When using the word option, does pubchem limit the number of results to a specific number like 10,000 for example. I have seen some other systems limit results unless being accessed from a verified user with a token or some key for verification that they are not a robot.

Is there a way to get images for a list of chemicals submitted or would they need to be submitted as separate individual searches? I notice a quick way to do this would be as shown below in the spreadsheet, but that looks like it is submitted as separate searches.

Im curious as to what type of database all of this is run by with so many different queries and data sets available? I would think that since its relational data that a database with those features would be needed, such as MySQL, Oracle or Microsoft SQL Maybe? My second question is would this all run on cloud servers or traditional style servers? The deeper we get into these modules, the more I am just amazed at the abilities that PubChem has.

Andrew

Im curious as to what individual pieces of the search happen synchronously as described in the term "fast"? Is this referring to something like multiple returns being processed similarily instead of one at a time based on a query result?

Andrew

Is this service mostly limited to an output in XML? I notice some services offered an output for ASN.1, SDF, CSV, etc, but can this be extended to all services with the possibility of a particular format or is XML the limit.

The reason i ask is that a lot of data can quickly cause excessively large files when put into XML vs something like a CSV if it only needs to contain one type of result.

Andrew

This is a really good site and I am glad it was mentioned. I use this site a lot because I am not a programmer but I often have research meetings with people who do lots of programming and it quickly lets me learn the basics of what they do.

Andrew

The PubChem BioAssay Classification Tree is really an amazing feature. Within a few minutes I was able to go through the classification of bacteria to a species I use to work with in microbiology, combine the sources with a few keywords and find the exact AID needed to run confirmation tests. This being coupled to the Pubmed side on the publication is a great feature for scientists to have access to.

This article was cited in the OLCC Cheminformatics Class Module 6 for atom-centered Gaussian-shape comparison method. I will see if i can access the full article from campus tomorrow, but its very difficult for me to understand how causing a gaussian adaptation to a molecule would help to provide information about the degree of chirality on certain molecules. for example, it would be difficult to understand the shape of a miniature model sailboat inside of a glass bottle if the only shape you see is the outer bottle and not whats contained inside.

Andrew

I assume that the ROCS description here that talks about volume overlays is what is mentioned on the olcc module 6 page about finding the best alignmentfor a 3D structure overlay. it seems that through the gaussian blur around the chemical being matched against others that many of the individual bonds would not be compared in the matching process.

Andrew

I am pretty familiar with the software that CAMEO Chemicals puts out that we use in emergency response but had no idea they also provided data to services like PubChem.

Andrew

Can this service be accessed by other methods instead of using the form?

Andrew

There are quite a few safer alternatives in this list, but none are listed on the PubCHem page under the EPA Safer Choice Label for Use and Manufacturing on the PubChem Classification Browser which links itself to this page.

Andrew

This says that an input list can be provided by a file. What types of files would work? CSV, XML, etc? Also is there a limit to how many identifiers can be in a single exchange?

This is very interesting that based on the marketing or how a company classifies their product, they can have different rules to follow when regardless the product is intended to be consumed.

This is a really great feature. With all data, I believe things should be preserved even as new things replace the old.

Andrew

I am really glad that this source was used in the write-up. Im not sure why I was so unfamiliar with some of the things that this resource provides given all of the articles i have read from TOXNET, but I will be using it more in the future.

Andrew

If i were a chemical supply vender and wanted to update the SDS sheets for important information updates, would this be recommended as the first place to perform a search? It seems like a perfect source, but with a lot of entries in SDS sheets, they may state that something is a possible carcinogin for example. Its not really clear to me if TOXNET includes possible hazards or only the ones that have been confirmed through scientific means.

Andrew

Over the years, we have seen some of the errors mentioned when pulling data sets and using APIs, especially when we would use database entries as the basis to perform conversions. The most difficult involved either, identifiers that had multiple possibilities or through use of a chemicals common name which had a lot of varyance in different databases.

Andrew

I know that PubChem houses a lot of data and also pulls data from many other sources. Due to this, would the 235 million deposited chemical structures mean that it holds that many in its own database or is that number a sum of entries held in many separate databases?

Andrew

I find it really fascinating that the NIST Webbook has versions that go back to 1996 for their database. Do they offer direct access to this database or would bulk data only be acquired through their product services or web scraping?

Andrew

I was unaware that this was very common. Its easy to wrap my head around secondary databases pulling from primary or even from other secondary sources, but I wonder if pulling secondary into primary would then make it primary data based on the way it may be used in the new database. Maybe the data exchange and integration mentioned in the following sentence causes a new way to directly use data in a primary way.

Andrew

How do you become a data contributor if you have things you would like to put into PubChem?

Surely, this would be a fairly simple process with millions of data sets already put into the system.

Andrew

Its seems just a matter of time before all of the online sources for spectra offer APIs, possibly including predictive spectra. I wonder how much of a load these types of things put on a server to request.

Although compression is nice for saving space, would the compression limit the ability to search spectral databases if reading compressed files makes things more complicated. when a lot of files need to be accessed in a single search, such as through an API or user interface search i would think this may take longer.

Would storing images in a database as a blob cause poor performance. This seems like a lot for a single entry. I would think storing a link to the image in the database would reduce the entry size.

One of the big drawbacks that I often hear when using XML with databasing is that it quickly starts making very large files in terms of storage. Would the same hold true for using CML with large chemical databases? If so, what size reduction could be expected for the same size collection of chemicals stored using connection tables?

Will a future release version of InChI include a layer to include inorganic molecules that can be standardized? I have come across things in the past saying that it really only works efficiently for organic molecules. I have the understanding that some inorganic things have been included, but not the more complex structures.

This is very similar to how I use to protect passwords on my server before SSH keys became the standard. We used similar protocols under the MD5 standard so its very interesting to see the same thing used to make something easier to find with search engines as it was to keep something from being found when used as a security measure.

What process or services would be needed for the databases to perform this interchange?

How would an aromatic bond be represented if needed to be used to bypass the multiple configuration possibilities?

This would be a very good project if all of the 3D data for the different conformations were all indexed and compared based on the influence type and how it changed a molecules shape.

Its very interesting that breaking apart a structure into fragments, performing a search and then rebuilding the structure as part of a screening process with a complex search would be more accurate than just using a connection table to compare each atom.