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The Terminology of Integrated Systems Biomedicine(ISBM)

 


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Pan-Complementary Principle(PCP) :

The binary relations are the most fundamental  or “bricks” for any other more complicated or higher-level relations, including movements, events, processes, …. PCP for a binary relation states that a binary relation is, in nature, based on so called complementary mechanism. That is to say, for both sides of a binary relation, on side is lack of or needs what the opposite sides exactly owns and is able to provide, and just this mechanism makes the binary relation carrying out.

The realization of a binary relation based on PCP is not only the mater of both sides and it makes the story of some new things starting(i.e. CBR), as mentioned elsewhere.

   PCP is consistent with Yin-Yang doctrine in the ancient Chinese philosophy.

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The Creativity of Binary Relation (CBR):

The creativity means something new occurs or appears as a result or a coexistent factor of an act. The creativity of binary relation (CBR) always accompanies the carrying out of a binary relation (or other relations). In another word, the realization of a  binary relation always starts a new story in the world which we are interested in. An example of CBR may be the attraction and combination of a positive magnetic pole and another negative magnetic pole with the same strengths make the magnetic field disappeared, liking doing a “physical calculation”, i.e.  1 + -1 = 0.

 

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Pan-Oscillation Principle(POP) :

POP states that any entities in the world, especially those in the living organisms, eternally involve all kinds of movements which takes some form of repetitiveness. The examples of the movements with repeated forms include the orbiting of an electron around the nucleus of an atom, which, as we know, is one of most universal moving in the nature, the wave-like curves of blood pressure or body temperature, the multiplications of cells or viruses, the rhythmic heart beat, tricarboxylic acid cycle,  making copy and inheritance of genetic material  between generations and generations, etc.

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High Organized System(HOS):

As we known, the goal of a game for a football team is to score more goals for own team and prevent the opposite team from scoring goals as much as possibly. And usually eleven players constitute a football team, one is goalkeeper, other ten players play as forwards, midfielders or defenders. Thus a football team is an most simple organization with its goal and the composition.

A High Organized System(HOS) is much complicated system, which consists of many parts or members, say, hundreds of millions, with many goals or functions, say, tens of millions. The parts or members and functions closely cooperate with each other and are highly coordinated, usually being compacted in a very limited space. Human body and its parts are typical HOSs.

(to be continued)

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The Knowledge Explosion in Biomedicine (KEBM)–means the imbalance in biomedical fields between the massive knowledge products and the big challenges in the connections and applications of those existing knowledge. It does not mean we have too much information or knowledge in these fields, but means we have not enough efficient innovations for the organisations or expressions of those knowledge and information in formatted or engineering way, which are able to be red, understood, and computed by the computer applications to help people to deal with those massive information or knowledge on integration basis. Thus KEBM implies the imbalance between the bigger efforts in new knowledge producing and the relatively smaller efforts in connecting, understanding and using of those existing knowledge as whole.

(to be continued)

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The Knowledge based-on Phenomenon (KP)–The knowledge gained by what people observed or measured in their scientific experiments or practical experiences.  From the systems viewpoint, this kind of knowledge describes the relationships between the inputs and outputs of a system rather than the inner mechanisms of that system. In other words, it is somewhat “black-box” knowledge. Most of biomedical knowledge nowadays may be, more or less, classified into that sort of knowledge.

(to be continued)

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The Engineering of Biomedical Knowledge(EBMK)–In the aspect of fully and effectively using the knowledge resources, Biomedcines are nowadays facing a challenge from the masssive or ever-growing and extremely-complex resources of biomedical information or knowledge discovered at the different levels ranged from nature environments and human societies, human individuals, inside human body (the systems, organs, tissues, cells, subcellular organelles,including cell membrane, endoplasmic reticulum, mitochondria, Golgi apparatus, cytoskeleton, etc), large biological molecules, general molecules, various molecular complexes and networks, submolecules such as chemical bonds or radicals inculding free randicals, and all forms of orther biomedical objects e.g. physiological or pathological miroorganisms, for instances, bacteria and viruses, and the inner environments where all the above factors exist and function.
Engineering of Biomedical Knowledge(EBMK)arises at these historic situations. EBMK is fousing on the formatted expressions of biomedical knowledge (e.g.in the forms of biomedical ontologies) which is expected to be read, “understood”, processed or calculated by computer applications and the relative new cognitive sciences and philosophy of the systems biomedicines and engineering biomedcine, and the new methodology and its programs developments, .

(to be continued)

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Systems BioMedicines(SBMs)– SBMs are taking all biomedical objects, such as societies, individuals, parts of individual, including body systems, organs, tissues, cells, subcellular organelles, biological large molecules, functional groups, atoms etc. as the generalized systems(GSs) surrounded by their own particular contexts depending on which those systems exist and function. Consequently the whole body is deemed the sophisticated organisation of the massive and diverse systems.

A main components of a GS include the input, output, border, and inside innate structures or mechanisms(ISMs).  If the ISMs of a system is unknown or ignored, then the system is called a “black-box” or “granule” in terms of cognition. A system may be called a “grey-box” or “white-box”, if ISMs of the system is partly known or paid attention to, respectively.

(to be continued)

The Knowledge About Biomedical Dynamics Based On Double-readability Language(DRL) (V1)

********The Knowledge About Biomedical Dynamics Based On Double-readability Language(DRL) (V1)********
********—-Hanfei Bao(包含飞)********

 

 

********Spaces,TrackSpace,BarrierInSpace ********

%%%BarrierInSpace:(空间屏障)
%%%\AbsoluteBarrierInSpace:(绝对空间屏障)
%%%\RaletiveBarrierInSpace:(相对空间屏障)
%%%\\BonyBarrier:(骨性屏障)
%%%\\TissueBarrier:(组织屏障)
%%%\\BiologicMembraneBarrier:(生物膜屏障)
%%%HomogeneousSpace:A space where the quality of any parts is all the same(匀质空间或同质空间)
%%%HeterogeneousSpace: A space where the quality of its parts may be different(异质空间)
%%%\StructuredSpace:(结构化空间)
%%%\SubstanceMixtureSpace:(物质混合空间, 如溶剂-溶质空间)
%%%\\DissolvantSolvendSpace(溶剂-溶质空间)
%%%\PartitionedSpac:The space where some its parts are separated by the barriers from the surroundings of them(分隔性空间)
%%%\SpaceWithSubstanceGradient:(物质梯度空间)
%%%\TrackSpace:(轨道空间)
%%%\\SubstanceTunnelSpace:(物质通道空间)
%%%\\\BloodVesselSpace:(血管)
%%%\\\LymphVesselSpace:(淋巴管)
%%%\\\TracheaAndBronchus:(气管与支气管)
%%%\\\DigestiveTract:(消化道)
%%%\\\UrinaryTract:(泌尿道)
%%%\\SignalTransmissionPathway:(信号传递通道)
%%%\SubstatialParticleOccupyingSpace:
%%%\\AtomOccupyingSpace:(原子占有空间)
%%%\\MoleculeOccupyingSpace:(分子占有空间)
%%%\\\LargeMoleculeOccupyingSpace:(大分子占有空间)
%%%WhiteBoxRelation:All the factors and their relations in a system are fully clarified(白箱关系,体系的所有的元素和机制全部清楚)
%%%GreyBoxRelation:Not all but parts of the factors and their relations in a system are clarified(灰箱关系,系统的部分元素和机制是清楚)
%%%BlackBoxRelation:All of the factors and their relations in a system are unknown(黑箱关系,系统的所有的元素和机制都未知)

 

********Basic Physical Forces********

 

%%%UniversalSubstance:(泛物质)
%%%UniversalMovement:(泛运动)
%%%OriginalConstitution:The universe is constituted by the universal substance and the universal movement(原始构成)
%%%UniversalHeterogenicity: the heterogenicty every where, the universal movement dertermines the Universal Heterogenicity(泛异质性)
%%%OriginalForceOfTheUniverse: An axiomatic existence is accepted generally. (宇宙原力)
%%%BasicStructuralUnit:
%%%Atom:
%%%Ion:
%%%Molecule:
%%%ChemicalBond:Lasting attraction between the chemical substances
%%%ComplexOfMolecules:
%%%\StrongChemicalBond:
%%%\\MetallicBond:
%%%\\IonicBondBond:
%%%\\CovalentBond:
%%%\WeakChemicalBond:
%%%\\VanDerWaalsForce:(范德华力)
%%%\\Dipole-DipoleInteractionAlsoNamedOrientationForce(取向力,极性分子-极性分子之间的作用力)
%%%\\InductionForce:(诱导力,非极性分子-极性分子之间的作用力)
%%%\\LondonDispersionForce:(色散力或伦敦力,非极性分子-非极性分子之间的作用力)
%%%\\HydrogenBonding:(氢键)
&&:(Dipole-DipoleInteractionAlsoNamedOrientationForce–or–InductionForce–or–LondonDispersionForce)—isPartOf—VanDerWaalsForce:&&
%%%ElectrostaticForce:
%%%OppositelyChargedParticles:
%%%StrengthOfChemicalBond:
%%%ConditionsDrivenUnreversibleProcess:(自发不可逆过程)
%%%SpontaneousUnreversibleProcess:(自发不可逆过程)
%%%SpontaneousReversibleProcess:(自发可逆过程)
%%%ReactionSystem:(反应体系)
%%%SurroundingsOfReactionSystem:(反应体系的环境)
%%%EntropyOfTheUniverse:(焓的改变)
%%%DeltaEntropy:(熵的改变)
%%%GibbsFreeEnergyOfSystem:(系统的吉布斯自由能)
%%%GibbsFreeEnergyOfInitialStateOfSystem:(系统初态的吉布斯自由能)
%%%GibbsFreeEnergyOfFinalStateOfSystem:(系统终态的吉布斯自由能)
%%%DeltaGibbsFreeEnergyOfSystem:the change in free energy of a system(系统的吉布斯自由能的改变)
&&:DeltaGibbsFreeEnergyOfSystem—equals—(EntropyOfTheUniverse—minus—(Tempratue—times—DeltaEntropy)):&&
&&:SpontaneousUnreversibleProcess—increases—EntropyOfTheUniverse:&&
&&:SpontaneousReversibleProcess—keepsUnchangedIn—EntropyOfTheUniverse:&&

 

 

 

 

********References********

********1. khanacademy:Free Energy,********
********https://www.khanacademy.org/science/biology/energy-and-enzymes/free-energy-tutorial/a/gibbs-free-energy********
********2.https://en.wikipedia.org/wiki/Chemical_bond********
********3.https://en.wikipedia.org/wiki/Van_der_Waals_force********
********4.https://chem.libretexts.org/Core/Physical_and_Theoretical_Chemistry/Physical_Properties_of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Specific_Interactions/Van_Der_Waals_Interactions********

********Updated 2018-02-14-21-27********

 

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********

A Bridge Between Natural Language— And Ontology-based Biomedical Resources The Examples of Biomedical Knowledge Expressed by SLHMR

A Bridge Between Natural Language- And Ontology-based Biomedical Resources

—-The Examples of Biomedical Knowledge Expressed by SLHMR

Hanfei Bao,BMKI Lab, Toronto, Canada Mail: hanfeib@gmail.com

I. The Structured Language Readable To Human And Machine(SLHMR)

The Structured Language Readable To Human And Machine(SLHMR) is a formatted language which is expected by the author to be used to express the biomedical knowledge in both the formatted (and therefore machine-readable) and still natural-text-like way.  The resources which are expressed  by SLHMR (SLHMRRs) are taken as a bridge between the traditional natural-text biomedical resources (NTBMRs) and the ontology-based formatted biomedical resources(OFBMRs) . The philosophic bases for SLHMR are the views that NTBMRs are usually only human-readable (rather than machine- or computer program-readable), whereas the OFBMRs are generally only machine-readable. Thus the biomedical resources expressed by SLHMR would help human reader to understand the corresponding OFBMRs by their natural language features and are expected to be more powerful in the expression capability than the ontology-technique, as well, especially in respects of expressing the knowledge about the super-complex systems like the molecular biomedicine, such as in HIV/AIDS area. Additionally, SLHMR are intedned to be readable by machine through the development of the powerful applications. (see Fig19-1)

Fig19-1.png

Fig19-1

II. The Examples of Knowledge About HIV/HIDS Expressed By SLHMR

1. (LTR–or—U3–or–R–or–U5)—isA—SequenceOfViralDNA
2. (U3–or–R–or–U5)—isA—RegionOfViralDNA
3.  LTR —physicalyContains—(U3–and–R–and–U5)
4.  LTR —isSubdividedInto—(U3–and–R–and–U5)
5.  LTR—physicalyContains—(Enhancer–and–Promotor–and–Cleavage/Poly(A))
6. U3—isEncodedBy—ViralRNA-SequencesUniquelyAt3′EndOfGenome
7. U5—isEncodedBy—ViralRNA-SequencesUniquelyAt5′EndOfGenome
8. R—isEncodedBy—RepeatedSequenceOfViralRNAAtEitherEndOfGenome
9. SiteOf(CleavageAlsoCalledPolyadenylation)—isLocatedAt—R
10. (Promoter–or–Eenhancer)—isLocatedAt—U3
11. (Enhancer–or–Promotor–or–SiteOf(CleavageAlsoCalledPolyadenylation)—isA—TranscriptionalSignal
12. Transcription —isInitiatedAt—BoundaryBetweenU3AndR
13. CleavageAlsoCalledPolyadenylation—takesPlaceAt— BoundaryBetweenU5AndR
14. BoundaryBetweenU3AndR—isLocatedAt—UpstreamLTR
15. BoundaryBetweenU5AndR—isLocatedAt—DownstreamLTR

 

III.  The Examples of Relations Drawn from the Particular References and Their Composite and the Granularity Evolution of Those Relations

We can draw the following set of the physical relations from ref. 2,3,4. They are

16. RNA-PolymeraseII—regulatesPositively—(TranscriptionOfDNA-ToSynthesizePrecursorsOf-mRNA–or–TranscriptionOfDNA-ToSynthesizePrecursorsOf-snRNA–or–TranscriptionOfDNA-ToSynthesizePrecursorsOf-microRNA)

17. PhosphorylationOfCTD-OfLargerSubUnitOfRNA-PolymeraseII—regulatesPositively—ActivityOfRNA-PolymeraseII

18. The compound form of the relations 16 and 17 would be
(RNA-PolymeraseII—regulatesPositively—(TranscriptionOfDNA-ToSynthesizePrecursorsOf-mRNA–or–TranscriptionOfDNA-ToSynthesizePrecursorsOf-snRNA–or–TranscriptionOfDNA-ToSynthesizePrecursorsOf-microRNA))—byMeansOf—PhosphorylationOfCTD-OfLargerSubUnitOfRNA-PolymeraseII

19. The more detailed form of 18 would be
(RNA-PolymeraseII—regulatesPositively—(TranscriptionOfDNA-ToSynthesizePrecursorsOf-mRNA–or–(TranscriptionOfDNA-ToSynthesizePrecursorsOf-snRNA—hasDescrPanWeightOfProportionOfPopulation—MostOfPopulation)–or–(TranscriptionOfDNA-ToSynthesizePrecursorsOf-microRNA—hasDescrPanWeightOfProportionOfPopulation—MostOfPopulation)))—byMeansOf—PhosphorylationOfCTD-OfLargerSubUnitOfRNA-PolymeraseII

20 The coarseness or granularity evolution here means the processes of turninng a content-detailed relation into its less detailed one or the coarser granularity form or even the blackbox-like form. For 19, we have the steps as the following:
(RNA-PolymeraseII—regulatesPositively—(TranscriptionOfDNA-ToSynthesizePrecursorsOf-mRNA–or–(TranscriptionOfDNA-ToSynthesizePrecursorsOf-snRNA—hasDescrPanWeightOfProportionOfPopulation—MostOfPopulation)(#st1)–or–(TranscriptionOfDNA-ToSynthesizePrecursorsOf-microRNA—hasDescrPanWeightOfProportionOfPopulation—MostOfPopulation)(#st2)))—byMeansOf—PhosphorylationOfCTD-OfLargerSubUnitOfRNA-PolymeraseII
—>
(RNA-PolymeraseII—regulatesPositively—(TranscriptionOfDNA-ToSynthesizePrecursorsOf-mRNA–or–(#st1)–or–(#st2))(#st3))—byMeansOf—PhosphorylationOfCTD-OfLargerSubUnitOfRNA-PolymeraseII
—>
(RNA-PolymeraseII—regulatesPositively—(#st3))(#st4)—byMeansOf—PhosphorylationOfCTD-OfLargerSubUnitOfRNA-PolymeraseII
—>
(#st4)—byMeansOf—PhosphorylationOfCTD-OfLargerSubUnitOfRNA-PolymeraseII

Thus a “simple” binary relation would be the last result of the granularization evolution.

IV. The Network-like Diagram For The Physical Relations Above And Some Necessary Logic Relations

The data file RNAPolII.sif, which is of the required form for Cytoscape, of the completed physical and logical relations for the network-like diagram is as the following:
Column1 Column2 Column3
st14 byMeansOf PhosphorylationOfCTD-OfLargerSubUnitOfRNA-PolymeraseII
RNA-PolymeraseII regulatesPositively TranscriptionOfDNA-ToSynthesizePrecursorsOf-mRNA
RNA-PolymeraseII regulatesPositively st11
RNA-PolymeraseII regulatesPositively st12
st14 represents RNA-PolymeraseII—regulatesPositively—st13
st13 represents RNA-PolymeraseII—regulatesPositively—TranscriptionOfDNA-ToSynthesizePrecursorsOf-mRNA
st13 represents RNA-PolymeraseII—regulatesPositively—st11
st13 represents RNA-PolymeraseII—regulatesPositively—st12
st12 represents TranscriptionOfDNA-ToSynthesizePrecursorsOf-microRNA—hasDescrPanWeightOfProportionOfPopulation—MostOfPopulation
st11 represents TranscriptionOfDNA-ToSynthesizePrecursorsOf-snRNA—hasDescrPanWeightOfProportionOfPopulation—MostOfPopulation
st12 hasSubjectOfRelation TranscriptionOfDNA-ToSynthesizePrecursorsOf-microRNA
st11 hasSubjectOfRelation TranscriptionOfDNA-ToSynthesizePrecursorsOf-snRNA
st13 hasObjectOfRelation st11
st13 hasObjectOfRelation st12
st13 hasObjectOfRelation TranscriptionOfDNA-ToSynthesizePrecursorsOf-mRNA
st14 hasObjectOfRelation st13

And the network diagram shown by Cytoscape can be seen in Fig. 19-2.

Fig19-2.png

Fig19-2 the diagram made by Cytoscape.

V. Realization Of Ontology Based On the Resources Expressed By SLHMR

From references 5-6, we have the SLHMR-expressed resources and based on which the author has built the corresponding ontology HIVGenetics00*.owl, which will be published as a open medical machine reading resource:

(1)LTR-FullNmLongTerminalRepeatOfHIV1ProViralDNA—isA—SequenceOfDNA;
(2)LTR-FullNmLongTerminalRepeatOfHIV1ProViralDNA—hasNumberOfBasePair— some 634(see Fig19-3)

Fig19-3.png

Fig. 19-3

(3)LTR-FullNmLongTerminalRepeatOfHIV1ProViralDNA—isLocatedInOrAt—EitherEndRegionOfHIV1ProviralDNA
(4)LTR-FullNmLongTerminalRepeatOfHIV1ProViralDNA—hasPhysicalComponentOrPhysicallyContains—
(U3RegionFullNmUnique3’Sequence–And–R-RegionFullNmRepeatedSequence–And–U5FullNmUnique5’Sequence)(see Fig.19-4)

Fig19-4.png

Fig.19-4

(5)U3RegionFullNmUnique3’Sequence—hasNumberOfBasePair—some 450
(6)U3RegionFullNmUnique3’Sequence—physicallyAndFunctionallyContains— CisActingDNA-Element
(7)CisActingDNA-Element—isA—SiteBindingCellularTranscriptionFactor(see Fig.19-5)

Fig19-5.png

Fig.19-5

(8)R-RegionFullNmRepeatedSequence—hasNumberOfBasePair—some 100
(9)Transcription—startsAtLocation—FirstBaseOfR-RegionFullNmRepeatedSequence(see Fig. 19-6)

Fig19-6.png

Fig. 19-6

(10)Polyadenylation—startsAtLocation— ImmediatelyAfterLastBaseOfR-RegionFullNmRepeatedSequence(see Fig, 19-7)

Fig-19-7.png

Fig. 19-7

(11)U5RegionFullNmUnique5’Sequence—hasNumberOfBasePair—some 180
(12)U5RegionFullNmUnique5’Sequence—binds—Tat(Fig. 19-8)
(13)U5RegionFullNmUnique5’Sequence—binds–PackagingSequenceOfHIV(Fig. 19-8)

Fig-19-8.png

Fig. 19-8

References

1, Warner C. Greene, and B. Matija Peterlin:Molecular Insights Into HIV Biology

http://hivinsite.ucsf.edu/InSite?page=kb-00&doc=kb-02-01-01

2, Nguyen V.T., Kiss T., Michels A.A., Bensaude O.:,7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes.
http://www.uniprot.org/citations/11713533

3,
https://en.wikipedia.org/wiki/RNA_polymerase_II

4, Steven Hahn:
Structure and mechanism of the RNA Polymerase II transcription machinery,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1189732/

5. Hope, PhD, Didier Trono, MD: Structure, Expression, and Regulation of the HIV Genome,http://hivinsite.ucsf.edu/InSite?page=kb-02-01-02#S3.1X
6. https://en.wikipedia.org/wiki/Long_terminal_repeat

 (Relative sites for ontologies and discussions:

https://bioportal.bioontology.org/ontologies/HIVO004
http://bioportal.bioontology.org/ontologies/HCODONONT/
http://bioportal.bioontology.org/ontologies/AIDSCLIN
http://blog.51.ca/u-345129/
http://wp.miforum.net/baohanfei/)

(All rights reserved),(Updates: 2017-01-18,2017-01-19,2017-01-24,2017-01-26,2017-02-10,2017-02-11)

To Make Biomedical Knowldge Storehouse To Medical Knowlege Systems--The Goals of The Ontology Sciences In HIV/AIDS Areas

The Preface Of A Pilot Project

Hanfei Bao,BMKI Lab, Toronto, Canada

Mail: hanfeib@gmail.com

 

One of the big challenges faced by human beings in the development of the Biomedicine is how to better understand, integrate and use those countless and ever growing biomedical data, information and knowledge, especcially in a precise or biomedical engineering way.

We would prefer taking the mass biomedical knowledge resources(BMKRs) as the complete systems, being precisely organized or tightly connected. But unfortunately it is not true. Our BMKRs nowadays are essentially only fragmentary ones in terms of their cognitive and operative features. They are kinds of well classified knowledge storehouses rather than well connected systems. Except those biomedical sciences such as the anatomy or the praxiology etc. which are obtained on basis of ordinary sense-organs like eyes (neither macro- nor micro-instruments), the most of our BMKRs, especially in the molecular biomedicine, are made up of numberless knowledge pieces which are, in most cases, isolated or separated from each other and poorly connected.

Secondly, our BMKRs are usually only partly known. Thus why they are described visuablly as the grey boxes rather than the white boxes in the Systems Theories. These situations are particularly true for the biomedical sciences at the levels of the molecular biology.

Thirdly, BMKRs are dominantly the knowledge or information of phenomenology in its cognitive nature. That means the knowledge or information are usually observable or measurable but hardly understandable.  About them, we generally know what have happened, but we don’t know why they happen or how the molecular mechanics make them happen, and therefore they usually lack of the capacities of precisely reasoning and calculation abilities. In other words, if you intend to use these knowledge in your health practices, you had better to retest them to your target again before a real clinical usage. This is, in fact, the way frequently used in the current clinic practices.

That is why we can’t only make our efforts to mine more and more new biomedical information and knowledge and express or accumulate them only in the traditional ways, i.e. in the way of the free text or the natural language(NL).

One of the goals of the Biomedical Informatics(BMI) and Biomedical Ontology Sciences(BMOS) is to help improve the above situations by formatedly organizations and expressions of biomedical knowledge and developments of powerful applications which operate on them.

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(Updates: 1017-01-11,)