petermr

# implementing * add `` child elements to dictionary `` elements * lookup unknowns in wikidata and identify synonyms of existing entries Will start by creating a bag of unknown...

# analysing isomerism and synonyms We need to sort compounds by WikidataID and PubchemCID to determine synonyms. Example: ``` para-cymen-7-ol 325 4-Isopropylbenzyl alcohol p-cymen-7-ol p-cymen-7-ol 325 4-Isopropylbenzyl alcohol ``` These...

Good, It gives us standardised terms, possibly. Am now close to being able to extract subtables and their column names automatically. We should start thinking about applying this to activity......

# searching with dictionaries ``` cd CEVOpen ``` verify that `oil186` is a subdirectory ``` ls oil186 ``` then search: ``` ami-search -p oil186 --dictionary species country mydictionaries/instrument.xml ``` `species`...

Simple `grep` that finds mass spec: ``` grep -r -E -o ".{0,50}mass spectromet{0,50}" PMC*/scholarly.html ``` will search all the HTML for "mass spectrom" and gives 50 characters either side

This is wonderful Tiago If you checkout oil186/ You will find fulldatatables.html which I think is what you want On Thu, 12 Sep 2019, 19:12 Tiago Lubiana, wrote: > Hello,...

Tiago, can you send me your email (by email to peter.murray.rust AT gmail DOT com) so I can connect you with others. Manny - meet TIago who is in Sao...

# Antioxidant DPPH Concentration μg/ml | % inhibition by T. bovei essential oil ± SD | % of inhibition by Trolox ± SD -- | -- | -- 1 |...

# antimicrobial (MIC) Microorganism | MIC value (mg/ml) for T. bovei essential oil -- | -- Escherichia coli (ATCC 25922) | 0.5 Pseudomonas aeruginosa (ATCC 27853) | 0.25 Staphylococcus aureus ...

I've made some headway in processing ContentMine output using KNIME. I can now read in the full text of articles and tag it up using OSCAR.  We should also...