EchoGO validation and reproducibility compendium

Zenodo (CERN European Organization for Nuclear Research)

Abstract

EchoGO validation and reproducibility compendium supporting the validation analyses presented in “EchoGO: annotation-context-aware functional interpretation of transcriptomic data.” The compendium contains the evidence, provenance, analysis products, and reproducibility materials for the three transcriptomic applications used to evaluate EchoGO: a reference-rich zebrafish analysis (ZEB) and two annotation-limited Gammarus pulex field contrasts (GAM1 and GAM2). Together, these exercises examine functional interpretation across different levels of identifier representation and annotation availability. The deposited materials include target GOseq evidence, g:Profiler results across selected annotation contexts, identifier-resolution and context-recognition information, exact-term evidence and provenance, RRvGO semantic-reduction products, gene-sharing networks, and case-level reports. Manuscript-facing resources include the validation summary underlying Table 3 and the complete reproducibility chain for Figure 2, including the selected GO terms, evidence matrix, semantic-selection provenance, generation scripts, and final figure exports. Source enrichment results from the original validation analyses are preserved as frozen evidence, while the accompanying interpretation and reporting products implement the finalized EchoGO v0.1.4 evidence framework. The compendium therefore preserves the original analytical provenance while providing the tables, figures, and supporting evidence used in the published EchoGO analysis. Offline regression and reproduction scripts are included to verify the deposited results without rerunning the original enrichment queries. EchoGO v0.1.4 is archived separately at Zenodo: DOI 10.5281/zenodo.23158481. See the included README for the structure of the compendium, provenance of individual resources, reproduction instructions, and licensing information.

Authors 4

1. Camilo Escobar-Sierra Aachen

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

2. Felix Langschied

   Goethe University Frankfurt

   Affiliation as printed

   Goethe University Frankfurt

3. Angelina Miller Aachen

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

4. Pedro A. Inostroza Aachen

   University of Gothenburg · RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

   University of Gothenburg