Aug 06

National Moth Week July 20-28, 2013

National Moth Week offers everyone, everywhere a unique opportunity to become a Citizen Scientist and contribute scientific data about moths. Through partnerships with major online biological data depositories such as EOL, National Moth Week participants can help map moth distribution and provide needed information on other life history aspects around the globe.

National Moth Week Website

Learn more about Moths on EOL

Watch the EOL Moths Audio Slideshow

Anita, iNaturalist.org. CC BY-NC. http://eol.org/data_objects/24048608

Progress of Colin’s 2013 Rubenstein Project (Ⅱ) —Glossary & Database Design

This article is to introduce some glossaries used or defined by us in this project and the work of database design.

1.       Glossaries

(1)     Taxon

Taxon is a taxonomic unit or group which may be named or not. A taxon encompasses all included taxa of lower rank and individual organisms. Taxonomic rank describes the level of a taxon in a taxonomic hierarchy for nomenclatural purposes. Each rank is either mandatory (e.g. kingdom, phylum, class, order, family, genus, species) or optional (e.g. subkingdom, subphylum, subclass, subfamily, subgenus, subspecies). Nominal taxon isa concept of a taxon which is denoted by an available name based on a name-bearing type.

(2)     Taxon Concept

The scope of a taxon may differ from one taxonomists to another, and changes with new data. Each opinion as to what is intended by the name of a taxon is a ‘taxon concept’.

(3)     Taxonomic Hierarchy

Taxa are arranged hierarchically from high rank to low rank, and compose a taxonomic hierarchy (or “taxonomic tree” and “taxonomic classification”) that reflects the view on classification. As well known, taxonomic hierarchy is usually tree-based and can be regarded as a special case of mathematical tree technically.

(4)     Nominal Relation (NR)

Because of the inexact nature of taxonomy, different taxonomies may use different names for the same taxon concepts and the same name for different taxon concepts (Homonym). When compare two taxon concepts from different hierarchies, scientific names including accepted name and synonyms for the concepts usually provide important clues about the relationship between them, and that is named as Nominal Relation.

(5)     Ancestor Relation (AR)

Ancestor Relation is defined to describe the relationship between two compared taxa by their parent paths.

(6)     Descendant Relation (DR)

Descendant Relation is intended for assessing the similarity of the branches under the compared taxa.

(7)     Taxon Link (TL)

Taxon Link is defined as a triple tuple (AR, NR, DR). It is the result of taxon to taxon comparison, and intended for representing the combined relationships among compared taxa.

(8)     Compared Tree and Reference Tree

Just like subtraction, the hierarchy to be compared on the left of the comparator is regarded as compared tree (CT) and the hierarchy for comparing on the right of the operator is called reference tree (RT).

2.       Database Design

(1)     Data Requirements

According to the analysis of THC’s requirements (refer to Progress of Colin’s 2013 Rubenstein Project ()), the database should consider the following main data requirements:

1.       The user information like username, password, self description, status.

2.       The tree information like tree name, creator, created date, description of the tree.

3.       The experiment information like name, creator, created date, compare tree, reference tree.

4.       The result of comparison like similarity index, taxon links.

5.       Taxon detail like scientific name, synonym, parents, rank.

This database will store as many as possible taxonomic trees (hierarchies) just like a forest, so it is named as “Taxonomic Forest” vividly. We will use MYSQL 5.0 or above as the database software.

(2)     Tables & Relationship

Table 1 shows the main tables of “Taxonomic Forest”.

Table

Cols

Description

experiment

8

Table “experiment” is for storing detail information about experiment.

synonyms

6

Table ‘synonyms’ is to store synonyms of taxon in ‘tree’.
Synonym is regarded as vice label for taxon.

taxonlinks

13

Table ‘taxonlinks’ stores the relationships of taxa in compared trees.
It is for the result of tree comparison and computation.

tree

10

Each record of ‘tree’ means a taxon including its propertis such as name, rank, position and so on.

tree_info

8

'tree_info' stores information about tree.

users

6

It is for user management, and records the information for registered users.

Figure1 shows the relationship of these main tables (detail fields are not displayed for the security reason).


                                      Fig 1 E-R Diagram of Database “Taxonomic Forest”

Fig 1 E-R Diagram of Database “Taxonomic Forest”

Relative article: Progress of Colin’s 2013 Rubenstein Project ()

This article is excerpted from “Database Design Specification for THC”

Author: Colin, 2013 EOL Rubenstein Fellow

Jul 11

Progress of Colin’s 2013 Rubenstein Project (Ⅰ)

Project Description

As a 2013 EOL Rubenstein Fellow, my project is “Using the multiple classifications harvested by EOL for analysis to obtain the degree of coverage and congruence among hierarchies and nomenclatures.” As we know, many taxonomic hierarchies have been created due to:

a.       Taxonomists have different views on biological classification

b.       New technologies like phylogenetics create new perspectives on taxa relationships.

c.       Biological classification is a job proceeding with time, and the old classification should be updated when new groups of species or specimens are found.

d.       The scopes and coverage of different classifications are usually geographically restricted.

Analysis on these hierarchies (or taxonomic trees) to find out the congruence and incongruence is interesting, and required both by researchers on biodiversity informatics and taxonomy according to our first stage requirement analysis. Considering the long term usage and the requirement of potential users, we plan to implement a mature tool Taxonomic Hierarchy Comparator (THC) for managing and comparing different taxonomic hierarchies.

 

Potential Users of THC:

1.       Researchers on Biodiversity Informatics who want to know where the differences are among the hierarchies, what biological group is hot, and where the gap to be filled is.

2.       Taxonomists who want to find out the incongruence between their taxonomic views and others’. They can analysis their own hierarchies against with EOL hierarchies.

 

Main Functional Requirement

1.       User management

User should have an account before using THC. That will help them to create and manage their own taxonomic hierarchies and keep analysis experiment result permanently for reuse. User management is required to manage user account including registration, authorization, log in/out, and account update.

2.       Hierarchy management

a.       Create hierarchy: hierarchy can be created from different methods. User can upload an Xml in BSBC format or DWCA file, or copy a hierarchy from shared hierarchies’ pool. EOL hierarchies will be imported to THC by web API provided by EOL.

b.       Edit hierarchy: a simple editor for user to modify the hierarchies. It will help user to edit scientific names, change position of taxon, insert new taxon, and delete taxon.

c.       Share hierarchy: user can share his own hierarchies to others for analysis, but others cannot modify the shared hierarchies.

d.       Export hierarchy: help users to save their hierarchy as standard DWCA file or BSBC xml.

3.       Analysis experiment

a.       Create experiment: give an identifier and some descriptions for the experiment; select which hierarchies for analysis. THC will keep the analysis result.

b.       Share experiment: result of analysis can be shared with other users

c.       Implementation: submit the analysis task to server, and waiting for response message. It is a time consuming process, so task queue is required to deal with multiple analysis tasks. Analysis is based on algorithm proposed by us.

d.       Visualization: it is an important function for expressing analysis result. It should show where the congruence and incongruence explicitly is.

e.       Computation: base on the result, “intersection” computation between two hierarchies is to extract the common part and “difference” is to produce the incongruence part.

 

Use Case

Some use cases have been designed to show how users or manager engage THC and how the requirements are realized in the context of software. Fig1 is the use case of experiment.

Fig1 Use Case of Experiment

Fig1 Use Case of Experiment

Another progress is a paper about the method and algorithm is being written, and we hope it can be published in a relative journal in next stage.

More progresses are about database design and interface design and will be posted at the end of July.

 

This article is excerpted from “requirement analysis of THC”

Author: Colin, 2013 EOL Rubenstein Fellow

Jul 10

New One Species at a Time Podcast: Saltwater Crocodile

The city of Darwin in Australia’s Northern Territory lies in the heart of crocodile country. In the 1950s, saltwater crocodiles were shot, skinned, and turned into shoes and handbags. After hunting was banned in the 1970s, crocodile numbers climbed. Now there’s a croc for every man, woman, and child in Darwin. Can the human citizens learn to live alongside their toothy neighbors?

