IST-Africa 2020 Conference Proceedings

Miriam Cunningham and Paul Cunningham (Eds)

IST-Africa Institute and IIMC, 2020
ISBN: 978-1-905824-64-9

WIDGET: the WatriImed knowleDGe

Exploration Tool
Borlli Michel Jonas SOME1, Zakaria TEGUERA1, Ibrahim TRAORE1, Rasmané
YAMEOGO1, Gayo DIALLO2
1
Ecole Supérieure d’Informatique, Université Nazi Boni, 01 BP : 1091, Bobo Dioulasso,
Burkina Faso, Email: borlli.some@tic.gov.bf
2
Team ERIAS, BPH Health INSERM 1219, Univ. Bordeaux, F-33000, Bordeaux, France
Abstract: In this paper, we describe the WATRIMed (West African Herbal
Traditional Medicine) Knowledge Graph visualisation tool, WIDGET. It enables a
set of e-health services and will contribute in increasing patient safety in the context
of herbal-based African Traditional Medicine. Users can browse in medicinal recipes
for a given symptom or disease. The recipes consist in medicinal plants with proven
effectiveness. It is therefore possible to access the information of the recipe
composition and that of the plants. It also allow cross-linking most of common
dialects of West Africa, their geographic distribution, and the name of plants in these
ethnic dialects. Thus, from the symptoms, available indications in different West
African regions are provided.
Keywords: African Traditional Medicine, Knowledge Graph, Knowledge
exploration, e-Health, Patient Safety, WATRIMed.

1. Introduction
In West Africa, nature has always been considered for millennia as the main source in
various fields, especially for traditional medicine (TM), whose practices are based on the
transmission of oral knowledge from generation to generation. There are indeed multitudes
of formulas, compositions, associations and herbal medicines scattered across Africa, which
can be used to treat many diseases that occurs in this region.
Four of the seventeen Sustainable Development Goals (SDGs)i call for specific
improvements in health, such as lowering child mortality, reducing maternal mortality and
slowing the spread of HIV (human immunodeficiency virus) / AIDS (acquired
immunodeficiency syndrome), malaria and tuberculosis. West Africa being one of the most
concerned parts of the world, has given itself the means through the WAHOii - West
African Health Organization. WAHO has developed and published several reference books
and guidelines in this field and has placed TM as its sixth priority program in its 2016-2020
strategic plan. Within this plan, an important action item is the standardisation of
descriptions of herbal and traditional medicines in terms of the above mentioned knowledge
representation assets. Together with the lack of computable TM data, it is difficult to take
benefit from them for primary and secondary use cases~: patient follow-up and public
health statistics, phytovigilance about available herbal medications, etc.
The development of the use of social networks and mobile money in West Africa,
favorited a free advertising space to people in herbal TM to promote, sell and distribute
herbal products. However, scams, fake products or even toxic are offered to people who are
looking for miraculous products. It is therefore very important to take the appropriate
measures to stem this phenomenon, which could fight again fake traditional drug
distribution.

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 It is important, and above all, essential to digitize and structure the numerous data
already collected on African plants, as well as their medicinal properties, so that they can be
exploited by computer. In this context, an important step was the launch of the first edition
of the West African pharmacopeia in 2013, with inputs from African TM experts coming
from different member statesiii. Indeed, WAHO has developed and published several
reference documents, including "West African Pharmacopoeia", and "Inventory of Proven
Efficacy Herbal Medicine Formulations", which are collections of verified practices from
pharmacopoeia and herbal recipes formulations from West Africa. In these various sources,
the plants used are well described scientifically and especially highlight the names of these
plants in the various local languages of the indigenous populations who use them in their
everyday life.
It is also very important to emphasize that African Traditional Medicine (ATM) is
practiced among indigenous peoples, without a great degree of formal instruction and who
especially speak only their local languages. As of consequences, WAHO publications have
introduced the multiple names of plants on the most common dialects of West Africa, their
geographic distribution. Data concern 122 dialects distributed in 15 countries.
In this paper, we describe the design and development of WIDGET, the West African
Herbal Traditional Medicine (WATRIMed) [1] knowledge visualisation tools. WATRIMed
aims at bringing West African TM to the digital world so as to help establish bridges with
conventional medicine and more general African TM [2], using a state-of-the art, flexible
and shareable knowledge representation approach. The core model comprises currently 556
concepts including 115 identified West African medicinal plants and 108 recipes used for
110 diseases and symptoms which are commonly encountered in this part of the world. As
WATRIMed Knowledge base is large with many relationships between the different
elements, it is necessary to find a simplified representation of the relationships between
these data in order to allow their easy understanding. Therefore, as in the SynMap system
[3] the two data sources (the WATRIMed Plant database and the WATRIMed Plant
Ontology) will be used for the realization of the "WatriImed knowleDGe Exploration
Tool". We recall that the WATRIMed's ambition was to extract from the WAHO’s
documents, the maximum information, to structure these information so that it can be used
in a database, to augment these data by associating them with online databases like
DBPedia, IPNI, Pubchem, etc., to build an ontological model with this enriched result in
order to offer a knowledge graph usable by other computer systems, by experts and the
public.

2. Materials and Methods

2.1 Materials
WAHO works with a set of experts specialized in various fields of ATM including
Pharmacognosy, Ethnobotany and Ethnopharmacology. In 2013, it launched the first
edition of the West African Herbal Pharmacopeia, which gathers information on medicinal
plants identified from the West African countries and regions. It is worth noting that the
first attempt in Africa was the publication of the 105-plant which was published by the
defunct Organization of African Unity's Scientific, Technical and Research Commission
(OAU/STRC) in 1985, followed by a book on medicinal plant analysis as the volume II in
1986.
Each plant within the WA pharmacopeia book is described with the following items~: a
general summary with information related to the general description of the plant, its ethno-
medicinal usage, clinical information and safety information. In addition, information about
its chemical constitution, indication of contraindication of the plants, the regions where it is

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found, a high resolution photography, biological and pharmacological activities of the
plants and possible dosages and mode of administration are recorded.
In order to enable the linkage of the data gathered from the WAHO herbal
pharmacopeia and TM resources we have identified a set of publicly available relevant
resources to link with [4]. They allow enriching the core information and widen its scope
while opening the perspective of wide-scale integration [4]. So far they are limited to open
and publicly available resources. They include the following knowledge bases.
DBpedia to describe Plants and Diseases. It is a crowd-sourced community effort to
extract structured content from the information created in various Wikimedia projects [5].
DBpedia leverages this gigantic source of knowledge by extracting structured information
from Wikipedia and by making this information accessible on the Web though Linked Data
[6].
STITCH and PubChem for chemical compounds. STITCH stands for ‘search tool for
interactions of chemicals’ and integrates information about interactions from metabolic
pathways, crystal structures, binding experiments and drug–target relationships [7]. It
enables understanding interactions between proteins and small molecules. PubChem is an
open chemistry database at the US National Institutes of Health (NIH) which
collects information including chemical structures, chemical and physical properties, etc.
[8]
IPNI for plants names and bibliographic references. The International Plant Names
Index (IPNI) is a database of the names and associated basic bibliographical details of seed
plants, ferns and lycophytes [9].
GeoNames for information about countries and regions. The GeoNames geographical
database covers all countries and contains over eleven million places names that are
available for download free of charge [10].
Wikidata and Yago for local dialects and vernacular names of plants and recipes. It is a
free and open knowledge base, which stores structured data from Wikimedia sister projects
including Wikipediaiv, Wikivoyage, Wikisource, and othersv. While Yago [11] is a
knowledge base derived from Wikipedia, Wordnet and GeoNames. It contains more than 10
million entities (like persons, organizations, cities, etc.) and contains more than 120 million
assertions about these entities.
2.1.1 Overview of the WATRIMed Knowledge Graph development
The designed and implemented workflow is depicted in figure 1. It comprises three main
components detailed as follows.
In order to structure information about TM in WA, the WAHO Herbal Pharmacopeia
book and the Inventory of WA Proven Medicinal Plant formulations provided by the
WAHO are looked up in order to extract the relevant information. From them, a relational
database, hosted in a PostgreSQL server has been designed and fed by the extracted
information (part 1 in figure 1), which has been manually done as they are not available in a
machine-readable format.
Starting from the resources made available by WAHO and interviews with local experts
in TM, the core schema of the TM knowledge model is designed as an Ontology (part 2 in
Figure 1). This design takes into account medicinal plants and their components both in
terms of chemical compounds and plant parts. Medicinal plant components intervene in the
composition of some recipes.

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 Figure 1: Workflow of the WATRIMed Knowledge Graph development
The purpose of the third step of the workflow is: (i) to instantiate the TM Ontology with
data residing within the WATRIMed plant database and (ii) to link the resulting instances
with entities from relevant external publicly available Knowledge Bases.
To do so, the workflow relies on the OpenRefine toolvi. For each selected external KB,
the relevant sub-categories (called type of resources in OpenRefine) that could match with
the tables’ columns of WATRIMed plant database are identified. It could happen that a
WATRIMed plant database column possibly matches several sub-categories of the targeted
KB resources. For instance, the botanical name of a plant could be matched both with IPNI
and DBPedia.
The database comprises 25 relational tables which totalize currently 6067 tuples. It is
hosted in a PostGreSQL server and the schema is available onlinevii. Table 1 indicates the
current statistics of the main entities of WATRIMed plant database. As can be seen, 115
plants are identified and documented from the sixteen WA countries.
Table 1– Current Statistics of the main entities of the WAHO WATRIMed plant database
Component Size (#tuples)
West African Plants 115
Countries 16
Therapeutic Indications 110
Contraindications 148
Local Dialects 122
Traditional Medicine Recipes 109
Chemical Compounds 171
Plant Parts 34
The schema of the Herbal Traditional Medicine knowledge model referred as the HTM
Ontology is depicted in Figure 2. It comprises 13 main Concepts and 36 Properties. The
latter are subdivided into 17 Datatype Properties and 19 Object Properties. The major
component is the MedicinalPlant entity. It is linked with the ChemicalCompound entity by
the object property HasChemicalComponent. Again, a MedicinalPlant has a BotanicalName
(which is a Datatype Property). The PlantInRecipe entity illustrates the n-ary relationship
pattern. A PlantInRecipe defines the plant part components which constitute a given
Recipe. Thus, two property restrictions are used to link PlantInRecipe respectively to
Recipe and PlantPart.

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 Figure 2: Herbal Traditional Medicine Knowledge Model - HTM Ontology
The following entities of the HTM Ontology have been linked to external resources
identified among the KBs described in the Materials Section: MedicinalPlant,
TheurapeuticIndication, ContraIndication, ChemicalComponent and Dialect [4]. The
WATRIMed graph is available onlineviii.
2.2 Methods
The visualisation tool allows rendering the information about a plant (list the plants of the
underlying knowledge model, to look for general information such as locality, names,
botanical name, give the properties of each plant). We can visualise the information of the
different diseases (suggest recipes related to each disease, view recipe information, show
how to make a recipe, give the dosage, list the plants needed).
We have opted for the Object Oriented Methodology system development approach
encouraging and facilitating re-use of software components. Within this methodology, a
computer system can be developed on a component basis which enables the effective re-use
of existing components and facilitates the sharing of its components by other systems.
2.2.1 Technology Description
The TM Ontology has been edited using the Protégé editor workbench [12].
The Back-end is developed in Java and the Front-end graphical representation was
inspired by the SymMap system. The programming languages that we used for the front-
end are respectively Python [13] and jQuery [14]. In correspondence with the chosen
language, Flaskix , a Python web framework, was used.
In WATRIMed data is stored in a PostgreSQL database. Then we used Psycopgx a
PostgreSQL database adapter for the Python programming language.
For the visualization we used Cytoscapexi, an Open Source Platform for visualizing
complex networks and integrating these with any type of attribute data, which is written
through the scripts. Cytoscape.js is an open-source graph theory library written in JS. You
can use it for graph analysis and visualisation. It allows you to easily display and
manipulate rich, interactive graphs. With also used plugins like qTipxii, a jQuery plugin that
allows us to display tooltips on HTML element.
2.2.2 Developments
Abstract visualization of large graphs has been widely studied in Information visualization
[14] and often refers to compound graph visualization [15]. It mainly consists in abstracting
the nodes and edges of the graph by collapsing each set of nodes of a partition of the graph
into a single node. Repeating iteratively that process allows building abstractions of higher
and higher levels. Such an abstraction can then be used to guide the user during his/her

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exploration as similar nodes should be clustered together and therefore reduce the scope of
his/her study on interesting parts of the graph. One can distinguish two main approaches,
classical compound visualization and multi-scale compound visualization. While in
classical compound visualizations, abstracted nodes are displayed as any other nodes, in
multi-scale compound visualizations, the interior of an abstracted node is filled with a
preview of the underlying sub graph. To build the abstraction of the graph, one needs a
partition of its nodes. The quality of the abstraction clearly relies on the quality of this
partition. The classical approach is that we have decided to implement at this stage.
Our main task is to represent WATRIMed data into a graphical form. The tool that we
have chosen, Cytoscape, has a layout parameter that corresponds to the desired graphical
display model. By default it has a number of default displays. In order for such
visualization to be possible on the WATRIMed graph, we not only used existing display
modes, but we also defined our own display mode by placing the points at custom
positions. In addition to this, we used Jquery’s qtip library to provide more details through
events such as mouse hovering over a node. When flying over the nodes, a bubble appears
with a certain amount of information.

3. Results
The visualisation tools represents, in several kinds of graphics and forms, information
related to the data described above. The first tool, as shown in Figure 3, the Knowledge
graph backend visualisation has been developed in Java. To ensure ontology data
processing by the application, we used a Java ontology manipulation API namely
OWLAPI. In this tool, you can see information about medicinal recipes for a given
symptom or disease. The recipes consist in medicinal plants with proven effectiveness; it is
therefore possible to browse the information of the recipe and that of the plants.

Figure 3: WATRIMed Back-end visualisation tool

As shown in Figure 4, the WIDGET Front-end visualisation tool, in (A) and (B) we
have the list of recipes and the graphical representation of the recipe with its related
elements. In the plants tab, we observe the list of plants through their botanical names. A
recipe is made up of parts of plants. Also, the contraindications of the recipe and the
diseases that can be cured by the recipe are highlighted. When flying over the nodes, a
bubble appears with a certain amount of information.
In (C) and (D) one can get a graphical view of the plant and the countries where it can
be found, the name of the plant in the local languages of the countries, the diseases that the
plant can treat and the contraindications. In addition, the chemical composition of the plant
can be look up.

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 (A) (B)

(C) (D)

Figure 4: WATRIMed Front-end visualisation tool

3.1 Societal Benefits

For many people in Africa, TM either is the first line of treatment or is used as a last resort
when all the available possibilities in the conventional medicine are exploited. Despite its
affordability, it comes with various issues, in particular due to the oral transmission of
knowledge and lack of digitalized resources that could contribute to improve the
sustainability of experiences gathered. The WATRIMed initiative is the first large-scale
attempt to overcome this issue in the context of West Africa. It benefits from decades of
experience gathered by the West African Health Organization, which promotes and
contributes to regulate TM usage among its member states. The WIDGET tool in this
context contributes to making available TM knowledge to potential users. And making the
WATRIMed resource available could help benefiting from crowdsourcing curation of the
content.
Moreover, it is important to facilitate the integration of ATM and conventional
medicine to ensure safer delivery of ATM-based healthcare because one of the main issues
with the ATM is its integration to the conventional health system. WATRIMed contribute
to this by providing a single access point to the targeted countries’ pharmacopoeia and
ATM related guidelines and resources for different end users (medical students, medical
doctors, general public, health agencies, etc.)
The prototype is functional. Its functionality will be completed to allow the experts of
TM to give their testimonials on data and especially for comments for its improvement. It
would be interesting to use the WARTRIMed ontology as a database to make the same
graphical representation with more relationship and detail.
In the future, the addition of scoring criteria, and users’ comments can be a best thing
who can make us have some feedbacks to the platform will complete make the software.

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4. Conclusions and Summary Recommendations
The current release of the West African Herbal Traditional Medicine KG is available to the
community at www.watrimed.org/wul.html together with a SPARQL endpoint. It could
therefore be processed both by human and machines. The WIDGET exploration tool is
directly accessible at www.watrimed.org/widget.html. The idea of setting up a new way of
representing the data in the WATRIMed database is important. Most of the time users use
the data without having a clear idea of the relationships between them. Graphical
visualization is an effective way to easily understand the data, and therefore to use it
properly.

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i
https://sustainabledevelopment.un.org/
ii
https://www.wahooas.org/
iii
WAHO (2013). WAHO Herbal pharmacopoeia for Economic Community of West African States. Bobo
Dioulasso, ISBN:978-9988-1-8015-7, KS Printkraft Ghana, Ltd
iv
www.wikipedia.org
v
https://www.wikidata.org
vi
http://openrefine.org/
vii
www.watrimed.org
viii
www.watrimed.org
ix
https://flask.palletsprojects.com/
x
http://initd.org/
xi
https://cytoscape.org
xii
http://qtip2.com/

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