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petermr
📚DICTIONARIES to consider creating/adding
New Dictionaries to consider:
Plant Related
- "Extracts"? of plants such as Oil, Resin, Balsam, etc..
- Further distinction of plants and plant substances, the way the European Medicines Evaluation Agency does: Latin name of herbal substance | Botanical name of plant | English common name of herbal substance Example: Tanaceti parthenii herba | Tanacetum parthenium (L.) Schultz Bip. | Feverfew
Activity Target Related
I suggest we start with broad Classes, Groups and Species first, and later add Sub-species by Taxomomy. Example:
- Class = Pest
- Group = Insect
- Species = Mosquito
- Subfamilies = Anophelinae or Culicinae
- Genera = Aedeomyia, Aedes, Anopheles... etc.
Pests
- Insects (General)
- Flies (Sub-typ
- Mosquitos
- Moths
- Ticks
- Worms
- etc.
Animals
- Human
- Weasel
- Etc.
Organisms/Microbes
- Bacteria
- Fungus
- Virus
- etc.
Body Parts or Organs
- Skin/Epidermis
- Heart
Body Systems
- Circulatory/Cardiovascular system:
- Digestive system and Excretory system:
- Endocrine system:
- Integumentary system / Exocrine system:
- Immune system and lymphatic system:
- Muscular system:
- Nervous system:
- Renal system and Urinary system:
- Reproductive system:
- Respiratory system:
- Skeletal system:
Enzymes
- Lipase
Enzymatic Activities?
- eg?
Enzyme Inhibitors?
- eg?
Pathogenesis Pathways
- Inflammation
- ?
Uses
- Medical
- Pest Control
- Animal Control
- ?
Indications (Specific Medical uses: an indication is a valid reason to use a certain test, medication, procedure, or surgery)
- Skin disorders and minor wounds
- Mouth and throat disorders
- Eye discomfort
- Urinary tract and genital disorders,
- Fatigue and weakness,
- Urinary tract and genital disorders
- Circulatory disorders
- Gastrointestinal disorders
- Sleep disorders and temporary insomnia
- Mental stress and mood disorders
- Constipation
- Cough and cold
- Pain and inflammation
- etc
Contraindications (a condition or factor that serves as a reason to withhold a certain medical treatment due to the harm that it would cause the patient)
- ?
Toxicity Type or Scale
- Description or scale?
All my comments relate to the usefulness of dictionaries against the 10000 articles
On Wed, Oct 23, 2019 at 8:56 PM Emanuel Faria [email protected] wrote:
New Dictionaries to consider: Plant Related
- "Extracts"? of plants such as Oil, Resin, Balsam, etc..
I think plant exudates may be useful. At present the corpus is based on search for "essential oils" but there may be other sources in the 10K articles
- Further distinction of plants and plant substances, the way the European Medicines Evaluation Agency does: Latin name of herbal substance | Botanical name of plant | English common name of herbal substance Example: Tanaceti parthenii herba | Tanacetum parthenium (L.) Schultz Bip. | Feverfew
The plants themselves are already captured by GBIF Wikidata. Herbal substances should be added IFF ( If and only if) we discover a significant number in 10K
Activity Target Related
I suggest we start with broad Classes, Groups and Species first, and later add Sub-species by Taxomomy. Example:
- Class = Pest
If there are significant pest articles this will be useful
- Group = Insect
If there are articles on attractants, repellents, insecticides
- Species = Mosquito
- Subfamilies = Anophelinae or Culicinae
IFF significant mosquito articles
- Genera = Aedeomyia, Aedes, Anopheles... etc.
Pests
- Insects (General)
- Flies (Sub-typ
- Mosquitos
- Moths
- Ticks
- Worms
- etc.
Animals
- Human
- Weasel
- Etc.
Organisms/Microbes
- Bacteria
- Fungus
- Virus
- etc.
Body Parts or Organs
- Skin/Epidermis
- Heart
Body Systems
- Circulatory/Cardiovascular system:
- Digestive system and Excretory system:
- Endocrine system:
- Integumentary system / Exocrine system:
- Immune system and lymphatic system:
- Muscular system:
- Nervous system:
- Renal system and Urinary system:
- Reproductive system:
- Respiratory system:
- Skeletal system:
Enzymes
- Lipase
Enzymatic Activities?
- eg?
Enzyme Inhibitors?
- eg?
Pathogenesis Pathways
- Inflammation
- ?
They all fall into this pattern IFF there are enough publications
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Too broad at present. Many of these dictionaries will be in Wikidata if and when we need them.
@petermr Consider a dictionary of "Tests" that could also help identify activities.
Examples: paw licking and Hot Plate tests = Antinocioceptive
Consider dictionary of "tests" that could provide another means to identify activities:
eg: The rota-rod test is a safe and efficient test to assess an animal's motor coordination and balance.
Antinocioceptive
- Paw Licking
- Hot plate
Dictionaries should be created in response to the data reported in the articles. I still suspect that 90+% of tested are simple inhibition tests and we should concentrate on them first.
On Fri, Nov 8, 2019 at 7:20 PM Emanuel Faria [email protected] wrote:
Consider dictionary of "tests" that could provide another means to identify activities:
eg: The rota-rod test is a safe and efficient test to assess an animal's motor coordination and balance.
Antinocioceptive
- Paw Licking
- Hot plate
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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
Dictionaries should be created in response to the data reported in the articles. I still suspect that 90+% of tested are simple inhibition tests and we should concentrate on them first.
Agreed. I do see these things popping up as I go through the articles in Oil186.
I'm using this issue as a "parking lot" for ideas to consider for future iterations. Also, I'm operating under the assumption that these other dictionaries could be used as other data points to "triangulate" on the data we most want.
@petermr , are we getting just "constituent compound concentrations", or are we also getting Nutritional Composition? I've seen the latter quite a few times, but wasn't sure if this is part of what Ambarish is pulling now.
Separate tables showing Nutritional Composition would be very useful to me in choosing ingredients not just for their phyto-medicinal activities, but to maximize the nutrition I provide (or restrict) the skin cells affected by different pathogenic conditions.
Here's an example table: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920425/table/foods-07-00060-t003/?report=objectonly
... and the original article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920425/