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Contentmining of Open phytochemical literature for medicinal activities
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Extraction of EO isolation method and analysis technique. #73

Closed ambarishK closed 4 years ago

ambarishK commented 4 years ago

Sir, please review test sheet for extraction of EO isolation method and analysis techniques - methodAndAnalysisExtraction20191225.tsv

There are extraction of first 20 articles of oil186.

PMC5307246 - No EO isolation method and analysis technique are mentioned.

PMC5426739 -  No EO isolation method and analysis technique are mentioned.

Column description is as follows.

petermr commented 4 years ago

Looks reasonable. I don't think it's worth extracting the instrument typre yet, but that may change

On Wed, Dec 25, 2019 at 12:13 PM Ambarish Kumar notifications@github.com wrote:

Sir, please review test sheet for extraction of EO isolation method and analysis techniques - methodAndAnalysisExtraction20191225.tsv https://github.com/petermr/CEVOpen/blob/master/articleAnalysis/oil186/raw/methodAndAnalysisExtraction20191225.tsv

There are extraction of first 20 articles of oil186.

PMC5307246 - No EO isolation method and analysis technique are mentioned.

PMC5426739 - No EO isolation method and analysis technique are mentioned.



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ambarishK commented 4 years ago

Looks reasonable. I don't think it's worth extracting the instrument typre yet, but that may change …

Sir, would you please give an example for making above change.

ambarishK commented 4 years ago

Sir, please review updated sheet for extraction of method for EO isolation and it's composition analysis techniques - methodAndAnalysisExtraction20191225.tsv.

There are extraction records from first 100 articles of oil186.

Notes:

There are articles which contains more than one extraction method names which have been put comma separated.

For example - 

PMC5694587  steam distillation, solvent extraction, soxhlet extraction, microwave-assisted hydrodistillation, dynamic headspace, static headspace, solvent flavor evaporation, solid-phase microextraction, and direct thermal desorption

PMC5622403  steam or hydro-distillation

PMC5661929  hydrodistillation, HS-SPME

PMC5723952  hydroalcoholic extract, hydrodistillation

PMC5742650  hydro-distillation, Microwave hydro-distillation
ambarishK commented 4 years ago

Sir, please review the extraction of EO isolation techniques and EO composition analysis - methodAndAnalysisExtraction20191225.tsv.

Suggest for making changes.

ambarishK commented 4 years ago

Sir, should I go for WIKIPEDIA lookup or WIKIDATA lookup for extraction method and analysis techniques?

ambarishK commented 4 years ago

Sir, EO isolation method - hydrodistillation/steam-distillation/microwave-ultrasonic/clevenger apparatus extraction etc - is explicitly mentioned into article sub-section.

Extracted value for EO composition analysis are abbreviation of technique names. As in gas chromatography coupled with mass spectrometry is extracted as GC-MS.

Most of articles mention composition analysis techniques as separate terms - gas chromatography separated of mass spectrometry - and that also into separate lines of corresponding sub-section.

Below is an example for it. Sub-section discusses gas chromatography coupled with mass-spectrometry but there is no explicit term as GC-MS.

PMC4391421

Gas chromatography-mass spectrometry. Samples were analyzed by gas chromatography using a HP6890 instrument coupled with a HP 5973 mass spectrometer. The gas chromatograph is equipped with a split-splitless injector and a Factor FourTM VF-35ms 5% fenil-methylpolysiloxane, 30 m, 0.25 mm, 0.25 μm film thickness capillary column. Gas chromatography conditions include a temperature range of 50 to 250°C at 40°C/min, with a solvent delay of 5 min. The injector was maintained at a temperature of 250°C. The inert gas was helium at a flow of 1.0 mL/min, and the injected volume in the splitless mode was 1 μL. The MS conditions were the following: ionization energy, 70 eV; quadrupole temperature, 100°C; scanning velocity, 1.6 scan/s; weight range, 40-500 amu.

GC-MS is not mentioned explicitly into EO composition analysis sub-section.

I have abbreviated them into single term - GC, GC-MS or GC-FID.

ambarishK commented 4 years ago

Sir, Please go through the added column for WIKIDATA query for EO isolation method and EO composition analysis techniques.

File - methodAndAnalysisExtraction20191225.tsv

Issues:

PMC5778200          Sample preparation and oil extraction

PMC5897738          Preparation of Herbal Extracts and Isolation of Reference Standards

microwave-ultrasonic

water distillation

maceration, bligh and dyer

WIKIPEDIA lookup for EO isolation methods are as follows.

method                     WIKIPEDIA_query

hydrodistillation   Steam_distillation

steam distillation  Steam_distillation

clevenger apparatus extraction  Steam_distillation

vacuum distillation        Vacuum_distillation

fractional distillation Fractional_distillation

soxhlet extraction      Soxhlet_extractor 

analysis        WIKIPEDIA_query

GC-MS    Gas_chromatography–mass_spectrometry

GC           Gas_chromatography

GC-FID   Flame_ionization_detector

SPME GC-MS       Gas_chromatography–mass_spectrometry

Thin Layer Chromatography (TLC)          Thin-layer_chromatography

HRGC-FID

HRGC-MS

GLC-MS

GC-MSD
ambarishK commented 4 years ago

There requires making the terms - GC-MS, GC/MS, Gas chromatography-mass spectrometry, gas-chromatography, hydrodistillation, hydro-distillation, steam-distillation, steam distillation etc uniform.

Apart, confirmation over extraction method - water extraction, clevenger apparatus extraction, steam-distillation and hydrodistillation as different extraction method is required to meet the extent of normalization.