Resources To Batch Map Long Gene Names To Entrez Ids?

Question

[Walter Jessen]

I frequently have a list of long gene names (not symbols) that I need to map to Entrez IDs. For example, instead of having the gene symbol PTEN, I have the long gene name "phosphatase and tensin homolog". I don't see where Biomart supports the mapping of long gene names (using database: Ensembl genes 64, Sanger UK).

I've tried using MatchMiner. However, often the list of long gene names I have uses something other than "official" gene names and MatchMiner has trouble mapping. It's also quite slow.

What other resources are people using to batch map large lists of long gene names? I'd appreciate any tips.

Answer 1

[Pierre Lindenbaum]

Did you try NCBI eSearch ? I got only one hit with your example (don't forget the quotes):

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=9606[TID]+"phosphatase+and+tensin+homolog"[GFN]

<eSearchResult>
  <Count>1</Count>
  <RetMax>1</RetMax>
  <RetStart>0</RetStart>
  <IdList>
    <Id>5728</Id>
  </IdList>
  <TranslationSet/>
  <TranslationStack>
    <TermSet>
      <Term>9606[TID]</Term>
      <Field>TID</Field>
      <Count>191183</Count>
      <Explode>Y</Explode>
    </TermSet>
    <TermSet>
      <Term>"phosphatase+and+tensin+homolog"[GFN]</Term>
      <Field>GFN</Field>
      <Count>17</Count>
      <Explode>Y</Explode>
    </TermSet>
    <OP>AND</OP>
  </TranslationStack>
  <QueryTranslation>9606[TID] AND "phosphatase+and+tensin+homolog"[GFN]</QueryTranslation>
</eSearchResult>

Edit:

Walter, you can run a loop with a shell script and call this query for each long name.

$ cat list.txt 
phosphatase and tensin homolog
notch 2

the script:

while read G 
do
    for I in `curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=9606%5BTID%5D+%22${G// /\+}%22%5BGFN%5D" |grep "<Id>" `
       do
         echo  $G $I
       done
done < list.txt

phosphatase and tensin homolog <Id>5728</Id>
notch 2 <Id>4853</Id>

[Walter Jessen]

I don't see how this supports batch submissions -- I typically have several hundred names to map.

[Walter Jessen]

Thanks Pierre. However, I don't see how this supports batch submissions -- I typically have several hundred names to map.

[Walter Jessen]

Ah, I see. Excellent! Thanks Pierre!