New One Species at a Time Podcast: Bats
The batman of Mexico has his own bat-cave. He just shares it with 4,000 Mexican long-nosed bats. In this episode, join researcher Rodrigo Medellin as he descends into the Devil’s Cave just north of Mexico City. It’s a journey that started decades ago when Medellin was on a game show as a boy. He lost the game show, but won a prize far more valuable—for himself, his students, and Mexico’s bats. Ari Daniel Shapiro reports from Tepoztlán.
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.
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.
Let us know what you think of M-EOL! Send your feedback to education (at) eol.org.
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.
New One Species at a Time Podcast: New Species in the Old World
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.
Newly described species of mammal!
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.
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.
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.
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 (Ⅰ)), 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 “experiment” is for storing detail information about experiment.
Table ‘synonyms’ is to store synonyms of taxon in ‘tree’.
Synonym is regarded as vice label for taxon.
Table ‘taxonlinks’ stores the relationships of taxa in compared trees.
It is for the result of tree comparison and computation.
Each record of ‘tree’ means a taxon including its propertis such as name, rank, position and so on.
'tree_info' stores information about tree.
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”
Relative article: Progress of Colin’s 2013 Rubenstein Project (Ⅰ)
This article is excerpted from “Database Design Specification for THC”
Author: Colin, 2013 EOL Rubenstein Fellow