Discussion

Damon Ridley's picture
Damon Ridley | Sat, 01/28/2017 - 02:27

People have asked about the indexing of salts in different databases.

There are two parts of the problem:
- there are different "classes" of salts;
- databases may (or may not) have different indexing policies for the different classes.

We can have salts of simple alkali/alkaline earth metals with non carbon-containing or carbon-containing acids, or of simple halides with non carbon-containing or carbon containing bases, or salts of carbon-containing acids with carbon-containing bases. We also talk about hard and soft acids and bases, but the chemical difference here usually relates to the extent of ionisation of the "bond" between the different atoms. Then, when is something a salt or a coordination compound? Calcium hydroxide is normally considered a salt, so is calcium acetate - but is calcium oxalate a salt or a coordination compound? Then, what happens with "hydrates" - are they hydrates, salts or coordination compounds? (Incidentally, I once made a lithium salt of a phosphinic acid, and it gave a strong molecular ion in the mass spectrum - possible only because of a very "covalent" Li - O bond.)

Given all that, the representation of substances in computer databases needs to have clear cut rules and the different databases may have different policies. Hence, in different databases, lithium acetylide may have a different representation from lithium acetate. Further, take ferrocene. When it was first made chemists thought of different ways to represent its structure. These structures were published in papers and databases entered the structures accodingly. However, years later it was realised the actual structure was quite different - that being the case should all the previous structures be deleted, or changed? Are databases always going to make "retrospective corrections"?

The issue here is not necessarily with computers, or the policies of people who create databases, but perhaps more with the (fascinating) complexities of chemical substances.

Damon

Damon Ridley's picture
Damon Ridley | Sat, 01/28/2017 - 00:58

Thanks for your question.

In cases like this I'd definitely go down the structure search route since structure searches are precise and comprehensive - provided you enter the right query.

So from the Landing Page, I'd click Create Structure or Reaction Drawing, then in Create structure template from name enter say: 2-hydroxypyridine. I'd search this structure As drawn and I'd definitely include Tautomers. I'd consider the defaults but at this stage I'd probably leave them as they are.

After you Transfer and Search you find each substance has its own Substance Record. I'd browse some of the other answers just for interest, but there are not many documents for them.

The question now is: Which tautomer is indexed? The answer is that it depends on what was in the original document. If 2-hydroxypyridine was the focus then that would be the indexed substance; similarly if 2-pyridone was the focus - it would be the indexed substance. If the original document discussed both, then while I am not certain of the indexing policy, I think both would be indexed.

I hope this helps.

Damon

olcc s16 | Fri, 01/27/2017 - 14:36

I'm trying to figure out if Reaxys treating 2-hydroxypyridine and 2-pyridone as one substance or not. We know that 2-hydroxypyridine and 2-pyridone are tautomer. When I perform quick text search for each, Reaxys retrieved strictly one either 2-hydroxypyridine or 2-pyridone. However, if I perform structure search with a check on "Tautomer", I received result of both 2-hydroxypyridine and 2-pyridone as tautomer of each other. So, how can I tell if Reaxys treated these substances as one or two? Because seems like it would depend on my searching method.

Best

Damon Ridley's picture
Damon Ridley | Fri, 01/27/2017 - 14:23

Hi

Yes you certainly need to put spaces between the terms entered. You may also wish to try: absor* phosphate* *water* *wood* which you will find gives a few different hits. Also remember that when you put in 4 concepts like this you are requiring that ALL FOUR be in the database record. (You are not searching the full text and it is possible that fewer concepts are in the database record although all concepts could be in the full text.) So you may wish to try in Search Reaxys: adsorb* *phosphate* *wood* (note that I have left-truncated phosphate in case there are records such as organophosphates (if you also want to include them)). Further: absorb* *phosphate* *wood* ?

Remember that you are requiring a potentially large number of terms to be searched and Reaxys may take a little while (30 seconds?) to find all the answers.

Remember also that you are trying to enter search terms that anticipate what was written by an author (in titles and abstracts) and entered by an indexer in Index Terms. In your search you don't have one or two "really good terms" that will always be used (and on which you can focus) - so you have to try them all (or perhaps three of them as I have indicated).

You may think this is all a bit cumbersome since in something like Google you can enter: adsorption of phosphates by wood whereupon you will find some interesting hits, but then you wonder what you may have missed. The learning point here is that you may have to search a few different sources.

I consider this a "tough" search question, but it seems to me that you can pick up around 200 document records in Reaxys (if you combine the various searches and particularly if you leave out the 'water' concept). Realistically I'd be pretty happy with this at least as a start.

Damon

Olcc S14 | Fri, 01/27/2017 - 12:14

I am trying to find out articles related with adsorption of phosphate from water using wood nanocomposites. I have tried using truncation as adsor*phosphate**water**wood* but the Reaxys does not read it. So can anybody tell me how to find articles in Reaxys related to my subject with truncation or any other methods?

Robert Belford's picture
Robert Belford | Fri, 01/27/2017 - 11:17

All,
A student posted a question to hypothes.is, but it did not go to everyone who is subscribing to this article, so I am pasting it here

I understand from the paragraph which databases are used for sodium acetylide. On the other hand, i don't understand which databases treat sodium acetate as 2 fragments. Any help?

Please note, this deals with the article by Cooke and Ridley, which is at the bottom of this page. Here is a google short URL to the hypothes.is link, and in case it gets depreciated, I am pasting the long one at the bottom of this comment https://goo.gl/fS7PJz . If you join the hypothes.is group called OLCCSendMail, these two links will take you right to the highlighted text the student is talking about.
Cheers,
Bob

https://hyp.is/b-v2sOStEeavIF_TnRkzXg/olcc.ccce.divched.org/sites/olcc.ccce.divched.org/files/Aust%20J%20Chem%20Article%20Cooke%20Ridley%20%282%29.pdf

Anja Brunner | Fri, 01/27/2017 - 05:05

With the complexity of naming chemical substances and the different ways in which substances are systematically indexed by database producers, searching information on a substance or group of substances can pose a challenge.

Reaxys houses a very extensive database of substances and associated information, and as you will see, that information comes from different sources and is organized into several types of records. The system also offers several opportunities to retrieve that information. Learning about some of those options is the objective of another resource we have posted (at the top of this module page).

Try some of the searches! And please do not hesitate to post comments and ask questions!
Cheers,
Anja

Anja Brunner | Wed, 01/25/2017 - 06:52

Research shows that the vast majority of information searches performed by scientists are text-based. So, Damon and I have posted (at the top of this module page) a new resource introducing text searching in Reaxys (Reaxys_TextSearch_230117). In it, we comment on general issues to consider for text searches, how systems build algorithms to interpret text-based queries, and we've worked through some of the ways in which Reaxys handles text searches.

Reaxys contains trillions of searchable words, not just in Document Records but also in Substance and Reaction Records. Creating a search engine that accesses and effectively unveils this content embedded in different types of records is challenging. However, with a little understanding of the background and a little practice, we can quickly see the opportunities available in Reaxys.

Please do take a look at the resource and try some of the activities it describes in Reaxys. And we look forward to any comments or questions on text searches in Reaxys!

Cheers,
Anja

Damon Ridley's picture
Damon Ridley | Wed, 01/25/2017 - 02:06

Hi Everyone,

In my reply to Chris I referred to terms 'entered' by authors and by indexers in database records.

As authors, it helps to remember that the terms we use in titles and abstracts will make up a large part of the text that is searched in databases. We want fellow scientists to find our papers, right? - so it follows that we should carefully consider the terms we use. I am not saying that we should be de facto indexers, but we definitely need to consider terms that have "meaning" within the context of being part of a searchable database.

Compare abstracts that contain:
"Compounds (1) to (5) had reduction potential between -1 and -1.2V ......" and
"Cyclovoltammetric studies of the zinc tetraphenylporphyrin derivatives prepared showed half-wave potential ....."

The first abstract has few searchable terms [and (1) to (5) means nothing as an entry in a database, right], whereas at least the second abstract has a few searchable terms.

Think about it when you write your next title and abstract!

Damon