1 / 24

UniProt

UniProt. Eric Jain Swiss Institute of Bioinformatics, Geneva W3C Workshop on Semantic Web for Life Sciences, October 2004. What is it?. 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)

minty
Télécharger la présentation

UniProt

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

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?

  3. 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 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=98163340; PubMed=9504812; 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 18:2795-2802(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 //

  4. What have we done so far?

  5. [DIR] Parent Directory 19-Jul-2004 13:02 - • [ ] cellular-components.rdf 11-Oct-2004 19:15 5k • [ ] databases.rdf 11-Oct-2004 19:15 45k • [ ] databases.rdf.gz 13-Sep-2004 11:34 6k • [ ] datasets.rdf 19-Oct-2004 16:32 4k • [ ] enzymes.rdf.gz 11-Oct-2004 19:15 309k • [ ] go.rdf.gz 11-Oct-2004 19:15 839k • [ ] intact.rdf.gz 11-Oct-2004 19:15 636k • [ ] keywords.rdf.gz 11-Oct-2004 19:15 96k • [ ] ontology.owl 19-Oct-2004 18:27 77k • [ ] taxonomy.rdf.gz 11-Oct-2004 19:15 4.0M • [ ] uniparc.rdf.gz 13-Oct-2004 10:54 762M • [ ] uniprot.rdf.gz 11-Oct-2004 19:39 768M • [ ] uniref.rdf.gz 01-Oct-2004 12:56 52.2M

  6. 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;

  7. Issues

  8. XML Syntax <?xml version="1.0" encoding="UTF-8"?> <rdf:RDF xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="urn:lsid:uniprot.org:ontology:" xmlns:owl="http://www.w3.org/2002/07/owl#" > <rdf:Description rdf:about="urn:lsid:uniprot.org:taxonomy:9606"> <rdf:type rdf:resource="urn:lsid:uniprot.org:ontology:Taxon"/> <mnemonic>HUMAN</mnemonic> <scientificName>Homo sapiens</scientificName> <commonName>Human</commonName> <rdfs:subClassOf rdf:resource="urn:lsid:uniprot.org:taxonomy:9605"/> </rdf:Description> </rdf:RDF>

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

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

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

  12. Embedded References • uniprot.rdf • <rdf:Description rdf:about="#_2F9A"> • <rdf:type rdf:resource="urn:lsid:uniprot.org:ontology:Caution_Annotation"/> • <rdfs:comment>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.</rdfs:comment> • <citation rdf:resource="#_2F8A"/> • </rdf:Description> • cyc.rdf • <owl:Class rdf:ID="Antigen"> • <rdfs:comment>The collection of substances that can stimulate immune response. For example, bacteria [#$Bacterium], #$Viruses, proteins [#$ProteinMolecule] can serve as #$Antigens.</rdfs:comment> • </owl:Class>

  13. Summary

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

  15. Credits

  16. <?xml version="1.0" encoding="UTF-8"?> • <rdf:RDF • xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" • xmlns:foaf="http://xmlns.com/foaf/0.1/" • > • <foaf:Project> • <foaf:name>UniProt</foaf:name> • <foaf:homepage rdf:resource="http://uniprot.org/"/> • <foaf:fundedBy> • <foaf:Organization> • <foaf:name>National Institutes of Health</foaf:name> • <foaf:homepage rdf:resource="http://www.nih.gov/"/> • </foaf:Organization> • </foaf:fundedBy> • </foaf:Project> • <foaf:Organization> • <foaf:name>Swiss Institute of Bioinformatics</foaf:name> • <foaf:nick>SIB</foaf:nick> • <foaf:homepage rdf:resource="http://www.isb-sib.ch/"/> • </foaf:Organization> • <foaf:Organization> • <foaf:name>European Bioinformatics Institute</foaf:name> • <foaf:nick>EBI</foaf:nick> • <foaf:homepage rdf:resource="http://www.ebi.ac.uk/"/> • </foaf:Organization> • <foaf:Organization> • <foaf:name>Georgetown University</foaf:name> • <foaf:homepage rdf:resource="http://www.georgetown.edu/"/> • </foaf:Organization> • ...

More Related