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petermr / CEVOpen

Contentmining of Open phytochemical literature for medicinal activities
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đź“• Documentation: Dictionary.xml and DictionaryDescription.md of: eoActivity #24

Open EmanuelFaria opened 4 years ago

EmanuelFaria commented 4 years ago

The Big WHY — Dictionary: Activities | Extended list/table for normalization

We are building the ACTIVITIES DICTIONARY so that:

Type of User: Verriclear Natural Skin Essentials™ can: confidently choose essential oil ingredients that perform HIGHLY SPECIFIC desired phytomedicinal activities optimally, and possess desired chemical properties (like absorption rate, pleasing or neutral fragrance) without: introducing undesirable activities and chemical properties (eg. skin irritants, carciongenic, toxic, etc.,)

Goals: Describe the Challenge, the solution we will bring, and the Desired End State by which all will know we have achieved excellence.

Desired Results: A clear and concise description / outline of the final "state or vision" of the project — the evidence we will see when our goals are achieved.

Guiding principles: What principles will guide our decisions as we do our part to fulfill the mission?

Responsibilities and Roles: Who will have what completed when?

Tips, Tools, Shortcuts and Resources: Anything done or used to make the desired outcome more likely to occur.

ambarishK commented 4 years ago

OK sir.

petermr commented 4 years ago

Thanks - this is shaping well

On Thu, Oct 3, 2019 at 4:30 AM Emanuel Faria notifications@github.com wrote:

The Big WHY

We are building the ACTIVITIES DICTIONARY so that:

Type of User: Verriclear Natural Skin Essentials™ can: confidently choose essential oil ingredients that perform HIGHLY SPECIFIC desired phytomedicinal activities optimally, and possess desired chemical properties (like absorption rate, pleasing or neutral fragrance) without: introducing undesirable activities and chemical properties (eg. skin irritants, carciongenic, toxic, etc.,)

Goals: Describe the Challenge, the solution we will bring, and the Desired End State by which all will know we have achieved excellence.

  • A. Deliver a diverse and useful set of activities that will serve as keywords when searching the literature, as well as tags to be associated with plants, essential oils, and their constituents

Desired Results: A clear and concise description / outline of the final "state or vision" of the project — the evidence we will see when our goals are achieved.

  • A. Identify and cross-reference as many specific Activity Classes, Activity Action Types, and Activity Targets as possible from the relevant fields in the provided RAW data table
  • B. Normalize their names and synonyms/aliases
  • C. Add Wikidata or other relevant IDs
  • D. Capture Activity descriptions for each

Guiding principles: What principles will guide our decisions as we do our part to fulfill the mission?

  • A. Review the notes in the column headings as well as the comments related to specific records. If you have questions, ask.

Responsibilities and Roles: Who will have what completed when?

  • A. @mannyrules https://github.com/mannyrules / Verriclear will provide the RAW expanded list of activities to be cross-referenced and normalized
  • B. @petermr https://github.com/petermr will analyze the RAW data and deliberate with Emanuel and other experts on how best to organize the data
  • C. @ambarishK https://github.com/ambarishK will perform the cross-referencing and normalization. (Once final version approved, please check with @gita https://github.com/gita to update EssOilDb entries that had multiple Activities assigned to single entries, as noted in the RAW table).

Tips, Tools, Shortcuts and Resources: Anything done or used to make the desired outcome more likely to occur.

  • A. @ambarishK https://github.com/ambarishK: Please search for synonyms in this column too. Hopefully, you can widen the scope by changing the suffixes of the words (eg. Carcinogen, Carcinogenic, Carcinogenicity). Also, try with and without hyphens (eg. Anti-Viral and antiviral)

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ambarishK commented 4 years ago

Hello!! Now going to process ( normalize ) activity sheet - https://github.com/petermr/CEVOpen/blob/master/dictionary/activity/raw/Manny's%20Activity%20Table%20RAW%20for%20Ambarish%202019-10-02.tsv

petermr commented 4 years ago

Please dont create long filenames with spaces or punctuation in. This file could be named:

.../raw/activityClassifcation20191001.tsv

variants should simply have a date:

/raw/activityClassifcation20191003.tsv

so we can tell it's a derivative of previous ones.

Please do NOT include "Manny", "Ambarish" "New", etc.

Also document these in README.md files.

EmanuelFaria commented 4 years ago

I've uploaded the correctly-named tsv (without the notes in the column header) and added a README.md file too. But the readme won't format properly, so I must have done something wrong.

ambarishK commented 4 years ago

Let me go through notes in column header of the file and correlate it with each description of README.md

EmanuelFaria commented 4 years ago

Thanks Ambarish

ambarishK commented 4 years ago

Normalizing the activities right now. I will post it soon.

EmanuelFaria commented 4 years ago

@ambarishK Please let me know if you have ANY questions at all about what I provided. Happy to help make your work less challenging or time-consuming

ambarishK commented 4 years ago

I am finding synonyms. I will tell you as it get done.

Have we to keep these as activities?

Calcium
Chloride
Chromium
Copper
Fluoride
Iodine
Iron
Magnesium
Manganese
Molybdenum
Phosphorus
Potassium
Selenium
Sodium
Sulphur
Zinc
Omega-3: Alpha-linolenic Acid (18:3)
Omega-3: Docosaehexaenoic Acid (Dha, 22:6)
Omega-3: Docosapentaenoic Acid (22:5)
Omega-3: Eicosapentaenoic Acid (Epa, 20:5)
Omega-3: Eicosatetraenoic Acid (20:4)
Omega-3: Stearidonic Acid (18:4)
Omega-6: Adrenic Acid (22:4)
Omega-6: Arachidonic Acid (Aa, Ara) (20:4)
Omega-6: Calendic Acid (18:3)
Omega-6: Dihomo-vamma-linolenic Acid (Dgla) (20:3)
Omega-6: Docosadienoic Acid (22:2)
Omega-6: Eicosadienoic Acid (20:2)
Omega-6: Gamma-linolenic Acid (Gla) (18:3)
Omega-6: Linoleic Acid (La) (18:2)
Omega-6: Osbond Acid (22:50
Omega-6: Tetracosapentaenoic Acid (24:5)
Omega-6: Tetracosatetraenoic Acid (24:4)
Omega-9: Elaidic Acid (18:1)
Omega-9: Erucic Acid (22:1)
Omega-9: Gondoic Acid (20:1)
Omega-9: Mead Acid (20:3)
Omega-9: Nervonic Acid (24:1)
Omega-9: Oleic Acid (18:1)
Omega-9: Palmitic Acid C16:0 14%
Omega-9: Stearic Acid C18:1 36%
Omega-9: Ximenic Acid (26:1)
Vitamin A: Retinol
Vitamin B1: Thiamine
Vitamin B12: Cobalamin
Vitamin B2: Riboflavin
Vitamin B3: Niacin
Vitamin B5: Pantothenic Acid
Vitamin B6: Pyroxidine
Vitamin B7: Biotin
Vitamin B9: Folate
Vitamin C: Ascorbic acid (C6H8O6)
Vitamin E: Tocopherols
Vitamin F:
Vitamin K1: Phylloquinone
Vitamin K2: (Menaquinone
EmanuelFaria commented 4 years ago

No. I called those "Nutritive" for my own personal use, but I don't think "Nutritive" is officially an activity. Happy to find out I'm wrong however.

Edit: Spelling: "Nutritive": "relating to nutrition. providing nourishment; nutritious"

ambarishK commented 4 years ago

OK. I am keeping them into the Original EssoilDb data column.

petermr commented 4 years ago

I would omit these. An activity is something that changes the state of an organism.

On Tue, Oct 8, 2019 at 6:04 PM Emanuel Faria notifications@github.com wrote:

No. I called those "Nutrative" for my own personal use, but I don't think "Nutrative" is officially an activity. Happy to find out I'm wrong however.

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EmanuelFaria commented 4 years ago

Agreed. If anything, they might be considered "synonyms" or lay terms for the chemical constituents of some oils. I don't know if we're doing that though. Are we @petermr ?

petermr commented 4 years ago

We will record anything that is in the oil. There are few examples where non-terpenes has been reported, especially lipids. This will probably depend on solvent extraction rather than distillation (the lipids are not volatile).

