search

gilienv / EssOilDB

Restructuring of Essential Oil Database
Apache License 2.0
8 stars 6 forks source link

narrative for OpenPlant poster #55

Open petermr opened 5 years ago

petermr commented 5 years ago

what is EssoilDB? why is it important? what is in it (as much detail compatible with clarity - this is hard!)? how can I use it? (also hard) how can I get more information? (and add more ideas here)

petermr commented 5 years ago

some Indian examples (e.g. phytochemical production and harvesting of terpenes (spices, fragrances, medicine,) or pheromones . This is a great chance to set the scene with photos. NOTE: all photos MUST have CC BY licences and attribution. Wikimedia is a good place to do this, but NIPGR may also have photos.

petermr commented 5 years ago

Have added a very crude wireframe to show a narrative. (The plant Nipgria and compound nipgren are fictitious - you have to change this to a real one). Start populating boxes and that will get us going. The profile table should be at the centre of the diagram - so we'll need to move bits around. This is NOT the final story - just a suggestion to get you going. In my experience the fewer words the better.

Shruthi-M commented 5 years ago

I have shortlisted 5 articles from JEOR, which contain the chemical composition of the essential oils of Ocimum basilicum. Ocimum basilicum has several functional characteristics including carminative, stimulant, diuretic, antiseptic, anesthetic, anti-spasmodic, analgesic and anti-tussive properties. The articles contain information about essential oils from this plant from the following parts of the world:

  1. Northeastern Brazil (Brazil) Essential Oils from Leaves and Inflorescence of Ocimum basilicum var purpurascens Benth from Northeastern Brazil.pdf

  2. Northeastern India (India) Composition of the Camphor rich Essential Oil of Ocimum basilicum L Native to Northeast India.pdf

  3. Iran (Iran) Composition and Antibacterial Activity of the Essential Oil of a Green Type and a Purple Type of Ocimum basilicum L from Iran.pdf

  4. Mali (West Africa) (Mali) Aromatic Plants of Mali I Chemical Composition of Essential Oils of Ocimum basilicum L.pdf

  5. Benin (West Africa) (Benin) Chemical Features of Some Essential Oils of Ocimum basilicum L from Benin.pdf

I have a few suggestions: In order to compare the profiles at different locations, we can consider Brazil, India, Mali and Benin as all these countries fall under the tropical climatic zone. It might provide us a good basis for comparison. We could also consider the 2 countries of West Africa for the comparison. The following article contains some key points regarding the importance of this plant: (Importance) Chemical composition radical scavenging and anti oxidant capacity of Ocimum Basilicum essential oil.pdf

vinitamehlawat commented 5 years ago

what is EssoilDB?

why is it important?

what is in it (as much detail compatible with clarity - this is hard!)?

This paragraph showing us that:

Plant-name Lantana camera Plant-part used is Fresh Leaves Location from oil extracted was Dehra Dun Analysis done by GC-MS Major constituents are β-caryophyllene, α-humulene, germacrene D, γ-curcumene etc.

how can I use it? (also hard)

petermr commented 5 years ago

Thank you Shruthi Well done for suggesting ideas. We will discuss them. Vinita, can you make sure that we include these on the agenda (which I will create now).

Shruthi-M commented 5 years ago

This is a rough sketch of the layout for the poster. Layout 1.pdf Page 1 has the overall layout for essential oils extracted from a flower. The compound names can be written inside the petals of the flower. Else, if the extract is from leaves of a plant, we could use the pictorial representation shown in page 2. In this the compound names can be written on each leaflet. I thought this would make the poster attractive and informative. This is just a suggestion. Thank you

petermr commented 5 years ago

That is a BRILLIANT idea. It's both eye-catching and informative and represents the structure of the database!

On Wed, Jul 10, 2019 at 10:22 AM Shruthi-M notifications@github.com wrote:

This is a rough sketch of the layout for the poster. Layout 1.pdf https://github.com/gilienv/EssOilDB/files/3376724/Layout.1.pdf Page 1 has the overall layout for essential oils extracted from a flower. The compound names can be written inside the petals of the flower. Else, if the extract is from leaves of a plant, we could use the pictorial representation shown in page 2. In this the compound names can be written on each leaflet. I thought this would make the poster attractive and informative. This is just a suggestion. Thank you

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS6Y6GPC22CRKZGL4W3P6WS7FA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZS33VQ#issuecomment-509984214, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCSYVGYCOGNSOWZVJN33P6WS7FANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

Shruthi-M commented 5 years ago

world map This is the image of a world map which shows the regions which grow O. basilicum. I hope this is relevant to our yesterday's discussion. The source is: http://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:452874-1#distribution-map

Green ----> Native Purple ----> Invasive

Shruthi-M commented 5 years ago

This is the image of the homeopathic medicine which is an extract of Osimum basilicum; manufactured by SBL PVT LTD. SBL

petermr commented 5 years ago

Thanks The maps are excellent. Will be useful to have the 5 papers you found pinpointed on the map.

Can we find a non-homeopathic example? Could be cooking, traditional, or pharmaceutical.

On Thu, Jul 11, 2019 at 7:23 AM Shruthi-M notifications@github.com wrote:

This is the image of the homeopathic medicine which is an extract of Osimum basilicum; manufactured by SBL PVT LTD. [image: SBL] https://user-images.githubusercontent.com/51472608/61025747-3983af80-a3cf-11e9-9972-765955536bd0.jpg

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCSYL2BQOQPO2QBSDI4TP63GWRA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZVUOLQ#issuecomment-510347054, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS2NFU3P2RWDB6NOUOTP63GWRANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

petermr commented 5 years ago

Typical amazon example: https://gb.pipingrock.com/essential-oils/basil-100-pure-essential-oil-2-fl-oz-59-ml-bottle-4758?prd=129738a3&gclid=CjwKCAjwvJvpBRAtEiwAjLuRPbaunnzh9Ca_LdEB6oC6i33VScX8F273NFnmcvJNy1p96Y71xR3UCBoCWtYQAvD_BwE

On Thu, Jul 11, 2019 at 8:35 AM Peter Murray-Rust < peter.murray.rust@googlemail.com> wrote:

Thanks The maps are excellent. Will be useful to have the 5 papers you found pinpointed on the map.

Can we find a non-homeopathic example? Could be cooking, traditional, or pharmaceutical.

On Thu, Jul 11, 2019 at 7:23 AM Shruthi-M notifications@github.com wrote:

This is the image of the homeopathic medicine which is an extract of Osimum basilicum; manufactured by SBL PVT LTD. [image: SBL] https://user-images.githubusercontent.com/51472608/61025747-3983af80-a3cf-11e9-9972-765955536bd0.jpg

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCSYL2BQOQPO2QBSDI4TP63GWRA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZVUOLQ#issuecomment-510347054, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS2NFU3P2RWDB6NOUOTP63GWRANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

Shruthi-M commented 5 years ago

Greetings! I have found the following papers on essential oil composition of Lanatana camara:

  1. Extract from Algeria (Algeria) Chemical composition and insecticidal properties of Lantana camara L leaf essential oils from Algeria.pdf
  2. Extract from Cuba (Cuba) Chemical Composition of the Essential Oil of Lantana camara L from Cuba.pdf
  3. Extract from India (India) Chemical Composition of the Leaf Oil of Lantana camara.pdf
  4. Extract from Madagascar (Madagascar) Chemical Compositions of Aerial Part Essential Oils of Lantana camara L Chemotypes from Madagascar.pdf
  5. Extract from Pernambuco (Northeast of Brazil (Brazil) Essential Oil Composition of Two Lantana Species from Mountain Forests of Pernambuco Northeast of Brazil.pdf
Shruthi-M commented 5 years ago

The articles containing information about the extracts from Cuba, India and Pernambuco, are found in EssoilDB.

petermr commented 5 years ago

Thank you

On Mon, 15 Jul 2019, 06:03 Shruthi-M, notifications@github.com wrote:

The articles containing information about the extracts from Cuba, India and Pernambuco, are found in EssoilDB.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS3ISFTBXSDFBBRAI3DP7QALZA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZ4XBYY#issuecomment-511275235, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS3D6KYWM7OB7LRWTOLP7QALZANCNFSM4H7EBVTQ .

