petermr
commented
5 years ago Thank you well done
On Wed, May 8, 2019 at 12:46 PM vinitamehlawat notifications@github.com wrote:
Table1. Observation Table. This should contain "Plant Profile data" - What plant makes what
Yes - this is the most important data in the table and the reason for EssOilDB
The Table should have (ATLEAST): *PlantName: // (Existing)
Actually should be link to plant table through primary key
*CompoundName: // (Existing)
link to compound table through primary key
*CompoundAmountEmitted: // (Existing)
what is the format of this? ("percent"?)
*PlantPartEmissionSource: // (Existing) yes either link to plant parft table OR unique strings
TimeOfExpt // (Experimental conditions are Existing) Bibliography-DOI // (Volume,Author,Title,Journal_name,Existing)
Need to show examples
- LocationofExpt // (Existing)
Yes
- Location-LinkToGoogleMaps // (NOT-Existing)
Can be added later
- DOI-LinkToArticle // (NOT-Existing)
can be added later
Table2. Plant Fact Table
This should contain EVERYTHING one may wish to know about a certain plant:
- PlantName (From Table1) // (Existing)
Essential to normalize. Suggest it is referenced by Wikidata or NCBI Taxonomy
- Synonym // (NOT-Existing)
Either opaque string or separate table
- Taxonomic Family // (Existing)
not necessary if the primary plant authority gives family, genus ..
- Genus // (NOT-Existing / To be extracted from Plant_Name)
- Species // (NOT-Existing / To be extracted from Plant_Name)
??? I though species binomial name was the unique key
- PlantHabit ( For eg. is this a Tree/Shrub/Herb etc) // (Existing)
Where is this from?
- LinkToWiki // (Existing Linked to NCBI, not to Wiki )
Table3. Compound Fact Table This should contain EVERYTHING one may wish to know about a certain compound:
- CompoundName (From Table1) // (Existing)
This MUST be normalised and this is non-trivial Menthol vs L-menthol vs (-+) menthol are all DIFFERENT compounds
- Synonym // (Existing)
- ChemicalFamily // (Existing)
derived data
- KnownBiologicalActivity // (Existing)
derived data
- SMILESCode // (NOT-Existing)
derived data
- LinkToPubChem // (Existing)
problematic - Pubchem is not curated. Suggest ChEBI where possible
- LinkToWiki/CheBI/Others // (NOT-Existing)
derived
- ImageOfStructure // (NOT-Existing)
derived
- LinkToGene/KEGGPathway // (NOT-Existing)
don't understand. There will be many pathways. Suggest this is separate
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vinitamehlawat
Table1. Observation Table. This should contain "Plant Profile data" - What plant makes what The Table should have (ATLEAST): PlantName: // (Existing) CompoundName: // (Existing) CompoundAmountEmitted: // (Existing) PlantPartEmissionSource: // (Existing) TimeOfExpt // (Experimental conditions are Existing) Bibliography-DOI // (Volume,Author,Title,Journal_name,Existing)
Table2. Plant Fact Table
This should contain EVERYTHING one may wish to know about a certain plant:
Table3. Compound Fact Table This should contain EVERYTHING one may wish to know about a certain compound: