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

[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 first draft copy below for discussion and direction.

[EmanuelFaria]

In this case there were two dictionary files (Linked in Headers below). @petermr please choose the one we will continue with from the links below, and I will delete the other.

Thanks

[EmanuelFaria]

Target Organisms

The organisms used as targets of experiments conducted to determine what effect(s) (Activities) tested EOs may have on them. They may occur as A) single-cells or colonies, such as bacteria, fungi, yeasts and molds, protozoa, algae, or viruses; B) insects such as mosquitos, flies, etc.; or, C) they may be helminths, such as Nematodes (roundworms), Cestodes (tapeworms), and Trematodes (flukes).

 

TargetOrganismDictionaryDescription.md

• Description: A dictionary of [55] organisms mentioned [as subjects of experiment?] in the 186 test articles downloaded from PubMed.

• Filename: targetOrganism.xml

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

 

TargetOrganismDictionaryDescription.md

• Description: A dictionary of 133 microrganisms mentioned in tests + WikidataID + frequencies (the number of times the organisms occurred in the 186 source papers)

• Filename: TargetOrganismCount.csv

• File Location: https://github.com/petermr/CEVOpen/blob/master/articleAnalysis/oil186/raw/targetOrganismCount.csv

[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 Target Organism​​​​ Dictionary

 

File Data

• Description: A dictionary of terms describing 307 target organisms resolved to wikidataIDs (including genus and species of bacteria, fungi, protist, protozoa, and other microorgnisms), with 154 terms including names of related diseases.

• Filename: eoTargetOrganism.xml

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

 

Table Column Headings

• id: serialized identifier

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

• wikidataID: Unique identifier for each normalized dictionary term, 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 plant part being identified in that row

• relatedDisease: examples of diseases related to the specific microorganism/pathogen

 

Contents/Results

• No. of Entries (Headers are not counted): 307

• No. of unique entries (including alternate spellings or synonyms): 55

• No. of terms resolved in Wikidata: 307

• No. of terms NOT resolved in Wikidata: 0

• No. of terms including related diseases: 154

 

Notes: