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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 l.jpg

Searching Biochemistry

SF-hbz meeting 2010


Biochemistry is a cornerstone of the cas databases l.jpg
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 l.jpg
Most common journals for German biochem research

SciFinder is a trademark of the American Chemical Society


Search example trisporic acids l.jpg
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 l.jpg
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


Some close derivatives of trisporic acids l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
Combining the results by name and structure

SciFinder is a trademark of the American Chemical Society


A broad answer set is obtained l.jpg
A broad answer set is obtained

SciFinder is a trademark of the American Chemical Society


This set produces 87 de duplicated literature refs l.jpg
This set produces 87 de-duplicated literature refs

SciFinder is a trademark of the American Chemical Society


The categorize analysis on organisms l.jpg
The Categorize analysis on Organisms:

SciFinder is a trademark of the American Chemical Society


How would this compare to a similarity search l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
Searching for organism names organisms or the therapeutic areas

Has 534 de-duplicated answers

SciFinder is a trademark of the American Chemical Society


Searching for organism names in registry l.jpg
Searching for organism names in REGISTRY organisms or the therapeutic areas

SciFinder is a trademark of the American Chemical Society


Comments on searching biological names l.jpg
Comments on searching biological names organisms or the therapeutic areas

  • 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 l.jpg
CAS has a project to look at biological entity searching organisms or the therapeutic areas

  • 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 l.jpg
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 l.jpg

Focus on Biochemistry used in the Categorize function, but not in the searching

Questions?

Comments?


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