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Searching Biochemistry SF-hbz meeting 2010. 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

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searching biochemistry sf hbz meeting 2010
Searching Biochemistry

SF-hbz meeting 2010

biochemistry is a cornerstone of the cas databases
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

most common journals for german biochem research
Most common journals for German biochem research

SciFinder is a trademark of the American Chemical Society

search example trisporic acids
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

let s meet the team of trisporic acids
Let’s meet the team of Trisporic acids

TSA-A

TSA-B (trans)

TSA-C

TSA-D

TSA-E (cis)

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some close derivatives of trisporic acids
Some close derivatives of Trisporic acids

Trisporol B

Trisporin B

Apotrisporin

Trisporone

Methyl trisporate B

SciFinder is a trademark of the American Chemical Society

how can these variations be searched by name
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

name searching example exact match
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

how could scifinder search name fragments
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

the systematic approach by structure
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

of which 24 are not retrieved in the name search
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

combining the results by name and structure
Combining the results by name and structure

SciFinder is a trademark of the American Chemical Society

a broad answer set is obtained
A broad answer set is obtained

SciFinder is a trademark of the American Chemical Society

this set produces 87 de duplicated literature refs
This set produces 87 de-duplicated literature refs

SciFinder is a trademark of the American Chemical Society

the categorize analysis on organisms
The Categorize analysis on Organisms:

SciFinder is a trademark of the American Chemical Society

how would this compare to a similarity search
How would this compare to a similarity search?

SciFinder is a trademark of the American Chemical Society

a ranked list of similar compounds are found
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

some fairly common compounds can be found uniquely in the similarity search result
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

the categorize on the similar compounds shows details of the organisms or the therapeutic areas
The categorize on the similar compounds shows details of the organisms or the therapeutic areas

SciFinder is a trademark of the American Chemical Society

searching for organism names
Searching for organism names

Has 534 de-duplicated answers

SciFinder is a trademark of the American Chemical Society

searching for organism names in registry
Searching for organism names in REGISTRY

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comments on searching biological names
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

cas has a project to look at biological entity searching
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

slide24
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

focus on biochemistry

Focus on Biochemistry

Questions?

Comments?