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petermr / CEVOpen

Contentmining of Open phytochemical literature for medicinal activities
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📚DICTIONARIES to consider creating/adding #42

Open EmanuelFaria opened 4 years ago

EmanuelFaria commented 4 years ago

Here we discuss new dictionaries that may be useful to D.A.V.E.

EmanuelFaria commented 4 years ago

New Dictionaries to consider:

Plant Related

Activity Target Related

I suggest we start with broad Classes, Groups and Species first, and later add Sub-species by Taxomomy. Example:

Pests

Animals

Organisms/Microbes

Body Parts or Organs

Body Systems

  1. Circulatory/Cardiovascular system:
  2. Digestive system and Excretory system:
  3. Endocrine system:
  4. Integumentary system / Exocrine system:
  5. Immune system and lymphatic system:
  6. Muscular system:
  7. Nervous system:
  8. Renal system and Urinary system:
  9. Reproductive system:
  10. Respiratory system:
  11. Skeletal system:

Enzymes

Enzymatic Activities?

Enzyme Inhibitors?

Pathogenesis Pathways

Uses

Indications (Specific Medical uses: an indication is a valid reason to use a certain test, medication, procedure, or surgery)

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

petermr commented 4 years ago

All my comments relate to the usefulness of dictionaries against the 10000 articles

On Wed, Oct 23, 2019 at 8:56 PM Emanuel Faria notifications@github.com 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

  1. Circulatory/Cardiovascular system:
  2. Digestive system and Excretory system:
  3. Endocrine system:
  4. Integumentary system / Exocrine system:
  5. Immune system and lymphatic system:
  6. Muscular system:
  7. Nervous system:
  8. Renal system and Urinary system:
  9. Reproductive system:
  10. Respiratory system:
  11. 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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petermr commented 4 years ago

Too broad at present. Many of these dictionaries will be in Wikidata if and when we need them.

EmanuelFaria commented 4 years ago

@petermr Consider a dictionary of "Tests" that could also help identify activities.

Examples: paw licking and Hot Plate tests = Antinocioceptive

EmanuelFaria commented 4 years ago

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

petermr commented 4 years ago

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 notifications@github.com 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

EmanuelFaria commented 4 years ago

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.

EmanuelFaria commented 4 years ago

@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/