From nickl at CALM.WA.GOV.AU Fri May 12 14:57:38 2000 From: nickl at CALM.WA.GOV.AU (Nick Lander) Date: Fri, 12 May 2000 14:57:38 Subject: Coverage of Floras? Message-ID: Jean-Marc Vanel , on 12/05/2000 14:01 PM, wrote: 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) I am not sure to what you are referring. Do you mean simply lists of names or are you after useful information such as descriptions, maps, illustrations? >The following are on the Web : >Flora of China >Flora of Australia >Flora of North America (www.fna.org) Where can one view a Flora of Australia on the Web, I wonder? FloraBase (http://www.calm.wa.gov.au/science/florabase.html), maintained by the Western Australian Herbarium, includes brief descriptions, specimen lists and maps of all 12,500 vascular plant species occuring in this state. This represents ca half of the continent's flora and covers ca one third of its area. For each species an information page can be retrieved on-line comprising its scientific and common names, an indication of its status (native, alien, priority if threatened), a description, a map and (if available) a composite colour photograph showing habitat, habit, floral and fruit characteristics. Form-based query tools enable one to retrieve information or identify species on the basis of nomenclatural, geographic and/or morphological fields. There are also facilities for users to suggest corrections (eg redeterminations) to the various databases which underlie FloraBase. Over the coming months FloraBase will be extended to include highly detailed descriptions of genera and families. Over the horizon, the descriptive data will be expanded by use of a much larger character set. Another Australian botanical information system that may be worth your attention is The National Herbarium of New South Wales' PlantNet site (http://plantnet.rbgsyd.gov.au/). The HISCOM site (http://www.rbgsyd.gov.au/HISCOM/default.htm) provides a springboard for those embarking on a virtual foray in search of the Australian flora. Nicholas Lander Western Australian Herbarium (PERTH) ---------- Original Text ---------- From: "Jean-Marc Vanel" , on 12/05/2000 14:01 PM: 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 -- Jean-Marc Vanel Veni, vidi, convici 9th International World Wide Web Conference - Amsterdam, May 15-19, 2000 site Worlwide Botanical Knowledge Base - making botany available on Internet site mail (possibly put "wwbota" in subject to route your mail in relevant folder) From jmvanel at FREE.FR Fri May 12 07:44:37 2000 From: jmvanel at FREE.FR (Jean-Marc Vanel) Date: Fri, 12 May 2000 7:44:37 Subject: Coverage of Floras? Message-ID: 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 -- Jean-Marc Vanel Veni, vidi, convici 9th International World Wide Web Conference - Amsterdam, May 15-19, 2000 site Worlwide Botanical Knowledge Base - making botany available on Internet site mail (possibly put "wwbota" in subject to route your mail in relevant folder) X-Mozilla-Status: 00090:16 2000 X-Mozilla-Status: 0801 X-Mozilla-Status2: 00000000 FCC: /D|/Programs/Netscape/Program/Users/jmv/mail/Sent Message-ID: <391B9940.8B85D4CE at free.fr> Date: Fri, 12 May 2000 07:40:16 +0200 From: Jean-Marc Vanel X-Mozilla-Draft-Info: internal/draft; vcard=0; receipt=0; uuencode=0; html=0; linewidth=0 X-Mailer: Mozilla 4.5 [fr]C-CCK-MCD {FREE} (Win95; I) X-Accept-Language: en,fr MIME-Version: 1.0 To: Jean Marc VANEL Subject: pres. WWW9 Content-Type: multipart/mixed; boundary="------------F0DEFDB499A8369AE40C44BD" Il s'agit d'un message multivolet au format MIME. --------------F0DEFDB499A8369AE40C44BD Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  

--
<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>
  --------------F0DEFDB499A8369AE40C44BD Content-Type: text/html; charset=iso-8859-1; name="index.htm" Content-Transfer-Encoding: 8bit Content-Disposition: inline; filename="index.htm" Worlwide Plant Database Project

Worldwide Botanical Knowledge Base

You will not find here botanical databases with queries on the species description - not yet. But this is the aim of this project, the techniques are here, the data are here. So why not join us, wether you are a computer specialist or a botanist. Or just drop a few lines for advice, encouragement or critics.

Call for a world botanical database
Test of the botanical resources on INTERNET
Short-term plan for a WWW botanical database

What's new
FAQ
En français (pas à jour)


Presentation at WWW9 Conference NEW

Technical:


Only english version is regularly updated.
To translate this in other languages: AltaVista Translations
Um dieses zu Übersetzen: AltaVista Translations
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Bases de données botaniques

mise à jour: 14 sept. 1999

Appel pour une base de données botanique mondiale
Essai des ressources botaniques sur INTERNET
Présentation synthétique du projet NOUVEAU

A paraître:

  • techniques informatiques applicables
  • schéma UML des données
  • contacts
--------------F0DEFDB499A8369AE40C44BD Content-Type: text/html; charset=us-ascii; name="presentationWWW9.htm" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="presentationWWW9.htm" Worldwide Botanical Knowledge Base

Worldwide Botanical Knowledge Base

http://wwbota.free.fr/

Biodiversity and nature conservancy

  • thousands of species are disappearing forever,
  • need quick identification of specimens from threatened areas, without qualified scientists;
  • the knowledge is on paper like in Linnaeus' time,
==> an inventory of the biological inheritance of our earth has to be done.

There is currently no other botanical project with this scope.
Why ?

  • funds go rather to biotechnologies than to descriptive biology,
  • pluri-displinarity is not easy

Aim

to make botanical data available on  Internet :
  • description of the species, including 2D and 3D pictures,
  • geographical distribution,
  • computer-aided identification of specimens

Initial intuitions:

  1. relational DB
  2. uncouple data (XML) and processing (relational DB, OO DB, AI engines)
  3. offer easy access to detailed knowledge both for the layman and the professional botanist
  4. federate existing resources and people

The metadata

  • Why a relational DB is not enough: example of bark and stem
    • bark is a part of stem (and trunk)
  • different levels of metadata
  • several sources of metadata: Floras, Wordnet
  • Abstract Data Model: UML diagrams
  • uses of metadata: GUI, reasoning

The data exists

  • more than 90% of the 250 000 species are on Floras on paper, and lots are on the Web in HTML (not XHTML!);
  • herbarium images; also many are on the Web (e.g. 30 000 species in Florida)

Vision

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.

A free sofware / free information project

  • nobody can own nature
  • a great project for humanity, and
  • a great, far-reaching, and enjoyable software project.

Collaborations

  • Flora of China ( http://flora.harvard.edu/china/ ),
  • Taxonomic Databases Working Group
  • Kew Botanical Gardens

New kind of software needed

A multi-everything browser will in fact be an empty shell
  • calls the appropriate processors when it sees certain XML namespaces and/or Processing Instructions.
  • multi-domain documents
  • manage drag'n drop and clipboard with an XML data model.
  • editor with the same multi-domain capabilities.
  • manage the display space between XML processors (tiling, resize, ...).
  • manage the mapping between raw XML and displayed XML transformed by XSLT
  • Generic display skills are also desirable:
    •     collapsable tree/graph views for:
      • document tree
      • inheritance graph
      • the ID/IDREF graph
    •     extended search/query
  • using a standard dictionary (e.g. wordnet) and some AI techniques will enable to treat well-formed XML with a natural vocabulary of tags
A general and modular tool for manipulating data, of the 3 main kinds:
  • document-oriented (HTML & word processor)
  • structure-oriented (database type)
  • knowledge-oriented (semantic network, AI, RDF, etc)
The next killer-app ... A role for Mozilla ? or Gnome? KDE ? or will the next Microsoft Wave submerge all ?

2D and 3D images

  • vectorized images (SVG) from bitmap images
  • 3D images (X3D, etc) generated from several pictures through stereoscopic software
  • very compact representations adapted to growing beings having recursive structure: L-Systems, MathML, etc
  • Artificial Vision techniques

Botany, Zoology, Ecology and the Semantic Web

  • express relations between plants and animals in a formal and flexible way (RDF/XLink)
  • plants (250 000) are just a beginning: insects alone have 1 000 000 species
  • all kinds of properties, and properties about properties
  • XML is not just to catalog consumers's preferences and locate the cheapest merchandise

Conclusions

  • do great things with little resources, like Ampère in the 19th century
  • plants are like software: you can clone easily, but some try to copyright them
  • make standards for 20 years or more

Issues

  • distributed knowledge on the Web
  • AI techniques and XML exchange formats/protocols for AI
  • authoring side
  • new ways of working for taxonomic scientists: new species created by Web transaction, etc
  • Problems with existing standards
    • overlapping concepts: RDF and Xlinks, RDF Schemas and XML Schemas
    • development of monolythic vocabularies, little reuse of Schemas and concepts


___________

structure the presentation as a semantic network

A VOIR: description logic
 
 
 
 
 
 
 
 
 
 
  --------------F0DEFDB499A8369AE40C44BD Content-Type: text/html; charset=us-ascii; name="wordnet.htm" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="wordnet.htm" wn daisy -hypen

Synonyms/Hypernyms (Ordered by Frequency) of noun daisy

1 sense of daisy

Sense 1
daisy
       => flower
           => angiosperm, flowering plant
               => spermatophyte, phanerogam, seed plant
                   => vascular plant, tracheophyte
                       => plant, flora, plant life
                           => life form, organism, being, living thing
                               => entity, something

wn sepal -hholn

Holonyms of noun sepal

1 sense of sepal

Sense 1
sepal
          PART OF: calyx
              PART OF: perianth, floral envelope
                  PART OF: flower, bloom, blossom
                      PART OF: angiosperm, flowering plant

wn hard -attra

Attributes of adj hard

2 of 11 senses of hard

Sense 1
difficult (vs. easy), hard
       => difficulty, difficultness

Sense 3
hard (vs. soft)
       => hardness --------------F0DEFDB499A8369AE40C44BD Content-Type: text/html; charset=us-ascii; name="image_processing.htm" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="image_processing.htm" Plant image processing

Botanical images

updated 2000-03-15

Visual plant identification

Here is some information about visual plant identification, for the non-botanists.

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.
A typical flower is composed, from bottom to top, of 5 rings (or verticillas) of pieces attached on a vertical axis:

  • bracts
  • sepals
  • petals
  • etamins (male part)
  • carpels (female part)
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.

Leaves also have discriminating characters, and are (generally) 2D. These characters are:
- shape
- veins (better seen on the underside)
- differents types of hairs, better distinguished by touch or by lenses
- sometimes color

So you see, plant images are a challenge for a 2D general purpose image system.

Bibliography on plant morphology

If you want to read more, or just see images, here are some good books I use on general botany:

In french:

  • Précis de botanique - 2. végétaux supérieurs; Gaussen, Leroy, Ozenda, éditions Masson
  • La botanique redécouverte; Aline Reynal, éditions Belin 1995
  • Les plantes à fleurs - Guide morphologique illustré; Adrian D. Bell, éditions Masson
In english:
  • Plant form - An illustrated Guide to flowering plant morphology; Adrian D. Bell, at Oxford Un. Press

Image generation

L-Systems

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:
 http://www.ctpm.uq.edu.au/virtualplants/ipiwww.html
http://www.cpsc.ucalgary.ca/projects/bmv/software.html

Of course L-Systems is a link in the chain we envision:

  • 2 or 3 pictures from different angles -->
  • 3D representation (with Bezier mappings or whatever) -->
  • pattern recognition --> L-Systems -->
  • static or growth simulation images
Sure this is a too big picture for now!

So we can enter L-Systems models in the database. I see the following advantages to this representation:

  • L-Systems capture truly biological features, like branching angles,
  • species in the same genus or family will share a lot of growth patterns,
  • this is a way to generate very accurate images with very little information.
I want to know more on this subject, especially are there many downloadable plants available, with a rigourous taxonomic identity ?

What is not clear now to me (this is not an urgent issue) is:
Will we develop, or is there, a XML vocabulary for L-Systems, or will a L-System definition remain "just" a character string.
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.

3D recognition

Here is a home page 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.

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.

The next stage in our project would be to generate from the 3D facets a compact, non proprietary, preferably XML, clean definition for complex 3D geometry in the form of reunions and intersections of volumes defined by equations:

f(x,y,z)>=0

and (e.g. NURBS and Beziers patches) surfaces defined by 3 functions R2 ---> R3

(u,v) ---> (X(u,v),Y(u,v),Z(u,v))

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. --------------F0DEFDB499A8369AE40C44BD Content-Type: text/html; charset=us-ascii; name="ApplicationSpec.htm" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="ApplicationSpec.htm" Specimen identification specification

Specimen identification

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.

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.

There will be an input field for a character with three ways of entering organ, property, and value:

  • automatic completion in an input field
  • point and click on an image of a schematic plant with all organs present (with a possibility to supress organs that are not present)
  • pull-down menu


This is possible because the relevant meta-data has been downloaded from server: list of organs, properties, and values (see XML protocol).

At any stage the following items are recomputed and proposed to the user:

  • the number of species corresponding to the list of characters entered
  • the most discriminating questions
  • the list of possible families or genus, possibly presented as a tree view
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. --------------F0DEFDB499A8369AE40C44BD-- From jmvanel at FREE.FR Fri May 12 07:38:44 2000 From: jmvanel at FREE.FR (Jean-Marc Vanel) Date: Fri, 12 May 2000 7:38:44 Subject: Coverage of Floras? Message-ID: 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 -- Jean-Marc Vanel Veni, vidi, convici 9th International World Wide Web Conference - Amsterdam, May 15-19, 2000 site Worlwide Botanical Knowledge Base - making botany available on Internet site mail (possibly put "wwbota" in subject to route your mail in relevant folder)