the Coding.\n", + "# Range: CrdchString\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "add2ee49", + "metadata": {}, + "outputs": [], + "source": [ + "uberon_larynx_coding = ccdh.Coding(code=\"UBERON:0001737\", system=\"http://purl.obolibrary.org/obo/uberon.owl\")\n", + "uberon_larynx_coding" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f1711256", + "metadata": {}, + "outputs": [], + "source": [ + "uberon_larynx__cc = ccdh.CodeableConcept(coding=[test_coding])\n", + "uberon_larynx__cc" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e8898458", + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "uberon_larynx_bs = ccdh.BodySite(site=test_cc)\n", + "uberon_larynx_bs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4bf85ea1", + "metadata": {}, + "outputs": [], + "source": [ + "ccdh.CodeableConcept(\n", + " coding=[\n", + " ccdh.Coding(\n", + " code=\"UBERON:0001737\",\n", + " system=\"http://purl.obolibrary.org/obo/uberon.owl\",\n", + " label=\"larynx\",\n", + " )\n", + " ]\n", + ")\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a5f085c6", + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { @@ -2059,7 +1884,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.6" + "version": "3.8.10" } }, "nbformat": 4, diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..9d0c7d0 --- /dev/null +++ b/Makefile @@ -0,0 +1,17 @@ +.PHONY: all clean instantiate + +all: clean gen_diag_with_stage_obs_set.yaml instantiate + +clean: + rm -rf gen_diag_with_stage_obs_set.yaml + rm -rf Pipfile.lock + pipenv --rm + pipenv install + pipenv run pip list + +gen_diag_with_stage_obs_set.yaml: gen_diag_with_stage_obs_set.py + pipenv run python $< + cat $@ + +instantiate: instantiate_diag_with_stage_obs_set.py + pipenv run python $< diff --git a/Pipfile b/Pipfile index a32e02f..16c6c16 100644 --- a/Pipfile +++ b/Pipfile @@ -13,4 +13,7 @@ pip = "*" crdch-model = "*" pandas = "*" +# conflicts? +# black = "*" + [dev-packages] diff --git a/Pipfile.lock b/Pipfile.lock index 7a24b85..9d6625e 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -23,9 +23,17 @@ }, "antlr4-python3-runtime": { "hashes": [ - "sha256:31f5abdc7faf16a1a6e9bf2eb31565d004359b821b09944436a34361929ae85a" + "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b" ], - "version": "==4.9.2" + "version": "==4.9.3" + }, + "appnope": { + "hashes": [ + "sha256:93aa393e9d6c54c5cd570ccadd8edad61ea0c4b9ea7a01409020c9aa019eb442", + "sha256:dd83cd4b5b460958838f6eb3000c660b1f9caf2a5b1de4264e941512f603258a" + ], + "markers": "platform_system == 'Darwin'", + "version": "==0.1.2" }, "argon2-cffi": { "hashes": [ @@ -41,6 +49,7 @@ "sha256:f710b61103d1a1f692ca3ecbd1373e28aa5e545ac625ba067ff2feca1b2bb870", "sha256:fa7e7d1fc22514a32b1761fdfa1882b6baa5c36bb3ef557bdd69e6fc9ba14a41" ], + "markers": "python_version >= '3.5'", "version": "==21.1.0" }, "argparse": { @@ -55,6 +64,7 @@ "sha256:149e90d6d8ac20db7a955ad60cf0e6881a3f20d37096140088356da6c716b0b1", "sha256:ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb" ], + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'", "version": "==21.2.0" }, "babel": { @@ -62,6 +72,7 @@ "sha256:ab49e12b91d937cd11f0b67cb259a57ab4ad2b59ac7a3b41d6c06c0ac5b0def9", "sha256:bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0" ], + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==2.9.1" }, "backcall": { @@ -76,6 +87,7 @@ "sha256:0900d8b37eba61a802ee40ac0061f8c2b5dee29c1927dd1d233e075ebf5a71da", "sha256:4d2651ab93271d1129ac9cbc679f524565cc8a1b791909c4a51eac4446a15994" ], + "markers": "python_version >= '3.6'", "version": "==4.1.0" }, "cachetools": { @@ -83,64 +95,70 @@ "sha256:89ea6f1b638d5a73a4f9226be57ac5e4f399d22770b92355f92dcb0f7f001693", "sha256:92971d3cb7d2a97efff7c7bb1657f21a8f5fb309a37530537c71b1774189f2d1" ], + "markers": "python_version ~= '3.5'", "version": "==4.2.4" }, "certifi": { "hashes": [ - "sha256:2bbf76fd432960138b3ef6dda3dde0544f27cbf8546c458e60baf371917ba9ee", - "sha256:50b1e4f8446b06f41be7dd6338db18e0990601dce795c2b1686458aa7e8fa7d8" + "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872", + 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--git a/gen_diag_with_stage_obs_set.py b/gen_diag_with_stage_obs_set.py new file mode 100644 index 0000000..863dcb9 --- /dev/null +++ b/gen_diag_with_stage_obs_set.py @@ -0,0 +1,31 @@ +import crdch_model as cm +from linkml_runtime.dumpers import yaml_dumper + +ncit_sys_url = "http://ncithesaurus.nci.nih.gov/" +harmonized_tag = "harmonized" +diagnosis_fn = "gen_diag_with_stage_obs_set.yaml" + +stage_obs_set = cm.CancerStageObservationSet() + +obs_type_coding = cm.Coding(code="C25605", system=ncit_sys_url, label="Overall") +obs_type_coding.tag.append(harmonized_tag) +obs_type_cc = cm.CodeableConcept(coding=obs_type_coding) + +stage_value_coding = cm.Coding(code="C96258", system=ncit_sys_url, label="FIGO Stage IIIC") +stage_value_coding.tag.append(harmonized_tag) +stage_value_cc = cm.CodeableConcept(coding=stage_value_coding) + +stage_obs = cm.CancerStageObservation(id=1, observation_type=obs_type_cc, value_codeable_concept=stage_value_cc) + +stage_obs_set.observations.append(stage_obs) + +meth_type_coding = cm.Coding(code="C125738", system=ncit_sys_url, label="FIGO Stage") +meth_type_coding.tag.append(harmonized_tag) +meth_type_cc = cm.CodeableConcept(coding=meth_type_coding) + +stage_obs_set.method_type.append(meth_type_cc) + +diag = cm.Diagnosis(id=1) +diag.stage.append(stage_obs_set) + +yaml_dumper.dump(diag, to_file=diagnosis_fn) diff --git a/instantiate_diag_with_stage_obs_set.py b/instantiate_diag_with_stage_obs_set.py new file mode 100644 index 0000000..a6febaf --- /dev/null +++ b/instantiate_diag_with_stage_obs_set.py @@ -0,0 +1,8 @@ +from crdch_model import Diagnosis +from linkml_runtime.loaders import yaml_loader + +diagnosis_fn = "gen_diag_with_stage_obs_set.yaml" + +diag = yaml_loader.load(diagnosis_fn, Diagnosis) + +print(diag) diff --git a/linkml_linkml_issue_463_test.py b/linkml_linkml_issue_463_test.py new file mode 100644 index 0000000..a27e863 --- /dev/null +++ b/linkml_linkml_issue_463_test.py @@ -0,0 +1,32 @@ +from crdch_model import Coding, CodeableConcept, CancerStageObservation, CancerStageObservationSet +from linkml_runtime.loaders import yaml_loader + +Coding_fn = "linkml_linkml_issue_463_test_data/Coding.yaml" +CodeableConcept_fn = "linkml_linkml_issue_463_test_data/CodeableConcept.yaml" +CancerStageObservation_fn = "linkml_linkml_issue_463_test_data/CancerStageObservation.yaml" +CancerStageObservationSet_fn = "linkml_linkml_issue_463_test_data/CancerStageObservationSet.yaml" + + +def load_and_type(fn, expected_type): + obj = None + try: + obj = yaml_loader.load(fn, expected_type) + except Exception: + print(f"Exception on loading {fn} vs crdch_model") + assert isinstance(obj, expected_type) + + +def test_Coding(): + load_and_type(Coding_fn, Coding) + + +def test_CodeableConcept(): + load_and_type(CodeableConcept_fn, CodeableConcept) + + +def test_CancerStageObservation(): + load_and_type(CancerStageObservation_fn, CancerStageObservation) + + +def test_CancerStageObservationSet(): + load_and_type(CancerStageObservationSet_fn, CancerStageObservationSet) diff --git a/linkml_linkml_issue_463_test_data/CancerStageObservation.yaml b/linkml_linkml_issue_463_test_data/CancerStageObservation.yaml new file mode 100644 index 0000000..190242f --- /dev/null +++ b/linkml_linkml_issue_463_test_data/CancerStageObservation.yaml @@ -0,0 +1,13 @@ +id: 1 +observation_type: + coding: + - code: 'abc1' + system: 'xxx' + - code: 'abc2' + system: 'xxx' +value_codeable_concept: + coding: + - code: 'abc1' + system: 'xxx' + - code: 'abc2' + system: 'xxx' diff --git a/linkml_linkml_issue_463_test_data/CancerStageObservationSet.yaml b/linkml_linkml_issue_463_test_data/CancerStageObservationSet.yaml new file mode 100644 index 0000000..8039600 --- /dev/null +++ b/linkml_linkml_issue_463_test_data/CancerStageObservationSet.yaml @@ -0,0 +1,28 @@ +id: '1' +observations: +- observation_type: + coding: + - code: abc1 + system: xxx + - code: abc2 + system: xxx + value_codeable_concept: + coding: + - code: abc1 + system: xxx + - code: abc2 + system: xxx + id: '1' +- observation_type: + coding: + - code: abc1 + system: xxx + - code: abc2 + system: xxx + value_codeable_concept: + coding: + - code: abc1 + system: xxx + - code: abc2 + system: xxx + id: '2' diff --git a/linkml_linkml_issue_463_test_data/CodeableConcept.yaml b/linkml_linkml_issue_463_test_data/CodeableConcept.yaml new file mode 100644 index 0000000..46b137c --- /dev/null +++ b/linkml_linkml_issue_463_test_data/CodeableConcept.yaml @@ -0,0 +1,5 @@ +coding: + - code: 'abc1' + system: 'xxx' + - code: 'abc2' + system: 'xxx' \ No newline at end of file diff --git a/linkml_linkml_issue_463_test_data/Coding.yaml b/linkml_linkml_issue_463_test_data/Coding.yaml new file mode 100644 index 0000000..520c448 --- /dev/null +++ b/linkml_linkml_issue_463_test_data/Coding.yaml @@ -0,0 +1,2 @@ +code: 'abc' +system: 'xxx' diff --git a/tobacco_expo.py b/tobacco_expo.py new file mode 100644 index 0000000..b7c1201 --- /dev/null +++ b/tobacco_expo.py @@ -0,0 +1,17 @@ +import crdch_model as cm +from linkml_runtime.dumpers import yaml_dumper +from linkml_runtime.loaders import yaml_loader + +obs_type_coding = cm.Coding(code="123", system="http://example.com/system") +obs_type_cc = cm.CodeableConcept(coding=obs_type_coding) +tobacco_expo = cm.TobaccoExposureObservation(observation_type=obs_type_cc) + +print(tobacco_expo) + +tobacco_expo_file = "tobacco_expo.yaml" + +yaml_dumper.dump(tobacco_expo, to_file=tobacco_expo_file) + +instantiated = yaml_loader.load(tobacco_expo_file, cm.TobaccoExposureObservation) + +print(instantiated) diff --git a/via_terminology_server.ipynb b/via_terminology_server.ipynb new file mode 100644 index 0000000..6a17d14 --- /dev/null +++ b/via_terminology_server.ipynb @@ -0,0 +1,580 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "f0aa79f9", + "metadata": {}, + "outputs": [], + "source": [ + "import requests\n", + "import pandas as pd\n", + "import json\n", + "import crdch_model as ccdh\n", + "from linkml_runtime.dumpers import yaml_dumper" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "74625ec4", + "metadata": {}, + "outputs": [], + "source": [ + "with open('head-and-mouth/gdc-head-and-mouth.json') as file:\n", + " gdc_head_and_mouth = json.load(file)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "ae7fb14c", + "metadata": {}, + "outputs": [], + "source": [ + "suggested_row_num = 131\n", + "suggested_diag_num = 0\n", + "suggested_row = gdc_head_and_mouth[suggested_row_num]\n", + "# suggested_row" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "536f4e1f", + "metadata": {}, + "outputs": [], + "source": [ + "suggested_diagnosis_dict = suggested_row[\"diagnoses\"][suggested_diag_num]\n", + "# suggested_diagnosis_dict" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "cae20189", + "metadata": {}, + "outputs": [], + "source": [ + "# derrived from Gaurav's code\n", + "# how to DISCOVER?\n", + "# close_mappings ?\n", + "# how to convert these legacy CRDC-H strings to codable concepts?