en Author: Adrien Coulet Contact: adrien dot coulet at loria dot fr Loria - Inria NGE, University of Lorraine en fr It is likely that this ontology contains errors, omissions. If you notice any, have suggestions, we would be happy to hear from you. You can send your comments to adrien dot coulet at loria dot fr. SO-Pharm SCOPE: SO-Pharm is a formal ontology that represents domain knowledge in pharmacogenomics. To achieve this goal SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e., genotype, phenotype, drug, trial representations). SO-Pharm enables to support knowledge about pharmacogenomic hypothesis, case study, and clinical investigations in pharmacogenomics. TODO: - update URI of concepts of outer ontologies The new release (March 02, 2017) 2.2 includes concept and properties labels in French. Imports have been abandoned in favor of simple references to distant URI Version: SO-Pharm 2.2 Release: 02 Mar 2017 Classical partition object property. is part of "is composed of" is the inverse of "is part of". It is an aggregation relationship. is composed of A clinical item could be measured during different events. E.g: Blood pressure could be measured during every patient visit. is measured during Temporarly, a clinical trial is composed of various "clinical trial events" (visits). During those a list of clinical item are systematically measured for every included patient. E.g: the first visit is moment for the measurement of the blood pressure and the genotype of some genomic variation. is the moment of measurement of Relation between a family member of a patient and the endophenotype item which is measured on the family member. on who endophentoype item is measured Since endophenotype items used to be phenotype item measured on relatives, this object property enables to link endophenotype item and the patient on who it is directly measured. is measured on relative A clinical item measured on the relative to a included patient could be an enophenotype item for this relative. is measured as endophenotype item An endophenotype item for an included patient is a "simple" clinical item for one of its relatives. In that way an endophenotype item measured on the patient x correspond to a clinical item (for instance, a phenotype item) which is actually measured on the patient y who is a relative of x and who could even not been included in the trial. is measured as clinical item A drug treatment is composed of only one drug. has drug Drugs are administrated to patients within drug treatments. is administrated in A posology has a dose that define the administrated dose of drug for each time it is administrated (see frequency [SOPHARM_22100]). has dose A dose composes one part of a posology. is dose in A posology has a frequency that define the frequency of the administration of the drug dose. has frequency A frequency composes one part of a posology. is frequency in A drug treatment is composed of a defined posology. has posology A posology is applied to a drug treatment. is the way of administration in If the genotyping of a genomic variation is include in the protocole of a trial, allele observed for this genomic variation will be different depending on individual genomes. E.g: the variation rs0001 has been genotyped as AA and AC. has been genotyped as An individual genotype is measured atomically for one genomic variation. The a genomic genotype (into an indivudal, during one event) is observed for a particular genomic variation. is the observed genotype for Various entity in relation with the clinicla trial have various role. Example 1: A person who has for role "patientRole" is a patient. Example 2: A treatment has for role "role_in_protocole_application". hasRole A role describes a specific function or usage for an entity. is the role for Patients presents various clinical item measured during the trial. presents clinical item Each instance of a clinical item is measured on an identified patient. is measured on A clinical trial protocol defines how a clinical trial will be developed. defines The development of clinical trial is guided by the clinical trial protocol that contains measurment methods, details on patient treatment and constraints for patient inclusion. is defined by a clinical trial enrolls various patient independently, and a clinical trial enrolls a clinical trial panel which is the global group of patient included in the trial. enrolls Patient could be enrolled in one or several clinical trials. A clinical trial panel, which is composed of patient, is enrolled in only one trial. is enrolled in A clinical trial enrolls only one clinical trial panel, which is the group of all the patient included in the trial. enrolls panel A clinical trial panel, which is composed of patient, is enrolled in only one trial. panel is enrolled in Each clinical item is measured according to a defined measurement method. describes measurement of Each kind of clinical item measured during a trial must be measured according to a defined method in regard to the protocol. is measured according to Some biological/chemical entities could interact together. interacts with Some biological/chemical entities could interact with a drug treatment. interacts with drug treatment Some biological/chemical entities could interact with a genotype item. interacts with genotype Some biological/chemical entities could interact with a phenotype item. interacts with phentoype An interaction (e.g. a pharmacogenomic property) has been evocated in a scientific paper. has been published in A scientific paper argues on the existence of an interaction. evokes An interaction has been experimentated (and potentially proved) on the basis of a clinical trial. has been experimented in A clinical study can experiments (or tests or validates) the validity of an interaction. experiments on Identifier of scientific publication in the NLM PubMed. PMID (PubMed Identifier) The value of the item. item value Name of generic drug. Ex: omeprazol, montelukast. generic name Commercial name of a drug. One drug could have several trade name depending on which pharmaceutical firm sells it. Trade name drug dose value administration frequency value patient id sex A given name of the population. Example: Afro-americans poulation name The name of the clinical trial clinical trial name Each clinical trial is undertaken by a scientific group which is the investigation group. investigation group The time form start is the time that is spend form the begin of the study to the current event. Example: For the study visit which is done 3 month after the intitial visit, the time to start is 3 month. TODO: separate the time unity with PATO concepts. time from start OBI:OBI_12 OBI:OBI_126 OBI:OBI_144 OBI:OBI_181 OBI:OBI_184 OBI:OBI_264 OBI:OBI_272 OBI:OBI_336 OBI:OBI_338 OBI:OBI_343 OBI:OBI_70 MP:MP_0000001 SO:SO_0000240 FB:family_member MEO:MEO_001 PATO:frequency PATO:physical_quality PATO:quality PATO:quantitative SNPO:chromosome SNPO:coding_variant SNPO:dbsnp SNPO:dna_sequence SNPO:exon SNPO:gene SNPO:ncbi_nucleotide SNPO:nucleotide SNPO:nucleotide_variation SNPO:population SNPO:sequence SNPO:sequence_position SNPO:variant CHEBI:CHEBI_23367 CHEBI:CHEBI_23888 CHEBI:CHEBI_27189 UO:unit 1 1 1 SOPHARM:SOPHARM_00100 A biological hypothesis of the existence of a relationship between at least one genotype item [SOPHARM_14000], one drug treatment [SOPHARM_23100] and one phentoype item[SOPHARM_15000]. Propriété pharmacogénomique pharmacogenomic property Created in SO-Pharm 2.0. 18/07/2007 SOPHARM:SOPHARM_00120 A scientific paper could be any kind of scientific publication (research article, position paper, lettre, book chapter,etc.). A scientific paper could evoke the existence of a pharmacogenomic property [SOPHARM_00100]. article scientifique scientific paper 1 1 SOPHARM:SOPHARM_10000 A clinical item is something that is measured on a patient, during a particular clinical event and according to a measuring method. Any variable related to a human individual and measured during a clinical trial is a clinical item. The same clinical item (i.e. the same variable) should be measured on different patients and at different times. Conversely the clinical item must be measured according to only one (or zero) defined method. Otherwise it is another clinical item. Example: the blood pressure - could be measured according to a describe method - could be measured several times (during several clinical events) - could be measured on every patient involved in a study. NB: the value of the measurment while be the value described by the data property "item value" [SOPHARM_01102]. NB: In some cases (e.g. endophenotype) a same clinical item could be both an endophentoype item (i.e. a clinical item) for a patient and a simple clinical item for one of his family members. clinical item item clinique SOPHARM:SOPHARM_11000 It is a clinical item relative to the patient behavior. E. g.: The patient behavior in regard to smoking. behavior item item comportemental SOPHARM:SOPHARM_11100 It is a clinical item informing about treatments of the patient which are not include in the protocole of the clinical trial. E.g.: antidiabetic treatment in a clinical trial not focusing on antidiabetics effects. comportement avec les médicaments drug behavior SOPHARM:SOPHARM_11200 It is a clinical item informing about the way the patient used to eat. E.g.: free-fat diet. alimentation feed behavior SOPHARM:SOPHARM_11300 It describes the life style of the patient. E.g: sedentary, sportsmanlike, etc. life style mode de vie SOPHARM:SOPHARM_11400 Discribing the behavior of a patient in regard to smoking. E. g.: non-smoker. It could be related to a quantity of smoking: x packet year. smoking behavior tabagisme SOPHARM:SOPHARM_12000 A clinical item related to the patient endophenotype. It is a clinical item that is measured on a family member of the patient. Then it is a same clinical item which is both a simple clinical item for the family member and an endophenotype item for the concerned patient. endophenotype item item endophénotypique SOPHARM:SOPHARM_12100 An endophenotype item which has been validated then is known to be involved in endophentoype. item endophénotypique connu known endophenotype item SOPHARM:SOPHARM_12200 An item that could be a endophenotype item, but this status is still a supposition. item endophénotypique hypothétique potential endophenotype item SOPHARM:SOPHARM_13000 A clinical item related to the patient epigenotype. epigenetic item item épigénétique SOPHARM:SOPHARM_14000 It is a clinical item bringing information from the patient genome. Example: the genotype of a mutation or of a SNP in a patient. genotype item item génotypique SOPHARM:SOPHARM_14100 Do the patient has chromosome variations? i.e.: Any variation in the chromosome number or morphology. chromosome variation variation chromosomique 1 SOPHARM:SOPHARM_14200 It is a clinical item that informs on the allele the patient presents for a genomic variation. Example: For the genomic variation rs0001, the patient PA_001 presents the genotype "wild" (which has the item value "AA") genomic genotype génotype génomique SOPHARM:SOPHARM_14210 The patient is heterozygote for the observed allele, i.e.: he presents to different versions of the allele. For a SNP, the item value can be AT, AC, AG, etc. génotype hétérozygote heterozygote genotype SOPHARM:SOPHARM_14220 The patient is homozygote for the observed allele, i.e.: he presents two times the same version of the allele. For a SNP, the item value can be AA, CC, GG or TT. génotype homozygote homozygote genotype 1 1 1 SOPHARM:SOPHARM_15000 20070215: new defintion of phenotype item using only QUALITY ontology (new PATO ontology) + UO to be tested for distinction is_magnitude_of (only symbolic) and is_measurment_of (only numeric) It is a clinical item related to the patient phenotype. It should be quantitative traits as qualitative traits. E. g.: blood pressure. item phénotypique phenotype item SOPHARM:SOPHARM_15100 A disease that as been diagnosed for the concerned patient. E.g.: diabetes. diagnostique disease diagnostic SOPHARM:SOPHARM_20000 A drug. We adopte there the FDCA definition: a drug is a substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease. E.g.: Methotrexate, Omeprazol, etc. SO-Pharm definition said that a drug is administrated in regard to a drug treatment and add that it is composed of chemical compounds. drug médicament TODO: to link with RXNORM 1 1 SOPHARM:SOPHARM_21000 It describes the dose of one atomic drug administration. It is composed of a numerical value and a unit. E.g: 500 mg, 30 mmol N.b:For constant drug administration (e.g. drip/IV) the drug dose value describe the dose administrate during the reference meantime (e.g. 1 g if the drip is tune at 1g/minute ). The reference meantime is then the administration frequency [SOPHARM_22100], 1 minute in this example. dose d'un traitment drug dose 1 1 SOPHARM:SOPHARM_22000 The posology of a drug is the specification of the dosage of the drug and of its administration frequency. posologie posology 1 1 SOPHARM:SOPHARM_22100 The frequence with which a drug or any treatment is administrated to a person (for example to a patient). It is composed of a numerical value and a frequency unit. E.g.: 3 per day (or 3 j^-1), 1 per minute administration frequency fréquence d'administration SOPHARM:SOPHARM_23000 A technique applied onto patient in a view of treating a pathology. traitement treatment 1 1 SOPHARM:SOPHARM_23100 A treatmement based on the administration of a (only one) drug according to a (only one) defined posology. It should be a part of a clinical trial protocol or be a patient behavior that must be take into account. drug treatment traitement médicamenteux SOPHARM:SOPHARM_23200 A regimen of eating and drinking dedicated to modified patient feed behavior. diet régime SOPHARM:SOPHARM_23300 It is a treatment based on physical manipulation of the patient body. physical treatment traitement physique SOPHARM:SOPHARM_23310 The treatment is based on physical therapy/physiotherapy. physical therapy treatment traitement par kinésithérapie SOPHARM:SOPHARM_23320 A treatment technique involving the practical application of surgery. opération chirurgicale surgical operation SOPHARM:SOPHARM_24000 Any chemical compound. It should be a component of a drug (active or inactive). It should be a biological chemical compound too (as the cholesterol that is measured during a trial event). chemical coumpound composé chimique SOPHARM:SOPHARM_30000 Genomic variations are observed modification in the DNA nucleotide sequences between two individuals. E.g.: A SNP, a mutation, a CNV, etc. genomic variation variation génomique SOPHARM:SOPHARM_31000 The exploration of genomic variations in individuals enables the definition of the genotype of individuals. In diploïd organisms, two versions (or two allele) of genes co-exist and both of them must be observed in order to define the genotype.Observed alleles could be the reference allele or a variant allele. For SNP, observed alleles should be two single nuclotides, e.g. A and G. observed allele SOPHARM:SOPHARM_31100 The observed allele should be the reference one if this one is observed in most of individual or if it is considered as a normal state of the genome. reference allele SOPHARM:SOPHARM_31200 The observed allele should be the variant one if this one is rare (in the considered population) or if it is considered as an abnormal state of the genome. variant allele SOPHARM:SOPHARM_40000 The genotype is the specific genetic genome of an individual, in the form of DNA. Source: wikipedia at http://en.wikipedia.org/wiki/Genotype There the genotype of an indivdual could be considered, briefly, as a composition of all its genotype items. genotype génotype SOPHARM:SOPHARM_41000 Neoplasm could has a variant genotype that differs from the "everwhere else normal genotype" in an individual. génotype tumoral neoplasm genotype SOPHARM:SOPHARM_42000 By opposition to a neoplasmic genotype, it is the genotype that is expressed in physiological conditions. génotype somatique normally expressed genotype SOPHARM:SOPHARM_43000 The genotype observed for the TPMT gene. génotype du gène TPMT tpmt genotype SOPHARM:SOPHARM_43100 The particular genotype TPMT*1 for the gene TPMT. tpmt1 tpmt1 SOPHARM:SOPHARM_43200 The particular genotype TPMT*3A for the gene TPMT. tpmt3a tpmt3a SOPHARM:SOPHARM_43300 The particular genotype TPMT*3B for the gene TPMT. tmpt3b tpmt3b SOPHARM:SOPHARM_43400 The particular genotype TPMT*3C for the gene TPMT. tpmt3c tpmt3c SOPHARM:SOPHARM_44000 Viruses from a same species/strain could differs individually in the genome (as indiviudal of any species). In some cases, viral genotype could be associated to the indivdual who hosts the virus. génotype viral viral genotype SOPHARM:SOPHARM_44100 The genotype observed for a VIH virus. Usually a virus that infects a patient. génotype de l'HIV vih genotype SOPHARM:SOPHARM_50000 A human individual. person personne SOPHARM:SOPHARM_51000 A human individual involved in a clinical trial or someone who has been subject for the measurement of a clinical item in the frame of a clinical trial (e.g. a family member who is not included in the clinical trial but who is related to an included patient). patient patient SOPHARM:SOPHARM_52000 A group of persons population population SOPHARM:SOPHARM_52100 A group of persons who are living in a definied area of the world. geographically localized population population associée à une zone géogrpahique SOPHARM:SOPHARM_52110 People living in the American Continent. american américain SOPHARM:SOPHARM_52120 People living in the African Continent. africain african SOPHARM:SOPHARM_52130 People living in the Oceanian Continent. oceanian océanien SOPHARM:SOPHARM_52140 People living in the European Continent. european européen SOPHARM:SOPHARM_52150 People living in the Asian Continent. asian asiatique SOPHARM:SOPHARM_52200 A population of human individuals whose members identify with each other, either on the basis of a presumed common genealogy or ancestry. Source: Wikipedia, http://en.wikipedia.org/wiki/Ethnicity ethnic group groupe éthnique SOPHARM:SOPHARM_52210 caucasian people from the HapMap project, for more details see http://www.hapmap.org/citinghapmap.html.en caucasian caucasien SOPHARM:SOPHARM_52220 yoruba people from the HapMap project, for more details see http://www.hapmap.org/citinghapmap.html.en le peuple yoruba yoruba people SOPHARM:SOPHARM_52230 chinese people from the HapMap project, for more details see http://www.hapmap.org/citinghapmap.html.en chinese chinois SOPHARM:SOPHARM_52240 japanese people from the HapMap project, for more details see http://www.hapmap.org/citinghapmap.html.en japanese japonais SOPHARM:SOPHARM_52300 A populaton that is involved into a clinical trial according to some criteria (criteria of inclusion). clinical trial panel panel d'essai clinique SOPHARM:SOPHARM_52400 A group of persons belonging to the same family. famille family 1 1 SOPHARM:SOPHARM_60000 A scientifically controlled study of the safety and effectiveness of a therapeutic agent (as a drug or vaccine) using consenting human subjects. Source: www.m-w.org In SO-Pharm, a clinical trial is defined by a precise protocole, that should be realize during one or several event, that is done on an selected population (named a panel). clinical trial essai clinique 1 SOPHARM:SOPHARM_61000 A clinical trial event is a moment of the clinical trial when some clinical items are measured. clinical trial event événement d'essai clinique SOPHARM:SOPHARM_62000 The clinical trial protocole defines one or several clinical trial. It is composed of some measurement methods that are employed for the measurement of clinical item during the trial. It also includes the description of studied treatments. clinical trial protocol protocole d'essai clinique SOPHARM:SOPHARM_62100 Every clinical item is measured, and should be measured according to a precisly defined method. measurement method méthode de mesure SOPHARM:SOPHARM_62110 It is measurement method for genotype item. genotype measurement method méthode de mesure du génotype SOPHARM:SOPHARM_62120 It is measurement method for phenotype item. méthode de mesure du phénotype phenotype measurement method SOPHARM:SOPHARM_62121 The medical history or anamnesis of a patient is information gained by a physician or other healthcare professional by asking specific questions, either of the patient or of other people who know the person and can give suitable information , with the aim of obtaining information useful in formulating a diagnosis and providing medical care to the patient. Source: wikipedia at http://en.wikipedia.org/wiki/Medical_history anamnesis anamnèse SOPHARM:SOPHARM_70000 The phenotype of an individual organism is either its total physical appearance and constitution or a specific manifestation of a trait, such as size, eye color, or behavior that varies between individuals. Source: wikipedia at http://en.wikipedia.org/wiki/Phenotype It is composed of phenotype items. phenotype phénotype SOPHARM:SOPHARM_80000 Any hereditary characteristic that is normally associated with some condition but is not a direct symptom of that condition. Source: wiktionary at http://en.wiktionary.org/wiki/endophenotype. It is composed of endophenotype items. endophenotype endophénotype SOPHARM:SOPHARM_90000 It can refer to reversible, heritable changes in gene regulation that occur without a change in DNA sequence (genotype). Source: wikipedia at http://en.wikipedia.org/wiki/Epigenetics. It is composed of epigentic items. epigenotype épigénotype CTO:observations owl:Thing 1 1 plus 2486854 2486854 NT_011295 11085052 11085052 NC_000019 dbSNP http://www.ncbi.nlm.nih.gov/SNP/ 125 CoreNucleotide http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore 36.2 rs28942078 rs28942078 1 1 1 1 1 TODO: - update URI of concepts of outer ontologies The new release (March 02, 2017) 2.2 includes concept and properties labels in French. Imports have been abandoned in favor of simple references to distant URI Version: SO-Pharm 2.2 Release: 02 Mar 2017 en Author: Adrien Coulet Contact: adrien dot coulet at loria dot fr Loria - Inria NGE, University of Lorraine en fr It is likely that this ontology contains errors, omissions. If you notice any, have suggestions, we would be happy to hear from you. You can send your comments to adrien dot coulet at loria dot fr. SO-Pharm SCOPE: SO-Pharm is a formal ontology that represents domain knowledge in pharmacogenomics. To achieve this goal SO-Pharm articulates ontologies from sub domains of phamacogenomics (i.e., genotype, phenotype, drug, trial representations). SO-Pharm enables to support knowledge about pharmacogenomic hypothesis, case study, and clinical investigations in pharmacogenomics. TODO: - update URI of concepts of outer ontologies The new release (March 02, 2017) 2.2 includes concept and properties labels in French. Imports have been abandoned in favor of simple references to distant URI Version: SO-Pharm 2.2 Release: 02 Mar 2017