Header lines formatting and SMILES for the core elements

README.md

@@ -3,4 +3,66 @@ Protein_Corona
 Files are from:
 
 Protein Corona Fingerprinting Predicts the Cell Association of Gold Nanoparticles, Supplementary Info. 
-pubs.acs.org/doi/abs/10.1021/nn406018q
+http://pubs.acs.org/doi/abs/10.1021/nn406018q
+
+
+File format 
+==============
+
+### Note: this 12-line header parser is deprecated in favour of more flexible Excel parser https://github.com/enanomapper/nmdataparser and [XLSX+JSON](https://apps.ideaconsult.net/enanomapper/ui/uploadsubstance1) upload
+
+* The file [MergetSheets.csv](https://github.com/ideaconsult/Protein_Corona/blob/master/MergedSheets.csv) contains all nanoparticles and related experiments from the above paper
+* Format: Comma separated, with 12 header lines
+* Parser: [loom-nm](https://github.com/vedina/loom/tree/master/loom-nm) package
+* Import: The CSV format and parser are sufficiently generic to allow import into [AMBIT substances](https://apps.ideaconsult.net/enanomapper/ui/uploadsubstance)
+
+###File header
+####Row	1 
+endpointcategory. Specifies an endpoint category. Should be one of [this list](endpointcategory.md).
+
+####Row	2 
+protocol
+
+####Row	3 
+guideline
+
+####Row	4 
+type_of_study
+
+####Row	5 
+type_of_method
+
+####Row	6 
+data_gathering_instruments
+
+####Row	7 
+endpoint
+
+####Row	8 
+condition1
+
+####Row	9 
+condition2
+
+####Row	10 
+condition3
+
+####Row	11 
+result
+
+####Row	12 
+units
+
+
+Examples
+-----
+
+* [Nano particles, experiments](example1.md)
+* [Chemicals, experiments](example2.md)
+
+
+API to use for upload to AMBIT
+----
+
+ See [Substance resource](https://github.com/ideaconsult/examples-ambit/blob/master/ambit-json-docs/substance.md)
+

endpointcategory.md

@@ -0,0 +1,5 @@
+Endpoint categories
+-------------------
+
+<table>
+<tr><td>GI_GENERAL_INFORM</td></tr><tr><td>PC_MELTING</td></tr><tr><td>PC_BOILING</td></tr><tr><td>PC_GRANULOMETRY</td></tr><tr><td>PC_VAPOUR</td></tr><tr><td>PC_PARTITION</td></tr><tr><td>PC_WATER_SOL</td></tr><tr><td>PC_SOL_ORGANIC</td></tr><tr><td>PC_NON_SATURATED_PH</td></tr><tr><td>PC_DISSOCIATION</td></tr><tr><td>AGGLOMERATION_AGGREGATION</td></tr><tr><td>CRYSTALLINE_PHASE</td></tr><tr><td>CRYSTALLITE_AND_GRAIN_SIZE</td></tr><tr><td>ASPECT_RATIO_SHAPE</td></tr><tr><td>SPECIFIC_SURFACE_AREA</td></tr><tr><td>ZETA_POTENTIAL</td></tr><tr><td>SURFACE_CHEMISTRY</td></tr><tr><td>DUSTINESS</td></tr><tr><td>POROSITY</td></tr><tr><td>POUR_DENSITY</td></tr><tr><td>PHOTOCATALYTIC_ACTIVITY</td></tr><tr><td>CATALYTIC_ACTIVITY</td></tr><tr><td>PC_UNKNOWN</td></tr><tr><td>TO_PHOTOTRANS_AIR</td></tr><tr><td>TO_HYDROLYSIS</td></tr><tr><td>TO_BIODEG_WATER_SCREEN</td></tr><tr><td>TO_BIODEG_WATER_SIM</td></tr><tr><td>EN_STABILITY_IN_SOIL</td></tr><tr><td>EN_BIOACCUMULATION</td></tr><tr><td>EN_BIOACCU_TERR</td></tr><tr><td>EN_ADSORPTION</td></tr><tr><td>EN_HENRY_LAW</td></tr><tr><td>EC_FISHTOX</td></tr><tr><td>EC_CHRONFISHTOX</td></tr><tr><td>EC_DAPHNIATOX</td></tr><tr><td>EC_CHRONDAPHNIATOX</td></tr><tr><td>EC_ALGAETOX</td></tr><tr><td>EC_BACTOX</td></tr><tr><td>EC_SEDIMENTDWELLINGTOX</td></tr><tr><td>EC_SOILDWELLINGTOX</td></tr><tr><td>EC_HONEYBEESTOX</td></tr><tr><td>EC_PLANTTOX</td></tr><tr><td>EC_SOIL_MICRO_TOX</td></tr><tr><td>TO_ACUTE_ORAL</td></tr><tr><td>TO_ACUTE_INHAL</td></tr><tr><td>TO_ACUTE_DERMAL</td></tr><tr><td>TO_SKIN_IRRITATION</td></tr><tr><td>TO_EYE_IRRITATION</td></tr><tr><td>TO_SENSITIZATION</td></tr><tr><td>TO_REPEATED_ORAL</td></tr><tr><td>TO_REPEATED_INHAL</td></tr><tr><td>TO_REPEATED_DERMAL</td></tr><tr><td>TO_GENETIC_IN_VITRO</td></tr><tr><td>TO_GENETIC_IN_VIVO</td></tr><tr><td>TO_CARCINOGENICITY</td></tr><tr><td>TO_REPRODUCTION</td></tr><tr><td>TO_DEVELOPMENTAL</td></tr><tr><td>UNKNOWN_TOXICITY</td></tr><tr><td>PROTEOMICS</td></tr></table>

example1.md

@@ -0,0 +1,42 @@
+Example file
+------------
+
+Defines nanoparticles and experiments.  Format supported by AMBIT Substance import.
+
+
+<table>
+<tr>
+<td>EndpointCategory</td><td>Core composition</td><td>Surface modifier</td><td>External Identifier</td><td>PC_GRANULOMETRY</td><td>PC_GRANULOMETRY</td><td>ZETA_POTENTIAL</td><td>ZETA_POTENTIAL</td>
+</tr><tr>
+<td>Protocol</td><td></td><td></td><td></td><td>TEM</td><td>TEM</td><td>DLS</td><td>DLS</td>
+</tr><tr>
+<td>Guideline</td><td></td><td></td><td></td><td>doi: 10.1021/nn406018q</td><td>doi: 10.1021/nn406018q</td><td>doi: 10.1021/nn406018q</td><td>doi: 10.1021/nn406018q</td>
+</tr><tr>
+<td>type_of_study</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td>
+</tr><tr>
+<td>type_of_method</td><td></td><td></td><td></td><td>TEM</td><td>TEM</td><td>DLS</td><td>DLS</td>
+</tr><tr>
+<td>data_gathering_instruments</td><td>Description</td><td></td><td></td><td>Tecnai 20 (FEI) microscope;Tecnai 20 (FEI) microscope;AMT 16000 camera</td><td>Tecnai 20 (FEI) microscope;Tecnai 20 (FEI) microscope;AMT 16000 camera</td><td>ZetaSizer Nano ZS (Malvern Instruments)</td><td>ZetaSizer Nano ZS (Malvern Instruments)</td>
+</tr><tr>
+<td>Endpoint</td><td>Element</td><td>Abbreviated</td><td>Classification</td><td>Core size</td><td>Core size</td><td>ZETA POTENTIAL</td><td>ZETA POTENTIAL</td>
+</tr><tr>
+<td>Cell</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td>
+</tr><tr>
+<td>MEDIUM</td><td></td><td></td><td></td><td></td><td></td><td>Human serum</td><td>Human serum</td>
+</tr><tr>
+<td>Condition</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td>
+</tr><tr>
+<td>Designation</td><td></td><td></td><td></td><td>Mean</td><td>SD</td><td>Mean</td><td>SD</td>
+</tr><tr>
+<td>Units</td><td></td><td></td><td></td><td>nm</td><td>nm</td><td>mV</td><td>nm</td>
+</tr><tr>
+<td>G15.AC</td><td>[Au]</td><td>AC</td><td>Anionic</td><td>14.9</td><td>1.2</td><td>-21.78</td><td>6.81</td>
+</tr><tr>
+<td>G15.AHT</td><td>[Au]</td><td>AHT</td><td>Cationic</td><td>14.9</td><td>1.2</td><td>15.22</td><td>3.05</td>
+</tr><tr>
+<td>G15.Ala-SH</td><td>[Au]</td><td>Ala-SH</td><td>Anionic</td><td>14.9</td><td>1.2</td><td>-24.08</td><td>0.68</td>
+</tr><tr>
+<td>G15.Asn-SH</td><td>[Au]</td><td>Asn-SH</td><td>Anionic</td><td>14.9</td><td>1.2</td><td>-20.27</td><td>6.1</td>
+</tr><tr>
+<td>G15.AUT</td><td>[Au]</td><td>AUT</td><td>Cationic</td><td></td><td></td><td>16.35</td><td>2.26</td>
+</table>

