Depth-First: Tag database

Yet Another Free Chemistry Database: Pherobase

Rich Apodaca — Tue, 15 Apr 2008 18:56:00 -0400

The creation of free chemical databases continues unabated. Today's entry is Pherobase, a service dedicated to documenting the relationship between chemical structures and the insect world.

Users can search Pherobase by text, or browse a large number of precompiled categories: alphabetical by genus; alphabetical by species; and compounds by genus or species. Each compound data sheet contains a wealth of data, all linked to the primary literature: mass spectrum; nmr; synthesis; and behavioral function. There's even an interactive Jmol model for each entry.

Pherobase is clearly designed to be useful to farmers and others involved in agriculture who are interested in using pheromones in pest control. Are insects eating your olive tree? Let pherobase help. Need help with fire ants? Pherobase can help there, too. Wonder what else besides Gypsy Moths might be affected by disparlure? Pherobase has the answer. And nearly all of this information is backed by references to the primary literature.

Pherobase clearly demonstrates the value of building comprehensive, focused chemical databases around a limited subject of high practical utility. After all, chemistry's most enduring contribution is in the production of useful properties, not the production of compounds.

Pherobase is also noteworthy for the way it's being used by its creator, Ashraf El-Sayed. Rather than standing on its own, Pherobase is designed to direct users to suppliers of pheromones and related pest control products by educating them about what might be possible. In this sense, Pherobase's approach offers another intriguing example of an Open Access business model that can actually work.

The Fundamental Cheminformatics Toolset

Rich Apodaca — Tue, 08 Jan 2008 09:37:00 -0500

Reference: W.J. Howe and T.R. Hogadone, J. Chem. Inf. Model.

Imagine you need to create a cheminformatics system that's useful to chemists in their daily work. What tools would you absolutely need, regardless of the specific system you're building?

The answer to this question is hardly academic. If you're looking for ways to disproportionately improve the state of cheminformatics, improving the performance of one or more of its fundamental tools would seem to be a logical path.

Here, in no particular order, are my picks for the five fundamental cheminformatics tools:

2D Structure Editor. Ubiquitous yet mostly-ignored, the 2D structure editor is the last mile connecting cheminformaticians with laboratory chemists. Take away the structure editor for data entry and building queries, and most cheminformatics systems become useless to the average chemist.
2D Structure Renderer. Chemists expect their cheminformatics systems to communicate with them the way that other chemists do - through 2D chemical structures. Rendering software makes this possible. Like the 2D structure editor, structure renderers are a widely-ignored yet critical link between producers and consumers of cheminformatics software. Although the 2D renderer and editor need not necessarily be related, the two technologies are so similar that most 2D editors are based on a related 2D rendering engine.
Structure Query System. The purpose of the vast majority of cheminformatics systems is to produce a set of chemical structure results based on a structure query. The structure query system makes this possible. As the datasets that chemists deal with become ever larger, the ability to specify query structures at a high level of detail, and retrieve the results efficiently, becomes increasingly important. This is an area ripe for big improvements.
Low-Level Cheminformatics Toolkit. Most cheminformatics systems involve one or more elements specific to their problem domain. For example, predictive tools may use molecular descriptors. A robust and versatile low-level cheminformatics toolkit makes it possible to build problem-specific cheminformatics libraries. This toolkit may or may not be used in the 2D structure editor and renderer, depending on whether an adequate text-based molecular language is available (see below).
Text-Based Molecular Language. Cheminformatics systems are frequently built from components developed independently by multiple groups. These systems may be developed in different programming languages, may even run on different operating systems, and may need to communicate over a network connection. A well-specified, open, text-based molecular language makes it possible for these systems to interoperate. Two widely-used examples include MDL's molfile format and Daylight's SMILES, both of which have significant limitations.

One of the reasons I consider this set of cheminformatics tools in particular to be fundamental is the perennial need to use and improve them. Elements of each of these tools can be seen, for example, in the COUSIN system developed by Howe and Hogadone at Upjohn over 25 years ago. Comparison of this system with PubChem shows just how little the basic problems change, despite major changes in underlying technology.

What are your fundamental cheminformatics tools and which of them are you working to improve?

Yet Another Free Chemistry Database: Heterocycles Web Edition

Rich Apodaca — Fri, 06 Jul 2007 09:57:00 -0400

Yet another free chemistry database comes in the form of a service run by the journal Heterocycles. The Heterocycles Web Edition offers two ways to search for heterocylic ring systems: by structure or by synthesis.

You may assume that these services would only search the contents of Heterocycles. It would then be a pleasant surprise to find a number of highly-regarded journals being covered. Here are some of titles:

Angew. Chem. Int. Ed. Engl.
Chem. Eur. J.
Eur. J. Org. Chem.
Heterocycles
J. Am. Chem. Soc.
J. Med. Chem.
J. Nat. Prod.
J. Org. Chem.
Org. Lett.
Synlett
Tetrahedron
Tetrahedron Lett.

The current query interface supports text only, although a number of important criteria can be used. I haven't searched for many heterocyles, but my results for indolizidine give a flavor for what you might expect (the actual number of hits was 115):

It would be interesting to know how Heterocycles populated its database. Is it text-mining, manual curation, both, or something else? Regardless of how it's done, Heterocycles Web Edition is definitely worth looking at.

Yet Another Free Chemical Database: Reaction Searching with CMLD-BU

Rich Apodaca — Mon, 18 Jun 2007 09:08:00 -0400

As chemical informatics continues its climb out of a decades-long stagnation, the number of free chemical databases continues to grow. But despite all the activity, reaction databases are notably under-represented. For this reason, I was delighted to stumble onto Boston University's Center for Chemical Methodology and Library Development Reaction Database (CMLD-BU).

According to their website, CMLD-BU:

...is a new center funded by the National Institute of General Medical Sciences ( NIGMS ) focused on the discovery of new methodologies to produce novel chemical libraries of unprecedented complexity for biological screening. The goal of the CMLD-BU is to explore and expand the diversity of small-molecule libraries by creating general, useful protocols for stereocontrolled synthesis. ... A major objective of the CMLD-BU is also to provide information and chemistry protocols to the public on parallel and chemical library synthesis. ...

Use this link to begin exploring their service. To date the CMLD-BU has deposited just over 1,600 Substances with PubChem and their site shows 125 reaction protocols.

Although CMLD-BU's user interface could use some tweaking, their content is right on the money: real examples of preparative reactions with links to the primary literature and even spectral data.

Are we at the end of this process or at the beginning? Only time will tell. But the nearly infinite shelflife and ubiquity of chemical information coupled with the inexorable approach of virtually zero-cost computer services leaves only one of those two possibilities worthy of serious consideration.

Free Chemistry Databases on the Web: Creating a Comprehensive Guide

Rich Apodaca — Mon, 07 May 2007 09:32:00 -0400

One of Depth-First's more popular articles is a summary of free databases titled Thirty-Two Free Chemistry Databases. Clearly there is a need to link the producers of free chemical databases (developers) with the potential users of these services (chemists). Chemistry is slowly emerging from a decades-long period of over-reliance on a single supplier of information. As new players enter, they'll need some way to have their message heard.

The Problem

As evidence of this need, I'm getting more requests to list additional services on the Thirty-Two Databases article - or to provide an updated review of a service already there. This is wonderful!

One approach would be for me to simply research and write an updated article reviewing the new additions myself. The problem is that thirty-two is already a very large number to deal with. My guess is that there must now be well over sixty or seventy free chemistry databases. That's far too many for one person to research properly on their own.

On the other hand, the Web is all about collaboration, so why no try to use it that way?

An Idea

Here's the idea: if you run a free database or other online chemistry service and would like to promote it, post a comment to this article containing a link and brief description of what makes your service different/useful. If you've used a free chemistry database, feel free to provide your thoughts on it. If there's a free database you wish existed but doesn't yet, feel free to write about that. Unlike the other articles on this site for which comments are closed after two weeks, this article's comments will remain open indefinitely.

After some period of time, I'll use these comments to write a new article highlighting the new material.

Notice the use of the word "free". A free database can be used by any member of the general public without fees or a lengthy registration process. This includes both free speech and free beer services. There are more restrictive definitions that could be applied, but let's not worry about those just yet. Free beer is better than no beer at all.

Links can either be in HTML or Markdown. Here's one example of each:

<a href="http://megamolecules.com">MegaMolecules</a> (HTML)

[MegaMolecules](http://megamolecules.com) (Markdown)

The Outcome

I have no idea what kind of response this experiment will generate. But if past experience is any guide, large numbers of chemists are keenly interested in free chemistry databases. All they need is a link.

Image Credit: Kate and Dave Hugh

Roll Your Own Chemical Database With Free Components

Rich Apodaca — Fri, 13 Apr 2007 10:27:00 -0400

Are you thinking of building a free chemical database but would rather not rent and maintain a bunch of proprietary software components? Norbert Haider has thought a lot about this problem and offers some helpful resources to get you started:

Creating a web-based, searchable molecular structure database using free software Step-by step case study
How to create a web-based molecular structure database with free software A presentation
checkmol/matchmol Open source command-line utility for 2D (sub)structure matching
mol2ps Command-line utility for converting molfiles into Postscript files

Haider's system can be deployed on commodity hardware running open source operating systems. In other words, the cost of setting up a system like the one he describes is practically zero.

Creating and open sourcing your own custom components is one way to go. Building on top of existing open source tools like CDK, Open Babel, Octet and JOELib is another.

Haider's work raises an interesting question. Has anyone assembled a complete, ready to install general purpose chemical database package built from open source components? It for no other reason, such an exercise would give an excellent idea of what the dogfood tastes like.

Thirty-Two Free Chemistry Databases

Rich Apodaca — Wed, 24 Jan 2007 02:32:00 -0500

Chemical information is in the early stages of a revolution. Long dominated by a handful of established players, the field has rather suddenly opened up to a variety of innovative newcomers. The Internet now offers a diverse array of free online chemistry databases, twelve of which were summarized in a recent article. This list has since been updated with new information and new entries. The following (incomplete) list summarizes some of the possibilities available for your next search.

PubChem- The granddaddy of all free chemistry databases. Search over 8 million compounds by a variety of criteria. Although some PubChem records are linked into the primary literature through MeSH, most are not. But this doesn't seem to be PubChem's true calling. Instead, PubChem may well evolve into the world's largest online collection of molecular data sheets. Increasingly, the other databases in this list are cross-referencing their entries into PubChem. PubChem's entire database can be downloaded by FTP. CAS Registry are correct to see PubChem as the first real competition they've had in decades.
ZINC- A free database of commercially-available compounds for virtual screening. Search over 4.6 million compounds by structure, IUPAC name, InChI, and a host of calculated properties. For noncommercial purposes, the ZINC database may be downloaded in whole or in part for local use.
eMolecules- Google for molecules. With a simple interface and super fast search engine, eMolecules augments PubChem with other information sources, including specialty chemical catalogs. Although eMolecules' emphasis seems to be on commercially-available compounds, it's only possible to get a link directly into a supplier's online catalog for a limited number of molecules. Most of the links are to PubChem records. For this reason, I don't find eMolecules very useful in its current form. If you remember something called "Chmoogle", this is the same service (moral: don't mess with Google).
CHEBI- "A freely available dictionary of molecular entities focused on ‘small’ chemical compounds." CHEBI draws its information from two main sources: Integrated Relational Enzyme Database of the EBI and the Kyoto Encyclopedia of Genes and Genomes. Find out what proteins a molecule has been associated with and in what context. Provides cross-links to CAS registry numbers, Beilstein registry numbers, and Gmelin registry numbers.
NIST Chemistry WebBook- Physical data (thermochemical, thermophysical, and ion energetics) for mostly organic compounds. Search by formula, structure, CAS number, and IUPAC name.
BioCyc- A collection of about 3,500 compounds involved as enzyme substrates, products, inhibitors, and activators. On accepting a license agreement, the entire database can be freely downloaded in Chemical Markup Language format.
ChemExper- Find a supplier for your specialty chemical needs. Search by structure, name, molecular formula, and CAS number. After finding you compound, get an offer from one or more suppliers. I can't vouch for how this works in practice, but it sounds like a good idea.
Compendium of Pesticide Common Names- More than 1,100 commonly-used pesticides. Compounds are located by browsing indexed lists (IUPAC name, CAS number, and trade name) rather than searching. Each entry lists, among other pieces of information, a chemical structure and sub-classifications (repellents, antifeedants, synergists, etc.).
NMRShiftDB- Organic structures and their nuclear magnetic resonance (nmr) chemical shifts. NMRShiftDB contains chemical shift data for over 22,000 organic compounds and 19,000 spectra. Records can be searched by structure, chemical shift and nucleus. NMRShiftDB is truly open; it can be accessed programmatically and the source code for the software that runs the online database can be freely downloaded. Individual users can submit their own spectral shifts for peer review and subsequent inclusion.
Chemical Structure Lookup Service (CSLS)- An address book for chemical structures. If you've ever used Metacrawler, then you'll recognize the idea behind SCLS, which is to aggregate several free chemistry databases. Search over 27 million molecules by IUPAC name, InChI, structure, SMILES, and a variety of molecular identifiers. Your results set will contain links into specific databases that host the molecules you find. The user interface isn't just unfriendly - it's downright antisocial. But if you can get past this, CSLS may well be one of the most useful services in this list.
DrugBank- Combines detailed drug data with comprehensive drug target information. Search over 4,300 drugs by trade name, SMILES, and InChI. Each record contains information on target of action, therapeutic indication, medications the drug is an ingredient of, and trade names. Searches can be limited to only approved drugs or experimental drugs. Both the concept and interface to this service are well thought-out. Note: this service was unavailable as of Jan 19, 2007
Wikipedia- Wikipedia? Yes, Wikipedia. Wikipedia offers several kinds of chemical information produced by a knowledgeable, all-volunteer army. Looking for information on organic compounds? Consider this datasheet on morphine as an example. For those interested in synthesis, Wikipedia is increasingly being used to collaboratively author short reviews on the topic. Search capabilities are currently limited to text and don't appear to work with IUPAC names or CAS numbers. Where this quintessential disruptive technology and its offspring end up taking chemical publishing is unclear, but the ride will be spectacular.
ChemDB- A chemical database is but one of the services offered by this site. Search over 4.1 million compounds by structure, or various calculated properties. ChemDB also offers a variety of free online cheminformatics tools such as Babel file format conversion, SMILES depict, and molecular property calculation. Read more about ChemDB in this Bioinformatics paper.
ChemBank- Structure search over 36,000 original biological assays of small molecules collected by Harvard's Institute of Chemistry and Cell Biology (ICCB). Many of the data contained in ChemBank have never been published, making this database particularly valuable.
National Institute of Allergy and Infectious Diseases Database- Structure search hundreds of thousands of screening datapoints collected by the NIAID in its HIV, Opportunistic Infection, and TB programs.
National Toxicology Program- Seach by name for compounds listed in the NTP database. Returns detailed internal reports and links to the primary literature.
NIST Chemical Kinetics Database- Search by reagent or product name or formula for gas phase rate constants collected from the primary literature.
Computational Chemstry Comparison and Benchmark Database- Search by formula for over 600 gas phase atom and molecule physical chemistry data obtained experimentally and by computation.
IUPAC-NIST Solubility Data Series- Search by name or CAS number through over 67,000 solubility measurements. Data were comprehensively compiled from over 1,800 references in primary literature.
SOLV-DB- Search over 200 common solvents by name, CAS number, or chemical formula physical. Available data include boiling point, water solubility, viscosity, octanol-water partition constant, flash point, and a variety of other properties.
NIMH Pyschoactive Drug Screening Program K_i Database- Search over 44,000 K_i determinations culled from the literature. Although this database appears to have no structure search capability, this is listed as a "Future Enhancement". This is a perfect example of a very useful service that could do with a major user interface redesign. There also appears to be another (defunct) service by the same name, but a different URL.
Kyoto Encyclopedia of Genes and Genomes (KEGG)- A Japanese counterpart to PubChem/PubMed. One of the most interesting services on this list, KEGG consists of four interconnected databases: KEGG Pathway; KEGG genes; KEGG Brite; and KEGG Ligand. KEGG Ligand contains over 14,000 compounds searchable by name, and crosslinked to over 45,000 biological pathways. The KEGG Ligand database can be searched by structure through KegDraw, a 2-D structure editor written in Java. With some minor configuration on my Linux system, I was able to perform some basic substructure searches using KegDraw. Your mileage may vary. A nice overview of KEGG is available in a recent article. The contents of KEGG can be downloaded by anonymous ftp for academic use.
BRENDA- Search over 40,000 structures as substrates, products, cofactors, or inhibitors for enzymes. Although my search was able to find compounds by substructure, I was not able to view any links to the results. Your mileage may vary.
Biochemical Pathways Database- Structure search over 1,100 small molecules as participants in biochemical pathways. A potentially useful service, but currently too slow to fully evaluate. A structure search for naphthalene hung for five minutes before I terminated it without success.
ChemMine- Search by structure for compounds collected from a variety of open databases. View assay results in annotated biological experiments. I find the layout and organization of this service annoyingly confusing, but the underlying information appears to be useful nevertheless. Behind the scenes, ChemMine uses two open source cheminformatics libraries: Open Babel and JOELib. For a more detailed view of ChemMine, see the recent article.
Organic Syntheses- Search by structure through the entire contents of synthetic organic chemistry's flagship resource. Substructure search requires Chime, so if you run Linux, or for some other reason can't install the plugin, you'll be out of luck.
WebReactions- Structure search organic reactions in four databases containing a total of over 391,000 reactions. Each reaction hit is linked to the primary literature through a bibliographical reference. Although the interface takes some getting used to, WebReactions may make a worthy companion to the traditional SciFinder search.
Spectral Database for Organic Compounds (SDBS)- Search by name, molecular formula, molecular weight range, or CAS number through over 14,000 full ¹H NMR spectra, 12,000 full ¹³C spectra, and 50,000 full FT-IR spectra collected from over 32,000 compounds.
BindingDB- Structure search over 24,000 K_i and IC₅₀ measurements from over 10,000 molecules. Data is collected from, and cross-referenced to, the primary literature. I was unable to determine how to submit a substructure search through the Marvin applet on my Linux system (there is no "Search" button, for example). A text search for "naphthalene", for example, showed some impressive potential for this database. Anyone can currently contribute to BindingDB, one of the few databases on this list to have such a policy.
PDBBind- Browse over 2,700 complexes of small molecules ligands with proteins found in the Protein Databank. Structure searching requires a license. 3-D rendering comes courtesy of the ever-popular Jmol applet.
AffinDB- Search affinity data for complexes found in the Protein Databank. Affinity data are cross-linked to the primary literature through PubMed. Small molecule searching is limited to IUPAC names provided in a pull-down menu. By registering, users can upload affinity data themselves. AffinDB is just one example of what might be possible as chemistry databases begin to combine multiple sources of data into easy-to-use packages.
ChemRefer- It doesn't get any simpler. Type in your keywords and get links to the matching full-text PDFs from the primary literature. As mentioned before, the legality of some of ChemRefer's holdings, for example its articles from ACS journals, is not clear. But as more chemistry journals go Open Access, look to services like ChemRefer to play an increasing role in the way scientists navigate the primary literature.