About the grammar for Double Readability Language(DRL) (V1)

 

 

About the grammar for Double Readability Language(DRL) (V1)

—-Hanfei Bao(包含飞)

Facing to nowadays the boundless and ever growing biomedical information or knowledge “sea”, where the entities (or classes or terms), statements (or relations) and their sophisticated combinations of all forms are mounting to nearly the astronomical figures, can we simply depend on the operations by human brain, changelessly following the traditional ways? The answer is NO, because nobody can ensure that in these ways people can get complete or accurate information or knowledge for their clinical or research purposes. And as we know, the incomplete and inaccurate information or knowledge will lead to an incomplete and inaccurate conclusions (or diagnoses and interventions). That’s why the author has for decades been questing the wide and deep conversations between human experts and computers “experts”(the applications). But first of all, we need a novel tool to build our special knowledge base, which both the human and computer can read, understand, and then communicate and discuss about their insights, drawn from their more complete and more accurate information or knowledge.  Thus, so called The Double Readability Language(DRL) or The Structured Language Readable To Human And Machine(SLHMR) is being developed and expected to be the tool to build our desired knowledge base to support us to accomplish our missions. This paper will be focused on the introduction to DRL and its development.

(面对当今无穷无尽的并不断增长的生物医学信息或知识海洋,其中实体(即类或术语),陈述(或关系)以及它们的复杂的形形色色的复合的数量已多达天文数字,我们能否一成不变地按照传统的方法,单一地依赖于人类大脑的操作吗?答案是否定的。理由是依靠这种传统的方法,没有人能保证在临床工作或科学研究方面获得全面的和准确的信息或知识。而我们知道,不全面的或不准确的信息或知识将会导致不全面的或不准确的结论(如诊断或行动)。这就是笔者几十年来追求人类专家和计算机“专家”展开广泛而深入的对话的原因。但首当其冲的是我们需要一种新型的工具来建立特殊的知识库,它可以被人类和计算机阅读和理解,并进而交流和讨论它们在更全面更准确信息或知识基础上获得的见解。因此,我们正在开发一种双读性语言(The Double Readability Language,DRL),又称为人机可读性结构化语言(The Structured Language Readable To Human And Machine,SLHMR),期望着它帮助我们完成这一历史使命。本文着重介绍RDL及其发展。 )

 

 

1.About the expressions for concepts

 

 

(1-1)“%%%”:The starting sign of a concept or entity or class.

(1-2)“%%%\”:The starting sign of a subconcept of the concept directly above.

(1-3)“%%%\\”:The starting sign of a subconcept of the subconcept directly above.,

(1-4) “%%%Concept:” The expression or the format of a concept or entity or a class,i.e. starting with “%%%” and ended with “:”.

(1-5) “%%%\SubConcept:” The expression or the format of the sub-concept of a concept. I.e. a sub concept of the concept directly above, meaning also

&&:SubConcept—isA—Concept:&&

(1-6) “***\\SubSubConcept:” The expression of the sub-concept of a sub-concept, i.e. a sub concept of the subconcept directly above,

,meaning also &&:SubSubConcept—isA—SubConcept:&&

(1-7) “which” is a grammatical concept, representing the concept directly before it.

 

2. About the expressions for statement

(2-1-1) “&&:Statement(s):&&”:The expression or format of statement(s).

(2-1-2) “&&:”:statement’s starting sign.

(2-1-3) “:&&”:statement’s ending sign.

(2-1-4) Thus, a basic statement has the format:  “&&:ConceptA—relationship—ConceptB:&&”

(2-2) The combinations of the relations (or statements) e.g.
&&:(ReverseTranscriptionComplex—adheresTo—ActinMicrofilament)—isModiatedBy—PhosphorylatedMatrix:&&
&&:((ViralReverseTranscriptionComplex—isReleasedFrom—Virion)–and—(ViralReverseTranscriptionComplex—isReleasedTo—CytoplasmOfHostCell))—isCarriedOutAfter—(VirionOfHIV-InsideCell—undergoes—UncoatingOfVirionOfHIV):&&

 

 

3. About other grammatical signs

 

(3-1) “(……)”: A pair of parenthesis completes a multiple-to-single conversion, any contents in the pair of parenthesis, no matter how complex they are organized, will become a single concept grammatically.

(3-2)“–conjunction–”:Here “conjunction” means “and” or “or”, to link two grammatically equivalent concepts.

Thus if we have “A–conjunction–B”, then A and B are equivalent grammatically. In most cases, we have the formats like “A–and–B–and–C–and–…”, “A–or–B–or–C–or–…”

(3-3) “-”: usually in RDL, if a concept is composed of several words, the adjacent words are separated by the small letter at the end of one word and the capital letter at the beginning of the next word, such as “StomachCancer”, “CytoskeletalStructure” ,”InsertionOfHIV1GeneticMaterialIntoHostGenome”…But some times we use “-” instead, if that method does not work, such as “cAMP-DependentProteinKinaseA”, “ARNTL-Gene”, etc.

(3-4)The explanatory notes have the format like:
********Explanatory note********
********http://hivinsite.ucsf.edu/InSite?page=kb-00&doc=kb-02-01-01********
They are not expected to be machine-readable or operated by machine.

 

4. The examples for the knowledge calculations

 

(4-1) example 1:
&&:Vif—overcomes—(CEM15/APOBEC3G—desstabilizes—ReverseTranscriptionComplex):&&
—>&&:Vif—stabilizes—ReverseTranscriptionComplex:&&

 

(4-2) example 2:
&&:(ReverseTranscriptionComplex—adheresTo—ActinMicrofilament)–and–(ActinMicrofilament—isLocatedIn—CytoplasmOfCell):&&—>
&&:ReverseTranscriptionComplex—isLocatedIn—CytoplasmOfCell:&&

 

 

 

 

 

The Knowledge About HIV Based On Double-readability Language(DRL) (V3)

The Knowledge About HIV Based On Double-readability Language(DRL) (V3)
—-Hanfei Bao(包含飞)

 

%%%Adenosine:(腺苷)
%%%Angiogenesis:(血管再生)
%%%ArylHydrocarbonReceptor:(芳香碳氢化合物受体)
%%%AP-1:ActivatorProtein1:(激活蛋白l)
&&:AP1—isA—TranscriptionFactor–and–
((TranscriptionFactor—regulates—GeneExpression)—isStimulatedBy—StimulatingFactor)–and–(StimulatingFactor—hasExamples—(Cytokine–Or–GrowthFactor–Or–Stress–Or–BacterialInfection–Or–ViralInfection)):&&
%%%AP-1:BindingSite(AP-1结合位点,被称为TPA效应原件(TRE))
%%%AP3-L/NF-AT-BindingSite:(AP3-L/NF-AT结合位点)
%%%Apoptosis:Cell suicide based on the specialized cellular machinery to control cell number and eliminate cells that threaten the body([细胞]凋亡)
%%%ARNT:aryl hydrocarbon receptor nuclear translocator (芳香烃受体核转移子)
%%%ATF:Activating transcription factor(激活性转录因子)
&&:(ATF—isPhosphorylatedAtSite—Serine63OfATF)–and—(Serine63OfATF—isLoactedIn—KinaseInducibelDomain):&&
%%%\Cyclic AMP-dependent transcription factor ATF-1(环一磷酸腺苷依赖性激活性转录因子1)
&&:(ATF-1)—isEncodedBy—(ATF1-gene):&&
%%%ATF1Gene:(激活性转录因子1基因)
%%%ATF2:Activating transcription factor 2(激活性转录因子2)
%%%ATF2Gene:(ATF2 基因)
%%%ATF3:(激活性转录因子3)
%%%ATF4:(激活性转录因子4)
%%%ATF5:(激活性转录因子5)
%%%ATF6:(激活性转录因子6)
%%%ATF7:(激活性转录因子7)
%%%ATF-Family:Family of Activating transcription factor(激活性转录因子家族)
%%%ATF/CREB:activating transcription factor (ATF)/cyclic AMP response element binding protein (CREB)
%%%ATF/CREB-BindingSite:(ATF/CREB结合位点)
%%%ATF/CREB-Family:(ATF/CREB家族)
%%%ATF/CREB_BindingSiteVariant:(结合点突变)
%%%ATP:adenosine triphosphate(三磷酸腺苷)
%%%Bcl-3:B-cell lymphoma 3-encoded protein(B细胞淋巴瘤3-编码蛋白质)
%%%BondingBetweentTwoMolecules:(两个分子间的键合)
%%%\CovalentBonding:(共价键键合)
%%%bHLH-Domain:Basic helix-loop-helix domain:(基本螺旋-袢-螺旋域)
%%%BromodomainOfPCAF-Aacetylase:(P300/CBP-连接因子(PCAF)溴区结构域)
%%%BTEB:Basic Transcription Element-binding Protein(基础转录元件结合蛋白)
%%%\BTEB1:Basic Transcription Element-binding Protein 1 基础转录元件结合蛋白 1)
%%%bZIP:basic-region leucine zipper(基本区域亮氨酸拉链)
%%%DistalModulatoryRegion:(远距离调节区域)
%%%CAK: CDK-ActivatingKinase:(CDK-激活激酶)
%%%cAMP:cyclic adenosine monophosphate((单磷酸)环腺苷酸)
%%%cAMP-DependentProteinKinaseA: (环腺苷酸-依赖性蛋白激酶A)
%%%Calmodulin-DependentProteinKinaseI/II:(调钙蛋白依赖性蛋白激酶I/II)
%%%CCAAT:cytosine-cytosine-adenosine-adenosine-thymidine box motif(胞嘧啶-胞嘧啶-腺苷-腺腺苷-胸苷盒基元)
%%%Cdk:Cyclin Dependent Kinase(细胞周期蛋白依赖性激酶)
%%%\Cdk1: Cyclin Dependent Kinase 1(细胞周期蛋白依赖性激酶1)
%%%\Cdk2:Cyclin Dependent Kinase 2(细胞周期蛋白依赖性激酶2)
%%%\Cdk4:Cyclin Dependent Kinase 4(细胞周期蛋白依赖性激酶4)
%%%\Cdk6: Cyclin Dependent Kinase 6(细胞周期蛋白依赖性激酶6)
%%%\Cdk9: Cyclin Dependent Kinase 9(细胞周期蛋白依赖性激酶9)
%%%Cdk-Family:(Cdk家族)
%%%C/EBP:CCAAT/enhancer-binding protein(CCAAT/增强子-结合蛋白)
&&:(C/EBP)—promotes—ExpressionOfGene:&&
%%%\C/EBPα:
%%%\C/EBPβ:
%%%\C/EBPγ:
%%%\C/EBPδ:
%%%\C/EBPε:
%%%\C/EBεζ:
%%%C/EBP-BindingSite:(CCAAT/增强子-结合蛋白结合位点)
%%%Cell:(细胞)
%%%CellSurvival:(细胞存活)
%%%\Long-livedLatentHIV-InfectedCell:(长期存活的HIV-感染细胞)
%%%\QuiescentMemoryT-Cell:(休止记忆T细胞)
%%%\Tissue-ResidentMacrophage:(组织内巨噬细胞)
%%%CellularTranscriptionFactor:(细胞转录因子)
%%%C-Fos:(为一种原癌基因)
&&:(C-Fos)—isA—(Proto-oncogene):&&
&&:(C-Fos)—isA—(HumanHomologOfRetroviralOncogene-(v-fos)):&&
&&:(C-Fos)—isFoundInAbnormality—Ratfibroblasts:&&
&&:(C-Fos)—isConsideredAs—TransformingGeneOf(FBJ-MSV):&&
&&:((c-Fos)–or–FosB–or–(Fra-1)–or–(Fra-2))—isA—FosFamilyOfTranscriptionFactor:&&
&&:(c-Fos)—isLocatedIn—ChromosomeRegion14Fromq21Toq31:&&
&&:(c-Fos)—isInvolvedIn—FormationOf(AP-1Complex):&&
&&:(AP-1Complex)—bindsAtGeneSite—(AP-1)SpecificSiteAtPromoterAndEnhancerRegionOfGene:&&
&&:(C-Fos)—isInvolvedIn—ManyCellarFunctions:&&
&&:(C-Fos)—isOverExpressedIn—SomeCancer:&&
%%%C-FosFamily:(c-Fos族)
%%%Chromatin:(染色质)
%%%ChromatinFiber:(染色质纤维)
%%%Chromosome:(染色体)
%%%Chromodomain:(染色质域或克罗莫结构域)
%%%C-JunFamily:(C-Jun族)
%%%CKIs:Cdk inhibitor proteins(Cdk抑制子蛋白)
%%%COUP-TF:chicken ovalbumin upstream promoter-transcription factor(鸡卵清蛋白上游启动子转录因子)
&&:(COUP-TF)—regulatesNegatively—ExpressionOfHIV1Gene:&&
&&:(COUP-TF)—isTransformedInto—DimerOf(COUP-TF):&&
%%%COUP-TF-BindingRegion:(COUP-TF结合区域)
%%%CodingSequence:(编码序列)
%%%CorePromoter:(核心启动子单位(-78 to -1))
%%%Cyclin:(细胞周期蛋白)
%%%\CyclinT1:
%%%Dementia:(痴呆)
%%%\HIV-AssociatedDementia:(HIV相关性痴呆)
%%%DC:Dendritic cell(树突细胞)
%%%DNA sequence:(DNA序列)
%%%\PlantPromoterSequence:(植物促进子序列)
%%%DRB:5,6-Dichloro-1-beta-D-ribofuranosylbenzimidazole(5,6-二氯-1-beta-D-呋喃糖苯并咪唑)
&&:DRB—inhibits—TranscriptionElongationByRNA-PolymeraseII:&&
&&:DRB—isAnalogueOf—Adenosine:&&
%%%DRL:Double-ReadabilityLanguage, and also called SLHMR standing for The Structured Language Readable To Human And Machine(SLHMR)(人机双读语言,又称人机可读性结构化语言)
%%%DSIF:DRB sensitivity inducing factor(DRB敏感性诱发因子)
&&:DSIF—isA—NELF:&&
%%%EnhancerElement(增强子单元(-105 to -79))
%%%Erythropoiesis(红细胞生成)
%%%FBJ-MSV:Finkel-Biskis-Jinkins murine osteogenic sarcoma virus(Finkel-Biskis-Jinkins鼠类骨源性肉瘤病毒)
