Joined SPARQLthon held at DBCLS Mishima. This was 78th SPARQLthon.
First, I tried to execute SPARQL from UNIX command line for the integration of unfamiliar data. According to the SPARQL book (p145), I could make it.
# command line execution of SPARQL
% curl -F query=@hoge.rq -H "Accept: application/sparql-results …I joined BioHackathon2018 held at Matsue. I also joined Common Workflow Language (CWL) Workshop Tokyo 2018 held at Shibuya prior to the hackathon, and learned a little bit about CWL.
I have other tasks (update searchability of All of gene expression (AOE)) to be discussed in the hackathon, but it …
Joined SPARQLthon held at DBCLS Kashiwa. This was 71st SPARQLthon.
Try to update AOE data for the latest one, but there was some trouble in this process. There might be unexpected characters in the contents of original data. It was because names in the header line were conflicted. After the …
Joined SPARQLthon held at DBCLS Mishima. This was 70th SPARQLthon.
After the intensive development of AOE system at BH18.7, we continued that work in this SPARQLthon.
Joined SPARQLthon held at DBCLS Kashiwa. This was 69th SPARQLthon.
We discussed a development of DBCLS SRA and AOE for this fiscal year.
How to get GEO metadata from NCBI was examined for sustainable retrieval system for AOE.
Joined SPARQLthon held at DBCLS Kashiwa. This was 68th SPARQLthon.
Updated version of AOE, which use Apache Solr as a back-end, officially released on this week, and we checked the web interface of AOE. It tentatively includes meta-data from NCBI Gene Expression Omnibus (GEO), which was taken from SRA/BioProject …
Joined SPARQLthon held at DBCLS Kashiwa. This was 67th SPARQLthon.
Discussed the development of two search systems (DBCLS SRA and AOE) and the integration of these. The specification will be fixed after the coming INSDC meeting of this year at NCBI.
I tried to add contents to how to make …
Joined SPARQLthon held at DBCLS Mishima located at National Institute of Genetics. This was 65th SPARQLthon.
Discussed the development of search system for public high-throughput sequencing data at Sequence Read Archive (SRA).
Joined SPARQLthon for Jan 2018 was held at DBCLS Kashiwa. This was 64th SPARQLthon.
I will hack for the development of AOE, index of public omics (gene expression) data.
Tackling to hack parsers for inputing metadata from NCBI GEO utilizing DBCLS SRA API. Thanks to this API, we …