LMSD: Lipid Maps Structure Database (LMSD)

In WMBEdmands/compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

This dataset contains fields from the LMSD database (http://www.lipidmaps.org/data/structure/index.html) The variables are as follows:

Usage

data(LMSD)

Format

A data frame with 34127 rows and 294 columns

Details

1. WebAddress web address for database (when combined with the Unique_DB_ID entry this will provide a direct link to the online database entry e.g. Web address : "LMFA00000001" + Unique_DB_ID : "LMFA00000001" = http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000001)

2. Unique_DB_ID. LMSD unique reference number

3. name. LMSD entry name

4. monoisotopic_weight. Monoisotopic weight of LMSD entry (58.04187 – 1199.439)

5. SMILES. Canonical SMILES code of LMSD entry (converted from sdf file using the ChemmineR::sdf2smiles)

6. molecular_formula. Molecular formula of LMSD entry

7. cas_number. CAS registry number of LMSD entry

8. compound_class. compound class information utilized by annoCompoundClass function.

9. - 294. (n=286) all molecular descriptors extracted from the chemistry development kit using the rcdk package and a 1024bit chemical fingerprint obtained using the ChemmineR package in the form of an index rather than full length 1024 binary representation. see table below for details:

category	className	molDescNames
topological	SmallRingDescriptor	MD_nSmallRings
topological	SmallRingDescriptor	MD_nAromRings
topological	SmallRingDescriptor	MD_nRingBlocks
topological	SmallRingDescriptor	MD_nAromBlocks
topological	SmallRingDescriptor	MD_nRings3
topological	SmallRingDescriptor	MD_nRings4
topological	SmallRingDescriptor	MD_nRings5
topological	SmallRingDescriptor	MD_nRings6
topological	SmallRingDescriptor	MD_nRings7
topological	SmallRingDescriptor	MD_nRings8
topological	SmallRingDescriptor	MD_nRings9
topological	FractionalPSADescriptor	MD_tpsaEfficiency
topological	ZagrebIndexDescriptor	MD_Zagreb
constitutional	XLogPDescriptor	MD_XLogP
topological	WienerNumbersDescriptor	MD_WPATH
topological	WienerNumbersDescriptor	MD_WPOL
hybrid	WHIMDescriptor	MD_Wlambda1.unity
hybrid	WHIMDescriptor	MD_Wlambda2.unity
hybrid	WHIMDescriptor	MD_Wlambda3.unity
hybrid	WHIMDescriptor	MD_Wnu1.unity
hybrid	WHIMDescriptor	MD_Wnu2.unity
hybrid	WHIMDescriptor	MD_Wgamma1.unity
hybrid	WHIMDescriptor	MD_Wgamma2.unity
hybrid	WHIMDescriptor	MD_Wgamma3.unity
hybrid	WHIMDescriptor	MD_Weta1.unity
hybrid	WHIMDescriptor	MD_Weta2.unity
hybrid	WHIMDescriptor	MD_Weta3.unity
hybrid	WHIMDescriptor	MD_WT.unity
hybrid	WHIMDescriptor	MD_WA.unity
hybrid	WHIMDescriptor	MD_WV.unity
hybrid	WHIMDescriptor	MD_WK.unity
hybrid	WHIMDescriptor	MD_WG.unity
hybrid	WHIMDescriptor	MD_WD.unity
topological	WeightedPathDescriptor	MD_WTPT.1
topological	WeightedPathDescriptor	MD_WTPT.2
topological	WeightedPathDescriptor	MD_WTPT.3
topological	WeightedPathDescriptor	MD_WTPT.4
topological	WeightedPathDescriptor	MD_WTPT.5
constitutional	WeightDescriptor	MD_MW
topological	VAdjMaDescriptor	MD_VAdjMat
topological	VABCDescriptor	MD_VABC
topological	TPSADescriptor	MD_TopoPSA
constitutional	RuleOfFiveDescriptor	MD_LipinskiFailures
constitutional	RotatableBondsCountDescriptor	MD_nRotB
topological	PetitjeanShapeIndexDescriptor	MD_topoShape
topological	PetitjeanShapeIndexDescriptor	MD_geomShape
topological	PetitjeanNumberDescriptor	MD_PetitjeanNumber
geometrical	MomentOfInertiaDescriptor	MD_MOMI.X
geometrical	MomentOfInertiaDescriptor	MD_MOMI.Y
geometrical	MomentOfInertiaDescriptor	MD_MOMI.Z
geometrical	MomentOfInertiaDescriptor	MD_MOMI.XY
geometrical	MomentOfInertiaDescriptor	MD_MOMI.XZ
geometrical	MomentOfInertiaDescriptor	MD_MOMI.YZ
geometrical	MomentOfInertiaDescriptor	MD_MOMI.R
topological	MDEDescriptor	MD_MDEC.11
topological	MDEDescriptor	MD_MDEC.12
topological	MDEDescriptor	MD_MDEC.13
topological	MDEDescriptor	MD_MDEC.14
topological	MDEDescriptor	MD_MDEC.22
topological	MDEDescriptor	MD_MDEC.23
topological	MDEDescriptor	MD_MDEC.24
topological	MDEDescriptor	MD_MDEC.33
topological	MDEDescriptor	MD_MDEC.34
topological	MDEDescriptor	MD_MDEC.44
topological	MDEDescriptor	MD_MDEO.11
topological	MDEDescriptor	MD_MDEO.12
topological	MDEDescriptor	MD_MDEO.22
topological	MDEDescriptor	MD_MDEN.11
topological	MDEDescriptor	MD_MDEN.12
topological	MDEDescriptor	MD_MDEN.13
topological	MDEDescriptor	MD_MDEN.22
topological	MDEDescriptor	MD_MDEN.23
topological	MDEDescriptor	MD_MDEN.33
constitutional	MannholdLogPDescriptor	MD_MLogP
constitutional	LongestAliphaticChainDescriptor	MD_nAtomLAC
geometrical	LengthOverBreadthDescriptor	MD_LOBMAX
geometrical	LengthOverBreadthDescriptor	MD_LOBMIN
constitutional	LargestPiSystemDescriptor	MD_nAtomP
constitutional	LargestChainDescriptor	MD_nAtomLC
topological	KierHallSmartsDescriptor	MD_khs.sLi
topological	KierHallSmartsDescriptor	MD_khs.ssBe
topological	KierHallSmartsDescriptor	MD_khs.ssssBe
topological	KierHallSmartsDescriptor	MD_khs.ssBH
topological	KierHallSmartsDescriptor	MD_khs.sssB
topological	KierHallSmartsDescriptor	MD_khs.ssssB
topological	KierHallSmartsDescriptor	MD_khs.sCH3
topological	KierHallSmartsDescriptor	MD_khs.dCH2
topological	KierHallSmartsDescriptor	MD_khs.ssCH2
topological	KierHallSmartsDescriptor	MD_khs.tCH
topological	KierHallSmartsDescriptor	MD_khs.dsCH
topological	KierHallSmartsDescriptor	MD_khs.aaCH
topological	KierHallSmartsDescriptor	MD_khs.sssCH
topological	KierHallSmartsDescriptor	MD_khs.ddC
topological	KierHallSmartsDescriptor	MD_khs.tsC
topological	KierHallSmartsDescriptor	MD_khs.dssC
topological	KierHallSmartsDescriptor	MD_khs.aasC
topological	KierHallSmartsDescriptor	MD_khs.aaaC
topological	KierHallSmartsDescriptor	MD_khs.ssssC
topological	KierHallSmartsDescriptor	MD_khs.sNH3
topological	KierHallSmartsDescriptor	MD_khs.sNH2
topological	KierHallSmartsDescriptor	MD_khs.ssNH2
topological	KierHallSmartsDescriptor	MD_khs.dNH
topological	KierHallSmartsDescriptor	MD_khs.ssNH
topological	KierHallSmartsDescriptor	MD_khs.aaNH
topological	KierHallSmartsDescriptor	MD_khs.tN
topological	KierHallSmartsDescriptor	MD_khs.sssNH
topological	KierHallSmartsDescriptor	MD_khs.dsN
topological	KierHallSmartsDescriptor	MD_khs.aaN
topological	KierHallSmartsDescriptor	MD_khs.sssN
topological	KierHallSmartsDescriptor	MD_khs.ddsN
topological	KierHallSmartsDescriptor	MD_khs.aasN
topological	KierHallSmartsDescriptor	MD_khs.ssssN
topological	KierHallSmartsDescriptor	MD_khs.sOH
topological	KierHallSmartsDescriptor	MD_khs.dO
topological	KierHallSmartsDescriptor	MD_khs.ssO
topological	KierHallSmartsDescriptor	MD_khs.aaO
topological	KierHallSmartsDescriptor	MD_khs.sF
topological	KierHallSmartsDescriptor	MD_khs.sSiH3
topological	KierHallSmartsDescriptor	MD_khs.ssSiH2
topological	KierHallSmartsDescriptor	MD_khs.sssSiH
topological	KierHallSmartsDescriptor	MD_khs.ssssSi
topological	KierHallSmartsDescriptor	MD_khs.sPH2
topological	KierHallSmartsDescriptor	MD_khs.ssPH
topological	KierHallSmartsDescriptor	MD_khs.sssP
topological	KierHallSmartsDescriptor	MD_khs.dsssP
topological	KierHallSmartsDescriptor	MD_khs.sssssP
topological	KierHallSmartsDescriptor	MD_khs.sSH
topological	KierHallSmartsDescriptor	MD_khs.dS
topological	KierHallSmartsDescriptor	MD_khs.ssS
topological	KierHallSmartsDescriptor	MD_khs.aaS
topological	KierHallSmartsDescriptor	MD_khs.dssS
topological	KierHallSmartsDescriptor	MD_khs.ddssS
topological	KierHallSmartsDescriptor	MD_khs.sCl
topological	KierHallSmartsDescriptor	MD_khs.sGeH3
topological	KierHallSmartsDescriptor	MD_khs.ssGeH2
topological	KierHallSmartsDescriptor	MD_khs.sssGeH
topological	KierHallSmartsDescriptor	MD_khs.ssssGe
topological	KierHallSmartsDescriptor	MD_khs.sAsH2
topological	KierHallSmartsDescriptor	MD_khs.ssAsH
topological	KierHallSmartsDescriptor	MD_khs.sssAs
topological	KierHallSmartsDescriptor	MD_khs.sssdAs
topological	KierHallSmartsDescriptor	MD_khs.sssssAs
topological	KierHallSmartsDescriptor	MD_khs.sSeH
topological	KierHallSmartsDescriptor	MD_khs.dSe
topological	KierHallSmartsDescriptor	MD_khs.ssSe
topological	KierHallSmartsDescriptor	MD_khs.aaSe
topological	KierHallSmartsDescriptor	MD_khs.dssSe
topological	KierHallSmartsDescriptor	MD_khs.ddssSe
topological	KierHallSmartsDescriptor	MD_khs.sBr
topological	KierHallSmartsDescriptor	MD_khs.sSnH3
topological	KierHallSmartsDescriptor	MD_khs.ssSnH2
topological	KierHallSmartsDescriptor	MD_khs.sssSnH
topological	KierHallSmartsDescriptor	MD_khs.ssssSn
topological	KierHallSmartsDescriptor	MD_khs.sI
topological	KierHallSmartsDescriptor	MD_khs.sPbH3
topological	KierHallSmartsDescriptor	MD_khs.ssPbH2
topological	KierHallSmartsDescriptor	MD_khs.sssPbH
topological	KierHallSmartsDescriptor	MD_khs.ssssPb
topological	KappaShapeIndicesDescriptor	MD_Kier1
topological	KappaShapeIndicesDescriptor	MD_Kier2
topological	KappaShapeIndicesDescriptor	MD_Kier3
topological	HybridizationRatioDescriptor	MD_HybRatio
electronic	HBondDonorCountDescriptor	MD_nHBDon
electronic	HBondAcceptorCountDescriptor	MD_nHBAcc
geometrical	GravitationalIndexDescriptor	MD_GRAV.1
geometrical	GravitationalIndexDescriptor	MD_GRAV.2
geometrical	GravitationalIndexDescriptor	MD_GRAV.3
geometrical	GravitationalIndexDescriptor	MD_GRAVH.1
geometrical	GravitationalIndexDescriptor	MD_GRAVH.2
geometrical	GravitationalIndexDescriptor	MD_GRAVH.3
geometrical	GravitationalIndexDescriptor	MD_GRAV.4
geometrical	GravitationalIndexDescriptor	MD_GRAV.5
geometrical	GravitationalIndexDescriptor	MD_GRAV.6
topological	FragmentComplexityDescriptor	MD_fragC
topological	FMFDescriptor	MD_FMF
topological	EccentricConnectivityIndexDescriptor	MD_ECCEN
electronic	CPSADescriptor	MD_PPSA.1
electronic	CPSADescriptor	MD_PPSA.2
electronic	CPSADescriptor	MD_PPSA.3
electronic	CPSADescriptor	MD_PNSA.1
electronic	CPSADescriptor	MD_PNSA.2
electronic	CPSADescriptor	MD_PNSA.3
electronic	CPSADescriptor	MD_DPSA.1
electronic	CPSADescriptor	MD_DPSA.2
electronic	CPSADescriptor	MD_DPSA.3
electronic	CPSADescriptor	MD_FPSA.1
electronic	CPSADescriptor	MD_FPSA.2
electronic	CPSADescriptor	MD_FPSA.3
electronic	CPSADescriptor	MD_FNSA.1
electronic	CPSADescriptor	MD_FNSA.2
electronic	CPSADescriptor	MD_FNSA.3
electronic	CPSADescriptor	MD_WPSA.1
electronic	CPSADescriptor	MD_WPSA.2
electronic	CPSADescriptor	MD_WPSA.3
electronic	CPSADescriptor	MD_WNSA.1
electronic	CPSADescriptor	MD_WNSA.2
electronic	CPSADescriptor	MD_WNSA.3
electronic	CPSADescriptor	MD_RPCG
electronic	CPSADescriptor	MD_RNCG
electronic	CPSADescriptor	MD_RPCS
electronic	CPSADescriptor	MD_RNCS
electronic	CPSADescriptor	MD_THSA
electronic	CPSADescriptor	MD_TPSA
electronic	CPSADescriptor	MD_RHSA
electronic	CPSADescriptor	MD_RPSA
topological	ChiPathDescriptor	MD_SP.0
topological	ChiPathDescriptor	MD_SP.1
topological	ChiPathDescriptor	MD_SP.2
topological	ChiPathDescriptor	MD_SP.3
topological	ChiPathDescriptor	MD_SP.4
topological	ChiPathDescriptor	MD_SP.5
topological	ChiPathDescriptor	MD_SP.6
topological	ChiPathDescriptor	MD_SP.7
topological	ChiPathDescriptor	MD_VP.0
topological	ChiPathDescriptor	MD_VP.1
topological	ChiPathDescriptor	MD_VP.2
topological	ChiPathDescriptor	MD_VP.3
topological	ChiPathDescriptor	MD_VP.4
topological	ChiPathDescriptor	MD_VP.5
topological	ChiPathDescriptor	MD_VP.6
topological	ChiPathDescriptor	MD_VP.7
topological	ChiPathClusterDescriptor	MD_SPC.4
topological	ChiPathClusterDescriptor	MD_SPC.5
topological	ChiPathClusterDescriptor	MD_SPC.6
topological	ChiPathClusterDescriptor	MD_VPC.4
topological	ChiPathClusterDescriptor	MD_VPC.5
topological	ChiPathClusterDescriptor	MD_VPC.6
topological	ChiClusterDescriptor	MD_SC.3
topological	ChiClusterDescriptor	MD_SC.4
topological	ChiClusterDescriptor	MD_SC.5
topological	ChiClusterDescriptor	MD_SC.6
topological	ChiClusterDescriptor	MD_VC.3
topological	ChiClusterDescriptor	MD_VC.4
