UniProt

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UniProt

• Eric Jain
• Swiss Institute of Bioinformatics, Geneva
• W3C Workshop on Semantic Web for Life Sciences,
  October 2004

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• What is it?

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ID ATPB_CANFA STANDARD PRT 19
AA. AC P99504 DT 15-JUL-1998 (Rel. 36,
Created) DT 15-JUL-1998 (Rel. 36, Last sequence
update) DT 05-JUL-2004 (Rel. 44, Last
annotation update) DE ATP synthase beta chain,
mitochondrial (EC 3.6.3.14) (Fragment). GN
NameATP5B OS Canis familiaris (Dog). OC
Eukaryota Metazoa Chordata Craniata
Vertebrata Euteleostomi OC Mammalia
Eutheria Carnivora Fissipedia Canidae
Canis. OX NCBI_TaxID9615 RN 1 RP
SEQUENCE. RC TISSUEHeart RX
MEDLINE98163340 PubMed9504812 RA Dunn M.J.,
Corbett J.M., Wheeler C.H. RT "HSC-2DPAGE and
the two-dimensional gel electrophoresis database
of RT dog heart proteins." RL
Electrophoresis 182795-2802(1997). CC -!-
FUNCTION Produces ATP from ADP in the presence
of a proton CC gradient across the
membrane. The beta chain is the catalytic CC
subunit. CC -!- CATALYTIC ACTIVITY ATP
H(2)O H()(In) ADP phosphate CC
H()(Out). CC -!- SUBUNIT F-type ATPases have
2 components, CF(1) - the catalytic CC core
- and CF(0) - the membrane proton channel. CF(1)
has five CC subunits alpha(3), beta(3),
gamma(1), delta(1), epsilon(1). CF(0) CC
has three main subunits a, b and c. CC -!-
SUBCELLULAR LOCATION Mitochondrial. CC -!-
SIMILARITY Belongs to the ATPase alpha/beta
chains family. DR HSC-2DPAGE P99504 DOG. DR
InterPro IPR000194 ATPase_a/bcentre. DR
PROSITE PS00152 ATPASE_ALPHA_BETA PARTIAL. KW
ATP synthesis ATP-binding CF(1) Direct
protein sequencing KW Hydrogen ion transport
Hydrolase Mitochondrion. FT UNSURE 8
8 FT UNSURE 17 19 FT NON_TER
19 19 SQ SEQUENCE 19 AA 1871 MW
BB9C163FDC60BB42 CRC64 ATQTSPSPKG
AAAXXXRVV //
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• What have we done so far?

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• DIR Parent Directory 19-Jul-2004 1302
  -
• cellular-components.rdf 11-Oct-2004 1915
  5k
• databases.rdf 11-Oct-2004 1915
  45k
• databases.rdf.gz 13-Sep-2004 1134
  6k
• datasets.rdf 19-Oct-2004 1632
  4k
• enzymes.rdf.gz 11-Oct-2004 1915
  309k
• go.rdf.gz 11-Oct-2004 1915
  839k
• intact.rdf.gz 11-Oct-2004 1915
  636k
• keywords.rdf.gz 11-Oct-2004 1915
  96k
• ontology.owl 19-Oct-2004 1827
  77k
• taxonomy.rdf.gz 11-Oct-2004 1915
  4.0M
• uniparc.rdf.gz 13-Oct-2004 1054
  762M
• uniprot.rdf.gz 11-Oct-2004 1939
  768M
• uniref.rdf.gz 01-Oct-2004 1256
  52.2M

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use ExpasyRDF my parser ExpasyRDFParser
-gtnew('P12345.rdf') while (my protein
parser-gtnext) my id protein-gtid my
mass protein-gtsequence-gtmass print "Mass of
id is mass.\n" print _-gttype, ' ',
_-gtcomment, "\n" foreach (protein-gtannotation
) parser-gtclose
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• Issues

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XML Syntax lt?xml version"1.0"
encoding"UTF-8"?gt ltrdfRDF
xmlnsrdfs"http//www.w3.org/2000/01/rdf-schema"
xmlnsrdf"http//www.w3.org/1999/02/22-rdf-sy
ntax-ns" xmlns"urnlsiduniprot.orgontology
" xmlnsowl"http//www.w3.org/2002/07/owl" gt
ltrdfDescription rdfabout"urnlsiduniprot.or
gtaxonomy9606"gt ltrdftype rdfresource"urnl
siduniprot.orgontologyTaxon"/gt
ltmnemonicgtHUMANlt/mnemonicgt ltscientificNamegtHomo
sapienslt/scientificNamegt ltcommonNamegtHumanlt/co
mmonNamegt ltrdfssubClassOf rdfresource"urnls
iduniprot.orgtaxonomy9605"/gt
lt/rdfDescriptiongt lt/rdfRDFgt
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• Triples, Quads and Quints
• What is the source of a triple?
• Compact reification.

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• Web Services
• Overkill for providing programmatic access to
  resources.
• Often impractical for performance reasons.

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• Life Science Identifiers
• Need special resolver.
• Resolution tied to retrieval.
• Explicit version numbers.
• Not widely used.

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• Embedded References
• uniprot.rdf
• ltrdfDescription rdfabout"_2F9A"gt
• ltrdftype rdfresource"urnlsiduniprot.orgontol
  ogyCaution_Annotation"/gt
• ltrdfscommentgtIn mouse, 5 genes homologous to
  human CD209/DC-SIGN and CD209L/DC-SIGNR have been
  identified. Mouse CD209A product was named
  DC-SIGN by citation 1 because of its similar
  expression pattern and chromosomal location in
  juxtaposition to CD23, but despite of the low
  sequence similarity.lt/rdfscommentgt
• ltcitation rdfresource"_2F8A"/gt
• lt/rdfDescriptiongt
• cyc.rdf
• ltowlClass rdfID"Antigen"gt
• ltrdfscommentgtThe collection of substances that
  can stimulate immune response. For example,
  bacteria Bacterium, Viruses, proteins
  ProteinMolecule can serve as
  Antigens.lt/rdfscommentgt
• lt/owlClassgt

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• Summary

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• People will adopt the technology if it provides
  immediate benefits and is simple to use.

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• Credits

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• lt?xml version"1.0" encoding"UTF-8"?gt
• ltrdfRDF
• xmlnsrdf"http//www.w3.org/1999/02/22-rdf-synta
  x-ns"
• xmlnsfoaf"http//xmlns.com/foaf/0.1/"
• gt
• ltfoafProjectgt
• ltfoafnamegtUniProtlt/foafnamegt
• ltfoafhomepage rdfresource"http//uniprot.org/
  "/gt
• ltfoaffundedBygt
• ltfoafOrganizationgt
• ltfoafnamegtNational Institutes of
  Healthlt/foafnamegt
• ltfoafhomepage rdfresource"http//www.nih.go
  v/"/gt
• lt/foafOrganizationgt
• lt/foaffundedBygt
• lt/foafProjectgt
• ltfoafOrganizationgt