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Given a list of UniProt IDs that are linked to an Ensembl ID, is there a way to systematically determine which is the primary accession number with no other information?

According to ExPasy

Researchers who wish to cite entries in their publications should always cite the first accession number. This is commonly referred to as the 'primary accession number'. 'Secondary accession numbers' are sorted alphanumerically.

But what if the order has been jumbled or compiled from a different source and resorted.

For example:

Ensembl:

ENSMUSG00000035642

Uniprot:

Q8R0P4, Q8CF11, D6RJK8, D6RJJ4, D3Z442, D3Z1Q3, D3YZD8, D3YY39, D3YX09, D3YWY5

This question is cross listed on the Bioinformatics stack-exchange.

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I think there is an issue with the terminology. The "primary" accession number, is the first accession number in cases where an entry has more than one accession number, as described in http://www.uniprot.org/help/accession_numbers:

Entries can have more than one accession number. This can be due to two distinct mechanisms:

a) When two or more entries are merged, the accession numbers from all entries are kept. The first accession number is referred to as the

‘Primary (citable) accession number’, while the others are referred to as ‘Secondary accession numbers’. These are listed in alphanumerical order.

b) If an existing entry is split into two or more entries (‘demerged’), new ‘primary’ accession numbers are attributed to all

the split entries while all original accession numbers are retained as ‘secondary’ accession numbers.

Example: P29358 which has been ‘demerged’ into P68250 and P68251.

Both reviewed and unreviewed entries can have primary accession numbers.

What you probably mean, as previous posters understood, are accession numbers of reviewed entries as opposed to unreviewed ones.

In that case, you can indeed add "reviewed:yes" to your query, e.g. when you are using the UniProt ID mapping, http://www.uniprot.org/help/uploadlists

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Swissprot is the reviewed section of Uniprot's holdings. TrEMBl contains everything else.

Q8R0P4 or Mth938 domain-containing protein (AAMDC_MOUSE) is the reviewed Swissprot, aka reliable, identifier.

When searching in Uniprot you can filter to only see Reviewed/Swissprot identifiers; see the top-left corner of the link above.

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