1. Group activities: Day Four
    1. The part of the MEDIE result XML that we should focus on
    2. How to generate RDF-friendly URIs for recognized entities
    3. RDF format discussion

Group activities: Day Four

The part of the MEDIE result XML that we should focus on

<set>
 <article>
  <PMID>19694806</PMID>

    ... <sentence>
	Treatment with 5-aza-2'-deoxycytidine and/or the histone deacetylase inhibitor trichostatin A increased 
	<entity_name gena_id="GMM040544" species="Mus musculus" db_site="EntrezGene:13138|MGI:101864|PIR:S59630|SWISS-PROT:Q62165|TrEMBL:Q8BPJ7" type="gene_prod" confidence="1" filter_confidence="0.284761" id="entity-10" gene_symbol="Dag1">Dag1</entity_name>
 	mRNA expression levels in myoblasts, and methylation decreased promoter activity in vitro.
	</sentence>

How to generate RDF-friendly URIs for recognized entities

<entity_name gena_id="GMM040544" species="Mus musculus" db_site="EntrezGene:13138|MGI:101864|PIR:S59630|SWISS-PROT:Q62165|TrEMBL:Q8BPJ7"

--->  http://purl.uniprot.org/uniprot/Q62165

Note: If given the choice, prefer Swissprot over TrEMBL 

<entity_name id="disease6" facta_id="UMLS:C0878544" type="disease">cardiomyopathy</entity_name>

---> Unfortunately we still don't have well accepted URIs for UMLS yet. We could do a lookup and provide URIs pointing to the OBO disease ontology, but this is a bit computationally expensive. 

<entity_name id="compound18615" facta_id="CAS:79-43-6" type="compound">Dichloroacetate</entity_name>
<entity_name id="enzyme1375" facta_id="EC:3.5.3.22" type="enzyme">
<entity_name id="compound18620" facta_id="CAS:61-78-9" type="compound">PAH</entity_name>
</entity_name>

---> CAS and EC numbers would need to be mapped as well

Using TogoDB, although not a primary database provider, you can use URI for UMLS (subset, those can be redistributed).
Note that currently we (DBCLS) haven't loaded the UMLS data to togoDB yet, so you will see an error page if you access to the following URL. But, we will prepare soon. 

http://togows.dbcls.jp/entry/togodb-umls/C08384423

RDF format discussion

<http://togows.dbcls.jp/entry/ncbi-pubmed/22333111> <ns:cites> <uniprot> .
<http://togows.dbcls.jp/entry/ncbi-pubmed/22333111> <ns:cites> <genbank> .
<http://togows.dbcls.jp/entry/ncbi-pubmed/22333111> <ns:contains> _:hasG1 .

_:hasG1 <http://www.w3.org/2000/01/rdf-schema#label> "p53" .
_:hasG1 <rdf:type> <something:protein> .
_:hasG1 <something:taxonomy> <taxid:9399> .
...

<http://togows.dbcls.jp/entry/ncbi-pubmed/22333111> <http://togosw.dbcls.jp/textmining#hasSentence> _:hasS1 .
<http://togows.dbcls.jp/entry/ncbi-pubmed/22333111> <http://togosw.dbcls.jp/textmining#hasSentence> _:hasS2 .
<http://togows.dbcls.jp/entry/ncbi-pubmed/22333111> <http://togosw.dbcls.jp/textmining#hasSentence> _:hasS3 .
...

_:hasS1 <http://togosw.dbcls.jp/textmining#hasSubject> _:sbj1 .
_:hasS1 <http://togosw.dbcls.jp/textmining#hasVerb> _:verb1 .
_:hasS1 <http://togosw.dbcls.jp/textmining#hasObject> _:obj1 .
_:sbj1 <http://www.w3.org/2000/01/rdf-schema#label> "peripheral lymphocytes" .
_:verb1 <http://www.w3.org/2000/01/rdf-schema#label> "secreting" .
_:obj1 <http://www.w3.org/2000/01/rdf-schema#label> "a specific cytokine" .


<http://purl.org/dc/elements/1.1/identifier> <http://pubmed.org/22333111>
<http://purl.org/dc/elements/1.1/title> "pmid:22333111"
<http://togows.dbcls.jp/entry/ncbi-pubmed/22333111>

TextMining