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:&&