example2.md

@@ -0,0 +1,25 @@
+Example file
+------------
+
+Defines chemicals and experiments.  Format supported by AMBIT Substance import.
+
+<table>
+<tr><td>Chemical</td><td>Chemical</td><td>External Identifier</td><td></td><td>TO_SENSITIZATION</td><td></td><td></tr>
+<tr><td>Protocol</td><td></td><td></td><td></td><td>The Local Lymph Node Assay (LLNA)</td><td>The Myeloid U937 Skin Sensitization Test </td><td>Direct Peptide Reactivity Assay (DPRA)</td></tr>
+<tr><td>Guideline</td><td></td><td></td><td></td><td>OECD TG 429 Local Lymph Node Assay (LLNA)</td><td>The Myeloid U937 Skin Sensitization Test </td><td>DB ALM Protocol No.154</td></tr>
+<tr><td>type_of_study</td><td></td><td></td><td></td><td>measurement of the proliferative activity of draining lymph node cells (LNC)</td><td>CD86 cell surface marker activation </td><td>measures depletion of synthetic heptapeptides containing either cysteine or lysine</td></tr>
+<tr><td>type_of_method</td><td></td><td></td><td></td><td>in vivo</td><td>in vitro</td><td>in chemico</td></tr>
+<tr><td>data_gathering_instruments</td><td></td><td></td><td></td><td>LLNA potency</td><td>Fluorescence</td><td>High-performance liquid chromatography</td></tr>
+<tr><td>Endpoint</td><td>SMILES</td><td>CASRN</td><td>Some property</td><td>LLNA </td><td>EC150</td><td>DPRACys</td></tr>
+<tr><td>Target gene</td><td></td><td></td><td></td><td></td><td>CD86</td><td></td></tr>
+<tr><td>Species</td><td></td><td></td><td></td><td>Murinae</td><td>U-937 cell</td><td></td></tr>
+<tr><td>Dose</td><td></td><td></td><td></td><td></td><td></td><td></td></tr>
+<tr><td>Designation</td><td></td><td></td><td></td><td>interpretation</td><td></td><td></td></tr>
+<tr><td></td><td></td><td></td><td></td><td></td><td>mM</td><td>% peptide remaining</td></tr>
+<tr><td>1-Bromobutane</td><td>BrCCCC</td><td>109-65-9</td><td>0</td><td>Non-sensitizer</td><td>10000</td><td>86.2</td></tr>
+<tr><td>1-Butanol</td><td>OCCCC</td><td>71-36-3</td><td>1</td><td>Non-sensitizer</td><td>10000</td><td>100</td></tr>
+<tr><td>4-Hydroxybenzoic acid</td><td>O=C(O)c(ccc(O)c1)c1</td><td>99-96-7</td><td>2</td><td>Non-sensitizer</td><td>10000</td><td>100</td></tr>
+<tr><td>Diethyl phthalate</td><td>CCOC(=O)c1ccccc1C(=O)OCC</td><td>84-66-2</td><td>3</td><td>Non-sensitizer</td><td>10000</td><td>99.2</td></tr>
+<tr><td>Glycerol</td><td>OCC(O)CO</td><td>56-81-5</td><td>4</td><td>Non-sensitizer</td><td>10000</td><td>100</td></tr>
+<tr><td>Hexane</td><td>C(CCCC)C</td><td>110-54-3</td><td>5</td><td>Non-sensitizer</td><td>10000</td><td>100</td></tr>
+</table>