\n", + "gdc_to_crdch_csoot_dict = [\n", + " {\"GDC\": \"ajcc_clinical_m\", \"CRDC-H\": \"Clinical Metastasis (M)\"},\n", + " {\"GDC\": \"ajcc_clinical_n\", \"CRDC-H\": \"Clinical Node (N)\"},\n", + " {\"GDC\": \"ajcc_clinical_stage\", \"CRDC-H\": \"Clinical Overall\"},\n", + " {\"GDC\": \"ajcc_clinical_t\", \"CRDC-H\": \"Clinical Tumor (T)\"},\n", + " {\"GDC\": \"tumor_stage\", \"CRDC-H\": \"Overall\"},\n", + " {\"GDC\": \"ajcc_pathologic_m\", \"CRDC-H\": \"Pathological Metastasis (M)\"},\n", + " {\"GDC\": \"ajcc_pathologic_n\", \"CRDC-H\": \"Pathological Node (N)\"},\n", + " {\"GDC\": \"ajcc_pathologic_stage\", \"CRDC-H\": \"Pathological Overall\"},\n", + " {\"GDC\": \"ajcc_pathologic_t\", \"CRDC-H\": \"Pathological Tumor (T)\"},\n", + " {\"GDC\": \"age_at_diagnosis\", \"CRDC-H\": None},\n", + " {\"GDC\": \"ajcc_staging_system_edition\", \"CRDC-H\": None},\n", + " {\"GDC\": \"classification_of_tumor\", \"CRDC-H\": None},\n", + " {\"GDC\": \"created_datetime\", \"CRDC-H\": None},\n", + " {\"GDC\": \"days_to_diagnosis\", \"CRDC-H\": None},\n", + " {\"GDC\": \"days_to_last_follow_up\", \"CRDC-H\": None},\n", + " {\"GDC\": \"days_to_last_known_disease_status\", \"CRDC-H\": None},\n", + " {\"GDC\": \"days_to_recurrence\", \"CRDC-H\": None},\n", + " {\"GDC\": \"diagnosis_id\", \"CRDC-H\": None},\n", + " {\"GDC\": \"icd_10_code\", \"CRDC-H\": None},\n", + " {\"GDC\": \"last_known_disease_status\", \"CRDC-H\": None},\n", + " {\"GDC\": \"morphology\", \"CRDC-H\": None},\n", + " {\"GDC\": \"primary_diagnosis\", \"CRDC-H\": None},\n", + " {\"GDC\": \"prior_malignancy\", \"CRDC-H\": None},\n", + " {\"GDC\": \"prior_treatment\", \"CRDC-H\": None},\n", + " {\"GDC\": \"progression_or_recurrence\", \"CRDC-H\": None},\n", + " {\"GDC\": \"site_of_resection_or_biopsy\", \"CRDC-H\": None},\n", + " {\"GDC\": \"state\", \"CRDC-H\": None},\n", + " {\"GDC\": \"submitter_id\", \"CRDC-H\": None},\n", + " {\"GDC\": \"synchronous_malignancy\", \"CRDC-H\": None},\n", + " {\"GDC\": \"tissue_or_organ_of_origin\", \"CRDC-H\": None},\n", + " {\"GDC\": \"tumor_grade\", \"CRDC-H\": None},\n", + " {\"GDC\": \"updated_datetime\", \"CRDC-H\": None},\n", + " {\"GDC\": \"year_of_diagnosis\", \"CRDC-H\": None},\n", + "]" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "a1b0bb2d", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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GDCCRDC-H
0ajcc_clinical_mClinical Metastasis (M)
1ajcc_clinical_nClinical Node (N)
2ajcc_clinical_stageClinical Overall
3ajcc_clinical_tClinical Tumor (T)
4tumor_stageOverall
5ajcc_pathologic_mPathological Metastasis (M)
6ajcc_pathologic_nPathological Node (N)
7ajcc_pathologic_stagePathological Overall
8ajcc_pathologic_tPathological Tumor (T)
\n", + "
" + ], + "text/plain": [ + " GDC CRDC-H\n", + "0 ajcc_clinical_m Clinical Metastasis (M)\n", + "1 ajcc_clinical_n Clinical Node (N)\n", + "2 ajcc_clinical_stage Clinical Overall\n", + "3 ajcc_clinical_t Clinical Tumor (T)\n", + "4 tumor_stage Overall\n", + "5 ajcc_pathologic_m Pathological Metastasis (M)\n", + "6 ajcc_pathologic_n Pathological Node (N)\n", + "7 ajcc_pathologic_stage Pathological Overall\n", + "8 ajcc_pathologic_t Pathological Tumor (T)" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "gdc_to_crdch_csoot_frame = pd.DataFrame(gdc_to_crdch_csoot_dict)\n", + "gdc_to_crdch_csoot_frame_complete = gdc_to_crdch_csoot_frame.loc[ ~ gdc_to_crdch_csoot_frame['CRDC-H'].isnull()]\n", + "gdc_to_crdch_csoot_frame_complete" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "cb104514", + "metadata": {}, + "outputs": [], + "source": [ + "# initialize\n", + "global_mapping_table = pd.DataFrame()\n", + "\n", + "def get_mapping_table(model_name, class_name, slot_name):\n", + " global global_mapping_table\n", + " current_url = f\"https://terminology.ccdh.io/models/{model_name}/entities/{class_name}/attributes/{slot_name}/mappings\"\n", + " response = requests.get(current_url)\n", + " resp_struct = response.json()\n", + " current_mappings = pd.DataFrame(resp_struct[\"mappings\"])\n", + " global_mapping_table = global_mapping_table.append(current_mappings)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "5949bcf5", + "metadata": {}, + "outputs": [], + "source": [ + "# add suggestion to pull new content into global_mapping_table if no hits\n", + "# add required predicate handling\n", + "# add handling for len(results.index) == 0 or > 1\n", + "# add option for closest match via difflib.get_close_matches \n", + "# or something more quantitative\n", + "def get_mapping(model_name, mf, sl, required_pred=\"\"):\n", + " prefixed_mf = model_name + \".\" + mf\n", + " # print(prefixed_mf)\n", + " results = global_mapping_table.loc[\n", + " global_mapping_table['subject_match_field'].eq(prefixed_mf) &\n", + " global_mapping_table['subject_label'].eq(sl)\n", + " ]\n", + " if len(results.index) == 1:\n", + " return results.to_dict(orient=\"records\")" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "d6494aad", + "metadata": {}, + "outputs": [], + "source": [ + "global_mapping_table = pd.DataFrame()" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "9019eece", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(0, 0)\n", + "(1402, 9)\n", + "(2081, 9)\n" + ] + } + ], + "source": [ + "\n", + "print(global_mapping_table.shape)\n", + "get_mapping_table(\"CRDC-H\", \"BodySite\", \"site\")\n", + "print(global_mapping_table.shape)\n", + "get_mapping_table(\"CRDC-H\", \"CancerStageObservation\", \"valueCodeableConcept\")\n", + "print(global_mapping_table.shape)" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "4cb0009b", + "metadata": {}, + "outputs": [], + "source": [ + "# global_mapping_table" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "18f879c7", + "metadata": {}, + "outputs": [], + "source": [ + "# get_mapping(\"GDC.Case\", \"primary_site\", \"Brain\")" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "21a48c20", + "metadata": {}, + "outputs": [], + "source": [ + "# suggested_row['samples'][0]['sample_id']" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "17d589e7", + "metadata": {}, + "outputs": [], + "source": [ + "# suggested_row['primary_site']" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "31005b07", + "metadata": {}, + "outputs": [], + "source": [ + "def transform_sample_to_specimen(sample):\n", + " \"\"\"\n", + " A method for transforming a GDC Sample into CCDH Specimen.\n", + " \"\"\"\n", + "\n", + " specimen = ccdh.Specimen(id = sample.get('sample_id'))\n", + " specimen.source_material_type = sample.get('sample_type')\n", + " specimen.general_tissue_morphology = sample.get('tissue_type')\n", + " specimen.specific_tissue_morphology = sample.get('tumor_code')\n", + " specimen.tumor_status_at_collection = sample.get('tumor_descriptor')\n", + " # we don't consistentely have created_datetimes\n", + " # need to check their format too\n", + "# if 'created_datetime' in sample and sample['created_datetime'] is not None :\n", + "# specimen.creation_activity = ccdh.SpecimenCreationActivity(\n", + "# date_ended=ccdh.TimePoint(\n", + "# dateTime=sample.get('created_datetime')\n", + "# )\n", + "# )\n", + "# else:\n", + "# print(\"creation_activity not created because created_datetime absent or equals None\")\n", + " return specimen\n", + "\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "d065d4cd", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Specimen(id='a118da56-784d-4b67-aade-d9a7a8b49f18', identifier=[], description=None, specimen_type=None, analyte_type=None, associated_project=None, data_provider=None, source_material_type='Primary Tumor', parent_specimen=[], source_subject=None, tumor_status_at_collection=None, creation_activity=None, processing_activity=[], storage_activity=[], transport_activity=[], contained_in=None, dimensional_measures=None, quantity_measure=[], quality_measure=[], cellular_composition_type=None, histological_composition_measures=[], general_tissue_pathology=None, specific_tissue_pathology=None, preinvasive_tissue_morphology=None, morphology_pathologically_confirmed=None, morphology_assessor_role=None, morphology_assessment_method=None, degree_of_dysplasia=None, dysplasia_fraction=None, related_document=[], section_location=None, derived_product=[], distance_from_paired_specimen=None)" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Let's try creating a test specimen.\n", + "test_specimen = transform_sample_to_specimen(suggested_row['samples'][0])\n", + "test_specimen" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "id": "53cad32f", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Diagnosis(id=None, identifier=[], subject=None, age_at_diagnosis=Quantity(value_decimal=Decimal('123'), value_codeable_concept=None, unit=None), diagnosis_date=None, condition=None, primary_site=[], metastatic_site=[], stage=[], grade=[], morphology=None, disease_status=None, prior_diagnosis=None, method_of_diagnosis=None, related_specimen=[], primary_tumor_dimensional_measures=None, supporting_observation=[])" + ] + }, + "execution_count": 41, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ccdh.Diagnosis(age_at_diagnosis = ccdh.Quantity(value_decimal=\"123\"))" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "id": "107150ad", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{'age_at_diagnosis': 22107, 'ajcc_clinical_m': 'M1', 'ajcc_clinical_n': 'N1', 'ajcc_clinical_stage': 'Stage IVC', 'ajcc_clinical_t': 'T3', 'ajcc_pathologic_m': 'M1', 'ajcc_pathologic_n': 'N1', 'ajcc_pathologic_stage': 'Stage IVC', 'ajcc_pathologic_t': 'T3', 'ajcc_staging_system_edition': '7th', 'classification_of_tumor': 'not reported', 'created_datetime': None, 'days_to_diagnosis': 0, 'days_to_last_follow_up': None, 'days_to_last_known_disease_status': None, 'days_to_recurrence': None, 'diagnosis_id': '9e30aa6c-91e6-5dd3-9512-75c162a89913', 'icd_10_code': 'C32.9', 'last_known_disease_status': 'not reported', 'morphology': '8070/3', 'primary_diagnosis': 'Squamous cell carcinoma, NOS', 'prior_malignancy': 'no', 'prior_treatment': 'No', 'progression_or_recurrence': 'not reported', 'site_of_resection_or_biopsy': 'Larynx, NOS', 'state': 'released', 'submitter_id': 'TCGA-QK-A8Z8_diagnosis', 'synchronous_malignancy': 'No', 'tissue_or_organ_of_origin': 'Larynx, NOS', 'tumor_grade': 'not reported', 'tumor_stage': 'stage ivc', 'updated_datetime': '2019-08-08T16:48:06.888156-05:00', 'year_of_diagnosis': 2013}\n", + "primary_diagnosis = Squamous cell carcinoma, NOS\n", + "morphology = 8070/3\n", + "grade = None\n", + "year_of_diagnosis = 2013\n" + ] + }, + { + "ename": "ValueError", + "evalue": " Unknown argument: year_at_diagnosis = Quantity(value_decimal=Decimal('2013'), ", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m/tmp/ipykernel_383721/3442452710.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 110\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 111\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 112\u001b[0;31m example_diagnosis = transform_diagnosis(\n\u001b[0m\u001b[1;32m 113\u001b[0m \u001b[0mgdc_head_and_mouth\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m131\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"diagnoses\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgdc_head_and_mouth\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m131\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 114\u001b[0m )\n", + "\u001b[0;32m/tmp/ipykernel_383721/3442452710.py\u001b[0m in \u001b[0;36mtransform_diagnosis\u001b[0;34m(diagnosis, case)\u001b[0m\n\u001b[1;32m 77\u001b[0m \u001b[0mlist_to_pii\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdiagnosis\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m\"primary_diagnosis\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"morphology\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"grade\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"year_of_diagnosis\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 78\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 79\u001b[0;31m ccdh_diagnosis = ccdh.Diagnosis(\n\u001b[0m\u001b[1;32m 80\u001b[0m \u001b[0mid\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdiagnosis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"diagnosis_id\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 81\u001b[0m related_specimen=[\n", + "\u001b[0;32m~/.local/share/virtualenvs/example-data-8chtNU61/lib/python3.8/site-packages/crdch_model.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, id, identifier, subject, age_at_diagnosis, diagnosis_date, condition, primary_site, metastatic_site, stage, grade, morphology, disease_status, prior_diagnosis, method_of_diagnosis, related_specimen, primary_tumor_dimensional_measures, supporting_observation, **kwargs)\u001b[0m\n", + "\u001b[0;32m~/.local/share/virtualenvs/example-data-8chtNU61/lib/python3.8/site-packages/crdch_model.py\u001b[0m in \u001b[0;36m__post_init__\u001b[0;34m(self, *_, **kwargs)\u001b[0m\n\u001b[1;32m 604\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_normalize_inlined_as_list\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mslot_name\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"supporting_observation\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mslot_type\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mObservation\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey_name\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"observation_type\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkeyed\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 605\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 606\u001b[0;31m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__post_init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 607\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 608\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;32m~/.local/share/virtualenvs/example-data-8chtNU61/lib/python3.8/site-packages/linkml_runtime/utils/yamlutils.py\u001b[0m in \u001b[0;36m__post_init__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m 46\u001b[0m \u001b[0mv\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrepr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m40\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreplace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'\\n'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'\\\\n'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[0mmessages\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mf\"{TypedNode.yaml_loc(k)} Unknown argument: {k} = {v}\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 48\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'\\n'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmessages\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 49\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 50\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_default\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfiltr\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mCallable\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mdict\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdict\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mValueError\u001b[0m: Unknown argument: year_at_diagnosis = Quantity(value_decimal=Decimal('2013'), " + ] + } + ], + "source": [ + "def create_body_site(site_input):\n", + " the_mapping = get_mapping(\"GDC.Case\", \"primary_site\", site_input)\n", + " mapped = ccdh.BodySite(\n", + " site=ccdh.CodeableConcept(\n", + " coding=[\n", + " ccdh.Coding(\n", + " code=the_mapping[0][\"object_id\"],\n", + " system=\"undefined\",\n", + " label=the_mapping[0][\"object_label\"],\n", + " )\n", + " ],\n", + " text=site_input,\n", + " )\n", + " )\n", + " return