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Questions: synonyms and Greek chars

andrew brian clegg a.clegg at
Tue Jul 2 00:57:28 PDT 2002

Two quick questions -- I'm working from the MySQL version of the data but
I assume there's no significant difference from the flatfile or XML

If no-one has a clue what I'm on about I'll assume they're MySQL-specific
quirks and ask on go-database instead.

1. What's with all the gene products that have a synonym of 'gene' in the
gene_product_synonym table? Isn't this rather unhelpful? After all, any
particular gene symbol isn't synonymous with the word 'gene', and it adds
complications if you're, for example, searching the literature for all
occurrences of a gene product by any of its known names. Unless you filter
out all the 'gene' synonyms you'll get lots of false hits.

2a. I assume that html character codes such as &agr; and &bgr; etc. in the
gene products stand for Greek alpha, beta etc. characters, as in
'&agr;-Cat'. Where do these tokens come from -- are they an ISO standard
or something? Internet Explorer uses α for lowercase-alpha and
Α for uppercase.

2b. There are also lots of gene products that have the appropriate Greek
letter spelt out in full, as in 'alpha-catenin-related'. Is there any
standard for this? Is it because 'alpha-catenin-related' is conventionally
written as such in the literature whereas '&agr;-Cat' is usually written
with an actual alpha character, or is it just random?

Thanks folks,



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