Retrieve Relevant Results with Reaxys
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This document provides an overview and examples of using the Reaxys database to search for natural products, reactions, and literature. It demonstrates how to search for substances from natural products containing 8-membered rings with anti-inflammatory activity. It also shows how to search for literature on the transfer hydrogenation of ketones and ketimines using Ask Reaxys, the Literature Search Form, and the Reaxys Tree. The document emphasizes using different search techniques and filters available in Reaxys to obtain tailored and relevant results.
Retrieve Relevant Results with Reaxys
- 1. REAXYS: RETRIEVING RELEVANT RESULTS Christine Flemming Elsevier Product Training Manager November 18, 2014 c.flemming@elsevier.com
- 2. 2 NATURAL PRODUCT Search for a list of substances isolated from natural products, containing eight-membered rings, that have known antiinflammatory activity….
- 3. NEW CONTENT IN REAXYS OVER 16000 PERIODICALS 3 Not just journals and patents… Now Reaxys also includes:
- 5. 5 Data needs to be: • Organized • Normalized • Compared REAXYS MEDICINAL CHEMISTRY pX values are calculated from the data so you can: • better compare biological results across publications (articles and Patents) and bioassays. • Use third party tools (Spotfire, Pipeline Pilot) through the export. IC50,Ki,% Inhibition, %,EC50,pKi,ED50,pIC50,AUC,Emax(%), Concentration,Cmax,nH,pA2,% Stimulation,Tmax,Fold increase,t1/2 el,Rate,Number,KD,pEC50,pKb,IA (%),Time,Km,ID50,Delta, Vmax,Cl,Clint,Ue (%),pD2,% Max,Kb,Bmax,Cavg,Pressure,Amount,t1/2, Cl/F,Cmin,MED,fu,F(%),Dose,ClR,AUC i/AUC,LD50,Frequency PARAMETERS RELATED TO CONCENTRATION pIC50, pEC50, pED50, pID50, pLC50, pLD50, pKi, pKd, pKb, pD2, pD’2, pA2 , IC50, EC50, ED50, ID50, LC50, LD50, Ki, Kd, Kb, Ka, Ke , % Inhibition pIC50, pEC50, pED50, pID50, pLC50, pLD50, pKi, pKd, pKb, pD2, pD’2, pA2 IC50, EC50, ED50, ID50, LC50, LD50, Ki, Kd, Kb, Ka, Ke , % Inhibition pX
- 6. 6 FIELD INDEX AND DROP-DOWN TEXT Data transparency • The index that lets you see if your query is in there BEFORE you hit the Search button • See different spellings, hyphens, and so forth. • Choose terms that may not have occurred to you.
- 7. 7 S3: DROP-DOWN TEXT WHILE TYPING A COMMENT ABOUT “ERRORS“ Drop-down text may give the impression that there are a lot of errors in a database since all terms in the database are shown Generally these errors make up <<0.5% of correct entries (e.g., asymmetric and asymmetric catalysis in the examples* on this slide are misspelt 0.3% and 0.1% respectively) Errors usually occur because of incorrect author text If needed, the effect of errors may sometimes be reduced by use of truncation * Examples below are from Lookup in the Citation Basic Index Querylet ASSYMETRIC ASYMMETRIC ASYMMETRIC CATALYS
- 8. EXAMPLES DATA SEARCH • RELATIONSHIP BETWEEN REFRACTIVE INDEX AND DENSITY OF INORGANICS REACTION SEARCH • SYNTHESIS OF PYRAZOLES • NON-REACTING NITRO GROUP • REACTION STEREOCHEMISTRY SEARCH LITERATURE SEARCH • ASK REAXYS • REAXYS TREE • LITERATURE SEARCH FORM
- 9. RELATIONSHIP BETWEEN REFRACTIVE INDEX AND DENSITY OF INORGANIC SUBSTANCES 9 Ask Reaxys retrieves a list of citations
- 10. 10 RELATIONSHIP BETWEEN REFRACTIVE INDEX AND DENSITY RI.W='589' PROXIMITY RI.T='18 - 25' NOT IDE.ELS='c' =440 substances Refine by density = 18-25 OF INORGANIC SUBSTANCES
- 11. 11 RELATIONSHIP BETWEEN REFRACTIVE INDEX AND DENSITY OF INORGANIC SUBSTANCES
- 12. 12 SYNTHESIS OF PYRAZOLES Literature search
- 13. 13
- 14. 14 SYNTHESIS OF PYRAZOLES Ask Reaxys retrieves a list of reactions
- 15. 15 SYNTHESIS OF PYRAZOLES Refine the list to exclude reactions with the pyrazole substructure in the starting material
- 16. FILTER BY AUTHOR 16
- 17. 17 REACTION SEARCH Reduction of a nitrile to an amine in the presence of a non-reacting nitro group = 459 reactions
- 18. 18 Different rings Same ring Example Results:
- 19. 19 Limit results to those with the NO2 and NH2 on different rings
- 20. (R) AND (S): REACTIONS Ritalin
- 21. INVERSION OF CONFIGURATION Apply the “Inv” label, then search by substructure.
- 22. INVERSION OF CONFIGURATION 4 reactions are retrieved.
- 23. 23 THREE WAYS TO DO A LITERATURE SEARCH Which one should I choose? You are interested in finding citations on the transfer hydrogenation of ketones or ketimines. •Try Ask Reaxys. Over 1000 citations are retrieved. Try adding or ketimines to the query. About 5 citations are retrieved. Ask Reaxys is designed to be a quick way to get information, but it does not use data operators or wild cards. (In the example above, “or” is not recognized as a data operator).
- 24. 24 Now try the same query using the Literature Search Form. Click the Literature icon and type transfer hydrogenation of (ketones or ketimines) into the Citation Basic Index field. This retrieves about 1092 citations. The parentheses are important to the syntax of the query. Without them you would retrieve over 1800 citations because the word OR would be interpreted as a data operator and the query would mean: “show me citations about transfer hydrogenation of ketones……..OR…….show me citations about ketimines”.
- 25. 25 Now try the Reaxys Tree. Click the icon.The tree contains indexed terms. Type hydrogenation into the search box. A drop-down menu is displayed showing you the options to choose from. Click the Search button to expand the Tree. The tree then expands and lets you choose the most appropriate query. This is useful when you are not sure about how to formulate a query in the Literature form or in Ask Reaxys. It lets you view terms you may not have thought of. You can then uncheck the ones you don’t want.
- 26. THANK YOU! 26 c.flemming@elsevier.com
Editor's Notes
- #2: The concept of Relevance in a chemical database is an interesting one because relevance is really in the eye of the beholder. If you want to be comprehensive, then everything is relevant…….for example if you need all articles published by a particular author.
- #3: But if you are looking for precision, then even the largest database won’t help you unless you have the right tools to get to the data. An example could be searching for a list of substances isolated from natural products, containing eight-membered rings, that have known anti-inflammatory activity.
- #4: The concept of relevance is not new to Reaxys. Improvements to the database over the years have enabled users to find information in unique ways….. the foundation being relevant sources of information, recently increased and now well over 15K periodicals.
- #5: Relevance is seen in, for example, “Reaxys Ranking” which is used when presenting reaction results. This is based on an algorithm that takes into account the yield, number of steps, and other reaction details and assigns a weight. Like, those with fewer steps and fewer reactants are weighted more and those with low yields are weighted lower than those with higher yields.
- #6: RMC is an excellent example of how a vast assortment of data can be turned into something that yields relevant results. In RMC, We’ve extracted data on bioactivity, targets, bioassays, cells; parameters, …and organized and normalized it using Px values to quantify the affinity of a compound.
- #7: Data transparency is yet another way that Reaxys strives to bring you the most relevant results. All data fields have an index that lets you see if your query is in there BEFORE you hit the Search button.
- #8: You can see different spellings, hyphens, and so forth. (Even mis-spellings that appeared in the original document). It also enables you to choose terms that may not have occurred to you.
- #10: Find out about the relationship between the refractive index and density of inorganic substances. The quickest and easiest way to find this info is to use Ask Reaxys, type in the query and retrieve a list of citations.
- #11: But another way would be to use the relevant data in Reaxys to come to a conclusion about the relationship between these 2 properties. Here’s the Advanced Search Theme. This allows you to access the entire data structure of, not only Reaxys, but also of PubChem and eMolecules. Here you can string together complex queries using any of the fields and various data operators. Look for the refractive index wavelength and temperature fields. Use “Proximity” to show that the fields are related to each other. Add the density, using “exists” and then use the “Element Symbol” field with the “Not” operator and “C” to ensure that only inorganics are retrieved. The results show inorganic substances with Refractive index data taken at a wavelength of 589 and temperature of 18-25. The density temperature should also be 18-25 for the comparison, so refine the list.
- #12: The results can be exported to Excel where the columns can be sorted …and this data seems to imply that the refractive index increases with increased density.
- #13: The next example is Synthesis of pyrazoles To do a literature search on this subject , use the Literature theme and the citation basic index field. This field searches over titles, abstracts, authors, and key words…..
- #14: ….and retrieves several thousand citations, like those shown here.
- #15: What if the results are not exactly what you had in mind? If you were really looking for cyclization-type reactions, than the first few reactions are probably irrelevant.
- #16: You can filter by reaction type, but filtering by substructure will result in more hits. This way you can eliminate all reactions where the reactants contain a pyrazole substructure or a dihydro pyrazole structure..
- #18: Here’s another Reaction search Reduction of a nitrile to an amine in the presence of a non-reacting nitro group The reaction shown here will retrieve hits with the nitro and the amine on the same rings, as well as hits with the nitro and amino on different rings. (see next slide).
- #19: What if you want to limit results to only those with the nitro and amino on different rings….
- #20: Revised query.
- #21: Ritalin is a chiral compound. You are not only interested in preparations of Ritalin (with substitution allowed), you would like to compare reactions where the configuration of the starting material was inverted in the product to reactions where the configuration of the starting material was retained in the product. How can your searches be limited in this manner? First, let’s do a substructure search for preparations of Ritalin without specifying stereochemistry. 906 reactions are found.
- #22: Now, we will specify “Inversion of configuration”. It is not necessary to pick a particular configuration by drawing up and down bonds, we’re just looking for the relative configurations. In Marvin, right click the chiral center and select Edit Atom>Reactions>Inversion.
- #23: Run the search. 4 reactions are retrieved.