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FAO-Carib-Agri <[log in to unmask]>
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FAO-Carib-Agri <[log in to unmask]>
Date:
Tue, 6 Nov 2012 10:04:37 -0400
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Dear Members,


From: FletcherPaul, Lystra (FAOGY)

The National Agricultural Research and Extension Institute (NAREI) recently developed the national report on the State of Plant Genetic Resources for Agriculture as well as a National Information Sharing Mechanism (NSIM), with assistance from FAO.  Attached, please find the link to the report
http://www.pgrfa.org/gpa/guy/docs/report2_pgrfa.pdf

Regards


From: Discussion group on Caribbian agriculture [mailto:[log in to unmask]] On Behalf Of FAO-Carib-Agri
Sent: Monday, November 05, 2012 3:41 PM
To: [log in to unmask]
Subject: FW: Caribbean Medicinal Plant Ontology


FAO-Carib-Agri is a service provided by the FAO Sub-Regional Office, Barbados =============================================================================



Dear Members,


From: Alana Abdool
Sent: 03 November 2012 10:37
To: FAO-Carib-Agri
Subject: RE: Caribbean Medicinal Plant Ontology

Hi everyone,


I would appreciate some feedback on my comments on existing databases that represent the plants of the Caribbean (medicinal and otherwise). I am assuming you guys have copies of the Caribbean Medicinal Pharmacopoeia. If not when giving feedback just state that you do not have access to the Pharmacopoeia. Unfortunately, due to copyright restrictions I cannot make copies for you. I am hoping that your comments on the existing databases will help me in my research. You can use the following questions as a guide in your analysis:


- What fields used to search the databases are useful and which are not? Are there any examples of additional search fields that would be useful?
- What combination of features on medicinal plants would you like to see together in a search result?
- Is there any data/knowledge on medicinal plants not represented in these databases that you would have liked to see?

Finally, please comment on my little analysis below:


"There is an existing database of medicinal plants of Latin America and the Caribbean researched and created by TRAMIL (Traditional Knowledge of the Use of Medicinal Plants in Central America and the Caribbean) (TRAMIL (2006)). The TRAMIL database is searchable alphabetically by names and contains photos, scans, drawings, plants herbarium, thin sections specimen and monographs of the Caribbean medicinal plants selected by TRAMIL network. The database can be accessed here:
http://www.tramil.net/fototeca/revision_botanica.php?lang=en
Additional information on the objectives of the database can be found here:
http://www.tramil.net/english/TramilInfo.html
An investigation of the listings and the search tool of the TRAMIL library revealed that while there were extensive listings of medicinal plants with associated pictorial and other documentation the search tool only allowed the user to search by the entire scientific name, part of the scientific name or botanical name to yield results. It was also noted that the TRAMIL library was not yet populated with medicinal attributes of plants or the common names of plants.
TRAMIL has also published a book "Caribbean Medicinal Pharmacopoeia" which is also available as an electronic resource. The second edition (electronic version) of this pharmacopoeia represents a comprehensive collection of plants with medicinal properties with monographs, scientific and common names, geographic location and ailments. It is stored and accessible in Adobe Reader version 7.0 or higher and is searchable using words or phrases. However, it was not possible to yield results based on meaningful, knowledge-rich search phrases e.g. no results for "Coffea arabica poor blood quality" although Coffea arabica is categorized in the pharmacopoeia as a treatment for "Poor blood quality". Phrases needed to be 'exact' or the sequence of words could only be found if occurring in the same order they are found in the text of the pharmacopoeia.
The University of the West Indies, Cave Hill Campus in Barbados has produced a database of plants of the Eastern Caribbean:
http://ecflora.cavehill.uwi.edu/index.html
While this database did not contain medicinal attributes it did have search tools to locate plants by scientific name, common name, family name, physical attribute information and distribution information:
http://ecflora.cavehill.uwi.edu/advsearch.php
The Faculty of Medicine at the Cave Hill Campus, U.W.I. also has proposed a "Database of Medicinal Plants of the Caribbean and Possible Interactions with Conventional Medication" found here:
http://www.cavehill.uwi.edu/fms/research.asp
No database has been developed to date.
All of this suggests that regional organizations and institutions have a keen and current interest in creating electronic records of plants and in particular medicinal plants and documenting indigenous knowledge of medicinal plants. Additionally, they are aware of the importance of documenting data pertinent to the continued acceptance and use of traditional knowledge of medicinal plants and the results of investigating issues surrounding this. The data is disparately stored across different sources, is redundant and in some cases mismatched e.g. Citrus aurantium is found in the Caribbean Herbal Pharmacopoeia but not in the database of Plants of the Eastern Caribbean.
Of note is the fact that while the drive is to represent traditional medicinal plant knowledge in a way that is semantically meaningful i.e. to elicit knowledge that would direct further research into phytochemical properties, the present electronic structures do not do much more than textually describe indigenous knowledge. The only move towards structuring indigenous medicinal knowledge in a manner that is more meaningful for further research by Western medicine and conventional scientific methods was found in the Caribbean Herbal Pharmacopoeia where ailments are categorized by traditional groupings e.g. "after anger", "clogged nose" and plants purported to have action to alleviate these ailments are listed alongside each category."

Thanks so much.

Alana.


________________________________
Date: Mon, 24 Sep 2012 08:14:50 -0400
From: [log in to unmask]<mailto:[log in to unmask]>
Subject: FW: Caribbean Medicinal Plant Ontology
To: [log in to unmask]<mailto:[log in to unmask]>
FAO-Carib-Agri is a service provided by the FAO Sub-Regional Office, Barbados =============================================================================

Dear Members,



From: Alana Abdool

Hi everyone,
Please excuse the extended time during which I have not followed up on the thread and posted more guidelines and supporting materials for my ontology project. The time lapse is due to a leave of absence on account of my last semester of pregnancy and delivery of my baby.
I have prepared a small resource package for the persons who have indicated an interest in assisting with my project. If, after reviewing the materials, you would like to join the group; either to participate or observe please send me an email and I will provide further instructions. The files can be downloaded at these links:


http://www9.zippyshare.com/v/13321148/file.html
http://www10.zippyshare.com/v/48285782/file.html
http://www10.zippyshare.com/v/13437124/file.html
http://www10.zippyshare.com/v/41579196/file.html
http://www10.zippyshare.com/v/24118505/file.html
http://www10.zippyshare.com/v/41501455/file.html
http://www10.zippyshare.com/v/20081245/file.html


Thanks.