mapped\n", + "\n", + "\n", + "def create_stage_from_gdc(current_prefix, diagnosis):\n", + " cancer_stage_method_type = None\n", + " \n", + " # if diagnosis.get('ajcc_staging_system_edition') == '7th':\n", + " # cancer_stage_method_type = 'AJCC staging system 7th edition'\n", + " \n", + " # Create an observation set\n", + " obs = ccdh.CancerStageObservationSet(method_type=cancer_stage_method_type)\n", + " for k, v in diagnosis.items():\n", + " # print(f\"trying {k} of {v}\")\n", + " qk = current_prefix + str(k)\n", + " current_mapping = get_mapping(current_prefix, k, v)\n", + " # print(current_mapping)\n", + " if current_mapping is not None:\n", + " crdch_diag_info_type = gdc_to_crdch_csoot_frame_complete[\"CRDC-H\"].loc[\n", + " gdc_to_crdch_csoot_frame_complete[\"GDC\"] == k\n", + " ]\n", + " crdch_diag_info_type = list(crdch_diag_info_type)\n", + " if len(crdch_diag_info_type) == 1:\n", + " crdch_diag_info_type = crdch_diag_info_type[0]\n", + " current_observation = ccdh.CancerStageObservation(\n", + " observation_type=ccdh.CodeableConcept(\n", + " coding=[\n", + " ccdh.Coding(\n", + " code=crdch_diag_info_type,\n", + " system=\"undefined\",\n", + " )\n", + " ],\n", + " text=k,\n", + " ),\n", + " value_codeable_concept=ccdh.CodeableConcept(\n", + " coding=[\n", + " ccdh.Coding(\n", + " code=current_mapping[0][\"object_id\"],\n", + " system=\"undefined\",\n", + " label=current_mapping[0][\"object_label\"],\n", + " )\n", + " ],\n", + " text=v,\n", + " ),\n", + " )\n", + " # print(current_observation)\n", + " obs.observations.append(current_observation)\n", + " # print(obs)\n", + " return obs\n", + "\n", + "def printifin(current_dict, current_key):\n", + " if current_key in current_dict:\n", + " print(f\"{current_key} = {current_dict[current_key]}\")\n", + " else:\n", + " print(f\"{current_key} = {None}\")\n", + " \n", + "def list_to_pii(current_dict, key_list):\n", + " for i in key_list:\n", + " printifin(current_dict, i)\n", + "\n", + "\n", + "def transform_diagnosis(diagnosis, case):\n", + " print(diagnosis)\n", + " list_to_pii(diagnosis, [\"primary_diagnosis\", \"morphology\", \"grade\", \"year_of_diagnosis\"])\n", + " \n", + " ccdh_diagnosis = ccdh.Diagnosis(\n", + " id=diagnosis.get(\"diagnosis_id\"),\n", + " related_specimen=[\n", + " transform_sample_to_specimen(sample) for sample in case.get(\"samples\")\n", + " ],\n", + " stage=create_stage_from_gdc(\"GDC.Diagnosis\", diagnosis),\n", + "# age_at_diagnosis = ccdh.Quantity(value_decimal=diagnosis['year_of_diagnosis'])\n", + " )\n", + "\n", + " # ccdh_diagnosis = ccdh.Diagnosis(\n", + " # condition=diagnosis.get('primary_diagnosis'),\n", + " # morphology=diagnosis.get('morphology'),\n", + " # grade=diagnosis.get('grade'),\n", + " # year_at_diagnosis=diagnosis.get('year_of_diagnosis'),\n", + " # )\n", + "\n", + " ccdh_diagnosis.identifier = [\n", + " ccdh.Identifier(system=\"GDC-submitter-id\", value=diagnosis.get(\"submitter_id\"))\n", + " ]\n", + "\n", + " if \"primary_site\" in case and case[\"primary_site\"] != \"\":\n", + " body_site = create_body_site(case[\"primary_site\"])\n", + " if body_site is not None:\n", + " ccdh_diagnosis.metastatic_site.append(body_site)\n", + " else:\n", + " print(\"returned body_site is None\")\n", + " else:\n", + " print(\"case didn't seem to have a populated primary_site\")\n", + "\n", + " return ccdh_diagnosis\n", + " pass\n", + "\n", + "\n", + "example_diagnosis = transform_diagnosis(\n", + " gdc_head_and_mouth[131][\"diagnoses\"][0], gdc_head_and_mouth[131]\n", + ")\n", + "print(\"\\n\")\n", + "print(yaml_dumper.dumps(example_diagnosis))\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1be21d55", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.10" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}