Re: drug side effects

2009-05-29 Thread Kingsley Idehen
Matthias Samwald wrote: The conversion of SIDER to aTags is now available, see http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags/datasets A small excerpt of the aTags: http://hcls.deri.org/atag/data/SIDER_atags_excerpt.html The aTags re-use URIs from DBpedia, OBO disease ontology and OBO sy

Re: drug side effects

2009-05-29 Thread Matthias Samwald
The conversion of SIDER to aTags is now available, see http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags/datasets A small excerpt of the aTags: http://hcls.deri.org/atag/data/SIDER_atags_excerpt.html The aTags re-use URIs from DBpedia, OBO disease ontology and OBO symptom ontology. Most stat

Re: drug side effects

2009-05-07 Thread Jun Zhao
Matthias Samwald wrote: As shown in the TCMGeneDIT web site, they have links to the STITCH database. I will need to contact them if this part of dataset is needed. When you have the STITCH/PubchemIDs, you can also use them for mapping to DBpedia. You can retrieve the IDs from DBpedia like th

Re: drug side effects

2009-05-06 Thread Matthias Samwald
As shown in the TCMGeneDIT web site, they have links to the STITCH database. I will need to contact them if this part of dataset is needed. When you have the STITCH/PubchemIDs, you can also use them for mapping to DBpedia. You can retrieve the IDs from DBpedia like this: SELECT * WHERE {?db

Re: drug side effects

2009-05-06 Thread Jun Zhao
Kei Cheung wrote: Matthias Samwald wrote: I have also started to convert SIDER into aTags, but our two conversions will be complementary. What I am doing is mapping the information to the OBO disease ontology and to DBpedia (for drug names), and reusing OBO and DBpedia URIs directly. The conv

Re: drug side effects

2009-05-05 Thread Peter Ansell
2009/5/6 Kei Cheung : > Matthias Samwald wrote: > >> I have also started to convert SIDER into aTags, but our two conversions >> will be complementary. What I am doing is mapping the information to the OBO >> disease ontology and to DBpedia (for drug names), and reusing OBO and >> DBpedia URIs dire

Re: drug side effects

2009-05-05 Thread Kei Cheung
Matthias Samwald wrote: I have also started to convert SIDER into aTags, but our two conversions will be complementary. What I am doing is mapping the information to the OBO disease ontology and to DBpedia (for drug names), and reusing OBO and DBpedia URIs directly. The conversion will be los

Re: drug side effects

2009-04-30 Thread Matthias Samwald
ll document to the HCLS KB. Cheers, Matthias -- From: "Peter Ansell" Sent: Wednesday, April 29, 2009 11:26 AM To: "Matthias Samwald" Cc: "public-semweb-lifesci" Subject: Re: drug side effects 2009/4/29 Matthias Sam

Re: drug side effects

2009-04-29 Thread Matthias Samwald
Peter Ansell wrote: I will have to investigate how aTags works more deeply. I developed my own tagging vocabulary [1] but it hasn't seen many uses so far. From a rough view, the terms:hasEvidence URI seems to map well to aTags although it might be a bit specialised. Is [2] the only place aTags ar

Re: drug side effects

2009-04-29 Thread Peter Ansell
they have reused the pubchem identifiers, so owl:sameAs should be appropriate to http://bio2rdf.org/pubchem:STITCHID. > By the way, some time back I also found two other datasets about drug side > effects / pharmacovigilance data that could be used for conversions. > > Maximum Recommende

Re: drug side effects

2009-04-29 Thread Matthias Samwald
found in these resources, but it will be bound more tightly to OBO and DBpedia. The STITCH ids for chemicals seem to be equivalent to Pubchem in all cases I checked. Are there deviations? By the way, some time back I also found two other datasets about drug side effects / pharmacovigilance data

Re: drug side effects

2009-04-28 Thread Peter Ansell
2009/4/29 Matthias Samwald : > We have metadata! The download page (http://sideeffects.embl.de/download/) > contains Creative Commons licensing HTML, which in  turn contains RDFa. > We can extract the RDF from the page with a web service: > > http://srv.buzzword.org.uk/turtle,strict=aegu/sideeffect

Re: drug side effects

2009-04-28 Thread Matthias Samwald
We have metadata! The download page (http://sideeffects.embl.de/download/) contains Creative Commons licensing HTML, which in turn contains RDFa. We can extract the RDF from the page with a web service: http://srv.buzzword.org.uk/turtle,strict=aegu/sideeffects.embl.de/download/ (The swignition

Re: drug side effects

2009-04-27 Thread Kei Cheung
It looks like we need metadata (e.g. license type and the type of data provided) describing this type of resources. Cheers, -Kei Egon Willighagen wrote: Just was told about this: http://sideeffects.embl.de/ Rather permissively licensed. "SIDER contains information on marketed medicines an

drug side effects

2009-04-22 Thread Egon Willighagen
Just was told about this: http://sideeffects.embl.de/ Rather permissively licensed. "SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect f