diff --git a/data/_models/shared/Resource counts.csv b/data/_models/shared/Resource counts.csv index cd58def91e..0de966bdcd 100644 --- a/data/_models/shared/Resource counts.csv +++ b/data/_models/shared/Resource counts.csv @@ -5,7 +5,11 @@ Resource counts,,age group,ontology,1,,CatalogueOntologies,Age groups,,,,,Select Resource counts,,population size,int,,,,,,,,,"Total number of unique individuals with records captured in the data source (most recent count). In the catalogue, this will accommodate counts per year","DataCatalogueFlat,RWEStaging,StudiesStaging,INTEGRATE", Resource counts,,active size,int,,,,,,,,,"Number of unique, active, or currently registered individuals with records captured in the data source (most recent count). In the catalogue, this will accommodate counts per year","DataCatalogueFlat,RWEStaging,StudiesStaging", Resource counts,,no individuals with samples,int,,,,,,,,,"Number of unique individuals with records of biological samples (e.g., blood, urine) (most recent count). In the catalogue, this will accommodate counts per year ","DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging", +Resource counts,,number of samples,int,,,,,,,,,Total number of samples included in this resource,"DataCatalogueFlat,CohortsStaging", +Resource counts,,sample type,ontology_array,,,CatalogueOntologies,BiospecimenType,,,,,Do the counts relate to one or more types of sample?,"DataCatalogueFlat,CohortsStaging", +Resource counts,,population diseases,ontology_array,,,CatalogueOntologies,Diseases,,,,,Do the counts relate to one or more medical conditions?,"DataCatalogueFlat,CohortsStaging,RWEStaging", Resource counts,,mean observation years,int,,,,,,,,,Median years for which unique individuals with records captured in the data source are observable (most recent count),"DataCatalogueFlat,RWEStaging,StudiesStaging", Resource counts,,mean years active,int,,,,,,,,,Median time for which unique individuals with records captured in the data source are observable (most recent count),"DataCatalogueFlat,RWEStaging,StudiesStaging", Resource counts,,median age,int,,,,,,,,,Median age of individuals within data source,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,INTEGRATE", +Resource counts,,sex types,ontology_array,,,CatalogueOntologies,Sex types,,,,http://purl.obolibrary.org/obo/PATO_0000047,The sex of the individuals in this resource - MIABIS-COLLECTION-08 (v3.0),"DataCatalogueFlat,CohortsStaging", Resource counts,,proportion female,int,,,,,,,,,Proportion of females in the data source,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,INTEGRATE", diff --git a/data/_models/shared/Resource qualities.csv b/data/_models/shared/Resource qualities.csv new file mode 100644 index 0000000000..31d6b8416c --- /dev/null +++ b/data/_models/shared/Resource qualities.csv @@ -0,0 +1,8 @@ +tableName,tableExtends,tableType,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,refLabel,defaultValue,validation,visible,computed,semantics,profiles,label,description +Resource qualities,,,,,,,,,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Quality information, i.e. standards, assessments and certifications relating to a resource or sample collection" +Resource qualities,,,resource,ref,1,TRUE,,Resources,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Resource the quality information pertains to" +Resource qualities,,,quality standard,ontology,1,TRUE,CatalogueOntologies,Quality standards,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Quality standard" +Resource qualities,,,assessment level,ontology,,TRUE,CatalogueOntologies,Assessment levels,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Assessment level" +Resource qualities,,,certification number,,,FALSE,,,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Certification Number" +Resource qualities,,,certification report,hyperlink,,FALSE,,,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Certification Report" +Resource qualities,,,certification image url,hyperlink,,FALSE,,,,,,,,,,,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging",,"Certification Image" \ No newline at end of file diff --git a/data/_models/shared/Resources.csv b/data/_models/shared/Resources.csv index 2ca832e7a8..18862d21ad 100644 --- a/data/_models/shared/Resources.csv +++ b/data/_models/shared/Resources.csv @@ -15,6 +15,7 @@ Resources,,network type,ontology_array,,,CatalogueOntologies,Network types,,,,,T Resources,,website,hyperlink,,,,,,,,"http://www.w3.org/ns/dcat#landingPage,foaf:homepage",Link to the website or homepage,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,description,text,,,,,,,,http://purl.org/dc/terms/description,Short description,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,keywords,string_array,,,,,,,,http://www.w3.org/ns/dcat#keyword,Keywords to increase findability of this resource. Try to use words that are not used in the description. Keywords are not displayed on the resource page,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,RWEStaging,UMCUCohorts,INTEGRATE" +Resources,,research domain,ontology_array,,,CatalogueOntologies,Research domains,,,,,The research domain(s) this resource is relevant to,"DataCatalogueFlat,CohortsStaging" Resources,,internal identifiers,refback,,,,Internal identifiers,,resource,,,Internal identifier(s) for this resource (e.g. UMCG register number),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging" Resources,,external identifiers,refback,,,,External identifiers,,resource,,,External identifier(s) for this resource (e.g. EUPASS number or BBMRI persistent identifer),"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,INTEGRATE" Resources,,start year,int,,,,,,,,http://www.w3.org/ns/dcat#startDate,"The year when the resource started, e.g. when data or samples started to be collected or extracted, or when the resource was established","DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,UMCGCohortsStaging,NetworksStaging,INTEGRATE" @@ -50,6 +51,7 @@ Resources,,population of interest other,text,,,,,,,,,"If population of interest Resources,,countries,ontology_array,,,CatalogueOntologies,Countries,,,,http://purl.org/dc/terms/spatial,Countries where data/samples from this resource largely originate from,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,regions,ontology_array,,,CatalogueOntologies,Regions,,,,http://purl.org/dc/terms/spatial,Geographical regions where data/samples from this resource largely originate from,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,population age groups,ontology_array,,,CatalogueOntologies,Age groups,,,,"urn:uuid:a7ef52b2-bd43-4294-a80f-3e7299af35e4#healthdcatap:minimumTypicalAge,urn:uuid:a7ef52b2-bd43-4294-a80f-3e7299af35e4#healthdcatap:maximumTypicalAge",Which population age groups are captured in this resource? Select all that are relevant,"DataCatalogueFlat,EMA,CohortsStaging,RWEStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" +Resources,,sex types,ontology_array,,,CatalogueOntologies,Sex types,,,,http://purl.obolibrary.org/obo/PATO_0000047,The sex of the individuals in this resource - MIABIS-COLLECTION-08 (v3.0),"DataCatalogueFlat,CohortsStaging" Resources,,inclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Inclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,other inclusion criteria,text,,,,,,,,,Other inclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" Resources,,exclusion criteria,ontology_array,,,CatalogueOntologies,Inclusion Exclusion Criteria,,,,,Exclusion criteria applied to the participants of this resource,"DataCatalogueFlat,CohortsStaging,UMCGCohortsStaging,UMCUCohorts,INTEGRATE" @@ -72,7 +74,9 @@ Resources,,publisher,ref,,,,Organisations,,,,http://purl.org/dc/terms/publisher, Resources,,creator,ref_array,,,,Organisations,,,,http://purl.org/dc/terms/creator,This attribute is read only and written during migration of data from staging areas and used to produce valid dcat output. Organisation(s) that created this resource,DataCatalogueFlat Resources,,networks involved,refback,,,,Resources,,resources,,,The consortia or networks that this resource is part of,"DataCatalogueFlat,EMA" Resources,,networks other,text,,,,,,,,,List the names of any other networks that are not listed and this resource is involved in,EMA -Resources,,available data and samples,heading,,,,,,,,,Data model and contents,"DataCatalogueFlat,EMA,RWEStaging,CohortsStaging" +Resources,,"available data, imaging and samples,heading",,,,,,,,,,Data model and contents,"DataCatalogueFlat,EMA,RWEStaging,CohortsStaging,UMCGCohortsStaging" +Resources,,data categories,ontology_array,,,CatalogueOntologies,Data categories,,,,http://www.w3.org/ns/dcat#theme,Types of data collected in this resource,"DataCatalogueFlat,CohortsStaging" +Resources,,number of samples,int,,,,,,,,,Total number of samples included in this resource,"DataCatalogueFlat,CohortsStaging" Resources,,datasets,refback,,,,Datasets,,resource,,,List of datasets contained in this resouce if applicable,"DataCatalogueFlat,CohortsStaging,RWEStaging,NetworksStaging,StudiesStaging" Resources,,samplesets,refback,,,,Samplesets,,resource,,,List of sample sets contained in this resource if applicable,"DataCatalogueFlat,CohortsStaging,RWEStaging,StudiesStaging" Resources,,areas of information,ontology_array,,,CatalogueOntologies,Areas of information cohorts,,,,,Areas of information that were collected,"DataCatalogueFlat,CohortsStaging" @@ -91,6 +95,11 @@ Resources,,diagnosis medical event vocabulary other,text,,,,,,,,,"If 'other', wh Resources,,data dictionary available,bool,,,,,,,,,Are a data dictionary and a data model available?,"DataCatalogueFlat,RWEStaging" Resources,,disease details,ontology_array,,,CatalogueOntologies,MedDRA,,,,,"If data on a specific disease is collected, which diseases does the data source collect information on","DataCatalogueFlat,EMA,RWEStaging" Resources,,disease details other,text,,,,,,,,,Specify disease details if not present in MedDRA,EMA +Resources,,biospecimen types,ontology_array,,,CatalogueOntologies,BiospecimenType,,,,,"If the data bank contains biospecimens, what types of specimen","DataCatalogueFlat,CohortsStaging" +Resources,,sample storage temperatures,ontology_array,,,CatalogueOntologies,Storage temperatures,,,,,"The long-term storage temperature at which the sample is stored after preparation, based on SPREC v3 - MIABIS-COLLECTION-15 (v3.0)","DataCatalogueFlat,CohortsStaging" +Resources,,image types,ontology_array,,,CatalogueOntologies,Image types,,,,,Types of imaging data collected in this resource,"DataCatalogueFlat,CohortsStaging" +Resources,,imaging modality,ontology_array,,,CatalogueOntologies,Imaging modalities,,,,,Imaging modalities used in this resource,"DataCatalogueFlat,CohortsStaging" +Resources,,imaging body parts,ontology_array,,,CatalogueOntologies,Body parts,,,,,The body parts examined during imaging,"DataCatalogueFlat,CohortsStaging" Resources,,biospecimen collected,ontology_array,,,CatalogueOntologies,Biospecimens,,,,,"If the data bank contains biospecimens, what types of specimen","DataCatalogueFlat,RWEStaging" Resources,,languages,ontology_array,,,CatalogueOntologies,Languages,,,,,Languages that the records are recorded in (ISO 639),"DataCatalogueFlat,EMA,RWEStaging" Resources,,multiple entries,bool,,,,,,,,,Can there be multiple entries for a single person in the data bank?,"DataCatalogueFlat,RWEStaging" @@ -121,6 +130,8 @@ Resources,,access non EU,bool,,,,,,,,,Can (an extract of) the data bank be acces Resources,,access non EU conditions,text,,,,,,,,,"If yes to the above, describe the conditions under which non-EU/EEA access may be granted","DataCatalogueFlat,RWEStaging" Resources,,biospecimen access,bool,,,,,,,,,"If the data bank contains biospecimens (e.g. tissue samples), can these be retrieved?","DataCatalogueFlat,EMA,RWEStaging,INTEGRATE" Resources,,biospecimen access conditions,text,,,,,,,,,"If yes to the above, describe the conditions under which permission to retrieve biospecimens may be granted","DataCatalogueFlat,EMA,RWEStaging,INTEGRATE" +Resources,,biospecimen access,bool,,,,,,,,,"If the data bank contains imaging data, can these be accessed?","DataCatalogueFlat,CohortsStaging" +Resources,,biospecimen access conditions,text,,,,,,,,,"If yes to the above, describe the conditions under which access to imaging data can be granted","DataCatalogueFlat,CohortsStaging" Resources,,governance details,text,,,,,,,,,"If available, provide a link to documents or webpages that describe the overall governance of the data source bank (governing data access or utilisation for research purposes by existing DAPs)","DataCatalogueFlat,RWEStaging" Resources,,approval for publication,bool,,,,,,,,,Is an approval needed to publish the results of a study using the data,"DataCatalogueFlat,EMA,RWEStaging" Resources,,updates,heading,,,,,,,,,Information on the regularity of updates and time lags,"DataCatalogueFlat,EMA,RWEStaging" @@ -138,6 +149,7 @@ Resources,,quality,heading,,,,,,,,,List of relevant studies conducted using the Resources,,standard operating procedures,bool,,,,,,,,,Is there a standard operating procedure document that defines the processes and procedures for data capture and management?,"DataCatalogueFlat,RWEStaging" Resources,,qualification,bool,,,,,,,,,"Has the data source successfully undergone a formal qualification process (e.g. from the EMA, ISO or other certifications)?","DataCatalogueFlat,EMA,RWEStaging,INTEGRATE" Resources,,qualifications description,text,,,,,,,,,"Has the data source successfully undergone a qualification process (e.g. from the EMA)? If yes, describe the qualification(s) granted","DataCatalogueFlat,EMA,RWEStaging" +Resources,,qualifications,refback,,,,Resource qualities,,resource,,,Quality standards that this resource meets,"DataCatalogueFlat,CohortsStaging" Resources,,audit possible,bool,,,,,,,,,"Are external parties allowed to audit the data? For example, is it possible for an external party to audit the quality or validity of the data source?","DataCatalogueFlat,RWEStaging" Resources,,completeness,text,,,,,,,,,Describe the completeness of the data bank (e.g. variables with more or fewer missing