sopharm
type: Ontology
comment: 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.
version info: 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 info: TODO: - update URI of concepts of outer ontologies
comment: 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.
default language: en
language: fr
version info: Version: SO-Pharm 2.2 Release: 02 Mar 2017
language: en
creator: Author: Adrien Coulet Contact: adrien dot coulet at loria dot fr Loria - Inria NGE, University of Lorraine

is part of
type: ObjectProperty
sub property of: part of
inverse of: is composed of
domain: Class
  union of: endophenotype item
  union of: epigenetic item
  union of: genotype item
  union of: phenotype item
  union of: drug
  union of: drug dose
  union of: posology
  union of: treatment
  union of: chemical coumpound
  union of: observed allele
  union of: genotype
  union of: person
  union of: clinical trial event
  union of: measurement method
  union of: phenotype
  union of: endophenotype
  union of: epigenotype
range: Class
  union of: genomic genotype
  union of: drug
  union of: posology
  union of: drug treatment
  union of: genotype
  union of: person
  union of: population
  union of: clinical trial
  union of: clinical trial protocol
  union of: phenotype
  union of: endophenotype
  union of: epigenotype
comment: Classical partition object property.

is composed of
type: ObjectProperty
sub property of: has part
domain: Class
  union of: genomic genotype
  union of: drug
  union of: posology
  union of: drug treatment
  union of: genotype
  union of: person
  union of: population
  union of: clinical trial
  union of: clinical trial protocol
  union of: phenotype
  union of: endophenotype
  union of: epigenotype
range: Class
  union of: endophenotype item
  union of: epigenetic item
  union of: genotype item
  union of: phenotype item
  union of: drug
  union of: drug dose
  union of: posology
  union of: treatment
  union of: chemical coumpound
  union of: observed allele
  union of: genotype
  union of: person
  union of: clinical trial event
  union of: measurement method
  union of: phenotype
  union of: endophenotype
  union of: epigenotype
comment: "is composed of" is the inverse of "is part of". It is an aggregation relationship.

is measured during
type: ObjectProperty
inverse of: is the moment of measurement of
domain: clinical item
range: clinical trial event
comment: A clinical item could be measured during different events. E.g: Blood pressure could be measured during every patient visit.

is the moment of measurement of
type: ObjectProperty
domain: clinical trial event
range: clinical item
comment: 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.

on who endophentoype item is measured
type: ObjectProperty
inverse of: is measured on relative
domain: family member
range: endophenotype item
comment: Relation between a family member of a patient and the endophenotype item which is measured on the family member.

is measured on relative
type: ObjectProperty
domain: endophenotype item
range: family member
comment: 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 as endophenotype item
type: ObjectProperty
inverse of: is measured as clinical item
domain: clinical item
range: endophenotype item
comment: A clinical item measured on the relative to a included patient could be an enophenotype item for this relative.

is measured as clinical item
type: ObjectProperty
domain: endophenotype item
range: clinical item
comment: 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.

has drug
type: ObjectProperty
inverse of: is administrated in
type: FunctionalProperty
domain: drug treatment
range: drug
comment: A drug treatment is composed of only one drug.

is administrated in
type: ObjectProperty
domain: drug
range: drug treatment
comment: Drugs are administrated to patients within drug treatments.

has dose
type: ObjectProperty
inverse of: is dose in
type: FunctionalProperty
domain: posology
range: drug dose
comment: A posology has a dose that define the administrated dose of drug for each time it is administrated (see frequency [SOPHARM_22100]).

is dose in
type: ObjectProperty
type: InverseFunctionalProperty
domain: drug dose
range: posology
comment: A dose composes one part of a posology.

has frequency
type: ObjectProperty
inverse of: is frequency in
type: FunctionalProperty
domain: posology
range: administration frequency
comment: A posology has a frequency that define the frequency of the administration of the drug dose.

is frequency in
type: ObjectProperty
type: InverseFunctionalProperty
domain: administration frequency
range: posology
comment: A frequency composes one part of a posology.

has posology
type: ObjectProperty
inverse of: is the way of administration in
type: FunctionalProperty
domain: drug treatment
range: posology
comment: A drug treatment is composed of a defined posology.

is the way of administration in
type: ObjectProperty
domain: posology
range: drug treatment
comment: A posology is applied to a drug treatment.

has been genotyped as
type: ObjectProperty
inverse of: is the observed genotype for
domain: genomic variation
range: genomic genotype
comment: 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.

is the observed genotype for
type: ObjectProperty
domain: genomic genotype
range: genomic variation
comment: 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.

hasRole
type: ObjectProperty
inverse of: is the role for
comment: 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".

is the role for
type: ObjectProperty
comment: A role describes a specific function or usage for an entity.

presents clinical item
type: ObjectProperty
inverse of: is measured on
domain: patient
range: clinical item
comment: Patients presents various clinical item measured during the trial.

is measured on
type: ObjectProperty
domain: clinical item
range: patient
comment: Each instance of a clinical item is measured on an identified patient.

defines
type: ObjectProperty
inverse of: is defined by
domain: clinical trial protocol
range: clinical trial
comment: A clinical trial protocol defines how a clinical trial will be developed.

is defined by
type: ObjectProperty
domain: clinical trial
range: clinical trial protocol
comment: 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.

enrolls
type: ObjectProperty
sub property of: has participant
inverse of: is enrolled in
domain: clinical trial
range: Class
  union of: patient
  union of: clinical trial panel
comment: 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.

is enrolled in
type: ObjectProperty
sub property of: participates in
domain: Class
  union of: patient
  union of: clinical trial panel
range: clinical trial
comment: 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.

enrolls panel
type: ObjectProperty
sub property of: enrolls
inverse of: panel is enrolled in
type: FunctionalProperty
comment: A clinical trial enrolls only one clinical trial panel, which is the group of all the patient included in the trial.

panel is enrolled in
type: ObjectProperty
sub property of: is enrolled in
type: InverseFunctionalProperty
comment: A clinical trial panel, which is composed of patient, is enrolled in only one trial.

describes measurement of
type: ObjectProperty
inverse of: is measured according to
domain: measurement method
range: clinical item
comment: Each clinical item is measured according to a defined measurement method.

is measured according to
type: ObjectProperty
domain: clinical item
range: measurement method
comment: Each kind of clinical item measured during a trial must be measured according to a defined method in regard to the protocol.

interacts with
type: ObjectProperty
comment: Some biological/chemical entities could interact together.

interacts with drug treatment
type: ObjectProperty
sub property of: interacts with
range: drug treatment
comment: Some biological/chemical entities could interact with a drug treatment.

interacts with genotype
type: ObjectProperty
sub property of: interacts with
range: genotype item
comment: Some biological/chemical entities could interact with a genotype item.

interacts with phentoype
type: ObjectProperty
sub property of: interacts with
range: phenotype item
comment: Some biological/chemical entities could interact with a phenotype item.

has been published in
type: ObjectProperty
inverse of: evokes
domain: pharmacogenomic property
range: scientific paper
comment: An interaction (e.g. a pharmacogenomic property) has been evocated in a scientific paper.

evokes
type: ObjectProperty
domain: scientific paper
range: pharmacogenomic property
comment: A scientific paper argues on the existence of an interaction.

has been experimented in
type: ObjectProperty
inverse of: experiments on
domain: pharmacogenomic property
range: clinical trial
comment: An interaction has been experimentated (and potentially proved) on the basis of a clinical trial.

experiments on
type: ObjectProperty
domain: clinical trial
range: pharmacogenomic property
comment: A clinical study can experiments (or tests or validates) the validity of an interaction.

PMID (PubMed Identifier)
type: DatatypeProperty
type: FunctionalProperty
domain: scientific paper
range: string
comment: Identifier of scientific publication in the NLM PubMed.

item value
type: DatatypeProperty
type: FunctionalProperty
domain: clinical item
range: string
comment: The value of the item.

generic name
type: DatatypeProperty
type: FunctionalProperty
domain: drug
range: string
comment: Name of generic drug. Ex: omeprazol, montelukast.

Trade name
type: DatatypeProperty
domain: drug
range: string
comment: Commercial name of a drug. One drug could have several trade name depending on which pharmaceutical firm sells it.

drug dose value
type: DatatypeProperty
domain: drug dose
range: string

administration frequency value
type: DatatypeProperty
type: FunctionalProperty
domain: administration frequency
range: string

patient id
type: DatatypeProperty
type: FunctionalProperty
domain: patient
range: string

sex
type: DatatypeProperty
type: FunctionalProperty
domain: patient
range: string

poulation name
type: DatatypeProperty
type: FunctionalProperty
domain: population
range: string
comment: A given name of the population. Example: Afro-americans

clinical trial name
type: DatatypeProperty
domain: clinical trial
range: string
comment: The name of the clinical trial

investigation group
type: DatatypeProperty
domain: clinical trial
range: string
comment: Each clinical trial is undertaken by a scientific group which is the investigation group.

time from start
type: DatatypeProperty
type: FunctionalProperty
domain: clinical trial event
range: string
comment: 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.

pharmacogenomic property
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: interacts with drug treatment
    min cardinality: 1
  intersection of: Restriction
    on property: interacts with genotype
    min cardinality: 1
  intersection of: Restriction
    on property: interacts with phentoype
    min cardinality: 1
subclass of: OBI 12
subclass of: Thing
subclass of: Restriction
  on property: has been published in
  some values from: scientific paper
subclass of: Restriction
  on property: has been experimented in
  some values from: clinical trial
comment: 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].
label: Propriété pharmacogénomique
version info: Created in SO-Pharm 2.0. 18/07/2007

scientific paper
type: Class
comment: 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].
label: article scientifique

clinical item
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is measured during
    all values from: clinical trial event
  intersection of: Restriction
    on property: is measured on
    all values from: person
  intersection of: Restriction
    on property: is measured according to
    all values from: measurement method
  intersection of: Restriction
    on property: is measured according to
    max cardinality: 1
  intersection of: Restriction
    on property: item value
    cardinality: 1
comment: 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.
label: item clinique

behavior item
type: Class
subclass of: clinical item
comment: It is a clinical item relative to the patient behavior. E. g.: The patient behavior in regard to smoking.
label: item comportemental

drug behavior
type: Class
subclass of: behavior item
subclass of: Restriction
  on property: is composed of
  some values from: treatment
comment: 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.
label: comportement avec les médicaments

feed behavior
type: Class
subclass of: behavior item
subclass of: Restriction
  on property: is composed of
  some values from: diet
comment: It is a clinical item informing about the way the patient used to eat. E.g.: free-fat diet.
label: alimentation

life style
type: Class
subclass of: behavior item
comment: It describes the life style of the patient. E.g: sedentary, sportsmanlike, etc.
label: mode de vie

smoking behavior
type: Class
subclass of: behavior item
comment: 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.
label: tabagisme

endophenotype item
type: Class
subclass of: clinical item
subclass of: Restriction
  on property: is measured on relative
  all values from: Class
    union of: Restriction
      on property: hasChild
      some values from: person
    union of: Restriction
      on property: hasParent
      some values from: person
    union of: Restriction
      on property: sibling
      some values from: person
subclass of: Restriction
  on property: is measured as clinical item
  all values from: clinical item
comment: 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.
label: item endophénotypique

known endophenotype item
type: Class
subclass of: endophenotype item
comment: An endophenotype item which has been validated then is known to be involved in endophentoype.
label: item endophénotypique connu

potential endophenotype item
type: Class
subclass of: endophenotype item
comment: An item that could be a endophenotype item, but this status is still a supposition.
label: item endophénotypique hypothétique

epigenetic item
type: Class
subclass of: clinical item
comment: A clinical item related to the patient epigenotype.
label: item épigénétique

genotype item
type: Class
subclass of: clinical item
subclass of: Restriction
  on property: is measured according to
  all values from: genotype measurement method
comment: It is a clinical item bringing information from the patient genome. Example: the genotype of a mutation or of a SNP in a patient.
label: item génotypique

chromosome variation
type: Class
subclass of: genotype item
comment: Do the patient has chromosome variations? i.e.: Any variation in the chromosome number or morphology.
label: variation chromosomique

genomic genotype
type: Class
subclass of: genotype item
subclass of: Class
  intersection of: Restriction
    on property: is the observed genotype for
    all values from: genomic variation
  intersection of: Restriction
    on property: is the observed genotype for
    cardinality: 1
subclass of: Restriction
  on property: is composed of
  some values from: observed allele
subclass of: Restriction
  on property: is composed of
  all values from: observed allele
comment: 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")
label: génotype génomique

heterozygote genotype
type: Class
subclass of: genomic genotype
comment: 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.
label: génotype hétérozygote

homozygote genotype
type: Class
subclass of: genomic genotype
comment: 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.
label: génotype homozygote

phenotype item
type: Class
subclass of: clinical item
subclass of: Class
  union of: Class
    intersection of: Restriction
      on property: is magnitude of
      all values from: quality
    intersection of: Restriction
      on property: is magnitude of
      cardinality: 1
  union of: Class
    intersection of: Restriction
      on property: is measurement of
      all values from: quantitative
    intersection of: Restriction
      on property: is measurement of
      cardinality: 1
subclass of: Restriction
  on property: has unit
  all values from: unit
subclass of: Restriction
  on property: is measured according to
  all values from: phenotype measurement method
subclass of: Restriction
  on property: has quality
  cardinality: 1
comment: 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)
comment: It is a clinical item related to the patient phenotype. It should be quantitative traits as qualitative traits. E. g.: blood pressure.
label: item phénotypique

disease diagnostic
type: Class
subclass of: OBI 338
subclass of: phenotype item
comment: A disease that as been diagnosed for the concerned patient. E.g.: diabetes.
label: diagnostique

drug
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is composed of
    some values from: chemical coumpound
  intersection of: Restriction
    on property: is administrated in
    some values from: drug treatment
comment: 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.
label: médicament
version info: TODO: to link with RXNORM

drug dose
type: Class
equivalent class: Restriction
  on property: drug dose value
  cardinality: 1
subclass of: Quality
subclass of: physical quality
subclass of: Thing
subclass of: Restriction
  on property: is dose in
  some values from: posology
subclass of: Restriction
  on property: has unit
  all values from: unit
subclass of: Restriction
  on property: has unit
  cardinality: 1
comment: 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.
label: dose d'un traitment

posology
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has dose
    all values from: drug dose
  intersection of: Restriction
    on property: has frequency
    all values from: administration frequency
  intersection of: Restriction
    on property: has dose
    cardinality: 1
  intersection of: Restriction
    on property: has frequency
    cardinality: 1
subclass of: Thing
subclass of: Restriction
  on property: is part of
  some values from: drug treatment
comment: The posology of a drug is the specification of the dosage of the drug and of its administration frequency.
label: posologie

administration frequency
type: Class
equivalent class: Restriction
  on property: administration frequency value
  cardinality: 1
subclass of: Quality
subclass of: frequency
subclass of: Thing
subclass of: Restriction
  on property: is frequency in
  some values from: posology
subclass of: Restriction
  on property: has unit
  all values from: unit
subclass of: Restriction
  on property: has unit
  cardinality: 1
comment: 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
label: fréquence d'administration

treatment
type: Class
subclass of: RealizableEntity
subclass of: Thing
subclass of: Class
  union of: Restriction
    on property: is part of
    some values from: behavior item
  union of: Restriction
    on property: is part of
    some values from: clinical trial protocol
subclass of: Restriction
  on property: hasRole
  some values from: OBI 343
comment: A technique applied onto patient in a view of treating a pathology.
label: traitement

drug treatment
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has drug
    all values from: drug
  intersection of: Restriction
    on property: has posology
    all values from: posology
  intersection of: Restriction
    on property: has drug
    cardinality: 1
  intersection of: Restriction
    on property: has posology
    cardinality: 1
subclass of: treatment
subclass of: Class
  union of: Restriction
    on property: is part of
    some values from: drug behavior
  union of: Restriction
    on property: is part of
    some values from: clinical trial protocol
comment: 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.
label: traitement médicamenteux

diet
type: Class
subclass of: treatment
comment: A regimen of eating and drinking dedicated to modified patient feed behavior.
label: régime

physical treatment
type: Class
subclass of: treatment
comment: It is a treatment based on physical manipulation of the patient body.
label: traitement physique

physical therapy treatment
type: Class
subclass of: physical treatment
comment: The treatment is based on physical therapy/physiotherapy.
label: traitement par kinésithérapie

surgical operation
type: Class
subclass of: physical treatment
comment: A treatment technique involving the practical application of surgery.
label: opération chirurgicale

chemical coumpound
type: Class
subclass of: Object
subclass of: Thing
subclass of: Restriction
  on property: is part of
  some values from: drug
comment: 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).
label: composé chimique

genomic variation
type: Class
subclass of: variant
subclass of: Thing
subclass of: Restriction
  on property: has been genotyped as
  some values from: genomic genotype
comment: Genomic variations are observed modification in the DNA nucleotide sequences between two individuals. E.g.: A SNP, a mutation, a CNV, etc.
label: variation génomique

observed allele
type: Class
equivalent class: Class
  intersection of: sequence
  intersection of: Restriction
    on property: is part of
    all values from: genomic genotype
comment: 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.

reference allele
type: Class
subclass of: observed allele
comment: 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.

variant allele
type: Class
subclass of: observed allele
comment: 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.

genotype
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is composed of
    some values from: genotype item
  intersection of: Restriction
    on property: is composed of
    all values from: genotype item
subclass of: Thing
subclass of: Restriction
  on property: is part of
  some values from: person
comment: 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.
label: génotype

neoplasm genotype
type: Class
subclass of: genotype
comment: Neoplasm could has a variant genotype that differs from the "everwhere else normal genotype" in an individual.
label: génotype tumoral

normally expressed genotype
type: Class
subclass of: genotype
comment: By opposition to a neoplasmic genotype, it is the genotype that is expressed in physiological conditions.
label: génotype somatique

tpmt genotype
type: Class
subclass of: normally expressed genotype
comment: The genotype observed for the TPMT gene.
label: génotype du gène TPMT

tpmt1
type: Class
subclass of: tpmt genotype
comment: The particular genotype TPMT*1 for the gene TPMT.

tpmt3a
type: Class
subclass of: tpmt genotype
comment: The particular genotype TPMT*3A for the gene TPMT.

tpmt3b
type: Class
subclass of: tpmt genotype
comment: The particular genotype TPMT*3B for the gene TPMT.
label: tmpt3b

tpmt3c
type: Class
subclass of: tpmt genotype
comment: The particular genotype TPMT*3C for the gene TPMT.

viral genotype
type: Class
subclass of: genotype
comment: 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.
label: génotype viral

vih genotype
type: Class
subclass of: viral genotype
comment: The genotype observed for a VIH virus. Usually a virus that infects a patient.
label: génotype de l'HIV

person
type: Class
subclass of: family member
subclass of: Thing
comment: A human individual.
label: personne

patient
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: person
    intersection of: Restriction
      on property: hasRole
      some values from: OBI 144
  intersection of: Class
    union of: Restriction
      on property: is part of
      some values from: clinical trial panel
    union of: Restriction
      on property: is enrolled in
      some values from: clinical trial
subclass of: person
comment: 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).

population
type: Class
equivalent class: Class
  intersection of: OBI 181
  intersection of: Restriction
    on property: is composed of
    some values from: person
subclass of: Thing
subclass of: Restriction
  on property: is composed of
  all values from: person
comment: A group of persons

geographically localized population
type: Class
subclass of: population
comment: A group of persons who are living in a definied area of the world.
label: population associée à une zone géogrpahique

american
type: Class
subclass of: geographically localized population
comment: People living in the American Continent.
label: américain

african
type: Class
subclass of: geographically localized population
comment: People living in the African Continent.
label: africain

oceanian
type: Class
subclass of: geographically localized population
comment: People living in the Oceanian Continent.
label: océanien

european
type: Class
subclass of: geographically localized population
comment: People living in the European Continent.
label: européen

asian
type: Class
subclass of: geographically localized population
comment: People living in the Asian Continent.
label: asiatique

ethnic group
type: Class
subclass of: population
comment: 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
label: groupe éthnique

caucasian
type: Class
subclass of: ethnic group
comment: caucasian people from the HapMap project, for more details see http://www.hapmap.org/citinghapmap.html.en
label: caucasien

yoruba people
type: Class
subclass of: ethnic group
comment: yoruba people from the HapMap project, for more details see http://www.hapmap.org/citinghapmap.html.en
label: le peuple yoruba

chinese
type: Class
subclass of: ethnic group
comment: chinese people from the HapMap project, for more details see http://www.hapmap.org/citinghapmap.html.en
label: chinois

japanese
type: Class
subclass of: ethnic group
comment: japanese people from the HapMap project, for more details see http://www.hapmap.org/citinghapmap.html.en
label: japonais

clinical trial panel
type: Class
subclass of: OBI 264
subclass of: population
subclass of: Restriction
  on property: is composed of
  some values from: patient
comment: A populaton that is involved into a clinical trial according to some criteria (criteria of inclusion).
label: panel d'essai clinique

family
type: Class
subclass of: population
comment: A group of persons belonging to the same family.
label: famille

clinical trial
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: Restriction
      on property: enrolls panel
      all values from: clinical trial panel
    intersection of: Restriction
      on property: enrolls panel
      cardinality: 1
  intersection of: Restriction
    on property: is composed of
    some values from: clinical trial event
  intersection of: Restriction
    on property: is defined by
    all values from: clinical trial protocol
  intersection of: Restriction
    on property: is defined by
    cardinality: 1
subclass of: ProcessAggregate
subclass of: Thing
comment: 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).
label: essai clinique

clinical trial event
type: Class
equivalent class: Restriction
  on property: is the moment of measurement of
  some values from: clinical item
subclass of: Process
subclass of: Thing
subclass of: Class
  intersection of: Restriction
    on property: is part of
    all values from: clinical trial
  intersection of: Restriction
    on property: is part of
    cardinality: 1
comment: A clinical trial event is a moment of the clinical trial when some clinical items are measured.
label: événement d'essai clinique

clinical trial protocol
type: Class
subclass of: OBI 272
subclass of: Thing
subclass of: Restriction
  on property: is composed of
  some values from: treatment
subclass of: Restriction
  on property: is composed of
  some values from: measurement method
subclass of: Restriction
  on property: defines
  all values from: clinical trial
comment: 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.
label: protocole d'essai clinique

measurement method
type: Class
subclass of: OBI 70
subclass of: Thing
subclass of: Restriction
  on property: is part of
  some values from: clinical trial protocol
subclass of: Restriction
  on property: describes measurement of
  all values from: clinical item
comment: Every clinical item is measured, and should be measured according to a precisly defined method.
label: méthode de mesure

genotype measurement method
type: Class
subclass of: measurement method
comment: It is measurement method for genotype item.
label: méthode de mesure du génotype

phenotype measurement method
type: Class
subclass of: measurement method
comment: It is measurement method for phenotype item.
label: méthode de mesure du phénotype

anamnesis
type: Class
subclass of: phenotype measurement method
comment: 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
label: anamnèse

phenotype
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is composed of
    some values from: phenotype item
  intersection of: Restriction
    on property: is composed of
    all values from: phenotype item
subclass of: Thing
subclass of: Restriction
  on property: is part of
  some values from: person
comment: 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.
label: phénotype

endophenotype
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is composed of
    some values from: endophenotype item
  intersection of: Restriction
    on property: is composed of
    all values from: endophenotype item
subclass of: Thing
subclass of: Restriction
  on property: is part of
  some values from: person
comment: 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.
label: endophénotype

epigenotype
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is composed of
    some values from: epigenetic item
  intersection of: Restriction
    on property: is composed of
    all values from: epigenetic item
subclass of: Thing
subclass of: Restriction
  on property: is part of
  some values from: person
comment: 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.
label: épigénotype

http://www.loria.fr/~coulet/sopharm/#A
type: NamedIndividual
type: dna sequence
is a sequence composed of: nt A
is one observed allele in: G A
length: 1

http://www.loria.fr/~coulet/sopharm/#G
type: NamedIndividual
type: dna sequence
is a sequence composed of: nt G
is one observed allele in: G A
length: 1

G A
type: NamedIndividual
type: nucleotide variation
has variant allele sequence: http://www.loria.fr/~coulet/sopharm/#A
has variant allele sequence: http://www.loria.fr/~coulet/sopharm/#G
is nucleotide variation of: rs28942078 contig
is nucleotide variation of: rs28942078 ref
strand: plus

NT 011295 2486854
type: NamedIndividual
type: sequence position
has variant: rs28942078 contig
is position in: NT 011295 36 2
start position: 2486854
stop position: 2486854

NT 011295 36 2
type: NamedIndividual
type: dna sequence
identifier in related seq db: NT_011295
is sequence in: LDLR
is stored in seq db: ncbi nucleotide 36 2
presents position: NT 011295 2486854

chr19 11085052 36 2
type: NamedIndividual
type: sequence position
has variant: rs28942078 ref
is position in: chr19 36 2
start position: 11085052
stop position: 11085052

chr19 36 2
type: NamedIndividual
type: dna sequence
identifier in related seq db: NC_000019
is dna sequence of: chr19
is stored in seq db: ncbi nucleotide 36 2
presents position: chr19 11085052 36 2

dbsnp build 125
type: NamedIndividual
type: dbsnp
db name: dbSNP
db url: http://www.ncbi.nlm.nih.gov/SNP/
db version: 125
stores variant: rs28942078 contig
stores variant: rs28942078 ref

ncbi nucleotide 36 2
type: NamedIndividual
type: ncbi nucleotide
db name: CoreNucleotide
db url: http://www.ncbi.nlm.nih.gov/sites/entrez
db version: 36.2
stores sequence: NT 011295 36 2
stores sequence: chr19 36 2

rs28942078 contig
type: NamedIndividual
type: coding variant
has nucleotide variation: G A
has position: NT 011295 2486854
identifier in related var db: rs28942078
is stored in var db: dbsnp build 125

rs28942078 ref
type: NamedIndividual
type: coding variant
has nucleotide variation: G A
has position: chr19 11085052 36 2
identifier in related var db: rs28942078
is dna variant in: LDLR
is dna variant in: LDLR exon 9
is dna variant in: chr19
is stored in var db: dbsnp build 125

cardinality: 1

cardinality: 1

cardinality: 1

cardinality: 1

cardinality: 1