sopharm.owl
type: Ontology
imports: pharmacogeneticsontology.owl
imports: snpontology full.owl
imports: chebi.owl
imports: familybond.owl
version info: TODO: - refine free text descriptions of classes - refine property hierarchy
imports: quality.owl
imports: OBI.owl
imports: disease ontology.owl
imports: http://www.ifomis.org/bfo/1.0
imports: OBO REL
imports: unit.owl
imports: MP
version info: Author: Adrien Coulet Version: SO-Pharm 2.1 Release: 01/15/2009 Contact: adrien dot coulet at loria dot fr University of Nancy
comment: It is likely that this ontology contains errors, omissions. If you notice any, have suggestions, we would be happy to heard from you. We welcome and appreciate your suggestions. You can send your comments to adrien dot coulet at loria dot fr.
default language: en
version info: SO-Pharm 2.1
imports: cto.owl
imports: sequence
imports: meo.owl
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.

clinical trial panel
type: Class
subclass of: OBI 264
subclass of: sopharm resource:arc1be8b1
subclass of: population
comment: A populaton that is involved into a clinical trial according to some criteria (criteria of inclusion).

is composed of
type: ObjectProperty
comment: "is composed of" is the inverse of "is part of". It is an aggregation relationship.
inverse of: is part of
sub property of: has part
range: sopharm resource:arc1be8b174
domain: sopharm resource:arc1be8b192

patient
type: Class
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).
equivalent class: sopharm resource:arc1be8b152
subclass of: person

population
type: Class
equivalent class: sopharm resource:arc1be8b105
comment: A group of persons
subclass of: Thing
subclass of: sopharm resource:arc1be8b109

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].

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.

genotype
type: Class
subclass of: sopharm resource:arc1be8b132
subclass of: Thing
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.
equivalent class: sopharm resource:arc1be8b133

epigenotype
type: Class
equivalent class: sopharm resource:arc1be8b2
subclass of: Thing
subclass of: sopharm resource:arc1be8b7
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.

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

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

is part of
type: ObjectProperty
sub property of: part of
range: sopharm resource:arc1be8b205
inverse of: is composed of
domain: sopharm resource:arc1be8b218
comment: Classical partition object property.

genotype item
type: Class
subclass of: sopharm resource:arc1be8b8
subclass of: clinical item
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.

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

genotype measurement method
type: Class
comment: It is measurement method for genotype item.
subclass of: measurement method

clinical item
type: Class
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.
equivalent class: sopharm resource:arc1be8b138

clinical trial event
type: Class
equivalent class: sopharm resource:arc1be8b9
subclass of: Process
subclass of: Thing
subclass of: sopharm resource:arc1be8b10
comment: A clinical trial event is a moment of the clinical trial when some clinical items are measured.

is the moment of measurement of
type: ObjectProperty
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.
inverse of: is measured during
domain: clinical trial event

sopharm resource:arc1be8b11
type: Restriction
cardinality: 1
on property: is part of

clinical trial
type: Class
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).
subclass of: ProcessAggregate
subclass of: Thing
equivalent class: sopharm resource:arc1be8b15

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

geographically localized population
type: Class
comment: A group of persons who are living in a definied area of the world.
subclass of: population

sopharm resource:arc1be8b16
type: Restriction
cardinality: 1
on property: is defined by

is defined by
type: ObjectProperty
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.
domain: clinical trial
range: clinical trial protocol
inverse of: defines

clinical trial protocol
type: Class
subclass of: OBI 272
subclass of: sopharm resource:arc1be8b149
subclass of: Thing
subclass of: sopharm resource:arc1be8b150
subclass of: sopharm resource:arc1be8b151
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.

sopharm resource:arc1be8b22
type: Restriction
cardinality: 1
on property: enrolls panel

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

observed allele
type: Class
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.
equivalent class: sopharm resource:arc1be8b28

genomic genotype
type: Class
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")
subclass of: sopharm resource:arc1be8b98
subclass of: genotype item
subclass of: sopharm resource:arc1be8b103
subclass of: sopharm resource:arc1be8b104

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

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

endophenotype item
type: Class
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.
subclass of: clinical item
subclass of: sopharm resource:arc1be8b32
subclass of: sopharm resource:arc1be8b33

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

is measured on relative
type: ObjectProperty
range: family member
inverse of: on who endophentoype item is measured
domain: endophenotype item
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.

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

endophenotype
type: Class
equivalent class: sopharm resource:arc1be8b41
subclass of: sopharm resource:arc1be8b46
subclass of: Thing
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.

posology
type: Class
subclass of: Thing
subclass of: sopharm resource:arc1be8b47
equivalent class: sopharm resource:arc1be8b48
comment: The posology of a drug is the specification of the dosage of the drug and of its administration frequency.

drug treatment
type: Class
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.
subclass of: sopharm resource:arc1be8b110
subclass of: treatment
equivalent class: sopharm resource:arc1be8b115

sopharm resource:arc1be8b49
type: Restriction
on property: has frequency
cardinality: 1

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

administration frequency
type: Class
subclass of: sopharm resource:arc1be8b62
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
subclass of: sopharm resource:arc1be8b63
subclass of: Thing
equivalent class: sopharm resource:arc1be8b64
subclass of: Quality
subclass of: frequency
subclass of: sopharm resource:arc1be8b65

drug dose
type: Class
subclass of: Quality
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.
subclass of: physical quality
subclass of: sopharm resource:arc1be8b128
subclass of: sopharm resource:arc1be8b129
subclass of: sopharm resource:arc1be8b130
equivalent class: sopharm resource:arc1be8b131
subclass of: Thing

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

sopharm resource:arc1be8b55
type: Restriction
on property: has dose
cardinality: 1

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

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

ethnic group
type: Class
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
subclass of: population

drug
type: Class
equivalent class: sopharm resource:arc1be8b57
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.
version info: TODO: to link with RXNORM

chemical coumpound
type: Class
subclass of: Object
subclass of: sopharm resource:arc1be8b125
subclass of: Thing
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).

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

sopharm resource:arc1be8b62
type: Restriction
on property: has unit
cardinality: 1

sopharm resource:arc1be8b64
type: Restriction
on property: administration frequency value
cardinality: 1

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

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

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

phenotype item
type: Class
subclass of: sopharm resource:arc1be8b75
subclass of: sopharm resource:arc1be8b76
subclass of: sopharm resource:arc1be8b89
subclass of: clinical item
subclass of: sopharm resource:arc1be8b90
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.

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

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

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

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

pharmacogenomic property
type: Class
subclass of: OBI 12
subclass of: Thing
subclass of: sopharm resource:arc1be8b66
subclass of: sopharm resource:arc1be8b67
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].
version info: Created in SO-Pharm 2.0. 18/07/2007
equivalent class: sopharm resource:arc1be8b68

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

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

sopharm resource:arc1be8b69
type: Restriction
min cardinality: 1
on property: interacts with drug treatment

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

sopharm resource:arc1be8b71
type: Restriction
min cardinality: 1
on property: interacts with genotype

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

sopharm resource:arc1be8b73
type: Restriction
on property: interacts with phentoype
min cardinality: 1

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

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.

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

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.

phenotype measurement method
type: Class
comment: It is measurement method for phenotype item.
subclass of: measurement method

sopharm resource:arc1be8b81
type: Restriction
on property: is magnitude of
cardinality: 1

sopharm resource:arc1be8b87
type: Restriction
cardinality: 1
on property: is measurement of

sopharm resource:arc1be8b90
type: Restriction
cardinality: 1
on property: has unit

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

drug behavior
type: Class
subclass of: sopharm resource:arc1be8b91
subclass of: behavior item
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.

treatment
type: Class
comment: A technique applied onto patient in a view of treating a pathology.
subclass of: RealizableEntity
subclass of: sopharm resource:arc1be8b165
subclass of: Thing
subclass of: sopharm resource:arc1be8b170

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.

phenotype
type: Class
equivalent class: sopharm resource:arc1be8b92
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.
subclass of: Thing
subclass of: sopharm resource:arc1be8b97

sopharm resource:arc1be8b99
type: Restriction
cardinality: 1
on property: is the observed genotype for

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

genomic variation
type: Class
subclass of: variant
subclass of: sopharm resource:arc1be8b164
subclass of: Thing
comment: Genomic variations are observed modification in the DNA nucleotide sequences between two individuals. E.g.: A SNP, a mutation, a CNV, etc.

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.

variant allele
type: Class
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.
subclass of: observed allele

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

sopharm resource:arc1be8b116
type: Restriction
cardinality: 1
on property: has drug

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

sopharm resource:arc1be8b120
type: Restriction
on property: has posology
cardinality: 1

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

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.

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

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

feed behavior
type: Class
comment: It is a clinical item informing about the way the patient used to eat. E.g.: free-fat diet.
subclass of: behavior item
subclass of: sopharm resource:arc1be8b124

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

measurement method
type: Class
subclass of: OBI 70
subclass of: sopharm resource:arc1be8b126
subclass of: sopharm resource:arc1be8b127
subclass of: Thing
comment: Every clinical item is measured, and should be measured according to a precisly defined method.

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.

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

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.

homozygote genotype
type: Class
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.
subclass of: genomic genotype

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

sopharm resource:arc1be8b128
type: Restriction
on property: has unit
cardinality: 1

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

sopharm resource:arc1be8b131
type: Restriction
on property: drug dose value
cardinality: 1

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

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

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

sopharm resource:arc1be8b139
type: Restriction
on property: is measured according to
max cardinality: 1

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

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

sopharm resource:arc1be8b147
type: Restriction
on property: item value
cardinality: 1

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

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.

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

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

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

is enrolled in
type: ObjectProperty
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.
sub property of: participates in
domain: sopharm resource:arc1be8b171
inverse of: enrolls
range: clinical trial

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

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

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.

vih genotype
type: Class
subclass of: viral genotype
comment: The genotype observed for a VIH virus. Usually a virus that infects a patient.

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

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.
inverse of: has been experimented in

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

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

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

enrolls
type: ObjectProperty
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.
range: sopharm resource:arc1be8b236
sub property of: has participant
inverse of: is enrolled in
domain: clinical trial

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

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

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

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

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

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

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

time from start
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.
type: DatatypeProperty

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

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

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

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

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

http://www.loria.fr/~coulet/ontology/sopharm/version2.1/sopharm.owl#G
type: dna sequence
is a sequence composed of: nt G
length: 1
is one observed allele in: G A

G A
type: nucleotide variation
strand: plus
has variant allele sequence: http://www.loria.fr/~coulet/ontology/sopharm/version2.1/sopharm.owl#G
has variant allele sequence: http://www.loria.fr/~coulet/ontology/sopharm/version2.1/sopharm.owl#A
is nucleotide variation of: rs28942078 ref
is nucleotide variation of: rs28942078 contig

http://www.loria.fr/~coulet/ontology/sopharm/version2.1/sopharm.owl#A
type: dna sequence
is one observed allele in: G A
is a sequence composed of: nt A
length: 1

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

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

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

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

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

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

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

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