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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 Terminology of Integrated Systems Biomedicine(ISBM)

 

 ***************************

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.

 ***************************

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.

 

***************************

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.

***************************

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)

***************************

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)

***************************

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)