Piotr Golkiewicz Life Sciences Solutions Consultant Central-Eastern Europe
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PIOTR GOLKIEWICZ LIFE SCIENCES SOLUTIONS CONSULTANT CENTRAL-EASTERN EUROPE 1 WHAT’S IN A TYPICAL CHEMISTRY DOCUMENT (PUBLICATION OR PATENT)? Scientific topic, author Chemical reactions Can be searched in full Cannot be searched by text, but difficult to find text terms in full text the right search term Can be searched in full text, but you don’t want to read the whole paper in you are interested only by this section! Experimental procedures Cannot be searched by Cannot be searched by Cannot be searched by text terms in full text text terms in full text text terms in full text Substances and their Chemical structure Chemical spectra physicochemical properties 2 REAXYS DESIGN Chemistry as the organizing principle With experimental data from journal REAXYS IS BUILT articles and patents Physical Data Physical Data Spectra Spectra Bioactivity Data Bioactivity Data Natural Product Natural Product Reaxys CHEMISTRY AS THE ORGANIZING PRINCIPLE Physicochemical Chemical Structures Reaxys excerpts all relevant data Properties even from footnotes and text Chemical Syntheses Pharmacology STRUCTURED TO HELP YOU SEARCH OTHER DATABASES REAXYS CATALOGUED AND TAXONMISED BY CHEMISTS FOR CHEMISTS ESSENTIAL TITLES BIBLIOGRAPHIC APPROACH ACROSS TIME/LITERATURE UNFOCUSED RESULTS USE-CASE DRIVEN FURTHER SEARCH NEEDED RELEVANT ANSWERS 50,000,000 RESULTS RETURNED 6 REAXYS INCLUDES Patent Content: English language only patents from the major chemistry patent LiteratureCoverage Content: from 1771 16,000 - present periodicals classes of the US, European, and World Patent Offices REAXYS INCLUDES Over 500 million facts Over 400+ searchable data fields HIGH QUALITY experimental results KEYWORDS A single bibliographic record in Reaxys contains index keywords from: Authors, Compendex, Embase, Geobase, Medline and Reaxys. Our competition has keywords only from two sources: CAplus and Medline Searching for classes of substances in Reaxys Found in REAXYS SUBSTANCE RECORDS Found in KEYWORDS in REAXYS BIBLIOGRAPHIC … and … RECORDS CLASSIC ORGANICS POLYMERS ALLOYS & METALS ORGANOMETALLICS COORDINATION COMPOUNDS CERAMICS CLASSIC INORGANICS NUCLEIC ACIDS & PROTEINS Search Substances Context Search Literature Context 10 WHAT IS REAXYS 2015? CONTENT: MANY DATABASES ALL IN ONE A Bibliographic A Substance Database Database >48 million records > 78 million substances (from ~16,000 journal titles (total) plus records from key patent organisations) ~ 57 million substances (unique) Reaxys 2015 A Chemical A Property Reaction Database Database > 500 million experimental properties > 38 million single- and in > 400 fields multi-step reactions in > 130 subject areas 11 SEARCH • What are the search options? • Substances • Reactions • Literature SEARCH • Properties • Is there “search REAXYS: SIMPLER TO SEARCH, MORE DISCOVERABLE INFORMATION intelligence”? • Truncation • Proximity • Algorithmic interpretation of natural language query Perform a literature Ask Reaxys, a quick, search easy topic ‘concept search’ Open Reaction search form Browse database via taxonomies rather Data search than search form by “property” database Access detailed Biodata, Open a structure Search using and MedChem specific search form chemical identifiers features 12 SEARCH SUBSTANCES SEARCH STRUCTURE, NAME, OR FORMULA – IN FULL, OR IN PART STRUCTURE CHEMICAL NAME FORMULA Formula Builder: easy way to find substances right across the Periodic Table As Drawn ✔ Chemical Name ✔ Formula ✔ Part of Chemical Name Substructure ✔ ✔ Part of Formula ✔ 13 Similarity ✔ Reaxys helps on the way ✔✔ Reaxys helps on the way ✔✔ SEARCH REACTIONS SEARCH BY STRUCTURE, DATA, OR TYPE STRUCTURE DATA TYPE Atom mapping Bond forming/breaking Search reactions by structure Search reactions by reaction Search reactions by type or conditions name ✔✔✔ ✔✔✔ ✔✔✔ 14 SEARCH LITERATURE OUR GOAL: MAKE CONTENT MORE DISCOVERABLE, MORE EASILY! Ask Reaxys Reaxys Tree You are in control Ask Reaxys provides new ReaxysTree lets users user experience for text “browse” the database by searching: content better taxonomies: helps with discoverable, answers more search precision and answer You can also search with immediately available comprehension truncation/proximity – like you do through other interfaces Intelligent interpretation of Browse through taxonomies Use truncation/proximity if topic query you like ✔✔✔ ✔✔✔ ✔✔✔ 15 SEARCH PROPERTIES >500 MILLION EXPERIMENTAL PROPERTIES, >400 FIELDS, >130 SUBJECT AREAS PRE-PROGRAMMED BUILD YOUR OWN MedChem PROPERTIES CONTENT FIELDS ✔✔✔ easy to set up ✔✔✔ easy to search ✔✔✔ 16 | 17 MAKE A COMPOUND 18 SYNTHESIS PLAN: AUTOMATES THE UNDERLYING PROCESSES IN CREATING SYNTHESIS ROUTES 19 SHOW EXPERIMENTAL PROCEDURE 20 PRESENTER | DATE | NAME OF PRESENTATION TI02 - PROPERTIES 21 | 22 FIND: A polymer shape EXAMPLE: Comb shaped polyacrylates The various shapes of polymer backbones may easily be searched by words: 23 FIND: Polymer Blends EXAMPLE: Blends using linear low density polyethylenes For simple text searches, try Ask Reaxys Ask Reaxys performs a text search, and usually gives satisfactory initial answers In order to discover ways to expand (or contract) the search, look carefully at a few of the answers and in particular look at the (more systematic) Keywords that have been added from several different sources • We may wish to use some of them in revised searches Note that for text searches, Ask Reaxys currently does not automatically add singulars/plurals If needed, more precise or comprehensive searches may be done through the CITATION BASIC INDEX QUERYLET Go to Next Slide 24 EXAMPLE: Mechanical Properties of FIND: Property of a Polymer Polytetrafluoroethylene General Mechanical Properties, or specific Mechanical Properties (such as Young’s modulus) may easily be found through searches in the CITATION BASIC INDEX QUERYLET. Simply type in the entry field, take note of the auto-suggest terms (and perhaps use them as a guide to application of truncation) 25 Back to ca. 1 minute fully meet expectations referring slide MOLECULAR FORMULA MOLECULAR FORMULA BUILDER 26 Chrome compounds 27 CHROME COMPOUNDS Find substances that contain Cr and C 28 CHROME COMPOUNDS All carbon + chromium- containing substances All “inorganic” chromium- containing substances All carbon + chromium- containing substances All chromium-containing substances 29 CHROME COMPOUNDS (Yellow Inorganics) > 900,000 YELLOW SUBSTANCES 30 CHROME COMPOUNDS (Yellow Inorganics) 31 CHROME COMPOUNDS (Yellow Inorganics) 32 borosilicate glass Power of lookup 33 ALLOYS USING THE ALLOY QUERY FORM INITIAL ALLOY SEARCH OPTIONS 34 PRESENTER | DATE | NAME OF PRESENTATION ROTATE 3D VIEW 35 CHECK COMMERCIAL AVAILABILITY 36 SUPPORTS DIFFERENT STRUCTURE EDITORS 37 REPORTING: GATHER AND PREPARE THE INFORMATION 38 INTEROPERABILITY REAXYS MEDICINAL CHEMISTRY 40 ESSENTIAL INFORMATION: 100+ EXPERIMENTAL FIELDS Reaxys Medicinal Chemistry excerpts all the relevant Quantitative data 41 … BUT IT'S NOT THAT SIMPLE, MEDICINAL CHEMISTS FOR INSTANCE NEED TO COLLECT, ORGANIZE AND COMPARE INFORMATION FROM DIFFERENT SOURCES… THIS IS TIME CONSUMING AND ERROR PRONE ? ? ? ? 42 … BUT IT'S NOT THAT SIMPLE, MEDICINAL CHEMISTS FOR INSTANCE NEED TO COLLECT, ORGANIZE AND COMPARE INFORMATION FROM DIFFERENT SOURCES… THIS IS TIME CONSUMING AND ERROR PRONE û ü û ü û ü ü 43 AND TO MAKE A DECISION ON WHICH EXPERIMENT TO DO, YOU WANT TO ORGANIZE YOUR CONTENT, NORMALIZE AND COMPARE, TO UNDERSTAND WHICH COMPOUND INTERACTS WITH WHICH TARGET AND TRIGGER WHICH BIOLOGICAL EFFECT—THAT'S A LOT OF MANUAL WORK! ü ü ü û ü û û û ü û ü û ü û ü û û û û û ü ü ü ü ü 44 RESULTS VIEW - HEATMAP Manage X and Y axis Bioactivity data based on pX values 45 46 RMC 2 CONTENT Patents Origin and starting date « The most comprehensive medicinal chemistry solution on the market » >90 000 Patents • US : 1971-present • EP : 1979-present • WO : 1978-present (English only) • Patents are coming from the A61K class mainly but not only. Articles and Journals • >5000 Journals Covered • >230 000 Articles • From 1980 to Present Drugable Targets • >9000 Drugable Targets 47 EXPORT CAPABILITIES 48 RMC2 EXPORT AND OUTPUT CAPABILITIES Export Import SD file RMC2 Export format includes : - XML, Excel, SD file RMC2 Export includes : - Substances and Physchem properties - Bioactivities and Bioassays - Targets - Bibliographic references RMC2 Export is compatible with : - Pipeline pilot 49 - Spotfire Etc… RMC2 EXCEL EXPORT AND SCATTER PLOT GENERATION No additional data TARGET SELECTIVITY improvement is need for Excel Scatterplot Performed Scatter plot Export For selectivity • Search for Substances tested on COX-1 and Cox-2 <20 minutes 12 COX2 versus COX1 Selectivity Based on pX COX 2 Selective compounds COX2 Selective compounds pX on COX >7 and pX on10 COX1 <6 at least a 10 fold Selectivity index 8 6 pX COX2 4 2 pX COX1 50 0 0 1 2 3 4 5 6 7 8 9 10 PIOTR GOLKIEWICZ LIFE SCIENCES SOLUTION CONSULTANT CENTRAL EASTERN EUROPE [email protected] MOBILE: +48 695 30 60 17 51 .