%%%Fos-FamilyOfTranscriptionFactors:(转录因子Fos族)
%%%\FosB:
%%%\Fra-1:
%%%\Fra-2:
%%%Gene:(基因)
%%%\HIF1A-Gene:(HIF1A-基因)
&&:HIF1A-Gene—encodes—HIF-1Alpha:&&
%%%\ARNT-Gene:(ARNT–基因)
&&:ARNT-Gene—encodes—HIF-1Beta:&&
%%%\EPAS1-Gene: &&:EPAS1-Gene—encodes—HIF-2Alpha:&&
%%%\ARNT2-gene:
&&:ARNT2-Gene—encodes—HIF-2Beta:&&
%%%\HIF3A-Gene:
&&:HIF3A-Gene—encodes—HIF-3Alpha:&&
%%%\ARNTL-Gene:
&&:ARNTL-Gene—encodes—HIF-3Beta:&&
%%%Genome:(基因组)
%%%Glycolysis:(糖酵解)
%%%GLS:gag leading sequence:(gag引导序列)
%%%GTF:General transcription factor:(通用转录因子)
%%%GrammaticalConcept:(语法概念)
%%%\Which:representing the previous adascent concept
%%%HAT:Histone Acetyltransferase(组蛋白乙酰转移酶)
%%%HDAC:Histone Deacetylases(组蛋白去乙酰化酶)
%%%HIF:hypoxia-inducible factor (低氧诱导因子)
%%%\HIF-1:hypoxia-inducible factor 1(低氧诱导因子1)
&&:HIF-1—isA—ROSTF:&&
&&HIF-1—isA—SubfamilyOfPAS:&&
%%%\\HIF-1Alpha:hypoxia-inducible factor 1 with alpha subunit
%%%\\HIF-1Beta:aryl hydrocarbon receptor nuclear translocator
%%%\HIF-2:(低氧诱导因子2)
%%%\\HIF-2Alpha:endothelial PAS domain protein 1
%%%\\HIF-2Beta:aryl hydrocarbon receptor nuclear translocator 2
%%%\HIF-3:(低氧诱导因子3)
%%%\\HIF-3Alpha:hypoxia inducible factor 3, alpha subunit
%%%\\HIF-3Beta:aryl hydrocarbon receptor nuclear translocator 3
&&:HIF—regulates—(Glycolysis–or–MitochondrialOxygenConsumption–or–Erythropoiesis–or–Angiogenesis–or–CellSurvival):&&
%%%HIV-1:Human Immunodeficiency Virus Type 1(人类免疫缺陷病毒1型)
%%%HRE:hypoxia response element (HRE) motif(低氧应答原件)
%%%Hypoxia(低氧状态)
&&:Hypoxia—isEquivalentOf—HypoxicCondition:&&
%%%HypoxicCondition(低氧环境)
%%%KDRL: Knowledge Expressed by DRL(以DRL形式表达的知识)
%%%LTR-Region: Long Terminal Repeat region(长的末端重复区)
%%%\LTR-RegionOfHIV:(HIV长的末端重复区)
%%%\5’LTR:(5’端长末端重复区)
%%%\3’LTR:(3’端长末端重复区)
&&:LTR—hasFunction—InsertionOfHIV1GeneticMaterialIntoHostGenome:&&
&&:LTR—isloatedAt—BothEndsOfRetrotransposon:&&
&&:LTR—containsPhysically—(U3–and–R–and–U5):&&
&&:U3—containsPhysically—(Modulatory–and–E–and–Basal):&&
&&:Modulatory—containsphysicallyAndSequentially—(Sp–and–GATAOf5–and–NFAT–and–C/EBP–and–NFAT–and–AP-1–and–GATA–and–C/EBP–and–USF–Ets–and–AP-1–and–C/EBP):&&
&&:E—containsphysicallyAndSequentially—(NF-kBOf2):&&
&&:Basal—containsphysicallyAndSequentially—(SpOf3–and–TATA):&&
&&:R—containsphysicallyAndSequentially—(NF-kB–and–TAR–and–NF-kB):&&
&&:U5—containsphysicallyAndSequentially—(AP-1Of3–and–NFAT):&&
%%%Lysines:(赖氨酸)
%%%Ligand:(配位体)
%%%Methylation:(甲基化)
%%%\DNAMethylation:(DNA甲基化)
%%%MitochondrialOxygenConsumption:(线粒体氧消耗)
%%%NELF:negative elongation factor(负性延长因子)
%%%NMP:nuclear matrix protein(核基质蛋白)
%%%NRE:negative modulatory region(负调节区,from -340 to -184)
%%%Nucleosomes(核小体)
%%%PAS-Domain:Per-Arnt-Sim (PAS) domain (一种被称为”尼龙搭扣”的生物大分子的基序(mottif))
&&:PAS-Domain—is-A—PhysicalForceOrMechanicalStructureInBiomacromolecule:&&
%%%PCAF:p300/CBP associated factor(p300/CBP结合因子)
%%%PCAF BRD:p300/CBP associated factor bromodomain (p300/CBP结合因子布罗姆结构域)
%%%PhysicalForceOrMechanicalStructure(力或力学结构)
%%%\PhysicalForceOrMechanicalStructureInBiomacromolecule(生物大分子中的力或力学结构)
%%%Proto-oncogene:(原癌基因)
%%%P-TEFb:positive transcription elongation factor b(阳性转录因子b)
%%%ROS:reactive oxygen species(活性氧类)
%%%\superoxide:(超氧化物())
%%%\hydrogen peroxide:(过氧化氢(H2O2))
%%%\hydroxyl radical:(羟基(OH))
%%%ROS-dependent pathway(活性氧类-依赖性通道)
%%%ROSTF:redox-sensitive transcription factor(氧化还原敏感性转录因子)
%%%RNS:reactive nitrogen species:(活性氮类)
%%%\NitricOxide:(一氧化氮(NO))
%%%\Peroxynitrite:(过氧化亚硝酸盐())
%%%SizeOfDistanceOfTimeOrSpace:(时空距离大小)
%%%\InfinitesimalDistanceOfTime:(无限小时间距离)
%%%\InfinitesimalDistanceOfSpace:(无限小空间距离)
%%%SOD:Superoxide Dismutase:(超氧物歧化酶)
%%%TAR:transactivating response element(反式激活效应元件,+1 to +59)
%%%Tat:Trans-Activator of Transcription(病毒反式转录因子)
%%%TBP:TATA box binding protein(TATA盒结合蛋白)
%%%TBP-associated factors:(TBP关联因子)
%%%Transcript cleavage factor:(转录子分裂因子)
%%%Transposon:(转座子)
%%%TranscriptionRegulation:(转录调节)
%%%\TranscriptionInitiation:(转录启动)
%%%\PolymeraseRecruitment:(多聚酶招募)
%%%\TranscriptionElongation:(转录延长)
%%%\ChromatinOrganization:(染色质组织)
%%%USF:Upstream stimulating factor(上游刺激因子)
&&:USF—mayStimulates—Transcription:&&
%%%UTR: Untranslated region(非翻译区)
%%%Vpr:Viral Protein R(一种病毒编码调节蛋白)
%%%YY1:nuclear motif-associated protein-1:(核基序关联蛋白)
%%%ZincFinger:(锌指结构)
%%%Ligand Binding:(配位体结合)
%%%\\ProteinLigandBinding:(蛋白质配位体结合)
%%%\\DNA-LigandBinding:(DNA配位体结合,指Target为DNA)
&&:ProteinLigandBinding—mayProduces—SignalAtSiteOnTargetProtein:&&
&&:ProteinLigandBinding—mayCauses—ChangeOfTargetProtein:&&
%%%ConceptRelatingToLigandBinding:
%%%\Ligand:(配位体)
%%%\\ProteinLigand:(蛋白质配位体)
%%%\Receptor:(受体)
%%%\TargetProtein:(目标蛋白)
&&:TargetProtein—equalsTo—Receptor:&&
%%%\ElectricCharge:(电荷)
%%%\Hydrophobicity:(疏水性)
%%%\MolecularStructure:(分子结构)
%%%\Association:(关联)
%%%\Dissociation:(离解,分开,脱离关系)
%%%\ChemicalConformationOrThreeDimensionalShapeOrientation:(三维构型改变)
%%%\Inhibitor:(抑制子)
%%%\Activator:(激活子)
%%%\Neurotransmitter:(神经递质)
%%%\Affinity:(亲和性)
%%%\\RateOfLigandBinding:(配位体结合速率)
%%%\SolventEffect:(溶剂效应。溶剂作用)
%%%\Non-covalentBinding:(非共价键结合)
%%%\ChemicalEnvironment:(化学环境)
&&:(Substance–or–Inhibitor–or–Activator–or–Neurotransmitter)—mayActAs—Ligand:&&
&&:(InteractionBetweenSubjectAndObject–and–ChemicalEnvironment)—Influences—RateOfLigandBinding:&&
%%%IntermolecularForce:(分子间力)
%%%\IonicBond:(离子键)
%%%\HydrogenBond:(氢键)
%%%\VDW:VanDerWaalsForce:(范德华力)
&&:(IonicBond–or–HydrogenBond–or–VanDerWaalsForce)—isA—IntermolecularForce:&&
%%%\CovalentBond:(共价键)
%%%LigandBinding:(配位键结合)

