There are numerous ways to obtain gene IDs for gene-based products. The most accurate methods require some sort of ID - whether it's from an Affymetrix chip or a protein PDB ID, but having only a species and gene symbol, or in some cases just the gene name itself, can be enough to obtain a gene ID.
The BioCompare product database uses Entrez GeneIDs to pull in various curated data, including species, full NCBI gene names and synonyms, so it is best to obtain the Entrez GeneID when possible. However, we are able to convert gene IDs from various sources to Entrez GeneIDs, so just about any ID-format is acceptable.
Some very good sources of gene IDs are the following websites:
NCBI Gene - searches any provided ID, symbol or gene name across many databases.
Strengths: ID conversion and free text lookup of gene names. Initial ID format can be specified but is not necessary.
Weakness: Output in "gene card" format; Limited to single lookups (multiple lookups not allowed).
http://www.ncbi.nlm.nih.gov/gene
SwissProt/UniProt - searches any provided ID or symbol
Strengths: Multiple lookups allowed by pasting or file uploads.
Weaknesses: Starting ID format is required.
http://www.uniprot.org/ (then select the "ID Mapping" tab)
bioDBnet - similar to UniProt website
Strengths (over SwissProt/UniProt): More programmatic tools allowing increased user control over mapping.
Weaknesses: ID formats are organized only alphabetically, not by database family as by SwissProt/UniProt.
http://biodbnet.abcc.ncifcrf.gov/db/db2db.php
Additional ID conversion websites can be found. Many of these have the ability for local installations of their databases or other programmatic interfaces simplifying the task of converting hundreds or thousands of IDs.