Banff Manifesto

From wikipedia: http://en.wiktionary.org/wiki/manifesto

Some participant from the HCLS-DI2007 workshop, and from the I3 Workshop propose to the community of life science to establish an authority for attributing namespaces used in semantic web to build URIs. This authority will also establish a set of rules for the construction of well formed RDF documents. When someone will use URI approved from the BM authority, they will know that some standard of naming are upheld. The set of rules are good pratices that need to be followed to be in recognized by the BM community.

Much in the way DOI work, BM will certified the appartenance of a namespace to a data provider and disambiguate the naming for it.

Banff Manifesto first rule

The syntax of normalized URI is composed of three parts separated by ':'. The autority_namespace is 'bm' an acronym for Banff Manifesto.  The literal of public_namespace are attributed by the BM community (for example go, uniprot, pubmed).  The private identifier is the responsibility of the RDF provider of the corresponding document (for example 0000007 with go, p26838 for uniprot).

 

authority_namespace:public_namespace:private_identifier

 

URI example

The official authoritative web page for uniprot:p26838 protein is http://www.ebi.uniprot.org/entry/uniprot:p26838

The proposed URI attributed according to Banff Manifesto will be bm:uniprot:p26838

 

Its LSID equivalent is urn:lsid:bm:uniprot:p26838

 

Bio2RDF implementation using URL to obtain the RDF copy of this document is already available at http://bio2rdf.org/bm:uniprot:p26838

Existing official URLs

• PDB use DOI
• http://www.rcsb.org/pdb/explore.do?structureId=2b3y
• http://dx.doi.org/10.2210/pdb2b3y/pdb
• UniProt at SwissProt, Pir and EBI
  
• http://www.expasy.org/enzyme/4.2.1.11
• http://www.expasy.org/uniprot/Q8NKC2
• http://www.pir.uniprot.org/cgi-bin/upEntry?id=ENO12_SCHPO
• http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinId=ENO12_SCHPO
• NCBI
• http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=gene&dopt=full_report&list_uids=15275
• http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9271679
• http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602080
• http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=ac008393
• So many
• same sequence AL732457 three sources EBI, DDBJ and NCBI
  
• http://www.ebi.ac.uk/cgi-bin/expasyfetch?AL732457
• http://getentry.ddbj.nig.ac.jp/search/get_entry?accnumber=AL732457
• http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=AL732457&doptcmdl=GenBank
• http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000941
• http://www.pantherdb.org/panther/family.do?clsAccession=PTHR11902
• http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00113
• http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=PR00148
• LSID
• http://lsid.biopathways.org/resolver/data/urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:genbank:30350027
• urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:genbank:30350027

    It is creepy ! Dont you think ?

Existing URIs for uniprot:p26838

• http://www.expasy.org/uniprot/Q8NKC2

• uniprot:p26838

• urn:lsid:uniprot.org:uniprot:p26838

• http://bio2rdf.org/uniprot:p26838
• http://dx.doi.org/10.9999/pdb2b3y/pdb  ($)

Banff Manifesto propositions

• bm:uniprot:p26838
• http://lsid.info/uniprot:p26838

         

Existing namespace lists

• BioMoby
• http://biomoby.org/RESOURCES/MOBY-S/Namespaces
• The BioMoby namespace list is taken from the Gene Ontology Cross Reference Abbreviations list
  
• UniProt
• GO
• http://mobycentral.icapture.ubc.ca/cgi-bin/XrefAbbs
• Note that this is the same document as from BioMoby above, but in GO XrefAbbs file format
  

Authoritative namespace table

The main resource defined  by the Banff Manifesto is the table of authoritative namespace used in URIs of the bioinformatics semantic web ressource.

 

 

Why Banff manifesto, because to build the semantic coordinate system based on URIs we need a reference to start from, 'bm' is the proposed namespace authority and if it is based in Banff, it will not move because the Rockies dont move !  Banff Manifesto wants to remove some creeps from bioinformatics semantic web.  Creeps rule the web, we gathered to adopt a share Banff Manifesto. Join our community, it is up to you.

References

• http://en.wikipedia.org/wiki/LSID
• http://lsid.biopathways.org/
  
• Life Sciences Identifiers final adopted specification
• 
  

Signatories (add your name and web site)

Francois Belleau, http://bio2rdf.org/

Marc-Alexandre Nolin, http://bio2rdf.org/