Cavalcante, J. V. F. | Search bioRxiv

bioRxiv2024

Bringing PanglaoDB to 5-star Linked Open Data using Wikidata

PanglaoDB is a database of cell-type markers widely used for single-cell RNA sequencing data analysis. However, cell types and genes in the database are encoded by free text, lacking proper identifiers. Wikidata, is a freely editable knowledge graph database useful for integrating biomedical knowledge. We thus reasoned that porting PanglaoDBs markers to the platform could improve their reusability and overall technical quality (FAIRness). We mapped 188 cell types from PanglaoDB to species-neutral terms on Wikidata and created 376 species-specific terms for cell types in Homo sapiens and Mus musculus. These terms were enriched with marker information via the has marker (P8872) property, totaling over 15.000 cell type X marker associations (w.wiki/9iw6). We explored this new subset of the graph via SPARQL queries, illustrating the discovery potential of structured, integrated knowledge. For example, we found a previously unexplored link between rosehip neurons, clozapine, and schizophrenia via the HRH1 marker. Besides the graph-based insights, we took time to describe the details of the reconciliation process, hoping to stimulate more resources for a move to a 5-star linked open data format.

bioinformatics↗

bioRxiv2022

Metagenomic analyses reveal the influence of depth layers on marine biodiversity in tropical and subtropical regions.

The emergence of open ocean global-scale studies provided important information about the genomics of oceanic microbial communities. Metagenomic analyses shed a light on the structure of marine habitats, unraveling the biodiversity of different water masses. Many biological and environmental factors can contribute to marine organism composition, such as depth. However, much remains unknown about the taxonomic and functional features of microbial communities in different water layer depths. Here, we performed a metagenomic analysis of 76 samples from the Tara Ocean Project, distributed in 8 collection stations located in tropical or subtropical regions, and sampled from three layers of depth (surface water layer - SRF, deep chlorophyll maximum layer - DCM, and mesopelagic zone - MES). In total, we assigned genomic sequences to 669.713.333 organisms. The SRF and DCM depth layers are similar in abundance and diversity, while the MES layer presents greater diversity than the other layers. Diversity clustering analysis shows differences regarding the taxonomic content of samples. At the domain level, bacteria prevail in the majority of samples, and the MES layer presents the highest proportion of archaea among all samples. A core of essential biological functions was identified between the depth layers, such as DNA replication, translation, transmembrane transport, and DNA repair. However, some biological functions were found exclusively in each depth layer, suggesting different functional profiles for each of them. Taken together, our results indicate that the depth layer influences microbial sample composition and diversity.

microbiology↗