Listen to the Podcast   

Meet the Scientist   

Learn more about the Saltwater Crocodile on EOL  

Image Credit: Gerald and Buff Corsi. CalPhotos. CC BY-NC-SA. http://eol.org/data_objects/12512171

Request for feedback regarding “Add to Reddit” button on EOL

The EOL development team is considering adding a “share with Reddit” button to EOL pages everywhere similar buttons to “Tweet” and “Like on Facebook” are found.

The debate comes down to the tension between supporting Reddit users who want to share EOL content with their various communities vs concerns about Reddit in general, especially in light of some of the content found on the site.

Do you have an opinion?  Please share it with me by email at bcorrigan@eol.org or tweeting a message to @eol or @eolpm - and thank you.

Image Credit: National Park Service, US Department of Interior, Public Domain.

In our latest podcast we venture to Santa Cruz Island, off the coast of California, to look into the mystery of the island’s tiny foxes, descendants of gray foxes who rafted over from the mainland more than ten thousand years ago and branched off to form a new, smaller species. 

Despite weighing a mere three pounds, these diminutive grey foxes thrived and for millennia they reigned as the island’s top predator. But twenty years ago, their numbers began to plummet, from three thousand in the early 1990s to fewer than one hundred by 2000. Learn how conservationists solved the puzzle of the vanishing foxes and helped them stage a comeback.

Listen to the podcast

Meet the Scientist

Learn more about the Island Fox on EOL

May 20

As they wing their way across North America, millions of migrating monarch butterflies form a living river of orange. In this episode, the second of two podcasts on monarchs, we’ll meet citizens young and old who are dipping a toe in that river in the name of science and of beauty.
Listen to the podcast
Watch the Monarch Butterflies Eastern Migration Google Earth Tour Video
También puede ver este vídeo con subtítulos en español aquí.
Photo: © Ted Kropiewnicki
CC-BY-NC-SA
Supplier: Tree of Life web project
Location Created: Bear, Delaware, USA
View source 

As they wing their way across North America, millions of migrating monarch butterflies form a living river of orange. In this episode, the second of two podcasts on monarchs, we’ll meet citizens young and old who are dipping a toe in that river in the name of science and of beauty.

Listen to the podcast

Watch the Monarch Butterflies Eastern Migration Google Earth Tour Video

También puede ver este vídeo con subtítulos en español aquí.


Photo: © Ted Kropiewnicki

CC-BY-NC-SA

Supplier: Tree of Life web project

Location Created: Bear, Delaware, USA

View source 

May 07

EOL/Google Earth Monarch Butterfly Tour Now Available

Every year eastern monarch butterflies begin a journey north from their overwintering grounds in Mexican forests. The epic migration spans generations and the better part of a continent.

EOL is pleased to announce a new Google Earth tour video showcasing the migration of monarch butterflies (Danaus plexippus) in North America, and the people that help them out along the way.

This Google Earth tour is accompanied by two companion podcasts, the first of which can be found here.

This Google Earth Tour was produced by Atlantic Public Media in cooperation with the Encyclopedia of Life Learning + Education group located at the Harvard Museum of Comparative Zoology.

Apr 18

More on Garlic Mustard (Alliaria petiolata) on EOL
(photo by Ondřej Zicha [CC BY-NC] via Biolib.cz)

More on Garlic Mustard (Alliaria petiolata) on EOL

(photo by Ondřej Zicha [CC BY-NC] via Biolib.cz)

Rodents of Unusual Size Do Exist | Around The Mallsmithsonianmag.com
But­ter­cup and West­ley may have doubt­ed the ROUS’ exis­tence in 1987′s The Princess Bride, but the love-stricken pair quick­ly caught on when the “Rodents of Unusu­al Size” attacked.A team of sci­en …

R.O.U.S. exist?  Inconceivable! (see esp. http://flip.it/H1eS8)

Rodents of Unusual Size Do Exist | Around The Mall
smithsonianmag.com

But­ter­cup and West­ley may have doubt­ed the ROUS’ exis­tence in 1987′s The Princess Bride, but the love-stricken pair quick­ly caught on when the “Rodents of Unusu­al Size” attacked.

A team of sci­en …

R.O.U.S. exist? Inconceivable! (see esp. http://flip.it/H1eS8)