Which URI to use in your RDF?

Guideline 1: Be polite. Use the data provider's URL as your identifier. Ideally there should be not get arguments, but if there are to avoid ambiguity for string comparison sort them in alphabetical order (e.g.  http://www.example.com/?a=100&b=2 sorting a before b).

Guideline 2. Often a provider offers multiple URLs for the same resource. e.g. the entrez query  http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=22177139 is the same as  http://www.ncbi.nlm.nih.gov/pubmed/22177139 (the community recommend to use the later) or  http://www.ebi.uniprot.org/entry/P05067 is the same as  http://purl.uniprot.org/uniprot/P05067 (where UniProt? asks you use the later, which will give RDF if your HTTP header requests it).

Document the URI pattern you use on freebase, to encourage uniformity.  http://www.freebase.com/view/user/biohackathon/default_domain/views/namespace_1 (is this the correct Freebase page? it doesn't seem to be providing URI patterns.) This is a first-come-first-served approach to pick preferred URL pattern; the first data provider to cross-reference to a third party, gets to decide what URL pattern is in Freebase as "approved" (ideally with the 'blessing' of the third-party data provider)

Guideline 3. Sometimes there is more than provider and thus more than one official URI for a record about a common concept, which can happen with consortia. e.g. PDB is available at PDBj, PDBe, RCSB PDB. Then choose the one that you prefer. Consider adding owl:seeAlso references between them, in strong preference over owl:sameAs due that giving misleading semantics.