Disambiguating chemistry and fixing typos

petermr commented 5 years ago

Chemical nomenclature is complex and ambiguous. Any attempt to disambiguate MUST record ambiguity. Thus acetyl-furan could be 1-acetyl-furan or 2-acetyl-furan, OPSIN (https://opsin.ch.cam.ac.uk) gives:

APPEARS_AMBIGUOUS: Connection of acet to furan

and this must be recorded

Always test with OPSIN.

ambarishK commented 4 years ago

Sir, Please go through the added chemical structure diagrams. 2D images and 3D images.

Count of 2D chemical structure diagrams is 2114. Count of 3D chemical structure diagram is 2004.

petermr commented 4 years ago

Egon Willighagen script ... yes, I can automate [creating Wikidata entry from PubChem].. Basically, just provide a list of smiles to the tool. Look for the "create" script in my ons-wikidata GitHub repo. More later. Have

petermr commented 4 years ago

@ambarishK the chemical structures look very nice. Thank you.

ambarishK commented 4 years ago

Yes, sir. I found SPARQL script into Egon Willighagen GitHub repository. I had seen him over twitter also. I followed him onto GitHub.

petermr commented 4 years ago

Ambarish, Please can you create an HTML table or CSV that we can browse and see the images. In your directory we would have something like

170

etc. On Tue, Aug 27, 2019 at 2:00 PM Ambarish Kumar wrote: > Sir, > Please go through the added chemical structure diagrams. 2D images > > and 3D images > > . > > Count of 2D chemical structure diagrams is 2114. > Count of 3D chemical structure diagram is 2004. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . > -- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

ambarishK commented 4 years ago

Yes sir.

petermr commented 4 years ago

Thanks It doesn't have to be the same document as the spreadsheet - a static HTMLwill do.

On Tue, Aug 27, 2019 at 8:15 PM Ambarish Kumar notifications@github.com wrote:

Yes sir.

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petermr commented 4 years ago

I have manually edited the TSV file into HTML to include images and links to Wikidata. It's static. At present Github does NOT render HTML; you have to download it, although it might be possible to view it as HTML from these suggestions: https://stackoverflow.com/questions/8446218/how-to-see-an-html-page-on-github-as-a-normal-rendered-html-page-to-see-preview Do not do anything to the current file.

resolveCompTable20190828.html

petermr commented 4 years ago

I am VERY pleased with the resolution of compounds in the resolveCompTable20190828.html table. Well done. As far as I can see there are only about 5-10 false positives (e.g SA3, NI) and I'll create a list to be removed. @gilienv and @mannyrules please also check.

ambarishK commented 4 years ago

Sir, even I prepared one table and added to repository now - compoundStructureDiagram.html but could not get an idea to embed images from repository folder. Current file has image path of my laptop i.e "E:/2D_images/*.png".

FPs would be only 07 - ni, sa2, sa3, sh1,sh2, sh3 and sh4. Also, there would be one repeat. Remove duplicated using cid column.

ambarishK commented 4 years ago

Sir, Table header for WIKIDATA is put into last most of the table. It should have been before cid column.

petermr commented 4 years ago

On Wed, Aug 28, 2019 at 11:39 AM Ambarish Kumar notifications@github.com wrote:

Sir, even I prepared one table and added to repository now - compoundStructureDiagram.html https://raw.githubusercontent.com/gilienv/EssOilDB/master/tables/chemistry/compoundStructureDiagram.html but could not get an idea to embed images from repository folder. Current file has image path of my laptop i.e "E:/2D_images/*.png".

If the images are in the same directory tree as the HTML you just need relative links. So if compoundStructureDiagram.html https://raw.githubusercontent.com/gilienv/EssOilDB/master/tables/chemistry/compoundStructureDiagram.html is in /tables/chemistry/ and the images are in tables/chemistry2D_images then the link from compoundStructureDiagram.html https://raw.githubusercontent.com/gilienv/EssOilDB/master/tables/chemistry/compoundStructureDiagram.html is simply: see my files. Or is there a separate problem?

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petermr commented 4 years ago

Thanks, That's a typical error in manual editing.

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ambarishK commented 4 years ago

Sir, synonym table for compounds as well as plants are below. compoundSynonymTable

column description

EID - EssoilDB unique ID for compound name.
SYNONYMS - compound synonym.

plantSynonymTable

column description

pid - EssoilDB unique ID for plant name.
synonyms - plant synonym.

Plant synonyms are from details.csv table.

ambarishK commented 4 years ago

Sir, all compound synonyms are from PubChem and plant synonyms are from details.csv. Plant synonyms are extracted using R-package-taxize from database - "col".

petermr commented 4 years ago

The plant table looks good, BUT the the column "pid" refers to the plant ID is EssoilDB and that should have a letter. We should have three columns,

id    pid name
EPS1 EP99 Foo baricus
EPS2 EP99 Foo xyzzy
EPS3 EP23 Bar fooicus

which says that Foo baricus has a synonym ID of EPS1 and is a synonym of EP99 Foo xyzzy has a synonym ID of EPS2 and is a synonym of EP99 EP99 in the plant table represents the plant and has an approved name (say Foo plughiensis)

On Fri, Sep 6, 2019 at 11:01 AM Ambarish Kumar notifications@github.com wrote:

Sir, synonym table for compounds as well as plants are below. compoundSynonymTable https://github.com/gilienv/EssOilDB/blob/master/tables/chemistry/compoundSynonymTable.tsv

column description

EID - EssoilDB unique ID for compound name.

SYNONYMS - compound synonym.

plantSynonymTable https://github.com/gilienv/EssOilDB/blob/master/tables/plant/plantSynonymTable.csv

column description

pid - EssoilDB unique ID for plant name.

synonyms - plant synonym.

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ambarishK commented 4 years ago

OK sir.

petermr commented 4 years ago

Pubchem is too verbose . We must try Wikidata or CheBI. These synonyms are going to be used for searching.

On Fri, Sep 6, 2019 at 12:23 PM Ambarish Kumar notifications@github.com wrote:

Sir, all compound synonyms are from PubChem and plant synonyms are from details.csv https://github.com/gilienv/EssOilDB/blob/master/tables/plant/details.csv. Plant synonyms are extracted using R-package-taxize from database - "col".

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petermr commented 4 years ago

Please create a flow diagram (with numbers) for where the compounds and the synonyms came from.

On Fri, Sep 6, 2019 at 12:24 PM Ambarish Kumar notifications@github.com wrote:

OK sir.

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ambarishK commented 4 years ago

sir, what is pid (property id) for compound synonyms?

petermr commented 4 years ago

On Fri, Sep 6, 2019 at 12:27 PM Ambarish Kumar notifications@github.com wrote:

sir, what is pid (property id) for compound synonyms?

Do you mean in our synonym table? If a Compound ID has the form C123 I suggest we have CS789 for Compound synonym IDs

Do we have a syntax for Plant IDs? It can't be Pddd as that clashes with Wikidata Did we decide on something like EPddd? If so then EPS9876 for synonym IDs

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ambarishK commented 4 years ago

Yes sir, I assign synonym IDs to plant synonyms as well as compound synonyms. For example -

Compound synonym IDs                     EID
CS789                                                   C123
CS790                                                   C123

Similarly, I will have to assign plant IDs as per the mentioned syntax.

EssoilDB plant ID                           synonym ID
EP123                                                EPS9876
EP123                                                EPS9877

Previous I meant to ask how to get compound synonyms from wikidata. In SPARQL query I will have to pass on wikidata property value for compound synonyms like p662 as wikidata property for PubChem CID.

ambarishK commented 4 years ago

Sir, please go through synonym tables with added synonym IDs. plant synonym table

Column description of plant synonym table is as follows.

EPSID - synonym ID assigned to plant synonym name.
EPID - Unique ID assigned to plant name (EssoilDB ID).
synonyms - plant synonym name.

For example.

EPSID                          EPID                             synonyms        
EPS1                               EP1                                 Abies alba apennina      
EPS2                               EP1                                 Abies alba pardei        
EPS3                                   EP1                                 Abies alba podolica      
EPS4                               EP1                                 Abies argentea       
EPS26                          EP2                                 Abies apollinis      
EPS27                          EP2                                 Abies borisii-regis pungenti-pilosa      
EPS28                          EP2                                 Abies cilicica borisii-regis     
EPS29                          EP3                                 Abies alba cephalonica       
EPS30                           EP3                                Abies apollinis      
EPS31                          EP3                                 Abies apollinis      
EPS32                          EP3                                 Abies apollinis panachaica

compound synonym table

Column description of compound synonym table is as follows.

