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Reading Between the Reads: A Decade On, Revisiting Sequencing Protocol Annotation in the Sequence Read Archive

Jamie J. Alnasir · 2026 · arXiv (Cornell University)

DOI: 10.48550/arxiv.2610.27331 · cited by 0 works (OpenAlex) · open-access PDF

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En 2015, Alnasir y Shanahan examinaron la anotación de la fragmentación, la preparación del adaptador y el enriquecimiento en el Archivo de lectura de secuencias (SRA). Este estudio revisó esas mediciones utilizando las definiciones de palabras clave SQL originales en un snapshot de datos de secuencias archivadas de la NCBI de septiembre de 2026 reconstruido en el esquema del protocolo histórico SRAdb. Resultados: La base de datos contemporánea contenía 41,593,302 experimentos de campo, en comparación con 419,620 en 2013. En bibliotecas_construcción_protocolo, la proporción que coincide con las tres definiciones de protocolos históricos de palabras clave disminuyó del 4,6% al 1,42%. El campo de la reconstrucción fue NULL en el 67,65% de los experimentos contemporáneos

Machine translation (Meta M2M100); the English original follows.

Abstract

Background: Experimental metadata are essential for interpreting archived sequencing data. In 2015, Alnasir and Shanahan examined the annotation of fragmentation, adapter ligation and enrichment in the Sequence Read Archive (SRA). This study revisits those measurements using the original SQL keyword definitions on a September 2026 NCBI metadata snapshot reconstructed in the historical SRAdb schema. Results: The contemporary database contained 41,593,302 experiments, compared with 419,620 in 2013. In library_construction_protocol, the proportion matching all three historical keyword groups declined from 4.06% to 1.42%. The protocol field was NULL in 67.65% of contemporary experiments. Searching design_description alongside the protocol field increased combined three-step keyword detection to 1,197,367 experiments (2.88%), with most additional matches occurring where the protocol field was NULL. Coverage varied across sequencing library strategies, ranging from 0.26% for AMPLICON to 7.69% for RNA-Seq. Independent comparison of 150 sampled experiment records against source XML confirmed agreement in all historical keyword classifications. Conclusions: The original criteria identify a smaller proportion of experiments in the designated protocol field than a decade earlier. Additional preparation-related terminology is detectable in general experiment descriptions, exposing the limitations of searches restricted to one metadata field. Differences among sequencing strategies complicate historical comparisons as preparation methods evolve. The findings support more consistent protocol annotation and the need to distinguish keyword occurrence from the adequacy of experimental documentation.

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Topics: Metadata, Annotation, Computer science, Information retrieval, Protocol (science), XML

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