format-version: 1.2
date: 02:05:2014 08:22
saved-by: martinschiller
auto-generated-by: OBO-Edit 2.3-beta7
default-namespace: HIV
idspace: ROP http://purl.org/obo/owl/OBO_REL#
idspace: ENVO http://purl.org/obo/owl/ENVO#
idspace: snap http://www.ifomis.org/bfo/1.1/snap#
idspace: VO http://purl.obolibrary.org/obo/VO
idspace: RO http://www.obofoundry.org/ro/ro.owl#
idspace: MOD http://www.berkeleybop.org/ontologies/mod.owl
idspace: BFO http://www.ifomis.org/bfo/1.1/
idspace: MI http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo
idspace: IDO http://purl.obolibrary.org/obo/ido.owl
idspace: CHEBI http://purl.org/obo/owl/CHEBI#
idspace: PRO http://purl.org/obo/owl/PRO#
idspace: PATO http://purl.org/obo/owl/PATO#
idspace: birn_anat http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#
idspace: HPO http://purl.org/obo/owl/HP#
idspace: UO http://purl.org/obo/owl/UO#
idspace: NCBITaxon http://purl.org/obo/owl/NCBITaxon#
idspace: OBI http://purl.obolibrary.org/obo/OBI_
idspace: SO http://purl.org/obo/owl/SO#
idspace: FMA http://purl.org/obo/owl/FMA#
idspace: IAO http://purl.obolibrary.org/obo/IAO
idspace: UBERON http://purl.org/obo/owl/UBERON#
idspace: GO http://purl.org/obo/owl/GO#
idspace: OGMS http://ogms.googlecode.com/svn/releases/2011-09-20/ontology/ogms.owl
idspace: CL http://purl.org/obo/owl/CL#
idspace: span http://www.ifomis.org/bfo/1.1/span#
remark: This version 1.3 contains additional sources and minor corrections in the spacing of some ids for the HIV Ontology
remark: This version 1.3 is of 2014-04-25

[Term]
id: HIV:00000
name: HIV
def: "Human immunodeficiency virus (HIV) is a lentivirus that causes acquired immunodeficiency syndrome (AIDS), a condition in humans in which progressive failure of the immune system allows life-threatening opportunistic infections and cancers to thrive." [http://digitaljournal.com/article/363078]
synonym: "HIV species" RELATED [PMID:24743531]
synonym: "Human Immunodeficiency Virus" RELATED [PMID:24757518]
xref: Source:NEWT\:11676
is_a: HIV:00029 ! retrovirus
is_a: HIV:00043 ! lentivirus

[Term]
id: HIV:00001
name: HIV gene
def: "A region (or regions) in the HIV genome that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:0000704]
comment: A region of the HIV genome that encodes an RNA and/or protein. Definition adapted from SO:0000704.
xref: Source:SO\:0000704
relationship: part_of HIV:00029
relationship: part_of HIV:00038

[Term]
id: HIV:00002
name: HIV transcript
def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:0000673]
comment: Definition adapted from SO:0000673.
xref: Source:SO\:0000673
relationship: part_of HIV:00029
relationship: is_transcribed_from HIV:00037

[Term]
id: HIV:00003
name: HIV protein
def: "A linear polymer of amino acids joined by peptide bonds in a specific sequence encoded by the HIV genome." [MI:0326]
comment: Definition adapted from MI:03264.
xref: Source:MI\:0326
relationship: is_transcribed_and_translated_from HIV:00037

[Term]
id: HIV:00004
name: antiretroviral drug
def: "A compound that inhibits the replication of retroviruses. Medications for the treatment of infection by retroviruses, primarily HIV." [http://www.sciencedaily.com/articles/a/antiretroviral_drug.htm]

[Term]
id: HIV:00005
name: FDA-approved antiretroviral drug
def: "An antiretroviral drug that has been approved by the Food and Drug Administration (FDA)." [http://medical-dictionary.thefreedictionary.com/Antiretroviral+drug]
synonym: "FDA approved ARV drug" RELATED [http://medical-dictionary.thefreedictionary.com/Antiretroviral+drug]
relationship: type_of HIV:00004

[Term]
id: HIV:00006
name: proteolytically processed protein
def: "A HIV protein that is cleaved at one or more peptide bonds by a protease to create multiple proteins derived from the precursor." [PubMed:18688235]
synonym: "processed" RELATED [PMID:18830418]
synonym: "proteolytic cleavage" RELATED [PMID:24755218]
xref: Source:GO\:0006508
xref: Source:MOD\:00000

[Term]
id: HIV:00007
name: HIV protein domain
def: "A HIV protein domain is a conserved part of a given HIV protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded." [http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C13379]
relationship: part_of HIV:00003

[Term]
id: HIV:00008
name: HIV protein sequence motif
def: "Signatures of protein families and can often be used as tools for the prediction of protein function." [PMID:8804823]
relationship: part_of HIV:00003

[Term]
id: HIV:00009
name: HIV minimotif
def: "Minimotifs are short peptide sequences which play important roles in many cellular functions." [PMID:19656396]
synonym: "HIV protein minimotif." RELATED [PMID:19656396]
synonym: "HIV Short Linear Motif" RELATED [PMID:19656396]
synonym: "HIV SLiM" RELATED [PMID:19656396]
relationship: part_of HIV:00003

[Term]
id: HIV:00010
name: HIV long terminal repeat
def: "The long terminal repeat (LTR) of the human immunodeficiency virus (HIV) contains the viral promoter, which is responsible for viral gene expression in eukaryotic cells." [http://www.pnas.org/content/86/7/2157.full.pdf]
synonym: "LTR" RELATED [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13251]
relationship: part_of HIV:00038

[Term]
id: HIV:00011
name: HIV group
def: "Scientists divide HIV types into groups. Each group is believed to represent an independent transmission of SIV into humans." [PMID:22229120]
relationship: type_of HIV:00000

[Term]
id: HIV:00012
name: HIV subtype
def: "Group is subdivided further into subtypes that are designated with a letter." [PMID:7723052]
synonym: "HIV clade" RELATED [http://www.projecthalo.com/aura#Clade]
relationship: type_of HIV:00011

[Term]
id: HIV:00013
name: HIV circulating recombinant form
def: "CRFs derived from recombination between viruses of different subtypes which are each given a number." [http://www.avert.org/hiv-types.htm]
synonym: "CRF" RELATED [http://www.avert.org/hiv-types.htm]
comment: CRF12_BF, for example, is a recombination between subtypes B and F.

[Term]
id: HIV:00014
name: HIV protein epitope
def: "The simplest form of an antigenic determinant, on a complex antigenic molecule, which can combine with antibody or T cell receptor." [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13189]
synonym: "antigenic determinant" RELATED [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13189]
synonym: "binding determinants" RELATED [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13189]
relationship: part_of HIV:00003

[Term]
id: HIV:00015
name: HIV drug binding site
def: "The reactive parts of an HIV macromolecule that directly participate in its specific combination with a drug." [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13405]
relationship: part_of HIV:00003

[Term]
id: HIV:00016
name: HIV posttranslational modification
def: "The process of covalently altering one or more amino acids in a HIV protein after the protein has been completely translated and released from the ribosome." [GO:0043687]
xref: GO:0043687
comment: Definition adapted from GO. [GO:0043687]
synonym: "HIV post-translational modification"[PMID:20170637]
synonym: "HIV PTM"[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738961/]
relationship: part_of HIV:00003

[Term]
id: HIV:00017
name: host protein that interacts with an HIV protein
def: "A human protein that binds to an HIV protein or covalently modifies a HIV protein." [PMID:18927109]
comment: Definition modified from PMID:18927109.
xref: [http://www.ncbi.nlm.nih.gov/projects/RefSeq/HIVInteractions/tat.html\][PMID\:18927109\]

[Term]
id: HIV:00018
name: host protein that interacts with an HIV RNA
def: "A human protein that binds to an HIV RNA or covalently modifies a HIV RNA." [PMID:24554657]

[Term]
id: HIV:00019
name: host protein required for HIV replication
def: "A class of human proteins that are essential for HIV replication, but are not lethal to the host cell when silenced." [PMID:21966263]
synonym: "HDF" RELATED [PMID:21966263]
synonym: "HIV dependency factor" RELATED [PMID:21966263]

[Term]
id: HIV:00020
name: HIV protein structure
def: "The three-dimensional structure of an HIV protein, part of an HIV protein, or a complex of an HIV protein with another protein. The structure of a protein is characterized in four ways: The primary structure is the order of the different amino acids in a protein chain, whereas the secondary structure consists of the geometry of chain segments in forms such as helices or sheets. The tertiary structure describes how a protein folds in on itself; the quaternary structure of a protein describes how different protein chains hook up with each other." [http://dictionary.reference.com/browse/protein+structure]
comment: Definition adapted from website source.
xref: FIX:0000327
relationship: part_of HIV:00003

[Term]
id: HIV:00021
name: HIV protein structured region
def: "Entire HIV proteins or regions that have a fixed tertiary structure." [PMID:24657436]
relationship: part_of HIV:00003

[Term]
id: HIV:00022
name: HIV unstructured protein
def: "Entire HIV proteins or regions of HIV proteins that lack a fixed tertiary structure." [:pondr.com/pondr-tut1.html]
comment: Definition and synonyms adapted from sources indicated.
synonym: "IDP" RELATED [PMID:24656084]
synonym: "Intrinsically disorded proteins" RELATED [PMID:11381529]
synonym: "Intrinsically unstructured proteins" RELATED [PMID:15738986]
synonym: "IUP" RELATED [PMID:12368089]
relationship: part_of HIV:00003

[Term]
id: HIV:00023
name: HIV isolate
def: "A specific individual microbe and its genetically identical progeny separated on a single occasion from a sample taken from a host or culture system." [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C53471]
synonym: "HIV strain" RELATED [http://www.avert.org/hiv-types.htm]
relationship: type_of HIV:00000

[Term]
id: HIV:00024
name: HIV protein subcellular localization
def: "Any process in which a HIV protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GO:0034613]
comment: Definition adapted from GO:0034613.
synonym: "cellular protein localisation " RELATED [GO:0034613]
synonym: "cellular protein localization " RELATED [GO:0034613]
synonym: "PSL" RELATED [PMID:19958518]

[Term]
id: HIV:00025
name: HIV protein-protein interaction
def: "Interactions between HIV and human proteins." [http://www.ncbi.nlm.nih.gov/projects/RefSeq/HIVInteractions/index.html, PMID:18927109]
comment: Database available at http://www.ncbi.nlm.nih.gov/projects/RefSeq/HIVInteractions/index.html. Definition adapted from PMID:18927109.

[Term]
id: HIV:00026
name: HIV protein-protein interaction residue
synonym: "HIV protein-protein interaction amino acid" RELATED [PMID:23867278]
def: "Amino acids in HIV protein involved in the interactions between HIV and human proteins" [PMID:23702796]
relationship: part_of HIV:00003
relationship: part_of HIV:00025

[Term]
id: HIV:00027
name: HIV protein sequence feature
def: "Regions or sites of interest in the protein sequence. In general this section lists post-translational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics." [http://www.uniprot.org/manual/sequence_annotation]
relationship: part_of HIV:00003

[Term]
id: HIV:00028
name: HIV drug binding site residue
def: "Drugs interact with HIV or host target proteins by bonding at specific binding sites. These binding sites are composed of amino acids that contact the drug which are called drug binding sites residues." [http://www.bio-toolkit.com/HIVTolbox/user_guide]
synonym: "HIV drug binding site amino acid" RELATED [http://www.merckmanuals.com/home/drugs/drug_dynamics/drug_action.html]
relationship: part_of HIV:00003
relationship: part_of HIV:00015

[Term]
id: HIV:00029
name: retrovirus
def: "Retroviruses from the family Retroviridae are composed of numerous non-icosahedral, enveloped viruses which possess two copies of a single-stranded RNA genome that has a short dimerized region." [http://www.ncbi.nlm.nih.gov/retroviruses/]
xref: Source:NEWT\:31931

[Term]
id: HIV:00030
name: reverse transcription
def: "A DNA synthesis process that uses RNA as the initial template for synthesis of DNA, but which also includes an RNase activity to remove the RNA strand of an RNA-DNA heteroduplex produced by the RNA-dependent synthesis step and use of the initial DNA strand as a template for DNA synthesis." [GO:0001171]
xref: Source:GO\:0001171

[Term]
id: HIV:00031
name: provirus integration
def: "A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage." [GO:0075713]
xref: Source:GO\:0075713

[Term]
id: HIV:00032
name: pre-integration complex
def: "A nucleoprotein complex containing viral genetic material and associated viral and host proteins, which is capable of inserting a viral genome into a host genome." [GO:0019035]
xref: Source:GO\:0019035

[Term]
id: HIV:00033
name: viral budding
def: "A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space." [GO:0046755]
xref: Source:GO\:0046755

[Term]
id: HIV:00034
name: viral assembly
def: "A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed." [GO:0019068]
xref: Source:GO\:0019068

[Term]
id: HIV:00035
name: viral envelope fusion
def: "Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm." [GO:0019064]
xref: Source:GO\:0019064

[Term]
id: HIV:00036
name: viral maturation
def: "The assembly of the component viral parts into an infectious virion." [GO:0019075]
xref: Source:GO\:0019075

[Term]
id: HIV:00037
name: genome
def: "The entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of viruses, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA." [PMID:_18258610]

[Term]
id: HIV:00038
name: HIV genome
def: "The entirety of HIV's hereditary information. It is encoded either in DNA as a provirus, or as RNA in the vision and host cell. The genome includes both the genes and the non-coding sequences of the DNA/RNA." [http://www.yale.edu/bio243/HIV/genome.html]
is_a: HIV:00037 ! genome
relationship: part_of HIV:00029

[Term]
id: HIV:00039
name: HIV RNA structure
def: "HIV RNA structure is often divided into four different levels primary, secondary, tertiary and quaternary. Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bonds. It is this linear sequence of nucleotides that make up the primary structure of RNA. Secondary structure is the set of interactions between bases, i.e., parts of which is strands are bound to each other. Tertiary structure is the locations of the atoms in three-dimensional space, taking into consideration geometrical and steric constraints. The quaternary structure of nucleic acids is similar to that of protein quaternary structure. Although some of the concepts are not exactly the same, the quaternary structure refers to a higher-level of organization of RNA. Moreover, it refers to interactions of the nucleic acids with other molecules." [PMID:9430589]
is_a: HIV:00037 ! genome
is_a: HIV:00042 ! HIV RNA

[Term]
id: HIV:00040
name: HIV drug resistance mutation
def: "Any mutation in the HIV genome that results in a change the susceptibility of HIV to one ore more antiretroviral drugs." [PMID:24746180]
synonym: "DRM" RELATED [http://www.bio-toolkit.com/GoMap/user_guide/]

[Term]
id: HIV:00041
name: HIV drug resistance mutation type
def: "There are six DRM categories of HIV drug resistance mutations(DRMs): (1) A primary DRM causes resistance without any other mutations; (2) A primary set DRM has two or more mutations that cause resistance only in the presence of other primary set mutation(s); (3) A secondary set DRM enhances resistance caused by a primary mutation; (4) A beneficial DRM attenuates/prevents resistance by overriding another mutation that promotes resistance; (5); A beneficial set DRM has two or more mutations that each normally cause resistance, override each other and attenuate/prevent resistance (6) ; and (6) A resistance precursor DRM has no effect on resistance, but must occur prior to another primary or primary set of mutations." [http://www.bio-toolkit.com/GoMap/user_guide/]
synonym: "DRM" RELATED [http://www.bio-toolkit.com/GoMap/user_guide/]
relationship: type_of HIV:00040

[Term]
id: HIV:00042
name: HIV RNA
def: "RNA that is transcribed from HIV proviral DNA." [PMID:24753416]
relationship: part_of HIV:00038

[Term]
id: HIV:00043
name: lentivirus
def: "A genus of viruses of the Retroviridae family, characterized by a long incubation period." [PMID:24749361]
is_a: HIV:00029 ! retrovirus

[Term]
id: HIV:00044
name: HIV RNA element
def: "A RNA structure found in HIV RNA that plays a role in one or more steps of the replication cycle." [http://dx.doi.org/10.1016/j.chom.2013.01.007]

[Term]
id: HIV:00045
name: HIV structural protein
def: "Protein products of gag, pol, and env genes which are essential components of the retroviral particle." [:LosAlamosHIVSequenceDatabaseCompendium2013]
relationship: type_of HIV:00003

[Term]
id: HIV:00046
name: HIV regulatory protein
def: "Tat and Rev proteins of HIV/SIV. They modulate transcriptional and posttranscriptional steps of virus gene expression and are essential for virus propagation." [:LosAlamosHIVSequenceDatabaseCompendium2013]
relationship: is_transcribed_and_translated_from HIV:00037
relationship: type_of HIV:00003

[Term]
id: HIV:00047
name: HIV accessory protein
def: "Additional virion and non-virion-associated proteins produced by HIV/SIV retroviruses: Vif, Vpr, Vpu, Vpx, Nef.  Although the accessory proteins are in general not necessary for viral propagation in tissue culture, they have been conserved in the different isolates; this conservation and experimental observations suggest that their role in vivo is very important. Their functional importance continues to be elucidated." [:LosAlamosHIVSequenceDatabaseCompendium2013]
synonym: "HIV auxiliary protein" RELATED [PMID:2202146]
relationship: is_transcribed_and_translated_from HIV:00037
relationship: type_of HIV:00003

[Term]
id: HIV:00048
name: HIV RNA dimerization
def: "The retroviral genome consists of two identical RNA molecules joined at their 5' ends." [PMID:2124274, PMID:22328732]
synonym: "HIV dimerization" RELATED [PMID:2124274]

[Term]
id: HIV:00049
name: viral genome packaging
def: "The encapsulation of the viral genome within the capsid." [GO:0019072]
synonym: "encapsidation" RELATED [PMID:24688060]
synonym: "packaging" RELATED [PMID:24530126]
xref: GO:0019072

[Term]
id: HIV:00050
name: viral enzyme
def: "Products of pol genes, which are essential components of the retroviral particle that catalyze different reactions." [:LosAlamosHIVSequenceDatabaseCompendium2013]
relationship: is_transcribed_and_translated_from HIV:00037
relationship: type_of HIV:00003

[Typedef]
id: binds_to
name: binds_to
is_transitive: true

[Typedef]
id: is_a
name: is_a

[Typedef]
id: is_transcribed_and_translated_from
name: is_transcribed_and_translated_from

[Typedef]
id: is_transcribed_from
name: is_transcribed_from

[Typedef]
id: is_translated_from
name: is_translated_from

[Typedef]
id: part_of
name: part_of
is_transitive: true

[Typedef]
id: type_of
name: type_of

[Typedef]
id: RO:instance_of
name: instance_of
is_transitive: true

[Instance]
id: HIV:00101
name: HIV-1
synonym: "HIV1" RELATED []
synonym: "HTLV-III" RELATED []
synonym: "Human Immunodeficiency Virus 1" RELATED []
synonym: "human immunodeficiency virus 1 HIV-1" RELATED []
synonym: "human immunodeficiency virus HIV-1" RELATED []
synonym: "human immunodeficiency virus type 1" RELATED []
synonym: "human immunodeficiency virus type 1 HIV 1" RELATED []
synonym: "human immunodeficiency virus type 1 HIV-1" RELATED []
synonym: "human immunodeficiency virus type 1 HIV1" RELATED []
synonym: "human immunodeficiency virus type 1, HIV-1" RELATED []
synonym: "human immunodeficiency virus type I HIV-1" RELATED []
synonym: "human immunodeficiency virus type-1 HIV-1" RELATED []
synonym: "human immunodeficiency virus-1 HIV-1" RELATED []
synonym: "LAV" RELATED []
xref: NCBITaxon:11676
instance_of: HIV:00010
property value: host_range human
type_of: HIV:00000