📕 Documentation: Dictionary.xml and DictionaryDescription.md of: eoAnalysisMethod

[EmanuelFaria]

Here we describe the process of creating a [DictionaryName]DictionaryDescription.md document, within which we will describe the contents of the individual dictionary (named in the title of this Issue), which was created (or is in the process of being created) from data collected for Oil186.

I will begin this thread by pasting the contents of the INDEX description, then follwed by first draft copy below for discussion and direction.

[EmanuelFaria]

EO Analysis Instruments

A dictionary of [24] makes/models of Gas chromatography–mass spectrometry equipment used to identify different substances within a test sample — in this case, Essential Oils mentioned in the 186 test articles downloaded from PubMed.

 

InstrumentDictionaryDescription.md

• Description: A dictionary of [24] makes/models of Gas chromatography–mass spectrometry equipment used to identify different substances within a test sample — in this case, Essential Oils mentioned in the 186 test articles downloaded from PubMed.

• Filename: instrument.xml

• File Location: https://github.com/petermr/CEVOpen/blob/master/dictionary/instrument/raw/instrument.xml

[EmanuelFaria]

Instrument​​ Dictionary

 

A dictionary of [24] makes/models of Gas chromatography–mass spectrometry equipment used to identify different substances within a test sample — in this case, Essential Oils mentioned in the 186 test articles downloaded from PubMed.

 

File Data

• Filename: instrument.xml

• File Location: https://github.com/petermr/CEVOpen/blob/master/dictionary/instrument/raw/instrument.xml

 

Table Column Headings

• title: type of data to be normalized and tagged with Wikidata ID.

• desc: data source / method of input

• name: a human readable string describing the concept.

• term: the precise string used to identify the concept. Name and Term are often the same.

 

Contents/Results

• No. of source papers: 1

• No. of Entries (Headers are not counted): 24

• No. of unique entries (including alternate spellings or synonyms): 23

 

Notes:

• I’m not sure if Gas chromatography–mass spectrometry equipment always go together, or if Gas chromatography can be one machine and mass spectrometry another.

• I believe there are duplicates yet to be normalized

• Potential errors: For example, I believe the Wiley references (lines 20 and

  1. are references to Spectral Databases.

• Once this dictionary is finalized, please update main description and the file location in this document and delete this note.

• Currently all entries for “desc”...

  • are from one source

    • are described as being “Hacked" from a few papers PMR 20190904 … is that the best way to describe the method of extration from the source material?

• As of Jan 27,2020 this equipment list contains only 24 models. Should we need to train software by providing some makes/models, many can be found here:

  • https://www.thomasnet.com/nsearch.html?cov=NA&heading=96153267&typed_term=Gas+chromatography&searchterm=Gas+Chromatography+%28GC%29+Instruments&what=Gas+Chromatography+%28GC%29+Instruments&WTZO=Find+Suppliers&searchsource=suppliers

  •  

[EmanuelFaria]

As of today, I believe this dictionary and it's description document are complete. Below I will copy the contents of the description document:

EO Analysis Method

Analytical chemistry studies and uses instruments and methods used to separate, identify, and quantify matter.[1] In practice, separation, identification or quantification may constitute the entire analysis or be combined with another method. Separation isolates analytes. Qualitative analysis identifies analytes, while quantitative analysis determines the numerical amount or concentration.

Analytical chemistry consists of classical, wet chemical methods and modern, instrumental methods.[2] Classical qualitative methods use separations such as precipitation, extraction, and distillation. Identification may be based on differences in color, odor, melting point, boiling point, radioactivity or reactivity. Classical quantitative analysis uses mass or volume changes to quantify amount. Instrumental methods may be used to separate samples using chromatography, electrophoresis or field flow fractionation. Then qualitative and quantitative analysis can be performed, often with the same instrument and may use light interaction, heat interaction, electric fields or magnetic fields. Often the same instrument can separate, identify and quantify an analyte.

(Source: https://en.wikipedia.org/wiki/Analytical_chemistry)

 

File Data

• Description: A dictionary of 117 entries describing instruments and methods used to separate, identify, and quantify matter, 105 being resolved to wikidata IDs, and 95 with short descriptions.

• Filename: eoAnalysisMethod.xml

• File Location: https://github.com/petermr/CEVOpen/blob/master/dictionary/eoAnalysisMethod/eoAnalysisMethod.xml

 

Table Column Headings

• id: serialized identification number

• term: The name is a human readable string describing the concept.

• acronym: standard abbreviations for the term

• wikidataID: Unique identifier linked to Wikidata.org — a free and open knowledge base that can be read and edited by both humans and machines.

• description: short description of the activity sourced from wikidata and/or wikipedia

 

Contents/Results

• No. of entries (Headers are not counted): 117

• No. of unique terms (including alternate spellings or synonyms): 117

• No. of activities resolved in wikidata (including alternate spellings or synonyms): 105

• Number of unique wikidata ids attributed to activities (normalizing for alternate spellings and synonyms): 78

• No. of entries withoug wikidataid: 13

• No. of entries with descriptions: 95

• No. of entries without descriptions: 22

 

Notes:

•