values),"DataCatalogueFlat,RWEStaging" Resources,,completeness over time,text,,,,,,,,,Describe any changes in completeness of the data bank (e.g. variables with more or fewer missing values) that have occurred over time,"DataCatalogueFlat,RWEStaging" diff --git a/data/_ontologies/Assessment levels.csv b/data/_ontologies/Assessment levels.csv new file mode 100644 index 0000000000..62181dbbb5 --- /dev/null +++ b/data/_ontologies/Assessment levels.csv @@ -0,0 +1,3 @@ +order,name,label,parent,codesystem,code,ontologyTermURI,definition +,eric,BBMRI-ERIC audited,,,,, +,accredited,Accredited/Certified by accredited body,,,,, \ No newline at end of file diff --git a/data/_ontologies/Body parts.csv b/data/_ontologies/Body parts.csv new file mode 100644 index 0000000000..a75de8364d --- /dev/null +++ b/data/_ontologies/Body parts.csv @@ -0,0 +1,119 @@ +order,name,label,parent,codesystem,code,ontologyTermURI,definition +,T-11503,LSPINE,,SNOMED CT,T-11503,http://purl.bioontology.org/ontology/SNOMEDCT/122496007,Lumbar spine +,T-11502,TSPINE,,SNOMED CT,T-11502,http://purl.bioontology.org/ontology/SNOMEDCT/122495006,Thoracic spine +,T-11501,CSPINE,,SNOMED CT,T-11501,http://purl.bioontology.org/ontology/SNOMEDCT/122494005,Cervical spine +,T-12710,FEMUR,,SNOMED CT,T-12710,http://purl.bioontology.org/ontology/SNOMEDCT/71341001,Femur +,T-11100,SKULL,,SNOMED CT,T-11100,http://purl.bioontology.org/ontology/SNOMEDCT/89546000,Skull +,T-12310,CLAVICLE,,SNOMED CT,T-12310,http://purl.bioontology.org/ontology/SNOMEDCT/51299004,Clavicle +,T-D9700,FOOT,,SNOMED CT,T-D9700,http://purl.bioontology.org/ontology/SNOMEDCT/56459004,Foot +,R-FAB53,NECKCHESTABDOMEN,,SNOMED CT,R-FAB53,http://purl.bioontology.org/ontology/SNOMEDCT/416152001,Neck +,T-12430,ULNA,,SNOMED CT,T-12430,http://purl.bioontology.org/ontology/SNOMEDCT/23416004,Ulna +,R-FAB54,NECKCHESTABDPELV,,SNOMED CT,R-FAB54,http://purl.bioontology.org/ontology/SNOMEDCT/416319003,Neck +,R-FAB52,NECKCHEST,,SNOMED CT,R-FAB52,http://purl.bioontology.org/ontology/SNOMEDCT/417437006,Neck and Chest +,R-FAB57,ABDOMENPELVIS,,SNOMED CT,R-FAB57,http://purl.bioontology.org/ontology/SNOMEDCT/416949008,Abdomen and Pelvis +,T-51000,MOUTH,,SNOMED CT,T-51000,http://purl.bioontology.org/ontology/SNOMEDCT/21082005,Mouth +,R-FAB55,CHESTABDOMEN,,SNOMED CT,R-FAB55,http://purl.bioontology.org/ontology/SNOMEDCT/416550000,Chest and Abdomen +,T-74000,BLADDER,,SNOMED CT,T-74000,http://purl.bioontology.org/ontology/SNOMEDCT/89837001,Bladder +,R-FAB56,CHESTABDPELVIS,,SNOMED CT,R-FAB56,http://purl.bioontology.org/ontology/SNOMEDCT/416775004,Chest +,T-15430,ELBOW,,SNOMED CT,T-15430,http://purl.bioontology.org/ontology/SNOMEDCT/16953009,Elbow joint +,T-45526,CIRCLEOFWILLIS,,SNOMED CT,T-45526,http://purl.bioontology.org/ontology/SNOMEDCT/362047009,Circle of Willis +,T-D00F9,LSSPINE,,SNOMED CT,T-D00F9,http://purl.bioontology.org/ontology/SNOMEDCT/297173004,Lumbo-sacral spine +,T-D00F7,CTSPINE,,SNOMED CT,T-D00F7,http://purl.bioontology.org/ontology/SNOMEDCT/297171002,Cervico-thoracic spine +,T-D00F8,TLSPINE,,SNOMED CT,T-D00F8,http://purl.bioontology.org/ontology/SNOMEDCT/297172009,Thoraco-lumbar spine +,T-15710,HIP,,SNOMED CT,T-15710,http://purl.bioontology.org/ontology/SNOMEDCT/24136001,Hip joint +,T-C8000,THYMUS,,SNOMED CT,T-C8000,http://purl.bioontology.org/ontology/SNOMEDCT/9875009,Thymus +,T-83000,UTERUS,,SNOMED CT,T-83000,http://purl.bioontology.org/ontology/SNOMEDCT/35039007,Uterus +,T-58600,ILEUM,,SNOMED CT,T-58600,http://purl.bioontology.org/ontology/SNOMEDCT/34516001,Ileum +,T-D2100,BACK,,SNOMED CT,T-D2100,http://purl.bioontology.org/ontology/SNOMEDCT/77568009,Back +,T-D2220,SHOULDER,,SNOMED CT,T-D2220,http://purl.bioontology.org/ontology/SNOMEDCT/16982005,Shoulder +,T-D8200,ARM,,SNOMED CT,T-D8200,http://purl.bioontology.org/ontology/SNOMEDCT/40983000,Upper arm +,T-AB959,IAC,,SNOMED CT,T-AB959,http://purl.bioontology.org/ontology/SNOMEDCT/361078006,Internal Auditory Canal +,T-D4000,ABDOMEN,,SNOMED CT,T-D4000,http://purl.bioontology.org/ontology/SNOMEDCT/113345001,Abdomen +,T-58200,DUODENUM,,SNOMED CT,T-58200,http://purl.bioontology.org/ontology/SNOMEDCT/38848004,Duodenum +,T-71000,KIDNEY,,SNOMED CT,T-71000,http://purl.bioontology.org/ontology/SNOMEDCT/64033007,Kidney +,T-12280,SCAPULA,,SNOMED CT,T-12280,http://purl.bioontology.org/ontology/SNOMEDCT/79601000,Scapula +,T-AA110,SCLERA,,SNOMED CT,T-AA110,http://purl.bioontology.org/ontology/SNOMEDCT/18619003,Sclera +,T-D14AE,ORBIT,,SNOMED CT,T-D14AE,http://purl.bioontology.org/ontology/SNOMEDCT/363654007,Orbital structure +,T-C3000,SPLEEN,,SNOMED CT,T-C3000,http://purl.bioontology.org/ontology/SNOMEDCT/78961009,Spleen +,T-45010,CAROTID,,SNOMED CT,T-45010,http://purl.bioontology.org/ontology/SNOMEDCT/69105007,Carotid Artery +,T-65000,PANCREAS,,SNOMED CT,T-65000,http://purl.bioontology.org/ontology/SNOMEDCT/15776009,Pancreas +,T-9200B,PROSTATE,,SNOMED CT,T-9200B,http://purl.bioontology.org/ontology/SNOMEDCT/181422007,Prostate +,T-A6000,CEREBELLUM,,SNOMED CT,T-A6000,http://purl.bioontology.org/ontology/SNOMEDCT/113305005,Cerebellum +,T-28000,LUNG,,SNOMED CT,T-28000,http://purl.bioontology.org/ontology/SNOMEDCT/39607008,Lung +,T-53000,TONGUE,,SNOMED CT,T-53000,http://purl.bioontology.org/ontology/SNOMEDCT/21974007,Tongue +,T-12730,PATELLA,,SNOMED CT,T-12730,http://purl.bioontology.org/ontology/SNOMEDCT/64234005,Patella +,T-D1200,FACE,,SNOMED CT,T-D1200,http://purl.bioontology.org/ontology/SNOMEDCT/89545001,Face +,T-D9200,KNEE,,SNOMED CT,T-D9200,http://purl.bioontology.org/ontology/SNOMEDCT/72696002,Knee +,T-15290,TMJ,,SNOMED CT,T-15290,http://purl.bioontology.org/ontology/SNOMEDCT/53620006,Temporomandibular joint +,T-D9440,CALF,,SNOMED CT,T-D9440,http://purl.bioontology.org/ontology/SNOMEDCT/53840002,Calf of leg +,T-D1160,SCALP,,SNOMED CT,T-D1160,http://purl.bioontology.org/ontology/SNOMEDCT/41695006,Scalp +,T-AA000,EYE,,SNOMED CT,T-AA000,http://purl.bioontology.org/ontology/SNOMEDCT/81745001,Eye +,T-D1206,CHEEK,,SNOMED CT,T-D1206,http://purl.bioontology.org/ontology/SNOMEDCT/60819002,Cheek +,T-D1600,NECK,,SNOMED CT,T-D1600,http://purl.bioontology.org/ontology/SNOMEDCT/45048000,Neck +,T-62000,LIVER,,SNOMED CT,T-62000,http://purl.bioontology.org/ontology/SNOMEDCT/10200004,Liver +,T-81000,VULVA,,SNOMED CT,T-81000,http://purl.bioontology.org/ontology/SNOMEDCT/45292006,Vulva +,T-D04FF,SPINE,,SNOMED CT,T-D04FF,http://purl.bioontology.org/ontology/SNOMEDCT/421060004,Spine +,T-D8104,AXILLA,,SNOMED CT,T-D8104,http://purl.bioontology.org/ontology/SNOMEDCT/91470000,Axilla +,T-12740,TIBIA,,SNOMED CT,T-12740,http://purl.bioontology.org/ontology/SNOMEDCT/12611008,Tibia +,T-12340,ILIUM,,SNOMED CT,T-12340,http://purl.bioontology.org/ontology/SNOMEDCT/22356005,Ilium +,T-98000,SCROTUM,,SNOMED CT,T-98000,http://purl.bioontology.org/ontology/SNOMEDCT/20233005,Scrotum +,T-56000,ESOPHAGUS,,SNOMED CT,T-56000,http://purl.bioontology.org/ontology/SNOMEDCT/32849002,Esophagus +,T-73000,URETER,,SNOMED CT,T-73000,http://purl.bioontology.org/ontology/SNOMEDCT/87953007,Ureter +,T-42000,AORTA,,SNOMED CT,T-42000,http://purl.bioontology.org/ontology/SNOMEDCT/15825003,Aorta +,T-AA810,EYELID,,SNOMED CT,T-AA810,http://purl.bioontology.org/ontology/SNOMEDCT/80243003,Eyelid +,T-25000,TRACHEA,,SNOMED CT,T-25000,http://purl.bioontology.org/ontology/SNOMEDCT/44567001,Trachea +,T-61300,SUBMANDIBULAR,,SNOMED CT,T-61300,http://purl.bioontology.org/ontology/SNOMEDCT/54019009,Submandibular gland +,T-D0010,WHOLEBODY,,SNOMED CT,T-D0010,http://purl.bioontology.org/ontology/SNOMEDCT/38266002,Entire body +,T-D1100,HEAD,,SNOMED CT,T-D1100,http://purl.bioontology.org/ontology/SNOMEDCT/69536005,Head +,T-59600,RECTUM,,SNOMED CT,T-59600,http://purl.bioontology.org/ontology/SNOMEDCT/34402009,Rectum +,T-32000,HEART,,SNOMED CT,T-32000,http://purl.bioontology.org/ontology/SNOMEDCT/80891009,Heart +,T-D3000,CHEST,,SNOMED CT,T-D3000,http://purl.bioontology.org/ontology/SNOMEDCT/51185008,Chest +,T-D8810,THUMB,,SNOMED CT,T-D8810,http://purl.bioontology.org/ontology/SNOMEDCT/76505004,Thumb +,T-11300,RIB,,SNOMED CT,T-11300,http://purl.bioontology.org/ontology/SNOMEDCT/113197003,Rib +,T-11AD0,SSPINE,,SNOMED CT,T-11AD0,http://purl.bioontology.org/ontology/SNOMEDCT/54735007,Sacrum +,T-11BF0,COCCYX,,SNOMED CT,T-11BF0,http://purl.bioontology.org/ontology/SNOMEDCT/64688005,Coccyx +,T-D9100,THIGH,,SNOMED CT,T-D9100,http://purl.bioontology.org/ontology/SNOMEDCT/68367000,Thigh +,T-55000,PHARYNX,,SNOMED CT,T-55000,http://purl.bioontology.org/ontology/SNOMEDCT/54066008,Pharynx +,T-15750,ANKLE,,SNOMED CT,T-15750,http://purl.bioontology.org/ontology/SNOMEDCT/70258002,Ankle joint +,T-24100,LARYNX,,SNOMED CT,T-24100,http://purl.bioontology.org/ontology/SNOMEDCT/4596009,Larynx +,T-14668,LOWER LIMB,,SNOMED CT,T-14668,http://purl.bioontology.org/ontology/SNOMEDCT/102292000,Lower limb +,T-26000,BRONCHUS,,SNOMED CT,T-26000,http://purl.bioontology.org/ontology/SNOMEDCT/955009,Bronchus +,T-83200,CERVIX,,SNOMED CT,T-83200,http://purl.bioontology.org/ontology/SNOMEDCT/71252005,Cervix +,T-87000,OVARY,,SNOMED CT,T-87000,http://purl.bioontology.org/ontology/SNOMEDCT/15497006,Ovary +,T-12403,RADIUSULNA,,SNOMED CT,T-12403,http://purl.bioontology.org/ontology/SNOMEDCT/110535000,Radius and ulna +,T-58400,JEJUNUM,,SNOMED CT,T-58400,http://purl.bioontology.org/ontology/SNOMEDCT/21306003,Jejunum +,T-D1213,JAW,,SNOMED CT,T-D1213,http://purl.bioontology.org/ontology/SNOMEDCT/661005,Jaw region +,T-D8800,FINGER,,SNOMED CT,T-D8800,http://purl.bioontology.org/ontology/SNOMEDCT/7569003,Finger +,T-B3000,ADRENAL,,SNOMED CT,T-B3000,http://purl.bioontology.org/ontology/SNOMEDCT/23451007,Adrenal gland +,T-75000,URETHRA,,SNOMED CT,T-75000,http://purl.bioontology.org/ontology/SNOMEDCT/13648007,Urethra +,T-15460,WRIST,,SNOMED CT,T-15460,http://purl.bioontology.org/ontology/SNOMEDCT/74670003,Wrist joint +,T-13600,MUSCLEOFUPPERLIMB,,SNOMED CT,T-13600,http://purl.bioontology.org/ontology/SNOMEDCT/30608006,Muscle of upper limb +,T-AB000,EAR,,SNOMED CT,T-AB000,http://purl.bioontology.org/ontology/SNOMEDCT/1910005,Ear +,T-82000,VAGINA,,SNOMED CT,T-82000,http://purl.bioontology.org/ontology/SNOMEDCT/76784001,Vagina +,T-D1000,HEADNECK,,SNOMED CT,T-D1000,http://purl.bioontology.org/ontology/SNOMEDCT/774007,Head and Neck +,T-D3300,MEDIASTINUM,,SNOMED CT,T-D3300,http://purl.bioontology.org/ontology/SNOMEDCT/72410000,Mediastinum +,T-D9800,TOE,,SNOMED CT,T-D9800,http://purl.bioontology.org/ontology/SNOMEDCT/29707007,Toe +,T-12410,HUMERUS,,SNOMED CT,T-12410,http://purl.bioontology.org/ontology/SNOMEDCT/85050009,Humerus +,T-11166,ZYGOMA,,SNOMED CT,T-11166,http://purl.bioontology.org/ontology/SNOMEDCT/13881006,Zygoma +,T-D9400,LEG,,SNOMED CT,T-D9400,http://purl.bioontology.org/ontology/SNOMEDCT/30021000,Lower leg +,T-12770,CALCANEUS,,SNOMED CT,T-12770,http://purl.bioontology.org/ontology/SNOMEDCT/80144004,Calcaneus +,T-A0100,BRAIN,,SNOMED CT,T-A0100,http://purl.bioontology.org/ontology/SNOMEDCT/12738006,Brain +,T-59300,COLON,,SNOMED CT,T-59300,http://purl.bioontology.org/ontology/SNOMEDCT/71854001,Colon +,T-57000,STOMACH,,SNOMED CT,T-57000,http://purl.bioontology.org/ontology/SNOMEDCT/69695003,Stomach +,T-91000,PENIS,,SNOMED CT,T-91000,http://purl.bioontology.org/ontology/SNOMEDCT/18911002,Penis +,T-43000,CORONARYARTERY,,SNOMED CT,T-43000,http://purl.bioontology.org/ontology/SNOMEDCT/41801008,Coronary artery +,T-B6000,THYROID,,SNOMED CT,T-B6000,http://purl.bioontology.org/ontology/SNOMEDCT/69748006,Thyroid +,T-AA200,CORNEA,,SNOMED CT,T-AA200,http://purl.bioontology.org/ontology/SNOMEDCT/28726007,Cornea +,T-04000,BREAST,,SNOMED CT,T-04000,http://purl.bioontology.org/ontology/SNOMEDCT/76752008,Breast +,T-12701,TIBIAFIBULA,,SNOMED CT,T-12701,http://purl.bioontology.org/ontology/SNOMEDCT/110536004,Tibia and fibula +,T-D0300,EXTREMITY,,SNOMED CT,T-D0300,http://purl.bioontology.org/ontology/SNOMEDCT/66019005,Extremity +,T-D2600,BUTTOCK,,SNOMED CT,T-D2600,http://purl.bioontology.org/ontology/SNOMEDCT/46862004,Buttock +,T-D8700,HAND,,SNOMED CT,T-D8700,http://purl.bioontology.org/ontology/SNOMEDCT/85562004,Hand +,T-11210,STERNUM,,SNOMED CT,T-11210,http://purl.bioontology.org/ontology/SNOMEDCT/56873002,Sternum +,T-12420,RADIUS,,SNOMED CT,T-12420,http://purl.bioontology.org/ontology/SNOMEDCT/62413002,Radius +,T-D6000,PELVIS,,SNOMED CT,T-D6000,http://purl.bioontology.org/ontology/SNOMEDCT/12921003,Pelvis +,T-94000,TESTIS,,SNOMED CT,T-94000,http://purl.bioontology.org/ontology/SNOMEDCT/40689003,Testis +,T-11170,MAXILLA,,SNOMED CT,T-11170,http://purl.bioontology.org/ontology/SNOMEDCT/70925003,Maxilla +,T-21000,NOSE,,SNOMED CT,T-21000,http://purl.bioontology.org/ontology/SNOMEDCT/45206002,Nose +,T-61100,PAROTID,,SNOMED CT,T-61100,http://purl.bioontology.org/ontology/SNOMEDCT/45289007,Parotid gland +,T-63000,GALLBLADER,,SNOMED CT,T-63000,http://purl.bioontology.org/ontology/SNOMEDCT/28231008,Gallbladder \ No newline at end of file diff --git a/data/_ontologies/Image types.csv b/data/_ontologies/Image types.csv new file mode 100644 index 0000000000..47390ab51d --- /dev/null +++ b/data/_ontologies/Image types.csv @@ -0,0 +1,121 @@ +order,name,label,parent,codesystem,code,ontologyTermURI,definition +,1.2.840.10008.5.1.4.1.1.88.70,Implantation Plan SR Document IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.70,, +,1.2.840.10008.5.1.4.1.1.1,Computed Radiography Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.1,, +,1.2.840.10008.5.1.4.1.1.78.1,Lensometry Measurements IOD,,DICOM,1.2.840.10008.5.1.4.1.1.78.1,, +,1.2.840.10008.5.1.4.1.1.78.2,Autorefraction Measurements IOD,,DICOM,1.2.840.10008.5.1.4.1.1.78.2,, +,1.2.840.10008.5.1.4.1.1.78.3,Keratometry Measurements IOD,,DICOM,1.2.840.10008.5.1.4.1.1.78.3,, +,1.2.840.10008.5.1.4.1.1.78.4,Subjective Refraction Measurements IOD,,DICOM,1.2.840.10008.5.1.4.1.1.78.4,, +,1.2.840.10008.5.1.4.1.1.77.1.5.6,Wide Field Ophthalmic Photography 3D Coordinates Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.5.6,, +,1.2.840.10008.5.1.4.1.1.78.5,Visual Acuity Measurements IOD,,DICOM,1.2.840.10008.5.1.4.1.1.78.5,, +,1.2.840.10008.5.1.4.1.1.78.6,Spectacle Prescription Report IOD,,DICOM,1.2.840.10008.5.1.4.1.1.78.6,, +,1.2.840.10008.5.1.4.1.1.77.1.5.4,Ophthalmic