predicted.csv

@@ -0,0 +1,133 @@
+EndpointCategory,ZETA_POTENTIAL,ZETA_POTENTIAL
+Protocol,Predictive model,Predictive model
+Guideline,http://example.com/model/123,http://example.com/model/456
+type_of_study,,
+type_of_method,,
+data_gathering_instruments,,
+Endpoint,ZETA POTENTIAL,ZETA POTENTIAL
+Cell,,
+MEDIUM,Human Serum,Human Serum
+Model,http://example.com/model/123,http://example.com/model/456
+Designation,,
+Units,mV,mV
+G15.AC,-21.78,-16.78
+G15.AHT,15.22,20.22
+G15.Ala-SH,-24.08,-19.08
+G15.Asn-SH,-20.27,-15.27
+G15.AUT,16.35,21.35
+G15.CALNN,-21.42,-16.42
+G15.CIT,-25.26,-20.26
+G15.cPEG5K-SH,-12.29,-7.29
+G15.cPEG5K-SH (LD),-6.33,-1.33
+G15.CTAB,-5.01,-0.01
+G15.DDT@BDHDA,13.49,18.49
+G15.DDT@CTAB,19.6,24.6
+G15.DDT@DOTAP,13.92,18.92
+G15.DDT@ODA,25.83,30.83
+G15.DDT@SA,-29.37,-24.37
+G15.DDT@SDS,-21.68,-16.68
+G15.DTNB,-24.32,-19.32
+G15.F127,-8.96,-3.96
+G15.Gly-SH,-17.77,-12.77
+G15.HDA,11.21,16.21
+G15.LA,-26.48,-21.48
+G15.MAA,-24.17,-19.17
+G15.MBA,-26.65,-21.65
+G15.MES,-25.55,-20.55
+G15.Met-SH,-22.2,-17.2
+G15.MHA,-24.38,-19.38
+G15.MHDA,-25.65,-20.65
+G15.MPA,-27.52,-22.52
+G15.mPEG1K-SH,-7.56,-2.56
+G15.mPEG20K-SH (LD),-2.47,2.53
+G15.mPEG2K-SH,-6.3,-1.3
+G15.mPEG5K-SH,-9.71,-4.71
+G15.mPEG5K(NH2)-SH,-12.31,-7.31
+G15.MSA,-24.92,-19.92
+G15.MUA,-21.13,-16.13
+G15.MUEG4,-2.84,2.16
+G15.MUTA,18.17,23.17
+G15.nPEG5K-SH,7.17,12.17
+G15.nPEG5K-SH (LD),-9.35,-4.35
+G15.NT@DCA,-4.78,0.22
+G15.NT@F127,-3.07,1.93
+G15.NT@PSMA-AAP,-20.23,-15.23
+G15.NT@PSMA-EA,-21.32,-16.32
+G15.NT@PSMA-EDA,-18.3,-13.3
+G15.NT@PSMA-Urea,-13.98,-8.98
+G15.NT@PVA,-2.02,2.98
+G15.ODA,18.85,23.85
+G15.PAH-SH,12.19,17.19
+G15.PEG3K(NH2)-SH,-7.85,-2.85
+G15.PEI-SH,15.27,20.27
+G15.Phe,-28.93,-23.93
+G15.Phe-SH,-16.94,-11.94
+G15.PLL-SH,19.01,24.01
+G15.PVA,-6.94,-1.94
+G15.PVP,-7.34,-2.34
+G15.SA,-24.63,-19.63
+G15.Ser-SH,-20.4,-15.4
+G15.SPP,-23.58,-18.58
+G15.T20,-10.71,-5.71
+G15.Thr-SH,-18.46,-13.46
+G15.TP,-21.75,-16.75
+G15.Trp-SH,-17.95,-12.95
+G30.AC,-33.12,-28.12
+G30.AUT,19.23,24.23
+G30.CALNN,-29.75,-24.75
+G30.CFGAILS,-28.75,-23.75
+G30.cPEG5K-SH,-20.96,-15.96
+G30.DDT@BDHDA,19.93,24.93
+G30.DDT@CTAB,7.35,12.35
+G30.DDT@DOTAP,20.08,25.08
+G30.DDT@HDA,18.93,23.93
+G30.LA,-32.37,-27.37
+G30.MAA,-28.55,-23.55
+G30.Met-SH,-30.57,-25.57
+G30.MHDA,-33.48,-28.48
+G30.mPEG20K-SH (LD),-6.89,-1.89
+G30.MUA,-32.67,-27.67
+G30.MUTA,24.34,29.34
+G30.NT@F127,-4.96,0.04
+G30.PAH-SH,16.08,21.08
+G30.Thr-SH,-27.78,-22.78
+G30.TP,-33.97,-28.97
+G60.AUT,19.11,24.11
+G60.CIT,-34.58,-29.58
+G60.cPEG5K-SH (LD),-19.12,-14.12
+G60.CTAB,-21.45,-16.45
+G60.CVVIT,-36.08,-31.08
+G60.DDT@BDHDA,22.78,27.78
+G60.DDT@DOTAP,25.73,30.73
+G60.DTNB,-37.05,-32.05
+G60.HDA,21.63,26.63
+G60.MBA,-34.72,-29.72
+G60.MPA,-38.62,-33.62
+G60.mPEG20K-SH,-0.6,4.4
+G60.mPEG5K-SH,-3.1,1.9
+G60.MUTA,24.14,29.14
+G60.nPEG5K-SH,9.82,14.82
+G60.NT@PSMA-AP,-41.68,-36.68
+G60.NT@PVA,-2.31,2.69
+G60.ODA,22.63,27.63
+G60.Phe-SH,-28.83,-23.83
+G60.PVA,-7.62,-2.62
+G60.Ser-SH,-34.23,-29.23
+G60.SPP,-30.7,-25.7
+G60.Trp-SH,-33.47,-28.47
+S40.AUT,,
+S40.CIT,,
+S40.cPEG5K-SH,,
+S40.DDT@DOTAP,,
+S40.HDA,,
+S40.LA,,
+S40.MAA,,
+S40.MBA,,
+S40.MES,,
+S40.MHDA,,
+S40.mPEG5K-SH,,
+S40.MUTA,,
+S40.nPEG5K-SH,,
+S40.PLL-SH,,
+S40.PVA,,
+S40.SA,,