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The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces

Adrian M Altenhoff, Natasha M Glover, Clément-Marie Train, Klara Kaleb, Alex Warwick Vesztrocy, David Dylus, Tarcisio M de Farias, Karina Zile, Charles Stevenson, Jiao Long, Henning Redestig, Gaston H Gonnet (+1 others)
2017 Nucleic Acids Research  
The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life.  ...  to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate  ...  OMA ('Orthologous Matrix') distinguishes itself through high-quality orthology inferences, a broad coverage of all three domains of life, feature-rich web interface, availability of data in a wide range  ... 
doi:10.1093/nar/gkx1019 pmid:29106550 pmcid:PMC5753216 fatcat:s5iawo2arvaq3dvcvtubr3v53a

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

Ana Claudia Sima, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, Tarcisio Mendes de Farias
2020 F1000Research  
The increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative  ...  In these protocols, we demonstrate through SPARQL queries how to retrieve pairwise orthologs, homologous groups, and hierarchical orthologous groups.  ...  OMA (Altenhoff et al., 2018) provides orthologous gene inferences covering all three domains of life: Archaea, Bacteria, and Eukarya.  ... 
doi:10.12688/f1000research.21027.2 fatcat:sdx3ddz2tvdtzeekyopsajasaa

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

Ana Claudia Sima, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, Tarcisio Mendes de Farias
2019 F1000Research  
The increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative  ...  Institute (EBI) RDF platform, the Database of Orthologous Groups (OrthoDB) and the Microbial Genome Database (MBGD).  ...  OMA (Altenhoff et al., 2018) provides orthologous gene inferences covering all three domains of life: Archaea, Bacteria, and Eukarya.  ... 
doi:10.12688/f1000research.21027.1 pmid:32612807 pmcid:PMC7324951 fatcat:dd4xuvlg6fbwhd3cbxjdgyx4s4

ULK1 and ULK2 are less redundant than previously thought: Computational analysis uncovers distinct regulation and functions of these autophagy induction proteins [article]

Amanda Demeter, Mari Carmen Romero-Mulero, Luca Csabai, Márton Ölbei, Padhmanand Sudhakar, Wilfried Haerty, Tamás Korcsmáros
2020 bioRxiv   pre-print
Despite the high similarity in their enzymatic domain, we found that ULK1 and ULK2 have major differences in their post-translational and transcriptional regulators.  ...  AbstractMacroautophagy, the degradation of cytoplasmic content by lysosomal fusion, is an evolutionary conserved process promoting homeostasis and intracellular defence.  ...  The OMA orthology database in 2018: retrieving evolutionary 486 relationships among all domains of life through richer web and programmatic 487 interfaces.  ... 
doi:10.1101/2020.02.27.967901 fatcat:gd4onv2q7jb6lkidorry23jju4

Short- and Long-Term Effects of UVA on Arabidopsis Are Mediated by a Novel cGMP Phosphodiesterase

Jean-Charles Isner, Vlad-Aris Olteanu, Alexander J. Hetherington, Aude Coupel-Ledru, Peng Sun, Ashley J. Pridgeon, Glyndyr S. Jones, Matthew Oates, Tom A. Williams, Frans J.M. Maathuis, Richard Kift, Ann R. Webb (+3 others)
2019 Current Biology  
We show that in Arabidopsis, short-term exposure to UVA inhibits the opening of stomata, and this requires a reduction in the cytosolic level of cGMP.  ...  These genes have been lost from the genomes of metazoans but are otherwise conserved as single-copy genes across the tree of life.  ...  ., et al. (2018). The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.  ... 
doi:10.1016/j.cub.2019.06.071 pmid:31353185 pmcid:PMC6692503 fatcat:4wzl65mgozhujjygldimhlubhi

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

Ana-Claudia Sima, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, Tarcisio Mendes De Farias
2020
.: The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. Nucleic Acids Res. 2018; 46(D1): 477-485.  ...  The increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative  ...  OMA (Altenhoff et al., 2018) provides orthologous gene inferences covering all three domains of life: Archaea, Bacteria, and Eukarya.  ... 
doi:10.21256/zhaw-20358 fatcat:yvrjtk7s7bau3lrrmxrrsefh6m