On Tue, Oct 8, 2019 at 6:43 PM Emanuel Faria notifications@github.com wrote:

Agreed. If anything, they might be considered "synonyms" or lay terms for the chemical constituents of some oils. I don't know if we're doing that though. Are we @petermr https://github.com/petermr ?

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ambarishK commented 4 years ago

Hello Sir.

I have found all synonyms for activities after normalizing them. I have added a column for normalized and unique activities - uactivity.

There are columns for match status as uniquely found or synonym - unique/synonym. First uniquely found activity is marked as F and S stands for synonym.

An additional column adjacent to unique/synonym is uactivityMatch. This one is for found status of unique activities. F stands for uniquely found into Original EssoilDB data.

All columns and data of the Manny's Activity Table RAW for Ambarish 2019-10-02.tsv are as it is.

File containing additional columns for finding synonyms is ActivityClassificationRAW20191009.tsv

Next is to edit multiple entries for activities into separate rows.
petermr commented 4 years ago

Something has gone wrong here. It's too complicated. All we need is the unique terms (probably in uactivity) Then we need to look them up in Wikidata. Do NOT include the chemicals (elements, acids, vitamins). These are NOT activities. At a first pass just include uactivity and a unique ID. I will edit out th chemical stuff. The dictionary is simply a iist of terms and links to wikidata. Do NOT attempt to include a classification. Wikidata will provide that.

On Wed, Oct 9, 2019 at 10:45 AM Ambarish Kumar notifications@github.com wrote:

Hello Sir.

I have found all synonyms for activities after normalizing them. I have added a column for normalized and unique activities - uactivity.

  • column for normalized and unique activities - uactivity.

There are columns for match status as uniquely found or synonym - unique/synonym. First uniquely found activity is marked as F and S stands for synonym.

  • columns for match status as uniquely found or synonym - unique/synonym.

An additional column adjacent to unique/synonym is uactivityMatch. This one is for found status of unique activities. F stands for uniquely found into Original EssoilDB data.

  • found status of unique activities. F stands for uniquely found into Original EssoilDB data - uactivityMatch.

All columns and data of the Manny's Activity Table RAW for Ambarish 2019-10-02.tsv https://github.com/petermr/CEVOpen/blob/master/dictionary/activity/raw/Manny's%20Activity%20Table%20RAW%20for%20Ambarish%202019-10-02.tsv are as it is.

File containing additional columns for finding synonyms is ActivityClassificationRAW20191009.tsv https://github.com/petermr/CEVOpen/blob/master/dictionary/activity/raw/ActivityClassificationRAW20191009.tsv

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ambarishK commented 4 years ago

OK sir.

EmanuelFaria commented 4 years ago

Peter, I haven't seen Ambarish' latest update, but I think you may be looking at the extra columns from my original file that I asked him to leave in so I could manually use his updates to revise the tables in my formulation database. I'll take a look when I get home in about an hour from now (that will be approximately 11h15 Brasilia time). Hang tight.

ambarishK commented 4 years ago

Hello Manny sir!

Please go through the updated file - ActivityClassificationRAW20191009.tsv . Columns and data are same as of your's file.

petermr commented 4 years ago

Please remove rows 156-212 inclusive. These are not activities.

Look at line 17 caname == bacteriostatic uactivity = anti-allergic

This makes no sense. Just create a SINGLE COLUMN of activities. and remove all other columns. I will edit that column.

On Wed, Oct 9, 2019 at 2:33 PM Ambarish Kumar notifications@github.com wrote:

Hello Manny sir!

Please go through the updated file - ActivityClassificationRAW20191009.tsv https://github.com/petermr/CEVOpen/blob/master/dictionary/activity/raw/ActivityClassificationRAW20191009.tsv . Columns and data are same as of your's file.

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EmanuelFaria commented 4 years ago

Thanks Ambarish. Peter is correct though. It seems that the normalized names are not in line with the originals. It would be best to just keep it simple with the few columns Peter suggests (Column J from my file is the most important column in terms of including activities that were in EssOildb as well as new ones I collected — and need). Sorry I made this more difficult.

ambarishK commented 4 years ago

Welcome Manny sir ! I make changes as per Peter sir suggestion and will edit my activity file - ActivityClassificationRAW20191009.tsv

ambarishK commented 4 years ago

Sir, Please check for normalized list of activities. ActivitiesNormalizedE1.020191010.tsv

I have excluded all elements, lipids and vitamins.

Total count is 228.

Few records has activities written as statement or comment. e.g

-  under testing as a skin penetration enhancer for the transdermal delivery of therapeutic drugs 

- used in manufacture of MDMA(ecstasy)

- used in traditional chinese medicine

Once finalised, will add WIKIDATA ID and run script for dictionary making.

ambarishK commented 4 years ago

Sir, please check the WIKIDATA ID links to first few activities. Should I proceed same way or change the approach?

I am getting WIKIDATA search for each activity and selecting most appropriate ID for the query.

First 15 records are as follows.


Activities              wikidataid              Description

Abortifacient          Q323047               activity agents: abortifacient Agents (Q323047)
Acaricide               Q416014                 activity agents: abortifacient Agents (Q323047)
ACE-inhibitor         Q288280               activity agents: abortifacient Agents (Q323047)
AChE-Inhibitor       Q63229690           activity agents: abortifacient Agents (Q323047)
Aldose-Reductase Inhibitor  Q4713968   activity: Aldose reductase inhibitor (Q4713968)
Allelochemic           Q39187846         scientific article: Allelochemic function for a primary metabolite: the case of l-tyrosine hyper-production in Inga umbellifera (Fabaceae). (Q39187846)
Allelopathic 
Allergenic               Q58646793          activity agent: Allergenic Pollen (Q58646793)
Analgesic               Q173235               activity: analgesic (Q173235)
Anaphylactic           Q168800              activity: anaphylaxis (Q168800)
Anesthetic              Q4990531           activity: anesthetic (Q4990531)
Anti-acetylcholinesterase   Q52211338   scientific article: Anti-acetylcholinesterase antibodies display cholinesterase-like activity. (Q52211338)
Anti-Acne                Q8106593              Category:Anti-acne preparations (Q8106593)
Anti-allergic             Q50430264            activity agent: Anti-Allergic Agents (Q50430264)
Anti-aggregant        Q67486978             scintific article: Anti-aggregants in clinical practice (Q67486978)
Anti-alzheimer         Q53327702            scintific article: Editorial: Anti Alzheimer agents. (Q53327702)

Sir, how to automate wikidata id extraction using SPARQL query .

petermr commented 4 years ago

Please make sure the description is for the correct activity and the WikidataIds match.

Remove scientific articles

petermr commented 4 years ago

On Thu, Oct 10, 2019 at 10:56 AM Ambarish Kumar notifications@github.com wrote:

Sir, Please check for normalized list of activities.

I have excluded all elements, lipids and vitamins.

Good

Total count is 228.

Few records has activities written as statement or comment. e.g

  • under testing as a skin penetration enhancer for the transdermal delivery of therapeutic drugs

  • used in manufacture of MDMA(ecstasy)

  • used in traditional chinese medicine

these are not actvities. Activities are normally a single word.

Once finalised, will run script for dictionary making.

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petermr commented 4 years ago

edited dictionary/activity/raw/ActivitiesNormalizedE1.020191010.tsv to remove non-activity terms.

Now add wikidata IDs and create dictionary using ami-dictionary

ambarishK commented 4 years ago

Sir, please go through the activity dictionary file activity/activities20191011.xml

Normalised activity file - ActivitiesNormalizedE1.020191010.tsv

Column description is as follows.

EmanuelFaria commented 4 years ago

@petermr @ambarishK I have some thoughts to address:

Maybe there’s a different way to go about this that we could consider. First some background on my thinking:

Single-word (or compound word) activities very often are top-level generic terms (ie. Anti-Fungal, Anti-Bacterial, Anti-Microbial, Anti-Viral). These are not very useful when trying to formulate solutions that get the root of a problem health condition. Be it a pimple or an ear infection: just as not every Essential Oil or EO constituent deemed “Anti-Bacterial” will work against acne, not all antibiotics are effective against an ear infection. To be fit for purpose, finer distinctions are required.

I’m concerned that when auto-processing data — be it from wikidata or elsewhere — we need to be careful that neither we, nor that data confuses/conflate "activity agents" (ie. Pollen) with "Activity" (ie. Antiallergenic) when the real target is “Histimine”, which means real/useful activity we’re looking for is Anti-histiminic, which I consider a sub-type of “Anti-Allergenic”.

This level of Activity classification is akin to “Kingdom, Phyllum, Class, Order, Family, Genus, Species. From months of gathering my own data, I’m convinced that no-one has created such a classification system for activity/target/pathway, but this is exactly what is needed. And I think that WE’RE the ones to do this with D.A.V.E..

To make D.A.V.E. truly fit for purpose, we need to distinguish activities in finer detail — which already exists in Wikidata to some extent* — but we may discover the need/opportunity to submit existing definitions that are not yet included in Wikidata, or coin new terms that need to be defined.

*I typed “Inhibitor” into Wikidata and got a pretty big list, but I’m hoping there is a better way to extract the entire Activity list from wikidata than guessing every type of prefix (Pro-, Anti-), suffix (-stat, -icide), or adjective (promotor, inhibitor) and copying and pasting the results by hand. https://www.wikidata.org/w/index.php?sort=relevance&search=inhibitor+inhibitor&title=Special%3ASearch&profile=advanced&fulltext=1&advancedSearch-current=%7B%22fields%22%3A%7B%22plain%22%3A%5B%22inhibitor%22%5D%7D%7D&ns0=1&ns120=1

For reference, take a look at this PDF with Anti-Allergenic data from the spreadsheet I provided. In it, Anti-Allergenic not only speaks to the Allergy trigger (ie. pollen), but also defines the activity by PATHWAY or PATHWAY COMPONENT upon which the action performs action.

To make D.A.V.E. a viable/reliable tool — one that the scientific communities and formulators alike can rely on to separate the wheat from the chaff — this level of activity distinction will absolutely be required. … and from what I understand so far about semantic search engines and NLP, I think it’s doable.

While not yet certain I have a firm handle on the operation of the Semantic search engine, what I imagine is that ultimately it will entail searching the literature for Natural Language variations like:

“inhibits Bradykinin action” “inhibition of Bradykinin(s)” “shows anti-Bradykinin activity” “counters Bradykinin activity” “counters Bradykinin activity”

...to relate it to either an existing activity or one newly defined by us — such as “Bradykinin inhibitor” — and the rest, I suppose, being treated as Synonyms in a lookup table that will be available when DAVE is online and users can input search requests that DAVE will relate to our top-level term. (Please correct me where I’m wrong).

So here’s my suggested approach with regard to ACTIVITIES:

I chatted with @ambarishK last night (2019-10-10), to find out more about how he accesses Wikidata to gather “categories” of information as well as to understand the steps he takes to manually normalize our activity data with what exists on Wikidata.

What I propose is: rather than starting with a LIMITED list of activities from EssOildb and Verriclear’s databases and then cross-referencing that to wikidata, that we instead:

  1. Determine which of the categories of interest listed below exist in Wikidata
  2. Download them all as a table with each category being the column header
  3. I will do the normalization using his steps (Since I’ve been working on collecting and defining activities for some months now, I’m more familiar with them than he is.)

I’ll update as soon as I see what @ambarishK can get.

This is the list of categories I HOPE exists in wikidata:

Besides being useful (I think) for creating more semantic phrases (?) that help us search articles, having the extra data in such table would help me make sure

BOTTOM LINE: I’m hoping we don’t have to… but if WE must be the ones to set the standards for new definitions that don't exist in Wikidata or even the general literature, then I’m definitely down for that. :)

P.S. Since I began searching for and distinguishing activities for my own purposes, I’ve been compiling a list of prefixes, suffixes and other words that describe “states or state changes” that may be useful in searching for and coining new activities. (This includes “modifiers” such as pro- vs anti-, inhibitor vs promotor, -static vs -icide, etc.,). Peter likely has lists like this too, but never hurts to double-check.

petermr commented 4 years ago

Suggest you propose a list of these as terms to the dictionary. They will be used as exact search terms only. But the only value of these terms will be if they actually occur in the papers. These papers are shrt and use simple concepts and language

Wikidata will be much more sporadic than your classification - don't expect too much.

On Fri, Oct 11, 2019 at 2:30 PM Emanuel Faria notifications@github.com wrote:

-- 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

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 Activity​​ Dictionary

 

File Data

 

Table Column Headings

 

Contents/Results

 

Notes: