Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals by Joseph A. Rothwell, Mireia Urpi-Sarda, Maria Boto-Ordoñez, Craig Knox, Rafael Llorach, Roman Eisner, Joseph Cruz, Vanessa Neveu, David Wishart, Claudine Manach, Cristina Andres-Lacueva, and Augustin Scalbert.
Abstract:
Phenol-Explorer, launched in 2009, is the only comprehensive web-based database on the content in foods of polyphenols, a major class of food bioactives that receive considerable attention due to their role in the prevention of diseases. Polyphenols are rarely absorbed and excreted in their ingested forms, but extensively metabolized in the body, and until now, no database has allowed the recall of identities and concentrations of polyphenol metabolites in biofluids after the consumption of polyphenol-rich sources. Knowledge of these metabolites is essential in the planning of experiments whose aim is to elucidate the effects of polyphenols on health. Release 2.0 is the first major update of the database, allowing the rapid retrieval of data on the biotransformations and pharmacokinetics of dietary polyphenols. Data on 375 polyphenol metabolites identified in urine and plasma were collected from 236 peer-reviewed publications on polyphenol metabolism in humans and experimental animals and added to the database by means of an extended relational design. Pharmacokinetic parameters have been collected and can be retrieved in both tabular and graphical form. The web interface has been enhanced and now allows the filtering of information according to various criteria. Phenol-Explorer 2.0, which will be periodically updated, should prove to be an even more useful and capable resource for polyphenol scientists because bioactivities and health effects of polyphenols are dependent on the nature and concentrations of metabolites reaching the target tissues. The Phenol-Explorer database is publicly available and can be found online at http://www.phenol-explorer.eu.
I wanted to call your attention to Table 1: Search Strategy and Terms, step 4 which reads:
Polyphenol* or flavan* or flavon*or anthocyan* or isoflav* or phytoestrogen* or phyto-estrogen* or lignin* or stilbene* or chalcon* or phenolic acid* or ellagic* or coumarin* or hydroxycinnamic* or quercetin* or kaempferol* or rutin* or apigenin* or luteolin* or catechin* or epicatechin* or gallocatechin* or epigallocatechin* or procyanidin* or hesperetin* or naringenin* or cyanidin* or malvidin* or petunid* or peonid*or daidz* or genist* or glycit* or equol* or gallic* or vanillic* or chlorogenic* or tyrosol* or hydoxytyrosol* or resveratrol* or viniferin*
Which of these terms are synonyms for “tyrosol?”
No peeking!
Wikipedia (a generalist source), lists five (5) names, including tyrosol, and 5 different identifiers.
Common Chemistry, which you can access by the CAS number, has twenty-one (21) synonyms.
Ready?
Would you believe 0?
See for yourself: Wikipedia Tyrosol; Common Chemistry – CAS 501-94-0.
Another question: In one week (or even tomorrow), how much of the query in step 4 will you remember?
Some obvious comments:
- The creators of Pehno-Explorer 2.0 have done a great service to the community by curating this data resource.
- Creating comprehensive queries is a creative enterprise and not easy to duplicate.
Perhaps less obvious comments:
- The terms in the query have synonyms, which is no great surprise.
- If the terms were represented as topics in a topic map, synonyms could be captured for those terms.
- Capturing of synonyms for terms would support expansion or contraction of search queries.
- Capturing terms (and their synonyms) in a topic map, would permit merging of terms/synonyms from other researchers.
Final question: Have you thought about using topic maps as search templates?