 

********after virion entering into host cell********
********The following knowledge is base on:********
********http://hivinsite.ucsf.edu/InSite?page=kb-00&doc=kb-02-01-01********
********Warner C. Greene, MD, PhD, University of California San Francisco********
********B. Matija Peterlin, MD, University of California San Francisco********

 

&&:VirionOfHIV-InsideCell—undergoes—UncoatingOfVirionOfHIV:&&
&&:(UncoatingOfVirionOfHIV—possiblyInvoloves—PhosphorylationOfViralMatrixProtean)—isCatalysedBy—MitogenActivatedProteinKinase:&&
&&:UncoatingOfVirionOfHIV—mayInvolve—(CyclophilinA–and–Nef–Vif):&&
&&:Nef—associatesWith—UniversalProtonPump:&&
&&:(UniversalProtonPump—promotes—UncoatingOfVirionOfHIV)—isFacilitatedBy—(UniversalProtonPump—makesChangeIn—Local-pH):&&
&&:ViralReverseTranscriptionComplex—isComposedOf—(LysineTransFerRNA-Abbr-tRNALys–and–ViralReverseTranscriptase–and–Matrix–and–NucleocapsidProtein–and–ViralProteinR-AbbrVpr–and–HostProtein):&&
&&:((ViralReverseTranscriptionComplex—isReleasedFrom—Virion)–and—(ViralReverseTranscriptionComplex—isReleasedTo—CytoplasmOfHostCell))—isCarriedOutAfter—(VirionOfHIV-InsideCell—undergoes—UncoatingOfVirionOfHIV):&&
&&:(VirionOfHIV-InsideCell—undergoes—UncoatingOfVirionOfHIV)—isCarriedOutAfter—(Virion—MovesInto—CytoplasmOfHostCell):&&
&&:(ReverseTranscriptionComplex—adheresTo—ActinMicrofilament)—isModiatedBy—PhosphorylatedMatrix:&&
&&:ActinMicrofilament—isLocatedIn—CytoplasmOfCell:&&
&&:Vif—stabilizes—ReverseTranscriptionComplex:&&
&&:Vif—overcomes—(CEM15/APOBEC3G—desstabilizes—ReverseTranscriptionComplex):&&
&&:ReverseTranscription—creates—HIV-PreintegrationComplexAbbrPIC:&&
&&:HIV-PreintegrationComplexAbbrPIC—isComposedOf—(Double-StrandedViral-cDNA–and–Integrase–and–Matrix–and–Vpr–and–ReverseTranscriptase–and–HighMobilityGroupDNA-binding-CellularProteinAbbrHMGI(Y)):&&
&&:HIV-PreintegrationComplexAbbrPIC—mayMoveInCellPerhapsTrough—CytoskeletalStructure:&&

%%%StructureOfChromatin:
%%%CellReplication:
%%%CellularRepair:
%%%INI1/hSNF5-Gene:
%%%DevelopmentOfTumor:
&&:(IntegraseInteractor1AbbrINI1/hSNF5—changes—StructureOfChromatin)—facilitates—(Transcription–and–CellReplication–and–CellularRepair):&&
&&:IntegraseInteractor1AbbrINI1/hSNF5—isAComponentOf—SWI/SNF-ChromatinRemodelingComplex:&&
&&:INI1/hSNF5-Gene—suppresses—DevelopmentOfTumor:&&
********!!!!!********
%%%NuclearImportOfPIC:
%%%Matrix:
%%%NuclearLocalizationSignal:
%%%ImportinAlpha:
%%%ImportinBeta:
%%%NuclearImportPathway:
%%%NuclearImportSignal:
%%%NuclearPoreComplex:
%%%NondividingCell:
%%%NuclearImportPathway:
%%%TerminallyDifferentiatedMacrophage:
%%%NuclearImportOfPIC:
%%%ImportinSystem:
&& :HIV-1—canInfect—NondividingCell:&&
&&:HIV-1—canInfect—TerminallyDifferentiatedMacrophage:&&
&&:TerminallyDifferentiatedMacrophage—isA—NondividingCell:&&
&&:(Integrase–and–Matrix–and–Vpr)—mayPossiblyMediate—NuclearImportOfPIC:&&
&&:(Matrix–or–Vpr)—shuttlesBetween—(CellNucleus–and–Cytoplasm):&&
&&:Matrix—containsPhysically—CanonicalNuclearLocalizationSignal:&&
&&:Integrase—containsPhysically—NuclearLocalizationSignal:&&
&&:NuclearLocalizationSignal—isRecognizedBy—(ImportinAlpha–and–ImportinBeta):&&
&&:(NuclearImportPathway–and–NuclearImportSignal)—isComponentOf—NuclearImportPathway):&&
&&:HIV-VprGeneProduct—containsPhysically—NoncanonicalNuclearTargetingSignal:&&

 

********!!!!!********
********References********
********1.Warner C. Greene,B. Matija Peterlin:Molecular Insights Into HIV Biology, http://hivinsite.ucsf.edu/InSite?page=kb-00&doc=kb-02-01-01********
********2.Das S. Integrase interactor 1 in health and disease, By Das S.https://www.ncbi.nlm.nih.gov/pubmed/25772157********

 

&&:Tat—mayIncreasesSignificantly—RateOfViralGeneExpression:&&
&&:((Tat—bindsTo—RNA-StemLoopStructureOfTAR)–and–(Tat—recruitsSthToSth—(CellularCyclinDependentKinase9AbbrCdk9,RNA-StemLoopStructureOfTAR)))—underConditionOf—(Tat—existsWith—CyclinT1AlsoNameCycT1):&&

%%%PositiveTranscriptionElongationFactor-bComplexAbbrP-TEFbComplex
&&:((CellularCyclinDependentKinase9AbbrCdk9—canCatalyze—PhosphorylationOfC-TerminalDomainOfRNAPII)—existsInStructureOf—PositiveTranscriptionElongationFactor-bComplexAbbrP-TEFbComplex)—marks—StartOfElongationOfEukaryoticTranscription:&&

