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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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Presentation on theme: "UniProt Eric Jain Swiss Institute of Bioinformatics, Geneva W3C Workshop on Semantic Web for Life Sciences, October 2004."— Presentation transcript:

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

2 What is it?

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5 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 ) (Fragment). GN Name=ATP5B; OS Canis familiaris (Dog). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Carnivora; Fissipedia; Canidae; Canis. OX NCBI_TaxID=9615; RN [1] RP SEQUENCE. RC TISSUE=Heart; RX MEDLINE= ; PubMed= ; 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 18: (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 FT NON_TER SQ SEQUENCE 19 AA; 1871 MW; BB9C163FDC60BB42 CRC64; ATQTSPSPKG AAAXXXRVV //

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7 What have we done so far?

8 [DIR] Parent Directory 19-Jul :02 - [ ] cellular-components.rdf 11-Oct :15 5k [ ] databases.rdf 11-Oct :15 45k [ ] databases.rdf.gz 13-Sep :34 6k [ ] datasets.rdf 19-Oct :32 4k [ ] enzymes.rdf.gz 11-Oct :15 309k [ ] go.rdf.gz 11-Oct :15 839k [ ] intact.rdf.gz 11-Oct :15 636k [ ] keywords.rdf.gz 11-Oct :15 96k [ ] ontology.owl 19-Oct :27 77k [ ] taxonomy.rdf.gz 11-Oct :15 4.0M [ ] uniparc.rdf.gz 13-Oct :54 762M [ ] uniprot.rdf.gz 11-Oct :39 768M [ ] uniref.rdf.gz 01-Oct : M

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13 use Expasy::RDF; my $parser = Expasy::RDF::Parser->new('P12345.rdf'); while (my $protein = $parser->next) { my $id = $protein->id; my $mass = $protein->sequence->mass; print "Mass of $id is $mass.\n"; print $_->type, ': ', $_->comment, "\n"; foreach ($protein->annotation) } $parser->close;

14 Issues

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16 XML Syntax HUMAN Homo sapiens Human

17 Triples, Quads and Quints ● What is the source of a triple? ● Compact reification.

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

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

20 Embedded References uniprot.rdf In 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. cyc.rdf The collection of substances that can stimulate immune response. For example, bacteria [#$Bacterium], #$Viruses, proteins [#$ProteinMolecule] can serve as #$Antigens.

21 Summary

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

23 Credits

24 UniProt National Institutes of Health Swiss Institute of Bioinformatics SIB European Bioinformatics Institute EBI Georgetown University...


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