LifeScience Knowledge Graph

# LifeScience Knowledge Graph This document describes about objective, scope of Knowledge graph and its applications in the field of life sciences and process of onbaording domain specific knowledge to knowledge graph and the reasoning part in Lifesciences domain. ### Objective: To build viable products/applications with help of knowledge graph in life sciences domain which can impact our daily life. ### Scope: Any application related to life sciences domain which involves knowledge graph information and capabilities in decision making, evaluating, reasoning etc. 1. Schema and KG for Biology 1.1. starting with elements of the periodic table as the foundation 1.2. Show how it is structured - entities, attributes, etc 1.3. Next stage will be some sort of validation and moving on to compounds 2. Listing down the application which we can building in the process as a by product of the knowledge capture ## Life Sciences Schema ### Entities The current entities present in Life Sciences ontology. **Biz Id : IUPAC notation for all currently** ##### Peroidic Table The periodic table, also known as the periodic table of the elements, is a tabular display of the chemical elements. ##### Chemical Elements A chemical element is a species of atoms that have a given number of protons in their nuclei, including the pure substance consisting only of that species. Unlike chemical compounds, chemical elements cannot be broken down into simpler substances by any chemical reaction. ![](https://i.imgur.com/nKehKS6.png) ##### Inorganic Compounds Inorganic compound, any substance in which two or more chemical elements (usually other than carbon) are combined, nearly always in definite proportions. Common examples of this are silica, carbides, common salt ##### Organic Compounds organic compound, any of a large class of chemical compounds in which one or more atoms of carbon are covalently linked to atoms of other elements, most commonly hydrogen, oxygen, or nitrogen. Eg. Benzene, Alchols , Organic Acid etc ##### Alkali Metals Alkali metals are any of the elements found in Group IA of the periodic table (the first column). Sodium, potasium, lithium are some examples of it. ##### Alkaline Earth Metals Alkaline-earth metal, any of the six chemical elements that comprise Group 2 (IIa) of the periodic table. Calsium, Magnesium fall in this category. ##### Transition Metals Transition metal, any of various chemical elements that have valence electrons—i.e., electrons that can participate in the formation of chemical bonds—in two shells instead of only one. Common transition metals include gold, iron, zinc etc ##### Post Transition Metals The metallic elements in the periodic table located between the transition metals and the chemically weak nonmetallic metalloids. Common post transition metals include aluminium, bismuth lead etc. ##### Metalloid A metalloid is a type of chemical element which has a preponderance of properties in between, or that are a mixture of, those of metals and nonmetals. Eg. Boron, silicon etc. ##### Non Metals Non-metals are elements that accept or gain electrons to generate negative ions. They often have 4, 5, 6, or 7 electrons in their outermost shell. Non-metals are materials that lack all of the characteristics of metals. They are excellent heat and electricity insulators. Common non metals include sulphur, oxygen, nitrogen etc. ##### Noble Gases noble gas, any of the seven chemical elements that make up Group 18 (VIIIa) of the periodic table. The elements include helium (He), neon (Ne), argon (Ar) etc. ##### Lanthanides Lanthanide, also called lanthanoid, any of the series of 15 consecutive chemical elements in the periodic table from lanthanum to lutetium (atomic numbers 57–71). With scandium and yttrium, they make up the rare-earth metals. Eg europium, cerium. ##### Actnides Actinoid element, also called actinide element, any of a series of 15 consecutive chemical elements in the periodic table from actinium to lawrencium (atomic numbers 89–103). As a group, they are significant largely because of their radioactivity. Common examples of this group includes uranium, plutonium, thorium. ##### Isotopes Isotopes are members of a family of an element that all have the same number of protons but different numbers of neutrons. ##### Toxic Elements These metals cause negative affect on human health. In very small amounts some of these metals contribute to support life. But, when there is an excess amount of these metals, they cause serious health issues. The metals are given below. ![](https://i.imgur.com/Dvbc9T6.png) ##### Biological process Biological processes are those processes that are vital for an organism to live, and that shape its capacities for interacting with its environment. Biological processes are made of many chemical reactions or other events that are involved in the persistence and transformation of life forms. Below image contains a few Biological Disease ![](https://i.imgur.com/1OcR04F.png) ##### Chemical process A chemical process is a method or means of somehow changing one or more chemicals or chemical compounds. Such a chemical process can occur by itself or be caused by an outside force, and involves a chemical reaction of some sort. ##### Biological Disease An abnormal condition of an organism which interrupts the normal bodily functions that often leads to feeling of pain and weakness, and usually associated with symptoms and signs. Below image contains a few Biological Disease ![](https://i.imgur.com/PEhqlnw.png) ##### Amino Acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most prevalent are the alpha-amino acids, which comprise proteins. Only 22 alpha amino acids appear in the genetic code. Eg alanine, valine, glycine etc. Resource: https://www.ncbi.nlm.nih.gov/books/NBK557845/ 1. Alanine 2. Aspartic Acid 3. Asparagine 4. Arginine 5. Cytosine 6. Cystine 7. Glycine 8. Glutamine 9. Histidine 10. Isoleucine 11. Leucine 12. Lysine 13. Methionine 14. Proline 15. Phenylalanine 16. Serine 17. Tyrosine 18. Threonine 19. Tryptophan 20. Valine 21. Selenocysteine 22. Pyrrolysine (not used ) Schema of Amino Acids: Resource: https://www.chemsrc.com/en/cas/302-72-7_958691.html | S.No. | Amino Acid | Chemical Formula | Molar Mass (g/mol) | Melting point | Boiling point | |-|-|-|-|-|-| | 1 | Alanine | C3H7NO2 | 89.09 | 272-275 | 212.9±23.0 | | 2 | Histidine | C6H9N3O2 | 155.1546 | 285 | 458.9±35.0 | ##### Proteins: The macronutrient which helps is building muscle mass of the body. Proteins are constructed as long chains of amino acids. ##### DNA: The information molecule which contains the instructions of an organism to develop, survive and reproduce. The Deoxyribonucleic acid is made up of 4 bases (A) Adenine, (C )Cytosine, (G) Guanine and (T) Thymine. It is a double helical structure. ##### RNA: The Ribonucleic Acid (RNA) helps in synthesis of protein in the body. It is derived form the DNA. RNA is a single helical structure made up of 4 bases (A) Adenine,(U) Uracil, (C ) Cytosine and (G) Guanine. ~~There are 3 types of RNA, mRNA, tRNA and rRNA.~~this is outdated information. There are many more types of RNA that have been identified (miRNA; lncRNA and others). ### Relation between Entities ##### is_a * Alkali Metal is a Chemical Element * Alkaline Earth Elements is a Chemical Element * Transition Metals is a Chemical Element * Post Transition Metals is a Chemical Element * Metalloid is a Chemical Element * Non Metals is a Chemical Element * Noble Gases is a Chemical Element * Lanthnides is a Chemical Element * Actnides is a Chemical Element * Amino Acid is a Organic Compounds ##### is_isotope_of * Chemical Element is_isotope_of Chemical Element ##### consists_of * Perodic table consists_of Chemical Element ##### causes * Eg. Arsenic causes Blackfoot Disease ##### triggers * Eg. Arsenic triggers breaking of red blood cells Graphical Representation ![](https://i.imgur.com/nBMpCDQ.png) ![](https://i.imgur.com/bi4bXCm.png) ### Attributes of Entities ##### Attributes of Chemical Element Entity (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Alkali Metals (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Alkaline Earth Metals (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Transition Metals (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Post Transition Metals (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Metalloid Metals (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Non Metals Metals (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Noble Gases Metals (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Lanthanides Metals (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Actinides Metals (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Toxic Elements (By default the elements attributes are inherited to subclass) * atomic_mass * atomic_radius * boiling_point * density * electron_affinity * electron_configuration * electronegativity * ionization_energy * melting_point * oxidation_states * year_discovered * natural_synthatic * standard_state ##### Attributes of Amino Acid (Not in the scope of initial development) * abundance_in_protiens * core_structural_functional_group * functional_group * hydropathy_index * molar_absorptivity_coefficient * molar_absorptivity_wavelength * molecular_mass * net_charge_at_pH_7.4 * side_chain_class * side_chain_polarity * 1_letter_symbol * 3_letter_symbol ##### Attributes of Periodic Table * To be decided ##### Attributes of Biolgical Disease * To be decided ##### Attributes of Biolgical Process * To be decided ##### Attributes of Chemical Process * To be decided ![](https://i.imgur.com/OFfeEx2.jpg) ## KG onboarding requirement * API for onboarding taxonomy. * Utlilising Taxonomy in Get calls. ## Life Science Applications 1. Real estate decision making 2. Environmental Impact calculation 3. Disease Inteceptor Slide URL : https://rilcloud-my.sharepoint.com/:p:/r/personal/krishna_tiwari_ril_com/_layouts/15/Doc.aspx?sourcedoc=%7BD84CF692-7695-45BE-BD80-988FF00CB576%7D&file=Environmental%20Graph.pptx&action=edit&mobileredirect=true&DefaultItemOpen=1&login_hint=Krishna.Tiwari%40ril.com&ct=1663219407940&wdOrigin=OFFICECOM-WEB.START.REC&cid=307fee19-d4af-4fe7-9b55-f11d15744dd0 All these above mentioned obbjective, scope, use cases can be achieved only when we can master about all the information available about the "elements" present around us in today's world. ### Environmental Graph ---- ##### HLD ![drawing](https://i.imgur.com/2IZ2i6P.jpg) ---- ##### Schema of Environmental Graph ![](https://i.imgur.com/FDkyiEd.jpg) ---- ### Disease Interceptor ##### Initial Schema of Disease Interceptor ![](https://i.imgur.com/LvFmpSQ.jpg) ### Q&A on Life Science KG #### General Reasoning questions in Life Sciences sector for Drug discovery: 1. Disease caused by excess of Fluorine? The system should be able to identify the limits of fluorine in the body and should be able to identify the disease dental fluorosis. 2. Which elements causes cancer. 3. Heavy metal deposition in human body is associated with diseases. 4. Many elements are toxic for the human body. 5. Excess amount of copper in liver. #### Questions that can be answered currently * Factoid Questions Examples * What is the density of lithium? * What is the IUPAC notation of oxygen? * Find all Alkali Metals? * One Hop Question using Enrich Services * What are the isotopes of hydrogen? #### Questions that need some implementation * Entity hierarchy related question? * Find all chemical elements? * Find out elements with electron affinity greater than 0.5? #### Questions that we will be answer after Environmental Graph buildup * (Simple) Is this a good place to buy a land ? * (Advanced) If I setup a car manufacturing units here what will be the impact of this on locality in terms of environment index? * (Next Level) Calculating impact of something for next few years timeline? * You have purchased 40 packs of cigaettes in 2 weeks, is there any trouble while breathing? * Your intake of coffee has been increased in past 2 months, are you experiencing any of these symptoms?

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