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The cBioPortal can be queried either using the web interface or through programmable application programming interface (API).
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The database can be queried either TF family-wise or using RGAP gene locus IDs.
Using Import.io, the data can be queried either manually or through an API.
The literature data can be queried either based on cancer type or gene name.
Two strategies were used: the cyanobacterial sxt genes were queried either against the assembled Alexandrium datasets or the unassembled 454 read datasets.
Most of those who were queried either fell silent or laughed in disbelief.
The transcript abundance associated with a given gene can be queried using either a Eutrema locus identifier (e.g. Thhalv10012839m.g) or an Arabidopsis locus identifier (e.g. At5g49740).
Genes/proteins can be queried using either the gene name (the official HGNC [ 20] name, Entrez Gene [ 11], Ensembl [ 21]), Affymetrix identifier, current UniGene/UniProt [ 1] cluster identifier, or GenBank [ 2] accession number of a sequence (Refseq ID) associated with the gene through UniGene/UniProt.
Both KBs can be queried using SPARQL and SQL.
They are queried simultaneously using the MIEL language.
HOCTARdb can be queried by information regarding either miRNAs or target genes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com