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From Wikipedia, the free encyclopedia

Description PubChem
Organisms Humans and other animals
Research center NCBI
Primary citation PMID 15879180
Download URL FTP
License Public domain

PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be freely downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds. More than 80 database vendors contribute to the growing PubChem database.[1]

YouTube Encyclopedic

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Molecular libraries program at NIH ended a few years ago, but PubChem continues to evolve grow. In addition to the data that came out from the molecular libraries program, PubChem now has more than 400 other data sources and has arguably become the largest database of publicly available chemical information in the world. So where does this data come from? Well, the data is provided by more than 400 contributors from all over the world, most of them in the United States and they are university labs and government agencies and pharmaceutical companies and chemical vendors and publishers and others. You can learn more by visiting our data sources page, but please do note that this page is getting an update very soon. Please watch for the announcement, and once the update is released, you will be able to do a lot more than the current interface allows. You will be able to filter the data sources by datatype and organization type or countries and so on. Next, let's talk about the actual data. So PubChem consists of three interlinked databases: Substance, Compound, and Bioassay. Substance contains chemical information submitted by individual contributors. On the other hand, compound database stores unique chemical structures that are extracted from the substance database. So there can be many substance records for aspirin, for example, but there is only one compound record for aspirin. So you can think of compound record as a summary of all of the data that has been submitted to PubChem as Substance records, and later we will talk about some other data that we call annotations. Biological activity data of chemical substances that are tested in experiments are contained in the bioassay database. Just to recap we have three databases PubChem Substance, Compound and Bioassay. If you are a PubChem user you may have noticed the look and feel of the website has been changing quite a bit. In addition to having more content, we also have been working on updating our interfaces to improve performance and make them mobile friendly so they can be used on your phones and tablets and phones and make them easy to use and so on. The update, however, is not yet complete. You will see some PubChem pages that look updated and some that are not; so, work in progress. Our content pages by which I mean our substance and bioassay record pages as well as compound summary pages, have all been updated within the past year and a half and we are also working on releasing a new set of pages that we are excited about that. It summarizes the everything we know about biological targets. I will show you a preview later. Our search and analysis tools have not been updated and is a work in progress. I will talk about that a little bit later on as well. Next we will go to a live demonstration and my goal is to give you a snapshot of PubChem as it is today. I will point out both new content and interface features that have been added recently, and I will provide some tips on getting the most out of the resource. I will also point out which interface and features are likely to change in the future. We will take a brief look at an example substance record for caffeine that has been submitted to us by a source name EPA DSSTox which is EPA's distributed structure search toxicity database. The URL is / substance / 48415680. This number is the substance identifier and we call it a S I D. This is a pretty typical substance record. It has chemical structure And I will scroll down to show you what it contains. It has chemical structure and it has some chemical names that you can see under synonyms. So here is a long chemical name and here is something that is a CAS number which we also include under synonyms and also there is a nice chemical name caffeine. And it has some bioactivity results. In fact, it looks like this record was -- the purpose of submitting this record was to post this test result. The source also submitted a bioassay record and we will take a look at that a little bit later. Going back to top I would like to point out the download menu and I will click on data provided by the source. I will choose display as the format. This is a very quick way to see what exactly was provided by the source. As you can see here, we provided a chemical structure and some comments and some synonyms, so this is just a way to displaying the same record as we displayed on the webpage. I am going back now. Generally, if you are looking up information about a chemical, you would want to look at the compound summary page, rather than the substance record page. We are looking at the substance record page right now as an example. But, generally, what you want is the page that is linked from here which is PubChem CID 2519, caffeine. The only time you should really be looking at the substance record is when you are specifically interested in information that has been provided by a particular source such as EPA DSSTox, in this case. I should also mention, another reason why you might want to look at the substance record would be when the substance does not have a well-defined chemical structure and thus we would not have a compound page for it. Let me quickly show you one such example for a substance described as safflower oil. You can see it under depositor supplied synonyms. It was also provided by EPA DSSTox. They also have biological test results for this substance but it doesn't have a well-defined chemical structure. One of the descriptions for this chemical that we have is in this chemical substance record. So there is value in this chemical substance description even though it doesn't have a chemical structure, which most chemists expect. Next, let's take a look at the compound summary page. These are the pages that you most often want to look at when you are looking up chemical information about chemicals. The URL is / compound / caffeine. Differently from substance pages because we care about compound pages a little bit more . We allow names and synonyms in the URLs so while PubChem CID 2519 would work if you put it in the URL. Let me type that here. So it will load [indescernible] So it will load caffeine and if you put any of these synonyms like methyltheobromime here in which are different names for the same compound, it would give you the same record. This is just for your convenience and you can browse PubChem via URLs to your hearts content if you would like. So differently from substance records, each of which contain information submitted by a single source, just like the record I showed you previously submitted by EPA, compound summary pages contain everything we, PubChem, know about the compound. This includes all information collated from all the different substance records that have been submitted by different sources to us by different sources about caffeine. And in addition, compound summaries also contain annotation information we pull from other authoritative sources. such as FDA and EPA and so on. Those are not substance records, those are just textual annotations. Let me show you some examples right here. At the top of the page we have some descriptions of compound records involving caffeine and this particular snippet of information that we call an annotation comes from the FDA and if I expand the source for this reference, there is information that you can see where it came from and the source name was FDA pharm classes which is just a classification that FDA has for chemicals and the record name was caffeine and you can click the URL and check exactly what data is available there. So here is another snippet of information from the National Cancer Institute and it gives you a little bit more of a description about this chemical. If you scroll down the page, you will see quite a bit of annotation information, including things like identifiers, like, for instance, here is an EC number and here if I open this tooltip you can see an explanation as to what exactly this piece of information is. If you expand the reference information under this, particular pieces of information you can see where it came from and what the URL is. So why do we collect all of this annotation information? Well, mostly, because a lot of it is very hard to find on that web. Some of the data are buried in PDF documents or sometimes they are available only via FTP downloads and so on. So we hope that collecting all of this information and putting it all into one page saves our users a lot of time to handle this information in one place. However, what this means, with some chemicals, like this one, caffeine, our compound summary pages are really really long. So I will point out a few features in the interface that may help you navigate these pages a little bit faster. Because if you try to scroll all the way down, it may take you a while and it would be hard to find exactly what you're looking for. Going back to the top of this page, these icons at the top, they are shortcuts to important sections you can click on. For instance, you can click on the patents icon and it will take you all the way down to the patents section. If you are only interested in patents, you can look at all of the patents and download them and sort them and click on these links to go to the patent pages at the US PTO or wherever they came from. If you are interested in downloading data, you can use download menu here at the top and to see what kind of information you can download for this compound. Note, that data used to display this page option includes all information on the page. So I will open this in JSON format and show you what this looks like. Basically, all information that you see on the pages included right here. So you can download and use it in any way you wish. What is not included in this particular file is information that is included in these sections that are too big. So for instance, if you want to do structure file to be downloaded, you have to use this particular option and you can get the sdf file or if you are interested in citations for instance you can use NLM Curated PubMed citations and download this file and so on. So there are lots of download options here, and you don't have to scroll all the way up and down the page to find out where to download the particular section. It is all available for you at the top of the page. When you scroll down the page, the table of contents stays visible, so you can quickly navigate between different sections. You can also expand this table of contents to get to even more detail. As you see, it can be very detailed, depending on what you are looking for. You can find exactly the particular piece of information. For instance, I will click on crystal structures, and this is content that we added fairly recently. We haven't advertised it very much, but what these are are links to our cambridge structural database and if you open them you can see crystal structures for this particular compound. Let’s see if this is going to load; here you go. This is quite nice. If you are interested in quickly finding all of the sources of annotation for this compound that we have and where we pull information from, at the bottom of the table of contents if you click on information sources, we list them all out for you in one place so you can look at all of the links that are available and see where it came from, click on them, and they are all in one place. However, these are the sources of annotations only. If you are interested in the sources for who submitted the substance records for the chemical, which is caffeine you would find them under related records section. Under substances subsection. From here, you can see there are a total of 1114 records that have been submitted by our sources about caffeine and 276 of them are caffeine exactly, while the other 838 records include mixtures that include caffeine. So those are all kinds of substances that have caffeine mixed with them. I will scroll back up a little bit so that I can point out the related compounds section could save you a lot of time searching for compounds similar to the one you are looking at. Under related compounds, with annotation you can find compounds that are similar to caffeine so here is theophylline and it has it is billed as a medication because it has annotations that are describing it as an medication. For instance, if you click on patent you will find the compounds that are related to caffeine that are mentioned in the patent records that we know about, so this can be a very quick way to find some important compounds that are related to the one you're looking at and don't necessarily have to go to any search interfaces or anything. You just look at this record and see what else is related to this record. I would also like to mention,drug and medication information section since it has been recently reorganized, in particular, we now show a lot of detailed data from the FDA Orange book and it includes sections on prescription drugs, drug products and over the counter drug products and discontinued drug products and so on. So it is all in one place, and we show three items in the list, but if you click on that button to show all of them, you can see that all 33 discontinued drug products that the FDA Orange book knows about, you can print it up or whatever. Hopefully this is convenient. The next type of information in the compound summary pages is safety and hazards information. This now includes a much improved GHS classification. I will open a tooltip to show the definition of GHS classification. This is globally harmonized system of classification and labeling of chemicals and is a United Nations system to identify hazardous chemicals and informs users about these hazards. GHS has been adopted by many countries around the world and is now also used as a basis for international and national transport regulations for dangerous goods. So we summarized all of the GHS hazard statements, categories and pictograms in a separate page which you can find up here in the URL. You can take a look at all the possible hazard statements. Going back to caffeine compound page, you can see exactly what is shown under GHS classification for caffeine in particular. We only show one source of information for GHS classification for caffeine by default, but if you click on this button down here, you can see that there are more other sources like EU regulation or Safe Work Australia provides hazard statements for caffeine that are a little bit less severe than those that are provided by the Japanese government chemical hazard classification. We can argue as to who is right or wrong, but it is up to you to decide which one you trust or which one you want to use. So going back to the top of the page, staying on the subject of chemical safety, I would like to point out that for compounds which we have GHS information available, we also provide a link to laboratory chemical safety summary view page for that chemical. So let's click that link and you can see another page for caffeine that is a subset of a full summary page. It focuses specifically on chemical information, so these pages have been created with -- in collaboration with chemical safety community and include a subset of compound summary information that is deemed important from the chemical safety perspective. It is still a work in progress, and you can read a bit about the project by following this link right here, read about the LCSS project. This link appears at the top of every page for LCSS so you can read about this at any time. So I talked quite a bit about compounds. Next, let's move on to an example of the bioassay record page. So the URL is / bioasay / 440. This number 440 is the AID and this is the bioassay identifier. This is a pretty typical record for bioassay and it has been submitted by the University of New Mexico, and if you scroll down, you will see that it includes the description of this experiment and includes the protocol and includes the biological target information, if there is such information available for the bioassay. Of course, it shows the results table, which is shown here in the data table. In this bioassay a large number of compounds were tested for activity against a particular protein target. It is human formyl peptide receptor one and a good number of compounds have been found to be active and have been reported active. As with other interfaces, there are numerous download options so you can download and analyze the data on your own so if you click the download menu option at the top you can see that you can have a description and data table or the description only or the data table only and you can download all the tested substances and you can download their structure and so on and so on. I would like to focus your attention on the target section for a moment. We have a protein target here and we have a link here which is a link to the NCBI protein page. The encoding gene for this protein is FPR1. And the link goes to the NCBI gene page and also we have all bioactivity data for this encoding gene that we know of in PubChem. So we will click on that. So this page collates all bioactivity results for this encoding gene FPR one from all of the bioassay records for which this gene is a target. While there is a lot of useful data here, I’ll let you observe it for a little bit, this page is not so easy to find. You have to find an assay that has this particular target and find the link or if you know a gene ID you can go to this URL up there at the top of the page. It is not easy to find, and it may not be as easy to understand or use. I am excited to tell you, however, that we are working on an entirely new set of content pages that we call target summary pages. Just like our compound summary pages they will summarize everything we know about a given target. I have a demo that is a work in progress at this point. The URL is not public, so I won't advertise it in any way. I will scroll down and show you that eventually it will contain complete summaries of anything and everything we know about this target as far as from a chemical biology perspective. So it will list all of the molecules that are known to be active against the target or inactive and everything that has been tested about it and any other annotation information we may find as to what diseases it might be involved in and so on. So we hope just like our compound summary pages that are popular that these target summary pages are going to be useful to the community as well. So watch out for the announcement for that. Those should be coming out later this year and we will go forward from there. So far, we talked quite a bit about the content that we have in PubChem. But there is another important aspect of any database resource. That is the ability to search and analyze the data. Unfortunately, I can say that creating effective search and analysis tools have been an ongoing challenge for us, and this part of the resource is currently under very active development. A few words I would like to say , interestingly, I have to say but the majority of our users search PubChem using generic web search such as Google. I will show you why. So using acetone. Here is acetone page in Wikipedia and then here it is in PubChem. If you click on this link you end up on a compound summary page for acetone and people find all kinds of useful information there. The question is, do we have internal search tools and what extra value can they provide over and above those as generic web searches such as Google? If you go to PubChem homepage, there is a search box there and you would have to choose which database you would like to search and at the moment you can't search all three of them at once. It's either bioassay compound or substance. So I’ll search acetone in the compound database and I end up on a page for PubChem compound Entrez database. It will list all of the results for acetone . And that is pretty great. You have a lot of filtering options here on the right-hand sidebar, and you can find all of the bioassays that this particular compound acetone has been found active in. You can find all of the bioassays that this compound has been tested in and so on. However, the caveat, and the drawback, is that the only field you can search in this interface are compound names and synonyms. There isn’t much else -- for instance, you can't search annotations such as safety results and so on. Also, you can't search compounds here by biomolecular structure. You can't write a molecular formula . So for instance if I type in something like h2so4 it might come up because somebody gave it as a synonym which is pretty nice. Let me type another formula. Quite a few of them are synonyms, so you may find those. This might be something similar. It finds some molecular formulas that correspond to these compounds but definitely not all of them. The point here is that if text search of compound names and synonyms is not sufficient to you, we have another interface, which you can find from the PubChem homepage which is called structure search and you end up on this interface where you can search by a similarity and here you can actually draw a structure and submit it for search. This may take a while. This is an old interface. Eventually you will get the result and you will end up in Entrez and we will give you a list of or just one compound record in this case. [Laughter]. This is called biphenyl. So we found what we were looking for, but nevertheless, the point is we have a separate interface for structures searching. It is not ideal. We realize that you have to go to one place to search by structure and another place to search by text and so on. So we made an attempt to combine these interfaces into one. So here is a step into the direction of improved search interfaces in PubChem . So we call it Beta because it is still beta. Anyway, in this interface you can search by chemical name or you can also search by similarity. So you can draw a structure right here and this saves you a little bit of time having to jump through different interfaces and so one. You can reuse the structure here and use the substructure search. However, we still are not so happy with interface, so currently we are working on another interface that would combine all collections into one where you don't have to choose compounds or bioassays or substances or what ever. You can just type your query and it will search both chemical names and annotations and molecular formulas, or if you happen to draw a structure or type in molecular formula, it should just work. So I don't have that for you just yet but this is something we are actively working