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The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
2017
Nucleic Acids Research
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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
2020
F1000Research
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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
2019
F1000Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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]
2020
bioRxiv
pre-print
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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
2019
Current Biology
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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
2020
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
.: 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