CSID - compound synonym ID.
EID - unique ID assigned to compounds (EssoilDB ID).
SYNONYM - compound sunonym name.

CSID                EID                   SYNONYM       
CS1             C214              acetate       
CS2                 C214             Acetate Ion        
CS3                 C214             Acetic acid, ion(1-)       
CS4             C214             Acetate ions       
CS5             C214             71-50-1    
CS431               C215             acetic aicd        
CS432           C215             acetic-acid        
CS433          C215                  Glacial acetate    
CS1160        C2776          ethanal        
CS1161        C2776          acetic aldehyde        
CS1162        C2776          ethyl aldehyde     
CS1163        C2776          75-07-0

petermr commented 4 years ago

Thanks, Something seems to have gone wrong here: A group of names are mapped to both EP1186 and EP1188

EPS12565 EP1186 Ocimum sanctum EPS12566 EP1186 Ocimum sanctum angustifolium EPS12567 EP1186 Ocimum sanctum cubensis EPS12568 EP1186 Ocimum sanctum hirsutum EPS12569 EP1186 Ocimum scutellarioides EPS12570 EP1186 Ocimum subserratum EPS12571 EP1186 Ocimum tenuiflorum anisodorum EPS12572 EP1186 Ocimum tenuiflorum villicaulis EPS12573 EP1186 Ocimum tomentosum EPS12574 EP1186 Ocimum villosum EPS12575 EP1186 Plectranthus monachorum EPS12576 EP1187 Lumnitzera carnosa EPS12577 EP1187 Ocimum atrovirens EPS12578 EP1187 Ocimum ebracteatum EPS12579 EP1187 Ocimum graveolens EPS12580 EP1187 Ocimum montevideanum EPS12581 EP1187 Ocimum selloi EPS12582 EP1187 Ocimum selloi angustifolium EPS12583 EP1187 Ocimum selloi carnosum EPS12584 EP1187 Ocimum selloi genuinum EPS12585 EP1187 Ocimum selloi serratum EPS12586 EP1187 Ocimum selloi subintegrifolium EPS12587 EP1187 Ocimum selloi tweedieanum EPS12588 EP1187 Ocimum tweedieanum

EPS12589 EP1188 Geniosporum tenuiflorum EPS12590 EP1188 Lumnitzera tenuiflora EPS12591 EP1188 Moschosma tenuiflorum EPS12592 EP1188 Ocimum anisodorum EPS12593 EP1188 Ocimum caryophyllinum EPS12594 EP1188 Ocimum hirsutum EPS12595 EP1188 Ocimum inodorum EPS12596 EP1188 Ocimum monachorum EPS12597 EP1188 Ocimum sanctum EPS12598 EP1188 Ocimum sanctum angustifolium EPS12599 EP1188 Ocimum sanctum cubensis EPS12600 EP1188 Ocimum sanctum hirsutum EPS12601 EP1188 Ocimum scutellarioides EPS12602 EP1188 Ocimum subserratum EPS12603 EP1188 Ocimum tenuiflorum anisodorum EPS12604 EP1188 Ocimum tenuiflorum villicaulis EPS12605 EP1188 Ocimum tomentosum EPS12606 EP1188 Ocimum villosum

In the details.csv file we have: 1186,Origanum adanense,Origanum adanense K.H.C.Baéªer & H.Duman,3895399,Q15349571,Origanum adanense,NOT A SYNONYM,"Geniosporum tenuiflorum,Lumnitzera tenuiflora,Moschosma tenuiflorum,Ocimum anisodorum,Ocimum caryophyllinum,Ocimum hirsutum,Ocimum inodorum,Ocimum monachorum,Ocimum sanctum,Ocimum sanctum angustifolium,Ocimum sanctum cubensis,Ocimum sanctum hirsutum,Ocimum scutellarioides,Ocimum subserratum,Ocimum tenuiflorum anisodorum,Ocimum tenuiflorum villicaulis,Ocimum tomentosum,Ocimum villosum,Plectranthus monachorum",NA, 1187,Origanum bargyli,Origanum bargyli Mouterde,3895268,Q12242088,Origanum bargyli,NOT A SYNONYM,"Lumnitzera carnosa,Ocimum atrovirens,Ocimum ebracteatum,Ocimum graveolens,Ocimum montevideanum,Ocimum selloi,Ocimum selloi angustifolium,Ocimum selloi carnosum,Ocimum selloi genuinum,Ocimum selloi serratum,Ocimum selloi subintegrifolium,Ocimum selloi tweedieanum,Ocimum tweedieanum",NA, 1188,Ocimum basilicum,Origanum Tourn. ex L.,2926611,Q38859,Origanum basilicum,NOT A SYNONYM,"Geniosporum tenuiflorum,Lumnitzera tenuiflora,Moschosma tenuiflorum,Ocimum anisodorum,Ocimum caryophyllinum,Ocimum hirsutum,Ocimum inodorum,Ocimum monachorum,Ocimum sanctum,Ocimum sanctum angustifolium,Ocimum sanctum cubensis,Ocimum sanctum hirsutum,Ocimum scutellarioides,Ocimum subserratum,Ocimum tenuiflorum anisodorum,Ocimum tenuiflorum villicaulis,Ocimum tomentosum,Ocimum villosum,Plectranthus monachorum,Geniosporum tenuiflorum,Lumnitzera tenuiflora,Moschosma tenuiflorum,Ocimum anisodorum,Ocimum caryophyllinum,Ocimum hirsutum,Ocimum inodorum,Ocimum monachorum,Ocimum sanctum,Ocimum sanctum angustifolium,Ocimum sanctum cubensis,Ocimum sanctum hirsutum,Ocimum scutellarioides,Ocimum subserratum,Ocimum tenuiflorum anisodorum,Ocimum tenuiflorum villicaulis,Ocimum tomentosum,Ocimum villosum,Plectranthus monachorum",sweet basil,Entry not found

Note the NOT A SYNONYM so I would exclude all these.

On Sun, Sep 8, 2019 at 4:16 AM Ambarish Kumar notifications@github.com wrote:

Sir, please go through synonym tables with added synonym IDs. plant synonym table https://github.com/gilienv/EssOilDB/blob/master/tables/plant/plantSynonymTableWithNewID.tsv

Column description of plant synonym table is as follows.

EPSID - synonym ID assigned to plant synonym name.

EPID - Unique ID assigned to plant name (EssoilDB ID).

synonyms - plant synonym name.

For example.

EPSID EPID synonyms
EPS1 EP1 Abies alba apennina
EPS2 EP1 Abies alba pardei
EPS3 EP1 Abies alba podolica
EPS4 EP1 Abies argentea
EPS26 EP2 Abies apollinis
EPS27 EP2 Abies borisii-regis pungenti-pilosa
EPS28 EP2 Abies cilicica borisii-regis
EPS29 EP3 Abies alba cephalonica
EPS30 EP3 Abies apollinis
EPS31 EP3 Abies apollinis
EPS32 EP3 Abies apollinis panachaica

[compound synonym table]

https://github.com/gilienv/EssOilDB/blob/master/tables/chemistry/compoundSynonymTableWithNewID.tsv

Column description of compound synonym table is as follows.

CSID - compound synonym ID.

EID - unique ID assigned to compounds (EssoilDB ID).

SYNONYM - compound sunonym name.

CSID EID SYNONYM
CS1 C214 acetate
CS2 C214 Acetate Ion
CS3 C214 Acetic acid, ion(1-)
CS4 C214 Acetate ions
CS5 C214 71-50-1
CS431 C215 acetic aicd
CS432 C215 acetic-acid
CS433 C215 Glacial acetate
CS1160 C2776 ethanal
CS1161 C2776 acetic aldehyde
CS1162 C2776 ethyl aldehyde
CS1163 C2776 75-07-0

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petermr commented 4 years ago

On Sun, Sep 8, 2019 at 4:16 AM Ambarish Kumar notifications@github.com wrote:

[compound synonym table]

https://github.com/gilienv/EssOilDB/blob/master/tables/chemistry/compoundSynonymTableWithNewID.tsv

Column description of compound synonym table is as follows.

CSID - compound synonym ID.

EID - unique ID assigned to compounds (EssoilDB ID).

SYNONYM - compound sunonym name.

CSID EID SYNONYM
CS1 C214 acetate
CS2 C214 Acetate Ion
CS3 C214 Acetic acid, ion(1-)
CS4 C214 Acetate ions
CS5 C214 71-50-1
CS431 C215 acetic aicd
CS432 C215 acetic-acid
CS433 C215 Glacial acetate
CS1160 C2776 ethanal
CS1161 C2776 acetic aldehyde
CS1162 C2776 ethyl aldehyde
CS1163 C2776 75-07-0

This is looking better. We don't want more synonyms than this if we can help it.

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ambarishK commented 4 years ago

Yes sir. Should we go for applying regex over compound name synonyms?

I am going through details.csv. synonyms are not consistent with available synonym names in db="col". For example.

pid | normalied_name | synonyms
1159 | Ocimum americanum | Dracocephalum sibiricum,Glechoma   sibirica,Moldavica elata,Nepeta macrantha
1160 | Ocimum basilicum | NA
1161 | Ocimum basilicum | Nepeta purpurea
1162 | Ocimum basilicum | Nicotiana alba,Nicotiana alipes,Nicotiana attenuata,Nicotiana   capensis,Nicotiana caudata,Nicotiana chinensis,Nicotiana crispula,Nicotiana   florida,Nicotiana frutescens,Nicotiana fruticosa,Nicotiana gigantea,Nicotiana   gracilipes,Nicotiana guatemalensis,Nicotiana havanensis,Nicotiana   lancifolia,Nicotiana lancifolia,Nicotiana latissima,Nicotiana   lehmanni,Nicotiana lingua,Nicotiana loxensis,Nicotiana macrophylla,Nicotiana   marylandica,Nicotiana mexicana,Nicotiana pallescens,Nicotiana   petiolata,Nicotiana pilosa,Nicotiana serotina,Nicotiana tabaca,Nicotiana   turcica,Nicotiana verdon,Nicotiana ybarrensis,Tabacum latissimum,Tabacum   nicotianum,Tabacum ovatofolium
1163 | Ocimum basilicum | Erobathos damascenum,Melanthium damascenum,Nigella bourgaei,Nigella   coerulea,Nigella damascena africana,Nigella damascena minor,Nigella damascena   minor,Nigella damascena oligogyna,Nigella elegans,Nigella involucrata,Nigella   multifida,Nigella romana,Nigella taurica
1164 | Ocimum basilicum | NA
1165 | Ocimum basilicum? | Gymnadenia nigra longibracteata,Gymnigritella brachystachya,Gymnigritella   megastachya,Habenaria nigra,Nigritella angustifolia,Nigritella angustifolia   longibracteata,Nigritella brachystachya,Nigritella fragrans,Nigritella   hybrida,Nigritella megastachya,Nigritella nigra,Nigritella nigra   longibracteata,Nigritella suaveolens,Nigritella suaveolens   nigroconopsea,Orchis atropurpurea,Orchis moritziana,Orchis nigra,Orchis nigra   flore-rosea,Orchis reichenbachii,Orchis variegata,Satyrium nigrum,Sieberia   nigra
1166 | Ocimum basilicum | Baeckea linearis
1167 | Ocimum basilicum | Ocimum adscendens,Ocimum diffusum,Ocimum glaucum,Ocimum menthoides,Ocimum   viscosum,Orthosiphon diffusus,Orthosiphon hispidus,Orthosiphon   tomentosus,Orthosiphon tristis,Plectranthus viscosus
1168 | Ocimum ciliatum | Becium obovatum glabrior,Ocimum album,Ocimum brachiatum,Ocimum   canum,Ocimum canum integrifolium,Ocimum dichotomum,Ocimum dinteri,Ocimum   fluminense,Ocimum fruticulosum,Ocimum hispidulum,Ocimum incanescens,Ocimum   serpyllifolium glabrius,Ocimum stamineum,Ocimum thymoides,Becium obovatum   glabrior,Ocimum album,Ocimum brachiatum,Ocimum canum,Ocimum canum   integrifolium,Ocimum dichotomum,Ocimum dinteri,Ocimum fluminense,Ocimum   fruticulosum,Ocimum hispidulum,Ocimum incanescens,Ocimum serpyllifolium   glabrius,Ocimum stamineum,Ocimum thymoides
1169 | Ocimum gratissimum | Ocimum album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum   album,Ocimum basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum   citrodorum,Ocimum cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum   integerrimum,Ocimum lanceolatum,Ocimum laxum,Ocimum majus,Ocimum   medium,Ocimum minus,Ocimum nigrum,Ocimum odorum,Ocimum scabrum,Ocimum   simile,Ocimum thyrsiflorum,Ocimum urticifolium,Plectranthus barrelieri,Ocimum   album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum album,Ocimum   basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum citrodorum,Ocimum   cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum integerrimum,Ocimum   lanceolatum,Ocimum laxum,Ocimum majus,Ocimum medium,Ocimum minus,Ocimum   nigrum,Ocimum odorum,Ocimum scabrum,Ocimum simile,Ocimum thyrsiflorum,Ocimum   urticifolium,Plectranthus barrelieri
1170 | Ocimum gratissimum | Ocimum album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum   album,Ocimum basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum   citrodorum,Ocimum cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum   integerrimum,Ocimum lanceolatum,Ocimum laxum,Ocimum majus,Ocimum   medium,Ocimum minus,Ocimum nigrum,Ocimum odorum,Ocimum scabrum,Ocimum   simile,Ocimum thyrsiflorum,Ocimum urticifolium,Plectranthus barrelieri,Ocimum   album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum album,Ocimum   basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum citrodorum,Ocimum   cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum integerrimum,Ocimum   lanceolatum,Ocimum laxum,Ocimum majus,Ocimum medium,Ocimum minus,Ocimum   nigrum,Ocimum odorum,Ocimum scabrum,Ocimum simile,Ocimum thyrsiflorum,Ocimum   urticifolium,Plectranthus barrelieri
1171 | Ocimum gratissimum | Ocimum album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum   album,Ocimum basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum   citrodorum,Ocimum cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum   integerrimum,Ocimum lanceolatum,Ocimum laxum,Ocimum majus,Ocimum   medium,Ocimum minus,Ocimum nigrum,Ocimum odorum,Ocimum scabrum,Ocimum   simile,Ocimum thyrsiflorum,Ocimum urticifolium,Plectranthus barrelieri,Ocimum   album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum album,Ocimum   basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum citrodorum,Ocimum   cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum integerrimum,Ocimum   lanceolatum,Ocimum laxum,Ocimum majus,Ocimum medium,Ocimum minus,Ocimum   nigrum,Ocimum odorum,Ocimum scabrum,Ocimum simile,Ocimum thyrsiflorum,Ocimum   urticifolium,Plectranthus barrelieri
1172 | Ocimum gratissimum | Ocimum album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum   album,Ocimum basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum   citrodorum,Ocimum cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum   integerrimum,Ocimum lanceolatum,Ocimum laxum,Ocimum majus,Ocimum   medium,Ocimum minus,Ocimum nigrum,Ocimum odorum,Ocimum scabrum,Ocimum   simile,Ocimum thyrsiflorum,Ocimum urticifolium,Plectranthus barrelieri,Ocimum   album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum album,Ocimum   basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum citrodorum,Ocimum   cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum integerrimum,Ocimum   lanceolatum,Ocimum laxum,Ocimum majus,Ocimum medium,Ocimum minus,Ocimum   nigrum,Ocimum odorum,Ocimum scabrum,Ocimum simile,Ocimum thyrsiflorum,Ocimum   urticifolium,Plectranthus barrelieri
1173 | Ocimum kilimandscharicum | Ocimum album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum   album,Ocimum basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum   citrodorum,Ocimum cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum   integerrimum,Ocimum lanceolatum,Ocimum laxum,Ocimum majus,Ocimum   medium,Ocimum minus,Ocimum nigrum,Ocimum odorum,Ocimum scabrum,Ocimum   simile,Ocimum thyrsiflorum,Ocimum urticifolium,Plectranthus barrelieri,Ocimum   album,Ocimum anisatum,Ocimum barrelieri,Ocimum basilicum album,Ocimum   basilicum bullatum,Ocimum basilicum densiflorum,Ocimum basilicum   difforme,Ocimum basilicum glabratum,Ocimum basilicum majus,Ocimum basilicum   pelvifolium,Ocimum basilicum purpurascens,Ocimum basilicum   thyrsiflorum,Ocimum basilicum violaceum,Ocimum basilicum violocrispum,Ocimum   basilicum viridicrispum,Ocimum basilicum vulgare,Ocimum bullatum,Ocimum   caryophyllatum,Ocimum chevalieri,Ocimum ciliare,Ocimum ciliatum,Ocimum citrodorum,Ocimum   cochleatum,Ocimum dentatum,Ocimum hispidum,Ocimum integerrimum,Ocimum   lanceolatum,Ocimum laxum,Ocimum majus,Ocimum medium,Ocimum minus,Ocimum   nigrum,Ocimum odorum,Ocimum scabrum,Ocimum simile,Ocimum thyrsiflorum,Ocimum   urticifolium,Plectranthus barrelieri

I have extracted plant synonym names. synonym column can be augmented from that after mapping normalized names with that of available name into EssoilDB1.0.

Column description of the table is as follows.

plantNameFound - EssoilDB1.0 plant names whose synonyms are available into db="col".
- synonyms - plant name synonyms.

All synonyms have been extracted using R taxize package.

R code snippet.

 > library(taxize)
> list<-c("Ocimum sanctum","Oryza sativa", "Millet")
> syn<-synonyms(list,db = "col")
> syn<-synonyms_df(syn)
> View(syn)

petermr commented 4 years ago

Suggest we discuss plants and compounds in different threads.

On Mon, Sep 9, 2019 at 8:38 AM Ambarish Kumar notifications@github.com wrote:

Yes sir. Should we go for applying regex over compound name synonyms?

Probably not. Regexes don't work well on chemical names. I suspect the best approach to chemicals is simply to collect the names used in phytochemical aricles. We already have these in E1.0. So collect the synonyms in that (about 300/2100 compound names I think). Maybe collect no more than 5 for a compound anyway.

P.

ambarishK commented 4 years ago

Yes sir.

petermr commented 4 years ago

Many of the synonyms in Pubchem are arbitrary and unlikely to occur in phyto chemistry. We only need a small list. Can we talk on Hangout?

On Mon, Sep 9, 2019 at 8:52 AM Ambarish Kumar notifications@github.com wrote:

Yes sir.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/76?email_source=notifications&email_token=AAFTCS6ZYZRKDN52QFJB2YTQIX6DRA5CNFSM4ICLYMF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6GSC7A#issuecomment-529342844, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCSZGHJC2CYA2WU4UV3LQIX6DRANCNFSM4ICLYMFQ .

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ambarishK commented 4 years ago

Yes sir.

Sir, There is no compound synonym information into EssoilDB1.0. Header of chemical compound sheet is as follows.


Paper_code | Compound_name | CAS | Qnt | Plant_parts | Technique | Classification | Activity | Plant_type | Exp_Condition

There is CAS, Classification and Activity which are directly related with chemical compounds.

ambarishK commented 4 years ago

Sir, please check for compound synonym names picked from EssoilDB1.0.

uniqueCompoundSynonym20190910.tsv

Each synonym is reported as one record per row.

Column description is as per follows.

CSID - Compound synonym ID.
EID - Unique identifiers assigned to each compound.
synonym - Compound synonym name.

Total number of records 2812

Example -

CSID         EID                     synonym
CS1              C214                       acetate
CS2              C215                       acetic acid
CS3              C2776            acetaldehyde
CS4              C170                3-hydroxy-2-butanone
CS5              C170                     3-hydroxybutan-2-one
CS6              C170                      acetoin
CS7              C2780                    acetone
CS8              C298                      benzaldehyde
CS9              C3196                   benzene

braaa11 commented 9 months ago

Ggg

braaa11 commented 9 months ago

Error CS0433

gilienv / EssOilDB

Disambiguating chemistry and fixing typos #76