%%%TranscriptionOfDNA-ToSynthesizePrecursorOf-mRNA
%%%TranscriptionOfDNA-ToSynthesizePrecursorOf-snRNA
%%%TranscriptionOfDNA-ToSynthesizePrecursorOf-microRNA
&&:RNA-PolymeraseIIAbbrRNAPII—existsInStrctureOf—EukaryoticCell:&&
&&:RNA-PolymeraseIIAbbrRNAPII—canCatalyze—TranscriptionOfDNA-ToSynthesizePrecursorOf-mRNA:&&
&&:RNA-PolymeraseIIAbbrRNAPII—canCatalyze—TranscriptionOfDNA-ToSynthesizePrecursorOf-snRNA:&&
&&:RNA-PolymeraseIIAbbrRNAPII—canCatalyze—TranscriptionOfDNA-ToSynthesizePrecursorOf-microRNA:&&

 

&&:RNA-PolymeraseII—isRecruitedTo—CorePromoter:&&
&&:GeneralTranscriptionFactorAbbrGTF—isRecruitedTo—CorePromoter:&&
&&:TranscriptionCoFactor—isRecruitedTo—CorePromoter:&&
&&:RNA-PolymeraseII—catalysesTranscriptionOfDNAInto—ProteinCodingRNA:&&
&&:RNA-PolymeraseII—catalysesTranscriptionOfDNAInto—NonProteinCodingRNA:&&
&&:LongNonCodingRNA—isA—NonProteinCodingRNA:&&
&&:miRNA—isA—NonProteinCodingRNA:&&
&&:Ribosome—isA—NonProteinCodingRNA:&&
&&:iRNA—isA—NonProteinCodingRNA:&&
&&:RegulatoryRNA—isA—NonProteinCodingRNA:&&
&&:InitiatorElementAbbrInrAlsoNameInitiatorMotif—isLocatedAt—TranscriptionStartSiteOfGeneOfEukaryocyte:&&
&&:InitiatorElementAbbrInrAlsoNameInitiatorMotif—isPartOf—CorePromoter:&&
&&:InitiatorElementAbbrInrAlsoNameInitiatorMotif—directs—TranscriptionInitiation:&&
&&:RNA—includesLogically—NonProteinCodingRNA:&&
&&:RNA—includesLogically—ProteinCodingRNA:&&

 

&&:RNA-PolymeraseII—isA—RNA-Polymerase:&&
&&:RNA-Polymerase—binds—Promoter:&&
&&:RNA-Polymerase—binds—ResponseElement:&&
&&:TranscriptionFactor—binds—ResponseElement:&&
&&:ResponseElement—isPartOf—Promoter:&&
&&:RNA-Polymerase—isRecruitedTo—TranscriptionFactor:&&
&&:Activator—isA—TranscriptionFactor:&&
&&:Reprssor—isA—TranscriptionFactor:&&
&&:Enhancer—isA—RegulatoryRegion:&&
&&:Silencer—isA—RegulatoryRegion:&&
&&:BoundaryElement—isA—RegulatoryRegion:&&
&&:Insulator—isA—RegulatoryRegion:&&
&&:(Promoter—cooperatesWith—RegulatoryRegion)—leadsTo—(TranscriptionFactor—recruits—RNA-Polymerase):&&

 

&&:5′LongTerminalRepeatOfHIVAbbrLTR-OfHIV—dominantlyRegulates—TranscriptionOfHIV:&&
&&:5′LongTerminalRepeatOfHIVAbbrLTR-OfHIV—containStructurely—(TatActivatingRegionAbbrTAR–and–Promotor–and–Enhancer–and—NegativeRegulatoryElement):&&
&&:((TatActivatingRegionAbbrTAR—forms—RNA-StemLoop)—underContextOf—NascentRNA)–and–(RNA-StemLoop—binds—VirusEncodedTransactivatorAbbrTatEncodedByVirus):&&
&&:((Promotor–or–Enhancer–or–ModulatoryElement)—recruits—HostTranscriptionFactor):&&
&&:HostTranscriptionFactor—functionsAS—ActivatorProtein–or–RepressorProtein–or–AdapterProtein:&&
&&:((AP-1–or–C/EBPb–or–NFAT–or–Ets/PU.1–or–TCF/LEF-1)—Transactivates—5′LongTerminalRepeatOfHIVAbbrLTR-OfHIV)—induces—TranscriptionOfHIV:&&
&&:(CorePromoter–or–ProximalPromoter–or–DistalPromoter)—isPartOf—Promoter:&&
&&:DistalPrpmoter—isLocatedUpStreamFrom—ProximalPromoter:&&
&&:ProximalPromoter—isLocatedUpStreamFrom—CorePromoter:&&
&&:CorePromoter—containsPhysically—(RNAPolymeraseBindingSite–and–TATA-Box–and–TranscriptionStartSiteAbbrTSS):&&
&&:RNA-Polymerase—hasSubtype—(RNA-PolymeraseI–and–RNA-PolymeraseII–and–RNA-PolymeraseIII):&&
&&:RNA-PolymeraseI—encodesFor—RiboSomalRNA-Abbr-rRNA:&&
&&:RNA-PolymeraseII—encodesFor—MessengerRNA-Abbr-mRNA:&&
&&:RNA-PolymeraseIII—encodesFor—TransforRNA-Abbr-tRNA:&&

 

********https://www.addgene.org/mol-bio-reference/promoter-background/********
********https://www.hindawi.com/journals/mbi/2012/614120/********
********Mechanisms of HIV Transcriptional Regulation and Their Contribution to Latency********
********Gillian M. Schiralli Lester and Andrew J. Henderson********

%%%CisActingTranscriptionalRegulatoryDNA-Element(同分子作用转录调节DNA元素)
%%%TransActingTranscriptionalRegulatoryDNA-Element(跨分子作用转录调节DNA元素)
&&:CisActingTranscriptionalRegulatoryDNA-Element—containsPhysically—(FamilyOfPromoter–and–FamilyOfDistalRegulatoryElement):&&
&&:FamilyOfDistalRegulatoryElement—containsPhysically—(Enhancer–and–Silencer–and–Insulator–and–LocusControlRegionAbbrLCR):&&

 

********Glenn A. Maston, Sara K. Evans, and Michael R. Green********
********“Transcriptional Regulatory Elements in the Human Genome”********
********http://web.stanford.edu/class/cs273a/papers.spr07/09/txRegulationReview.pdf********

 

 

&&:TransActingElement—isA—DNA-Sequence:&&
&&:TransActingElement—containsPhysically—GenesForTranscriptionOfOtherGene:&&
&&:GenesForTranscriptionOfOtherGene—encodesFor—ProteinForTranscriptionOfGene:&&
&&:GenesForTranscriptionOfOtherGene—encodesFor—microRNAForTranscriptionOfGene:&&

 

&&:TranscriptionInitiationComplex—consisteOf—(PromoterSequence–and–DNA-BindingProtein):&&
&&:CisActingElement—isA—DNA-Sequence:&&
&&:CisActingElement—isLocatedIn—VicinityOfStructuralPortionOfGene:&&
&&:ResponseElement—isA–CisActingElemen:&&
&&:TransActingFactor—isA—Protein:&&
&&:TransActingFactor—combines—CisActingElement:&&
&&:TransActingFactor—controls—ExpressionOfGene:&&
&&:ExpressionOfGene—isFunctionOf—Gene:&&
&&:TransActingFactor—isExpressedByGeneUnderContextOf—SpecificTissue:&&
&&:TransActingFactor—isExpressedByGeneUnderContextOf—SpecificStageOfDevelopmentOfOrganism:&&
&&:TransActingFactor—controlsExpressionOfGeneUnderContextOf—Phosphorylation:&&
&&:TransActingFactor—controlsExpressionOfGeneUnderContextOf—BeingActivatedByLigandBinding:&&
&&:TransActingFactor—controlsExpressionOfGeneUnderContextOf—EffectOfEnvironmentSignal:&&

 

********References********
********https://www.ndsu.edu/pubweb/~mcclean/plsc731/cis-trans/cis-trans6.htm********
********Copyright ? 1998. Phillip McClean********

 

&&:GTF-FLNM-GeneralTranscriptionFactor isA TF-FLNM-TranscriptionFactor-AlsoNameSequenceSpecificDNA-BindingFactor:&&
&&:(TFIIA-FLNM-TranscriptionFactorII-A–or–TFIIB-FLNM-TranscriptionFactorII-B–or–TFIID-FLNM-TranscriptionFactorII-D–or–TFIIE-FLNM-TranscriptionFactorII-E–or–TFIIF-FLNM-TranscriptionFactorII-F–or–TFIIH-FLNM-TranscriptionFactorII-H)—isA—GTF-FLNM-GeneralTranscriptionFactor:&&

&&:UpstreamTranscriptionFactor isA TF-FLNM-TranscriptionFactor-AlsoNameSequenceSpecificDNA-BindingFactor:&&
&&:(Otc1-FLNM-OctamerTranscriptionFactor1–or–Sp1-FLNM-SpecificityProtein1–or–C/EBP-FLNM-CCAAT/EnhancerBindingProteinBeta–or–AP-1-FLNM-ActivatorProtein1–or–NF-1-FLNM-NeurofibromatosisType1–or–ATF/CREB-FLNM-ActivatingTranscriptionFactor/cAMP-ResponseElementBindingProtein–or–HSF-FLNM-HeatShockFactor–or–bHLH-FLNM-BasicHelixLoopHelix)—isA—UpstreamTranscriptionFactor:&&

********Reference: https://en.wikipedia.org/wiki/Transcription_factor********

 

 

********edited 2018-02-08,02-09,03-14,-16,-20,04-01********