Tomography Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.5.4,, +,1.2.840.10008.5.1.4.1.1.78.7,Ophthalmic Axial Measurements IOD,,DICOM,1.2.840.10008.5.1.4.1.1.78.7,, +,1.2.840.10008.5.1.4.1.1.77.1.5.5,Wide Field Ophthalmic Photography Stereographic Projection Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.5.5,, +,1.2.840.10008.5.1.4.1.1.78.8,Intraocular Lens Calculations IOD,,DICOM,1.2.840.10008.5.1.4.1.1.78.8,, +,1.2.840.10008.5.1.4.1.1.77.1.5.2,Ophthalmic Photography 16 Bit Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.5.2,, +,1.2.840.10008.5.1.4.1.1.77.1.5.3,Stereometric Relationship IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.5.3,, +,1.2.840.10008.5.1.4.1.1.77.1.4.1,Video Photographic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.4.1,, +,1.2.840.10008.5.1.4.1.1.88.65,Chest CAD SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.65,, +,1.2.840.10008.5.1.4.1.1.6.2,Enhanced US Volume IOD,,DICOM,1.2.840.10008.5.1.4.1.1.6.2,, +,1.2.840.10008.5.1.4.1.1.88.67,X-Ray Radiation Dose SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.67,, +,1.2.840.10008.5.1.4.1.1.88.69,Colon CAD SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.69,, +,1.2.840.10008.5.1.4.1.1.88.68,Radiopharmaceutical Radiation Dose SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.68,, +,1.2.840.10008.5.1.4.1.1.2.1,Enhanced CT Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.2.1,, +,1.2.840.10008.5.1.4.1.1.7,Secondary Capture Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.7,, +,1.2.840.10008.5.1.4.1.1.6.1,Ultrasound Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.6.1,, +,1.2.840.10008.5.1.4.1.1.2,Computed Tomography Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.2,, +,1.2.840.10008.5.1.4.1.1.2.2,Legacy Converted Enhanced CT Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.2.2,, +,1.2.840.10008.5.1.4.1.1.4,Magnetic Resonance Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.4,, +,1.2.840.10008.5.1.4.1.1.82.1,Corneal Topography Map IOD,,DICOM,1.2.840.10008.5.1.4.1.1.82.1,, +,1.2.840.10008.5.1.4.1.1.9.4.2,General Audio Waveform IOD,,DICOM,1.2.840.10008.5.1.4.1.1.9.4.2,, +,1.2.840.10008.5.1.4.1.1.9.4.1,Basic Voice Audio IOD,,DICOM,1.2.840.10008.5.1.4.1.1.9.4.1,, +,1.2.840.10008.5.1.4.1.1.1.2.1,Digital Mammography X-Ray Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.1.2.1,, +,1.2.840.10008.5.1.4.1.1.67,Real World Value Mapping IOD,,DICOM,1.2.840.10008.5.1.4.1.1.67,, +,1.2.840.10008.5.1.4.1.1.66,Raw Data IOD,,DICOM,1.2.840.10008.5.1.4.1.1.66,, +,1.2.840.10008.5.1.4.1.1.88.59,Key Object Selection Document IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.59,, +,1.2.840.10008.5.1.4.1.1.128.1,Legacy Converted Enhanced PET Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.128.1,, +,1.2.840.10008.5.1.4.1.1.66.6,Tractography Results IOD,,DICOM,1.2.840.10008.5.1.4.1.1.66.6,, +,1.2.840.10008.5.1.4.1.1.66.5,Surface Segmentation IOD,,DICOM,1.2.840.10008.5.1.4.1.1.66.5,, +,1.2.840.10008.5.1.4.1.1.66.4,Segmentation IOD,,DICOM,1.2.840.10008.5.1.4.1.1.66.4,, +,1.2.840.10008.5.1.4.1.1.66.3,Deformable Spatial Registration IOD,,DICOM,1.2.840.10008.5.1.4.1.1.66.3,, +,1.2.840.10008.5.1.4.1.1.66.2,Spatial Fiducials IOD,,DICOM,1.2.840.10008.5.1.4.1.1.66.2,, +,1.2.840.10008.5.1.4.1.1.66.1,Spatial Registration IOD,,DICOM,1.2.840.10008.5.1.4.1.1.66.1,, +,1.2.840.10008.5.1.4.1.1.88.50,Mammography CAD SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.50,, +,1.2.840.10008.5.1.4.1.1.12.1.1,Enhanced X-Ray Angiographic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.12.1.1,, +,1.2.840.10008.5.1.4.34.10,RT Brachy Application Setup Delivery Instruction IOD,,DICOM,1.2.840.10008.5.1.4.34.10,, +,1.2.840.10008.5.1.4.1.1.7.4,Multi-frame True Color Secondary Capture Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.7.4,, +,1.2.840.10008.5.1.4.1.1.7.3,Multi-frame Grayscale Word Secondary Capture Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.7.3,, +,1.2.840.10008.5.1.4.1.1.77.1.5.1,Ophthalmic Photography 8 Bit Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.5.1,, +,1.2.840.10008.5.1.4.1.1.88.40,Procedure Log IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.40,, +,1.2.840.10008.5.1.4.1.1.7.2,Multi-frame Grayscale Byte Secondary Capture Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.7.2,, +,1.2.840.10008.5.1.4.1.1.7.1,Multi-frame Single Bit Secondary Capture Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.7.1,, +,1.2.840.10008.5.1.4.1.1.77.1.1.1,Video Endoscopic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.1.1,, +,1.2.840.10008.5.1.4.1.1.12.2,X-Ray RF Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.12.2,, +,1.2.840.10008.5.1.4.1.1.12.1,X-Ray Angiographic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.12.1,, +,1.2.840.10008.5.1.4.1.1.9.3.1,Basic Cardiac Electrophysiology IOD,,DICOM,1.2.840.10008.5.1.4.1.1.9.3.1,, +,1.2.840.10008.5.1.4.1.1.128,Positron Emission Tomography Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.128,, +,1.2.840.10008.5.1.4.1.1.81.1,Ophthalmic Thickness Map IOD,,DICOM,1.2.840.10008.5.1.4.1.1.81.1,, +,1.2.840.10008.5.1.4.1.1.3.1,Ultrasound Multi-frame Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.3.1,, +,1.2.840.10008.5.1.4.34.7,RT Beams Delivery Instruction IOD,,DICOM,1.2.840.10008.5.1.4.34.7,, +,1.2.840.10008.5.1.4.1.1.104.2,Encapsulated CDA IOD,,DICOM,1.2.840.10008.5.1.4.1.1.104.2,, +,1.2.840.10008.5.1.4.1.1.104.1,Encapsulated PDF IOD,,DICOM,1.2.840.10008.5.1.4.1.1.104.1,, +,1.2.840.10008.5.1.4.1.1.131,Basic Structured Display IOD,,DICOM,1.2.840.10008.5.1.4.1.1.131,, +,1.2.840.10008.5.1.4.1.1.1.1.1,Digital X-Ray Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.1.1.1,, +,1.2.840.10008.5.1.4.1.1.130,Enhanced PET Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.130,, +,1.2.840.10008.5.1.4.1.1.30,Parametric Map IOD,,DICOM,1.2.840.10008.5.1.4.1.1.30,, +,1.2.840.10008.5.1.4.1.1.88.34,Comprehensive 3D SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.34,, +,1.2.840.10008.5.1.4.1.1.88.33,Comprehensive SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.33,, +,1.2.840.10008.5.1.4.1.1.88.35,Extensible SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.35,, +,1.2.840.10008.5.1.4.1.1.77.1.2,VL Microscopic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.2,, +,1.2.840.10008.5.1.4.1.1.77.1.1,VL Endoscopic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.1,, +,1.2.840.10008.5.1.4.1.1.77.1.4,VL Photographic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.4,, +,1.2.840.10008.5.1.4.1.1.77.1.3,VL Slide-coordinates Microscopic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.3,, +,1.2.840.10008.5.1.4.1.1.77.1.6,VL Whole Slide Microscopy Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.6,, +,1.2.840.10008.5.1.4.1.1.12.2.1,Enhanced X-Ray RF Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.12.2.1,, +,1.2.840.10008.5.1.4.1.1.77.1.2.1,Video Microscopic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.77.1.2.1,, +,1.2.840.10008.5.1.4.1.1.4.4,Legacy Converted Enhanced MR Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.4.4,, +,1.2.840.10008.5.1.4.1.1.11.5,XA/XRF Grayscale Softcopy Presentation State IOD,,DICOM,1.2.840.10008.5.1.4.1.1.11.5,, +,1.2.840.10008.5.1.4.1.1.11.4,Blending Softcopy Presentation State IOD,,DICOM,1.2.840.10008.5.1.4.1.1.11.4,, +,1.2.840.10008.5.1.4.1.1.88.22,Enhanced SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.22,, +,1.2.840.10008.5.1.4.1.1.11.1,Grayscale Softcopy Presentation State IOD,,DICOM,1.2.840.10008.5.1.4.1.1.11.1,, +,1.2.840.10008.5.1.4.1.1.11.3,Pseudo-color Softcopy Presentation State IOD,,DICOM,1.2.840.10008.5.1.4.1.1.11.3,, +,1.2.840.10008.5.1.4.1.1.11.2,Color Softcopy Presentation State IOD,,DICOM,1.2.840.10008.5.1.4.1.1.11.2,, +,1.2.840.10008.5.1.4.1.1.4.3,Enhanced MR Color Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.4.3,, +,1.2.840.10008.5.1.4.1.1.4.2,MR Spectroscopy IOD,,DICOM,1.2.840.10008.5.1.4.1.1.4.2,, +,1.2.840.10008.5.1.4.1.1.80.1,Ophthalmic Visual Field Static Perimetry Measurements IOD,,DICOM,1.2.840.10008.5.1.4.1.1.80.1,, +,1.2.840.10008.5.1.4.1.1.9.2.1,Hemodynamic IOD,,DICOM,1.2.840.10008.5.1.4.1.1.9.2.1,, +,1.2.840.10008.5.1.4.1.1.4.1,Enhanced MR Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.4.1,, +,1.2.840.10008.5.1.4.1.1.9.6.1,Respiratory Waveform IOD,,DICOM,1.2.840.10008.5.1.4.1.1.9.6.1,, +,1.2.840.10008.5.1.4.1.1.20,Nuclear Medicine Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.20,, +,1.2.840.10008.5.1.4.1.1.13.1.3,Breast Tomosynthesis Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.13.1.3,, +,1.2.840.10008.5.1.4.1.1.13.1.4,Breast Projection X-Ray Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.13.1.4,, +,1.2.840.10008.5.1.4.1.1.13.1.5,Breast Projection X-Ray Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.13.1.5,, +,1.2.840.10008.5.1.4.1.1.88.11,Basic Text SR IOD,,DICOM,1.2.840.10008.5.1.4.1.1.88.11,, +,1.2.840.10008.5.1.4.1.1.13.1.1,X-Ray 3D Angiographic Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.13.1.1,, +,1.2.840.10008.5.1.4.1.1.13.1.2,X-Ray 3D Craniofacial Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.13.1.2,, +,1.2.840.10008.5.1.4.1.1.68.2,Surface Scan Point Cloud IOD,,DICOM,1.2.840.10008.5.1.4.1.1.68.2,, +,1.2.840.10008.5.1.4.1.1.68.1,Surface Scan Mesh IOD,,DICOM,1.2.840.10008.5.1.4.1.1.68.1,, +,1.2.840.10008.5.1.4.1.1.90.1,Content Assessment Results IOD,,DICOM,1.2.840.10008.5.1.4.1.1.90.1,, +,1.2.840.10008.5.1.4.1.1.79.1,Macular Grid Thickness and Volume Report IOD,,DICOM,1.2.840.10008.5.1.4.1.1.79.1,, +,1.2.840.10008.5.?1.?4.?1.?1.?88.?71,Acquisition Context SR IOD,,DICOM,1.2.840.10008.5.?1.?4.?1.?1.?88.?71,, +,1.2.840.10008.?5.?1.?4.?1.?1.?11.?7,Planar MPR Volumetric Presentation State IOD Description,,DICOM,1.2.840.10008.?5.?1.?4.?1.?1.?11.?7,, +,1.2.840.10008.5.1.4.1.1.481.2,RT Dose IOD,,DICOM,1.2.840.10008.5.1.4.1.1.481.2,, +,1.2.840.10008.5.1.4.1.1.481.1,RT Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.481.1,, +,1.2.840.10008.?5.?1.?4.?1.?1.?11.?6,Planar MPR Volumetric Presentation State IOD Description,,DICOM,1.2.840.10008.?5.?1.?4.?1.?1.?11.?6,, +,1.2.840.10008.5.1.4.1.1.481.4,RT Beams Treatment Record IOD,,DICOM,1.2.840.10008.5.1.4.1.1.481.4,, +,1.2.840.10008.5.1.4.1.1.481.3,RT Structure Set IOD,,DICOM,1.2.840.10008.5.1.4.1.1.481.3,, +,1.2.840.10008.5.1.4.1.1.481.6,RT Brachy Treatment Record IOD,,DICOM,1.2.840.10008.5.1.4.1.1.481.6,, +,1.2.840.10008.5.1.4.1.1.481.5,RT Plan IOD,,DICOM,1.2.840.10008.5.1.4.1.1.481.5,, +,1.2.840.10008.5.1.4.1.1.14.2,Intravascular OCT IOD,,DICOM,1.2.840.10008.5.1.4.1.1.14.2,, +,1.2.840.10008.5.1.4.1.1.481.8,RT Ion Plan IOD,,DICOM,1.2.840.10008.5.1.4.1.1.481.8,, +,1.2.840.10008.5.1.4.1.1.14.1,Intravascular OCT IOD,,DICOM,1.2.840.10008.5.1.4.1.1.14.1,, +,1.2.840.10008.5.1.4.1.1.481.7,RT Treatment Summary Record IOD,,DICOM,1.2.840.10008.5.1.4.1.1.481.7,, +,1.2.840.10008.5.1.4.1.1.481.9,RT Ion Beams Treatment Record IOD,,DICOM,1.2.840.10008.5.1.4.1.1.481.9,, +,1.2.840.10008.5.1.4.1.1.1.2,Digital Mammography X-Ray Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.1.2,, +,1.2.840.10008.5.1.4.1.1.1.1,Digital X-Ray Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.1.1,, +,1.2.840.10008.5.1.4.1.1.9.1.3,Ambulatory Electrocardiogram IOD,,DICOM,1.2.840.10008.5.1.4.1.1.9.1.3,, +,1.2.840.10008.5.1.4.1.1.9.1.2,General Electrocardiogram IOD,,DICOM,1.2.840.10008.5.1.4.1.1.9.1.2,, +,1.2.840.10008.5.1.4.1.1.9.1.1,12-Lead Electrocardiogram IOD,,DICOM,1.2.840.10008.5.1.4.1.1.9.1.1,, +,1.2.840.10008.5.1.4.1.1.1.3,Digital Intra-Oral X-Ray Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.1.3,, +,1.2.840.10008.5.1.4.1.1.9.5.1,Arterial Pulse Waveform IOD,,DICOM,1.2.840.10008.5.1.4.1.1.9.5.1,, +,1.2.840.10008.5.1.4.1.1.1.3.1,Digital Intra-Oral X-Ray Image IOD,,DICOM,1.2.840.10008.5.1.4.1.1.1.3.1,, \ No newline at end of file diff --git a/data/_ontologies/Imaging modalities.csv b/data/_ontologies/Imaging modalities.csv new file mode 100644 index 0000000000..5e3632df43 --- /dev/null +++ b/data/_ontologies/Imaging modalities.csv @@ -0,0 +1,55 @@ +order,name,label,parent,codesystem,code,ontologyTermURI,definition +,OCT,Optical Coherence Tomography (non-Ophthalmic),,DICOM,OCT,,"An acquisition device, process or method that uses an interferometric, non-invasive optical tomographic technique to image 2D slices and 3D volumes of tissue using visible and near visible frequencies." +,DG,Diaphanography,,DICOM,DG,,"An acquisition device, process or method that performs diaphanography." +,RTSTRUCT,Radiotherapy Structure Set,,DICOM,RTSTRUCT,,"A device, process or method that produces Radiotherapy Structure Sets." +,PT,Positron emission tomography (PET),,DICOM,PT,,"An acquisition device, process or method that performs positron emission tomography (PET)." +,LS,Laser surface scan,,DICOM,LS,,"An acquisition device, process or method that performs laser surface scanning." +,RTIMAGE,Radiotherapy Image,,DICOM,RTIMAGE,,"An acquisition device, process or method that performs radiotherapy imaging; includes portal imaging." +,PX,Panoramic X-Ray,,DICOM,PX,,"An acquisition device, process or method that performs panoramic X-Rays." +,EPS,Cardiac Electrophysiology,,DICOM,EPS,,"An acquisition device, process or method that performs cardiac electrophysiology." +,OPM,Ophthalmic Mapping,,DICOM,OPM,,"An acquisition device, process or method that measures corneal topography, corneal or retinal thickness, and other similar parameters that are typically displayed as maps." +,OPT,Ophthalmic Tomography,,DICOM,OPT,,"An acquisition device, process or method that performs tomography of the eye that is based on light and optical principles. Tomography based on other principles, such as ultrasound, is excluded." +,DX,Digital Radiography,,DICOM,DX,,"An acquisition device, process or method that performs digital radiography." +,OPV,Ophthalmic Visual Field,,DICOM,OPV,,"An acquisition device, process or method that measures visual fields and perform visual perimetry." +,RTRECORD,RT Treatment Record,,DICOM,RTRECORD,,"A device, process or method that records radiotherapy treatment records." +,MG,Mammography,,DICOM,MG,,"An acquisition device, process or method that performs mammography." +,US,Ultrasound,,DICOM,US,,"An acquisition device, process or method that performs ultrasound." +,IVOCT,Intravascular Optical Coherence Tomography,,DICOM,IVOCT,,"An acquisition device, process or method that performs intravascular optical coherence tomography" +,MR,Magnetic Resonance,,DICOM,MR,,"An acquisition device, process or method that performs magnetic resonance imaging." +,IO,Intra-Oral Radiography,,DICOM,IO,,"An acquisition device, process or method that performs intra-oral radiography." +,IVUS,Intravascular Ultrasound,,DICOM,IVUS,,"An acquisition device, process or method that performs intravascular ultrasound." +,VA,Visual Acuity,,DICOM,VA,,"An acquisition device, process or method that measures visual acuity." +,ES,Endoscopy,,DICOM,ES,,"An acquisition device, process or method that records images during endoscopy." +,AR,Autorefraction,,DICOM,AR,,"An acquisition device, process or method that measures autorefraction." +,AU,Audio,,DICOM,AU,,"An acquisition device, process or method that records audio." +,RF,Radio Fluoroscopy,,DICOM,RF,,"An acquisition device, process or method that performs radiofluoroscopy." +,SEG,SEG Segmentation,,DICOM,SEG,,"An image processing device, process or method that performs segmentation." +,RG,Radiographic imaging (conventional film/screen),,DICOM,RG,,"An acquisition device, process or method that performs radiographic imaging (conventional film/screen)." +,KER,Keratometry,,DICOM,KER,,"An acquisition device, process or method that performs keratometry." +,SMR,Stereometric Relationship,,DICOM,SMR,,"A device, process or method that records relationships between stereometric image pairs." +,OAM,Ophthalmic Axial Measurements,,DICOM,OAM,,"An acquisition device, process or method that measures the axial length of the eye." +,NM,Nuclear Medicine,,DICOM,NM,,"An acquisition device, process or method that performs nuclear medicine imaging." +,SRF,Subjective Refraction,,DICOM,SRF,,"An acquisition device, process or method that records subjective refraction." +,BI,Biomagnetic imaging,,DICOM,BI,,"An acquisition device, process or method that performs biomagnetic imaging." +,BMD,Bone Densitometry (X-Ray),,DICOM,BMD,,"An acquisition device, process or method that performs bone mineral densitometry by X-Ray, including dual-energy X-Ray absorptiometry (DXA) and morphometric X-Ray absorptiometry (MXA)." +,RTPLAN,Radiotherapy Plan,,DICOM,RTPLAN,,"A device, process or method that produces radiotherapy plans." +,SM,Slide Microscopy,,DICOM,SM,,"An acquisition device, process or method that performs slide microscopy." +,SR,SR Document,,DICOM,SR,,"A device, process or method that creates Structured Report documents." +,OP,Ophthalmic Photography,,DICOM,OP,,"An acquisition device, process or method that performs ophthalmic photography." +,KO,Key Object Selection,,DICOM,KO,,"A device, process or method that creates Key Object Selection objects." +,GM,General Microscopy,,DICOM,GM,,"An acquisition device, process or method that performs general microscopy." +,IOL,Intraocular Lens Data,,DICOM,IOL,, +,ECG,Electrocardiography,,DICOM,ECG,,"An acquisition device, process or method that performs electrocardiography." +,XA,X-Ray Angiography,,DICOM,XA,,"An acquisition device, process or method that performs X-Ray angiography." +,XC,External-camera Photography,,DICOM,XC,,"An acquisition device, process or method that performs photography with an external camera." +,OSS,Optical Surface Scan,,DICOM,OSS,,"An acquisition device, process or method that performs optical surface scanning." +,CR,Computed Radiography,,DICOM,CR,,"An acquisition device, process or method that performs computed radiography." +,CT,Computed Tomography,,DICOM,CT,,"An acquisition device, process or method that performs computed tomography." +,RTDOSE,Radiotherapy Dose,,DICOM,RTDOSE,,"A device, process or method that records radiotherapy dose." +,TG,Thermography,,DICOM,TG,,"An acquisition device, process or method that performs thermography." +,LEN,Lensometry,,DICOM,LEN,,"An acquisition device, process or method that performs lensometry." +,REG,Registration,,DICOM,REG,,"An image processing device, process or method that creates Registration objects." +,RESP,Respiratory Waveform,,DICOM,RESP,, +,HC,Hard Copy,,DICOM,HC,,"A device, process or method that creates images to be printed as hard copy." +,HD,Hemodynamic Waveform,,DICOM,HD,,"An acquisition device, process or method that records hemodynamic waveforms." +,BDUS,Bone Densitometry (ultrasound),,DICOM,BDUS,,"An acquisition device, process or method that performs ultrasound bone densitometry." \ No newline at end of file diff --git a/data/_ontologies/Quality standards.csv b/data/_ontologies/Quality standards.csv new file mode 100644 index 0000000000..6f619122c8 --- /dev/null +++ b/data/_ontologies/Quality standards.csv @@ -0,0 +1,44 @@ +order,name,label,parent,codesystem,code,ontologyTermURI,definition +,cen-ts-16945-2016,BBMRI audited CEN/TS 16945:2016,,,cen-ts-16945-2016,,"Specifications for pre-examination processes for metabolomics in urine, serum and plasma" +,iso-21899-2020,ISO 21899:2020,,,iso-21899-2020,,Biotechnology - Biobanking - General requirements for the validation and verification of processing methods for biological material in biobanks +,cen-ts-16835-3-2015,BBMRI audited CEN/TS 16835-3:2015,,,cen-ts-16835-3-2015,,Specifications for pre-examination processes for venous whole blood - Part 3: Isolated circulating cell free DNA from plasma +,iso-23118-2021,BBMRI audited ISO 23118:2021,,,iso-23118-2021,,"Specifications for pre-examination processes in metabolomics in urine, venous blood serum and plasma" +,iso-27001-2022,ISO 27001:2022,,,iso-27001-2022,,Information security management systems - Requirements +,cen-ts-16827-2-2015,BBMRI audited CEN/TS 16827-2:2015,,,cen-ts-16827-2-2015,,Specifications for pre-examination processes for FFPE tissue - Part 2: Isolated proteins +,iso-17043-2010,ISO 17043:2010,,,iso-17043-2010,,Conformity assessment - General requirements for proficiency testing +,iso-15190-2020,ISO 15190:2020,,,iso-15190-2020,,Medical laboratories – Requirements for safety +,iso-15189-2012,ISO 15189:2012,,,iso-15189-2012,,Medical laboratories – Requirements for quality and competence +,ISO-20387-2018,ISO 20387:2018,,,ISO-20387-2018,,Biotechnology - Biobanking - General requirements for biobanking +,oecd-guidelines,OECD Guidelines,,,oecd-guidelines,, +,nfs96-900,NFS96-900,,,nfs96-900,,Quality of Biological Resource Centres (BRCS) - Management system of a BRC and quality of biological resources +,iso-15189-2014,ISO 15189:2014,,,iso-15189-2014,,Medical laboratories – Requirements for quality and competence +,cen-ts-16826-1-2015,BBMRI audited CEN/TS 16826-1:2015,,,cen-ts-16826-1-2015,,Specifications for pre-examination processes for snap frozen tissue - Part 1: Isolated RNA +,cen-ts-16827-1-2015,BBMRI audited CEN/TS 16827-1:2015,,,cen-ts-16827-1-2015,,Specifications for pre-examination processes for FFPE tissue - Part 1: Isolated RNA +,others,Others,,,others,, +,iso-fdis-20387,BBMRI audited ISO 20387:2018,,,iso-fdis-20387,,Biotechnology - Biobanking - General requirements for biobanking +,cen-ts-16835-1-2015,BBMRI audited CEN/TS 16835-1:2015,,,cen-ts-16835-1-2015,,Specifications for pre-examination processes for venous whole blood - Part 1: Isolated cellular RNA +,iso-27001-2013,ISO 27001:2013,,,iso-27001-2013,,Information security management systems - Requirements +,iso-9001,ISO 9001:2015,,,iso-9001,,Quality management systems - Requirements +,iso-15189,ISO-15189:2012,,,iso-15189,,Medical laboratories – Requirements for quality and competence +,iso-17025,ISO-17025:2017,,,iso-17025,,General requirements for the competence of testing and calibration laboratories +,iso-20166-2,BBMRI audited ISO 20166-2:2018,,,iso-20166-2,,Specifications for pre-examination processes for FFPE tissue - Part 2: Isolated proteins +,iso-20166-3,BBMRI audited ISO 20166-3:2018,,,iso-20166-3,,Specifications for pre-examination processes for FFPE tissue - Part 3: Isolated DNA +,oeci_accreditation,OECI Accreditation,,,oeci_accreditation,, +,iso-17025-2017,ISO 17025:2017,,,iso-17025-2017,,General requirements for the competence of testing and calibration laboratories +,iso-17025-2018,ISO 17025:2018,,,iso-17025-2018,,General requirements for the competence of testing and calibration laboratories +,cen-ts-16826-2-2015,BBMRI audited CEN/TS 16826-2:2015,,,cen-ts-16826-2-2015,,Specifications for pre-examination processes for snap frozen tissue - Part 2: Isolated proteins +,iso-20184-1,BBMRI audited ISO 20184-1:2018,,,iso-20184-1,,Specifications for pre-examination processes for frozen tissue - Part 1: Isolated RNA +,iso-20184-3,BBMRI audited ISO 20184-3:2021,,,iso-20184-3,,Specifications for pre-examination processes for frozen tissue - Part 3: Isolated DNA +,iso-20186-1,BBMRI audited ISO 20186-1:2019,,,iso-20186-1,,Specifications for pre-examination processes for venous whole blood - Part 1: Isolated cellular RNA +,iso-20184-2,BBMRI audited ISO 20184-2:2018,,,iso-20184-2,,Specifications for pre-examination processes for frozen tissue - Part 2: Isolated proteins +,iso-15189-2022,ISO 15189:2022,,,iso-15189-2022,,Medical laboratories – Requirements for quality and competence +,iso-17020-2012,ISO 17020:2012,,,iso-17020-2012,,Conformity assessment - Requirements for the operation of various types of bodies performing inspection +,iso-20186-3,BBMRI audited ISO 20186-3:2019,,,iso-20186-3,,Specifications for pre-examination processes for venous whole blood - Part 3: Isolated circulating cell free DNA from plasma +,cen-ts-16835-2-2015,BBMRI audited CEN/TS 16835-2:2015,,,cen-ts-16835-2-2015,,Specifications for pre-examination processes for venous whole blood - Part 2: Isolated genomic DNA +,iso-20166-1,BBMRI audited ISO 20166-1:2018,,,iso-20166-1,,Specifications for pre-examination processes for FFPE tissue - Part 1: Isolated RNA +,iso-20186-2,BBMRI audited ISO 20186-2:2019,,,iso-20186-2,,Specifications for pre-examination processes for venous whole blood - Part 2: Isolated genomic DNA +,cen-ts-16827-3-2015,BBMRI audited CEN/TS 16827-3:2015,,,cen-ts-16827-3-2015,,Specifications for pre-examination processes for FFPE tissue - Part 3: Isolated DNA +,iso-17034-2016,ISO 17034:2016,,,iso-17034-2016,,General requirements for the competence of reference material producers +,iso-15190,ISO-15190:2020,,,iso-15190,,Medical laboratories – Requirements for safety +,iso-20186-1-EPND,BBMRI audited ISO 20186-1:2019,,,iso-20186-1-EPND,,"Specifications for pre-examination processes for venous whole blood - Part 1: Isolated cellular RNASpecifications for pre-examination processes for venous whole blood - Part 1: Isolated cellular RNA --EPND, H2020-JTI-IMI2, GA: 101034344--" +,iso-20186-2-EPND,BBMRI audited ISO 20186-2:2019,,,iso-20186-2-EPND,,"Specifications for pre-examination processes for venous whole blood - Part 2: Isolated genomic DNA --EPND, H2020-JTI-IMI2, GA: 101034344--" \ No newline at end of file diff --git a/data/_ontologies/Research domains.csv b/data/_ontologies/Research domains.csv new file mode 100644 index 0000000000..b8e3b5b749 --- /dev/null +++ b/data/_ontologies/Research domains.csv @@ -0,0 +1,11 @@ +order,name,label,parent,codesystem,code,ontologyTermURI,definition +,rare_disease,Rare Diseases,,,,http://edamontology.org/topic_3325,"The study of rare diseases." +,covid19,Covid-19,,,,,"" +,paediatrics,Paediatrics,,,,http://edamontology.org/topic_3418,"The branch of medicine that deals with the medical care of infants, children and adolescents." +,oncology,Oncology,,,,http://edamontology.org/topic_2640,"The study of cancer, for example, genes and proteins implicated in cancer." +,infectious,Infectious Diseases,,,,http://edamontology.org/topic_3324,"The branch of medicine that deals with the prevention, diagnosis and management of transmissible disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions)." +,population,Population/ Reference Samples,,,,,"Samples suitable to be used as population reference samples, e.g. samples from population studies or samples from donors free of the disease of interest" +,metabolic,Metabolic Disorders,,,,http://purl.obolibrary.org/obo/NCIT_C3235,"A congenital (due to inherited enyme abnormality) or acquired (due to failure of a metabolic important organ) disorder resulting from an abnormal metabolic process & A non-neoplastic or neoplastic disorder that affects the endocrine system. Representative examples of non-neoplastic disorders include diabetes mellitus, hyperthyroidism, and adrenal gland insufficiency. Representative examples of neoplastic disorders include carcinoid tumor, neuroendocrine carcinoma, and pheochromocytoma." +,cardiovascular,Cardiovascular Diseases,,,,http://purl.obolibrary.org/obo/NCIT_C2931,"A non-neoplastic or neoplastic disorder affecting the heart or the vessels (arteries, veins and lymph vessels). Representative examples of non-neoplastic cardiovascular disorders are endocarditis and hypertension. Representative examples of neoplastic cardiovascular disorders are endocardial myxoma and angiosarcoma. [Definition Source: NCI]" +,nervous_system,Nervous System Disorders,,,,http://purl.obolibrary.org/obo/NCIT_C26835,"A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves." +,autoimmune,Autoimmune Diseases,,,,http://purl.obolibrary.org/obo/OBI_1110054,"Is a disease characterized by an immune response of an organism against parts of itself."" \ No newline at end of file diff --git a/data/_ontologies/Sex types.csv b/data/_ontologies/Sex types.csv new file mode 100644 index 0000000000..436112648e --- /dev/null +++ b/data/_ontologies/Sex types.csv @@ -0,0 +1,7 @@ +name +Male +Female +Unknown +Undifferentiated +Not applicable +* \ No newline at end of file diff --git a/data/_ontologies/Storage temperatures.csv b/data/_ontologies/Storage temperatures.csv new file mode 100644 index 0000000000..107c439e0c --- /dev/null +++ b/data/_ontologies/Storage temperatures.csv @@ -0,0 +1,9 @@ +name +RT (Room temperature) +2 °C to 10°C +-18 °C to -35 °C +-60 °C to -85 °C +<-135 °C +Liquid nitrogen vapor-phase +Liquid nitrogen liquid-phase +Other \ No newline at end of file