Overview¶
The software and data resources of the Department of Translational Genomics, collected once a week from public sources.
Per-source detail is on the Methods page.
Maps identifiers between biological databases, so that one gene or metabolite can be recognised across resources that each name it differently.
13 registries
An open, community-curated pathway database. The department maintains its semantic layer and the clients most people actually use.
10 registries
8 papers
- WikiPathways 2024: next generation pathway database
- WikiPathways: connecting communities
- WikiPathways: a multifaceted pathway database bridging metabolomics to other omics researc
- Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online
- WikiPathways: capturing the full diversity of pathway knowledge
- WikiPathways: building research communities on biological pathways
- Mining Biological Pathways Using WikiPathways Web Services
- WikiPathways: Pathway Editing for the People
Desktop editor for biological pathways, and the origin of the GPML format.
Chemistry Development Kit
Java library for cheminformatics: structure handling, fingerprints, descriptors. Widely used well beyond this department.
1 link
10 registries
Bacting
Scriptable cheminformatics and bioinformatics, usable from Java and Python.
ArrayAnalysis
Transcriptomics analysis workflows and quality control for microarray and RNA-seq data.
R-ODAF
Reproducible RNA-seq differential expression analysis, packaged as a Shiny app for regulatory toxicogenomics.
The VHP4Safety portal: a single entry point to the chemical safety assessment services the consortium runs.
Converts the AOP-Wiki to RDF, versions every release as its own named graph, and serves it over a public SPARQL endpoint with a query interface and dashboard.
Maps Adverse Outcome Pathway key events onto molecular pathways, and analyses the resulting molecular AOPs.
pyBiodatafuse
Queries many biomedical databases at once and merges what comes back into a single knowledge graph, so a gene or compound list can be annotated from all of them in one step.
pysec2pri
Generates and use secondary identifier and symbol/label mapping sets for life sciences databases.
rdfsolve
Mine typed RDF schemas, convert between formats, and derive cross-dataset mappings.
Blue Obelisk
International team of chemists who share a belief in the concepts of Open Data, Open Standards, and Open Source (ODOSOS) (but not necessarily Open Access).
12 registries
Builds profile pages for researchers, topics, journals and chemicals out of what Wikidata already records, so the works, citations and co-authors behind a name can be read without writing a query.
NanoJava
Minimal cheminformatics Java library for nanomaterials.
2 registries
jQUDT
Java library to handle units and convert quantities.
3 registries
CyTargetLinker
Extend your biological networks in Cytoscape.
Releases¶
Releases per year. A tagged release of a project's repositories, from GitHub Releases and git tags.
Source: github · collected 2026-09-01 · download CSV
Downloads¶
Each registry counts over its own window, and the two are never added together.
Registry downloads, all time. The registry's own lifetime download counter, for registries that publish one.
Source: ecosystems · collected 2026-09-01 · download CSV
Registry downloads, last 30 days. Downloads in the last 30 days, as reported by registries that publish no lifetime counter.
Source: ecosystems · collected 2026-09-01 · download CSV
Bioconductor distinct IPs per month. Distinct IP addresses downloading a package in a month.
Source: bioconductor · collected 2026-09-01 · download CSV
Dependents¶
Maven Central publishes no download figures, so for the Java libraries this is the only measure of use a registry offers. It is counted the same way everywhere, and the registries do not see each other.
Packages depending on it. Other published packages that declare a dependency on one of these, as counted by the registry it is published in.
Source: ecosystems · collected 2026-09-01 · download CSV
Citations¶
Citations of the tool's papers. Citations to every paper describing a tool, summed across its update papers.
Source: citations · collected 2026-09-01 ⚠ incomplete · download CSV
Software mentions¶
Papers mentioning the software. Works the Research Software Directory records as mentioning a tool.
Source: rsd · collected 2026-09-01 · download CSV
Containers¶
Container pulls, all time. Docker Hub's lifetime pull counter for an image.
Source: dockerhub · collected 2026-09-01 · download CSV