topological	ChiClusterDescriptor	MD_VC.5
topological	ChiClusterDescriptor	MD_VC.6
topological	ChiChainDescriptor	MD_SCH.3
topological	ChiChainDescriptor	MD_SCH.4
topological	ChiChainDescriptor	MD_SCH.5
topological	ChiChainDescriptor	MD_SCH.6
topological	ChiChainDescriptor	MD_SCH.7
topological	ChiChainDescriptor	MD_VCH.3
topological	ChiChainDescriptor	MD_VCH.4
topological	ChiChainDescriptor	MD_VCH.5
topological	ChiChainDescriptor	MD_VCH.6
topological	ChiChainDescriptor	MD_VCH.7
topological	CarbonTypesDescriptor	MD_C1SP1
topological	CarbonTypesDescriptor	MD_C2SP1
topological	CarbonTypesDescriptor	MD_C1SP2
topological	CarbonTypesDescriptor	MD_C2SP2
topological	CarbonTypesDescriptor	MD_C3SP2
topological	CarbonTypesDescriptor	MD_C1SP3
topological	CarbonTypesDescriptor	MD_C2SP3
topological	CarbonTypesDescriptor	MD_C3SP3
topological	CarbonTypesDescriptor	MD_C4SP3
electronic	BPolDescriptor	MD_bpol
constitutional	BondCountDescriptor	MD_nB
hybrid	BCUTDescriptor	MD_BCUTw.1l
hybrid	BCUTDescriptor	MD_BCUTw.1h
hybrid	BCUTDescriptor	MD_BCUTc.1l
hybrid	BCUTDescriptor	MD_BCUTc.1h
hybrid	BCUTDescriptor	MD_BCUTp.1l
hybrid	BCUTDescriptor	MD_BCUTp.1h
constitutional	BasicGroupCountDescriptor	MD_nBase
topological	AutocorrelationDescriptorPolarizability	MD_ATSp1
topological	AutocorrelationDescriptorPolarizability	MD_ATSp2
topological	AutocorrelationDescriptorPolarizability	MD_ATSp3
topological	AutocorrelationDescriptorPolarizability	MD_ATSp4
topological	AutocorrelationDescriptorPolarizability	MD_ATSp5
topological	AutocorrelationDescriptorMass	MD_ATSm1
topological	AutocorrelationDescriptorMass	MD_ATSm2
topological	AutocorrelationDescriptorMass	MD_ATSm3
topological	AutocorrelationDescriptorMass	MD_ATSm4
topological	AutocorrelationDescriptorMass	MD_ATSm5
topological	AutocorrelationDescriptorCharge	MD_ATSc1
topological	AutocorrelationDescriptorCharge	MD_ATSc2
topological	AutocorrelationDescriptorCharge	MD_ATSc3
topological	AutocorrelationDescriptorCharge	MD_ATSc4
topological	AutocorrelationDescriptorCharge	MD_ATSc5
constitutional	AtomCountDescriptor	MD_nAtom
constitutional	AromaticBondsCountDescriptor	MD_nAromBond
constitutional	AromaticAtomsCountDescriptor	MD_naAromAtom
electronic	APolDescriptor	MD_apol
constitutional	ALOGPDescriptor	MD_ALogP
constitutional	ALOGPDescriptor	MD_ALogp2
constitutional	ALOGPDescriptor	MD_AMR
constitutional	AcidicGroupCountDescriptor	MD_nAcid

Source

http://www.lipidmaps.org/resources/downloads/index.html

1. Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz CR, Russell DW, Subramaniam S. LMSD: LIPID MAPS structure database Nucleic Acids Research 35: p. D527-32. PMID:17098933 [doi:10.1093/nar/gkl838] PMID: 17098933

2. Fahy E, Sud M, Cotter D & Subramaniam S. LIPID MAPS online tools for lipid research Nucleic Acids Research (2007) 35: p. W606-12.PMID:17584797 [doi:10.1093/nar/gkm324] PMID: 17584797

WMBEdmands/compMS2Miner documentation built on May 9, 2019, 10:04 p.m.