torchcell.adapters

BioCypher adapters that turn a built torchcell dataset into knowledge-graph nodes and edges. There is one adapter class per registered dataset (for example SmfCostanzo2016Adapter or BetaxanthinCachera2023Adapter), and most inherit from CellAdapter, which reads the dataset’s LMDB records and yields BioCypherNode and BioCypherEdge objects through get_nodes and get_edges. The knowledge-graph builders in torchcell.knowledge_graphs pair each dataset class with its adapter through dataset_adapter_map.

Classes

CellAdapter	Convert a cell experiment dataset into BioCypher nodes and edges for import.
SmfCostanzo2016Adapter	Adapter exposing the single-mutant fitness Costanzo 2016 dataset.
DmfCostanzo2016Adapter	Adapter exposing the double-mutant fitness Costanzo 2016 dataset.
DmiCostanzo2016Adapter	Adapter exposing the double-mutant interaction Costanzo 2016 dataset.
SmfKuzmin2018Adapter	Adapter for the Kuzmin 2018 single-mutant fitness (SMF) dataset.
DmfKuzmin2018Adapter	Adapter for the Kuzmin 2018 double-mutant fitness (DMF) dataset.
TmfKuzmin2018Adapter	Adapter for the Kuzmin 2018 triple-mutant fitness (TMF) dataset.
DmiKuzmin2018Adapter	Adapter for the Kuzmin 2018 double-mutant interaction (DMI) dataset.
TmiKuzmin2018Adapter	Adapter for the Kuzmin 2018 triple-mutant interaction (TMI) dataset.
SmfKuzmin2020Adapter	Adapter exposing the Kuzmin 2020 single-mutant fitness dataset to BioCypher.
DmfKuzmin2020Adapter	Adapter exposing the Kuzmin 2020 double-mutant fitness dataset to BioCypher.
TmfKuzmin2020Adapter	Adapter exposing the Kuzmin 2020 triple-mutant fitness dataset to BioCypher.
DmiKuzmin2020Adapter	Adapter exposing the Kuzmin 2020 double-mutant interaction dataset to BioCypher.
TmiKuzmin2020Adapter	Adapter exposing the Kuzmin 2020 triple-mutant interaction dataset to BioCypher.
GeneEssentialitySgdAdapter	CellAdapter that loads the SGD gene-essentiality dataset into BioCypher.
SynthLethalityYeastSynthLethDbAdapter	BioCypher adapter for the SynthLethDB synthetic lethality dataset.
SynthRescueYeastSynthLethDbAdapter	BioCypher adapter for the SynthLethDB synthetic rescue dataset.
ScmdOhya2005Adapter	Cell adapter that serves the Ohya 2005 SCMD morphology dataset to BioCypher.
SmfODuibhir2014Adapter	Adapter for the O'Duibhir 2014 single-mutant fitness (SMF) dataset.
MicroarrayKemmeren2014Adapter	Cell adapter that serves the Kemmeren 2014 deletion microarray expression dataset to BioCypher.
SmMicroarraySameith2015Adapter	Cell adapter that serves the Sameith 2015 single-mutant microarray expression dataset to BioCypher.
DmMicroarraySameith2015Adapter	Cell adapter that serves the Sameith 2015 double-mutant microarray expression dataset to BioCypher.
CaudalPanTranscriptome2024Adapter	Cell adapter that serves the Caudal 2024 natural-isolate pan-transcriptome dataset to BioCypher.
NadalRibellesPerturbSeq2025Adapter	Cell adapter that serves the Nadal-Ribelles 2025 pseudobulk Perturb-seq dataset to BioCypher.
ScmdOhnuki2018Adapter	Cell adapter that serves the Ohnuki 2018 SCMD CalMorph morphology dataset to BioCypher.
ScmdOhnuki2022Adapter	Cell adapter that serves the Ohnuki 2022 SCMD CalMorph morphology dataset to BioCypher.
CarotenoidOzaydin2013Adapter	Cell adapter that serves the Ozaydin 2013 carotenoid visual-score screen dataset to BioCypher.
BetaxanthinCachera2023Adapter	Cell adapter that serves the Cachera 2023 betaxanthin metabolite screen dataset to BioCypher.
MetaboliteDaSilveira2014Adapter	Cell adapter serving the da Silveira 2014 lipidome (MS lipidomics) dataset to BioCypher.
OrganicAcidYoshida2012Adapter	Cell adapter serving the Yoshida 2012 organic-acid titer dataset to BioCypher.
IsobutanolScreenLopez2024Adapter	Cell adapter serving the Lopez 2024 genome-wide isobutanol biosensor SCREEN to BioCypher.
IsobutanolValidatedLopez2024Adapter	Cell adapter serving the Lopez 2024 validated isobutanol strains to BioCypher.
FattyAcidXue2025Adapter	Cell adapter serving the Xue 2025 free-fatty-acid titer dataset to BioCypher.
MetaboliteZelezniak2018Adapter	Cell adapter that serves the Zelezniak 2018 metabolome dataset to BioCypher.
ProteomeZelezniak2018Adapter	Cell adapter that serves the Zelezniak 2018 SWATH-MS proteome dataset to BioCypher.
ProteomeMessner2023Adapter	Cell adapter serving the Messner 2023 genome-wide KO proteome dataset to BioCypher.
AminoAcidMulleder2016Adapter	Cell adapter that serves the Mulleder 2016 amino-acid metabolome dataset to BioCypher.
AminoAcidCooper2010Adapter	Cell adapter that serves the Cooper 2010 amino-acid metabolome dataset to BioCypher.
Bloom2019Adapter	Cell adapter that serves the Bloom 2019 segregant growth dataset to BioCypher.
EnvChemgenCostanzo2021Adapter	Cell adapter serving the Costanzo 2021 condition-SGA dataset to BioCypher.
EnvChemgenAuesukaree2009Adapter	Cell adapter serving the Auesukaree 2009 stress-sensitivity dataset.
EnvChemgenMota2024Adapter	Cell adapter serving the Mota 2024 weak-acid chemogenomic dataset.
Smith2006Adapter	Cell adapter that serves the the Smith 2006 fatty-acid clear-zone screen to BioCypher.
Smith2016Adapter	Cell adapter that serves the the Smith 2016 CRISPRi chemical-genetic screen to BioCypher.
Lian2019Adapter	Cell adapter that serves the the Lian 2019 MAGIC CRISPRa/i/d furfural screen to BioCypher.
Mormino2022Adapter	Cell adapter that serves the the Mormino 2022 CRISPRi acetic-acid biosensor screen to BioCypher.
EnvChemgenVanacloig2022Adapter	Cell adapter that serves the Vanacloig-Pedros 2022 chemical-genomic screen.
EnvChemgenWildenhain2015Adapter	Cell adapter that serves the Wildenhain 2015 chemical-genetic matrix.
EnvChemgenHoepfner2014Adapter	Cell adapter that serves the Hoepfner 2014 HIP-HOP atlas to BioCypher.
HetHillenmeyer2008Adapter	Cell adapter serving the HIP (heterozygous) log2-ratio dataset to BioCypher.
HomHillenmeyer2008Adapter	Cell adapter serving the HOP (homozygous) z-score dataset to BioCypher.
SmfBaryshnikova2010Adapter	Cell adapter that serves the Baryshnikova 2010 SMF dataset to BioCypher.