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

[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]

Plants

Layman and Botanical Names / Species

 

PlantOilDictionaryDescription.md

• Description: A dictionary of 1678 constituent chemical compounds extracted from the Essential Oils of [XX] plants mentioned in the 186 test articles downloaded from PubMed. Of the 1678 entries, ?????? had their names normalized and tagged with corresponding Wikidata IDs, the other 112 remain to be resolved.

• Filename: PlantOil.xml

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

[EmanuelFaria]

Plant Essential Oils​​ Dictionary

 

Description

A dictionary of 1678 constituent chemical compounds extracted from the Essential Oils of [XX] plants mentioned in the 186 test articles downloaded from PubMed. Of the 1678 entries, ?????? had their names normalized and tagged with corresponding Wikidata IDs, the other 112 remain to be resolved.

 

File Data

• Filename: PlantOil.xml

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

 

Table Column Headings

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

• desc: data source

• id: ID correlated to the row number of this table (not including first two column heading rows)

• term: The term is the precise string used to identify the concept.

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

 

Contents/Results

• No. of source papers: 186

• No. of Entries (Headers are not counted): 1678

• No. of unique plant names (including alternate spellings or synonyms): 1678 - DUPLICATES = ??

• No. of Chemical Compounds resolved in Wikidata: ????

• No. of Chemical Compounds NOT resolved in Wikidata: 112

 

Notes:

• I propose we rename this Dictionary to “Plants”. (If we do, will we need to update links elsewhere in GitHub, or will they resolve themselves?)

• I’m not sure how to deal with the duplicates… do we re-serialize the “id”?

• Once the duplicates are removed, please update the figures in this document description as well as the results.

• Duplicates (some of them more than once): 48

  • (See oil OilPlantCopy.xlsx for duplicates I’ve highlighted in yellow boxes.)

  1. Artemisia lobelii

  2. Artemisia roxburghiana

  3. Artemisia caerulescens

  4. Bunium persicum

  5. Cedrus libani

  6. Citrus limon

  7. Citrus paradisii

  8. Citrus sinensis

  9. Conyza canadensis

  10. Curcuma longa

  11. Cymbopogon citratus

  12. Cymbopogon nardus

  13. Hedychium gardnerianum

  14. Hyssopus officinalis

  15. Helichrysum stoechas

  16. Lavandula latifolia

  17. Melaleuca alternifolia

  18. Mentha piperita

  19. Myrtus communis

  20. Micromeria cristata

  21. Nepeta betonicifolia

  22. Neolitsea dealbata

  23. Ocimum basilicum

  24. Ocimum micranthum

  25. Pistacia lentiscus

  26. Pourouma cecropiifolia

  27. Psidium guajava

  28. Psidium guineense

  29. Rosmarinus officinalis

  30. Salvia aucheri

  31. Salvia euphratica

  32. Salvia moorcroftiana

  33. Salvia officinalis

  34. Salvia sclarea

  35. Sideritis raeseri

  36. Sphaerantia discolor

  37. Tanacetum cadmeum

  38. Tanacetum polycephalum

  39. Teucrium chamaedrys

  40. Teucrium montanum

  41. Valeriana officinalis

  42. Vetiveria zizanioides

[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 Plant​​ Dictionary

 

File Data

• Description: A dictionary of 1678 plant names extracted mentioned in the 186 test articles downloaded from PubMed. Of the 1678 entries, 1567 had their names normalized and tagged with corresponding Wikidata IDs.

• Filename: eoPlant.xml

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

 

Table Column Headings

• id: serialized identification number

• term: The term is the precise string used to identify the concept.

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

• desc: data source

 

Contents/Results

• No. of source papers: 186

• No. of Entries (Headers are not counted): 1678

• No. of unique plant names (including alternate spellings or synonyms): 1678

• No. of entries resolved to wikidataIDs: 1567

 

 

Notes: