| | 1 | == The part of the MEDIE result XML that we should focus on == |
| | 2 | |
| | 3 | {{{ |
| | 4 | <set> |
| | 5 | <article> |
| | 6 | <PMID>19694806</PMID> |
| | 7 | |
| | 8 | ... <sentence> |
| | 9 | Treatment with 5-aza-2'-deoxycytidine and/or the histone deacetylase inhibitor trichostatin A increased |
| | 10 | <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> |
| | 11 | mRNA expression levels in myoblasts, and methylation decreased promoter activity in vitro. |
| | 12 | </sentence> |
| | 13 | }}} |
| | 14 | |
| | 15 | |
| | 16 | == How to generate RDF-friendly URIs for recognized entities == |
| | 17 | |
| | 18 | |
| | 19 | {{{ <entity_name gena_id="GMM040544" species="Mus musculus" db_site="EntrezGene:13138|MGI:101864|PIR:S59630|SWISS-PROT:Q62165|TrEMBL:Q8BPJ7" }}} |
| | 20 | |
| | 21 | ---> http://purl.uniprot.org/uniprot/Q62165 |
| | 22 | |
| | 23 | Note: If given the choice, prefer Swissprot over TrEMBL |
| | 24 | |
| | 25 | {{{ |
| | 26 | <entity_name id="disease6" facta_id="UMLS:C0878544" type="disease">cardiomyopathy</entity_name> |
| | 27 | }}} |
| | 28 | |
| | 29 | ---> 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. |
| | 30 | |
| | 31 | {{{ |
| | 32 | <entity_name id="compound18615" facta_id="CAS:79-43-6" type="compound">Dichloroacetate</entity_name> |
| | 33 | <entity_name id="enzyme1375" facta_id="EC:3.5.3.22" type="enzyme"> |
| | 34 | <entity_name id="compound18620" facta_id="CAS:61-78-9" type="compound">PAH</entity_name> |
| | 35 | </entity_name> |
| | 36 | }}} |
| | 37 | |
| | 38 | ---> CAS and EC numbers would need to be mapped as well |
| | 39 | |
