From 1cbb261c4db0819e5a10a183b012c49175041732 Mon Sep 17 00:00:00 2001 From: Oudijk Date: Tue, 7 Jan 2025 10:57:38 +0100 Subject: [PATCH 01/11] Changed columnType in Biosamples --- data/portal/Biosamples.csv | 52 +++++++++++++++++++------------------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/data/portal/Biosamples.csv b/data/portal/Biosamples.csv index ec384d0a7b..c52d02819f 100644 --- a/data/portal/Biosamples.csv +++ b/data/portal/Biosamples.csv @@ -1,26 +1,26 @@ -tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles -Biosamples,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43376,"A natural substance derived from living organisms such as cells, tissues, proteins, and DNA","Beacon v2, FAIR Genomes, DCAT examples, RD3" -Biosamples,,id,string,1,TRUE,,,,,,http://purl.obolibrary.org/obo/NCIT_C93400,A unique proper name or character sequence that identifies this particular material,"Beacon v2, FAIR Genomes, DCAT examples, RD3" -Biosamples,,alternate ids,string_array,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C90353,A backup sequence of characters used to identify an entity,RD3 -Biosamples,,material type,ontology,,,,BiospecimenType,,,,http://purl.obolibrary.org/obo/NCIT_C70713,"The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes","FAIR Genomes, RD3" -Biosamples,,pathological state,ontology,,TRUE,,PathologicalState,,,,http://purl.obolibrary.org/obo/NCIT_C28257,"An examination that is performed to determine the extent of the spread of cancer based on histopathologic examination of one or more pathology specimens. Pathologic staging uses evidence acquired during the process of clinical staging, supplemented by histopathologic examination of surgical specimens.","Beacon v2, FAIR Genomes, DCAT examples, RD3" -Biosamples,,anatomical location,ontology,,TRUE,,AnatomicalLocation,,,,http://purl.obolibrary.org/obo/NCIT_C170983,The specific anatomical or biological region associated with a tissue or organ specimen.,"Beacon v2, FAIR Genomes, DCAT examples, RD3" -Biosamples,,anatomical location other,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C170983,Additional description on the anatomical or biological region associated with a tissue or organ specimen,"Beacon v2, FAIR Genomes, DCAT examples, RD3" -Biosamples,,collected at organisation,ref,,,,Organisations,,,,http://purl.obolibrary.org/obo/OBIB_0000085,The geographic location where biosample collection took place,RD3 -Biosamples,,collected by,ontology_array,,,,Contacts,,,,http://purl.obolibrary.org/obo/OBI_0001769,The person or persons responsible for biosample collection,RD3 -Biosamples,,date of collection,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C82515,Date on which the material was collected,"Beacon v2, FAIR Genomes, DCAT examples" -Biosamples,,age group of individual at collection,ontology,,,,Age groups,,,,http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual by age at the time of sample collection (e.g., ""Adult"", ""18-24 years"", etc.)", -Biosamples,,age of individual at collection,period,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0001775,The age of the individual at the time of sample collection,"Beacon v2, DCAT examples" -Biosamples,,affiliated organisations,ref_array,,,,Organisations,,,,http://purl.obolibrary.org/obo/NCIT_C25412,One or more associations between the record and an organisation or institution.,RD3 -Biosamples,,collected from individual,ref,,,,Individuals,,,,http://semanticscience.org/resource/SIO_000244,Reference to the person from whom this material was collected.,"FAIR Genomes, RD3" -Biosamples,,protocol used,refback,,,,Protocol parameters,,identifier,,http://www.ebi.ac.uk/efo/EFO_0005518,A description of the procedures whereby biological samples for an experiment are sourced.,"Beacon v2, FAIR Genomes, DCAT examples, RD3" -Biosamples,,registration timestamp,datetime,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25646,"Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.",FAIR Genomes -Biosamples,,storage conditions,ontology,,,,Storage conditions,,,,http://purl.obolibrary.org/obo/NCIT_C96145,The conditions under which this biological material was stored.,FAIR Genomes -Biosamples,,storage location,ontology,,,,Storage locations,,,,http://purl.obolibrary.org/obo/GENEPIO_0100594,"A place on the Earth where this material is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which freezer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).",FAIR Genomes -Biosamples,,date of expiration,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C164516,The date on which this material is no longer regarded as fit for use.,FAIR Genomes -Biosamples,,percentage tumor cells,decimal,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C127771,The percentage of tumor cells compared to total cells present in this material.,"FAIR Genomes, RD3" -Biosamples,,derived from biosample,ref,,,,Biosamples,,,,http://purl.obolibrary.org/obo/OBI_0002077,"If applicable, a reference to a biosample that this material was derived from",FAIR Genomes -Biosamples,,failed quality control,bool,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0100564,An indication confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.,RD3 -Biosamples,,files,refback,,,,Files,,biosamples,,http://semanticscience.org/resource/SIO_000396,A reference to one or more files that contain information about this individual,RD3 -Biosamples,,included in datasets,ref_array,,,,Datasets,,,,http://purl.obolibrary.org/obo/HSO_0000370,"A reference to one or more datasets that organises records for in a meaningful way (e.g., data releases, subpopulations, cohorts, etc.)",RD3 -Biosamples,,comments,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25393,"A written explanation, observation or criticism added to textual material.",RD3 \ No newline at end of file +tableName;tableExtends;columnName;columnType;key;required;refSchema;refTable;refLink;refBack;validation;semantics;description;profiles +Biosamples;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C43376;A natural substance derived from living organisms such as cells, tissues, proteins, and DNA;Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples;;id;string;1;TRUE;;;;;;http://purl.obolibrary.org/obo/NCIT_C93400;A unique proper name or character sequence that identifies this particular material;Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples;;alternate ids;string_array;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C90353;A backup sequence of characters used to identify an entity;RD3 +Biosamples;;material type;ontology;;;;BiospecimenType;;;;http://purl.obolibrary.org/obo/NCIT_C70713;The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes;FAIR Genomes, RD3 +Biosamples;;pathological state;ontology;;TRUE;;PathologicalState;;;;http://purl.obolibrary.org/obo/NCIT_C28257;An examination that is performed to determine the extent of the spread of cancer based on histopathologic examination of one or more pathology specimens. Pathologic staging uses evidence acquired during the process of clinical staging, supplemented by histopathologic examination of surgical specimens.;Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples;;anatomical location;ontology;;TRUE;;AnatomicalLocation;;;;http://purl.obolibrary.org/obo/NCIT_C170983;The specific anatomical or biological region associated with a tissue or organ specimen.;Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples;;anatomical location other;string;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C170983;Additional description on the anatomical or biological region associated with a tissue or organ specimen;Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples;;collected at organisation;ref;;;;Organisations;;;;http://purl.obolibrary.org/obo/OBIB_0000085;The geographic location where biosample collection took place;RD3 +Biosamples;;collected by;ref_array;;;;Contacts;;;;http://purl.obolibrary.org/obo/OBI_0001769;The person or persons responsible for biosample collection;RD3 +Biosamples;;date of collection;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C82515;Date on which the material was collected;Beacon v2, FAIR Genomes, DCAT examples +Biosamples;;age group of individual at collection;ontology;;;;Age groups;;;;http://purl.obolibrary.org/obo/NCIT_C20587;"A categorical value that groups this individual by age at the time of sample collection (e.g., ""Adult"", ""18-24 years"", etc.)"; +Biosamples;;age of individual at collection;period;;;;;;;;http://purl.obolibrary.org/obo/GENEPIO_0001775;The age of the individual at the time of sample collection;Beacon v2, DCAT examples +Biosamples;;affiliated organisations;ref_array;;;;Organisations;;;;http://purl.obolibrary.org/obo/NCIT_C25412;One or more associations between the record and an organisation or institution.;RD3 +Biosamples;;collected from individual;ref;;;;Individuals;;;;http://semanticscience.org/resource/SIO_000244;Reference to the person from whom this material was collected.;FAIR Genomes, RD3 +Biosamples;;protocol used;refback;;;;Protocol parameters;;identifier;;http://www.ebi.ac.uk/efo/EFO_0005518;A description of the procedures whereby biological samples for an experiment are sourced.;Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples;;registration timestamp;datetime;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25646;Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.;FAIR Genomes +Biosamples;;storage conditions;ontology;;;;Storage conditions;;;;http://purl.obolibrary.org/obo/NCIT_C96145;The conditions under which this biological material was stored.;FAIR Genomes +Biosamples;;storage location;ontology;;;;Storage locations;;;;http://purl.obolibrary.org/obo/GENEPIO_0100594;A place on the Earth where this material is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which freezer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).;FAIR Genomes +Biosamples;;date of expiration;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C164516;The date on which this material is no longer regarded as fit for use.;FAIR Genomes +Biosamples;;percentage tumor cells;decimal;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C127771;The percentage of tumor cells compared to total cells present in this material.;FAIR Genomes, RD3 +Biosamples;;derived from biosample;ref;;;;Biosamples;;;;http://purl.obolibrary.org/obo/OBI_0002077;If applicable, a reference to a biosample that this material was derived from;FAIR Genomes +Biosamples;;failed quality control;bool;;;;;;;;http://purl.obolibrary.org/obo/GENEPIO_0100564;An indication confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.;RD3 +Biosamples;;files;refback;;;;Files;;biosamples;;http://semanticscience.org/resource/SIO_000396;A reference to one or more files that contain information about this individual;RD3 +Biosamples;;included in datasets;ref_array;;;;Datasets;;;;http://purl.obolibrary.org/obo/HSO_0000370;A reference to one or more datasets that organises records for in a meaningful way (e.g., data releases, subpopulations, cohorts, etc.);RD3 +Biosamples;;comments;text;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25393;A written explanation, observation or criticism added to textual material.;RD3 \ No newline at end of file From 5ecc373352741f260f75c94c3802c454130a448a Mon Sep 17 00:00:00 2001 From: Oudijk Date: Wed, 8 Jan 2025 10:30:51 +0100 Subject: [PATCH 02/11] changed the id for Individual obserevations' ' --- data/portal/Individual observations.csv | 87 ++++++++++++------------- 1 file changed, 43 insertions(+), 44 deletions(-) diff --git a/data/portal/Individual observations.csv b/data/portal/Individual observations.csv index d1782d1867..00d46a46ec 100644 --- a/data/portal/Individual observations.csv +++ b/data/portal/Individual observations.csv @@ -1,44 +1,43 @@ -tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles -Individual observations,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25398,Findings and circumstances relating to the examination and treatment of a individual,"FAIR Genomes, JRC-CDE,RD3" -Individual observations,,id,auto_id,1,TRUE,,,,,,http://purl.obolibrary.org/obo/NCIT_C87853,A unique proper name or character sequence that identifies this particular clinical examination,"FAIR Genomes, JRC-CDE, RD3" -Individual observations,,individual,ref,,,,Individuals,,,,http://purl.obolibrary.org/obo/IAO_0000136,A reference to the individual whom this clinical information is about,"FAIR Genomes, JRC-CDE, RD3" -Individual observations,,date of observation,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C119798,The date on which the clinical assement was made,RD3 -Individual observations,,age at observation,period,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C192236,"The age of the individual at the time of observation (e.g., ""P55Y8M12D"")","Beacon v2,RD3" -Individual observations,,type of visit,ontology,,,,Visit type,,,,http://purl.obolibrary.org/obo/NCIT_C103165,"The kind of visit undertaken by the individual within a study, such as inpatient, outpatient, telephone, baseline, follow up, etc.","FAIR Genomes, JRC-CDE, RD3" -Clinical observations,Individual observations,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C87853,This table extends observations with clinical details compatible with phenopacket,RD3 -Clinical observations,,phenotypes,refback,,,,Phenotype observations,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C16977,"The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. In medical context, these are often the symptoms caused by a disease.","FAIR Genomes, RD3" -Clinical observations,,diseases,refback,,,,Disease history,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C15607,"Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function.","FAIR Genomes, RD3" -Clinical observations,,measurements,refback,,,,Measurements,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C25209,Annotation used to indicate the size or magnitude of something that was determined by comparison to a standard,"FAIR Genomes, RD3" -Clinical observations,,molecular diagnosis gene,ontology_array,,,,Genes,,,,http://purl.obolibrary.org/obo/NCIT_C36391,Gene affected by pathogenic variation that is causal for disease of the individual,FAIR Genomes -Clinical observations,,molecular diagnosis other,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C20826,Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.,FAIR Genomes -Clinical observations,,is solved,bool,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25587,An indication that diagnosis is given and the case is no longer considered unsolved.,RD3 -Clinical observations,,date solved,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C119798,"The date on which a case was considered solved (i.e., a diagnosis was made)",RD3 -Clinical observations,,medication,ontology_array,,,,Medication,,,,http://purl.obolibrary.org/obo/NCIT_C459,"A drug product that contains one or more active and/or inactive ingredients used by the individual intended to treat, prevent or alleviate the symptoms of disease. Any hormone therapies, gender-related or otherwise, should also be recorded here.",FAIR Genomes -Clinical observations,,drug regimen,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C142516,"The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.",FAIR Genomes -Clinical observations,,medical history,ontology_array,,,,MedicalHistory,,,,http://purl.obolibrary.org/obo/NCIT_C18772,"A record of a individual's background regarding health, occurrence of disease events and surgical procedures",FAIR Genomes -Clinical observations,,date of first contact,date,,,,,,,,http://purl.bioontology.org/ontology/LNC/MTHU048806,The date on which contact with the individual was initiated,"FAIR Genomes, JRC-CDE" -Clinical observations,,date of last contact,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C156916,The date on which contact with the individual was last made, -Clinical observations,,classification of functioning,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C21007,An individual's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF),"FAIR Genomes, JRC-CDE" -Clinical observations,,material used in diagnosis,text,,,,,,,,http://semanticscience.org/resource/SIO_000641,A description of one or more materials used to make a diagnosis,FAIR Genomes -Phenotype observations,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C16977,Beacon v2 Individuals PhenotypicFeatures,"Beacon v2,RD3" -Phenotype observations,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")","Beacon v2,RD3" -Phenotype observations,,type,ontology,1,TRUE,,Phenotypes,,,,http://semanticscience.org/resource/SIO_010056,"A term denoting a phenotypic feature. E.g. ""Abnormality of body height""","Beacon v2,RD3" -Phenotype observations,,excluded,bool,,,,,,,,http://purl.obolibrary.org/obo/HP_0040285,"An indication if the phenotype was observed or not. The default is ÔfalseÕ, in other words the phenotype was observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be absent.","Beacon v2,RD3" -Phenotype observations,,modifiers,ontology_array,,,,Phenotypes,,,,http://purl.obolibrary.org/obo/HP_0012823,"Additional terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. E.g. Exacerbated by tobacco use","Beacon v2,RD3" -Phenotype observations,,severity,ontology,,,,Severity,,,,http://purl.obolibrary.org/obo/HP_0012824,"A value that describes the intensity of the phenotype (e.g., ""Profound"")","Beacon v2,RD3" -Disease history,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C15607,History of diagnoses of an individual at a specific timepoints,"Beacon v2,RD3" -Disease history,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")","Beacon v2,RD3" -Disease history,,disease,ontology,1,TRUE,,Diseases,,,,http://semanticscience.org/resource/SIO_001331,"The diagnosis assigned for this particular observation (e.g., ""Spinocerebellar ataxia type 34"")","Beacon v2,RD3" -Disease history,,age group at onset,ontology,,,,Age groups,,,,"http://www.ebi.ac.uk/efo/EFO_0004847, http://purl.obolibrary.org/obo/NCIT_C20587","A categorical value that groups this individual's age of onset into groups (e.g., ""Adult"", ""18-24 years"", etc.)","Beacon v2,RD3" -Disease history,,age of onset,period,,,,,,,,http://www.ebi.ac.uk/efo/EFO_0004847,"The age at which manifestations of the diseaese first appeared (e.g., ""P32Y6M1D"")","Beacon v2,RD3" -Disease history,,age group at diagnosis,ontology,,,,Age groups,,,,"http://www.ebi.ac.uk/efo/EFO_0004918, http://purl.obolibrary.org/obo/NCIT_C20587","A categorical value that groups this individual's age at diagnosis into groups (e.g., ""Adult"", ""18-24 years"", etc.)","RD3,Beacon v2 Vivify add-on" -Disease history,,age at diagnosis,period,,,,,,,,http://www.ebi.ac.uk/efo/EFO_0004918,"The age at which the diagnosis was made (e.g., ""P32Y6M1D"")","RD3,Beacon v2 Vivify add-on" -Disease history,,has family history,bool,,,,,,,,http://purl.obolibrary.org/obo/HP_0032316,An indication if the diagnosis is present in one or more family members or other relatives,"Beacon v2,RD3" -Disease history,,disease severity,ontology,,,,Severity,,,,http://purl.obolibrary.org/obo/HP_0012824,"A value that describes the intensity of the disease (e.g., ""Profound"")","Beacon v2,RD3" -Disease history,,disease stage,ontology,,,,DiseaseStage,,,,http://purl.obolibrary.org/obo/OBI_0000278,"A part of an occurrence of a disease process which is associated with position in the normal progression of the disease (e.g., ""acute onset"")","Beacon v2,RD3" -Measurements,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25209,Additional clinical measurements collected as part of the clinical observation,"Beacon v2,RD3" -Measurements,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")","Beacon v2,RD3" -Measurements,,code,ontology,1,TRUE,,AnalysesPerformed,,,,http://purl.obolibrary.org/obo/NCIT_C25162,"A unique code that identifies or categorises this measurement (e.g., ""Metabolomics"")","Beacon v2,RD3" -Measurements,,variable,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C54166,"A name that describes the measurement (e.g.. ""Blood platelet count"")","RD3,Beacon v2 EMX2 add-on" -Measurements,,value,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25712,"The value that was measured, collected, derived, etc. (e.g. ""55345"")","Beacon v2,RD3" -Measurements,,unit,ontology,,,,Units,,,,http://purl.obolibrary.org/obo/NCIT_C25709,"A value that specifes the measured value (e.g., ""Per Millimeter"")","Beacon v2,RD3" \ No newline at end of file +tableName;tableExtends;columnName;columnType;key;required;refSchema;refTable;refLink;refBack;validation;semantics;description;profiles +Individual observations;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25398;Findings and circumstances relating to the examination and treatment of a individual;FAIR Genomes, JRC-CDE,RD3 +Individual observations;;individual;ref;1;TRUE;;Individuals;;;;http://purl.obolibrary.org/obo/IAO_0000136;A reference to the individual whom this clinical information is about;FAIR Genomes, JRC-CDE, RD3 +Individual observations;;date of observation;date;1;TRUE;;;;;;http://purl.obolibrary.org/obo/NCIT_C119798;The date on which the clinical assement was made;RD3 +Individual observations;;age at observation;period;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C192236;"The age of the individual at the time of observation (e.g., ""P55Y8M12D"")";Beacon v2,RD3 +Individual observations;;type of visit;ontology;;;;Visit type;;;;http://purl.obolibrary.org/obo/NCIT_C103165;The kind of visit undertaken by the individual within a study, such as inpatient, outpatient, telephone, baseline, follow up, etc.;FAIR Genomes, JRC-CDE, RD3 +Clinical observations;Individual observations;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C87853;This table extends observations with clinical details compatible with phenopacket;RD3 +Clinical observations;;phenotypes;refback;;;;Phenotype observations;;part of clinical observation;;http://purl.obolibrary.org/obo/NCIT_C16977;The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. In medical context, these are often the symptoms caused by a disease.;FAIR Genomes, RD3 +Clinical observations;;diseases;refback;;;;Disease history;;part of clinical observation;;http://purl.obolibrary.org/obo/NCIT_C15607;Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function.;FAIR Genomes, RD3 +Clinical observations;;measurements;refback;;;;Measurements;;part of clinical observation;;http://purl.obolibrary.org/obo/NCIT_C25209;Annotation used to indicate the size or magnitude of something that was determined by comparison to a standard;FAIR Genomes, RD3 +Clinical observations;;molecular diagnosis gene;ontology_array;;;;Genes;;;;http://purl.obolibrary.org/obo/NCIT_C36391;Gene affected by pathogenic variation that is causal for disease of the individual;FAIR Genomes +Clinical observations;;molecular diagnosis other;text;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C20826;Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.;FAIR Genomes +Clinical observations;;is solved;bool;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25587;An indication that diagnosis is given and the case is no longer considered unsolved.;RD3 +Clinical observations;;date solved;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C119798;The date on which a case was considered solved (i.e., a diagnosis was made);RD3 +Clinical observations;;medication;ontology_array;;;;Medication;;;;http://purl.obolibrary.org/obo/NCIT_C459;A drug product that contains one or more active and/or inactive ingredients used by the individual intended to treat, prevent or alleviate the symptoms of disease. Any hormone therapies, gender-related or otherwise, should also be recorded here.;FAIR Genomes +Clinical observations;;drug regimen;text;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C142516;The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.;FAIR Genomes +Clinical observations;;medical history;ontology_array;;;;MedicalHistory;;;;http://purl.obolibrary.org/obo/NCIT_C18772;A record of a individual's background regarding health, occurrence of disease events and surgical procedures;FAIR Genomes +Clinical observations;;date of first contact;date;;;;;;;;http://purl.bioontology.org/ontology/LNC/MTHU048806;The date on which contact with the individual was initiated;FAIR Genomes, JRC-CDE +Clinical observations;;date of last contact;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C156916;The date on which contact with the individual was last made; +Clinical observations;;classification of functioning;text;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C21007;An individual's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF);FAIR Genomes, JRC-CDE +Clinical observations;;material used in diagnosis;text;;;;;;;;http://semanticscience.org/resource/SIO_000641;A description of one or more materials used to make a diagnosis;FAIR Genomes +Phenotype observations;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C16977;Beacon v2 Individuals PhenotypicFeatures;Beacon v2,RD3 +Phenotype observations;;part of clinical observation;ref;1;TRUE;;Clinical observations;;;;http://purl.obolibrary.org/obo/NCIT_C87853;"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")";Beacon v2,RD3 +Phenotype observations;;type;ontology;1;TRUE;;Phenotypes;;;;http://semanticscience.org/resource/SIO_010056;"A term denoting a phenotypic feature. E.g. ""Abnormality of body height""";Beacon v2,RD3 +Phenotype observations;;excluded;bool;;;;;;;;http://purl.obolibrary.org/obo/HP_0040285;An indication if the phenotype was observed or not. The default is ÔfalseÕ, in other words the phenotype was observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be absent.;Beacon v2,RD3 +Phenotype observations;;modifiers;ontology_array;;;;Phenotypes;;;;http://purl.obolibrary.org/obo/HP_0012823;Additional terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. E.g. Exacerbated by tobacco use;Beacon v2,RD3 +Phenotype observations;;severity;ontology;;;;Severity;;;;http://purl.obolibrary.org/obo/HP_0012824;"A value that describes the intensity of the phenotype (e.g., ""Profound"")";Beacon v2,RD3 +Disease history;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C15607;History of diagnoses of an individual at a specific timepoints;Beacon v2,RD3 +Disease history;;part of clinical observation;ref;1;TRUE;;Clinical observations;;;;http://purl.obolibrary.org/obo/NCIT_C87853;"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")";Beacon v2,RD3 +Disease history;;disease;ontology;1;TRUE;;Diseases;;;;http://semanticscience.org/resource/SIO_001331;"The diagnosis assigned for this particular observation (e.g., ""Spinocerebellar ataxia type 34"")";Beacon v2,RD3 +Disease history;;age group at onset;ontology;;;;Age groups;;;;http://www.ebi.ac.uk/efo/EFO_0004847, http://purl.obolibrary.org/obo/NCIT_C20587;"A categorical value that groups this individual's age of onset into groups (e.g., ""Adult"", ""18-24 years"", etc.)";Beacon v2,RD3 +Disease history;;age of onset;period;;;;;;;;http://www.ebi.ac.uk/efo/EFO_0004847;"The age at which manifestations of the diseaese first appeared (e.g., ""P32Y6M1D"")";Beacon v2,RD3 +Disease history;;age group at diagnosis;ontology;;;;Age groups;;;;http://www.ebi.ac.uk/efo/EFO_0004918, http://purl.obolibrary.org/obo/NCIT_C20587;"A categorical value that groups this individual's age at diagnosis into groups (e.g., ""Adult"", ""18-24 years"", etc.)";RD3,Beacon v2 Vivify add-on +Disease history;;age at diagnosis;period;;;;;;;;http://www.ebi.ac.uk/efo/EFO_0004918;"The age at which the diagnosis was made (e.g., ""P32Y6M1D"")";RD3,Beacon v2 Vivify add-on +Disease history;;has family history;bool;;;;;;;;http://purl.obolibrary.org/obo/HP_0032316;An indication if the diagnosis is present in one or more family members or other relatives;Beacon v2,RD3 +Disease history;;disease severity;ontology;;;;Severity;;;;http://purl.obolibrary.org/obo/HP_0012824;"A value that describes the intensity of the disease (e.g., ""Profound"")";Beacon v2,RD3 +Disease history;;disease stage;ontology;;;;DiseaseStage;;;;http://purl.obolibrary.org/obo/OBI_0000278;"A part of an occurrence of a disease process which is associated with position in the normal progression of the disease (e.g., ""acute onset"")";Beacon v2,RD3 +Measurements;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25209;Additional clinical measurements collected as part of the clinical observation;Beacon v2,RD3 +Measurements;;part of clinical observation;ref;1;TRUE;;Clinical observations;;;;http://purl.obolibrary.org/obo/NCIT_C87853;"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")";Beacon v2,RD3 +Measurements;;code;ontology;1;TRUE;;AnalysesPerformed;;;;http://purl.obolibrary.org/obo/NCIT_C25162;"A unique code that identifies or categorises this measurement (e.g., ""Metabolomics"")";Beacon v2,RD3 +Measurements;;variable;string;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C54166;"A name that describes the measurement (e.g.. ""Blood platelet count"")";RD3,Beacon v2 EMX2 add-on +Measurements;;value;int;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25712;"The value that was measured, collected, derived, etc. (e.g. ""55345"")";Beacon v2,RD3 +Measurements;;unit;ontology;;;;Units;;;;http://purl.obolibrary.org/obo/NCIT_C25709;"A value that specifes the measured value (e.g., ""Per Millimeter"")";Beacon v2,RD3 \ No newline at end of file From c4913ba8be142c09ecafc1af305d01c0504cbbca Mon Sep 17 00:00:00 2001 From: dcruvolo Date: Wed, 8 Jan 2025 11:17:53 +0100 Subject: [PATCH 03/11] fix: reverted auto_id --- data/portal/Individual observations.csv | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/data/portal/Individual observations.csv b/data/portal/Individual observations.csv index 00d46a46ec..a7e4afb9b5 100644 --- a/data/portal/Individual observations.csv +++ b/data/portal/Individual observations.csv @@ -1,7 +1,9 @@ tableName;tableExtends;columnName;columnType;key;required;refSchema;refTable;refLink;refBack;validation;semantics;description;profiles Individual observations;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25398;Findings and circumstances relating to the examination and treatment of a individual;FAIR Genomes, JRC-CDE,RD3 -Individual observations;;individual;ref;1;TRUE;;Individuals;;;;http://purl.obolibrary.org/obo/IAO_0000136;A reference to the individual whom this clinical information is about;FAIR Genomes, JRC-CDE, RD3 -Individual observations;;date of observation;date;1;TRUE;;;;;;http://purl.obolibrary.org/obo/NCIT_C119798;The date on which the clinical assement was made;RD3 +Individual observations;;id;auto_id;1;TRUE;;;;;;;; +Individual observations;;individual;ref;;TRUE;;Individuals;;;;http://purl.obolibrary.org/obo/IAO_0000136;A reference to the individual whom this clinical information is about;FAIR Genomes, JRC-CDE, RD3 +Individual observations;;date saved in database;date;;;;;;;;;; +Individual observations;;date of observation;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C119798;The date on which the clinical assement was made;RD3 Individual observations;;age at observation;period;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C192236;"The age of the individual at the time of observation (e.g., ""P55Y8M12D"")";Beacon v2,RD3 Individual observations;;type of visit;ontology;;;;Visit type;;;;http://purl.obolibrary.org/obo/NCIT_C103165;The kind of visit undertaken by the individual within a study, such as inpatient, outpatient, telephone, baseline, follow up, etc.;FAIR Genomes, JRC-CDE, RD3 Clinical observations;Individual observations;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C87853;This table extends observations with clinical details compatible with phenopacket;RD3 From 13f356528dd272e1779ce3fcc4ac61e341ec47ab Mon Sep 17 00:00:00 2001 From: dcruvolo Date: Wed, 8 Jan 2025 12:07:25 +0100 Subject: [PATCH 04/11] fixed separator --- data/portal/Biosamples.csv | 52 +++++++------- data/portal/Individual observations.csv | 90 ++++++++++++------------- 2 files changed, 71 insertions(+), 71 deletions(-) diff --git a/data/portal/Biosamples.csv b/data/portal/Biosamples.csv index c52d02819f..b37d0d57c1 100644 --- a/data/portal/Biosamples.csv +++ b/data/portal/Biosamples.csv @@ -1,26 +1,26 @@ -tableName;tableExtends;columnName;columnType;key;required;refSchema;refTable;refLink;refBack;validation;semantics;description;profiles -Biosamples;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C43376;A natural substance derived from living organisms such as cells, tissues, proteins, and DNA;Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples;;id;string;1;TRUE;;;;;;http://purl.obolibrary.org/obo/NCIT_C93400;A unique proper name or character sequence that identifies this particular material;Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples;;alternate ids;string_array;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C90353;A backup sequence of characters used to identify an entity;RD3 -Biosamples;;material type;ontology;;;;BiospecimenType;;;;http://purl.obolibrary.org/obo/NCIT_C70713;The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes;FAIR Genomes, RD3 -Biosamples;;pathological state;ontology;;TRUE;;PathologicalState;;;;http://purl.obolibrary.org/obo/NCIT_C28257;An examination that is performed to determine the extent of the spread of cancer based on histopathologic examination of one or more pathology specimens. Pathologic staging uses evidence acquired during the process of clinical staging, supplemented by histopathologic examination of surgical specimens.;Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples;;anatomical location;ontology;;TRUE;;AnatomicalLocation;;;;http://purl.obolibrary.org/obo/NCIT_C170983;The specific anatomical or biological region associated with a tissue or organ specimen.;Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples;;anatomical location other;string;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C170983;Additional description on the anatomical or biological region associated with a tissue or organ specimen;Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples;;collected at organisation;ref;;;;Organisations;;;;http://purl.obolibrary.org/obo/OBIB_0000085;The geographic location where biosample collection took place;RD3 -Biosamples;;collected by;ref_array;;;;Contacts;;;;http://purl.obolibrary.org/obo/OBI_0001769;The person or persons responsible for biosample collection;RD3 -Biosamples;;date of collection;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C82515;Date on which the material was collected;Beacon v2, FAIR Genomes, DCAT examples -Biosamples;;age group of individual at collection;ontology;;;;Age groups;;;;http://purl.obolibrary.org/obo/NCIT_C20587;"A categorical value that groups this individual by age at the time of sample collection (e.g., ""Adult"", ""18-24 years"", etc.)"; -Biosamples;;age of individual at collection;period;;;;;;;;http://purl.obolibrary.org/obo/GENEPIO_0001775;The age of the individual at the time of sample collection;Beacon v2, DCAT examples -Biosamples;;affiliated organisations;ref_array;;;;Organisations;;;;http://purl.obolibrary.org/obo/NCIT_C25412;One or more associations between the record and an organisation or institution.;RD3 -Biosamples;;collected from individual;ref;;;;Individuals;;;;http://semanticscience.org/resource/SIO_000244;Reference to the person from whom this material was collected.;FAIR Genomes, RD3 -Biosamples;;protocol used;refback;;;;Protocol parameters;;identifier;;http://www.ebi.ac.uk/efo/EFO_0005518;A description of the procedures whereby biological samples for an experiment are sourced.;Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples;;registration timestamp;datetime;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25646;Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.;FAIR Genomes -Biosamples;;storage conditions;ontology;;;;Storage conditions;;;;http://purl.obolibrary.org/obo/NCIT_C96145;The conditions under which this biological material was stored.;FAIR Genomes -Biosamples;;storage location;ontology;;;;Storage locations;;;;http://purl.obolibrary.org/obo/GENEPIO_0100594;A place on the Earth where this material is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which freezer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).;FAIR Genomes -Biosamples;;date of expiration;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C164516;The date on which this material is no longer regarded as fit for use.;FAIR Genomes -Biosamples;;percentage tumor cells;decimal;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C127771;The percentage of tumor cells compared to total cells present in this material.;FAIR Genomes, RD3 -Biosamples;;derived from biosample;ref;;;;Biosamples;;;;http://purl.obolibrary.org/obo/OBI_0002077;If applicable, a reference to a biosample that this material was derived from;FAIR Genomes -Biosamples;;failed quality control;bool;;;;;;;;http://purl.obolibrary.org/obo/GENEPIO_0100564;An indication confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.;RD3 -Biosamples;;files;refback;;;;Files;;biosamples;;http://semanticscience.org/resource/SIO_000396;A reference to one or more files that contain information about this individual;RD3 -Biosamples;;included in datasets;ref_array;;;;Datasets;;;;http://purl.obolibrary.org/obo/HSO_0000370;A reference to one or more datasets that organises records for in a meaningful way (e.g., data releases, subpopulations, cohorts, etc.);RD3 -Biosamples;;comments;text;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25393;A written explanation, observation or criticism added to textual material.;RD3 \ No newline at end of file +tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles +Biosamples,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43376,A natural substance derived from living organisms such as cells, tissues, proteins, and DNA,Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples,,id,string,1,TRUE,,,,,,http://purl.obolibrary.org/obo/NCIT_C93400,A unique proper name or character sequence that identifies this particular material,Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples,,alternate ids,string_array,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C90353,A backup sequence of characters used to identify an entity,RD3 +Biosamples,,material type,ontology,,,,BiospecimenType,,,,http://purl.obolibrary.org/obo/NCIT_C70713,The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes,FAIR Genomes, RD3 +Biosamples,,pathological state,ontology,,TRUE,,PathologicalState,,,,http://purl.obolibrary.org/obo/NCIT_C28257,An examination that is performed to determine the extent of the spread of cancer based on histopathologic examination of one or more pathology specimens. Pathologic staging uses evidence acquired during the process of clinical staging, supplemented by histopathologic examination of surgical specimens.,Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples,,anatomical location,ontology,,TRUE,,AnatomicalLocation,,,,http://purl.obolibrary.org/obo/NCIT_C170983,The specific anatomical or biological region associated with a tissue or organ specimen.,Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples,,anatomical location other,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C170983,Additional description on the anatomical or biological region associated with a tissue or organ specimen,Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples,,collected at organisation,ref,,,,Organisations,,,,http://purl.obolibrary.org/obo/OBIB_0000085,The geographic location where biosample collection took place,RD3 +Biosamples,,collected by,ref_array,,,,Contacts,,,,http://purl.obolibrary.org/obo/OBI_0001769,The person or persons responsible for biosample collection,RD3 +Biosamples,,date of collection,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C82515,Date on which the material was collected,Beacon v2, FAIR Genomes, DCAT examples +Biosamples,,age group of individual at collection,ontology,,,,Age groups,,,,http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual by age at the time of sample collection (e.g., ""Adult"", ""18-24 years"", etc.)", +Biosamples,,age of individual at collection,period,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0001775,The age of the individual at the time of sample collection,Beacon v2, DCAT examples +Biosamples,,affiliated organisations,ref_array,,,,Organisations,,,,http://purl.obolibrary.org/obo/NCIT_C25412,One or more associations between the record and an organisation or institution.,RD3 +Biosamples,,collected from individual,ref,,,,Individuals,,,,http://semanticscience.org/resource/SIO_000244,Reference to the person from whom this material was collected.,FAIR Genomes, RD3 +Biosamples,,protocol used,refback,,,,Protocol parameters,,identifier,,http://www.ebi.ac.uk/efo/EFO_0005518,A description of the procedures whereby biological samples for an experiment are sourced.,Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples,,registration timestamp,datetime,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25646,Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.,FAIR Genomes +Biosamples,,storage conditions,ontology,,,,Storage conditions,,,,http://purl.obolibrary.org/obo/NCIT_C96145,The conditions under which this biological material was stored.,FAIR Genomes +Biosamples,,storage location,ontology,,,,Storage locations,,,,http://purl.obolibrary.org/obo/GENEPIO_0100594,A place on the Earth where this material is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which freezer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).,FAIR Genomes +Biosamples,,date of expiration,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C164516,The date on which this material is no longer regarded as fit for use.,FAIR Genomes +Biosamples,,percentage tumor cells,decimal,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C127771,The percentage of tumor cells compared to total cells present in this material.,FAIR Genomes, RD3 +Biosamples,,derived from biosample,ref,,,,Biosamples,,,,http://purl.obolibrary.org/obo/OBI_0002077,If applicable, a reference to a biosample that this material was derived from,FAIR Genomes +Biosamples,,failed quality control,bool,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0100564,An indication confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.,RD3 +Biosamples,,files,refback,,,,Files,,biosamples,,http://semanticscience.org/resource/SIO_000396,A reference to one or more files that contain information about this individual,RD3 +Biosamples,,included in datasets,ref_array,,,,Datasets,,,,http://purl.obolibrary.org/obo/HSO_0000370,A reference to one or more datasets that organises records for in a meaningful way (e.g., data releases, subpopulations, cohorts, etc.),RD3 +Biosamples,,comments,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25393,A written explanation, observation or criticism added to textual material.,RD3 \ No newline at end of file diff --git a/data/portal/Individual observations.csv b/data/portal/Individual observations.csv index a7e4afb9b5..128e54a6c8 100644 --- a/data/portal/Individual observations.csv +++ b/data/portal/Individual observations.csv @@ -1,45 +1,45 @@ -tableName;tableExtends;columnName;columnType;key;required;refSchema;refTable;refLink;refBack;validation;semantics;description;profiles -Individual observations;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25398;Findings and circumstances relating to the examination and treatment of a individual;FAIR Genomes, JRC-CDE,RD3 -Individual observations;;id;auto_id;1;TRUE;;;;;;;; -Individual observations;;individual;ref;;TRUE;;Individuals;;;;http://purl.obolibrary.org/obo/IAO_0000136;A reference to the individual whom this clinical information is about;FAIR Genomes, JRC-CDE, RD3 -Individual observations;;date saved in database;date;;;;;;;;;; -Individual observations;;date of observation;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C119798;The date on which the clinical assement was made;RD3 -Individual observations;;age at observation;period;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C192236;"The age of the individual at the time of observation (e.g., ""P55Y8M12D"")";Beacon v2,RD3 -Individual observations;;type of visit;ontology;;;;Visit type;;;;http://purl.obolibrary.org/obo/NCIT_C103165;The kind of visit undertaken by the individual within a study, such as inpatient, outpatient, telephone, baseline, follow up, etc.;FAIR Genomes, JRC-CDE, RD3 -Clinical observations;Individual observations;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C87853;This table extends observations with clinical details compatible with phenopacket;RD3 -Clinical observations;;phenotypes;refback;;;;Phenotype observations;;part of clinical observation;;http://purl.obolibrary.org/obo/NCIT_C16977;The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. In medical context, these are often the symptoms caused by a disease.;FAIR Genomes, RD3 -Clinical observations;;diseases;refback;;;;Disease history;;part of clinical observation;;http://purl.obolibrary.org/obo/NCIT_C15607;Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function.;FAIR Genomes, RD3 -Clinical observations;;measurements;refback;;;;Measurements;;part of clinical observation;;http://purl.obolibrary.org/obo/NCIT_C25209;Annotation used to indicate the size or magnitude of something that was determined by comparison to a standard;FAIR Genomes, RD3 -Clinical observations;;molecular diagnosis gene;ontology_array;;;;Genes;;;;http://purl.obolibrary.org/obo/NCIT_C36391;Gene affected by pathogenic variation that is causal for disease of the individual;FAIR Genomes -Clinical observations;;molecular diagnosis other;text;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C20826;Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.;FAIR Genomes -Clinical observations;;is solved;bool;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25587;An indication that diagnosis is given and the case is no longer considered unsolved.;RD3 -Clinical observations;;date solved;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C119798;The date on which a case was considered solved (i.e., a diagnosis was made);RD3 -Clinical observations;;medication;ontology_array;;;;Medication;;;;http://purl.obolibrary.org/obo/NCIT_C459;A drug product that contains one or more active and/or inactive ingredients used by the individual intended to treat, prevent or alleviate the symptoms of disease. Any hormone therapies, gender-related or otherwise, should also be recorded here.;FAIR Genomes -Clinical observations;;drug regimen;text;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C142516;The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.;FAIR Genomes -Clinical observations;;medical history;ontology_array;;;;MedicalHistory;;;;http://purl.obolibrary.org/obo/NCIT_C18772;A record of a individual's background regarding health, occurrence of disease events and surgical procedures;FAIR Genomes -Clinical observations;;date of first contact;date;;;;;;;;http://purl.bioontology.org/ontology/LNC/MTHU048806;The date on which contact with the individual was initiated;FAIR Genomes, JRC-CDE -Clinical observations;;date of last contact;date;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C156916;The date on which contact with the individual was last made; -Clinical observations;;classification of functioning;text;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C21007;An individual's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF);FAIR Genomes, JRC-CDE -Clinical observations;;material used in diagnosis;text;;;;;;;;http://semanticscience.org/resource/SIO_000641;A description of one or more materials used to make a diagnosis;FAIR Genomes -Phenotype observations;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C16977;Beacon v2 Individuals PhenotypicFeatures;Beacon v2,RD3 -Phenotype observations;;part of clinical observation;ref;1;TRUE;;Clinical observations;;;;http://purl.obolibrary.org/obo/NCIT_C87853;"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")";Beacon v2,RD3 -Phenotype observations;;type;ontology;1;TRUE;;Phenotypes;;;;http://semanticscience.org/resource/SIO_010056;"A term denoting a phenotypic feature. E.g. ""Abnormality of body height""";Beacon v2,RD3 -Phenotype observations;;excluded;bool;;;;;;;;http://purl.obolibrary.org/obo/HP_0040285;An indication if the phenotype was observed or not. The default is ÔfalseÕ, in other words the phenotype was observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be absent.;Beacon v2,RD3 -Phenotype observations;;modifiers;ontology_array;;;;Phenotypes;;;;http://purl.obolibrary.org/obo/HP_0012823;Additional terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. E.g. Exacerbated by tobacco use;Beacon v2,RD3 -Phenotype observations;;severity;ontology;;;;Severity;;;;http://purl.obolibrary.org/obo/HP_0012824;"A value that describes the intensity of the phenotype (e.g., ""Profound"")";Beacon v2,RD3 -Disease history;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C15607;History of diagnoses of an individual at a specific timepoints;Beacon v2,RD3 -Disease history;;part of clinical observation;ref;1;TRUE;;Clinical observations;;;;http://purl.obolibrary.org/obo/NCIT_C87853;"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")";Beacon v2,RD3 -Disease history;;disease;ontology;1;TRUE;;Diseases;;;;http://semanticscience.org/resource/SIO_001331;"The diagnosis assigned for this particular observation (e.g., ""Spinocerebellar ataxia type 34"")";Beacon v2,RD3 -Disease history;;age group at onset;ontology;;;;Age groups;;;;http://www.ebi.ac.uk/efo/EFO_0004847, http://purl.obolibrary.org/obo/NCIT_C20587;"A categorical value that groups this individual's age of onset into groups (e.g., ""Adult"", ""18-24 years"", etc.)";Beacon v2,RD3 -Disease history;;age of onset;period;;;;;;;;http://www.ebi.ac.uk/efo/EFO_0004847;"The age at which manifestations of the diseaese first appeared (e.g., ""P32Y6M1D"")";Beacon v2,RD3 -Disease history;;age group at diagnosis;ontology;;;;Age groups;;;;http://www.ebi.ac.uk/efo/EFO_0004918, http://purl.obolibrary.org/obo/NCIT_C20587;"A categorical value that groups this individual's age at diagnosis into groups (e.g., ""Adult"", ""18-24 years"", etc.)";RD3,Beacon v2 Vivify add-on -Disease history;;age at diagnosis;period;;;;;;;;http://www.ebi.ac.uk/efo/EFO_0004918;"The age at which the diagnosis was made (e.g., ""P32Y6M1D"")";RD3,Beacon v2 Vivify add-on -Disease history;;has family history;bool;;;;;;;;http://purl.obolibrary.org/obo/HP_0032316;An indication if the diagnosis is present in one or more family members or other relatives;Beacon v2,RD3 -Disease history;;disease severity;ontology;;;;Severity;;;;http://purl.obolibrary.org/obo/HP_0012824;"A value that describes the intensity of the disease (e.g., ""Profound"")";Beacon v2,RD3 -Disease history;;disease stage;ontology;;;;DiseaseStage;;;;http://purl.obolibrary.org/obo/OBI_0000278;"A part of an occurrence of a disease process which is associated with position in the normal progression of the disease (e.g., ""acute onset"")";Beacon v2,RD3 -Measurements;;;;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25209;Additional clinical measurements collected as part of the clinical observation;Beacon v2,RD3 -Measurements;;part of clinical observation;ref;1;TRUE;;Clinical observations;;;;http://purl.obolibrary.org/obo/NCIT_C87853;"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")";Beacon v2,RD3 -Measurements;;code;ontology;1;TRUE;;AnalysesPerformed;;;;http://purl.obolibrary.org/obo/NCIT_C25162;"A unique code that identifies or categorises this measurement (e.g., ""Metabolomics"")";Beacon v2,RD3 -Measurements;;variable;string;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C54166;"A name that describes the measurement (e.g.. ""Blood platelet count"")";RD3,Beacon v2 EMX2 add-on -Measurements;;value;int;;;;;;;;http://purl.obolibrary.org/obo/NCIT_C25712;"The value that was measured, collected, derived, etc. (e.g. ""55345"")";Beacon v2,RD3 -Measurements;;unit;ontology;;;;Units;;;;http://purl.obolibrary.org/obo/NCIT_C25709;"A value that specifes the measured value (e.g., ""Per Millimeter"")";Beacon v2,RD3 \ No newline at end of file +tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles +Individual observations,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25398,Findings and circumstances relating to the examination and treatment of a individual,FAIR Genomes, JRC-CDE,RD3 +Individual observations,,id,auto_id,1,TRUE,,,,,,,, +Individual observations,,individual,ref,,TRUE,,Individuals,,,,http://purl.obolibrary.org/obo/IAO_0000136,A reference to the individual whom this clinical information is about,FAIR Genomes, JRC-CDE, RD3 +Individual observations,,date saved in database,date,,,,,,,,,, +Individual observations,,date of observation,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C119798,The date on which the clinical assement was made,RD3 +Individual observations,,age at observation,period,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C192236,"The age of the individual at the time of observation (e.g., ""P55Y8M12D"")",Beacon v2,RD3 +Individual observations,,type of visit,ontology,,,,Visit type,,,,http://purl.obolibrary.org/obo/NCIT_C103165,The kind of visit undertaken by the individual within a study, such as inpatient, outpatient, telephone, baseline, follow up, etc.,FAIR Genomes, JRC-CDE, RD3 +Clinical observations,Individual observations,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C87853,This table extends observations with clinical details compatible with phenopacket,RD3 +Clinical observations,,phenotypes,refback,,,,Phenotype observations,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C16977,The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. In medical context, these are often the symptoms caused by a disease.,FAIR Genomes, RD3 +Clinical observations,,diseases,refback,,,,Disease history,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C15607,Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function.,FAIR Genomes, RD3 +Clinical observations,,measurements,refback,,,,Measurements,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C25209,Annotation used to indicate the size or magnitude of something that was determined by comparison to a standard,FAIR Genomes, RD3 +Clinical observations,,molecular diagnosis gene,ontology_array,,,,Genes,,,,http://purl.obolibrary.org/obo/NCIT_C36391,Gene affected by pathogenic variation that is causal for disease of the individual,FAIR Genomes +Clinical observations,,molecular diagnosis other,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C20826,Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.,FAIR Genomes +Clinical observations,,is solved,bool,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25587,An indication that diagnosis is given and the case is no longer considered unsolved.,RD3 +Clinical observations,,date solved,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C119798,The date on which a case was considered solved (i.e., a diagnosis was made),RD3 +Clinical observations,,medication,ontology_array,,,,Medication,,,,http://purl.obolibrary.org/obo/NCIT_C459,A drug product that contains one or more active and/or inactive ingredients used by the individual intended to treat, prevent or alleviate the symptoms of disease. Any hormone therapies, gender-related or otherwise, should also be recorded here.,FAIR Genomes +Clinical observations,,drug regimen,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C142516,The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.,FAIR Genomes +Clinical observations,,medical history,ontology_array,,,,MedicalHistory,,,,http://purl.obolibrary.org/obo/NCIT_C18772,A record of a individual's background regarding health, occurrence of disease events and surgical procedures,FAIR Genomes +Clinical observations,,date of first contact,date,,,,,,,,http://purl.bioontology.org/ontology/LNC/MTHU048806,The date on which contact with the individual was initiated,FAIR Genomes, JRC-CDE +Clinical observations,,date of last contact,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C156916,The date on which contact with the individual was last made, +Clinical observations,,classification of functioning,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C21007,An individual's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF),FAIR Genomes, JRC-CDE +Clinical observations,,material used in diagnosis,text,,,,,,,,http://semanticscience.org/resource/SIO_000641,A description of one or more materials used to make a diagnosis,FAIR Genomes +Phenotype observations,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C16977,Beacon v2 Individuals PhenotypicFeatures,Beacon v2,RD3 +Phenotype observations,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")",Beacon v2,RD3 +Phenotype observations,,type,ontology,1,TRUE,,Phenotypes,,,,http://semanticscience.org/resource/SIO_010056,"A term denoting a phenotypic feature. E.g. ""Abnormality of body height""",Beacon v2,RD3 +Phenotype observations,,excluded,bool,,,,,,,,http://purl.obolibrary.org/obo/HP_0040285,An indication if the phenotype was observed or not. The default is ÔfalseÕ, in other words the phenotype was observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be absent.,Beacon v2,RD3 +Phenotype observations,,modifiers,ontology_array,,,,Phenotypes,,,,http://purl.obolibrary.org/obo/HP_0012823,Additional terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. E.g. Exacerbated by tobacco use,Beacon v2,RD3 +Phenotype observations,,severity,ontology,,,,Severity,,,,http://purl.obolibrary.org/obo/HP_0012824,"A value that describes the intensity of the phenotype (e.g., ""Profound"")",Beacon v2,RD3 +Disease history,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C15607,History of diagnoses of an individual at a specific timepoints,Beacon v2,RD3 +Disease history,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")",Beacon v2,RD3 +Disease history,,disease,ontology,1,TRUE,,Diseases,,,,http://semanticscience.org/resource/SIO_001331,"The diagnosis assigned for this particular observation (e.g., ""Spinocerebellar ataxia type 34"")",Beacon v2,RD3 +Disease history,,age group at onset,ontology,,,,Age groups,,,,http://www.ebi.ac.uk/efo/EFO_0004847, http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual's age of onset into groups (e.g., ""Adult"", ""18-24 years"", etc.)",Beacon v2,RD3 +Disease history,,age of onset,period,,,,,,,,http://www.ebi.ac.uk/efo/EFO_0004847,"The age at which manifestations of the diseaese first appeared (e.g., ""P32Y6M1D"")",Beacon v2,RD3 +Disease history,,age group at diagnosis,ontology,,,,Age groups,,,,http://www.ebi.ac.uk/efo/EFO_0004918, http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual's age at diagnosis into groups (e.g., ""Adult"", ""18-24 years"", etc.)",RD3,Beacon v2 Vivify add-on +Disease history,,age at diagnosis,period,,,,,,,,http://www.ebi.ac.uk/efo/EFO_0004918,"The age at which the diagnosis was made (e.g., ""P32Y6M1D"")",RD3,Beacon v2 Vivify add-on +Disease history,,has family history,bool,,,,,,,,http://purl.obolibrary.org/obo/HP_0032316,An indication if the diagnosis is present in one or more family members or other relatives,Beacon v2,RD3 +Disease history,,disease severity,ontology,,,,Severity,,,,http://purl.obolibrary.org/obo/HP_0012824,"A value that describes the intensity of the disease (e.g., ""Profound"")",Beacon v2,RD3 +Disease history,,disease stage,ontology,,,,DiseaseStage,,,,http://purl.obolibrary.org/obo/OBI_0000278,"A part of an occurrence of a disease process which is associated with position in the normal progression of the disease (e.g., ""acute onset"")",Beacon v2,RD3 +Measurements,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25209,Additional clinical measurements collected as part of the clinical observation,Beacon v2,RD3 +Measurements,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")",Beacon v2,RD3 +Measurements,,code,ontology,1,TRUE,,AnalysesPerformed,,,,http://purl.obolibrary.org/obo/NCIT_C25162,"A unique code that identifies or categorises this measurement (e.g., ""Metabolomics"")",Beacon v2,RD3 +Measurements,,variable,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C54166,"A name that describes the measurement (e.g.. ""Blood platelet count"")",RD3,Beacon v2 EMX2 add-on +Measurements,,value,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25712,"The value that was measured, collected, derived, etc. (e.g. ""55345"")",Beacon v2,RD3 +Measurements,,unit,ontology,,,,Units,,,,http://purl.obolibrary.org/obo/NCIT_C25709,"A value that specifes the measured value (e.g., ""Per Millimeter"")",Beacon v2,RD3 \ No newline at end of file From 202d36202bc7af2a241969fac609e3c673b4b97c Mon Sep 17 00:00:00 2001 From: Oudijk Date: Thu, 9 Jan 2025 15:16:36 +0100 Subject: [PATCH 05/11] fix merge conflict --- data/_ontologies/AllowRecontacting.csv | 20 ++++++++-------- data/portal/Biosamples.csv | 32 +++++++++++++------------- 2 files changed, 27 insertions(+), 25 deletions(-) diff --git a/data/_ontologies/AllowRecontacting.csv b/data/_ontologies/AllowRecontacting.csv index d5241a6b96..d571e709ee 100644 --- a/data/_ontologies/AllowRecontacting.csv +++ b/data/_ontologies/AllowRecontacting.csv @@ -1,9 +1,11 @@ -name,definition,codesystem,code,ontologyTermURI -"Recontacting for additional sampling","Willingness to be recontacted to collect additional material or data from the patient.","FG","0000744","https://w3id.org/fair-genomes/resource/FG_0000744" -"Recontacting for incidental findings","Willingness to be recontacted when new knowledge regarding incidental findings becomes available to benefit the patient.","FG","0000745","https://w3id.org/fair-genomes/resource/FG_0000745" -"Recontacting for diagnostic question","Willingness to be recontacted when new knowledge regarding the diagnostic question becomes available to benefit the patient.","FG","0000746","https://w3id.org/fair-genomes/resource/FG_0000746", -"No recontacting for additional sampling",,,,, -"No recontacting for incidential findings",,,,, -"No recontacting for diagnostic question",,,,, -"Allow use in MatchMaker",,,,, -"No use in MatchMaker",,,,, +name;definition;codesystem;code;ontologyTermURI; +Recontacting for additional sampling;Willingness to be recontacted to collect additional material or data from the patient.;FG;744;https://w3id.org/fair-genomes/resource/FG_0000744; +Recontacting for incidental findings;Willingness to be recontacted when new knowledge regarding incidental findings becomes available to benefit the patient.;FG;745;https://w3id.org/fair-genomes/resource/FG_0000745; +Recontacting for diagnostic question;Willingness to be recontacted when new knowledge regarding the diagnostic question becomes available to benefit the patient.;FG;746;https://w3id.org/fair-genomes/resource/FG_0000746; +No recontacting for additional sampling;;;;; +No recontacting for incidential findings;;;;; +No recontacting for diagnostic question;;;;; +Allow use in MatchMaker;;;;; +No use in MatchMaker;;;;; +Report incidental findings back;;;;; +No reporting of incidental findings;;;;; \ No newline at end of file diff --git a/data/portal/Biosamples.csv b/data/portal/Biosamples.csv index b37d0d57c1..ec5e2d6186 100644 --- a/data/portal/Biosamples.csv +++ b/data/portal/Biosamples.csv @@ -1,26 +1,26 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles -Biosamples,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43376,A natural substance derived from living organisms such as cells, tissues, proteins, and DNA,Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples,,id,string,1,TRUE,,,,,,http://purl.obolibrary.org/obo/NCIT_C93400,A unique proper name or character sequence that identifies this particular material,Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43376,"A natural substance derived from living organisms such as cells, tissues, proteins, and DNA","Beacon v2, FAIR Genomes, DCAT examples, RD3" +Biosamples,,id,string,1,TRUE,,,,,,http://purl.obolibrary.org/obo/NCIT_C93400,A unique proper name or character sequence that identifies this particular material,"Beacon v2, FAIR Genomes, DCAT examples, RD3" Biosamples,,alternate ids,string_array,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C90353,A backup sequence of characters used to identify an entity,RD3 -Biosamples,,material type,ontology,,,,BiospecimenType,,,,http://purl.obolibrary.org/obo/NCIT_C70713,The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes,FAIR Genomes, RD3 -Biosamples,,pathological state,ontology,,TRUE,,PathologicalState,,,,http://purl.obolibrary.org/obo/NCIT_C28257,An examination that is performed to determine the extent of the spread of cancer based on histopathologic examination of one or more pathology specimens. Pathologic staging uses evidence acquired during the process of clinical staging, supplemented by histopathologic examination of surgical specimens.,Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples,,anatomical location,ontology,,TRUE,,AnatomicalLocation,,,,http://purl.obolibrary.org/obo/NCIT_C170983,The specific anatomical or biological region associated with a tissue or organ specimen.,Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples,,anatomical location other,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C170983,Additional description on the anatomical or biological region associated with a tissue or organ specimen,Beacon v2, FAIR Genomes, DCAT examples, RD3 +Biosamples,,material type,ontology,,,,BiospecimenType,,,,http://purl.obolibrary.org/obo/NCIT_C70713,"The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes","FAIR Genomes, RD3" +Biosamples,,pathological state,ontology,,,,PathologicalState,,,,http://purl.obolibrary.org/obo/NCIT_C28257,"An examination that is performed to determine the extent of the spread of cancer based on histopathologic examination of one or more pathology specimens. Pathologic staging uses evidence acquired during the process of clinical staging, supplemented by histopathologic examination of surgical specimens.","Beacon v2, FAIR Genomes, DCAT examples, RD3" +Biosamples,,anatomical location,ontology,,,,AnatomicalLocation,,,,http://purl.obolibrary.org/obo/NCIT_C170983,The specific anatomical or biological region associated with a tissue or organ specimen.,"Beacon v2, FAIR Genomes, DCAT examples, RD3" +Biosamples,,anatomical location other,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C170983,Additional description on the anatomical or biological region associated with a tissue or organ specimen,"Beacon v2, FAIR Genomes, DCAT examples, RD3" Biosamples,,collected at organisation,ref,,,,Organisations,,,,http://purl.obolibrary.org/obo/OBIB_0000085,The geographic location where biosample collection took place,RD3 Biosamples,,collected by,ref_array,,,,Contacts,,,,http://purl.obolibrary.org/obo/OBI_0001769,The person or persons responsible for biosample collection,RD3 -Biosamples,,date of collection,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C82515,Date on which the material was collected,Beacon v2, FAIR Genomes, DCAT examples +Biosamples,,date of collection,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C82515,Date on which the material was collected,"Beacon v2, FAIR Genomes, DCAT examples" Biosamples,,age group of individual at collection,ontology,,,,Age groups,,,,http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual by age at the time of sample collection (e.g., ""Adult"", ""18-24 years"", etc.)", -Biosamples,,age of individual at collection,period,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0001775,The age of the individual at the time of sample collection,Beacon v2, DCAT examples +Biosamples,,age of individual at collection,period,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0001775,The age of the individual at the time of sample collection,"Beacon v2, DCAT examples" Biosamples,,affiliated organisations,ref_array,,,,Organisations,,,,http://purl.obolibrary.org/obo/NCIT_C25412,One or more associations between the record and an organisation or institution.,RD3 -Biosamples,,collected from individual,ref,,,,Individuals,,,,http://semanticscience.org/resource/SIO_000244,Reference to the person from whom this material was collected.,FAIR Genomes, RD3 -Biosamples,,protocol used,refback,,,,Protocol parameters,,identifier,,http://www.ebi.ac.uk/efo/EFO_0005518,A description of the procedures whereby biological samples for an experiment are sourced.,Beacon v2, FAIR Genomes, DCAT examples, RD3 -Biosamples,,registration timestamp,datetime,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25646,Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.,FAIR Genomes +Biosamples,,collected from individual,ref,,,,Individuals,,,,http://semanticscience.org/resource/SIO_000244,Reference to the person from whom this material was collected.,"FAIR Genomes, RD3" +Biosamples,,protocol used,refback,,,,Protocol parameters,,identifier,,http://www.ebi.ac.uk/efo/EFO_0005518,A description of the procedures whereby biological samples for an experiment are sourced.,"Beacon v2, FAIR Genomes, DCAT examples, RD3" +Biosamples,,registration timestamp,datetime,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25646,"Date and time at which this material was listed or recorded officially, i.e. officially qualified or enrolled.",FAIR Genomes Biosamples,,storage conditions,ontology,,,,Storage conditions,,,,http://purl.obolibrary.org/obo/NCIT_C96145,The conditions under which this biological material was stored.,FAIR Genomes -Biosamples,,storage location,ontology,,,,Storage locations,,,,http://purl.obolibrary.org/obo/GENEPIO_0100594,A place on the Earth where this material is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which freezer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).,FAIR Genomes +Biosamples,,storage location,ontology,,,,Storage locations,,,,http://purl.obolibrary.org/obo/GENEPIO_0100594,"A place on the Earth where this material is located, by its name or by its geographical location. This definition is intentionally vague to allow reuse locally (e.g. which freezer), for contacting (e.g. which institute), broadly for logistical or legal reasons (e.g. city, country or continent).",FAIR Genomes Biosamples,,date of expiration,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C164516,The date on which this material is no longer regarded as fit for use.,FAIR Genomes -Biosamples,,percentage tumor cells,decimal,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C127771,The percentage of tumor cells compared to total cells present in this material.,FAIR Genomes, RD3 -Biosamples,,derived from biosample,ref,,,,Biosamples,,,,http://purl.obolibrary.org/obo/OBI_0002077,If applicable, a reference to a biosample that this material was derived from,FAIR Genomes +Biosamples,,percentage tumor cells,decimal,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C127771,The percentage of tumor cells compared to total cells present in this material.,"FAIR Genomes, RD3" +Biosamples,,derived from biosample,ref,,,,Biosamples,,,,http://purl.obolibrary.org/obo/OBI_0002077,"If applicable, a reference to a biosample that this material was derived from",FAIR Genomes Biosamples,,failed quality control,bool,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0100564,An indication confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.,RD3 Biosamples,,files,refback,,,,Files,,biosamples,,http://semanticscience.org/resource/SIO_000396,A reference to one or more files that contain information about this individual,RD3 -Biosamples,,included in datasets,ref_array,,,,Datasets,,,,http://purl.obolibrary.org/obo/HSO_0000370,A reference to one or more datasets that organises records for in a meaningful way (e.g., data releases, subpopulations, cohorts, etc.),RD3 -Biosamples,,comments,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25393,A written explanation, observation or criticism added to textual material.,RD3 \ No newline at end of file +Biosamples,,included in datasets,ref_array,,,,Datasets,,,,http://purl.obolibrary.org/obo/HSO_0000370,"A reference to one or more datasets that organises records for in a meaningful way (e.g., data releases, subpopulations, cohorts, etc.)",RD3 +Biosamples,,comments,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25393,"A written explanation, observation or criticism added to textual material.",RD3 From cbc4c7a34ae88a77890d068c9da2dac524ff043b Mon Sep 17 00:00:00 2001 From: Oudijk Date: Thu, 9 Jan 2025 15:09:01 +0100 Subject: [PATCH 06/11] Added two ontology files with no changes --- data/_ontologies/AnatomicalLocation.csv | 152 ++++++++++++------------ data/_ontologies/PathologicalState.csv | 16 +-- 2 files changed, 84 insertions(+), 84 deletions(-) diff --git a/data/_ontologies/AnatomicalLocation.csv b/data/_ontologies/AnatomicalLocation.csv index 888d9b0d64..c59288711a 100644 --- a/data/_ontologies/AnatomicalLocation.csv +++ b/data/_ontologies/AnatomicalLocation.csv @@ -1,6 +1,6 @@ name,label,codesystem,code,ontologyTermURI 106004,Structure of posterior carpal region,SNOMED CT,106004,http://purl.bioontology.org/ontology/SNOMEDCT/106004 -110001,"Structure of visceral layer of Bowman's capsule",SNOMED CT,110001,http://purl.bioontology.org/ontology/SNOMEDCT/110001 +110001,Structure of visceral layer of Bowman's capsule,SNOMED CT,110001,http://purl.bioontology.org/ontology/SNOMEDCT/110001 111002,Parathyroid structure,SNOMED CT,111002,http://purl.bioontology.org/ontology/SNOMEDCT/111002 116007,Subcutaneous tissue structure of medial surface of index finger,SNOMED CT,116007,http://purl.bioontology.org/ontology/SNOMEDCT/116007 124002,Structure of coronoid process of mandible,SNOMED CT,124002,http://purl.bioontology.org/ontology/SNOMEDCT/124002 @@ -213,7 +213,7 @@ name,label,codesystem,code,ontologyTermURI 2675006,Structure of anterior ethmoidal artery,SNOMED CT,2675006,http://purl.bioontology.org/ontology/SNOMEDCT/2675006 2682005,Structure of mucous membrane of urinary bladder,SNOMED CT,2682005,http://purl.bioontology.org/ontology/SNOMEDCT/2682005 2686008,Structure of medial olfactory gyrus,SNOMED CT,2686008,http://purl.bioontology.org/ontology/SNOMEDCT/2686008 -2687004,"Structure of Bowman's space",SNOMED CT,2687004,http://purl.bioontology.org/ontology/SNOMEDCT/2687004 +2687004,Structure of Bowman's space,SNOMED CT,2687004,http://purl.bioontology.org/ontology/SNOMEDCT/2687004 2695000,Left maxillary sinus structure,SNOMED CT,2695000,http://purl.bioontology.org/ontology/SNOMEDCT/2695000 2712006,Structure of capsule of ankle joint,SNOMED CT,2712006,http://purl.bioontology.org/ontology/SNOMEDCT/2712006 2718005,Structure of apical foramen of tooth,SNOMED CT,2718005,http://purl.bioontology.org/ontology/SNOMEDCT/2718005 @@ -724,7 +724,7 @@ name,label,codesystem,code,ontologyTermURI 8560002,Structure of interclavicular ligament,SNOMED CT,8560002,http://purl.bioontology.org/ontology/SNOMEDCT/8560002 8568009,Abdominal lymph node structure,SNOMED CT,8568009,http://purl.bioontology.org/ontology/SNOMEDCT/8568009 8590009,Neck of sixteenth rib,SNOMED CT,8590009,http://purl.bioontology.org/ontology/SNOMEDCT/8590009 -8595004,"Structure of Meissner's plexus",SNOMED CT,8595004,http://purl.bioontology.org/ontology/SNOMEDCT/8595004 +8595004,Structure of Meissner's plexus,SNOMED CT,8595004,http://purl.bioontology.org/ontology/SNOMEDCT/8595004 8598002,Vestibulocochlear nerve structure,SNOMED CT,8598002,http://purl.bioontology.org/ontology/SNOMEDCT/8598002 8600008,Cricoid cartilage structure,SNOMED CT,8600008,http://purl.bioontology.org/ontology/SNOMEDCT/8600008 8603005,Adductor hallucis muscle structure,SNOMED CT,8603005,http://purl.bioontology.org/ontology/SNOMEDCT/8603005 @@ -787,7 +787,7 @@ name,label,codesystem,code,ontologyTermURI 9262003,Pelvic fascia structure,SNOMED CT,9262003,http://purl.bioontology.org/ontology/SNOMEDCT/9262003 9290004,Structure of posterior intraoccipital synchondrosis,SNOMED CT,9290004,http://purl.bioontology.org/ontology/SNOMEDCT/9290004 9305001,Structure of labial vein,SNOMED CT,9305001,http://purl.bioontology.org/ontology/SNOMEDCT/9305001 -9317004,"Merkel's tactile disc",SNOMED CT,9317004,http://purl.bioontology.org/ontology/SNOMEDCT/9317004 +9317004,Merkel's tactile disc,SNOMED CT,9317004,http://purl.bioontology.org/ontology/SNOMEDCT/9317004 9320007,Structure of subtendinous iliac bursa,SNOMED CT,9320007,http://purl.bioontology.org/ontology/SNOMEDCT/9320007 9325002,Structure of interdental papilla of gingiva,SNOMED CT,9325002,http://purl.bioontology.org/ontology/SNOMEDCT/9325002 9332006,Structure of lateral ligament of temporomandibular joint,SNOMED CT,9332006,http://purl.bioontology.org/ontology/SNOMEDCT/9332006 @@ -1085,7 +1085,7 @@ name,label,codesystem,code,ontologyTermURI 12844004,Inferior frontomarginal sulcus,SNOMED CT,12844004,http://purl.bioontology.org/ontology/SNOMEDCT/12844004 12850009,Structure of inferior brachium of corpora quadrigemina,SNOMED CT,12850009,http://purl.bioontology.org/ontology/SNOMEDCT/12850009 12857007,Structure of ependyma of third ventricle,SNOMED CT,12857007,http://purl.bioontology.org/ontology/SNOMEDCT/12857007 -12858002,"Bonnet's plexus",SNOMED CT,12858002,http://purl.bioontology.org/ontology/SNOMEDCT/12858002 +12858002,Bonnet's plexus,SNOMED CT,12858002,http://purl.bioontology.org/ontology/SNOMEDCT/12858002 12872006,Head of rib structure,SNOMED CT,12872006,http://purl.bioontology.org/ontology/SNOMEDCT/12872006 12880004,Structure of posterior meniscofemoral ligament,SNOMED CT,12880004,http://purl.bioontology.org/ontology/SNOMEDCT/12880004 12881000,Bone structure of proximal radius,SNOMED CT,12881000,http://purl.bioontology.org/ontology/SNOMEDCT/12881000 @@ -1473,7 +1473,7 @@ name,label,codesystem,code,ontologyTermURI 17847004,Structure of nucleus pulposus of intervertebral disc of third cervical vertebra,SNOMED CT,17847004,http://purl.bioontology.org/ontology/SNOMEDCT/17847004 17856007,Structure of palatine portion of dorsum of tongue,SNOMED CT,17856007,http://purl.bioontology.org/ontology/SNOMEDCT/17856007 17858008,Entire angle of eleventh rib,SNOMED CT,17858008,http://purl.bioontology.org/ontology/SNOMEDCT/17858008 -17861009,"Waldeyer's ring structure",SNOMED CT,17861009,http://purl.bioontology.org/ontology/SNOMEDCT/17861009 +17861009,Waldeyer's ring structure,SNOMED CT,17861009,http://purl.bioontology.org/ontology/SNOMEDCT/17861009 17864001,Subserosal tissue of liver,SNOMED CT,17864001,http://purl.bioontology.org/ontology/SNOMEDCT/17864001 17879008,Habenula structure,SNOMED CT,17879008,http://purl.bioontology.org/ontology/SNOMEDCT/17879008 17911004,Cranial thoracic air sac,SNOMED CT,17911004,http://purl.bioontology.org/ontology/SNOMEDCT/17911004 @@ -1542,7 +1542,7 @@ name,label,codesystem,code,ontologyTermURI 18770002,Short sesamoidean ligament of forelimb,SNOMED CT,18770002,http://purl.bioontology.org/ontology/SNOMEDCT/18770002 18782006,Structure of cavernous sinus,SNOMED CT,18782006,http://purl.bioontology.org/ontology/SNOMEDCT/18782006 18787000,Structure of anti-mesenteric border of small intestine,SNOMED CT,18787000,http://purl.bioontology.org/ontology/SNOMEDCT/18787000 -18812005,"Structure of Held's space",SNOMED CT,18812005,http://purl.bioontology.org/ontology/SNOMEDCT/18812005 +18812005,Structure of Held's space,SNOMED CT,18812005,http://purl.bioontology.org/ontology/SNOMEDCT/18812005 18855009,Right lacrimal gland structure,SNOMED CT,18855009,http://purl.bioontology.org/ontology/SNOMEDCT/18855009 18882001,Entire costal groove of first rib,SNOMED CT,18882001,http://purl.bioontology.org/ontology/SNOMEDCT/18882001 18930002,Structure of phalanx of great toe,SNOMED CT,18930002,http://purl.bioontology.org/ontology/SNOMEDCT/18930002 @@ -1796,7 +1796,7 @@ name,label,codesystem,code,ontologyTermURI 21671001,Structure of mid thigh region,SNOMED CT,21671001,http://purl.bioontology.org/ontology/SNOMEDCT/21671001 21672008,Skin of parietal region,SNOMED CT,21672008,http://purl.bioontology.org/ontology/SNOMEDCT/21672008 21684005,Structure of ureteral plexus,SNOMED CT,21684005,http://purl.bioontology.org/ontology/SNOMEDCT/21684005 -21694000,"Henle's loop structure",SNOMED CT,21694000,http://purl.bioontology.org/ontology/SNOMEDCT/21694000 +21694000,Henle's loop structure,SNOMED CT,21694000,http://purl.bioontology.org/ontology/SNOMEDCT/21694000 21696003,Entire costal groove of eighth rib,SNOMED CT,21696003,http://purl.bioontology.org/ontology/SNOMEDCT/21696003 21699005,Dewclaw of hindlimb,SNOMED CT,21699005,http://purl.bioontology.org/ontology/SNOMEDCT/21699005 21740000,Trigonal structure,SNOMED CT,21740000,http://purl.bioontology.org/ontology/SNOMEDCT/21740000 @@ -1878,7 +1878,7 @@ name,label,codesystem,code,ontologyTermURI 22560007,Dense fibrous connective tissue,SNOMED CT,22560007,http://purl.bioontology.org/ontology/SNOMEDCT/22560007 22565002,Bone structure of ninth rib,SNOMED CT,22565002,http://purl.bioontology.org/ontology/SNOMEDCT/22565002 22577007,Posterior abdominal wall structure,SNOMED CT,22577007,http://purl.bioontology.org/ontology/SNOMEDCT/22577007 -22578002,"Structure of Huxley's layer",SNOMED CT,22578002,http://purl.bioontology.org/ontology/SNOMEDCT/22578002 +22578002,Structure of Huxley's layer,SNOMED CT,22578002,http://purl.bioontology.org/ontology/SNOMEDCT/22578002 22586002,Entire tendon of ring finger,SNOMED CT,22586002,http://purl.bioontology.org/ontology/SNOMEDCT/22586002 22593003,Talotibial joint structure,SNOMED CT,22593003,http://purl.bioontology.org/ontology/SNOMEDCT/22593003 22599004,Skin structure of all fingers,SNOMED CT,22599004,http://purl.bioontology.org/ontology/SNOMEDCT/22599004 @@ -1919,7 +1919,7 @@ name,label,codesystem,code,ontologyTermURI 23090001,Structure of capsule of carpometacarpal joint,SNOMED CT,23090001,http://purl.bioontology.org/ontology/SNOMEDCT/23090001 23094005,Structure of capsule of proximal interphalangeal joint of little finger,SNOMED CT,23094005,http://purl.bioontology.org/ontology/SNOMEDCT/23094005 23114008,Structure of gum of maxilla,SNOMED CT,23114008,http://purl.bioontology.org/ontology/SNOMEDCT/23114008 -23127007,"Structure of Bruch's basal membrane",SNOMED CT,23127007,http://purl.bioontology.org/ontology/SNOMEDCT/23127007 +23127007,Structure of Bruch's basal membrane,SNOMED CT,23127007,http://purl.bioontology.org/ontology/SNOMEDCT/23127007 23153004,Ileocecal valve structure,SNOMED CT,23153004,http://purl.bioontology.org/ontology/SNOMEDCT/23153004 23158008,Lamina of sixth lumbar vertebra,SNOMED CT,23158008,http://purl.bioontology.org/ontology/SNOMEDCT/23158008 23161009,Structure of angle of mouth,SNOMED CT,23161009,http://purl.bioontology.org/ontology/SNOMEDCT/23161009 @@ -1927,7 +1927,7 @@ name,label,codesystem,code,ontologyTermURI 23194007,Entire left commissure of pulmonic valve,SNOMED CT,23194007,http://purl.bioontology.org/ontology/SNOMEDCT/23194007 23198005,Structure of medial lacunar lymph node,SNOMED CT,23198005,http://purl.bioontology.org/ontology/SNOMEDCT/23198005 23215003,Bone structure of T12,SNOMED CT,23215003,http://purl.bioontology.org/ontology/SNOMEDCT/23215003 -23220003,"Structure of Fleischmann's bursa",SNOMED CT,23220003,http://purl.bioontology.org/ontology/SNOMEDCT/23220003 +23220003,Structure of Fleischmann's bursa,SNOMED CT,23220003,http://purl.bioontology.org/ontology/SNOMEDCT/23220003 23224007,Structure of zygomatic process of maxilla,SNOMED CT,23224007,http://purl.bioontology.org/ontology/SNOMEDCT/23224007 23226009,Structure of maxillary left second premolar tooth,SNOMED CT,23226009,http://purl.bioontology.org/ontology/SNOMEDCT/23226009 23230007,Intestinal villus,SNOMED CT,23230007,http://purl.bioontology.org/ontology/SNOMEDCT/23230007 @@ -2002,7 +2002,7 @@ name,label,codesystem,code,ontologyTermURI 24136001,Hip joint structure,SNOMED CT,24136001,http://purl.bioontology.org/ontology/SNOMEDCT/24136001 24142002,Nipple structure,SNOMED CT,24142002,http://purl.bioontology.org/ontology/SNOMEDCT/24142002 24160002,Structure of head of skeletal muscle,SNOMED CT,24160002,http://purl.bioontology.org/ontology/SNOMEDCT/24160002 -24166008,"Krause's end bulb",SNOMED CT,24166008,http://purl.bioontology.org/ontology/SNOMEDCT/24166008 +24166008,Krause's end bulb,SNOMED CT,24166008,http://purl.bioontology.org/ontology/SNOMEDCT/24166008 24170000,Structure of paraumbilical vein,SNOMED CT,24170000,http://purl.bioontology.org/ontology/SNOMEDCT/24170000 24176006,Structure of plantar interosseous muscle of foot,SNOMED CT,24176006,http://purl.bioontology.org/ontology/SNOMEDCT/24176006 24201007,All ribs,SNOMED CT,24201007,http://purl.bioontology.org/ontology/SNOMEDCT/24201007 @@ -2143,7 +2143,7 @@ name,label,codesystem,code,ontologyTermURI 25758003,Left nasolacrimal duct structure,SNOMED CT,25758003,http://purl.bioontology.org/ontology/SNOMEDCT/25758003 25763004,Skin of anterior surface of lower leg,SNOMED CT,25763004,http://purl.bioontology.org/ontology/SNOMEDCT/25763004 25768008,Rostral frontal sinus,SNOMED CT,25768008,http://purl.bioontology.org/ontology/SNOMEDCT/25768008 -25776005,"Entire Forel's H2 bundle",SNOMED CT,25776005,http://purl.bioontology.org/ontology/SNOMEDCT/25776005 +25776005,Entire Forel's H2 bundle,SNOMED CT,25776005,http://purl.bioontology.org/ontology/SNOMEDCT/25776005 25794004,Omohyoid muscle structure,SNOMED CT,25794004,http://purl.bioontology.org/ontology/SNOMEDCT/25794004 25805003,Subcutaneous tissue structure of palmar area of hand,SNOMED CT,25805003,http://purl.bioontology.org/ontology/SNOMEDCT/25805003 25866004,Structure of temporal operculum,SNOMED CT,25866004,http://purl.bioontology.org/ontology/SNOMEDCT/25866004 @@ -2524,7 +2524,7 @@ name,label,codesystem,code,ontologyTermURI 30216009,Structure of accessory nerve nucleus,SNOMED CT,30216009,http://purl.bioontology.org/ontology/SNOMEDCT/30216009 30220008,Right dorsal colon,SNOMED CT,30220008,http://purl.bioontology.org/ontology/SNOMEDCT/30220008 30241002,Arch of eighteenth thoracic vertebra,SNOMED CT,30241002,http://purl.bioontology.org/ontology/SNOMEDCT/30241002 -30249000,"Structure of parietal layer of Bowman's capsule",SNOMED CT,30249000,http://purl.bioontology.org/ontology/SNOMEDCT/30249000 +30249000,Structure of parietal layer of Bowman's capsule,SNOMED CT,30249000,http://purl.bioontology.org/ontology/SNOMEDCT/30249000 30267007,Structure of ostium of inferior vena cava,SNOMED CT,30267007,http://purl.bioontology.org/ontology/SNOMEDCT/30267007 30282002,Structure of inferior tarsal plate,SNOMED CT,30282002,http://purl.bioontology.org/ontology/SNOMEDCT/30282002 30284001,Subcutaneous tissue structure of toe,SNOMED CT,30284001,http://purl.bioontology.org/ontology/SNOMEDCT/30284001 @@ -2730,7 +2730,7 @@ name,label,codesystem,code,ontologyTermURI 32672002,Structure of descending thoracic aorta,SNOMED CT,32672002,http://purl.bioontology.org/ontology/SNOMEDCT/32672002 32679006,Lateral malleolar arterial network structure,SNOMED CT,32679006,http://purl.bioontology.org/ontology/SNOMEDCT/32679006 32696007,Structure of right lower leg,SNOMED CT,32696007,http://purl.bioontology.org/ontology/SNOMEDCT/32696007 -32704008,"Structure of Hesselbach's triangle",SNOMED CT,32704008,http://purl.bioontology.org/ontology/SNOMEDCT/32704008 +32704008,Structure of Hesselbach's triangle,SNOMED CT,32704008,http://purl.bioontology.org/ontology/SNOMEDCT/32704008 32713005,Cecum structure,SNOMED CT,32713005,http://purl.bioontology.org/ontology/SNOMEDCT/32713005 32731006,Structure of subfascial bursa,SNOMED CT,32731006,http://purl.bioontology.org/ontology/SNOMEDCT/32731006 32742002,Structure of medial arch of foot (instep),SNOMED CT,32742002,http://purl.bioontology.org/ontology/SNOMEDCT/32742002 @@ -2870,7 +2870,7 @@ name,label,codesystem,code,ontologyTermURI 34190003,Subcutaneous tissue structure of wrist,SNOMED CT,34190003,http://purl.bioontology.org/ontology/SNOMEDCT/34190003 34201000,Structure of soft tissues of head and neck,SNOMED CT,34201000,http://purl.bioontology.org/ontology/SNOMEDCT/34201000 34202007,Aortic valve structure,SNOMED CT,34202007,http://purl.bioontology.org/ontology/SNOMEDCT/34202007 -34223001,"Hassal's corpuscle",SNOMED CT,34223001,http://purl.bioontology.org/ontology/SNOMEDCT/34223001 +34223001,Hassal's corpuscle,SNOMED CT,34223001,http://purl.bioontology.org/ontology/SNOMEDCT/34223001 34260002,Structure of superficial head of flexor pollicis brevis muscle,SNOMED CT,34260002,http://purl.bioontology.org/ontology/SNOMEDCT/34260002 34265007,Structure of subcutaneous vein of abdomen,SNOMED CT,34265007,http://purl.bioontology.org/ontology/SNOMEDCT/34265007 34269001,Entire articular part of tubercle of twelfth rib,SNOMED CT,34269001,http://purl.bioontology.org/ontology/SNOMEDCT/34269001 @@ -3109,7 +3109,7 @@ name,label,codesystem,code,ontologyTermURI 37047006,Structure of supramammillary decussation,SNOMED CT,37047006,http://purl.bioontology.org/ontology/SNOMEDCT/37047006 37065005,Periventricular white matter,SNOMED CT,37065005,http://purl.bioontology.org/ontology/SNOMEDCT/37065005 37072006,Pedicle of eighteenth thoracic vertebra,SNOMED CT,37072006,http://purl.bioontology.org/ontology/SNOMEDCT/37072006 -37074007,"Structure of Luschka's ducts",SNOMED CT,37074007,http://purl.bioontology.org/ontology/SNOMEDCT/37074007 +37074007,Structure of Luschka's ducts,SNOMED CT,37074007,http://purl.bioontology.org/ontology/SNOMEDCT/37074007 37108007,Skin structure of nasolabial fold,SNOMED CT,37108007,http://purl.bioontology.org/ontology/SNOMEDCT/37108007 37111008,Hair shaft structure,SNOMED CT,37111008,http://purl.bioontology.org/ontology/SNOMEDCT/37111008 37117007,Right inguinal region structure,SNOMED CT,37117007,http://purl.bioontology.org/ontology/SNOMEDCT/37117007 @@ -3469,7 +3469,7 @@ name,label,codesystem,code,ontologyTermURI 41346001,Circular sinus,SNOMED CT,41346001,http://purl.bioontology.org/ontology/SNOMEDCT/41346001 41347005,Structure of subcutaneous lateral malleolar bursa,SNOMED CT,41347005,http://purl.bioontology.org/ontology/SNOMEDCT/41347005 41376008,Structure of terminal hair,SNOMED CT,41376008,http://purl.bioontology.org/ontology/SNOMEDCT/41376008 -41421000,"Meissner's corpuscle",SNOMED CT,41421000,http://purl.bioontology.org/ontology/SNOMEDCT/41421000 +41421000,Meissner's corpuscle,SNOMED CT,41421000,http://purl.bioontology.org/ontology/SNOMEDCT/41421000 41425009,Structure of anterior wall of stomach,SNOMED CT,41425009,http://purl.bioontology.org/ontology/SNOMEDCT/41425009 41442003,Structure of reflected head of rectus femoris muscle,SNOMED CT,41442003,http://purl.bioontology.org/ontology/SNOMEDCT/41442003 41474005,Harderian gland,SNOMED CT,41474005,http://purl.bioontology.org/ontology/SNOMEDCT/41474005 @@ -3602,7 +3602,7 @@ name,label,codesystem,code,ontologyTermURI 42977008,Structure of crura membranacea of membranous labyrinth,SNOMED CT,42977008,http://purl.bioontology.org/ontology/SNOMEDCT/42977008 42978003,Colonic epithelium,SNOMED CT,42978003,http://purl.bioontology.org/ontology/SNOMEDCT/42978003 42981008,Structure of mammillary peduncle,SNOMED CT,42981008,http://purl.bioontology.org/ontology/SNOMEDCT/42981008 -42983006,"Structure of Descemet's membrane",SNOMED CT,42983006,http://purl.bioontology.org/ontology/SNOMEDCT/42983006 +42983006,Structure of Descemet's membrane,SNOMED CT,42983006,http://purl.bioontology.org/ontology/SNOMEDCT/42983006 42991002,Medulla oblongata internal arcuate fibers,SNOMED CT,42991002,http://purl.bioontology.org/ontology/SNOMEDCT/42991002 43015003,Lateral ear canal,SNOMED CT,43015003,http://purl.bioontology.org/ontology/SNOMEDCT/43015003 43022006,Skin structure of dorsal surface of fifth toe,SNOMED CT,43022006,http://purl.bioontology.org/ontology/SNOMEDCT/43022006 @@ -4499,7 +4499,7 @@ name,label,codesystem,code,ontologyTermURI 53123009,Structure of transverse muscle of tongue,SNOMED CT,53123009,http://purl.bioontology.org/ontology/SNOMEDCT/53123009 53134007,Structure of paraurethral ducts,SNOMED CT,53134007,http://purl.bioontology.org/ontology/SNOMEDCT/53134007 53135008,Subcutaneous tissue structure of crura of antihelix,SNOMED CT,53135008,http://purl.bioontology.org/ontology/SNOMEDCT/53135008 -53140000,"Ruffini's corpuscle",SNOMED CT,53140000,http://purl.bioontology.org/ontology/SNOMEDCT/53140000 +53140000,Ruffini's corpuscle,SNOMED CT,53140000,http://purl.bioontology.org/ontology/SNOMEDCT/53140000 53154008,Structure of ductus reuniens,SNOMED CT,53154008,http://purl.bioontology.org/ontology/SNOMEDCT/53154008 53159003,Articular part of tubercle of fourteenth rib,SNOMED CT,53159003,http://purl.bioontology.org/ontology/SNOMEDCT/53159003 53170005,Right nasolacrimal duct structure,SNOMED CT,53170005,http://purl.bioontology.org/ontology/SNOMEDCT/53170005 @@ -4639,7 +4639,7 @@ name,label,codesystem,code,ontologyTermURI 54815004,Teat,SNOMED CT,54815004,http://purl.bioontology.org/ontology/SNOMEDCT/54815004 54827001,Arch of sixth lumbar vertebra,SNOMED CT,54827001,http://purl.bioontology.org/ontology/SNOMEDCT/54827001 54829003,Salivary gland interstitial tissue,SNOMED CT,54829003,http://purl.bioontology.org/ontology/SNOMEDCT/54829003 -54833005,"Structure of Fontana's spaces",SNOMED CT,54833005,http://purl.bioontology.org/ontology/SNOMEDCT/54833005 +54833005,Structure of Fontana's spaces,SNOMED CT,54833005,http://purl.bioontology.org/ontology/SNOMEDCT/54833005 54834004,Structure of posterior spinal artery,SNOMED CT,54834004,http://purl.bioontology.org/ontology/SNOMEDCT/54834004 54863001,Structure of base of phalanx of fourth toe,SNOMED CT,54863001,http://purl.bioontology.org/ontology/SNOMEDCT/54863001 54881003,Structure of common tendon sheath of peroneal muscle,SNOMED CT,54881003,http://purl.bioontology.org/ontology/SNOMEDCT/54881003 @@ -4661,7 +4661,7 @@ name,label,codesystem,code,ontologyTermURI 55097004,Structure of ulnar branch of medial antebrachial cutaneous nerve,SNOMED CT,55097004,http://purl.bioontology.org/ontology/SNOMEDCT/55097004 55111001,Structure of paranasal sinus cavity,SNOMED CT,55111001,http://purl.bioontology.org/ontology/SNOMEDCT/55111001 55139000,Sympathetic ganglion structure,SNOMED CT,55139000,http://purl.bioontology.org/ontology/SNOMEDCT/55139000 -55143001,"Structure of Bowman's layer",SNOMED CT,55143001,http://purl.bioontology.org/ontology/SNOMEDCT/55143001 +55143001,Structure of Bowman's layer,SNOMED CT,55143001,http://purl.bioontology.org/ontology/SNOMEDCT/55143001 55155007,Structure of anterior cerebral vein,SNOMED CT,55155007,http://purl.bioontology.org/ontology/SNOMEDCT/55155007 55173005,Structure of apex of thoracic spinal cord posterior horn,SNOMED CT,55173005,http://purl.bioontology.org/ontology/SNOMEDCT/55173005 55190004,Structure of long head of biceps femoris muscle,SNOMED CT,55190004,http://purl.bioontology.org/ontology/SNOMEDCT/55190004 @@ -4758,7 +4758,7 @@ name,label,codesystem,code,ontologyTermURI 56399000,Structure of collateral radial ligament of elbow,SNOMED CT,56399000,http://purl.bioontology.org/ontology/SNOMEDCT/56399000 56400007,Structure of renal vein,SNOMED CT,56400007,http://purl.bioontology.org/ontology/SNOMEDCT/56400007 56401006,Bone structure of T5,SNOMED CT,56401006,http://purl.bioontology.org/ontology/SNOMEDCT/56401006 -56411004,"Entire Waldeyer's ring",SNOMED CT,56411004,http://purl.bioontology.org/ontology/SNOMEDCT/56411004 +56411004,Entire Waldeyer's ring,SNOMED CT,56411004,http://purl.bioontology.org/ontology/SNOMEDCT/56411004 56439003,Structure of right gastroepiploic artery,SNOMED CT,56439003,http://purl.bioontology.org/ontology/SNOMEDCT/56439003 56450000,Entire crest of head of eighth rib,SNOMED CT,56450000,http://purl.bioontology.org/ontology/SNOMEDCT/56450000 56459004,Foot structure,SNOMED CT,56459004,http://purl.bioontology.org/ontology/SNOMEDCT/56459004 @@ -5208,7 +5208,7 @@ name,label,codesystem,code,ontologyTermURI 61787008,Structure of subcapital part of humerus,SNOMED CT,61787008,http://purl.bioontology.org/ontology/SNOMEDCT/61787008 61791003,Subcutaneous tissue structure of lateral region of trunk,SNOMED CT,61791003,http://purl.bioontology.org/ontology/SNOMEDCT/61791003 61840008,Structure of endocardium of atrium,SNOMED CT,61840008,http://purl.bioontology.org/ontology/SNOMEDCT/61840008 -61847006,"Structure of Reil's limiting sulcus",SNOMED CT,61847006,http://purl.bioontology.org/ontology/SNOMEDCT/61847006 +61847006,Structure of Reil's limiting sulcus,SNOMED CT,61847006,http://purl.bioontology.org/ontology/SNOMEDCT/61847006 61853006,Spinal canal structure,SNOMED CT,61853006,http://purl.bioontology.org/ontology/SNOMEDCT/61853006 61868007,Structure of deciduous mandibular right second molar tooth,SNOMED CT,61868007,http://purl.bioontology.org/ontology/SNOMEDCT/61868007 61878005,Structure of subarachnoid cistern,SNOMED CT,61878005,http://purl.bioontology.org/ontology/SNOMEDCT/61878005 @@ -5900,7 +5900,7 @@ name,label,codesystem,code,ontologyTermURI 69833005,Structure of right femoral artery,SNOMED CT,69833005,http://purl.bioontology.org/ontology/SNOMEDCT/69833005 69838001,Right external ear structure,SNOMED CT,69838001,http://purl.bioontology.org/ontology/SNOMEDCT/69838001 69842003,Structure of left lobe of liver,SNOMED CT,69842003,http://purl.bioontology.org/ontology/SNOMEDCT/69842003 -69854003,"Structure of Auerbach's plexus",SNOMED CT,69854003,http://purl.bioontology.org/ontology/SNOMEDCT/69854003 +69854003,Structure of Auerbach's plexus,SNOMED CT,69854003,http://purl.bioontology.org/ontology/SNOMEDCT/69854003 69856001,Structure of transverse process of axis,SNOMED CT,69856001,http://purl.bioontology.org/ontology/SNOMEDCT/69856001 69857005,Structure of superior thalamic radiation of internal capsule,SNOMED CT,69857005,http://purl.bioontology.org/ontology/SNOMEDCT/69857005 69898003,Structure of medial head of triceps brachii muscle,SNOMED CT,69898003,http://purl.bioontology.org/ontology/SNOMEDCT/69898003 @@ -6523,7 +6523,7 @@ name,label,codesystem,code,ontologyTermURI 76986006,Structure of distal phalanx of second toe,SNOMED CT,76986006,http://purl.bioontology.org/ontology/SNOMEDCT/76986006 76990008,Bronchiole structure of caudal lobe,SNOMED CT,76990008,http://purl.bioontology.org/ontology/SNOMEDCT/76990008 76993005,Enamel structure,SNOMED CT,76993005,http://purl.bioontology.org/ontology/SNOMEDCT/76993005 -77011004,"Tenon's capsule structure",SNOMED CT,77011004,http://purl.bioontology.org/ontology/SNOMEDCT/77011004 +77011004,Tenon's capsule structure,SNOMED CT,77011004,http://purl.bioontology.org/ontology/SNOMEDCT/77011004 77024004,Structure of free margin of eyelid,SNOMED CT,77024004,http://purl.bioontology.org/ontology/SNOMEDCT/77024004 77030004,Structure of ligament of midcarpal joint,SNOMED CT,77030004,http://purl.bioontology.org/ontology/SNOMEDCT/77030004 77052008,Structure of body of ilium,SNOMED CT,77052008,http://purl.bioontology.org/ontology/SNOMEDCT/77052008 @@ -6657,7 +6657,7 @@ name,label,codesystem,code,ontologyTermURI 78464007,Retrocecal tissue,SNOMED CT,78464007,http://purl.bioontology.org/ontology/SNOMEDCT/78464007 78472009,Serrated suture structure,SNOMED CT,78472009,http://purl.bioontology.org/ontology/SNOMEDCT/78472009 78480002,Structure of right pulmonary artery,SNOMED CT,78480002,http://purl.bioontology.org/ontology/SNOMEDCT/78480002 -78486008,"Structure of descending limb of Henle's loop",SNOMED CT,78486008,http://purl.bioontology.org/ontology/SNOMEDCT/78486008 +78486008,Structure of descending limb of Henle's loop,SNOMED CT,78486008,http://purl.bioontology.org/ontology/SNOMEDCT/78486008 78492002,Structure of midshaft of tibia,SNOMED CT,78492002,http://purl.bioontology.org/ontology/SNOMEDCT/78492002 78497008,Structure of external sheath of optic nerve,SNOMED CT,78497008,http://purl.bioontology.org/ontology/SNOMEDCT/78497008 78501003,Structure of inner part of cartilaginous portion of auditory canal,SNOMED CT,78501003,http://purl.bioontology.org/ontology/SNOMEDCT/78501003 @@ -6921,7 +6921,7 @@ name,label,codesystem,code,ontologyTermURI 81606001,Structure of anterior portion of interventricular septum,SNOMED CT,81606001,http://purl.bioontology.org/ontology/SNOMEDCT/81606001 81623005,Visceral pleura structure,SNOMED CT,81623005,http://purl.bioontology.org/ontology/SNOMEDCT/81623005 81628001,Entire neck of fourth rib,SNOMED CT,81628001,http://purl.bioontology.org/ontology/SNOMEDCT/81628001 -81636005,"Structure of Henle's layer",SNOMED CT,81636005,http://purl.bioontology.org/ontology/SNOMEDCT/81636005 +81636005,Structure of Henle's layer,SNOMED CT,81636005,http://purl.bioontology.org/ontology/SNOMEDCT/81636005 81657002,Structure of inferior margin of lung,SNOMED CT,81657002,http://purl.bioontology.org/ontology/SNOMEDCT/81657002 81661008,Structure of anterior ethmoidal nerve,SNOMED CT,81661008,http://purl.bioontology.org/ontology/SNOMEDCT/81661008 81668002,Structure of malleolar articular facet of fibula,SNOMED CT,81668002,http://purl.bioontology.org/ontology/SNOMEDCT/81668002 @@ -7030,8 +7030,8 @@ name,label,codesystem,code,ontologyTermURI 82858008,Skin structure of fossa triangularis of ear,SNOMED CT,82858008,http://purl.bioontology.org/ontology/SNOMEDCT/82858008 82859000,Macula lutea structure,SNOMED CT,82859000,http://purl.bioontology.org/ontology/SNOMEDCT/82859000 82875002,Structure of third metatarsal articular facet of second metatarsal bone,SNOMED CT,82875002,http://purl.bioontology.org/ontology/SNOMEDCT/82875002 -82880006,"Structure of Broca's area",SNOMED CT,82880006,http://purl.bioontology.org/ontology/SNOMEDCT/82880006 -82881005,"Structure of Roller's nucleus",SNOMED CT,82881005,http://purl.bioontology.org/ontology/SNOMEDCT/82881005 +82880006,Structure of Broca's area,SNOMED CT,82880006,http://purl.bioontology.org/ontology/SNOMEDCT/82880006 +82881005,Structure of Roller's nucleus,SNOMED CT,82881005,http://purl.bioontology.org/ontology/SNOMEDCT/82881005 82905002,Structure of lateral crus of superficial inguinal ring,SNOMED CT,82905002,http://purl.bioontology.org/ontology/SNOMEDCT/82905002 82910003,Structure of dorsal surface of fourth toe,SNOMED CT,82910003,http://purl.bioontology.org/ontology/SNOMEDCT/82910003 82925003,Structure of apex of arytenoid cartilage,SNOMED CT,82925003,http://purl.bioontology.org/ontology/SNOMEDCT/82925003 @@ -7095,7 +7095,7 @@ name,label,codesystem,code,ontologyTermURI 83693006,Entire superior pancreatic lymph node,SNOMED CT,83693006,http://purl.bioontology.org/ontology/SNOMEDCT/83693006 83697007,Entire under border of third rib,SNOMED CT,83697007,http://purl.bioontology.org/ontology/SNOMEDCT/83697007 83708004,Structure of capsule of midcarpal joint,SNOMED CT,83708004,http://purl.bioontology.org/ontology/SNOMEDCT/83708004 -83711003,"Structure of ascending limb of Henle's loop",SNOMED CT,83711003,http://purl.bioontology.org/ontology/SNOMEDCT/83711003 +83711003,Structure of ascending limb of Henle's loop,SNOMED CT,83711003,http://purl.bioontology.org/ontology/SNOMEDCT/83711003 83713000,Subcutaneous tissue structure of interscapular region of back,SNOMED CT,83713000,http://purl.bioontology.org/ontology/SNOMEDCT/83713000 83730003,Oblique sesamoidean ligament of forelimb,SNOMED CT,83730003,http://purl.bioontology.org/ontology/SNOMEDCT/83730003 83738005,Index finger structure,SNOMED CT,83738005,http://purl.bioontology.org/ontology/SNOMEDCT/83738005 @@ -7153,7 +7153,7 @@ name,label,codesystem,code,ontologyTermURI 84421000,Structure of abdominal vein,SNOMED CT,84421000,http://purl.bioontology.org/ontology/SNOMEDCT/84421000 84441005,Structure of bifurcated ligament,SNOMED CT,84441005,http://purl.bioontology.org/ontology/SNOMEDCT/84441005 84462006,Structure of spinous process of seventh thoracic vertebra,SNOMED CT,84462006,http://purl.bioontology.org/ontology/SNOMEDCT/84462006 -84465008,"Structure of Kerckring's valve",SNOMED CT,84465008,http://purl.bioontology.org/ontology/SNOMEDCT/84465008 +84465008,Structure of Kerckring's valve,SNOMED CT,84465008,http://purl.bioontology.org/ontology/SNOMEDCT/84465008 84507004,Skin structure of popliteal fossa,SNOMED CT,84507004,http://purl.bioontology.org/ontology/SNOMEDCT/84507004 84522009,Structure of arch of cervical vertebra,SNOMED CT,84522009,http://purl.bioontology.org/ontology/SNOMEDCT/84522009 84526007,Structure of uvula of bladder,SNOMED CT,84526007,http://purl.bioontology.org/ontology/SNOMEDCT/84526007 @@ -7328,7 +7328,7 @@ name,label,codesystem,code,ontologyTermURI 86682003,Structure of ceruminous gland,SNOMED CT,86682003,http://purl.bioontology.org/ontology/SNOMEDCT/86682003 86689007,Bursa of Fabricius,SNOMED CT,86689007,http://purl.bioontology.org/ontology/SNOMEDCT/86689007 86690003,Greater occipital nerve,SNOMED CT,86690003,http://purl.bioontology.org/ontology/SNOMEDCT/86690003 -86718003,"Structure of Nuel's space",SNOMED CT,86718003,http://purl.bioontology.org/ontology/SNOMEDCT/86718003 +86718003,Structure of Nuel's space,SNOMED CT,86718003,http://purl.bioontology.org/ontology/SNOMEDCT/86718003 86719006,Skin structure of preauricular region,SNOMED CT,86719006,http://purl.bioontology.org/ontology/SNOMEDCT/86719006 86721001,Structure of labrum glenoidale,SNOMED CT,86721001,http://purl.bioontology.org/ontology/SNOMEDCT/86721001 86722008,Entire interosseous talocalcaneal ligament,SNOMED CT,86722008,http://purl.bioontology.org/ontology/SNOMEDCT/86722008 @@ -7387,7 +7387,7 @@ name,label,codesystem,code,ontologyTermURI 87483006,Tunica intima of vessel,SNOMED CT,87483006,http://purl.bioontology.org/ontology/SNOMEDCT/87483006 87488002,Structure of inferior mesenteric ganglion,SNOMED CT,87488002,http://purl.bioontology.org/ontology/SNOMEDCT/87488002 87497003,Structure of acromial facet of clavicle,SNOMED CT,87497003,http://purl.bioontology.org/ontology/SNOMEDCT/87497003 -87501008,"Entire His' perivascular space",SNOMED CT,87501008,http://purl.bioontology.org/ontology/SNOMEDCT/87501008 +87501008,Entire His' perivascular space,SNOMED CT,87501008,http://purl.bioontology.org/ontology/SNOMEDCT/87501008 87508002,Entire dorsal tarsometatarsal ligament,SNOMED CT,87508002,http://purl.bioontology.org/ontology/SNOMEDCT/87508002 87516006,Extrapyramidal tract structure,SNOMED CT,87516006,http://purl.bioontology.org/ontology/SNOMEDCT/87516006 87517002,Structure of hilum of olivary nucleus,SNOMED CT,87517002,http://purl.bioontology.org/ontology/SNOMEDCT/87517002 @@ -7873,7 +7873,7 @@ name,label,codesystem,code,ontologyTermURI 105584000,Interphalangeal toe joint structure,SNOMED CT,105584000,http://purl.bioontology.org/ontology/SNOMEDCT/105584000 105585004,Interarytenoid fold structure,SNOMED CT,105585004,http://purl.bioontology.org/ontology/SNOMEDCT/105585004 105586003,Femoropopliteal vein,SNOMED CT,105586003,http://purl.bioontology.org/ontology/SNOMEDCT/105586003 -105587007,"Zymbal's gland",SNOMED CT,105587007,http://purl.bioontology.org/ontology/SNOMEDCT/105587007 +105587007,Zymbal's gland,SNOMED CT,105587007,http://purl.bioontology.org/ontology/SNOMEDCT/105587007 108348009,Spinal cord root AND/OR ganglion,SNOMED CT,108348009,http://purl.bioontology.org/ontology/SNOMEDCT/108348009 108350001,"Abdomen, excluding retroperitoneal region",SNOMED CT,108350001,http://purl.bioontology.org/ontology/SNOMEDCT/108350001 108371006,Bone structure of tarsus,SNOMED CT,108371006,http://purl.bioontology.org/ontology/SNOMEDCT/108371006 @@ -8552,11 +8552,11 @@ name,label,codesystem,code,ontologyTermURI 128530007,Entire bony skeleton,SNOMED CT,128530007,http://purl.bioontology.org/ontology/SNOMEDCT/128530007 128546004,Perforating vein structure of lower extremity,SNOMED CT,128546004,http://purl.bioontology.org/ontology/SNOMEDCT/128546004 128547008,Retro-tibial perforating vein of lower extremity,SNOMED CT,128547008,http://purl.bioontology.org/ontology/SNOMEDCT/128547008 -128548003,"Boyd's perforating vein",SNOMED CT,128548003,http://purl.bioontology.org/ontology/SNOMEDCT/128548003 -128549006,"Cockett's perforating vein",SNOMED CT,128549006,http://purl.bioontology.org/ontology/SNOMEDCT/128549006 +128548003,Boyd's perforating vein,SNOMED CT,128548003,http://purl.bioontology.org/ontology/SNOMEDCT/128548003 +128549006,Cockett's perforating vein,SNOMED CT,128549006,http://purl.bioontology.org/ontology/SNOMEDCT/128549006 128550006,Ventro-lateral perforating vein,SNOMED CT,128550006,http://purl.bioontology.org/ontology/SNOMEDCT/128550006 128553008,Structure of antecubital vein,SNOMED CT,128553008,http://purl.bioontology.org/ontology/SNOMEDCT/128553008 -128554002,"Dodd's perforating vein",SNOMED CT,128554002,http://purl.bioontology.org/ontology/SNOMEDCT/128554002 +128554002,Dodd's perforating vein,SNOMED CT,128554002,http://purl.bioontology.org/ontology/SNOMEDCT/128554002 128559007,Structure of genicular artery,SNOMED CT,128559007,http://purl.bioontology.org/ontology/SNOMEDCT/128559007 128560002,Hunterian perforating vein,SNOMED CT,128560002,http://purl.bioontology.org/ontology/SNOMEDCT/128560002 128564006,Structure of apex of left ventricle,SNOMED CT,128564006,http://purl.bioontology.org/ontology/SNOMEDCT/128564006 @@ -10373,7 +10373,7 @@ name,label,codesystem,code,ontologyTermURI 243973003,Greater sac of peritoneum,SNOMED CT,243973003,http://purl.bioontology.org/ontology/SNOMEDCT/243973003 243974009,Subphrenic space,SNOMED CT,243974009,http://purl.bioontology.org/ontology/SNOMEDCT/243974009 243975005,Suprahepatic area,SNOMED CT,243975005,http://purl.bioontology.org/ontology/SNOMEDCT/243975005 -243977002,"Rutherford Morrison's pouch",SNOMED CT,243977002,http://purl.bioontology.org/ontology/SNOMEDCT/243977002 +243977002,Rutherford Morrison's pouch,SNOMED CT,243977002,http://purl.bioontology.org/ontology/SNOMEDCT/243977002 243979004,Paracolic region,SNOMED CT,243979004,http://purl.bioontology.org/ontology/SNOMEDCT/243979004 243980001,Paracolic gutter,SNOMED CT,243980001,http://purl.bioontology.org/ontology/SNOMEDCT/243980001 243981002,Supracolic region,SNOMED CT,243981002,http://purl.bioontology.org/ontology/SNOMEDCT/243981002 @@ -10484,7 +10484,7 @@ name,label,codesystem,code,ontologyTermURI 244090002,Entire skin of tip of nose,SNOMED CT,244090002,http://purl.bioontology.org/ontology/SNOMEDCT/244090002 244091003,Skin of external naris,SNOMED CT,244091003,http://purl.bioontology.org/ontology/SNOMEDCT/244091003 244092005,Entire skin of lip,SNOMED CT,244092005,http://purl.bioontology.org/ontology/SNOMEDCT/244092005 -244093000,"Entire visceral layer of Bowman's capsule",SNOMED CT,244093000,http://purl.bioontology.org/ontology/SNOMEDCT/244093000 +244093000,Entire visceral layer of Bowman's capsule,SNOMED CT,244093000,http://purl.bioontology.org/ontology/SNOMEDCT/244093000 244094006,Entire skin of philtrum,SNOMED CT,244094006,http://purl.bioontology.org/ontology/SNOMEDCT/244094006 244095007,Entire skin of jaw,SNOMED CT,244095007,http://purl.bioontology.org/ontology/SNOMEDCT/244095007 244096008,Skin of side of jaw,SNOMED CT,244096008,http://purl.bioontology.org/ontology/SNOMEDCT/244096008 @@ -10601,7 +10601,7 @@ name,label,codesystem,code,ontologyTermURI 244259008,Right dominant posterior descending artery,SNOMED CT,244259008,http://purl.bioontology.org/ontology/SNOMEDCT/244259008 244260003,Extended left ventricular branch artery,SNOMED CT,244260003,http://purl.bioontology.org/ontology/SNOMEDCT/244260003 244261004,Abdominal visceral artery,SNOMED CT,244261004,http://purl.bioontology.org/ontology/SNOMEDCT/244261004 -244284006,"Entire Bowman's space",SNOMED CT,244284006,http://purl.bioontology.org/ontology/SNOMEDCT/244284006 +244284006,Entire Bowman's space,SNOMED CT,244284006,http://purl.bioontology.org/ontology/SNOMEDCT/244284006 244286008,Anterior abdominal wall artery,SNOMED CT,244286008,http://purl.bioontology.org/ontology/SNOMEDCT/244286008 244289001,Superficial inferior epigastric artery,SNOMED CT,244289001,http://purl.bioontology.org/ontology/SNOMEDCT/244289001 244291009,Anterior division of internal iliac artery,SNOMED CT,244291009,http://purl.bioontology.org/ontology/SNOMEDCT/244291009 @@ -11256,7 +11256,7 @@ name,label,codesystem,code,ontologyTermURI 245347004,Entire superior mesenteric lymph node,SNOMED CT,245347004,http://purl.bioontology.org/ontology/SNOMEDCT/245347004 245348009,Entire inferior mesenteric lymph node,SNOMED CT,245348009,http://purl.bioontology.org/ontology/SNOMEDCT/245348009 245349001,Entire pararectal lymph node,SNOMED CT,245349001,http://purl.bioontology.org/ontology/SNOMEDCT/245349001 -245350001,"Entire descending limb of Henle's loop",SNOMED CT,245350001,http://purl.bioontology.org/ontology/SNOMEDCT/245350001 +245350001,Entire descending limb of Henle's loop,SNOMED CT,245350001,http://purl.bioontology.org/ontology/SNOMEDCT/245350001 245351002,Mesorectal node,SNOMED CT,245351002,http://purl.bioontology.org/ontology/SNOMEDCT/245351002 245353004,Common iliac node,SNOMED CT,245353004,http://purl.bioontology.org/ontology/SNOMEDCT/245353004 245354005,Posterior common iliac node,SNOMED CT,245354005,http://purl.bioontology.org/ontology/SNOMEDCT/245354005 @@ -11295,7 +11295,7 @@ name,label,codesystem,code,ontologyTermURI 245390003,Entire lesser duodenal papilla,SNOMED CT,245390003,http://purl.bioontology.org/ontology/SNOMEDCT/245390003 245391004,Entire fundus of gallbladder,SNOMED CT,245391004,http://purl.bioontology.org/ontology/SNOMEDCT/245391004 245392006,Entire body of gallbladder,SNOMED CT,245392006,http://purl.bioontology.org/ontology/SNOMEDCT/245392006 -245393001,"Hartmann's pouch",SNOMED CT,245393001,http://purl.bioontology.org/ontology/SNOMEDCT/245393001 +245393001,Hartmann's pouch,SNOMED CT,245393001,http://purl.bioontology.org/ontology/SNOMEDCT/245393001 245394007,Entire neck of gallbladder,SNOMED CT,245394007,http://purl.bioontology.org/ontology/SNOMEDCT/245394007 245395008,Proximal third of main bile duct,SNOMED CT,245395008,http://purl.bioontology.org/ontology/SNOMEDCT/245395008 245396009,Middle third of main bile duct,SNOMED CT,245396009,http://purl.bioontology.org/ontology/SNOMEDCT/245396009 @@ -11329,7 +11329,7 @@ name,label,codesystem,code,ontologyTermURI 245431002,Supra-ampullary part of rectum,SNOMED CT,245431002,http://purl.bioontology.org/ontology/SNOMEDCT/245431002 245432009,Entire rectal ampulla,SNOMED CT,245432009,http://purl.bioontology.org/ontology/SNOMEDCT/245432009 245433004,Flexure of rectum,SNOMED CT,245433004,http://purl.bioontology.org/ontology/SNOMEDCT/245433004 -245434005,"Entire ascending limb of Henle's loop",SNOMED CT,245434005,http://purl.bioontology.org/ontology/SNOMEDCT/245434005 +245434005,Entire ascending limb of Henle's loop,SNOMED CT,245434005,http://purl.bioontology.org/ontology/SNOMEDCT/245434005 245435006,Entire sacral flexure of rectum,SNOMED CT,245435006,http://purl.bioontology.org/ontology/SNOMEDCT/245435006 245436007,Entire perineal flexure of rectum,SNOMED CT,245436007,http://purl.bioontology.org/ontology/SNOMEDCT/245436007 245437003,Lateral flexure of rectum,SNOMED CT,245437003,http://purl.bioontology.org/ontology/SNOMEDCT/245437003 @@ -11902,7 +11902,7 @@ name,label,codesystem,code,ontologyTermURI 251302002,Entire rectovesical septum,SNOMED CT,251302002,http://purl.bioontology.org/ontology/SNOMEDCT/251302002 254198003,Lymph nodes of multiple sites,SNOMED CT,254198003,http://purl.bioontology.org/ontology/SNOMEDCT/254198003 255416003,Entire capillary blood vessel (organ),SNOMED CT,255416003,http://purl.bioontology.org/ontology/SNOMEDCT/255416003 -255571004,"Little's area",SNOMED CT,255571004,http://purl.bioontology.org/ontology/SNOMEDCT/255571004 +255571004,Little's area,SNOMED CT,255571004,http://purl.bioontology.org/ontology/SNOMEDCT/255571004 256423008,Structure of hair of skin region,SNOMED CT,256423008,http://purl.bioontology.org/ontology/SNOMEDCT/256423008 256583008,Structure of neuromyoarterial glomus,SNOMED CT,256583008,http://purl.bioontology.org/ontology/SNOMEDCT/256583008 256661003,Entire pectineal ligament,SNOMED CT,256661003,http://purl.bioontology.org/ontology/SNOMEDCT/256661003 @@ -11993,7 +11993,7 @@ name,label,codesystem,code,ontologyTermURI 262408004,Entire serous layer of visceral peritoneum,SNOMED CT,262408004,http://purl.bioontology.org/ontology/SNOMEDCT/262408004 262511001,Entire peritoneal mesothelium,SNOMED CT,262511001,http://purl.bioontology.org/ontology/SNOMEDCT/262511001 262586001,Entire serous capsule of liver,SNOMED CT,262586001,http://purl.bioontology.org/ontology/SNOMEDCT/262586001 -262666009,"Entire Luschka's ducts",SNOMED CT,262666009,http://purl.bioontology.org/ontology/SNOMEDCT/262666009 +262666009,Entire Luschka's ducts,SNOMED CT,262666009,http://purl.bioontology.org/ontology/SNOMEDCT/262666009 262753003,Entire serous coat of spleen,SNOMED CT,262753003,http://purl.bioontology.org/ontology/SNOMEDCT/262753003 262844004,Entire subserous tissue of parietal peritoneum,SNOMED CT,262844004,http://purl.bioontology.org/ontology/SNOMEDCT/262844004 262929001,Entire subserous tissue of visceral peritoneum,SNOMED CT,262929001,http://purl.bioontology.org/ontology/SNOMEDCT/262929001 @@ -12370,9 +12370,9 @@ name,label,codesystem,code,ontologyTermURI 267281000,Entire mesenteric border of small intestine,SNOMED CT,267281000,http://purl.bioontology.org/ontology/SNOMEDCT/267281000 267378008,Entire anti-mesenteric border of small intestine,SNOMED CT,267378008,http://purl.bioontology.org/ontology/SNOMEDCT/267378008 267457009,Entire small intestinal lumen,SNOMED CT,267457009,http://purl.bioontology.org/ontology/SNOMEDCT/267457009 -267547005,"Entire Kerckring's valve",SNOMED CT,267547005,http://purl.bioontology.org/ontology/SNOMEDCT/267547005 +267547005,Entire Kerckring's valve,SNOMED CT,267547005,http://purl.bioontology.org/ontology/SNOMEDCT/267547005 267632005,Entire sympathetic enteric plexus,SNOMED CT,267632005,http://purl.bioontology.org/ontology/SNOMEDCT/267632005 -267716001,"Entire Auerbach's plexus",SNOMED CT,267716001,http://purl.bioontology.org/ontology/SNOMEDCT/267716001 +267716001,Entire Auerbach's plexus,SNOMED CT,267716001,http://purl.bioontology.org/ontology/SNOMEDCT/267716001 267901006,Entire lymphatic vessel of stomach,SNOMED CT,267901006,http://purl.bioontology.org/ontology/SNOMEDCT/267901006 268168004,Entire angular incisure of stomach,SNOMED CT,268168004,http://purl.bioontology.org/ontology/SNOMEDCT/268168004 268250007,Entire cardiac incisure of stomach,SNOMED CT,268250007,http://purl.bioontology.org/ontology/SNOMEDCT/268250007 @@ -12851,7 +12851,7 @@ name,label,codesystem,code,ontologyTermURI 278826002,Body internal region,SNOMED CT,278826002,http://purl.bioontology.org/ontology/SNOMEDCT/278826002 278827006,Superior lumbar triangle,SNOMED CT,278827006,http://purl.bioontology.org/ontology/SNOMEDCT/278827006 278828001,Inferior lumbar triangle,SNOMED CT,278828001,http://purl.bioontology.org/ontology/SNOMEDCT/278828001 -278829009,"Entire Hesselbach's triangle",SNOMED CT,278829009,http://purl.bioontology.org/ontology/SNOMEDCT/278829009 +278829009,Entire Hesselbach's triangle,SNOMED CT,278829009,http://purl.bioontology.org/ontology/SNOMEDCT/278829009 278830004,Entire inguinal ring,SNOMED CT,278830004,http://purl.bioontology.org/ontology/SNOMEDCT/278830004 278831000,Entire deep inguinal ring,SNOMED CT,278831000,http://purl.bioontology.org/ontology/SNOMEDCT/278831000 278842009,Third of esophagus,SNOMED CT,278842009,http://purl.bioontology.org/ontology/SNOMEDCT/278842009 @@ -13053,8 +13053,8 @@ name,label,codesystem,code,ontologyTermURI 279254007,Vestibular area,SNOMED CT,279254007,http://purl.bioontology.org/ontology/SNOMEDCT/279254007 279255008,Auditory area of cortex,SNOMED CT,279255008,http://purl.bioontology.org/ontology/SNOMEDCT/279255008 279256009,Taste area,SNOMED CT,279256009,http://purl.bioontology.org/ontology/SNOMEDCT/279256009 -279257000,"Entire Broca's area",SNOMED CT,279257000,http://purl.bioontology.org/ontology/SNOMEDCT/279257000 -279258005,"Wernicke's area",SNOMED CT,279258005,http://purl.bioontology.org/ontology/SNOMEDCT/279258005 +279257000,Entire Broca's area,SNOMED CT,279257000,http://purl.bioontology.org/ontology/SNOMEDCT/279257000 +279258005,Wernicke's area,SNOMED CT,279258005,http://purl.bioontology.org/ontology/SNOMEDCT/279258005 279259002,Sensory speech area,SNOMED CT,279259002,http://purl.bioontology.org/ontology/SNOMEDCT/279259002 279260007,Entire inferior sagittal sinus,SNOMED CT,279260007,http://purl.bioontology.org/ontology/SNOMEDCT/279260007 279261006,Entire straight sinus,SNOMED CT,279261006,http://purl.bioontology.org/ontology/SNOMEDCT/279261006 @@ -13128,7 +13128,7 @@ name,label,codesystem,code,ontologyTermURI 279344005,Entire superior temporal sulcus,SNOMED CT,279344005,http://purl.bioontology.org/ontology/SNOMEDCT/279344005 279345006,Entire middle temporal sulcus,SNOMED CT,279345006,http://purl.bioontology.org/ontology/SNOMEDCT/279345006 279346007,Entire inferior temporal sulcus,SNOMED CT,279346007,http://purl.bioontology.org/ontology/SNOMEDCT/279346007 -279347003,"Entire Reil's limiting sulcus",SNOMED CT,279347003,http://purl.bioontology.org/ontology/SNOMEDCT/279347003 +279347003,Entire Reil's limiting sulcus,SNOMED CT,279347003,http://purl.bioontology.org/ontology/SNOMEDCT/279347003 279348008,Central sulcus of insula,SNOMED CT,279348008,http://purl.bioontology.org/ontology/SNOMEDCT/279348008 279349000,Callosal sulcus,SNOMED CT,279349000,http://purl.bioontology.org/ontology/SNOMEDCT/279349000 279350000,Entire cingulate sulcus,SNOMED CT,279350000,http://purl.bioontology.org/ontology/SNOMEDCT/279350000 @@ -13648,7 +13648,7 @@ name,label,codesystem,code,ontologyTermURI 280198003,Inferior vagus ganglion,SNOMED CT,280198003,http://purl.bioontology.org/ontology/SNOMEDCT/280198003 280205004,Entire superior branch of oculomotor nerve,SNOMED CT,280205004,http://purl.bioontology.org/ontology/SNOMEDCT/280205004 280206003,Entire inferior branch of oculomotor nerve,SNOMED CT,280206003,http://purl.bioontology.org/ontology/SNOMEDCT/280206003 -280207007,"Killian's dehiscence",SNOMED CT,280207007,http://purl.bioontology.org/ontology/SNOMEDCT/280207007 +280207007,Killian's dehiscence,SNOMED CT,280207007,http://purl.bioontology.org/ontology/SNOMEDCT/280207007 280208002,Motor root of ciliary ganglion,SNOMED CT,280208002,http://purl.bioontology.org/ontology/SNOMEDCT/280208002 280209005,Division of trigeminal nerve,SNOMED CT,280209005,http://purl.bioontology.org/ontology/SNOMEDCT/280209005 280210000,Entire ophthalmic nerve,SNOMED CT,280210000,http://purl.bioontology.org/ontology/SNOMEDCT/280210000 @@ -14020,7 +14020,7 @@ name,label,codesystem,code,ontologyTermURI 280649008,Valve of medial palpebral ligament,SNOMED CT,280649008,http://purl.bioontology.org/ontology/SNOMEDCT/280649008 280650008,Entire posterior part of uveal tract,SNOMED CT,280650008,http://purl.bioontology.org/ontology/SNOMEDCT/280650008 280651007,Valve of Huscke,SNOMED CT,280651007,http://purl.bioontology.org/ontology/SNOMEDCT/280651007 -280652000,"Entire Bruch's basal membrane",SNOMED CT,280652000,http://purl.bioontology.org/ontology/SNOMEDCT/280652000 +280652000,Entire Bruch's basal membrane,SNOMED CT,280652000,http://purl.bioontology.org/ontology/SNOMEDCT/280652000 280653005,Valve of Beraud,SNOMED CT,280653005,http://purl.bioontology.org/ontology/SNOMEDCT/280653005 280654004,Valve of Taillefer,SNOMED CT,280654004,http://purl.bioontology.org/ontology/SNOMEDCT/280654004 280655003,Valve of Hasner,SNOMED CT,280655003,http://purl.bioontology.org/ontology/SNOMEDCT/280655003 @@ -14032,7 +14032,7 @@ name,label,codesystem,code,ontologyTermURI 280661000,Entire posterior pole of eye,SNOMED CT,280661000,http://purl.bioontology.org/ontology/SNOMEDCT/280661000 280662007,Entire retinal pigment epithelium,SNOMED CT,280662007,http://purl.bioontology.org/ontology/SNOMEDCT/280662007 280663002,Structure of conjunctival zone,SNOMED CT,280663002,http://purl.bioontology.org/ontology/SNOMEDCT/280663002 -280664008,"Henle's fiber layer",SNOMED CT,280664008,http://purl.bioontology.org/ontology/SNOMEDCT/280664008 +280664008,Henle's fiber layer,SNOMED CT,280664008,http://purl.bioontology.org/ontology/SNOMEDCT/280664008 280665009,Nuclear layer of retina,SNOMED CT,280665009,http://purl.bioontology.org/ontology/SNOMEDCT/280665009 280666005,Entire palpebral conjunctiva,SNOMED CT,280666005,http://purl.bioontology.org/ontology/SNOMEDCT/280666005 280667001,Limiting membrane of retina,SNOMED CT,280667001,http://purl.bioontology.org/ontology/SNOMEDCT/280667001 @@ -14047,12 +14047,12 @@ name,label,codesystem,code,ontologyTermURI 280677004,Internal limiting membrane of retina,SNOMED CT,280677004,http://purl.bioontology.org/ontology/SNOMEDCT/280677004 280678009,Entire outer nuclear layer of retina,SNOMED CT,280678009,http://purl.bioontology.org/ontology/SNOMEDCT/280678009 280679001,Structure of conjunctival fold,SNOMED CT,280679001,http://purl.bioontology.org/ontology/SNOMEDCT/280679001 -280680003,"Stieda's conjunctival groove",SNOMED CT,280680003,http://purl.bioontology.org/ontology/SNOMEDCT/280680003 +280680003,Stieda's conjunctival groove,SNOMED CT,280680003,http://purl.bioontology.org/ontology/SNOMEDCT/280680003 280681004,Conjunctival papilla,SNOMED CT,280681004,http://purl.bioontology.org/ontology/SNOMEDCT/280681004 280682006,Entire inner plexiform layer of retina,SNOMED CT,280682006,http://purl.bioontology.org/ontology/SNOMEDCT/280682006 280683001,Structure of subtarsal fold of conjunctiva,SNOMED CT,280683001,http://purl.bioontology.org/ontology/SNOMEDCT/280683001 280684007,Entire outer plexiform layer of retina,SNOMED CT,280684007,http://purl.bioontology.org/ontology/SNOMEDCT/280684007 -280685008,"Structure of Stieda's conjunctival fold",SNOMED CT,280685008,http://purl.bioontology.org/ontology/SNOMEDCT/280685008 +280685008,Structure of Stieda's conjunctival fold,SNOMED CT,280685008,http://purl.bioontology.org/ontology/SNOMEDCT/280685008 280686009,Entire semilunar fold of conjunctiva,SNOMED CT,280686009,http://purl.bioontology.org/ontology/SNOMEDCT/280686009 280687000,Smooth part of ciliary body,SNOMED CT,280687000,http://purl.bioontology.org/ontology/SNOMEDCT/280687000 280688005,Corneal surface zone,SNOMED CT,280688005,http://purl.bioontology.org/ontology/SNOMEDCT/280688005 @@ -14212,13 +14212,13 @@ name,label,codesystem,code,ontologyTermURI 280864005,Epichoroidal star of ciliary muscle,SNOMED CT,280864005,http://purl.bioontology.org/ontology/SNOMEDCT/280864005 280865006,Entire meridional fibers of ciliary muscle,SNOMED CT,280865006,http://purl.bioontology.org/ontology/SNOMEDCT/280865006 280866007,Entire circular fibers of ciliary muscle,SNOMED CT,280866007,http://purl.bioontology.org/ontology/SNOMEDCT/280866007 -280867003,"Muller's ciliary muscle",SNOMED CT,280867003,http://purl.bioontology.org/ontology/SNOMEDCT/280867003 +280867003,Muller's ciliary muscle,SNOMED CT,280867003,http://purl.bioontology.org/ontology/SNOMEDCT/280867003 280868008,Ciliary stroma,SNOMED CT,280868008,http://purl.bioontology.org/ontology/SNOMEDCT/280868008 280869000,Ciliary epithelium structure,SNOMED CT,280869000,http://purl.bioontology.org/ontology/SNOMEDCT/280869000 280870004,Entire ciliary epithelium,SNOMED CT,280870004,http://purl.bioontology.org/ontology/SNOMEDCT/280870004 280872007,Inner layer of ciliary epithelium,SNOMED CT,280872007,http://purl.bioontology.org/ontology/SNOMEDCT/280872007 280873002,Entire pigmented layer of ciliary body,SNOMED CT,280873002,http://purl.bioontology.org/ontology/SNOMEDCT/280873002 -280874008,"Ciliary part of Bruch's membrane",SNOMED CT,280874008,http://purl.bioontology.org/ontology/SNOMEDCT/280874008 +280874008,Ciliary part of Bruch's membrane,SNOMED CT,280874008,http://purl.bioontology.org/ontology/SNOMEDCT/280874008 280875009,Internal limiting membrane of ciliary body,SNOMED CT,280875009,http://purl.bioontology.org/ontology/SNOMEDCT/280875009 280876005,Iridociliary junction,SNOMED CT,280876005,http://purl.bioontology.org/ontology/SNOMEDCT/280876005 280877001,Zone of iris,SNOMED CT,280877001,http://purl.bioontology.org/ontology/SNOMEDCT/280877001 @@ -14239,7 +14239,7 @@ name,label,codesystem,code,ontologyTermURI 280897006,Layer of large choroidal vessels,SNOMED CT,280897006,http://purl.bioontology.org/ontology/SNOMEDCT/280897006 280898001,Layer of medium vessels,SNOMED CT,280898001,http://purl.bioontology.org/ontology/SNOMEDCT/280898001 280899009,Entire lamina choroidocapillaris,SNOMED CT,280899009,http://purl.bioontology.org/ontology/SNOMEDCT/280899009 -280900004,"Choroidal part of Bruch's membrane",SNOMED CT,280900004,http://purl.bioontology.org/ontology/SNOMEDCT/280900004 +280900004,Choroidal part of Bruch's membrane,SNOMED CT,280900004,http://purl.bioontology.org/ontology/SNOMEDCT/280900004 280903002,Pulp of finger,SNOMED CT,280903002,http://purl.bioontology.org/ontology/SNOMEDCT/280903002 280904008,Pulp of thumb,SNOMED CT,280904008,http://purl.bioontology.org/ontology/SNOMEDCT/280904008 280908006,Entire skin of supraclavicular region of neck,SNOMED CT,280908006,http://purl.bioontology.org/ontology/SNOMEDCT/280908006 @@ -14276,8 +14276,8 @@ name,label,codesystem,code,ontologyTermURI 281070008,Gland of Zeis,SNOMED CT,281070008,http://purl.bioontology.org/ontology/SNOMEDCT/281070008 281073005,Junction of small intestine,SNOMED CT,281073005,http://purl.bioontology.org/ontology/SNOMEDCT/281073005 281074004,Duodenojejunal junction,SNOMED CT,281074004,http://purl.bioontology.org/ontology/SNOMEDCT/281074004 -281075003,"Entire Bowman's layer",SNOMED CT,281075003,http://purl.bioontology.org/ontology/SNOMEDCT/281075003 -281076002,"Entire Descemet's membrane",SNOMED CT,281076002,http://purl.bioontology.org/ontology/SNOMEDCT/281076002 +281075003,Entire Bowman's layer,SNOMED CT,281075003,http://purl.bioontology.org/ontology/SNOMEDCT/281075003 +281076002,Entire Descemet's membrane,SNOMED CT,281076002,http://purl.bioontology.org/ontology/SNOMEDCT/281076002 281079009,Superior division of central artery of retina,SNOMED CT,281079009,http://purl.bioontology.org/ontology/SNOMEDCT/281079009 281081006,Inferior division of central artery of retina,SNOMED CT,281081006,http://purl.bioontology.org/ontology/SNOMEDCT/281081006 281082004,Macular arteriole,SNOMED CT,281082004,http://purl.bioontology.org/ontology/SNOMEDCT/281082004 @@ -15803,8 +15803,8 @@ name,label,codesystem,code,ontologyTermURI 319024007,Entire hair matrix,SNOMED CT,319024007,http://purl.bioontology.org/ontology/SNOMEDCT/319024007 319123004,Entire hair papilla,SNOMED CT,319123004,http://purl.bioontology.org/ontology/SNOMEDCT/319123004 319224003,Entire outer root sheath,SNOMED CT,319224003,http://purl.bioontology.org/ontology/SNOMEDCT/319224003 -319322001,"Entire Henle's layer",SNOMED CT,319322001,http://purl.bioontology.org/ontology/SNOMEDCT/319322001 -319423007,"Entire Huxley's layer",SNOMED CT,319423007,http://purl.bioontology.org/ontology/SNOMEDCT/319423007 +319322001,Entire Henle's layer,SNOMED CT,319322001,http://purl.bioontology.org/ontology/SNOMEDCT/319322001 +319423007,Entire Huxley's layer,SNOMED CT,319423007,http://purl.bioontology.org/ontology/SNOMEDCT/319423007 319522000,Entire infundibulum of hair follicle,SNOMED CT,319522000,http://purl.bioontology.org/ontology/SNOMEDCT/319522000 319622005,Entire infundibular canal of hair follicle,SNOMED CT,319622005,http://purl.bioontology.org/ontology/SNOMEDCT/319622005 319720006,Entire vellus hair,SNOMED CT,319720006,http://purl.bioontology.org/ontology/SNOMEDCT/319720006 @@ -15833,7 +15833,7 @@ name,label,codesystem,code,ontologyTermURI 322050006,Entire appendicular skeleton,SNOMED CT,322050006,http://purl.bioontology.org/ontology/SNOMEDCT/322050006 322151008,Entire venous network,SNOMED CT,322151008,http://purl.bioontology.org/ontology/SNOMEDCT/322151008 322249004,Entire gastrointestinal mucous membrane,SNOMED CT,322249004,http://purl.bioontology.org/ontology/SNOMEDCT/322249004 -322349001,"Entire Meissner's plexus",SNOMED CT,322349001,http://purl.bioontology.org/ontology/SNOMEDCT/322349001 +322349001,Entire Meissner's plexus,SNOMED CT,322349001,http://purl.bioontology.org/ontology/SNOMEDCT/322349001 322449002,Entire gastrointestinal serosa,SNOMED CT,322449002,http://purl.bioontology.org/ontology/SNOMEDCT/322449002 322548008,Entire gastrointestinal subserosa,SNOMED CT,322548008,http://purl.bioontology.org/ontology/SNOMEDCT/322548008 322648002,Entire esophageal lumen,SNOMED CT,322648002,http://purl.bioontology.org/ontology/SNOMEDCT/322648002 @@ -15848,10 +15848,10 @@ name,label,codesystem,code,ontologyTermURI 323810003,Entire parasympathetic fibers to bladder,SNOMED CT,323810003,http://purl.bioontology.org/ontology/SNOMEDCT/323810003 323907009,Entire parasympathetic fibers to external genitalia,SNOMED CT,323907009,http://purl.bioontology.org/ontology/SNOMEDCT/323907009 323998008,Entire medial root of optic tract,SNOMED CT,323998008,http://purl.bioontology.org/ontology/SNOMEDCT/323998008 -324097006,"Entire Held's space",SNOMED CT,324097006,http://purl.bioontology.org/ontology/SNOMEDCT/324097006 +324097006,Entire Held's space,SNOMED CT,324097006,http://purl.bioontology.org/ontology/SNOMEDCT/324097006 324194002,Entire meningeal spaces,SNOMED CT,324194002,http://purl.bioontology.org/ontology/SNOMEDCT/324194002 324289009,Entire virchow-Robin space,SNOMED CT,324289009,http://purl.bioontology.org/ontology/SNOMEDCT/324289009 -324385000,"Structure of His' perivascular space",SNOMED CT,324385000,http://purl.bioontology.org/ontology/SNOMEDCT/324385000 +324385000,Structure of His' perivascular space,SNOMED CT,324385000,http://purl.bioontology.org/ontology/SNOMEDCT/324385000 324478000,Entire sympathetic trunk ganglia,SNOMED CT,324478000,http://purl.bioontology.org/ontology/SNOMEDCT/324478000 324571009,Structure of sympathetic trunk intermediate ganglia,SNOMED CT,324571009,http://purl.bioontology.org/ontology/SNOMEDCT/324571009 324663003,Entire ganglion terminale of cephalic portion of sympathetic nervous system,SNOMED CT,324663003,http://purl.bioontology.org/ontology/SNOMEDCT/324663003 @@ -16395,7 +16395,7 @@ name,label,codesystem,code,ontologyTermURI 361331000,Entire glomerular capsule,SNOMED CT,361331000,http://purl.bioontology.org/ontology/SNOMEDCT/361331000 361332007,Entire renal tubule,SNOMED CT,361332007,http://purl.bioontology.org/ontology/SNOMEDCT/361332007 361333002,Entire convoluted renal tubule,SNOMED CT,361333002,http://purl.bioontology.org/ontology/SNOMEDCT/361333002 -361335009,"Entire henle's loop",SNOMED CT,361335009,http://purl.bioontology.org/ontology/SNOMEDCT/361335009 +361335009,Entire henle's loop,SNOMED CT,361335009,http://purl.bioontology.org/ontology/SNOMEDCT/361335009 361336005,Entire distal convoluted renal tubule,SNOMED CT,361336005,http://purl.bioontology.org/ontology/SNOMEDCT/361336005 361337001,Entire nephron,SNOMED CT,361337001,http://purl.bioontology.org/ontology/SNOMEDCT/361337001 361339003,Entire endocrine pancreas,SNOMED CT,361339003,http://purl.bioontology.org/ontology/SNOMEDCT/361339003 @@ -16471,7 +16471,7 @@ name,label,codesystem,code,ontologyTermURI 361572002,Entire medial lemniscus in pons,SNOMED CT,361572002,http://purl.bioontology.org/ontology/SNOMEDCT/361572002 361573007,Lateral lemniscus of pons,SNOMED CT,361573007,http://purl.bioontology.org/ontology/SNOMEDCT/361573007 361574001,Entire diencephalic periventricular fibers,SNOMED CT,361574001,http://purl.bioontology.org/ontology/SNOMEDCT/361574001 -361575000,"Entire luys' nucleus",SNOMED CT,361575000,http://purl.bioontology.org/ontology/SNOMEDCT/361575000 +361575000,Entire luys' nucleus,SNOMED CT,361575000,http://purl.bioontology.org/ontology/SNOMEDCT/361575000 361576004,Entire rhinencephalon,SNOMED CT,361576004,http://purl.bioontology.org/ontology/SNOMEDCT/361576004 361579006,Entire corpora quadrigemina,SNOMED CT,361579006,http://purl.bioontology.org/ontology/SNOMEDCT/361579006 361586003,Rubro-olivary tract,SNOMED CT,361586003,http://purl.bioontology.org/ontology/SNOMEDCT/361586003 @@ -16979,7 +16979,7 @@ name,label,codesystem,code,ontologyTermURI 362215008,Entire area cribrosa of renal papilla,SNOMED CT,362215008,http://purl.bioontology.org/ontology/SNOMEDCT/362215008 362216009,Entire perirenal tissue,SNOMED CT,362216009,http://purl.bioontology.org/ontology/SNOMEDCT/362216009 362217000,Entire glomerulus,SNOMED CT,362217000,http://purl.bioontology.org/ontology/SNOMEDCT/362217000 -362218005,"Entire parietal layer of Bowman's capsule",SNOMED CT,362218005,http://purl.bioontology.org/ontology/SNOMEDCT/362218005 +362218005,Entire parietal layer of Bowman's capsule,SNOMED CT,362218005,http://purl.bioontology.org/ontology/SNOMEDCT/362218005 362219002,Entire juxtaglomerular apparatus,SNOMED CT,362219002,http://purl.bioontology.org/ontology/SNOMEDCT/362219002 362220008,Entire proximal convoluted renal tubule,SNOMED CT,362220008,http://purl.bioontology.org/ontology/SNOMEDCT/362220008 362221007,Entire renal pelvis,SNOMED CT,362221007,http://purl.bioontology.org/ontology/SNOMEDCT/362221007 @@ -18520,7 +18520,7 @@ name,label,codesystem,code,ontologyTermURI 368822003,Entire corneal spaces,SNOMED CT,368822003,http://purl.bioontology.org/ontology/SNOMEDCT/368822003 368825001,All corneal epithelium,SNOMED CT,368825001,http://purl.bioontology.org/ontology/SNOMEDCT/368825001 368827009,Entire corneal endothelium,SNOMED CT,368827009,http://purl.bioontology.org/ontology/SNOMEDCT/368827009 -368828004,"Entire Fontana's spaces",SNOMED CT,368828004,http://purl.bioontology.org/ontology/SNOMEDCT/368828004 +368828004,Entire Fontana's spaces,SNOMED CT,368828004,http://purl.bioontology.org/ontology/SNOMEDCT/368828004 368830002,Entire pars plana,SNOMED CT,368830002,http://purl.bioontology.org/ontology/SNOMEDCT/368830002 368832005,Entire lamina basalis of ciliary body,SNOMED CT,368832005,http://purl.bioontology.org/ontology/SNOMEDCT/368832005 368834006,Entire pigmented layer of iris,SNOMED CT,368834006,http://purl.bioontology.org/ontology/SNOMEDCT/368834006 @@ -18641,7 +18641,7 @@ name,label,codesystem,code,ontologyTermURI 368962003,Entire pectinate zone of organ of Corti,SNOMED CT,368962003,http://purl.bioontology.org/ontology/SNOMEDCT/368962003 368963008,Entire vas spirale of cochlea,SNOMED CT,368963008,http://purl.bioontology.org/ontology/SNOMEDCT/368963008 368964002,Entire habenula perforata of organ of Corti,SNOMED CT,368964002,http://purl.bioontology.org/ontology/SNOMEDCT/368964002 -368965001,"Entire Nuel's space",SNOMED CT,368965001,http://purl.bioontology.org/ontology/SNOMEDCT/368965001 +368965001,Entire Nuel's space,SNOMED CT,368965001,http://purl.bioontology.org/ontology/SNOMEDCT/368965001 368966000,Entire reticular membrane of cochlear duct,SNOMED CT,368966000,http://purl.bioontology.org/ontology/SNOMEDCT/368966000 368967009,Entire tight junction of cochlear duct,SNOMED CT,368967009,http://purl.bioontology.org/ontology/SNOMEDCT/368967009 368968004,Entire intermediary junction of cochlear duct,SNOMED CT,368968004,http://purl.bioontology.org/ontology/SNOMEDCT/368968004 @@ -18726,7 +18726,7 @@ name,label,codesystem,code,ontologyTermURI 369072005,Entire nucleus cuneatus,SNOMED CT,369072005,http://purl.bioontology.org/ontology/SNOMEDCT/369072005 369073000,Structure of accessory cuneate nucleus,SNOMED CT,369073000,http://purl.bioontology.org/ontology/SNOMEDCT/369073000 369075007,Entire medulla oblongata lateral nucleus,SNOMED CT,369075007,http://purl.bioontology.org/ontology/SNOMEDCT/369075007 -369076008,"Entire Roller's nucleus",SNOMED CT,369076008,http://purl.bioontology.org/ontology/SNOMEDCT/369076008 +369076008,Entire Roller's nucleus,SNOMED CT,369076008,http://purl.bioontology.org/ontology/SNOMEDCT/369076008 369077004,Entire nucleus intercalatus,SNOMED CT,369077004,http://purl.bioontology.org/ontology/SNOMEDCT/369077004 369078009,Entire nucleus prepositus,SNOMED CT,369078009,http://purl.bioontology.org/ontology/SNOMEDCT/369078009 369079001,Entire fasciculus gracilis,SNOMED CT,369079001,http://purl.bioontology.org/ontology/SNOMEDCT/369079001 @@ -18835,7 +18835,7 @@ name,label,codesystem,code,ontologyTermURI 369187003,Entire subthalamic fasciculus,SNOMED CT,369187003,http://purl.bioontology.org/ontology/SNOMEDCT/369187003 369188008,Structure of ansa lenticularis,SNOMED CT,369188008,http://purl.bioontology.org/ontology/SNOMEDCT/369188008 369189000,Structure of lenticular fasciculus,SNOMED CT,369189000,http://purl.bioontology.org/ontology/SNOMEDCT/369189000 -369190009,"Structure of Forel's H2 bundle",SNOMED CT,369190009,http://purl.bioontology.org/ontology/SNOMEDCT/369190009 +369190009,Structure of Forel's H2 bundle,SNOMED CT,369190009,http://purl.bioontology.org/ontology/SNOMEDCT/369190009 369191008,Structure of nucleus of the tegmented field of Forel,SNOMED CT,369191008,http://purl.bioontology.org/ontology/SNOMEDCT/369191008 369192001,Structure of endopeduncular nucleus,SNOMED CT,369192001,http://purl.bioontology.org/ontology/SNOMEDCT/369192001 369193006,Entire subcommissural organ,SNOMED CT,369193006,http://purl.bioontology.org/ontology/SNOMEDCT/369193006 @@ -19359,7 +19359,7 @@ name,label,codesystem,code,ontologyTermURI 386059001,Guinea-pig hair,SNOMED CT,386059001,http://purl.bioontology.org/ontology/SNOMEDCT/386059001 386060006,Hamster hair,SNOMED CT,386060006,http://purl.bioontology.org/ontology/SNOMEDCT/386060006 386061005,Mouse hair,SNOMED CT,386061005,http://purl.bioontology.org/ontology/SNOMEDCT/386061005 -386062003,"Pig's bristles",SNOMED CT,386062003,http://purl.bioontology.org/ontology/SNOMEDCT/386062003 +386062003,Pig's bristles,SNOMED CT,386062003,http://purl.bioontology.org/ontology/SNOMEDCT/386062003 386063008,Rabbit hair,SNOMED CT,386063008,http://purl.bioontology.org/ontology/SNOMEDCT/386063008 386064002,Rat hair,SNOMED CT,386064002,http://purl.bioontology.org/ontology/SNOMEDCT/386064002 386096005,Foot joint synovium,SNOMED CT,386096005,http://purl.bioontology.org/ontology/SNOMEDCT/386096005 @@ -20225,4 +20225,4 @@ name,label,codesystem,code,ontologyTermURI 442320004,Hypothalamic-pituitary-adrenal axis,SNOMED CT,442320004,http://purl.bioontology.org/ontology/SNOMEDCT/442320004 442396004,Right labyrinth structure,SNOMED CT,442396004,http://purl.bioontology.org/ontology/SNOMEDCT/442396004 442698007,Hypothalamic-pituitary-testicular axis,SNOMED CT,442698007,http://purl.bioontology.org/ontology/SNOMEDCT/442698007 -442757008,Hypothalamic-pituitary-ovarian axis,SNOMED CT,442757008,http://purl.bioontology.org/ontology/SNOMEDCT/442757008 +442757008,Hypothalamic-pituitary-ovarian axis,SNOMED CT,442757008,http://purl.bioontology.org/ontology/SNOMEDCT/442757008 \ No newline at end of file diff --git a/data/_ontologies/PathologicalState.csv b/data/_ontologies/PathologicalState.csv index eb83dbc11d..c6f13a966b 100644 --- a/data/_ontologies/PathologicalState.csv +++ b/data/_ontologies/PathologicalState.csv @@ -1,13 +1,13 @@ name,definition,codesystem,code,ontologyTermURI -reference sample,"A material sample derived from cells or tissue representing a physiologically or phenotypically normal state.",EFO,0009654,http://www.ebi.ac.uk/efo/EFO_0009654 -abnormal sample,"A material sample derived from cells or tissue representing an observed or suspected physiologically, genomically or phenotypically abnormal state.",EFO,0009655,http://www.ebi.ac.uk/efo/EFO_0009655 -neoplastic sample,"A material sample derived from neoplastic cells or tissue.",EFO,0009656,http://www.ebi.ac.uk/efo/EFO_0009656 -cancer cell line sample,"A neoplastic sample derived from a cancer cell line.",EFO,0030035,http://www.ebi.ac.uk/efo/EFO_0030035 -metastasis sample,"A neoplastic sample derived from a cancer metastasis (not from a primary tumor).",EFO,0010941,http://www.ebi.ac.uk/efo/EFO_0010941 -primary tumor sample,"A neoplastic sample derived from a primary tumor (not from a cancer metastasis).",EFO,0010942,http://www.ebi.ac.uk/efo/EFO_0010942 -recurrent tumor sample,"A neoplastic sample derived from a recurrent tumor (not from a primary occurrence of a neoplasm).",EFO,0010943,http://www.ebi.ac.uk/efo/EFO_0010943 +reference sample,A material sample derived from cells or tissue representing a physiologically or phenotypically normal state.,EFO,9654,http://www.ebi.ac.uk/efo/EFO_0009654 +abnormal sample,"A material sample derived from cells or tissue representing an observed or suspected physiologically, genomically or phenotypically abnormal state.",EFO,9655,http://www.ebi.ac.uk/efo/EFO_0009655 +neoplastic sample,A material sample derived from neoplastic cells or tissue.,EFO,9656,http://www.ebi.ac.uk/efo/EFO_0009656 +cancer cell line sample,A neoplastic sample derived from a cancer cell line.,EFO,30035,http://www.ebi.ac.uk/efo/EFO_0030035 +metastasis sample,A neoplastic sample derived from a cancer metastasis (not from a primary tumor).,EFO,10941,http://www.ebi.ac.uk/efo/EFO_0010941 +primary tumor sample,A neoplastic sample derived from a primary tumor (not from a cancer metastasis).,EFO,10942,http://www.ebi.ac.uk/efo/EFO_0010942 +recurrent tumor sample,A neoplastic sample derived from a recurrent tumor (not from a primary occurrence of a neoplasm).,EFO,10943,http://www.ebi.ac.uk/efo/EFO_0010943 Affected,Skin region is determined to be affected by a skin disease.,,, Normal,The area within a sample that is represented by non-tumor tissue.,NCIT,C166238,http://purl.obolibrary.org/obo/NCIT_C166238 Organoid,A three dimensional mass comprised of a cultured cell or tissue sample that resembles an in vivo tissue or organ. Organoids are grown in vitro from a combination of cells or tissue fragments cultured in medium containing a variety of biochemical factors.,NCIT,C172259,http://purl.obolibrary.org/obo/NCIT_C172259 Tumor,"A tumor sample, or entire tumor that is removed for microscopic examination.",NCIT,C18009,http://purl.obolibrary.org/obo/NCIT_C18009 -Tumoroid,A three dimensional mass comprised of a cultured tumor cell or tumor sample that resembles an in vivo tumor. Tumoroid are grown in vitro from a combination of cells or tissue fragments cultured in medium containing a variety of biochemical factors.,FG,0000124,https://w3id.org/fair-genomes/resource/FG_0000124 +Tumoroid,A three dimensional mass comprised of a cultured tumor cell or tumor sample that resembles an in vivo tumor. Tumoroid are grown in vitro from a combination of cells or tissue fragments cultured in medium containing a variety of biochemical factors.,FG,124,https://w3id.org/fair-genomes/resource/FG_0000124 \ No newline at end of file From e6270e37661b6f1a7446d36e0aaf5eb077f7c3d1 Mon Sep 17 00:00:00 2001 From: Oudijk Date: Tue, 21 Jan 2025 13:48:23 +0100 Subject: [PATCH 07/11] added ontology table for age group at onset --- data/_ontologies/Age groups at onset.csv | 23 ++++++ data/portal/Individual observations.csv | 90 ++++++++++++------------ 2 files changed, 68 insertions(+), 45 deletions(-) create mode 100644 data/_ontologies/Age groups at onset.csv diff --git a/data/_ontologies/Age groups at onset.csv b/data/_ontologies/Age groups at onset.csv new file mode 100644 index 0000000000..e153c1c4ad --- /dev/null +++ b/data/_ontologies/Age groups at onset.csv @@ -0,0 +1,23 @@ +name,parent,codesystem,code,ontologyTermURI,definition +Postmenopausal onset,,hp,HP_6000315,http://purl.obolibrary.org/obo/HP_6000315,Onset of signs or symptoms of disease during the period of a woman's life after the occurrence of the menopause. +Perimenopausal onset,,hp,HP_6000314,http://purl.obolibrary.org/obo/HP_6000314,Onset of signs or symptoms of disease during the period of a woman's life shortly before the occurrence of the menopause. +Puerpural onset,,hp,HP_4000040,http://purl.obolibrary.org/obo/HP_4000040,Onset of a phenotypic abnormality or a disease during childbirth or in the period immediately following. +Pediatric onset,,hp,HP_0410280,http://purl.obolibrary.org/obo/HP_0410280,"Onset of disease manifestations before adulthood, defined here as before the age of 16 years, but excluding neonatal or congenital onset." +Childhood onset,Pediatric onset,hp,HP_0011463,http://purl.obolibrary.org/obo/HP_0011463,Onset of disease at the age of between 1 and 5 years.; This term refers to ages up to but not including the fifth birthday (see Juvenile onset). +Juvenile onset,Pediatric onset,hp,HP_0003621,http://purl.obolibrary.org/obo/HP_0003621,Onset of signs or symptoms of disease between the age of 5 and 15 years. +Infantile onset,Pediatric onset,hp,HP_0003593,http://purl.obolibrary.org/obo/HP_0003593,Onset of signs or symptoms of disease between 28 days to one year of life.; Onset of signs or symptoms of disease within the first 12 months of life. +Antenatal onset,,hp,HP_0030674,http://purl.obolibrary.org/obo/HP_0030674,Onset prior to birth. +Fetal onset,Antenatal onset,hp,HP_0011461,http://purl.obolibrary.org/obo/HP_0011461,"Onset prior to birth but after 8 weeks of embryonic development (corresponding to a gestational age of 10 weeks).; The time interval of a gestation is called the gestation period. In human obstetrics, gestational age refers to the fertilization age plus two weeks. This is approximately the duration since the woman's last menstrual period began." +Late first trimester onset,Fetal onset,hp,HP_0034199,http://purl.obolibrary.org/obo/HP_0034199,"This term refers to a phenotypic feature that was first observed prior to birth in the first trimester during the early fetal period, which is defined as 11 0/7 to 13 6/7 weeks of gestation (inclusive)." +Second trimester onset,Fetal onset,hp,HP_0034198,http://purl.obolibrary.org/obo/HP_0034198,"This term refers to a phenotypic feature that was first observed prior to birth during the second trimester, which comprises the range of gestational ages from 14 0/7 weeks to 27 6/7 (inclusive)." +Third trimester onset,Fetal onset,hp,HP_0034197,http://purl.obolibrary.org/obo/HP_0034197,"This term refers to a phenotypic feature that was first observed prior to birth during the third trimester, which is defined as 28 weeks and zero days (28+0) of gestation and beyond." +Embryonal onset,Antenatal onset,hp,HP_0011460,http://purl.obolibrary.org/obo/HP_0011460,"Onset of disease at up to 8 weeks following fertilization (corresponding to 10 weeks of gestation).; The time interval of a gestation is called the gestation period. In human obstetrics, gestational age refers to the fertilization age plus two weeks. This is approximately the duration since the woman's last menstrual period began." +Neonatal onset,,hp,HP_0003623,http://purl.obolibrary.org/obo/HP_0003623,Onset of signs or symptoms of disease within the first 28 days of life. +Adult onset,,hp,HP_0003581,http://purl.obolibrary.org/obo/HP_0003581,"Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later." +Young adult onset,Adult onset,hp,HP_0011462,http://purl.obolibrary.org/obo/HP_0011462,Onset of disease at the age of between 16 and 40 years. +Late young adult onset,Young adult onset,hp,HP_0025710,http://purl.obolibrary.org/obo/HP_0025710,"Onset of disease at an age of greater than or equal to 25 to under 40 years.; This term includes the full 25th year of age up to the completed 40th year of age (i.e., less than the 40th birthday)." +Intermediate young adult onset,Young adult onset,hp,HP_0025709,http://purl.obolibrary.org/obo/HP_0025709,"Onset of disease at an age of greater than or equal to 19 to under 25 years.; This term includes the full 19th year of age up to the completed 25th year of age (i.e., less than the 25th birthday)." +Early young adult onset,Young adult onset,hp,HP_0025708,http://purl.obolibrary.org/obo/HP_0025708,"Onset of disease at an age of greater than or equal to 16 to under 19 years.; This term includes the full 16th year of age up to the completed 18th year of age (i.e., less than the 19th birthday)." +Middle age onset,Adult onset,hp,HP_0003596,http://purl.obolibrary.org/obo/HP_0003596,A type of adult onset with onset of symptoms at the age of 40 to 60 years.; Middle age is of course not amenable to precise definitions. We suggest using this term for onset of disease symptoms between the age of 40 and 60 years. +Late onset,Adult onset,hp,HP_0003584,http://purl.obolibrary.org/obo/HP_0003584,A type of adult onset with onset of symptoms after the age of 60 years. +Congenital onset,,hp,HP_0003577,http://purl.obolibrary.org/obo/HP_0003577,"A phenotypic abnormality that is present at birth.; Congenital onset literally means present at birth. Congenital abnormalities are thus generally acquired during fetal development. Congenital abnormalities are often but not always hereditary in nature. Whether a disease manifestation is diagnosed to be intrauterine or congenital may depend on the time at which diagnostic procedures are performed. Thus, most congenital abnormalities are also intrauterine. This term should be used for phenotypic abnormalities or diseases initially observed at the time of birth. For abnormalities observed prior to (e.g., by fetal ultrasound), use the term Antenatal onset (HP:0030674)." diff --git a/data/portal/Individual observations.csv b/data/portal/Individual observations.csv index 128e54a6c8..4adc35bee3 100644 --- a/data/portal/Individual observations.csv +++ b/data/portal/Individual observations.csv @@ -1,45 +1,45 @@ -tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles -Individual observations,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25398,Findings and circumstances relating to the examination and treatment of a individual,FAIR Genomes, JRC-CDE,RD3 -Individual observations,,id,auto_id,1,TRUE,,,,,,,, -Individual observations,,individual,ref,,TRUE,,Individuals,,,,http://purl.obolibrary.org/obo/IAO_0000136,A reference to the individual whom this clinical information is about,FAIR Genomes, JRC-CDE, RD3 -Individual observations,,date saved in database,date,,,,,,,,,, -Individual observations,,date of observation,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C119798,The date on which the clinical assement was made,RD3 -Individual observations,,age at observation,period,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C192236,"The age of the individual at the time of observation (e.g., ""P55Y8M12D"")",Beacon v2,RD3 -Individual observations,,type of visit,ontology,,,,Visit type,,,,http://purl.obolibrary.org/obo/NCIT_C103165,The kind of visit undertaken by the individual within a study, such as inpatient, outpatient, telephone, baseline, follow up, etc.,FAIR Genomes, JRC-CDE, RD3 -Clinical observations,Individual observations,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C87853,This table extends observations with clinical details compatible with phenopacket,RD3 -Clinical observations,,phenotypes,refback,,,,Phenotype observations,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C16977,The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. In medical context, these are often the symptoms caused by a disease.,FAIR Genomes, RD3 -Clinical observations,,diseases,refback,,,,Disease history,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C15607,Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function.,FAIR Genomes, RD3 -Clinical observations,,measurements,refback,,,,Measurements,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C25209,Annotation used to indicate the size or magnitude of something that was determined by comparison to a standard,FAIR Genomes, RD3 -Clinical observations,,molecular diagnosis gene,ontology_array,,,,Genes,,,,http://purl.obolibrary.org/obo/NCIT_C36391,Gene affected by pathogenic variation that is causal for disease of the individual,FAIR Genomes -Clinical observations,,molecular diagnosis other,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C20826,Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.,FAIR Genomes -Clinical observations,,is solved,bool,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25587,An indication that diagnosis is given and the case is no longer considered unsolved.,RD3 -Clinical observations,,date solved,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C119798,The date on which a case was considered solved (i.e., a diagnosis was made),RD3 -Clinical observations,,medication,ontology_array,,,,Medication,,,,http://purl.obolibrary.org/obo/NCIT_C459,A drug product that contains one or more active and/or inactive ingredients used by the individual intended to treat, prevent or alleviate the symptoms of disease. Any hormone therapies, gender-related or otherwise, should also be recorded here.,FAIR Genomes -Clinical observations,,drug regimen,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C142516,The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.,FAIR Genomes -Clinical observations,,medical history,ontology_array,,,,MedicalHistory,,,,http://purl.obolibrary.org/obo/NCIT_C18772,A record of a individual's background regarding health, occurrence of disease events and surgical procedures,FAIR Genomes -Clinical observations,,date of first contact,date,,,,,,,,http://purl.bioontology.org/ontology/LNC/MTHU048806,The date on which contact with the individual was initiated,FAIR Genomes, JRC-CDE -Clinical observations,,date of last contact,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C156916,The date on which contact with the individual was last made, -Clinical observations,,classification of functioning,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C21007,An individual's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF),FAIR Genomes, JRC-CDE -Clinical observations,,material used in diagnosis,text,,,,,,,,http://semanticscience.org/resource/SIO_000641,A description of one or more materials used to make a diagnosis,FAIR Genomes -Phenotype observations,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C16977,Beacon v2 Individuals PhenotypicFeatures,Beacon v2,RD3 -Phenotype observations,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")",Beacon v2,RD3 -Phenotype observations,,type,ontology,1,TRUE,,Phenotypes,,,,http://semanticscience.org/resource/SIO_010056,"A term denoting a phenotypic feature. E.g. ""Abnormality of body height""",Beacon v2,RD3 -Phenotype observations,,excluded,bool,,,,,,,,http://purl.obolibrary.org/obo/HP_0040285,An indication if the phenotype was observed or not. The default is ÔfalseÕ, in other words the phenotype was observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be absent.,Beacon v2,RD3 -Phenotype observations,,modifiers,ontology_array,,,,Phenotypes,,,,http://purl.obolibrary.org/obo/HP_0012823,Additional terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. E.g. Exacerbated by tobacco use,Beacon v2,RD3 -Phenotype observations,,severity,ontology,,,,Severity,,,,http://purl.obolibrary.org/obo/HP_0012824,"A value that describes the intensity of the phenotype (e.g., ""Profound"")",Beacon v2,RD3 -Disease history,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C15607,History of diagnoses of an individual at a specific timepoints,Beacon v2,RD3 -Disease history,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")",Beacon v2,RD3 -Disease history,,disease,ontology,1,TRUE,,Diseases,,,,http://semanticscience.org/resource/SIO_001331,"The diagnosis assigned for this particular observation (e.g., ""Spinocerebellar ataxia type 34"")",Beacon v2,RD3 -Disease history,,age group at onset,ontology,,,,Age groups,,,,http://www.ebi.ac.uk/efo/EFO_0004847, http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual's age of onset into groups (e.g., ""Adult"", ""18-24 years"", etc.)",Beacon v2,RD3 -Disease history,,age of onset,period,,,,,,,,http://www.ebi.ac.uk/efo/EFO_0004847,"The age at which manifestations of the diseaese first appeared (e.g., ""P32Y6M1D"")",Beacon v2,RD3 -Disease history,,age group at diagnosis,ontology,,,,Age groups,,,,http://www.ebi.ac.uk/efo/EFO_0004918, http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual's age at diagnosis into groups (e.g., ""Adult"", ""18-24 years"", etc.)",RD3,Beacon v2 Vivify add-on -Disease history,,age at diagnosis,period,,,,,,,,http://www.ebi.ac.uk/efo/EFO_0004918,"The age at which the diagnosis was made (e.g., ""P32Y6M1D"")",RD3,Beacon v2 Vivify add-on -Disease history,,has family history,bool,,,,,,,,http://purl.obolibrary.org/obo/HP_0032316,An indication if the diagnosis is present in one or more family members or other relatives,Beacon v2,RD3 -Disease history,,disease severity,ontology,,,,Severity,,,,http://purl.obolibrary.org/obo/HP_0012824,"A value that describes the intensity of the disease (e.g., ""Profound"")",Beacon v2,RD3 -Disease history,,disease stage,ontology,,,,DiseaseStage,,,,http://purl.obolibrary.org/obo/OBI_0000278,"A part of an occurrence of a disease process which is associated with position in the normal progression of the disease (e.g., ""acute onset"")",Beacon v2,RD3 -Measurements,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25209,Additional clinical measurements collected as part of the clinical observation,Beacon v2,RD3 -Measurements,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")",Beacon v2,RD3 -Measurements,,code,ontology,1,TRUE,,AnalysesPerformed,,,,http://purl.obolibrary.org/obo/NCIT_C25162,"A unique code that identifies or categorises this measurement (e.g., ""Metabolomics"")",Beacon v2,RD3 -Measurements,,variable,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C54166,"A name that describes the measurement (e.g.. ""Blood platelet count"")",RD3,Beacon v2 EMX2 add-on -Measurements,,value,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25712,"The value that was measured, collected, derived, etc. (e.g. ""55345"")",Beacon v2,RD3 -Measurements,,unit,ontology,,,,Units,,,,http://purl.obolibrary.org/obo/NCIT_C25709,"A value that specifes the measured value (e.g., ""Per Millimeter"")",Beacon v2,RD3 \ No newline at end of file +tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles,,,,,,,, +Individual observations,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25398,Findings and circumstances relating to the examination and treatment of a individual,FAIR Genomes, JRC-CDE,RD3,,,,,, +Individual observations,,id,auto_id,1,TRUE,,,,,,,,,,,,,,,, +Individual observations,,individual,ref,,TRUE,,Individuals,,,,http://purl.obolibrary.org/obo/IAO_0000136,A reference to the individual whom this clinical information is about,FAIR Genomes, JRC-CDE,RD3,,,,,, +Individual observations,,date saved in database,date,,,,,,,,,,,,,,,,,, +Individual observations,,date of observation,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C119798,The date on which the clinical assement was made,RD3,,,,,,,, +Individual observations,,age at observation,period,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C192236,"The age of the individual at the time of observation (e.g., ""P55Y8M12D"")",Beacon v2,RD3,,,,,,, +Individual observations,,type of visit,ontology,,,,Visit type,,,,http://purl.obolibrary.org/obo/NCIT_C103165,The kind of visit undertaken by the individual within a study, such as inpatient, outpatient, telephone, baseline, follow up, etc.,FAIR Genomes, JRC-CDE,RD3 +Clinical observations,Individual observations,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C87853,This table extends observations with clinical details compatible with phenopacket,RD3,,,,,,,, +Clinical observations,,phenotypes,refback,,,,Phenotype observations,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C16977,The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. In medical context, these are often the symptoms caused by a disease.,FAIR Genomes,RD3,,,,,, +Clinical observations,,diseases,refback,,,,Disease history,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C15607,Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function.,FAIR Genomes,RD3 +Clinical observations,,measurements,refback,,,,Measurements,,part of clinical observation,,http://purl.obolibrary.org/obo/NCIT_C25209,Annotation used to indicate the size or magnitude of something that was determined by comparison to a standard,FAIR Genomes,RD3,,,,,,, +Clinical observations,,molecular diagnosis gene,ontology_array,,,,Genes,,,,http://purl.obolibrary.org/obo/NCIT_C36391,Gene affected by pathogenic variation that is causal for disease of the individual,FAIR Genomes,,,,,,,, +Clinical observations,,molecular diagnosis other,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C20826,Causal variant in HGVS notation with optional classification or free text explaining any other molecular mechanisms involved.,FAIR Genomes,,,,,,,, +Clinical observations,,is solved,bool,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25587,An indication that diagnosis is given and the case is no longer considered unsolved.,RD3,,,,,,,, +Clinical observations,,date solved,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C119798,The date on which a case was considered solved (i.e., a diagnosis was made),RD3,,,,,,, +Clinical observations,,medication,ontology_array,,,,Medication,,,,http://purl.obolibrary.org/obo/NCIT_C459,A drug product that contains one or more active and/or inactive ingredients used by the individual intended to treat, prevent or alleviate the symptoms of disease. Any hormone therapies, gender-related or otherwise, should also be recorded here.,FAIR Genomes,,,,, +Clinical observations,,drug regimen,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C142516,The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration.,FAIR Genomes,,, +Clinical observations,,medical history,ontology_array,,,,MedicalHistory,,,,http://purl.obolibrary.org/obo/NCIT_C18772,A record of a individual's background regarding health, occurrence of disease events and surgical procedures,FAIR Genomes,,,,,,, +Clinical observations,,date of first contact,date,,,,,,,,http://purl.bioontology.org/ontology/LNC/MTHU048806,The date on which contact with the individual was initiated,FAIR Genomes, JRC-CDE,,,,,,, +Clinical observations,,date of last contact,date,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C156916,The date on which contact with the individual was last made,,,,,,,,, +Clinical observations,,classification of functioning,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C21007,An individual's classification of functioning i.e. disability profile according to International Classification of Functioning and Disability (ICF),FAIR Genomes, JRC-CDE,,,,,,, +Clinical observations,,material used in diagnosis,text,,,,,,,,http://semanticscience.org/resource/SIO_000641,A description of one or more materials used to make a diagnosis,FAIR Genomes,,,,,,,, +Phenotype observations,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C16977,Beacon v2 Individuals PhenotypicFeatures,Beacon v2,RD3,,,,,,, +Phenotype observations,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")",Beacon v2,RD3,,,,,,, +Phenotype observations,,type,ontology,1,TRUE,,Phenotypes,,,,http://semanticscience.org/resource/SIO_010056,"A term denoting a phenotypic feature. E.g. ""Abnormality of body height""",Beacon v2,RD3,,,,,,, +Phenotype observations,,excluded,bool,,,,,,,,http://purl.obolibrary.org/obo/HP_0040285,An indication if the phenotype was observed or not. The default is ÔfalseÕ, in other words the phenotype was observed. Therefore it is only required in cases to indicate that the phenotype was looked for, but found to be absent.,Beacon v2,RD3,,,,, +Phenotype observations,,modifiers,ontology_array,,,,Phenotypes,,,,http://purl.obolibrary.org/obo/HP_0012823,Additional terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. E.g. Exacerbated by tobacco use,Beacon v2,RD3,,, +Phenotype observations,,severity,ontology,,,,Severity,,,,http://purl.obolibrary.org/obo/HP_0012824,"A value that describes the intensity of the phenotype (e.g., ""Profound"")",Beacon v2,RD3,,,,,,, +Disease history,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C15607,History of diagnoses of an individual at a specific timepoints,Beacon v2,RD3,,,,,,, +Disease history,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")",Beacon v2,RD3,,,,,,, +Disease history,,disease,ontology,1,TRUE,,Diseases,,,,http://semanticscience.org/resource/SIO_001331,"The diagnosis assigned for this particular observation (e.g., ""Spinocerebellar ataxia type 34"")",Beacon v2,RD3,,,,,,, +Disease history,,age group at onset,ontology,,,,Age groups at onset,,,,http://www.ebi.ac.uk/efo/EFO_0004847,http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual's age of onset into groups (e.g., ""Adult"", ""18-24 years"", etc.)",Beacon v2,RD3,,,,,, +Disease history,,age of onset,period,,,,,,,,http://www.ebi.ac.uk/efo/EFO_0004847,"The age at which manifestations of the diseaese first appeared (e.g., ""P32Y6M1D"")",Beacon v2,RD3,,,,,,, +Disease history,,age group at diagnosis,ontology,,,,Age groups,,,,http://www.ebi.ac.uk/efo/EFO_0004918,http://purl.obolibrary.org/obo/NCIT_C20587,"A categorical value that groups this individual's age at diagnosis into groups (e.g., ""Adult"", ""18-24 years"", etc.)",RD3,Beacon v2 Vivify add-on,,,,,, +Disease history,,age at diagnosis,period,,,,,,,,http://www.ebi.ac.uk/efo/EFO_0004918,"The age at which the diagnosis was made (e.g., ""P32Y6M1D"")",RD3,Beacon v2 Vivify add-on,,,,,,, +Disease history,,has family history,bool,,,,,,,,http://purl.obolibrary.org/obo/HP_0032316,An indication if the diagnosis is present in one or more family members or other relatives,Beacon v2,RD3,,,,,,, +Disease history,,disease severity,ontology,,,,Severity,,,,http://purl.obolibrary.org/obo/HP_0012824,"A value that describes the intensity of the disease (e.g., ""Profound"")",Beacon v2,RD3,,,,,,, +Disease history,,disease stage,ontology,,,,DiseaseStage,,,,http://purl.obolibrary.org/obo/OBI_0000278,"A part of an occurrence of a disease process which is associated with position in the normal progression of the disease (e.g., ""acute onset"")",Beacon v2,RD3,,,,,,, +Measurements,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25209,Additional clinical measurements collected as part of the clinical observation,Beacon v2,RD3,,,,,,, +Measurements,,part of clinical observation,ref,1,TRUE,,Clinical observations,,,,http://purl.obolibrary.org/obo/NCIT_C87853,"A reference to a specific clinical observation (e.g., ""Ind001_Phen001"")",Beacon v2,RD3,,,,,,, +Measurements,,code,ontology,1,TRUE,,AnalysesPerformed,,,,http://purl.obolibrary.org/obo/NCIT_C25162,"A unique code that identifies or categorises this measurement (e.g., ""Metabolomics"")",Beacon v2,RD3,,,,,,, +Measurements,,variable,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C54166,"A name that describes the measurement (e.g.. ""Blood platelet count"")",RD3,Beacon v2 EMX2 add-on,,,,,,, +Measurements,,value,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25712,"The value that was measured, collected, derived, etc. (e.g. ""55345"")",Beacon v2,RD3,,,,,,, +Measurements,,unit,ontology,,,,Units,,,,http://purl.obolibrary.org/obo/NCIT_C25709,"A value that specifes the measured value (e.g., ""Per Millimeter"")",Beacon v2,RD3,,,,,,, \ No newline at end of file From 90351f5ff90e20dd96df4c778aaa2772ee25c31c Mon Sep 17 00:00:00 2001 From: Oudijk Date: Wed, 22 Jan 2025 16:17:13 +0100 Subject: [PATCH 08/11] Renamed ontology --- .../{Age groups at onset.csv => Age group at onset.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename data/_ontologies/{Age groups at onset.csv => Age group at onset.csv} (100%) diff --git a/data/_ontologies/Age groups at onset.csv b/data/_ontologies/Age group at onset.csv similarity index 100% rename from data/_ontologies/Age groups at onset.csv rename to data/_ontologies/Age group at onset.csv From 4ef03e89ba2c8d280f3df02a59511bf1d03b854e Mon Sep 17 00:00:00 2001 From: Oudijk Date: Wed, 22 Jan 2025 16:29:41 +0100 Subject: [PATCH 09/11] changed ontology name back --- .../{Age group at onset.csv => Age groups at onset.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename data/_ontologies/{Age group at onset.csv => Age groups at onset.csv} (100%) diff --git a/data/_ontologies/Age group at onset.csv b/data/_ontologies/Age groups at onset.csv similarity index 100% rename from data/_ontologies/Age group at onset.csv rename to data/_ontologies/Age groups at onset.csv From 7f53c20fcba609566342a0bcc3954f126afea2e7 Mon Sep 17 00:00:00 2001 From: Oudijk Date: Tue, 28 Jan 2025 12:06:47 +0100 Subject: [PATCH 10/11] fix: new ontology for library layout and removed camelcase in columns in Protocol parameters.csv --- data/_ontologies/LibraryLayout.csv | 3 + data/portal/Protocol parameters.csv | 94 ++++++++++++++--------------- 2 files changed, 50 insertions(+), 47 deletions(-) create mode 100644 data/_ontologies/LibraryLayout.csv diff --git a/data/_ontologies/LibraryLayout.csv b/data/_ontologies/LibraryLayout.csv new file mode 100644 index 0000000000..cef232affd --- /dev/null +++ b/data/_ontologies/LibraryLayout.csv @@ -0,0 +1,3 @@ +name,definition +SINGLE,Single-end reads +PAIRED,Paired-end reads \ No newline at end of file diff --git a/data/portal/Protocol parameters.csv b/data/portal/Protocol parameters.csv index c7fe2f15eb..ae12933ee8 100644 --- a/data/portal/Protocol parameters.csv +++ b/data/portal/Protocol parameters.csv @@ -1,13 +1,13 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles Protocol parameters,,,,,,,,,,,,Generic supertable for capturing protocol specific parameters,RD3 -Protocol parameters,,identifier,auto_id,1,,,,,,,http://purl.obolibrary.org/obo/NCIT_C204540,"Processing identifier","RD3" +Protocol parameters,,identifier,string,1,,,,,,,http://purl.obolibrary.org/obo/NCIT_C204540,Processing identifier,RD3 Protocol parameters,,protocol,ontology,,,,Protocols,,,,,Link to the protocol that was used,RD3 -Protocol parameters,,date,datetime,,,,,,,,,"When the processing happened","RD3" -Protocol parameters,,persons involved,ref_array,,,,Contacts,,,,,"Who was involved in the processing","RD3" +Protocol parameters,,date,datetime,,,,,,,,,When the processing happened,RD3 +Protocol parameters,,persons involved,ref_array,,,,Contacts,,,,,Who was involved in the processing,RD3 Protocol parameters,,institutions involved,ref_array,,,,Organisations,,,,http://purl.obolibrary.org/obo/NCIT_C25412,One or more associations between the individual and a organisation or institution.,Delete? -Protocol parameters,,description,text,,,,,,,,,"Human readible description of the protocol used. In case of standard protocol describe deviations. Could also be a log","RD3" -Protocol parameters,,input files,ref_array,,,,Files,,,,,"links to files used as input","RD3" -Protocol parameters,,input samples,ref_array,,,,Biosamples,,,,,"links to samples used as input","RD3" +Protocol parameters,,description,text,,,,,,,,,Human readible description of the protocol used. In case of standard protocol describe deviations. Could also be a log,RD3 +Protocol parameters,,input files,ref_array,,,,Files,,,,,links to files used as input,RD3 +Protocol parameters,,input samples,ref_array,,,,Biosamples,,,,,links to samples used as input,RD3 Protocol parameters,,comments,text,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25393,"A written explanation, observation or criticism added to textual material.",RD3 Sample preparations,Protocol parameters,,,,,,,,,,http://purl.obolibrary.org/obo/OBI_0001902,A sample preparation for a nucleic acids sequencing assay.,"FAIR Genomes, RD3" Sample preparations,,input amount,int,,,,,,,,http://purl.allotrope.org/ontologies/role#AFRL_0000010,Amount of input material in nanogram (ng).,"FAIR Genomes, RD3" @@ -19,46 +19,46 @@ Sample preparations,,intended insert size,int,,,,,,,,https://w3id.org/fair-genom Sample preparations,,intended read length,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C153362,The number of nucleotides intended to be ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.,"FAIR Genomes, RD3" Sample preparations,,barcode,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43361,A machine-readable representation of information in a visual format on a surface.,RD3 Sequencing runs,Protocol parameters,,,,,,,,,,http://edamontology.org/topic_3168,"The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. In FAIR Genomes: Sequencing. Ideally: SequencingRuns.","Beacon v2, FAIR Genomes, DCAT examples,RD3" -Sequencing runs,,individualId,ref,,,,Individuals,,,,http://purl.obolibrary.org/obo/NCIT_C164337,E.g. Ind001,"Beacon v2,RD3" -Sequencing runs,,Sequencing centre,ref,,,,Organisations,,,,http://purl.obolibrary.org/obo/GENEPIO_0001202,A data field which describes the name of the third party company or laboratory that provided services.,"Beacon v2,RD3" -Sequencing runs,,librarySource,ontology,,,,LibrarySource,,,,http://purl.obolibrary.org/obo/GENEPIO_0001965,E.g. genomic source,"Beacon v2,RD3" -Sequencing runs,,librarySelection,string,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0001940,Edat.g. RANDOM method,"Beacon v2,RD3" -Sequencing runs,,libraryStrategy,ontology,,,,SequencingMethods,,,,http://purl.obolibrary.org/obo/FIX_0000704,Method used to determine the order of bases in a nucleic acid sequence. In FAIR Genomes: SequencingMethod.,"Beacon v2, FAIR Genomes,RD3" -Sequencing runs,,libraryLayout,string,,,,,,,,http://purl.obolibrary.org/obo/FBcv_0003208,Either PAIRED or SINGLE,"Beacon v2,RD3" +Sequencing runs,,individual,ref,,,,Individuals,,,,http://purl.obolibrary.org/obo/NCIT_C164337,E.g. Ind001,"Beacon v2,RD3" +Sequencing runs,,sequencing centre,ref,,,,Organisations,,,,http://purl.obolibrary.org/obo/GENEPIO_0001202,A data field which describes the name of the third party company or laboratory that provided services.,"Beacon v2,RD3" +Sequencing runs,,library source,ontology,,,,LibrarySource,,,,http://purl.obolibrary.org/obo/GENEPIO_0001965,E.g. genomic source,"Beacon v2,RD3" +Sequencing runs,,library selection,string,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0001940,Edat.g. RANDOM method,"Beacon v2,RD3" +Sequencing runs,,library strategy,ontology,,,,SequencingMethods,,,,http://purl.obolibrary.org/obo/FIX_0000704,Method used to determine the order of bases in a nucleic acid sequence. In FAIR Genomes: SequencingMethod.,"Beacon v2, FAIR Genomes,RD3" +Sequencing runs,,library layout,ontology,,,,LibraryLayout,,,,http://purl.obolibrary.org/obo/FBcv_0003208,Either PAIRED or SINGLE,"Beacon v2,RD3" Sequencing runs,,platform,ontology,,,,SequencingPlatforms,,,,http://purl.obolibrary.org/obo/GENEPIO_0000071,"The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment). In FAIR Genomes: SequencingPlatform.","Beacon v2, FAIR Genomes,RD3" -Sequencing runs,,platformModel,ontology,,,,SequencingInstrumentModels,,,,http://purl.obolibrary.org/obo/GENEPIO_0001921,The used product name and model number of a manufacturer's genomic (dna) sequencer. In FAIR Genomes: SequencingInstrumentModel.,"Beacon v2, FAIR Genomes,RD3" -Sequencing runs,,Mean read depth,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C167285,The mean number of times each gene encoding an RNA transcript was fully sequenced.,"FAIR Genomes,RD3" -Sequencing runs,,MedianReadDepth,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C155320,"The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.","FAIR Genomes,RD3" -Sequencing runs,,ObservedReadLength,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C153362,The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.,"FAIR Genomes,RD3" -Sequencing runs,,ObservedInsertSize,int,,,,,,,,https://w3id.org/fair-genomes/resource/FG_0000002,"In paired-end sequencing, the DNA between the adapter sequences is the insert. The length of this sequence is known as the insert size, not to be confused with the inner distance between reads. So, fragment length equals read adapter length (2x) plus insert size, and insert size equals read lenght (2x) plus inner distance.","FAIR Genomes,RD3" -Sequencing runs,,PercentageQ30,decimal,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0000089,"Percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly.","FAIR Genomes,RD3" -Sequencing runs,,PercentageTr20,decimal,,,,,,,,https://w3id.org/fair-genomes/resource/FG_0000003,Percentage of the target sequence on which 20 or more unique reads were successfully mapped.,"FAIR Genomes,RD3" -Sequencing runs,,OtherQualityMetrics,text,,,,,,,,http://edamontology.org/data_3914,"Other NGS quality control metrics, including but not limited to (i) sequencer metrics such as yield, error rate, density (K/mm2), cluster PF (%) and phas/prephas (%), (ii) alignment metrics such as QM insert size, GC content, QM duplicated reads (%), QM error rate, uniformity/evenness of coverage and maternal cell contamination, and (iii) variant call metrics such as number of SNVs/CNVs/SVs called, number of missense/nonsense variants, common variants (%), unique variants (%), gender match and trio inheritance check.","FAIR Genomes,RD3" -Sequencing runs,,Flow cell,string,,,,,,,,http://purl.obolibrary.org/obo/OBI_0400043,"Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.","FAIR Genomes,RD3" -Sequencing runs,,Sequencing lane identifier,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C182081,The numerical identifier for the lane or machine unit where a sample was located during nucleotide sequencing.,"FAIR Genomes,RD3" -MetabolomicMaterialProcessing,Protocol parameters,,,,,,,,,,http://purl.obolibrary.org/obo/OBI_0000073,"A metabolomics material processing is a protocol application including material enrollments and biomaterial transformations.",FAIR Genomes metabolomics add-on -MetabolomicMaterialProcessing,,ProcessingType,ontology,,,,MetabolomicProcessingType,,,,http://purl.obolibrary.org/obo/OBI_0000094,"A planned process which results in physical changes in a specified input material.",FAIR Genomes metabolomics add-on -MetabolomicMaterialProcessing,,SampleExtraction,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0001577,"The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it.",FAIR Genomes metabolomics add-on -MetabolomicMaterialProcessing,,FilterUsed,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0001640,"The filter used in separating of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.",FAIR Genomes metabolomics add-on -MetabolomicMaterialProcessing,,PassingRate,int,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0002751,"The volume of carrier gas passing through a chromatography column in unit time.",FAIR Genomes metabolomics add-on -MetabolomicMaterialProcessing,,SPECartridge,string,,,,,,,,http://purl.obolibrary.org/obo/OMIT_0025161,"A sample preparation technique using a solid adsorbent contained most commonly in a cartridge device, or on a disk to adsorb select species from solution.",FAIR Genomes metabolomics add-on -MetabolomicMaterialProcessing,,WashingProtocol,text,,,,,,,,http://purl.obolibrary.org/obo/OBI_0302888,"Washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.",FAIR Genomes metabolomics add-on -MetabolomicMassSpecAssays,Protocol parameters,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C60819,"A qualitative or quantitative analysis performed to determine the amount of a particular constituent in a sample or the biological or pharmacological properties of a drug.",FAIR Genomes metabolomics add-on -MetabolomicMassSpecAssays,,AssayType,ontology,,,,MetabolomicAssayType,,,,http://purl.obolibrary.org/obo/CHMO_0000470,"Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.",FAIR Genomes metabolomics add-on -MetabolomicMassSpecAssays,,Inlet,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C50251,"A valve that controls the flow of fluids in through the wall of a chamber.",FAIR Genomes metabolomics add-on -MetabolomicMassSpecAssays,,MassSpectrometer,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0000982,"A piece of apparatus that consists of at least an ion source, a mass-to-charge analyser, a detector and a vacuum system and is used to measure mass spectra.",FAIR Genomes metabolomics add-on -MetabolomicMassSpecAssays,,IonizationSource,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0000960,"A piece of apparatus that takes an analyte and generates ions which are passed to the rest of a mass spectrometer for analysis.",FAIR Genomes metabolomics add-on -MetabolomicMassSpecAssays,,ChromatographyColumn,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0000997,"A piece of apparatus that has the form of a tube with a diameter between 5 to 50 mm and hosts the stationary bed in chromatography.",FAIR Genomes metabolomics add-on -MetabolomicMassSpecAssays,,PhaseSeparationProtocol,text,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0002214,"Any method for the synthesis of polymer membranes that involves the polymer transforming from the liquid phase of the cast solution to the solid phase.",FAIR Genomes metabolomics add-on -MetabolomicMassSpecAssays,,MassSpecSourceConditions,string,,,,,,,,http://purl.obolibrary.org/obo/ZECO_0000104,"Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition.",FAIR Genomes metabolomics add-on +Sequencing runs,,platform model,ontology,,,,SequencingInstrumentModels,,,,http://purl.obolibrary.org/obo/GENEPIO_0001921,The used product name and model number of a manufacturer's genomic (dna) sequencer. In FAIR Genomes: SequencingInstrumentModel.,"Beacon v2, FAIR Genomes,RD3" +Sequencing runs,,mean read depth,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C167285,The mean number of times each gene encoding an RNA transcript was fully sequenced.,"FAIR Genomes,RD3" +Sequencing runs,,median read depth,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C155320,"The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.","FAIR Genomes,RD3" +Sequencing runs,,observed read length,int,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C153362,The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.,"FAIR Genomes,RD3" +Sequencing runs,,observed insert size,int,,,,,,,,https://w3id.org/fair-genomes/resource/FG_0000002,"In paired-end sequencing, the DNA between the adapter sequences is the insert. The length of this sequence is known as the insert size, not to be confused with the inner distance between reads. So, fragment length equals read adapter length (2x) plus insert size, and insert size equals read lenght (2x) plus inner distance.","FAIR Genomes,RD3" +Sequencing runs,,percentage Q30,decimal,,,,,,,,http://purl.obolibrary.org/obo/GENEPIO_0000089,"Percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly.","FAIR Genomes,RD3" +Sequencing runs,,percentage Tr20,decimal,,,,,,,,https://w3id.org/fair-genomes/resource/FG_0000003,Percentage of the target sequence on which 20 or more unique reads were successfully mapped.,"FAIR Genomes,RD3" +Sequencing runs,,other quality metrics,text,,,,,,,,http://edamontology.org/data_3914,"Other NGS quality control metrics, including but not limited to (i) sequencer metrics such as yield, error rate, density (K/mm2), cluster PF (%) and phas/prephas (%), (ii) alignment metrics such as QM insert size, GC content, QM duplicated reads (%), QM error rate, uniformity/evenness of coverage and maternal cell contamination, and (iii) variant call metrics such as number of SNVs/CNVs/SVs called, number of missense/nonsense variants, common variants (%), unique variants (%), gender match and trio inheritance check.","FAIR Genomes,RD3" +Sequencing runs,,flow cell,string,,,,,,,,http://purl.obolibrary.org/obo/OBI_0400043,"Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.","FAIR Genomes,RD3" +Sequencing runs,,sequencing lane identifier,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C182081,The numerical identifier for the lane or machine unit where a sample was located during nucleotide sequencing.,"FAIR Genomes,RD3" +MetabolomicMaterialProcessing,Protocol parameters,,,,,,,,,,http://purl.obolibrary.org/obo/OBI_0000073,A metabolomics material processing is a protocol application including material enrollments and biomaterial transformations.,FAIR Genomes metabolomics add-on +MetabolomicMaterialProcessing,,processing type,ontology,,,,MetabolomicProcessingType,,,,http://purl.obolibrary.org/obo/OBI_0000094,A planned process which results in physical changes in a specified input material.,FAIR Genomes metabolomics add-on +MetabolomicMaterialProcessing,,sample extraction,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0001577,The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it.,FAIR Genomes metabolomics add-on +MetabolomicMaterialProcessing,,filter used,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0001640,"The filter used in separating of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.",FAIR Genomes metabolomics add-on +MetabolomicMaterialProcessing,,passing rate,int,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0002751,The volume of carrier gas passing through a chromatography column in unit time.,FAIR Genomes metabolomics add-on +MetabolomicMaterialProcessing,,SPE cartridge,string,,,,,,,,http://purl.obolibrary.org/obo/OMIT_0025161,"A sample preparation technique using a solid adsorbent contained most commonly in a cartridge device, or on a disk to adsorb select species from solution.",FAIR Genomes metabolomics add-on +MetabolomicMaterialProcessing,,washing protocol,text,,,,,,,,http://purl.obolibrary.org/obo/OBI_0302888,Washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.,FAIR Genomes metabolomics add-on +MetabolomicMassSpecAssays,Protocol parameters,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C60819,A qualitative or quantitative analysis performed to determine the amount of a particular constituent in a sample or the biological or pharmacological properties of a drug.,FAIR Genomes metabolomics add-on +MetabolomicMassSpecAssays,,assay type,ontology,,,,MetabolomicAssayType,,,,http://purl.obolibrary.org/obo/CHMO_0000470,Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.,FAIR Genomes metabolomics add-on +MetabolomicMassSpecAssays,,inlet port valve,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C50251,A valve that controls the flow of fluids in through the wall of a chamber.,FAIR Genomes metabolomics add-on +MetabolomicMassSpecAssays,,mass spectrometer,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0000982,"A piece of apparatus that consists of at least an ion source, a mass-to-charge analyser, a detector and a vacuum system and is used to measure mass spectra.",FAIR Genomes metabolomics add-on +MetabolomicMassSpecAssays,,ionization source,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0000960,A piece of apparatus that takes an analyte and generates ions which are passed to the rest of a mass spectrometer for analysis.,FAIR Genomes metabolomics add-on +MetabolomicMassSpecAssays,,chromatography column,string,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0000997,A piece of apparatus that has the form of a tube with a diameter between 5 to 50 mm and hosts the stationary bed in chromatography.,FAIR Genomes metabolomics add-on +MetabolomicMassSpecAssays,,phase separation protocol,text,,,,,,,,http://purl.obolibrary.org/obo/CHMO_0002214,Any method for the synthesis of polymer membranes that involves the polymer transforming from the liquid phase of the cast solution to the solid phase.,FAIR Genomes metabolomics add-on +MetabolomicMassSpecAssays,,source conditions,string,,,,,,,,http://purl.obolibrary.org/obo/ZECO_0000104,Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition.,FAIR Genomes metabolomics add-on MetabolomicAnalyses,Protocol parameters,,,,,,,,,,http://edamontology.org/data_0949,"Basic information, annotation or documentation concerning a metabolomics analysis workflow (but not the workflow itself).",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,AnalysisType,ontology,,,,MetabolomicAnalysisType,,,,http://edamontology.org/operation_2945,"Apply analytical methods to existing data of a specific type.",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,WorkflowDefinition,text,,,,,,,,http://semanticscience.org/resource/SIO_000127,"File content or location that encapsulates the analysis workflow, i.e. a sequence of operations to achieve one or more objectives.",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,WorkflowEngine,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C48293,"The engine used to execute the workflow such as Papermill, Jupyter, Galaxy or Nextflow.",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,WorkflowPublished,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C48471,"A printed or electronic work offered for distribution.",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,ContainerizedBy,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43186,"The analysis has been boxed by a container engine such as Singularity or Docker.",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,SoftwareTools,string,,,,,,,,http://purl.obolibrary.org/obo/ERO_0000071,"A general term primarily used for digitally stored data such as computer programs and other kinds of information read and written by computers.",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,Parameters,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C44175,"Any factor that defines a system and determines (or limits) its performance.",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,DataformatsStored,ontology_array,,,,FileFormats,,,,http://purl.obolibrary.org/obo/NCIT_C142494,"Which data file formats (i.e. defined ways or layouts of representing and structuring data in a computer file, blob, string, message, or elsewhere) are stored and potentially available.",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,StandardsUsed,string,,,,,,,,http://semanticscience.org/resource/SIO_000618,"Any socially-agreed upon specifications used such as Common Workflow Language, mzML, ISA-TAB, FAIR Genomes, etc.",FAIR Genomes metabolomics add-on -MetabolomicAnalyses,,StatisticalMethodsApplied,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C19044,"A method of analyzing or representing statistical data or a procedure for calculating a statistic, such as principal component analysis, affinity propagation clustering, T-test, etc.",FAIR Genomes metabolomics add-on \ No newline at end of file +MetabolomicAnalyses,,analysis type,ontology,,,,MetabolomicAnalysisType,,,,http://edamontology.org/operation_2945,Apply analytical methods to existing data of a specific type.,FAIR Genomes metabolomics add-on +MetabolomicAnalyses,,workflow definition,text,,,,,,,,http://semanticscience.org/resource/SIO_000127,"File content or location that encapsulates the analysis workflow, i.e. a sequence of operations to achieve one or more objectives.",FAIR Genomes metabolomics add-on +MetabolomicAnalyses,,workflow engine,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C48293,"The engine used to execute the workflow such as Papermill, Jupyter, Galaxy or Nextflow.",FAIR Genomes metabolomics add-on +MetabolomicAnalyses,,workflow published,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C48471,A printed or electronic work offered for distribution.,FAIR Genomes metabolomics add-on +MetabolomicAnalyses,,containerized by,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43186,The analysis has been boxed by a container engine such as Singularity or Docker.,FAIR Genomes metabolomics add-on +MetabolomicAnalyses,,software tools,string,,,,,,,,http://purl.obolibrary.org/obo/ERO_0000071,A general term primarily used for digitally stored data such as computer programs and other kinds of information read and written by computers.,FAIR Genomes metabolomics add-on +MetabolomicAnalyses,,parameters,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C44175,Any factor that defines a system and determines (or limits) its performance.,FAIR Genomes metabolomics add-on +MetabolomicAnalyses,,dataformats stored,ontology_array,,,,FileFormats,,,,http://purl.obolibrary.org/obo/NCIT_C142494,"Which data file formats (i.e. defined ways or layouts of representing and structuring data in a computer file, blob, string, message, or elsewhere) are stored and potentially available.",FAIR Genomes metabolomics add-on +MetabolomicAnalyses,,standards used,string,,,,,,,,http://semanticscience.org/resource/SIO_000618,"Any socially-agreed upon specifications used such as Common Workflow Language, mzML, ISA-TAB, FAIR Genomes, etc.",FAIR Genomes metabolomics add-on +MetabolomicAnalyses,,statistical methods applied,string,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C19044,"A method of analyzing or representing statistical data or a procedure for calculating a statistic, such as principal component analysis, affinity propagation clustering, T-test, etc.",FAIR Genomes metabolomics add-on \ No newline at end of file From 04700ce2a3ecc2abbf0d8c1a98d4e514a09e3d89 Mon Sep 17 00:00:00 2001 From: Oudijk Date: Tue, 28 Jan 2025 12:09:52 +0100 Subject: [PATCH 11/11] fix: add order to age groups ontology --- data/_ontologies/Age groups at onset.csv | 46 ++++++++++++------------ 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/data/_ontologies/Age groups at onset.csv b/data/_ontologies/Age groups at onset.csv index e153c1c4ad..4cdb000c75 100644 --- a/data/_ontologies/Age groups at onset.csv +++ b/data/_ontologies/Age groups at onset.csv @@ -1,23 +1,23 @@ -name,parent,codesystem,code,ontologyTermURI,definition -Postmenopausal onset,,hp,HP_6000315,http://purl.obolibrary.org/obo/HP_6000315,Onset of signs or symptoms of disease during the period of a woman's life after the occurrence of the menopause. -Perimenopausal onset,,hp,HP_6000314,http://purl.obolibrary.org/obo/HP_6000314,Onset of signs or symptoms of disease during the period of a woman's life shortly before the occurrence of the menopause. -Puerpural onset,,hp,HP_4000040,http://purl.obolibrary.org/obo/HP_4000040,Onset of a phenotypic abnormality or a disease during childbirth or in the period immediately following. -Pediatric onset,,hp,HP_0410280,http://purl.obolibrary.org/obo/HP_0410280,"Onset of disease manifestations before adulthood, defined here as before the age of 16 years, but excluding neonatal or congenital onset." -Childhood onset,Pediatric onset,hp,HP_0011463,http://purl.obolibrary.org/obo/HP_0011463,Onset of disease at the age of between 1 and 5 years.; This term refers to ages up to but not including the fifth birthday (see Juvenile onset). -Juvenile onset,Pediatric onset,hp,HP_0003621,http://purl.obolibrary.org/obo/HP_0003621,Onset of signs or symptoms of disease between the age of 5 and 15 years. -Infantile onset,Pediatric onset,hp,HP_0003593,http://purl.obolibrary.org/obo/HP_0003593,Onset of signs or symptoms of disease between 28 days to one year of life.; Onset of signs or symptoms of disease within the first 12 months of life. -Antenatal onset,,hp,HP_0030674,http://purl.obolibrary.org/obo/HP_0030674,Onset prior to birth. -Fetal onset,Antenatal onset,hp,HP_0011461,http://purl.obolibrary.org/obo/HP_0011461,"Onset prior to birth but after 8 weeks of embryonic development (corresponding to a gestational age of 10 weeks).; The time interval of a gestation is called the gestation period. In human obstetrics, gestational age refers to the fertilization age plus two weeks. This is approximately the duration since the woman's last menstrual period began." -Late first trimester onset,Fetal onset,hp,HP_0034199,http://purl.obolibrary.org/obo/HP_0034199,"This term refers to a phenotypic feature that was first observed prior to birth in the first trimester during the early fetal period, which is defined as 11 0/7 to 13 6/7 weeks of gestation (inclusive)." -Second trimester onset,Fetal onset,hp,HP_0034198,http://purl.obolibrary.org/obo/HP_0034198,"This term refers to a phenotypic feature that was first observed prior to birth during the second trimester, which comprises the range of gestational ages from 14 0/7 weeks to 27 6/7 (inclusive)." -Third trimester onset,Fetal onset,hp,HP_0034197,http://purl.obolibrary.org/obo/HP_0034197,"This term refers to a phenotypic feature that was first observed prior to birth during the third trimester, which is defined as 28 weeks and zero days (28+0) of gestation and beyond." -Embryonal onset,Antenatal onset,hp,HP_0011460,http://purl.obolibrary.org/obo/HP_0011460,"Onset of disease at up to 8 weeks following fertilization (corresponding to 10 weeks of gestation).; The time interval of a gestation is called the gestation period. In human obstetrics, gestational age refers to the fertilization age plus two weeks. This is approximately the duration since the woman's last menstrual period began." -Neonatal onset,,hp,HP_0003623,http://purl.obolibrary.org/obo/HP_0003623,Onset of signs or symptoms of disease within the first 28 days of life. -Adult onset,,hp,HP_0003581,http://purl.obolibrary.org/obo/HP_0003581,"Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later." -Young adult onset,Adult onset,hp,HP_0011462,http://purl.obolibrary.org/obo/HP_0011462,Onset of disease at the age of between 16 and 40 years. -Late young adult onset,Young adult onset,hp,HP_0025710,http://purl.obolibrary.org/obo/HP_0025710,"Onset of disease at an age of greater than or equal to 25 to under 40 years.; This term includes the full 25th year of age up to the completed 40th year of age (i.e., less than the 40th birthday)." -Intermediate young adult onset,Young adult onset,hp,HP_0025709,http://purl.obolibrary.org/obo/HP_0025709,"Onset of disease at an age of greater than or equal to 19 to under 25 years.; This term includes the full 19th year of age up to the completed 25th year of age (i.e., less than the 25th birthday)." -Early young adult onset,Young adult onset,hp,HP_0025708,http://purl.obolibrary.org/obo/HP_0025708,"Onset of disease at an age of greater than or equal to 16 to under 19 years.; This term includes the full 16th year of age up to the completed 18th year of age (i.e., less than the 19th birthday)." -Middle age onset,Adult onset,hp,HP_0003596,http://purl.obolibrary.org/obo/HP_0003596,A type of adult onset with onset of symptoms at the age of 40 to 60 years.; Middle age is of course not amenable to precise definitions. We suggest using this term for onset of disease symptoms between the age of 40 and 60 years. -Late onset,Adult onset,hp,HP_0003584,http://purl.obolibrary.org/obo/HP_0003584,A type of adult onset with onset of symptoms after the age of 60 years. -Congenital onset,,hp,HP_0003577,http://purl.obolibrary.org/obo/HP_0003577,"A phenotypic abnormality that is present at birth.; Congenital onset literally means present at birth. Congenital abnormalities are thus generally acquired during fetal development. Congenital abnormalities are often but not always hereditary in nature. Whether a disease manifestation is diagnosed to be intrauterine or congenital may depend on the time at which diagnostic procedures are performed. Thus, most congenital abnormalities are also intrauterine. This term should be used for phenotypic abnormalities or diseases initially observed at the time of birth. For abnormalities observed prior to (e.g., by fetal ultrasound), use the term Antenatal onset (HP:0030674)." +order,name,parent,codesystem,code,ontologyTermURI,definition +22,Postmenopausal onset,,hp,HP_6000315,http://purl.obolibrary.org/obo/HP_6000315,Onset of signs or symptoms of disease during the period of a woman's life after the occurrence of the menopause. +21,Perimenopausal onset,,hp,HP_6000314,http://purl.obolibrary.org/obo/HP_6000314,Onset of signs or symptoms of disease during the period of a woman's life shortly before the occurrence of the menopause. +20,Puerpural onset,,hp,HP_4000040,http://purl.obolibrary.org/obo/HP_4000040,Onset of a phenotypic abnormality or a disease during childbirth or in the period immediately following. +9,Pediatric onset,,hp,HP_0410280,http://purl.obolibrary.org/obo/HP_0410280,"Onset of disease manifestations before adulthood, defined here as before the age of 16 years, but excluding neonatal or congenital onset." +11,Childhood onset,Pediatric onset,hp,HP_0011463,http://purl.obolibrary.org/obo/HP_0011463,Onset of disease at the age of between 1 and 5 years.; This term refers to ages up to but not including the fifth birthday (see Juvenile onset). +12,Juvenile onset,Pediatric onset,hp,HP_0003621,http://purl.obolibrary.org/obo/HP_0003621,Onset of signs or symptoms of disease between the age of 5 and 15 years. +10,Infantile onset,Pediatric onset,hp,HP_0003593,http://purl.obolibrary.org/obo/HP_0003593,Onset of signs or symptoms of disease between 28 days to one year of life.; Onset of signs or symptoms of disease within the first 12 months of life. +1,Antenatal onset,,hp,HP_0030674,http://purl.obolibrary.org/obo/HP_0030674,Onset prior to birth. +3,Fetal onset,Antenatal onset,hp,HP_0011461,http://purl.obolibrary.org/obo/HP_0011461,"Onset prior to birth but after 8 weeks of embryonic development (corresponding to a gestational age of 10 weeks).; The time interval of a gestation is called the gestation period. In human obstetrics, gestational age refers to the fertilization age plus two weeks. This is approximately the duration since the woman's last menstrual period began." +4,Late first trimester onset,Fetal onset,hp,HP_0034199,http://purl.obolibrary.org/obo/HP_0034199,"This term refers to a phenotypic feature that was first observed prior to birth in the first trimester during the early fetal period, which is defined as 11 0/7 to 13 6/7 weeks of gestation (inclusive)." +5,Second trimester onset,Fetal onset,hp,HP_0034198,http://purl.obolibrary.org/obo/HP_0034198,"This term refers to a phenotypic feature that was first observed prior to birth during the second trimester, which comprises the range of gestational ages from 14 0/7 weeks to 27 6/7 (inclusive)." +6,Third trimester onset,Fetal onset,hp,HP_0034197,http://purl.obolibrary.org/obo/HP_0034197,"This term refers to a phenotypic feature that was first observed prior to birth during the third trimester, which is defined as 28 weeks and zero days (28+0) of gestation and beyond." +2,Embryonal onset,Antenatal onset,hp,HP_0011460,http://purl.obolibrary.org/obo/HP_0011460,"Onset of disease at up to 8 weeks following fertilization (corresponding to 10 weeks of gestation).; The time interval of a gestation is called the gestation period. In human obstetrics, gestational age refers to the fertilization age plus two weeks. This is approximately the duration since the woman's last menstrual period began." +8,Neonatal onset,,hp,HP_0003623,http://purl.obolibrary.org/obo/HP_0003623,Onset of signs or symptoms of disease within the first 28 days of life. +13,Adult onset,,hp,HP_0003581,http://purl.obolibrary.org/obo/HP_0003581,"Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later." +14,Young adult onset,Adult onset,hp,HP_0011462,http://purl.obolibrary.org/obo/HP_0011462,Onset of disease at the age of between 16 and 40 years. +17,Late young adult onset,Young adult onset,hp,HP_0025710,http://purl.obolibrary.org/obo/HP_0025710,"Onset of disease at an age of greater than or equal to 25 to under 40 years.; This term includes the full 25th year of age up to the completed 40th year of age (i.e., less than the 40th birthday)." +16,Intermediate young adult onset,Young adult onset,hp,HP_0025709,http://purl.obolibrary.org/obo/HP_0025709,"Onset of disease at an age of greater than or equal to 19 to under 25 years.; This term includes the full 19th year of age up to the completed 25th year of age (i.e., less than the 25th birthday)." +15,Early young adult onset,Young adult onset,hp,HP_0025708,http://purl.obolibrary.org/obo/HP_0025708,"Onset of disease at an age of greater than or equal to 16 to under 19 years.; This term includes the full 16th year of age up to the completed 18th year of age (i.e., less than the 19th birthday)." +18,Middle age onset,Adult onset,hp,HP_0003596,http://purl.obolibrary.org/obo/HP_0003596,A type of adult onset with onset of symptoms at the age of 40 to 60 years.; Middle age is of course not amenable to precise definitions. We suggest using this term for onset of disease symptoms between the age of 40 and 60 years. +19,Late onset,Adult onset,hp,HP_0003584,http://purl.obolibrary.org/obo/HP_0003584,A type of adult onset with onset of symptoms after the age of 60 years. +7,Congenital onset,,hp,HP_0003577,http://purl.obolibrary.org/obo/HP_0003577,"A phenotypic abnormality that is present at birth.; Congenital onset literally means present at birth. Congenital abnormalities are thus generally acquired during fetal development. Congenital abnormalities are often but not always hereditary in nature. Whether a disease manifestation is diagnosed to be intrauterine or congenital may depend on the time at which diagnostic procedures are performed. Thus, most congenital abnormalities are also intrauterine. This term should be used for phenotypic abnormalities or diseases initially observed at the time of birth. For abnormalities observed prior to (e.g., by fetal ultrasound), use the term Antenatal onset (HP:0030674)." \ No newline at end of file