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13. PubChem and Reaxys: Complementary Databases?

Project Mentors: Damon Ridley, Sunghwan Kim and Anja Brunner.

The wealth of information available creates information overload problems, and more than ever it is helpful if scientists understand the core collections in their field and know which sources to use and when.  At some stage, evaluations of the different options need to be made, and since elsewhere in this course PubChem and Reaxys have been introduced, we now have the opportunity to evaluate them together.

We shall explore answers to questions such as: in what ways are they similar and in what ways are they complementary; what is their combined landscape, and how are the different systems searched?

Those interested in teaching chemical information retrieval may wish to explore the “big picture”, i.e., the overall content and search functionality of PubChem/Reaxys; those interested in finding information in their special field of study or research may wish to explore subject-specific information.

Evaluating systems is fraught with numerous difficulties pertaining not only to the database(s) but also to the knowledge and skills of the searchers.  In this project we shall work as a team, with different participants evaluating areas of their choice.  The outcome should be of interest to everyone in the OLCC program … and beyond …

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Olcc S14 | Tue, 03/07/2017 - 08:47

Hello,

I am interested in this project as a part of this course. I am hopeful to use both PubChem and Reaxys in research work. Before I begin with it, can you tell me about PubChem and Reaxys, their similarity and differents? How can they get collaborated?

Looking forward to hearing from you.

Thank you

Amita

Damon Ridley's picture
Damon Ridley | Tue, 03/07/2017 - 10:10

Amita

The history here is that Sunghwan, Anja, and I thought it may be interesting for students to make their own assessments on similarities and differences - in other words, exactly what you are asking is the type of thing we would like you to assess in the student project.

While we haven't designed the exact way the project would be run (we would rather students decide that), we are thinking that if we can get a few students interested then each of them may tackle one aspect.  Finally the results students come up with would be collated.

In making comparisons like this you have to consider the content, which could be broken into documents, substances, reactions and properties - but that's not just a simple matter of saying (in comparing "substances"), e.g., there are 250 million PubChem Substances, 95 million PubChem Compounds and 28 million Reaxys Substance Records (or whatever the latest numbers are).  What you have to do is to look at what type of information, on average, is in the Substance/Compound records.  

Then you have to do the same for comparing "documents", "reactions", and "properties". 

Another thing to consider is the search interface - how you search.  Here I can perhaps let you know (without giving too much away) that you can indeed search PubChem Compounds through the Reaxys interface, but you cannot search Reaxys Substance Records through the PubChem interface.  So one student may, for example, wish to investigate the different results you get when searching PubChem Compounds through the PubChem interface and the Reaxys interface.   You may think you'd get the same result (you are searching the same data), but, NO, you may get different results because of the way the two systems search.

From memory you were interested in nanomaterials and water-treatment, right?   That being the case, you may wish to compare ways of searching for such topics in PubChem/Reaxys.  Probably the way it would work is that Sunghwan would work with you on options in PubChem, while Anja/I would help you with Reaxys.  However, while such an analysis may be of interest to you (and others working in the area), such a topic (and other very specific topics) may not be suitable for such analysis because it may turn out that you can only find this information in one of the products - and that can be found out very quickly.

Of course one of the huge differences between PubChem and Reaxys is that one is in the public domain (and is funded effectively though "public money") whereas the other is a proprietary product (and is funded through charges to those who access it). 

I don't want set down rules at this stage, and we'd rather interested students let us know and once we have a group then together we would work out sub-projects.   Having said that one of the things that does not seem to have been discussed during this Spring 2017 course is, out of all the available information "out there" which sources should I choose and when - and we shall try to answer the question relating to PubChem/Reaxys either together or separately at least for the projects that we undertake together.

Damon

OLCC S197 | Fri, 03/24/2017 - 21:48
HY , everyone my name is nwume chinenye from ualr i was directed by my instructor to talk to you about my project . i am working on different drugs that can treat mental illness using both reaxys and pubchem. please can you please help me cos i dont know where to start. .

Damon Ridley's picture
Damon Ridley | Mon, 03/27/2017 - 02:07
Nwume I am not quite sure whether the background to your question is to check whether you should take the Student Project or whether you already have signed up and want to start. If the former, then you will find the type of information you get from PubChem and from Reaxys is quite different, so it would be good for you to explore options in both databases. As you have learnt from other sections of the course, different databases organise (and excerpt) data in different ways and you really need to understand a bit about each database in order to extract the best results (for your needs). If the latter, then I think the first thing to do is to list a couple of the mental illnesses you wish to study. Since you have already attended the course on PubChem you probably know how to proceed - although Sunghwan will certainly help if you need it. Regarding Reaxys, then as soon as you give me a list of illnesses then we can work together on a plan to understand how to proceed in Reaxys. Damon

Sunghwan Kim | Thu, 03/30/2017 - 10:57

Hi, Amita and Nwume,

Thank you for showing interest in this project.  By the way, it seems that both of you are from UALR and Professor Belford (at UALR) told me that each student at UALR would be required to work on different project (for grading purposes), while it is okay for him or her to work with students at other schools.  Considering that both of you are from UALR, I suggest that both of you discuss this issue with Professor Belford before starting working on it. Because your school is getting closer to the end of semester, I recommend you to do it as soon as possible (if both of you are still interested in this project).

 

Bob Belford's picture
Bob Belford | Thu, 03/30/2017 - 12:16
I know Amita is involved with a research group, and she can orient this to assist her graduate research work. I do not believe Nwume is involved with research. The bottom line, is there is so much in Reaxys and PubChem, that they can work on total different projects that have no overlap. So I am not seeing a problem, as long as they pick different topics, that take them through different information spaces. I also know that Amita's work is more material sciences oriented, and there may not be significant usage of PubChem, while Nwume can pick a topic more in line with PubChem's mission and resources.

Olcc S14 | Fri, 03/31/2017 - 09:20
Sorry for late reply. I was not registered to this topic previously so I didn't see yours' comments. Regarding my class project, I want to connect with my research work. Yes, I am working on nanomaterials and waste water purification. I am making nanocomposites from waste materials like wood chips and utilize it in waste water purification. So my research is based on utilization of renewable resources based nanomaterials for waste water treatment. I am trying to remove heavy metals and some inorganic compound from waste water. So I wonder how can I use these two databases to get useful information for my research work? I have search document related to my project on Reaxys but I don't know about PubChem. Does PubChem search useful for my research? Does PubChem search document related to my research work? In my research, there is some chemical reaction occurs during preparation and phosphorous treatment so I want to use these databases to get information on those chemical reactions. I know Reaxys can be used to draw chemical structures and reactions but I am not sure about PubChem. I know PubChem can also draw chemical structure but I am not sure about reactions. Does PubChem draw chemical reactions? Looking forward to hearing from you. Thank you Amita

Sunghwan Kim | Fri, 03/31/2017 - 14:23

It seems that you are having hard time figuring out where to start from. To help you get started, let me tell you how you should approach. Typically, a project has a specific goal or specific questions to answer and needs to have tasks/steps that you will need to take to achieve that goal.

I guess your goal is to compare PubChem and Reaxys, but what tasks should you do to achieve the goal?  One issue here is that your goal is somewhat broad, making it difficult to identify necessary tasks.  A questions that you answered in your comment above is a process to narrow down the scope of your study, probably making your goal is more specific.

You asked how you can use the two databases to get useful information for your research on waste water treatment using nanomaterials.  However, you did not really say "what specific information" (or specific analysis tools/services) you need for your research.  Once you can identify specific pieces of information relevant to your study, now you can compare the two databases in the context of that information content.  Does both databases provide what you need?  Does one database have incorrect information?  Is a particular type of information found in one database, but not in the other?  So, essentially, you need to identifiy a set of specific questions that you can use when comparing the two databases.

Actually, you have asked me a series of questions, including:

  • how can I use these two databases to get useful information for my research work?
  • Does PubChem search useful for my research?
  • Does PubChem search document related to my research work?
  • Does PubChem draw chemical reactions?

While some of these questions are very subjective and ambiguous, I think they are a sort of good starting point.  Please define your questions more narrowly.  For example, in the fist question, what do you mean by "useful information"?  By narrowing down your questions and searching for answers to them, you will be able to compare two information resources.

Olcc S14 | Fri, 03/31/2017 - 16:18
Sorry for the confusion. My goal for my research work as well as for class projects is to find out chemical reactions occur in my synthesis of nanocomposites. I use chemicals like quat-188, sodium hydroxide, metal chlorides, ammonium hydroxide and wood (cellulose). The information I am looking from PubChem and Reaxys are properties of these chemicals such as reactivity and toxicity. And I am also looking for the reported documents which are related to my research work " removal and recovery of phosphorus and heavy metals (Selenium, Arsenic, cobalt, lead etc.) from waste water using renewable resources based nanomaterials prepare from wood or cellulose. So I am looking papers related to this topic. It's not my research topic but it is quite similar. I know I can find properties of the chemicals that I am using but I am not sure about the documents. So can I find documents related to my research topic? Looking forward to hearing from you. Thank you Amita

Anja Brunner | Sat, 04/01/2017 - 13:12
Hello Amita, I concur with Dr. Kim with regards to his advice to define specific information for your research that you would like to find and then explore PubChem and Reaxys to see what kind of answers they can provide. PubChem and Reaxys were designed for different objectives and thus, I think that you will find them to be complementary -- one being better for one kind of search and the other for another type. The key is first to know what specific type of information you want to find. Above you list the following: (1) What are the reactivity and toxicity properties of quat-188, sodium hydroxide, metal chlorides, ammonium hydroxide and cellulose? (2) What reactions occur in your synthesis of nanocomposites (you need to define which syntheses/nanocomposites)? (3) What work has already been reported in the literature and patents on "removal and recovery of phosphorus and heavy metals from waste water using cellulose-based nanomaterials"? Each of those questions calls for a different type of search. 1 is a search for specific property data. 2 is a search for reactions that lead to a specific product, o maybe even the elucidation of new reactions that could lead to that specific product. And 3 is broader search for literature on a topic. Maybe it would make sense to start with one question, define the specific information you are looking for (e.g., toxicity of ammonium hydroxide) and then perform the search in PubChem and then Reaxys. You already have experience using PubChem from the excellent modules Dr. Kim prepared and we have provided some detailed instructions on the search functionalities of Reaxys. Then, compare the two systems-- you could do so in terms of the information you found in each, or in terms of the functionality each affords. It might make sense to first sit down and think of specific evaluation criteria you could use to assess the search and results in each of the systems. Those criteria should be important to you as a researcher and in terms of what advances your research. So, for example, is it more important to have comprehensive answers or specific information that has been excerpted from source documents? See how it goes with one question and write down what works well in each system, what surprises you about the answer sets you get, what helps with your research. Then perhaps, you can tackle another question that requires searching differently and compare the two systems. The best thing you can do is to define your question and dive in! When you get stuck, contact us and we can try to help you along. I hope that helps! Anja

Olcc S14 | Sat, 04/01/2017 - 14:03
Thank you. I will follow the instructions that you, Dr. Kim and Dr. Damon have provided me so far. I will keep in touch.

Damon Ridley's picture
Damon Ridley | Sun, 04/02/2017 - 22:19

Amita Greetings from Sydney! I am on a different time zone so was unable to reply earlier, although I note Anja and Dr Kim have commented on your project. Everything they have said is absolutely correct, and, in particular, that you need to refine the project a little. A comment here is that there are a few steps in any search: first, define the question; second, understand the search landscape; third, then proceed with the search(es).

Let me start from the third part first. Here you almost invariably need to trial a few searches first, so don't just do a single search and then stop.

The second part (the landscape) means that you need to have some idea what is in the database(s) and then start to think of searches based on that knowledge.

Which brings me to the first part, where my suggestion is that you focus on two general problems:
1. How to find relevant substances and then specific properties on them. I suggest you choose QUAT 188 (perhaps also include some related quaternary ammonium salts) and find biological activity information on them.

2. How to formulate and execute a (text) search relating to "removal and recovery of phosphorus and heavy metals (Selenium, Arsenic, cobalt, lead etc.) from waste water using renewable resources based nanomaterials prepared from wood or cellulose". In starting this search, you need to define the concepts then formulate a search based on a few of the concepts (the ones for which you feel you can search more efficiently).

Since you probably have not had a lot of experience with general strategies for the second problem, let me start you off with the concepts I see (and comments on how to search them):

- removal/recovery (authors/indexers would use all sorts of terms here, so I don't think this would be a good concept at least initially);

- phosphorus (problem here is that you don't mean 'phosphorus' (the element) at all - rather you mean phosphate. Herein lies a common problem in this field. Yes, I know that fertilisers are often defined in N:K:P content and I know some authors would write about phosphorus and mean phosphate - but the question is how to search for it. Again, I don't think this would be a good concept at least initially);

- heavy metals (similar problem. Some authors/indexers would talk about heavy metals, but others would be more specific - as you suggest: Se, As, Co, Pb etc. So yet again, I don't think I'd be searching for this concept at least initially);

- waste water (at last - something that is quite specific and commonly mentioned, although you have to think about searching wastewater/wastewaters and so forth);

- nanomaterials ('synonyms' may be nanosponges, nanoparticles, nano materials and so forth. These probably could be included in an initial search, and there is a very simple way to search them - right? :-) );

- wood/cellulose (this concept also would be worth considering in an initial search).

So, what do you think? If you agree with my suggestions, then the next thing I suggest you do is formulate specific search strategies in PubChem and in Reaxys, and then get them checked by Dr Kim and Anja/me. Damon

Olcc S14 | Tue, 04/11/2017 - 15:06
I try to search Quat 188 and able find some of the data. In my search, it shows 6 bioactivities. When I clicked on it, it showed 6 hits of pharmacological data. In this section, I saw 1 of 6....., in a comment, there is reference only. So how can I know what type of bioactivity are there in quat-188? (use Reaxys for the search) Looking for your help. Thank you

Damon Ridley's picture
Damon Ridley | Wed, 04/12/2017 - 02:28
Amita, What you did was exactly correct. Bioactivity Data in Substance Records may appear in one of two ways: 1. There simply is a reference with a note that bioactivities are present (and unfortunately you have to go to the original literature to find the data); 2. extensive bioactivity data is actually given. Unfortunately in the case of Quat 188 all the information in the Substance Record is of the first type. Good news is that you have found relevant documents; bad news is that you would have to go through the original papers to find the specific information - but you don't have to do that for the purposes of this project. You will note that the record for Quat 188 (Reaxys Registry Number 6576172) contains information under Other Data and there are 88 documents relating to the specific substance. You could browse through some of these to see if there is anything of interest. You could also Search Reaxys: quat 188 in which case you find a few Document Records, but at a quick glance they don't appear to have biological activity data. The other thing you could do is Google: MSDS quat 188. When you do that you find the MSDS (Materials Safety Data Sheet). I shall comment on your other search in a separate comment. Damon

Damon Ridley's picture
Damon Ridley | Wed, 04/12/2017 - 03:06
Amita How are you going finding information on the use of nanomaterials to clean up wastewater? As I suggested in my earlier note it probably is best to search for three of the concepts: "nano", wastewater, wood/cellulose, so one of the starting points could be simply to search in Search Reaxys (the text option from the landing page): nanomaterials wood wastewater. When you do this you get 6 Documents and you can browse through them. However, the question is: "How did Reaxys perform the search?" Well, a couple of weeks ago (yes, Reaxys is constantly adding functions and features) Reaxys added the Edit Query feature which shows you exactly what was searched. To see this feature, from the list of choices you get after you do the search above, hover with the mouse over Preview Results for the 6 Documents and a link: Edit Query will appear. Click it. It tells you the search was done in the Document Basic Index (which contains single terms from all the 54+ million Document Records) and you will note that a number of synonyms for 'nanomaterials' were searched automatically (the semi-colon ; between the terms shows that the terms were ORed together), but only a few terms were searched automatically for 'wood' and 'wastewater'. The good thing is that you can easily modify the search so let's now think about it. In the top line, if you click the down arrow on the left you find some options, so why don't you chose 'starts with'. What then happens is that Reaxys automatically applies "right-hand truncation' for the term you now enter. On that line then delete all the suggested terms and simply enter: nano. What Reaxys then will do is search for all terms starting with the letters NANO. Next think about the next line (the one with wood). We need to allow for wood, woodchip (and various other 'woody things'). We also need to consider synonyms relating to 'cellulose'. Are you with me? If you are then adjust the down arrow to 'contains' and enter: wood; cellulose. 'Contains' applies left- AND right-truncation, so with ; meaning OR what we are asking for is any term in the Document Basic Index that has the letters WOOD or the letters CELLULOSE. That should reasonably cover the woody concept. Finally, change the last line to 'contains' and enter: waste which will pick up wastewater, waste water ... or any term that contains WASTE somewhere. Note that Reaxys will AND these together. That is, we are searching all concepts in the one go. At the top, click Search (Documents) and have a look at what you get (well over one thousand document records, right). That is, click Abstract, Index Terms, play around with some of the Filters and Analysis tools (although remember that Index Terms under Filters and Analysis only looks at Reaxys terms; for Emtree or Compendex terms we have to do something else, which I can help you with if you are interested). I think that's enough clues at the moment. Have a go and let me know what you think. I shall send you some contact information to get to me through your contact Information. In summary, all we did was try a few of the terms in Search Reaxys. We looked at Edit Query and learnt how Reaxys searched. We then used this information to guide us what to do next - in other words with Reaxys' initial help we 'took control of the search'. We thought like scientists (not like dummy Googlers) and we came up with a really good answer set which we could look at further. Have fun! Damon

Sunghwan Kim | Wed, 04/12/2017 - 12:52

Hi, Amita.

Try to search PubChem for the same compound. You will be able to find one record for the query. Go to its compound summary page and look into what kind of information is available and what is missing in PubChem that does exist in Reaxys, vice versa. And figure out how to go from this record to records in other databases (e.g., literature, protein, gene, disease, and so on). In this way, you will start noticing differences between the two databases.

OLCC S197 | Tue, 04/11/2017 - 16:50
Hy Dr kim, i am working on drugs for controlling psychotic disorder please if there is any idea you can give me on how to use reaxys and pubchem to do my project thanks from NWUME .

Anja Brunner | Wed, 04/12/2017 - 03:47
Hello Nwume! The topic "drugs for controlling psychotic disorders" is very broad. To do justice to this project, where you really look at how PubChem and Reaxys might complement each other in answering an information research question, it would make sense to narrow down your topic; that is, to define a specific question you want to answer about these drugs. Are you interested in a particular drug? Are you interested in the properties of these drugs? There are a lot of mental disorders; which specific one would you like to tackle? Dr. Kim and Damon gave some very sound advice in the comments above about how to narrow down your research topic, which will make it easier to define what kind of search you need to perform. Take a look at what they wrote above and please get back to us with the question you want to address in your search. Then, the three of us can help guide you through the searches that can be performed in PubChem and Reaxys. Looking forward to working with you! Anja

Damon Ridley's picture
Damon Ridley | Wed, 04/12/2017 - 04:05
Nwume Dr Kim will help you with researching this topic in PubChem. Below are suggestions for finding information in Reaxys. From the Landing Page, in the text search box enter: psychotic disorders. Click Search. You will see a list of options. Choose the top one and you will retrieve over 10,000 Document Records. You can browse through these (e.g., click Abstract and Index Terms). You can also try Filters and Analysis options. At the top of the list is Index Terms and when you click the down arrow you see the most listed Index Terms IN REAXYS. However, even this list shows up a number of options that will enable you to narrow the answers by various drug terms That's quite neat, right? However, uniquely Reaxys can directly answer what you really want to find, that is all the substances that have been tested for 'psychotic disorders'. The point is that Substance Records in Reaxys have information in over 400 'property' fields. This information can be text (millions and millions and millions of terms!) or numeric (things like melting points, electrical conductivities, mechanical properties that have numeric terms and so forth). What we really want to do is find all those substances that have text terms relating to 'psychotic disorders' and we search for such terms in Substance Records in the Substance Basic Index. To get to it, click Query builder at the top of the screen. Then under Search properties enter: substance basic. Then click, drag and drop the top-listed one (for Reaxys) into the main workspace. Click the down arrow on the left and choose 'contains'. Terms you now enter will be searched with left- and right- truncation. I suggest you enter terms: psychotic; schizophen; bipolar (the semi-colons ; indicate OR). Click Search (Substances) on the top-right. You now get over 23,000 substances. They are listed by number of references so fairly trivial substances appear at the top of the list. Nevertheless when you click Hit Data (and the the field) you get an idea of what was searched. It is up to you now to decide how you want to narrow the substances. If you don't have anything in particular, then I suggest as an example that you click Structure (under Filters and Analysis), then draw the structure of 1,4-piperazine (a saturated 6-membered ring with N's in the 1 and 4 positions), click (on the right panel) substructure and check boxes: tautomers. Finally, click Transfer to filter. From the next screen, click Limit to and you get all the substances with the 1,4-piperazine structure that have been tested for the text terms you initially searched. Browse through some of the substances and the Hit Data, and you will see a lot of actual data, right?! Damon

Sunghwan Kim | Wed, 04/12/2017 - 12:06

Hi, Nwume,

First of all, you really need to have a specific question that you want to answer, and then need to find a way to how to answer that question.  When you don’t have a good question to answer, you just can’t answer it.  So, please write down your question that ends with a question mark, and then list a set of tasks that you need to do to answer that question.  If you can’t identify a specific task(s) for finding the answer, it is likely to mean that your question is too broad, so need to write a new question (or questions) that is narrower than the original one.  Repeat this until you see what you really want to ask and how you find the answer to it.

By the way, to find psychoactive drugs from PubChem, probably the best approach is to user the PubChem classification browser (https://pubchem.ncbi.nlm.nih.gov/classification).

 

(1) Go to the classification browser, select “MeSH” from the “Select classification” drop-down menu (on the top-left) and “Compound” for the “Data type counts to display” option.

(2) Type “antipsychotic agents” in the text box and run a search by hitting the search button.   This returns ~9 MeSH terms with which any PubChem Compounds are annotated.

(3) Click the record count for one of the hits to explore (for example, “Antipsychotic Agents”).  This gives you a list of 207 compounds annotated with the MeSH term “antipsychotic agents”.

(4a) Refine the resulting compound list using various filters available under “Refine your results” on the right column.  You can retrieve the compounds with protein-bound experimental 3-D structures by clicking “Protein 3D Structure”, or retrieve the compounds with bioactivity data by clicking “BioAssays, Tested”.

(4b) Alternatively, you can click the “Structure Clustering” button under the “Actions on your results” section (on the top-right).

(4c) Another thing that you can try is to retrieve records in other databases associated with the antipsychotic drugs, using the dropdown menus in the “Find related data” section (on the right column).  For example, by selecting “BioSystems” from the dropdown menu, you will get a list of pathways associated with the psychotic drugs.

 

Well, there are many other things you can do with PubChem as well as Reaxys, but you can get the most out of these resources, only if you have a clear question that you want to answer.  I think you need to come up with some good idea about it.

 

OLCC S197 | Thu, 04/13/2017 - 17:26
hy, to be be specific i am working on finding the properties of ziprasidone which is an anti-psychotic drug using pubchem and reaxys i want to compare the result gotten from the two. from nwume

Anja Brunner | Fri, 04/14/2017 - 02:49
Hi Nwume, I think that the search in Reaxys that Dr. Ridley describes above is an excellent way to delve into a topic and explore what areas are of most interest to you. He also shows you how to use the filters to narrow down hitsets. If you are specifically interested in Ziprasidone, enter that name into the Quick Search in Reaxys. You will get a Substance Record and over 7000 Document Records. I encourage you to spend some time exploreing the Substance Record to get a feel for the tremendous amount of information it contains. You have identifier information, a link to the Synthesis Planner, and a large body of property information: physical, spectral, bioactivity, uses and more. Each excerpted property entry is connected to the citation of the source document so you can always look at the context in which the data were reported. Also explore the Document Records. They are first organized by Relevance but you can use the filters to, for example, look at only Reviews or other document types. I personally like using the Index Term Filter. It quickly gives me an overview of the topics addressed in the full set of documents to (a) get a feel for what topics are most commonly associated with and addressed regarding Ziprazidone and (b) select the documents that address topics that I find interesting. The Index Terms in each Document Record is also a very interesting way of finding other search terms you may not have thought of and that can help narrow or expand your search. Give it a shot and see what you find. Have fun! Anja

Olcc S14 | Wed, 04/19/2017 - 14:30
I tried to search some documents related to my project. When I searched just entering nanomaterial, I got 452 records for nanomaterials and 205,760 records for nanomaterial. When I used nanomaterial* it gave me 153,536 records and with *nanomaterial* I got 153,651 records. I am confused about using truncation. Why do I get a greater number of records when I put "*" in both side of text? Thank you

