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Searching Biochemistry SF-hbz meeting 2010

Searching Biochemistry SF-hbz meeting 2010

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Searching Biochemistry SF-hbz meeting 2010

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  1. Searching Biochemistry SF-hbz meeting 2010

  2. Biochemistry is a cornerstone of the CAS databases • Dedicated 19 sections for Biochemistry • Almost 25,000 journal references in the biochemistry section from German universities in 2008-now • Published in over 2600 different journals • Indexing of biological species, thesaurus of taxa, CAS Registry numbers for biochemical compounds SciFinder is a trademark of the American Chemical Society

  3. Most common journals for German biochem research SciFinder is a trademark of the American Chemical Society

  4. Search example: Trisporic acids • Trisporic acids are a group of related compounds that are pheromones for fungi of the Mucorales species • In the terminology there is Trisporic acid A, B, C, D and E, sometimes in different enantiomers • Trisporic acids are a group of related compounds that are pheromones for fungi of the Mucorales species • In the terminology there is Trisporic acid A, B, C, D and E, sometimes in different enantiomers • There are some slight chemically different derivatives, esters, and hydrogenated compounds derived from trisporic acids SciFinder is a trademark of the American Chemical Society

  5. Let’s meet the team of Trisporic acids TSA-A TSA-B (trans) TSA-C TSA-D TSA-E (cis) SciFinder is a trademark of the American Chemical Society

  6. Some close derivatives of Trisporic acids Trisporol B Trisporin B Apotrisporin Trisporone Methyl trisporate B SciFinder is a trademark of the American Chemical Society

  7. How can these variations be searched by name? • SciFinder’s Substance Identifier Explore is designed to find one exact compound • If the substance name is not found as an exact match of the full name • The name is searched as natural name fragments • TRISPORATE doesn’t retrieve TETRAHYDROTRISPORATE • If that also doesn’t produce any results the name is searched as smallest chemically relevant fragments • TRISPOR will retrieve DEOXYTRISPORONE • When the search for name fragments retrieves more than 100 answers, SciFinder will only indicate there will be too many answers SciFinder is a trademark of the American Chemical Society

  8. Name searching example: exact match Only one answer is retrieved because there is a compound with that exact name This compound is indexed when the author doesn’t specify which variation is used SciFinder is a trademark of the American Chemical Society

  9. How could SciFinder search name fragments? We may miss compounds only indexed with a systematic name Retrieves 24 answers that has “trisporic” as a natural name fragment SciFinder is a trademark of the American Chemical Society

  10. The systematic approach by structure Retrieves 41 answers But not the unknown substance R1=H/O SciFinder is a trademark of the American Chemical Society

  11. Of which 24 are not retrieved in the name search Answers include several esters and stereoisomers without trivial names SciFinder is a trademark of the American Chemical Society

  12. Combining the results by name and structure SciFinder is a trademark of the American Chemical Society

  13. A broad answer set is obtained SciFinder is a trademark of the American Chemical Society

  14. This set produces 87 de-duplicated literature refs SciFinder is a trademark of the American Chemical Society

  15. The Categorize analysis on Organisms: SciFinder is a trademark of the American Chemical Society

  16. How would this compare to a similarity search? SciFinder is a trademark of the American Chemical Society

  17. A ranked list of similar compounds are found • The 41 substructure search answers are all included in the 75-99% similarity search result SciFinder is a trademark of the American Chemical Society

  18. Some fairly common compounds can be found uniquely in the similarity search result Total number of substances for the search with at least 75% similarity is 368 These lead to 650 de-duplicated references SciFinder is a trademark of the American Chemical Society

  19. The categorize on the similar compounds shows details of the organisms or the therapeutic areas SciFinder is a trademark of the American Chemical Society

  20. Searching for organism names Has 534 de-duplicated answers SciFinder is a trademark of the American Chemical Society

  21. Searching for organism names in REGISTRY SciFinder is a trademark of the American Chemical Society

  22. Comments on searching biological names • Narrower terms are not included in the research topic explore smart searching today • Full genus-species names are often indexed, but abbreviations also occur (B. Trispora) • Names of genes, clones, receptors, antagonists, etc. are often written in codes with special symbols (no standardization), e.g., 5-HT, 5-hydroxy-tryptophan, 5-HTP, serotonin receptor • Sequenced biological entities should be searched in Registry with name fragments • Patented sequences often only have SEQID codes and no biological descriptions SciFinder is a trademark of the American Chemical Society

  23. CAS has a project to look at biological entity searching • What is needed to attract biologists/biochemists • How often would a search by species and subspecies be needed? • How much control should be given to the user? • How could this be made most intuitive? • Should specific sequences from these biological entities be automatically searched? • How often would extremely broad families be searched (all vertebrates, all fungi)? SciFinder is a trademark of the American Chemical Society

  24. CAplus has a rich thesaurus for biological taxa which is used in the Categorize function, but not in the searching • Search all subspecies of Mucorales • Absidia • Absidia anomala • Actinomucor • Backusella • Blakeslea • Blakeslea trispora • Cunninghamella • Mucor • Rhizopus • Zygorhynchus SciFinder is a trademark of the American Chemical Society

  25. Focus on Biochemistry Questions? Comments?