Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python

Kaleb, Klara; Vesztrocy, Alex Warwick; Altenhoff, Adrian M.; Dessimoz, Christophe

doi:10.12688/f1000research.17548.2

Cited by 15 publications

(12 citation statements)

References 28 publications

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“…OMA has been available in RDF for several years, in addition to other interfaces, namely the web browser, bulk file downloads and the REST API (and associated R and Python omadb libraries) ( 35 ). We have made several improvements to the RDF representation of OMA data.…”

Section: Semantic Interoperability and Federated Queries Based On Rdfmentioning

confidence: 99%

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

Altenhoff

Train

Gilbert

et al. 2020

Nucleic Acids Research

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188

167

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OMA is an established resource to elucidate evolutionary relationships among genes from currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise orthologs, functional annotations, local and global gene order conservation (synteny) information, among many other functions. This update paper describes the reorganisation of the database into gene-, group- and genome-centric pages. Other new and improved features are detailed, such as reporting of the evolutionarily best conserved isoforms of alternatively spliced genes, the inferred local order of ancestral genes, phylogenetic profiling, better cross-references, fast genome mapping, semantic data sharing via RDF, as well as a special coronavirus OMA with 119 viruses from the Nidovirales order, including SARS-CoV-2, the agent of the COVID-19 pandemic. We conclude with improvements to the documentation of the resource through primers, tutorials and short videos. OMA is accessible at https://omabrowser.org.

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Section: Semantic Interoperability and Federated Queries Based On Rdfmentioning

confidence: 99%

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

Altenhoff

Train

Gilbert

et al. 2020

Nucleic Acids Research

Self Cite

188

167

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“…The protein sequences of the SOTP and their corresponding orthologs in R.norvegicus (rat), C.familiaris (dog), and M. fascicularis (macaque), were obtained from the OMA orthology database using OMA IDs as queries (Altenhoff et al, 2018). These data were downloaded from the PyOMADB library (Kaleb et al, 2019) using a python script based on OMA Browser's REST API. With the sequence pairs downloaded, pairwise global Needleman-Wunsch sequence alignments were conducted with BioPython (Cock et al, 2009).…”

Section: Comparison Of Sotp Between Human and Nonclinical Speciesmentioning

confidence: 99%

A Proteomic Platform to Identify Off-Target Proteins Associated with Therapeutic Modalities that Induce Protein Degradation or Gene Silencing

Liu

Zhang

Ward

et al. 2020

Preprint

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Novel modalities such as Proteolysis Targeting Chimera (PROTAC) and RNA interference (RNAi) have a mechanism of action-based potential to alter the abundance of off-target proteins. The current in vitro secondary pharmacology assays, which evaluate off-target binding or activity of small molecules, do not fully assess the off-target effects of PROTAC and are not applicable to RNAi. To address this gap, we developed a proteomics-based platform to comprehensively evaluated abundance of off-target proteins. The first part of the manuscript describes the rationale and process through which the off-target proteins and cell lines were selected. The off-target proteins were selected from the entire human proteome based on genetics and pharmacology data (Deaton et al., 2018). The selection yielded 2,813 proteins, forming the nexus of a panel that we refer to as the “selected off-target proteome” (SOTP). An algorithm was then used to identify appropriate cell lines. Four human cell lines out of 932 were selected that, collectively, expressed ~ 80% of the SOTP based on transcriptome data. The second part of the manuscript describes the LC-MS/MS experimentation to quantify the intracellular and extracellular proteins of interest in the 4 selected cell lines. Among over 10,000 quantifiable proteins identified, 1,828 were part of the predefined SOTP. The SOTP was designed to be easily modified or expanded, owing rationale selection process developed and the label free LC-MS/MS approach chosen. This versatility inherent to our platform is essential to design fit-for-purpose studies that can address the dynamic questions faced in investigative toxicology.

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“…• Identifying orthologs with OMA: A primer (Software Tool article) 3 • How to build phylogenetic species trees with OMA (Method article) 4 • A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL (Method article) 5 • Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python (Software Tool article) 6 All the aforementioned protocols use publicly available software, and we provide scripts, code snippets, practical examples, and plenty of explanations in order to facilitate the use of OMA in user analyses. We have several more tutorials planned for this collection and aim to continually add more resources to this collection in order to help our users.…”

mentioning

confidence: 99%

“…So far, this collection contains four papers: Identifying orthologs with OMA: A primer ( Software Tool article ) 3 How to build phylogenetic species trees with OMA ( Method article ) 4 A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL ( Method article ) 5 Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python ( Software Tool article ) 6 …”

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confidence: 99%

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Making the most of genomic data with OMA

Glover

2020

F1000Res

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Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python

Cited by 15 publications

References 28 publications

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

A Proteomic Platform to Identify Off-Target Proteins Associated with Therapeutic Modalities that Induce Protein Degradation or Gene Silencing

Making the most of genomic data with OMA

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