Alana.
> Date: Mon, 30 Apr 2012 10:08:04 -0400
> From: [log in to unmask]<mailto:[log in to unmask]>
> Subject: FW: Caribbean Medicinal Plant Ontology
> To: [log in to unmask]<mailto:[log in to unmask]>
>
> FAO-Carib-Agri is a service provided by the FAO Sub-Regional Office, Barbados =============================================================================
>
> Dear Members,
>
>
>
>
> The discussion continues. Please see below the comments from Anthony, Osmond, Alana and Jerry
>
> --------
>
> From: Anthony Richards
>
> What is an ontology and what is it for?
>
> I needed a little help (see below)
>
> After a bit of reflection I remembered (back in 1987, Warwick University, uK) working with doctoral candidates who were trying to transfer both my science and craft approaches to fermentation process control into an artificial intelligence "Blackboard" architecture. http://en.wikipedia.org/wiki/Blackboard_system They told me that the system would eventually be capable of making complex decisions in bio-process operations management.
>
> If you working towards producing an "e-bush doctor", perhaps the best people to consult might be the bush doctors, themselves.
>
> A good place to obtain knowledge of a more summarised, academic nature is the basin-wide, TRAMIL study for the validation of Caribbean herbal medicine use http://www.tramil.net/
> Dr Sylvia Mitchel leads the Jamaica team..
>
> In your island, leading contributors to the study include Dr Compton Seaforth at University of Trinidad & Tobago (UTT) and Dr Yuri Clement at UWI, Mount Hope. TRAMIL has produced a number of handy booklets for the diffusion of results back into the community. There is also an atlas "Towards a Caribbean Herbal Pharmacopia" which is availble on CD in English or in hard copy in Spanish and French.
>
> Dr Gilbertha St Rose in St Lucia, leads CAPSICUM ( Caribbean Association for Plant Science, Industry, Commerce and Use in Medicine). http://www.open.uwi.edu/st_lucia/sites/www.open.uwi.edu.st_lucia/files/UWISPEAK%20Article%20UWI-CAPSICUM%20Collaboration%20A%20Resounding%20Success%20VM.pdf
>
> Dr Sonia Peter at Barbados Community College is organising the Caribbean Chapter of the Society of Economic Botany. http://www.econbot.org/chapters/Caribbean.html
>
> Clearly, both the sources and sinks of resources are scattered among institutions, as Dr Mitchell's shocking slide suggests.
>
> Ontology ?
> http://en.wikipedia.org/wiki/Ontology_(information_science)
>
> What is an ontology for?
> http://www-ksl.stanford.edu/kst/what-is-an-ontology.html
>
>
> Dr Anthony Richards
> Consultant in Chemistry, Food & Biotechnology Management
> Barbados
> ---------
>
> From: OSMOND BARON
>
> Thank you Esther for inviting me through Alana Abdool to participate in the Caribbean Medicinal Plant Ontology. Alana, my name is Osmond Baron. I am from Dominica now residing in the USA. My plant background is plant crop farmer, undergrad agricultural science degree, and Doctor of Plant Medicine (plant health degree). I am presently actively involved in biotechnology research with the USDA-ARS. Medicinal plant is a traditional concept that is gaining much attention today. Curently I am working on a project with the Dominica Academy of Arts & Sciences (DAAS) to identify in Dominica, plants of essential oils and medicinal properties and to perform chemical analyses on them.
>
> Osmond Baron, D.P.M.
>
> --------
>
> From: Alana Abdool
>
> Hi Lennox,
>
> Thanks for the sentiments expressed. No need to wait on my data. There are a number of online resources that have already been established. TRAMIL has done some great work and their online library can be accessed here:
> http://www.tramil.net/fototeca/revision_botanica.php?lang=en
>
> You need to click on the letters to the top to get an alphabetical listing of their entries.
> There is also a database of plants of the Eastern Caribbean:
> http://ecflora.cavehill.uwi.edu/index.html
>
> Additionally if you contact TRAMIL you should be able to get more info on the book Caribbean Herbal Pharmacopoeia.
>
> UWI, Cave Hill campus has some work in the pipeline on a database but I have not heard of any online publication thus far:
> http://www.cavehill.uwi.edu/fms/research.asp
>
> My ontology won't provide you with the sort of raw data that these databases provide. Rather, it will provide something like an upper structure for organizing and accessing the data contained in all databases that are plant related. Even after I construct such a ontology I would still need the cooperation of persons and organizations running said databases for the ontology to work effectively.
> It is actually the participation of these persons and organizations and other plant experts who would be most pertinent to the success of the ontology. The ontology can also be used to set a sort of standard for data and reduce ambiguity across different resources.
>
> My proposed database is still not on my immediate agenda.
>
>
> Dr. Mitchell,
> For the time being I just hope that I can at least get people to work together on my little project. As for vision, I would appreciate any guidance you can give.
>
> I do believe I need to give the feed members a clearer picture of my ontology but I need to revise my existing project proposal to be more appropriate to my potential resource group members. Forgive me. I am an avid computational biologist but as for my marketing skills...well, I have next to none.
>
>
>
> --------
>
> From: HAYES JR, GERALD W (AG/1000)
>
> This is a great opportunity and discussion. We had a brief conversation about Propolis, those plant gums and resins that honey bees collect that have medicinal value for them and also for humans and their livestock earlier. Seems like a good extension to loop in those interested in Honey Bees and how Honey Bees participate with plants for our good. Medicinal Plants with Medicinal Propolis. Thanks.
>
> Jerry Hayes
>
>
> --------
>
> -----Original Message-----
> From: FAO-Carib-Agri
> Sent: 27 April 2012 10:19
> To: [log in to unmask]
> Subject: FW: Caribbean Medicinal Plant Ontology
>
> FAO-Carib-Agri is a service provided by the FAO Sub-Regional Office, Barbados =============================================================================
>
> Dear Members,
>
> A response from Dr Mitchell.
>
> -----
>
>
> From: MITCHELL,Sylvia A
>
>
> I wish it were that simple.
>
> The problem is not money. It is lack of vision. And where there is lack of vision, the people perish.
>
> I am attaching a very telling slide from the 'Planet Under Pressure' conference we were at. And this is not all the institutions! A lot of people working to help the SIDS but bearing in mind our small size, and how hard we all work, its going to take some fortitude to take a couple of steps back and make some sense out of all this. And get people to work together more than defending their own turf. I just hope we can work it out before some of us give up.
>
> In the meantime, we pray and hope.
>
> SM
>
>
> Dr. Sylvia Mitchell,
> Medicinal Plant Research Group
> The Biotechnology Centre, University of the West Indies, Jamaica
>
> ------
>
>
> From: FAO-Carib-Agri [[log in to unmask]]
> Sent: Thursday, April 26, 2012 10:31 AM
> To: [log in to unmask]
> Subject: FW: Caribbean Medicinal Plant Ontology
>
> FAO-Carib-Agri is a service provided by the FAO Sub-Regional Office, Barbados =============================================================================
>
>
>
> Dear Members,
>
>
> From: Lennox Lampkin
>
> Dear Alana,
>
> This is an excellent imitative that should garner wide support! As I am not a synthetic toxin farmer I am particularly interested in this data! Based on the geographical location of Thailand maybe some of their research, if available and accessible could be applicable to our region.
>
> It would be excellent if Dr Mitchell's work is more widely available but also if she could be supported in researching plants on different islands. In fact we should all be focusing far more on medicinal agriculture both as a niche and as a means of improving general health. Proper analysis and sharing of the nutrition value of many of our indigenous foods is badly lacking and should have been a focus of a food sovereignty drive if the Caricom region is really serious about combating the epidemic of Non Communicable diseases that plague us today!
>
> Lennox D. Lampkin
>
>
>
> From: FAO-Carib-Agri [mailto:[log in to unmask]]
> Sent: Tuesday, April 24, 2012 10:47 AM
> To: [log in to unmask]
> Subject: Caribbean Medicinal Plant Ontology
>
>
> FAO-Carib-Agri is a service provided by the FAO Sub-Regional Office, Barbados =============================================================================
>
>
>
> Dear Members,
>
>
> From: Alana Abdool [mailto:[log in to unmask]]
> Sent: 23 April 2012 21:51
> To: FAO-Carib-Agri
> Subject: Caribbean Medicinal Plant Ontology
>
> Colleagues,
> I am working on constructing a Caribbean Medicinal Plant Ontology and eventually a database. The ontology is expected to take one year to completion of a first prototype thereafter upgrades will be done based on continued advice of plant experts and expansion of the existing model. The database construction will begin after completing the ontology and is expected to take approximately three years to complete. The project will be open access but will require funding to be maintained after completion. While I have some background experience in my undergraduate degree in biology my focus has been on computational biology in my postgraduate studies. I have little expert knowledge in the domain of medicinal plants and more specifically, those found in the Caribbean. I would like to create a network of persons, with indigenous or scholarly knowledge of medicinal plants in the region to assist me in developing this ontology. Please supply me with your name, some background on your experience with plants and contact information (phone, email) once you are interested in helping out for this year long project. Note that no remuneration can be given for time spent working on the project as it is entirely voluntary. I am including an excerpt of the brief project proposal below. Thanks.
>
> The Caribbean medicinal plant industry is rapidly expanding in its commercial endeavours and scientific research (Mitchell (2008)). The development of a Caribbean Medicinal Plant Ontology would enable domain experts to share common understanding of the structure of medicinal plants' terminology facilitating continued database revisions. The domain experts in turn would then contribute to ontology evaluation and subsequent further conceptualization, encoding and implementation. The proposed ontology will be developed using existing literature on Caribbean medicinal plants and their attributes and by consultation with domain experts.
>
> 1. Mitchell S. A. (2008), A Journey through the Medicinal Plant Industry of the Caribbean Highlighting Mona's Contribution, Caribbean Quarterly URL: http://mona-uwi.academia.edu/SylviaMitchell/Papers/751702/A_journey_through_the_Medicinal_Plant_Industry_of_the_Caribbean_highlighting_Monas_Contribution_Un_voyage_a_travers_lindustrie_de_plantes_medicinales_aux_Antilles_
>
> Alana Abdool
> Computational Biologist,
> Zaref Engineering,
> #64 Rosalind Drive,
> Block 6,
> Palmiste,
> San Fernando,
> Trinidad W.I.
> Contact - 1-868-365-5735
> Website - www.zarefengineering.com<http://www.zarefengineering.com<http://www.zarefengineering.com%3chttp:/www.zarefengineering.com>>
> ------
> Judith

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