EmanuelFaria commented 5 years ago

what is EssoilDB? why is it important? what is in it (as much detail compatible with clarity - this is hard!)? how can I use it? (also hard) how can I get more information? (and add more ideas here)

Who is it for? What can be done/created/answered with it? How can you (I) contribute?

petermr commented 5 years ago

These papers seem well suited to the poster, thank you.

Shruthi-M commented 5 years ago

This is a world map that depicts the distribution of L. camara: L camara distribution Citation: Taylor, Subhashni & Kumar, Lalit. (2012). Sensitivity Analysis of CLIMEX Parameters in Modelling Potential Distribution of Lantana camara L.. PloS one. 7. e40969. 10.1371/journal.pone.0040969.

petermr commented 5 years ago

Thanks, My guess is that is the potential distribution not the actual. It will make a good story. We have papers from round the world .

Are you online at 1530 IST?

On Tue, Jul 16, 2019 at 5:05 AM Shruthi-M notifications@github.com wrote:

This is a world map that depicts the distribution of L. camara: [image: L camara distribution] https://user-images.githubusercontent.com/51472608/61265173-d7e78a80-a7ac-11e9-936d-ef0deb528c08.png Citation: Taylor, Subhashni & Kumar, Lalit. (2012). Sensitivity Analysis of CLIMEX Parameters in Modelling Potential Distribution of Lantana camara L.. PloS one. 7. e40969. 10.1371/journal.pone.0040969.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS32FRKVDRXTEKMJNBDP7VCHFA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZ7UCEI#issuecomment-511656209, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS2VCQALCOLWXMNPC7LP7VCHFANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

Shruthi-M commented 5 years ago

Greetings! These are the drafts of some parts of the poster - that I have prepared. I have included details regarding introduction and snippets of the paper (India) with important parts highlighted. I have created a separate draft for the methodology followed in the corresponding paper (if needed). Slide1 Slide2 Slide3

petermr commented 5 years ago

Shruthi, thank you so much! This is an excellent start and not only provides material but also encourages us all.

I suggest we put this as PPT in the Github repo so I and you can annotate it.

On Wed, Jul 17, 2019 at 8:07 AM Shruthi-M notifications@github.com wrote:

Greetings! These are the drafts of some parts of the poster - that I have prepared. I have included details regarding introduction and snippets of the paper (India) with important parts highlighted. I have created a separate draft for the methodology followed in the corresponding paper (if needed). [image: Slide1] https://user-images.githubusercontent.com/51472608/61353969-ad6dfe00-a88e-11e9-86ad-3bf90ea8caae.jpg [image: Slide2] https://user-images.githubusercontent.com/51472608/61353972-ae069480-a88e-11e9-9a5a-06f1c06d0592.jpg [image: Slide3] https://user-images.githubusercontent.com/51472608/61353973-ae069480-a88e-11e9-8f8c-8c1c8b6aa6e7.jpg

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS3TUBIJEYCHOAJXXFLP73AMJA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2DIF2A#issuecomment-512131816, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS6HITGS7OLZQVXLBXDP73AMJANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

Shruthi-M commented 5 years ago

I have done that! Its named "Poster.pptx"

Shruthi-M commented 5 years ago

@petermr Greetings Sir! I have started working on the poster. I am not able to design the poster based on the wireframe3.jpg. Is it possible for you to mention the same as points? Thank you

Shruthi-M commented 5 years ago

I am unable to find the sample tables (from our database) that have to be included in the poster. Please help me regarding the same

petermr commented 5 years ago

On Thu, Jul 18, 2019 at 7:34 AM Shruthi-M notifications@github.com wrote:

@petermr https://github.com/petermr Greetings Sir! I have started working on the poster. I am not able to design the poster based on the wireframe3.jpg. Is it possible for you to mention the same as points? Thank you

Yes, wireframe3 is really a set of concepts, not a graphic design. Here are the key points.

—

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS7ZTPMCSA7Y7E7WIJ3QAAFI3A5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2HPE5Q#issuecomment-512684662, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS76NPALG4ZGK4VJ47TQAAFI3ANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

petermr commented 5 years ago

Have you checked out the whole Github repo?

Then you will have the files on your laptop I can also point at the web page

On Thu, Jul 18, 2019 at 8:13 AM Shruthi-M notifications@github.com wrote:

I am unable to find the sample tables (from our database) that have to be included in the poster. Please help me regarding the same

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS25ECFG6A26FPMIRJTQAAJ3HA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2HRXSY#issuecomment-512695243, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS3D4SWCJXOGP536YSTQAAJ3HANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

Shruthi-M commented 5 years ago

Greetings Sir! I have uploaded the copy of the poster as Final_poster.pdf, in the repository. Thanks.

petermr commented 5 years ago

Thanks, I will look now. Who will be on the call today?

On Fri, Jul 19, 2019 at 10:26 AM Shruthi-M notifications@github.com wrote:

Greetings Sir! I have uploaded the copy of the poster as Final_poster.pdf, in the repository. Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS7BSUDQIIB66BRPUM3QAGCEVA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2LDPRI#issuecomment-513161157, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS75R7B33QOYL3TUWG3QAGCEVANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

petermr commented 5 years ago

This is good progress. I will read it now. We have to add:

On Fri, Jul 19, 2019 at 10:51 AM Peter Murray-Rust < peter.murray.rust@googlemail.com> wrote:

Thanks, I will look now. Who will be on the call today?

On Fri, Jul 19, 2019 at 10:26 AM Shruthi-M notifications@github.com wrote:

Greetings Sir! I have uploaded the copy of the poster as Final_poster.pdf, in the repository. Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS7BSUDQIIB66BRPUM3QAGCEVA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2LDPRI#issuecomment-513161157, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS75R7B33QOYL3TUWG3QAGCEVANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

petermr commented 5 years ago

Are we going to have a hangout?

On Fri, Jul 19, 2019 at 10:56 AM Peter Murray-Rust < peter.murray.rust@googlemail.com> wrote:

This is good progress. I will read it now. We have to add:

  • addresses and affiliations for authors, also ORCID and check the order
  • logos for institutions (NIPGR, Univ Cambridge, ContentMine)
  • funders

On Fri, Jul 19, 2019 at 10:51 AM Peter Murray-Rust < peter.murray.rust@googlemail.com> wrote:

Thanks, I will look now. Who will be on the call today?

On Fri, Jul 19, 2019 at 10:26 AM Shruthi-M notifications@github.com wrote:

Greetings Sir! I have uploaded the copy of the poster as Final_poster.pdf, in the repository. Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS7BSUDQIIB66BRPUM3QAGCEVA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2LDPRI#issuecomment-513161157, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS75R7B33QOYL3TUWG3QAGCEVANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

Shruthi-M commented 5 years ago

Greetings Sir! I have uploaded the copy of the poster as Final_poster.pdf, in the repository. Thanks.

I have uploaded another layout as Final_poster_2.pdf. @petermr I will incorporate the changes you have mentioned and send another copy soon. Thanks

petermr commented 5 years ago

Thank you, Don't make more changes as we will probably use a new template from Gita. Can you make the PPT files available as I will need to extract images for them into Gita's template.

Thanks

On Fri, Jul 19, 2019 at 11:53 AM Shruthi-M notifications@github.com wrote:

Greetings Sir! I have uploaded the copy of the poster as Final_poster.pdf, in the repository. Thanks.

I have uploaded another layout as Final_poster_2.pdf. @petermr https://github.com/petermr I will incorporate the changes you have mentioned and send another copy soon. Thanks

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS2UZYZL7266FR5FCKTQAGMLDA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2LJSJI#issuecomment-513186085, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS7MCNDK2U44IHOA4GDQAGMLDANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

Shruthi-M commented 5 years ago

I have uploaded the files in ppt format.

petermr commented 5 years ago

Many thanks.

On Fri, Jul 19, 2019 at 3:13 PM Shruthi-M notifications@github.com wrote:

I have uploaded the files in ppt format.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/55?email_source=notifications&email_token=AAFTCS5JPMBHYTSM7KL7ZK3QAHDYHA5CNFSM4H7EBVT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2LXXIA#issuecomment-513244064, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCS7A77FEEQF6EW4ZF6LQAHDYHANCNFSM4H7EBVTQ .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK