Coverage of Floras?
Jean-Marc Vanel
jmvanel at FREE.FR
Fri May 12 07:44:37 CEST 2000
Hello
To prepare my presentation at the 9th International World Wide Web
Conference - Amsterdam, May 15-19, 2000 (http://www.www9.org/) , I would
like to have the pourcentage of species among the estimated
250 000 plant species that are on regional Floras :
1. - on paper,
2. - in some computerized form (HTML, etc)
The following are on the Web :
Flora of China
Flora of Australia
Flora of North America (www.fna.org)
Thank you
--
<person>
<firstName>Jean-Marc</firstName>
<lastName>Vanel</LastName>
<motto>Veni, vidi, convici</motto>
<conference>9th International World Wide Web Conference - Amsterdam,
May 15-19, 2000
<a href="http://www.www9.org/">site</a>
</conference>
<project>Worlwide Botanical Knowledge Base -
making botany available on Internet
<a href="http://wwbota.free.fr/" >site</a>
</project>
<a href="http://jmvanel.free.fr/>home page</a>
<a href="mailto:jmvanel at free.fr">mail (possibly put "wwbota" in
subject to route your mail in relevant folder)</a>
</person>
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Date: Fri, 12 May 2000 07:40:16 +0200
From: Jean-Marc Vanel <jmvanel at free.fr>
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<p>--
<br><person>
<br> <firstName>Jean-Marc</firstName>
<br> <lastName>Vanel</LastName>
<br> <motto>Veni, vidi, convici</motto>
<br> <conference>9th International World Wide Web Conference -
Amsterdam, May 15-19, 2000
<br> <a href="<A
HREF="http://www.www9.org/">http://www.www9.org/</A>">site</a>
<br> </conference>
<br> <project>Worlwide Botanical Knowledge Base -
<br> making botany available on Internet
<br> <a href="<A
HREF="http://wwbota.free.fr/">http://wwbota.free.fr/</A>" >site</a>
<br> </project>
<br> <a href="<A
HREF="http://jmvanel.free.fr/">http://jmvanel.free.fr/</A>>home
page</a>
<br> <a href="<A
HREF="mailto:jmvanel at free.fr">mailto:jmvanel at free.fr</A>">mail (possibly
put "wwbota"
in subject to route your mail in relevant folder)</a>
<br></person>
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<head>
<meta http-equiv="Content-Type" content="text/html;
charset=iso-8859-1">
<meta name="Author" content="Jean-Marc Vanel">
<meta name="GENERATOR" content="Mozilla/4.5 [fr]C-CCK-MCD {FREE}
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<meta name="Description" content="The aim of this project is to make
available botanical data through the Internet : description of the
species, including pictures, geographical distribution.">
<meta name="KeyWords" content="botany, database, species description,
taxonomy, biodiversity, ecology, INTERNET, natural language, XML, RDF,
L-Systems, 3D, image, semantic">
<title>Worlwide Plant Database Project</title>
</head>
<body>
<h2>
Worldwide Botanical Knowledge Base</h2>
You will not find here botanical databases with <b><font
color="#006600">queries
on the species description</font></b> - not yet. But this is the aim of
this project, the techniques are here, the data are here. So why not <a
href="join.htm">join
us</a>, wether you are a computer specialist or a botanist. Or just <a
href="mailto:jmvanel at free.fr">drop
a few lines</a> for advice, encouragement or critics.
<p><a href="call.htm">Call for a world botanical database</a>
<br><a href="existing.htm">Test of the botanical resources on
INTERNET</a>
<br><a href="shortterm_plan.htm">Short-term plan</a> for a WWW botanical
database
<br><p/><a href="What_s_new.htm">What's new</a>
<br><a href="FAQ.htm">FAQ</a>
<br><a href="#français">En français (pas à jour)</a><p/>
<br><a href="presentationWWW9.htm">Presentation</a> at WWW9 Conference
<font color="#FF0000">NEW</font>
<p>Technical:
<ul>
<li>
<a href="Architecture.htm">overall architecture</a></li>
<li>
<a href="XML.htm">why XML?</a>; about <a href="XMLReport/index.htm">XML
& related technologies</a> <font color="#FF0000">NEW to
appear</font></li>
<li>
plant <a href="image_processing.htm">image processing</a> (botany for
computer
scientists)</li>
<li>
<a href="Samples/parsing.htm">syntaxic processing</a> (parsing) of
floristic
texts</li>
<li>
sample <a href="User_Interfaces.htm">User Interfaces</a></li>
<li>
<a href="Links.htm">links</a></li>
<li>
<a href="UML_diagrams.htm">UML diagrams</a> (Abstract Data Model) <font
color="#FF0000">NEW</font></li>
<li>
<font color="#000000"><a href="RDF.htm">RDF mapping</a>
(XML)</font></li>
<li>
<font color="#000000"><a href="3Dgeometry.htm">3D geometry
representation</a></font><font color="#FF0000">
NEW</font></li>
<li>
<font color="#000000"><a href="XMLprotocol.htm">XML protocol</a>
</font><font color="#FF0000">NEW</font></li>
</ul>
<p/>
<br><font size=-1>Only english version is regularly updated.</font>
<br><font size=-1>To translate this in other languages: <a
href="http://babelfish.altavista.com/">AltaVista
Translations</a></font>
<br><font size=-1>Um dieses zu Übersetzen: <a
href="http://babelfish.altavista.com/">AltaVista
Translations</a></font>
<br><font size=-1>Pour traduire ceci : <a
href="http://babelfish.altavista.com/">AltaVista
Translations</a></font>
<h2>
<hr WIDTH="100%"><a NAME="français"></a>Bases de données
botaniques</h2>
mise à jour: 14 sept. 1999
<p><a href="Appel.htm">Appel pour une base de données botanique
mondiale</a>
<br><a href="Existant.htm">Essai des ressources botaniques sur
INTERNET</a>
<br><a href="présentation_fr.htm">Présentation
synthétique</a>
du projet <font color="#FF0000">NOUVEAU</font>
<p>A paraître:
<ul>
<li>
techniques informatiques applicables</li>
<li>
schéma UML des données</li>
<li>
contacts</li>
</ul>
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<head>
<meta http-equiv="Content-Type" content="text/html;
charset=iso-8859-1">
<meta name="Author" content="Jean-Marc Vanel">
<meta name="GENERATOR" content="Mozilla/4.5 [fr]C-CCK-MCD {FREE}
(Win95; I) [Netscape]">
<title>Worldwide Botanical Knowledge Base</title>
</head>
<body>
<center>
<h1>
Worldwide Botanical Knowledge Base</h1></center>
<center>http://wwbota.free.fr/</center>
<h4>
Biodiversity and nature conservancy</h4>
<ul>
<li>
thousands of species are disappearing forever,</li>
<li>
need quick identification of specimens from threatened areas, without
qualified
scientists;</li>
<li>
the knowledge is on paper like in Linnaeus' time,</li>
</ul>
==> an inventory of the biological inheritance of our earth has to be
done.
<p>There is currently no other botanical project with this scope.
<br>Why ?
<ul>
<li>
funds go rather to biotechnologies than to descriptive biology,</li>
<li>
pluri-displinarity is not easy</li>
</ul>
<hr WIDTH="100%">
<h4>
Aim</h4>
to make botanical data available on Internet :
<ul>
<li>
description of the species, including 2D and 3D pictures,</li>
<li>
geographical distribution,</li>
<li>
computer-aided identification of specimens</li>
</ul>
<h4>
Initial intuitions:</h4>
<ol>
<li>
<a href="Samples/protoGUI.htm">relational DB</a></li>
<li>
uncouple data (XML) and processing (relational DB, OO DB, AI
engines)</li>
<li>
offer <a href="User_Interfaces.htm">easy access</a> to detailed
knowledge
both for the layman and the professional botanist</li>
<li>
federate existing resources and people</li>
</ol>
<hr WIDTH="100%">
<h4>
The metadata</h4>
<ul>
<li>
Why a relational DB is not enough: example of bark and stem</li>
<ul>
<li>
bark is a part of stem (and trunk)</li>
</ul>
<li>
different levels of metadata</li>
<li>
several sources of metadata: Floras, <a
href="wordnet.htm">Wordnet</a></li>
<li>
Abstract Data Model: <a href="UML_diagrams.htm">UML diagrams</a></li>
<li>
uses of metadata: GUI, reasoning</li>
</ul>
<h4>
The data exists</h4>
<ul>
<li>
more than 90% of the 250 000 species are on Floras on paper, and lots
are
<a href="existing.htm">on the Web</a> in HTML (not XHTML!);</li>
<li>
herbarium images; also many are on the Web (e.g. 30 000 species in
Florida)</li>
</ul>
<h4>
Vision</h4>
Imagine you're in nature, with a portable computer running the
botanical
database, with a camera, a GPS, and a wireless Internet connection.
Suddenly
you meet a remarkable plant; you show it to the computer, which asks you
two questions about the number of carpels, and the shape of hairs
(answers
needs a cutting of the ovary, and lenses). The computer tells you that
this a new location of Strasburgeria robusta, which was thought to exist
only in New Caledonia. You are proposed to send e-mails to the
specialists
of the Strasburgeriaceae, and of the region, and to collect a herbarium
specimen. Meanwhile this discovery, complete with images and
geographical
coordinates, is sent to the global database, and the updated repartition
map appears on the screen.
<h4>
A free sofware / free information project</h4>
<ul>
<li>
nobody can own nature</li>
<li>
a great project for humanity, and</li>
<li>
a great, far-reaching, and enjoyable software project.</li>
</ul>
<h4>
Collaborations</h4>
<ul>
<li>
Flora of China ( http://flora.harvard.edu/china/ ),</li>
<li>
Taxonomic Databases Working Group</li>
<li>
Kew Botanical Gardens</li>
</ul>
<h4>
New kind of software needed</h4>
A multi-everything browser will in fact be an empty shell
<ul>
<li>
calls the appropriate processors when it sees certain XML namespaces
and/or
Processing Instructions.</li>
<li>
multi-domain documents</li>
<li>
manage drag'n drop and clipboard with an XML data model.</li>
<li>
editor with the same multi-domain capabilities.</li>
<li>
manage the display space between XML processors (tiling, resize,
...).</li>
<li>
manage the mapping between raw XML and displayed XML transformed by
XSLT</li>
<li>
Generic display skills are also desirable:</li>
<ul>
<li>
collapsable tree/graph views for:</li>
<ul>
<li>
document tree</li>
<li>
inheritance graph</li>
<li>
the ID/IDREF graph</li>
</ul>
<li>
extended search/query</li>
</ul>
<li>
using a standard dictionary (e.g. wordnet) and some AI techniques will
enable to treat well-formed XML with a natural vocabulary of tags</li>
</ul>
A general and modular tool for manipulating data, of the 3 main kinds:
<ul>
<li>
document-oriented (HTML & word processor)</li>
<li>
structure-oriented (database type)</li>
<li>
knowledge-oriented (semantic network, AI, RDF, etc)</li>
</ul>
The next killer-app ... A role for Mozilla ? or Gnome? KDE ? or will the
next Microsoft Wave submerge all ?
<h4>
2D and 3D images</h4>
<ul>
<li>
vectorized images (SVG) from bitmap images</li>
<li>
3D images (X3D, etc) generated from several pictures through
stereoscopic
software</li>
<li>
very compact representations adapted to growing beings having recursive
structure: L-Systems, <a href="3Dgeometry.htm">MathML</a>, etc</li>
<li>
<a href="image_processing.htm#image_chain">Artificial Vision</a>
techniques</li>
</ul>
<h4>
Botany, Zoology, Ecology and the Semantic Web</h4>
<ul>
<li>
express relations between plants and animals in a formal and flexible
way
(RDF/XLink)</li>
<li>
plants (250 000) are just a beginning: insects alone have 1 000 000
species</li>
<li>
all kinds of properties, and properties about properties</li>
<li>
XML is not just to catalog consumers's preferences and locate the
cheapest
merchandise</li>
</ul>
<h4>
Conclusions</h4>
<ul>
<li>
do great things with little resources, like Ampère in the 19th
century</li>
<li>
plants are like software: you can clone easily, but some try to
copyright
them</li>
<li>
make standards for 20 years or more</li>
</ul>
<h4>
Issues</h4>
<ul>
<li>
<a href="XMLprotocol.htm">distributed knowledge</a> on the Web</li>
<li>
AI techniques and XML exchange formats/protocols for AI</li>
<li>
authoring side</li>
<li>
new ways of working for taxonomic scientists: new species created by Web
transaction, etc</li>
<li>
Problems with existing standards</li>
<ul>
<li>
overlapping concepts: RDF and Xlinks, RDF Schemas and XML Schemas</li>
<li>
development of monolythic vocabularies, little reuse of Schemas and
concepts</li>
</ul>
</ul>
<p><br>___________
<p>structure the presentation as a semantic network
<p>A VOIR: description logic
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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wn daisy -hypen
<p>Synonyms/Hypernyms (Ordered by Frequency) of noun daisy
<p>1 sense of daisy
<p>Sense 1
<br>daisy
<br> => flower
<br> =>
angiosperm,
flowering plant
<br>
=> spermatophyte, phanerogam, seed plant
<br>
=> vascular plant, tracheophyte
<br>
=> plant, flora, plant life
<br>
=> life form, organism, being, living thing
<br>
=> entity, something
<p>wn sepal -hholn
<p>Holonyms of noun sepal
<p>1 sense of sepal
<p>Sense 1
<br>sepal
<br> PART OF:
calyx
<br>
PART OF: perianth, floral envelope
<br>
PART OF: flower, bloom, blossom
<br>
PART OF: angiosperm, flowering plant
<p>wn hard -attra
<p>Attributes of adj hard
<p>2 of 11 senses of hard
<p>Sense 1
<br>difficult (vs. easy), hard
<br> => difficulty, difficultness
<p>Sense 3
<br>hard (vs. soft)
<br> => hardness
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<head>
<meta http-equiv="Content-Type" content="text/html;
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<meta name="Author" content="Jean-Marc Vanel">
<meta name="GENERATOR" content="Mozilla/4.5 [fr]C-CCK-MCD {FREE}
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<title>Plant image processing</title>
</head>
<body>
<h2>
Botanical images</h2>
updated 2000-03-15
<h3>
Visual plant identification</h3>
Here is some information about visual plant identification, for the
non-botanists.
<p>Since Linnaeus and until today, plant classification is based on
flowers.
Flowers, unlike flat leaves and linear stems, are essentially 3D
structures.
This means that one can rarelly see all the significant features on a
single
flat image. Also equal but differently orientated organs (like petals)
will appear unequal. Also there is possible confusion beetwen an
individual
flower and an inflorescence (gathering of small flowers, like the
clover).
The color is often not a discriminating character, since it can vary
within
a single species.
<br>A typical flower is composed, from bottom to top, of 5 rings (or
verticillas)
of pieces attached on a vertical axis:
<ul>
<li>
bracts</li>
<li>
sepals</li>
<li>
petals</li>
<li>
etamins (male part)</li>
<li>
carpels (female part)</li>
</ul>
Any of those 5 verticillas can be missing, or be joined within a
verticilla
or with the next one. The number of pieces in a verticilla can be
beetwin
1 and several tens, 5 being a frequent number.
<p>Leaves also have discriminating characters, and are (generally) 2D.
These characters are:
<br>- shape
<br>- veins (better seen on the underside)
<br>- differents types of hairs, better distinguished by touch or by
lenses
<br>- sometimes color
<p>So you see, plant images are a challenge for a 2D general purpose
image
system.
<h3>
Bibliography on plant morphology</h3>
If you want to read more, or just see images, here are some good books
I use on general botany:
<p>In french:
<ul>
<li>
Précis de botanique - 2. végétaux
supérieurs;
Gaussen, Leroy, Ozenda, éditions Masson</li>
<li>
La botanique redécouverte; Aline Reynal, éditions Belin
1995</li>
<li>
Les plantes à fleurs - Guide morphologique illustré;
Adrian
D. Bell, éditions Masson</li>
</ul>
In english:
<ul>
<li>
Plant form - An illustrated Guide to flowering plant morphology; Adrian
D. Bell, at Oxford Un. Press</li>
</ul>
<h3>
Image generation</h3>
<h4>
L-Systems</h4>
There is a classic book on L-Systems applied to modelize plant growth 2
years ago (Prusinkiewicz, P. and Lindenmayer, A.,1990, The Algorithmic
Beauty of Plants, Springer Verlag), and there is a French Institute
called
Cirad which does this sort of things for plants (they are on WWW but I
haven't seen pictures). Here are some links, having a wealth of
information
and links to other sites:
<br> <a
href="http://www.ctpm.uq.edu.au/virtualplants/ipiwww.html">http://www.ctpm.uq.edu.au/virtualplants/ipiwww.html</a>
<br><a
href="http://www.cpsc.ucalgary.ca/projects/bmv/software.html">http://www.cpsc.ucalgary.ca/projects/bmv/software.html</a>
<p><a NAME="image_chain"></a>Of course L-Systems is a link in the chain
we envision:
<ul>
<li>
2 or 3 pictures from different angles --></li>
<li>
3D representation (with Bezier mappings or whatever) --></li>
<li>
pattern recognition --> L-Systems --></li>
<li>
static or growth simulation images</li>
</ul>
Sure this is a too big picture for now!
<p>So we can enter L-Systems models in the database. I see the following
advantages to this representation:
<ul>
<li>
L-Systems capture truly biological features, like branching angles,</li>
<li>
species in the same genus or family will share a lot of growth
patterns,</li>
<li>
this is a way to generate very accurate images with very little
information.</li>
</ul>
I want to know more on this subject, especially are there many
downloadable
plants available, with a rigourous taxonomic identity ?
<p>What is not clear now to me (this is not an urgent issue) is:
<br>Will we develop, or is there, a XML vocabulary for L-Systems, or
will
a L-System definition remain "just" a character string.
<br>The avantage of a XML vocabulary would be to have a unified syntax,
from which a non-graphical processor could extract information of
taxonomic
relevance. From a XML representation, it is easy to generate a standart
L-System definition, using a XSLT stylesheet.
<h3>
3D recognition</h3>
Here is a <a href="http://cermics.enpc.fr/~keriven/home.html">home
page</a>
about stereoscopic and other algorithms for extracting 3D information
out
of 2D images. We currently try to learn more about stereoscopic systems,
especially for shapes having edges and folds.
<p>I'm currently evaluating free downloads, notably Geometra. The demo
I saw in their site is a house, having sharp edges; the user must click
on 2 or more points in the 2D pictures, before 3D information is
computed.
<p>The next stage in our project would be to generate from the 3D facets
a compact, non proprietary, preferably XML, clean <a
href="3Dgeometry.htm">definition
for complex 3D geometry</a> in the form of reunions and intersections of
volumes defined by equations:
<p>f(x,y,z)>=0
<p>and (e.g. NURBS and Beziers patches) surfaces defined by 3 functions
R2 ---> R3
<p>(u,v) ---> (X(u,v),Y(u,v),Z(u,v))
<p>But this "next stage" is probably still a research subject. But this
should not prevent us from gathering pictures from different angles, and
generate 3D information out of it.
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<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=iso-8859-1">
<meta name="Author" content="jmv">
<meta name="GENERATOR" content="Mozilla/4.5 [fr]C-CCK-MCD {FREE}
(Win95; I) [Netscape]">
<title>Specimen identification specification</title>
</head>
<body>
<center>
<h2>
Specimen identification</h2></center>
This is a beginning of specification for an application, that could be
a browser extension, realizing a Specimen identification. For now it
doesn't
take into account the contribution of image recognition.
<p>The user narrows its choice until there is only one species possible.
But the user has more freedom than in a tree-driven dialog à la
Delta, (s)he can enter at any time a character that appears particular
and discriminating. On the other hand, the classical identification keys
of Floras are tree-structured, and take in account only a kew
characters.
<p>There will be an input field for a character with three ways of
entering
organ, property, and value:
<ul>
<li>
automatic completion in an input field</li>
<li>
point and click on an image of a schematic plant with all organs present
(with a possibility to supress organs that are not present)</li>
<li>
pull-down menu</li>
</ul>
<p><br>This is possible because the relevant meta-data has been
downloaded
from server: list of organs, properties, and values (see <a
href="XMLprotocol.htm">XML
protocol</a>).
<p>At any stage the following items are recomputed and proposed to the
user:
<ul>
<li>
the number of species corresponding to the list of characters
entered</li>
<li>
the most discriminating questions</li>
<li>
the list of possible families or genus, possibly presented as a tree
view</li>
</ul>
When the identification is advanced enough, the system will display an
identikit picture (portrait-robot) of the plant or flower or leaf, that
will be recomputed at each step.
</body>
</html>
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