Group activities

• TextMiningDayOne
• TextMiningDayTwo
• TextMiningDayThree
• TextMiningDayFour

Hacking, hacking, hacking

Implementation

• Make Reflect generate RDFa.
• Query Whatizit, Reflect and Medie.
• Get the RDFa data and use RDFa distiller or XSLT Transform to get RDF.
• Get Pubmed data from !TogoWS
• Get Uniprot RDF
• Deploy in Sesame
• Make queries
• Expose as linked data with Pubby

Accessing existing services

Here is some code:  http://scientifik.info/biohack/code/

Building RDF (Uniprot style)

(rdflib.URIRef('http://www.uniprot.org/uniprot/P12345.rdf#_1'), 
 rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#object'), 
 rdflib.URIRef('http://purl.uniprot.org/citations/4030726'))

(rdflib.URIRef('http://www.uniprot.org/uniprot/P12345.rdf#_1'), 
 rdflib.URIRef('http://purl.uniprot.org/core/scope'), 
 rdflib.Literal(u'PROTEIN SEQUENCE'))

(rdflib.URIRef('http://www.uniprot.org/uniprot/P12345.rdf#_1'), 
 rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), 
 rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#Statement'))

(rdflib.URIRef('http://www.uniprot.org/uniprot/P12345.rdf#_1'), 
 rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), 
 rdflib.URIRef('http://purl.uniprot.org/core/Citation_Statement'))

(rdflib.URIRef('http://www.uniprot.org/uniprot/P12345.rdf#_1'), 
 rdflib.URIRef('http://purl.uniprot.org/core/context'), 
 rdflib.URIRef('http://www.uniprot.org/uniprot/P12345.rdf#_2'))

(rdflib.URIRef('http://www.uniprot.org/uniprot/P12345.rdf#_1'), 
 rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#subject'), 
 rdflib.URIRef('http://purl.uniprot.org/uniprot/P12345'))

(rdflib.URIRef('http://www.uniprot.org/uniprot/P12345.rdf#_1'), 
 rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate'), 
 rdflib.URIRef('http://purl.uniprot.org/core/citation'))

(rdflib.URIRef('http://purl.uniprot.org/citations/4030726'), 
 rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), 
 rdflib.URIRef('http://purl.uniprot.org/core/Journal_Citation'))

(rdflib.URIRef('http://purl.uniprot.org/citations/4030726'), 
 rdflib.URIRef('http://www.w3.org/2004/02/skos/core#exactMatch'), 
 rdflib.URIRef('http://purl.uniprot.org/pubmed/4030726'))

(rdflib.URIRef('http://purl.uniprot.org/citations/4030726'), 
 rdflib.URIRef('http://www.w3.org/2004/02/skos/core#exactMatch'), 
 rdflib.URIRef('http://purl.uniprot.org/medline/85289123'))

Obtaining Subject, Verb, and Object of each sentence of MEDLINE titles/abstracts

• Endpoint:  http://docman.dbcls.jp/medieconv
  • argument: pmid (PubMed ID, multiple IDs can be accepted using bar "|" as a delimiter)
  • Example:  http://docman.dbcls.jp/medieconv?pmid=17551671|18424370