on right now. I would encourage you to look for announcements sometime later this year. We will try to replace this PubChem Beta structured search. We will keep the Entrez interfaces available but perhaps they won't be used as much by our users since we should have a better way or easier way for people to search this information. If I have a little bit of time, there is just one more interface that I would like to show you. This is not used as much, but if people will discover it, they may realize how useful it is. This is PubChem classification browser. We have multiple classifications and ontologies that you can use to browse PubChem data. One of them is the MeSH tree and this is an ontology from here at NLM. So these are medical subject headings and if you take a look here we have almost 1,000,000 compounds that fall into this classification that we have classified under chemicals and drugs category. You can expand and take a look, for instance, organic chemicals. Here we have 11,000 compounds that are classified as aldehydes and we will click on this number and so it will retrieve for me all the chemical compounds that we have that have been classified as aldehydes using MeSH. Hopefully, this will load at some point. I will come back to it a little bit later. One other classification here that I would like to point out is PubChem , and in particular PubChem compounds TOC. This is PubChem Compound table of contents and what you can use this for is to find all the compound records that happen to have a particular section in their table of contents. For instance, if you want to find all the compounds that have safety and hazards information, it would be just 11,000 at this point. We are working at getting more, but here are some subsections that you can also find. So under safety and hazards, we have subsections for accidental release measures and here we have 7000 compounds that have that and you could take a look at their records. Unfortunately, this is taking a bit of time, but here we are. So all of these compounds happen to have this section about accidental release measures, so there is something known about them that they should not be accidentally released or might be dangerous to the environment or humans. I will open one and take a look. So here under safety and hazards, here is a compound that has a subsection accidental release measures. So while this interface is not particularly well integrated with the rest of our interfaces or homepage, we are working on changing that. But for the time being, it can be very useful and in quickly locating information you may be interested in. We will go back to my slides. So we just had the live demonstration and I talked about the content in PubChem and I talked about recently updated substance, bioassay and compound summary pages. Watch for announcements about our upcoming target summary pages . We then talked a little bit about searching and browsing PubChem. We may have to do a bit more in-depth installments about searching and browsing some other time. We are doing quite a bit of work in the area, so hopefully there will be more exciting things to report. Now for the acknowledgments . I would like to thank the PubChem team. All of the PubChem depostors, users and collaborators from without whom PubChem would not be possible. It would not be possible without funding provided by the US national Library of medicine. I would also like to thank Ben Busby and the NCBI webinar team for making this webinar possible and thank you all for joining us. Finally while we check if there are any questions, and I will remind everyone to stay up-to-date on us an email if you have any questions or feedback or suggestions. Thanks, Asta. That was an information dense presentation, which I am sure everyone on the line will be watching the video of over and over again as soon as we release it. I do have one question. What's the best way for people to stay up-to-date with PubChem announcements? Follow the PubChem blog also follow us on Facebook and Twitter and Google plus. Are there any other questions? There is one question. What are all the different chemical notations you can use to search? So let's go to the PubChem search interface here and under query hints we will hit structure and you can search of course by keyword and name, whatever, but under structure you can search with any integer that would be treated as PubChem CID. You can use a smile string and that is one of the chemical notations and you can also use an InChi from the structur search interface and that would work. If you want to search by molecular formula, that is possible as well. So I hope that answers the question. How would you batch download the CID and names and synonyms in the PubChem compound database? Yes. I haven't talked about this much because it is quite a bit of content to cover, but if you go to the PubChem homepage, we have a PubChem FTP site. If you go there, under compound, you can download just about anything and everything you would like. We also have programmatic access interfaces available. I haven't talked about them that much as well because of that would probably be about two or three or four hours of talking, but if you are interested in programmatic services, I would encourage you to take a look at Pug Rest documentation for PubChem and see what you can get there programmatically. So it depends on what you are looking for, whether it is FTP or you want to download everything and process data offline, or if you are just wanting one record at a time where you make a Restful call and you get your data that way. Thank you, Asta. Any other questions? Well, with that, we will end today's webinar. Have a great day, and watch NCBI news for announcements of other webinars. Thanks again. Goodbye.



