TextMiningDayOne – BioHackathon 2010

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Version 5 (modified by alabarga, 15 years ago)
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Reflect RDFa snippets

Idea 1 (interlaced with the text):

<div xmlns:sioc="http://rdfs.org/sioc/ns#" typeof="sioc:Item">
<span class='reflect_protein'><a rel="sioc:topic" resource="http://purl.uniprot.org/uniprot/P05113"></a>IL-5</span>
</div>

Idea 2 (at the end of the document, non-redundant):

<div xmlns:sioc="http://rdfs.org/sioc/ns#" typeof="sioc:Item">
<span id='reflectEntity0'>9606.ENSP00000231454</span>
<a rel="sioc:topic" resource="http://purl.uniprot.org/uniprot/P05113"></a>
</div>

Whatizit RDFa service

IL-5 Example: http://whatizit.neurocommons.org/index.py/text_query?pipeline=whatizitEBIMedDiseaseChemicals&query=IL-5&format=atag&max_results=10

Converted to Turtle: http://www.w3.org/2007/08/pyRdfa/extract?uri=http://whatizit.neurocommons.org/index.py/text_query?pipeline=whatizitEBIMedDiseaseChemicals&query=IL-5&format=atag&max_results=10

This uses a W3 service ( http://www.w3.org/2007/08/pyRdfa/extract)

Uniprot RDF

http://www.uniprot.org/uniprot/P12345.n4

uniprot:P12345
  rdf:type Protein
  alternativeName 
    rdf:type Structured_Name
    fullName "Transaminase A"
  citation <http://purl.uniprot.org/citations/4030726>
    rdf:type Journal_Citation
    title 
      "Aspartate aminotransferase isozymes from rabbit liver. Purification 
       and properties."
    author "Kuramitsu S."
    author "Inoue K."
    author "Kondo K."
    author "Aki K."
    author "Kagamiyama H."
    skos:exactMatch <http://purl.uniprot.org/medline/85289123>
    skos:exactMatch <http://purl.uniprot.org/pubmed/4030726>
    date 1985
    name "J. Biochem."
    volume 97
    pages "1337-1345"
    +rdf:type Citation_Statement
    +scope "PROTEIN SEQUENCE"
    +context 
      rdf:type Tissue
      rdfs:label "Liver"

Pubmed RDF @ TogoWS

http://togows.dbcls.jp/entry/pubmed/4030726.ttl

<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#pmid>	"4030726" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://www.w3.org/2000/01/rdf-schema#label>	"pmid:4030726" .          
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://purl.org/dc/elements/1.1/title>	"pmid:4030726" .          
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://purl.org/dc/elements/1.1/identifier>	<http://pubmed.org/4030726> .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#own>	"NLM" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#stat>	"MEDLINE" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#da>	"1985-10-09" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#dcom>	"1985-10-09" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#lr>	"2007-12-19" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#vi>	"97" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://prismstandard.org/namespaces/2.0/basic/volume>	"97" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#dp>	"1985 May" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://prismstandard.org/namespaces/2.0/basic/prism:publicationDate>	"1985-05" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#ti>	"Aspartate aminotransferase isozymes from rabbit liver. Purification and properties." .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://purl.org/dc/elements/1.1/title>	"Aspartate aminotransferase isozymes from rabbit liver. Purification and properties." .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#pg>	"1337-45" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://prismstandard.org/namespaces/2.0/basic/startingPage>	"1337" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#ab>	"Cytosolic and mitochondrial isozymes of aspartate aminotransferase (L-aspartate:2-oxoglutarate aminotransferase [EC 2.6.1.1] ) were purified to homogeneity from rabbit liver. The rabbit liver isozymes were closely similar to the corresponding isozymes from other sources, including human heart, pig heart, chicken heart, and rat liver, in their molecular weights, absorption spectra, amino acid compositions, isoelectric points, and Michaelis constants for the substrates. The NH2-terminal amino acid sequences of rabbit liver isozymes were identified up to 30 residues, and showed some differences from those of the corresponding isozymes obtained from other animals so far studied." .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#ad>	"" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#fau>	"Kuramitsu, S" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://purl.org/dc/terms/creator>	"Kuramitsu, S" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#fau>	"Inoue, K" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://purl.org/dc/terms/creator>	"Inoue, K" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#fau>	"Kondo, K" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://purl.org/dc/terms/creator>	"Kondo, K" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#fau>	"Aki, K" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://purl.org/dc/terms/creator>	"Aki, K" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#fau>	"Kagamiyama, H" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://purl.org/dc/terms/creator>	"Kagamiyama, H" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#au>	"Kuramitsu S" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#au>	"Inoue K" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#au>	"Kondo K" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#au>	"Aki K" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#au>	"Kagamiyama H" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#pt>	"Journal Article Research Support, Non-U.S. Gov't" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#pl>	"JAPAN" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#ta>	"J Biochem" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://prismstandard.org/namespaces/2.0/basic/publicationName>	"J Biochem" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#jt>	"Journal of biochemistry" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#jid>	"0376600" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#rn>	"0 (Isoenzymes)" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#sb>	"IM" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Amino Acid Sequence" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Amino Acids/analysis" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Animals" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Aspartate Aminotransferases/*isolation & purification/metabolism" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Isoelectric Point" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Isoenzymes/*isolation & purification/metabolism" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Kinetics" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Liver/*enzymology" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Molecular Weight" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Rabbits" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mh>	"Spectrum Analysis" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#edat>	"1985-05-01" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#mhda>	"1985-05-01 00:01" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#crdt>	"1985-05-01 00:00" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#pst>	"ppublish" .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#so>	"J Biochem. 1985 May;97(5):1337-45." .
<http://togows.dbcls.jp/entry/ncbi-pubmed/4030726>	<http://togows.dbcls.jp/ns/ncbi-pubmed#la>	"eng" .

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