Oct 17

The Global Biodiversity Informatics Outlook

The recently released Global Biodiversity Informatics Outlook (GBIO) proposes a framework for work to be done in the next five to ten years by projects such as EOL. It is the main product produced from the 2012 Global Biodiversity Informatics Conference held in Copenhagen.

Some will argue that we don’t need another acronym — certainly we already have plenty! The important thing is for future investments in biodiversity informatics to have the most impact. A visionary document like the GBIO helps funders, tool builders and data providers most efficiently provide the data and knowledge that consumers need.

Encyclopedia of Life aims to play an essential role in several of GBIO’s interconnected components. Like many projects, we provide comprehensive knowledge access and promote a culture of open access and reuse.  We are serious about increasing data accuracy via a biodiversity knowledge network; most EOL curation actions and community-generated annotations are already routed to providers of source data. With the upcoming release of Traitbank(TM) we aim to be a premier provider of aggregated species trait data.

EOL also serves secondary roles in the rapid capture and dissemination of collections and specimen data (e.g. the National Museum of Natural history specimen images). We are exploring how best to mine published materials (see Rubenstein projects and the upcoming Research Sprint). Finally, EOL can contribute to an overall taxonomic framework

There is still much work to be done. Watch for future blog posts on these topics, and visit http://biodiversityinformatics.org for more information on how you can get involved.

Sep 12

New EOL Mobile App and Game for iPad and Android Tablets

Introducing M-EOL, a new mobile app for iPad and Android tablets and the winner of the EOL Education Innovation Challenge! Created by Natural Solutions and available on iTunes and Google Play.

Become an explorer, discovering different plant and animal species by travelling around the world. Improve your knowledge about each species through descriptions, images, distribution information, and conservation status from the Encyclopedia of Life website. Explore how organisms in each game collection are related to each other by browsing a dynamic, interactive graph. 

M-EOL App on iTunes

M-EOL App on Google Play

Let us know what you think of M-EOL! Send your feedback to education (at) eol.org.

M-EOL

Sep 06

Update on the EOL Private Beta program

I’m happy to report that the private beta for the EOL release codenamed Bocce began yesterday without a hiccup - if you accepted an invitation to participate, you will have received a detailed email from us yesterday with instructions on how to access the beta platform, credentials for logging in, a list of tasks to perform, and guidance on how to access the post-beta survey.

If you did not receive your beta instructions, drop me a note.  We want your feedback.

It’s fair to say we’re all a bit excited about this release.  It’s different than anything we’ve done before, and I think it has the possibility to change the world.  I don’t get to say that about everything we do, but this time, we’re on to something big.

The private beta will run for the next two weeks, then we will hunker down, digest the feedback, tune up what needs tuning up, push some final features, then ramp up for a public beta coming later this fall.

Stay tuned.

Sep 05

New One Species at a Time Podcast: New Species in the Old World

Image Credit: Ari Daniel Shapiro

You don’t always have to venture into the heart of a rain forest to discover a new species. Sometimes all you have to do is look more closely, right where you are. In Europe, experts and enthusiasts alike are looking high and low, from alpine meadows to underground caves, in search of Old World species new to science.

Listen to the podcast

Aug 15

Newly described species of mammal!

Olinguito (Bassaricyon neblina) at Tandayapa Bird Lodge, Ecuador. © Mark Gurney, CC-BY

Meet the olinguito, Bassaricyon neblina, the first new species of carnivore found in the Western Hemisphere in 35 years!

The olinguito lives in high elevation Andean cloud forests of Colombia and Ecuador. It spends most of its time high up in trees and is active at night. 

Specimens had been in museum cabinets for more than a century, but Smithsonian researchers confirmed its status as a distinct species only recently.  

Read more about the discovery on the Smithsonian Science website.

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.