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Confusing Search Results in the NPC Browser

16 Jun

For the past few days I have been in Prague at the PharmSciFair meeting. Beautiful city (with a little too much graffiti on the glorious architecture), good meeting and way too long a flight. I am traveling alone and despite the networking the disrupted sleep patterns have me working on various projects as I struggle to get more than 4 hours of sleep a night. The joys of sleep deprivation include productivity! After a break from looking at the NPC Browser and my earlier commentaries I did an update of the browser when I restarted it last night as Sean’s Collabchem blog has been keeping me updated on new changes.  Sean had informed me in two separate posts (X, Y) about the new disclaimer that states:

We are very much aware of a number of issues with the database and software. Please bear with us as we work meticulously to resolve them. Below are some of the specific issues we are addressing in the next update (which is likely to be version 1.1.0) of the software in a couple of weeks:

  • A new database release that incorporates a number of improvements to compound records (e.g., stereochemistry annotations, 2D layout, etc.).
  • There exists an indicator associated with each compound record to notify whether the record has or has not been manually curated. If the record has been curated, curators are acknowledged with proper attribution. .
  • A simple curation mechanism is integrated with each compound record so as to facilitate error reporting at finer resolutions (e.g., on an attribute basis).
  • Access to all curated records can be done through a single filter mechanism.
  • About ~2,000 QC LC/MS spectra are available for the “NPC screening” subset, courtesy of NCGC’s Bill Leister and the Analytical Chemistry group.
  • Other minor bug fixes and enhancements.

I started to poke around looking for the new features and discuss some below. Some definite moves in the right direction! Like it. I’ll comment on them in a separate post.

As I played more with the system and tried some new searches I started to get very concerned with the results I received. For example, a search on Taxol gives TWO answers. One is Taxol and the other is Ixabepilone, see below. This is weird. They are NOT the same structure at all so why would a search on one compound name bring back a separate “drug” which is really what the browser is supposed to provide us access to. The original paper reports “the creation of a definitive, complete, and non-redundant list of all approved molecular entities”. Certainly the two compounds are non-redundant (compare Taxol, and Ixabepilone). My first thought is that the search is looking for associated information that has been attached to the compound somehow. I found it under the therapeutic tab where it says…”Like taxol, Ixabepilone binds to the αβ-tubulin heterodimer subunit.” If it’s that subtle that will likely give rise to some very interesting challenges (see below). That will mean that I might search for a drug and ANY mention of that drug will retrieve hits. I expect that most people would expect to retrieve the drug itself, not all mentions ever of that drug. Maybe I’m wrong.

 

To take this to an extreme lets search for “Manganese” and see what we get in the NPC Browser…for one we see elemental manganese as the “compound” but associated with the label for the ionic form.

but also a LOT of organic compounds….one shown below. This is not an inherently obvious result but maybe exactly as its expected to be.

Of the 17 compounds retrieved with a search on Manganese only 5 actually have manganese in the formula. Do you find these results confusing? I would expect a Synonym only search would occur to retrieve just Mn++ (and maybe Mn if that is distinguished from Mn++ as a drug).

 

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.

2 Responses to Confusing Search Results in the NPC Browser

  1. Sean Ekins

    June 16, 2011 at 2:39 pm

    I randomly selected the following to search on yesterday and returned more than one structure.
    fenfluramine – 3 molecules returned
    verapamil – 4 differenrt structures returned
    perindopril 2 different cpds returnded

    Are we missing something in order to just pull back one compound when you put that name in?

     
    • Antony Williams, ChemConnector

      June 16, 2011 at 2:44 pm

      Sean…there are some times when I am typing a simple name and pulling back a couple of dozen structures. Maybe I am too “ChemSpider” in my expectations…I expect to type in a name and get one structure back. By the way…it doesn’t always work that way in ChemSpider either!!! But we generally get the same connection table with different stereo and then we curate…

       

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