Building InterMine databases from RDF Portal
Abstract
InterMine databases such as HumanMine integrate many biological data sources, but each source needs its own loader, and keeping those loaders current is costly. The public HumanMine has not had a data release since February 2022. RDF Portal, operated by the Database Division for Life Science, now serves many of the same sources as reviewed RDF, and describes each dataset with an rdf-config model. At the DBCLS BioHackathon 2026 we developed rdfc2im, a tool that maps rdf-config models onto the InterMine data model, keeps the mapping as reviewable data with the evidence for every row, uses RDF Config to generate SPARQL queries to acquire data from RDF Portal, and writes the data into a form that InterMine's standard loader integrates without new code. We used it to build a working demonstration HumanMine from nine sources and a panel of 113 food- and drug-metabolism genes, with NCBI Gene, the Gene Ontology and Reactome loaded in full. The mine supports search, template queries and list analysis. Real loads found problems that static checks did not, most of them related to the way objects from different sources are identified and merged, and to the limits of public SPARQL endpoints. This report describes our proof of concept. We list what remains to be done before rdfc2im can rebuild a full HumanMine from each RDF Portal release.
Related
- The use of sequence databases for taxonomic research in phytovirology and the application of factor analysis of correspondences to the clustering of geminiviruses
- Lossless compression of protein databases for efficient and accurate metagenomic sequence classification with Centrifuger
- Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species
- In-silico Tandem Mass Spectral Libraries for the Blood Exposome and Metabolomics Workbench Databases: Application of Gemini Large Language Model
- Democratizing Agentic Access to Bioinformatics and Biopharmaceutical Databases and Analyses with BioMCP-TS
BibTeX
@misc{neches2026building,
title = {{Building InterMine databases from RDF Portal}},
author = {Russell Y. Neches and Gos Micklem and Toshiaki Katayama and Shuichi Kawashima},
howpublished = {BioHackrXiv},
year = {2026},
month = sep,
doi = {10.37044/osf.io/dqm3j_v1},
url = {https://osf.io/preprints/biohackrxiv/dqm3j_v1/},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - Building InterMine databases from RDF Portal
AU - Russell Y. Neches
AU - Gos Micklem
AU - Toshiaki Katayama
AU - Shuichi Kawashima
PY - 2026
DA - 2026/09/18
PB - BioHackrXiv
DO - 10.37044/osf.io/dqm3j_v1
UR - https://osf.io/preprints/biohackrxiv/dqm3j_v1/
AB - InterMine databases such as HumanMine integrate many biological data sources, but each source needs its own loader, and keeping those loaders current is costly. The public HumanMine has not had a data release since February 2022. RDF Portal, operated by the Database Division for Life Science, now serves many of the same sources as reviewed RDF, and describes each dataset with an rdf-config model. At the DBCLS BioHackathon 2026 we developed rdfc2im, a tool that maps rdf-config models onto the InterMine data model, keeps the mapping as reviewable data with the evidence for every row, uses RDF Config to generate SPARQL queries to acquire data from RDF Portal, and writes the data into a form that InterMine's standard loader integrates without new code. We used it to build a working demonstration HumanMine from nine sources and a panel of 113 food- and drug-metabolism genes, with NCBI Gene, the Gene Ontology and Reactome loaded in full. The mine supports search, template queries and list analysis. Real loads found problems that static checks did not, most of them related to the way objects from different sources are identified and merged, and to the limits of public SPARQL endpoints. This report describes our proof of concept. We list what remains to be done before rdfc2im can rebuild a full HumanMine from each RDF Portal release.
ER -