Damon Ridley's picture
Damon Ridley | Wed, 04/19/2017 - 18:50
Amita OK. Here is a summary. From the Landing Page, there is a text box and when you hover over it you see it changes to Search Reaxys. In Search Reaxys you may enter either: a. just natural language terms, or b. terms with truncation. (Yes, there are other things you can enter and the outcomes may be different, but right now let's keep it simple and focus on a. or b. above.) When you go down route a., Reaxys interprets the query as best it can by applying hundreds (yes, hundreds) of algorithms to try to work out what the user wants and then provides a list of options from which to choose. These algorithms include, inter alia, building queries in Substance, Reaction and/or Document Records and include automatic addition of 'synonyms'. However, when you go down route b. all these algorithms ARE TURNED OFF and Reaxys searches only in Document Records - and applies truncation or whatever else you have done including use of semi-colon (for Boolean OR). So, in Search Reaxys: nanomaterial you have just used 'natural language' and route a. kicks in. You see the first two entries say: Documents Journal. What is happening here is that one of the algorithms tracks to titles of journals, and there is indeed a Journal called Nanomaterials. So if you View Results (for the 452) you will find hits in the Journal. The last entry says 205,760 Documents Titles, Abstract, Keywords: nanomaterial. This tells you that the search has been done in Titles, Abstract, Keywords in Document Records and you can go and View Results. From these results you can work out what Reaxys searched, but there is an even easier way to find this out, namely: hover (with mouse) over Preview Results for these 205,760 Document and you see Edit Query comes up. Click this and Reaxys tells you exactly what was searched, specifically the search was done in the Document Basic Index (that is single words in Titles, Abstract, Keywords) and you can see the bunch of 'synonyms' that Reaxys automatically applied. Note a semi-colon is between them = OR. (Note: unlike for every other natural language search engine which applies algorithms and doesn't tell you what it searched, Reaxys is fully transparent, shows you what was searched and then enables you to learn from that and modify it if you want.) However, with either of Search Reaxys: nanomaterial* or (separately) *nanomaterial or (separately) *nanomaterial* route b. kicks in, and the outcomes are either right, left, or right and left truncation respectively. (Note that Edit Query in these cases has yet to be fully implemented and what you see if you go down this path has 'errors'. Don't worry. Edit Query only came out a month ago and details like this are being attended to, but in reality the correct truncation as stated above has been used/searched.) I hope you can follow. It's all logical - once you know the (simple) rules. NEVERTHELESS where I really wanted to get you was to learn from everything you did above and then think your way (eventually) to the following search. DOCUMENT BASIC INDEX: *NANO* *WASTE* AND DOCUMENT BASIC INDEX: *WOOD*; *CELLULOS* (You need to do this through Query builder, then Search properties: document basic, then drag the querylet twice into the main working space, and enter the terms above - although you don't have to use capitals.) It is easiest to build two querylets (basically you want nano AND waste, AND (wood OR cellulos) ... and it is easiest to do these separately). The first one defaults to a search *nano* AND *waste* (meaning you search nano, nanocluster, nanostructure, nanocarbon, nanomaterial, bionanomaterial, and all their plurals and so forth, AND waste, waste water, wastewater and so forth). The second one truncates both right and left and searches the terms OR. When you do this you get over 1,200 documents and you pretty much has covered all variations. Interestingly you get NANOCELLULOSE(s) and this could well be of interest. I am not sure. It seems to me that this is a super answer set that you could modify further if you wanted (e.g., if you really wanted the water bit, then you would search *water* separately and combine this search with the 1,200+ documents...if you need help then let me know). Searching the literature is an ART and a SCIENCE. We have to think - and not like a Googler. We want to do comprehensive/precise searches in quite complex scientific databases (with all types of author word variations), and we don't want to "stop at the first few pages of answers". I hope this helps. Damon PS In your answer to your assignment, or in your presentation, please understand that you will need to communicate to people who may be say Googlers, WebofScience, Scopus, or SciFinder etc users. They may not be aware of how Reaxys works, so please take your time and explain everything step by step. In the long run, and having used all these products, I think that the Reaxys way is very neat. You have only to learn a couple of things and then you think your way through the problem logically. That's true science, right?

Olcc S14 | Wed, 04/19/2017 - 14:57
When I search (3-chloor-2-hydroxypropyl)trimethylammonium chloride, it did not get any result but when I enter Quat-188 or CAS number, I will get a result. Why do we do not get any results on compound search with a chemical name? Thank you

Olcc S14 | Tue, 04/25/2017 - 11:10
While using Reaxys and PubChem for compound search, I found "safety and hazard" on PubChem but I am unable to find that in Reaxys. So does Reaxys give an information about safety and hazard of searched compound?

Anja Brunner | Fri, 04/28/2017 - 05:19
Hello! Sorry for the delay in my response. So, good observation. The specific kind of safety and hazard information that you would find on an MSDS (so, standard GHS Hazard statements, precautionary statement codes and such) is not covered in Reaxys. I talked to some of our colleagues about this and there are lengthy historical reason for this (that we don't need to discuss). Having said that, Reaxys covers toxicity and environmental toxicity, for example, very nicely. And if you are specifically looking for H&S information, Reaxys links directly to substance records in third party databases where you DO find that kind of information. So, look up a substance, go to the hit list of Substance Records, and in the upper right corner you will find a dropdown menu titled "Database:". The menu will most likely be set to "Reaxys". You can change that to, for example, "PubChem". This will show you records available in PubChem and links you directly to the records where you can find that information (as you mentioned). While you are there, you might also want to look at the linked records in eMolecules. This is a database designed for the sourcing (purchase and supply) of chemicals. Their records may also contain interesting information. This is a good example of how Reaxys tries to bring together information across multiple sources and position them in one location so they can all be easily accessed and used. I hope this answers your question! Anja