PubChem consists of three dynamically growing primary databases. As of 1 November 2017:

  • Compounds, 93.9 million entries [2] (up from 54 million entries in Sept 2014), contains pure and characterized chemical compounds.[3]
  • Substances, 236 million entries[4] (up from 163 million entries in Sept 2014[5]), contains also mixtures, extracts, complexes and uncharacterized substances.
  • BioAssay, bioactivity results from 1.25 million[6] (up from 6000 in Sept 2014[7]) high-throughput screening programs with several million values.


Searching the databases is possible for a broad range of properties including chemical structure, name fragments, chemical formula, molecular weight, XLogP, and hydrogen bond donor and acceptor count.

PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments.

Each hit provides information about synonyms, chemical properties, chemical structure including SMILES and InChI strings, bioactivity, and links to structurally related compounds and other NCBI databases like PubMed.

In the text search form the database fields can be searched by adding the field name in square brackets to the search term. A numeric range is represented by two numbers separated by a colon. The search terms and field names are case-insensitive. Parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used.

Example (Lipinski's Rule of Five):

0:500[mw] 0:5[hbdc] 0:10[hbac] -5:5[logp]


PubChem was released in 2004.[8]

ACS's concerns

The American Chemical Society has raised concerns about the publicly supported PubChem database, since it appears to directly compete with their existing Chemical Abstracts Service.[9] They have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the society's revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress.

Soon after PubChem's creation, the American Chemical Society lobbied U.S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service.[10]

Database fields

Identification numbers
Identification number in current database [UID]
Substance identification number [SID]
Compound identification number [CID]
BioAssay identification number [BAID], [AID]

Any database field [ALL]
Comment [CMT]
Deposition date [DDAT], [DEPDAT]
Depositor's external ID [SRID], [SRCID]
Source name [SRC], [SRCNAM], [SRCNAME]
Source release date [SRD], [SRDAT], [RLSDAT]
Medical Subject Heading (MeSH) term [MSHT], [MESHT]
MeSH tree node [MSHN], [MESHTN]
MeSH pharmacological actions [PHMA], [PHARMA]

Substance properties
Substance synonyms [SYNO]
International Chemical Identifier (InChI) [INCHI]
Molecular weight [MW], [MWT], [MOLWT]
Chemical elements [ELMT], [EL]
Non-Hydrogen atoms [HAC], [HACNT]
Isotope count [IAC], [IACNT]
Total formal charge [TFC], [CHG], [CHRG]
Chiral atom count [ACC], [ACCNT]
Defined chiral atom count [ACDC], [ACDCNT]
Undefined chiral atom count [ACUC], [ACUCNT]
Hydrogen bond acceptor count [HBAC], [HBACNT]
Hydrogen bond donor count [HBDC], [HBDCNT]
Tautomer count [TC], [TCNT], [TTMC]
Rotatable bond count [RBC], [RBCNT]
XLogP[11] [XLGP], [LOGP]

Compound properties
Compound synonyms [CSYN], [CSYNO]
Component count [CC], [CCNT]
Covalent unit (molecule) count [CUC], [CUCNT]
Total bioactivity count [TAC]

See also


  1. ^ "PubChem Source Information". The PubChem Project. USA: National Center for Biotechnology Information. 
  2. ^ "Search Results for all compounds". Retrieved 28 January 2016. 
  3. ^ "all[filt] - PubChem Compound Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 7 January 2011. 
  4. ^ "all[filt] - PubChem Substance Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 28 January 2016. 
  5. ^ "all[filt] - PubChem Substance Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 7 January 2011. 
  6. ^ "all[filt] - PubChem BioAssay Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 28 January 2016. 
  7. ^ "all[filt] - PubChem BioAssay Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 7 January 2011. 
  8. ^ "About PubChem". Retrieved 3 May 2014. 
  9. ^ Kaiser J (May 2005). "Science resources. Chemists want NIH to curtail database". Science. 308 (5723): 774. doi:10.1126/science.308.5723.774a. PMID 15879180. 
  10. ^ "PubChem and the American Chemical Society". Reshaping Scholarly Communication. USA: University of California. 
  11. ^ Cheng T (Nov 2007). "Computation of octanol-water partition coefficients by guiding an additive model with knowledge". Journal of Chemical Information and Modeling. 47 (6): 2140–2148. doi:10.1021/ci700257y. PMID 17985865. 

External links

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