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).