Archive for the ‘Environment’ Category

Biodiversity Heritage Library (BHL)

Thursday, March 28th, 2013

Biodiversity Heritage Library (BHL)

Best described by their own “about” page:

The Biodiversity Heritage Library (BHL) is a consortium of natural history and botanical libraries that cooperate to digitize and make accessible the legacy literature of biodiversity held in their collections and to make that literature available for open access and responsible use as a part of a global “biodiversity commons.” The BHL consortium works with the international taxonomic community, rights holders, and other interested parties to ensure that this biodiversity heritage is made available to a global audience through open access principles. In partnership with the Internet Archive and through local digitization efforts , the BHL has digitized millions of pages of taxonomic literature , representing tens of thousands of titles and over 100,000 volumes.

The published literature on biological diversity has limited global distribution; much of it is available in only a few select libraries in the developed world. These collections are of exceptional value because the domain of systematic biology depends, more than any other science, upon historic literature. Yet, this wealth of knowledge is available only to those few who can gain direct access to significant library collections. Literature about the biota existing in developing countries is often not available within their own borders. Biologists have long considered that access to the published literature is one of the chief impediments to the efficiency of research in the field. Free global access to digital literature repatriates information about the earth’s species to all parts of the world.

The BHL consortium members digitize the public domain books and journals held within their collections. To acquire additional content and promote free access to information, the BHL has obtained permission from publishers to digitize and make available significant biodiversity materials that are still under copyright.

Because of BHL’s success in digitizing a significant mass of biodiversity literature, the study of living organisms has become more efficient. The BHL Portal allows users to search the corpus by multiple access points, read the texts online, or download select pages or entire volumes as PDF files.

The BHL serves texts with information on over a million species names. Using UBio’s taxonomic name finding tools, researchers can bring together publications about species and find links to related content in the Encyclopedia of Life. Because of its commitment to open access, BHL provides a range of services and APIs which allow users to harvest source data files and reuse content for research purposes.

Since 2009, the BHL has expanded globally. The European Commission’s eContentPlus program has funded the BHL-Europe project, with 28 institutions, to assemble the European language literature. Additionally, the Chinese Academy of Sciences (BHL-China), the Atlas of Living Australia (BHL-Australia), Brazil (through BHL-SciELO) and the Bibliotheca Alexandrinahave created national or regional BHL nodes. Global nodes are organizational structures that may or may not develop their own BHL portals. It is the goal of BHL to share and serve content through the BHL Portal developed and maintained at the Missouri Botanical Garden. These projects will work together to share content, protocols, services, and digital preservation practices.

A truly remarkable effort!

Would you believe they have a copy of “Aristotle’s History of animals.” In ten books. Tr. by Richard Cresswell? For download as a PDF?

Tell me, how would you reconcile the terminology of Aristotle or of Cresswell for that matter in translation, with modern terminology both for species and their features?

In order to enable navigation from this work to other works in the collection?

Moreover, how would you preserve that navigation for others to use?

Document level granularity is better than not finding a document at all but it is a far cry from being efficient.

BHL-Europe web portal opens up…

Thursday, March 28th, 2013

BHL-Europe web portal opens up the world’s knowledge on biological diversity

From the post:

The goal of the Biodiversity Heritage Library for Europe (BHL-Europe) project is to make published biodiversity literature accessible to anyone who’s interested. The project will provide a multilingual access point (12 languages) for biodiversity content through the BHL-Europe web portal with specific biological functionalities for search and retrieval and through the EUROPEANA portal. Currently BHL-Europe involves 28 major natural history museums, botanical gardens and other cooperating institutions.

BHL-Europe is a 3 year project, funded by the European Commission under the eContentplus programme, as part of the i2010 policy.

Unlimited access to biological diversity information

The libraries of the European natural history museums and botanical gardens collectively hold the majority of the world’s published knowledge on the discovery and subsequent description of biological diversity. However, digital access to this knowledge is difficult.

The BHLproject, launched 2007 in the USA, is systematically attempting to address this problem. In May 2009 the ambitious and innovative EU project ‘Biodiversity Heritage Library for Europe’ (BHL-Europe) was launched. BHL-Europe is coordinated by the Museum für Naturkunde Berlin, Germany, and combines the efforts of 26 European and 2 American institutions. For the first time, the wider public, citizen scientists and decision makers will have unlimited access to this important source of information.

A project with enormous potential, although three (3) years seems a bit short.

Mentioned but without a link, the BHLproject has digitized over 100,000 volumes, with information on more than one million species names.

DataONE

Friday, March 22nd, 2013

DataONE

From the “about” page:

Data Observation Network for Earth (DataONE) is the foundation of new innovative environmental science through a distributed framework and sustainable cyberinfrastructure that meets the needs of science and society for open, persistent, robust, and secure access to well-described and easily discovered Earth observational data.

Supported by the U.S. National Science Foundation (Grant #OCI-0830944) as one of the initial DataNets, DataONE will ensure the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program.

“…preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data….”

Sounds like they are playing our song!

See also: DataONE: Survey of Earth Scientists, To Share or Not to Share Data, abstract of a poster from the American Geophysical Union, Fall Meeting 2010, abstract #IN11A-1062.

Interesting summary of the current data habits and preferences of scientists.

Starting point for shaping a topic map solution to problems as perceived by a group of users.

Processing Public Data with R

Monday, July 16th, 2012

Processing Public Data with R

From the post:

I use R aplenty in analysis and thought it might be worthwhile for some to see the typical process a relative newcomer goes through in extracting and analyzing public datasets

In this instance I happen to be looking at Canadian air pollution statistics.

The data I am interested in is available on the Ontario Ministry of Environment’s website. I have downloaded the hourly ozone readings from two weather stations (Grand Bend and Toronto West) for two years (2000 and 2011) which are available in several formats , including my preference, csv. According to the 2010 annual report from the Ministry, the two selected represent the extremes in readings for that year

I firstly set the directory in which the code and the associated datafiles will reside and import the data. I would normally load any R packages I will utilize at the head of the script (if not already in my start up file) but will hold off here until they are put to use.

I had to do a small amount of row deletion in the csv files so that only the readings data was included

A useful look at using R to manipulate public data.

Do you know of any articles on using R to output topic maps?

I Dream of “Jini”

Thursday, June 7th, 2012

The original title reads: Argus Labs Celebrates The Launch Of The Beta Version Of Jini, The App That Goes Beyond The Check-In, And Unveils 2012 Roadmap For The First Time. See what you think:

Argus Labs, a deep data, machine learning and mobile start-up operating out of Antwerp (Belgium), will celebrate the closed beta of the mobile application the night before LeWeb 2012 at Tiger-Tiger, Haymarket in London’s West-End. From 18th June, registered users will be able to download and start evaluating the first version of the intelligent application, called Jini.

Jini is a personal advisor that helps discover unknown relations and hyper-personalised opportunities. Jini feels best when helping the user out in serendipitous moments, or propose things that respond to the affinity its user has with its environment. Having access to hot opportunities and continuously being ‘in the know’ means a user can boost the quality of offline life.

Jini aims to raise the bar for private social networks by going beyond the check-in, saving the user the effort of doing too many manual actions. Jini applies machine learning with ambient sensing technology, so that the user can focus exclusively on having an awesome social sharing and discovery experience on smart-phones.

During the London launch event users will be able to sign up and exclusively download the first beta release of the app. The number of beta users is limited, so be fast. Argus Labs love to pioneer and will also have some goodies in store for the first 250 beta-users of the app.

See the post for registration information.

I sense a contradiction between being “…continuously being ‘in the know’ means a user can boost the quality of offline life.” How am I going to be ‘in the know’ if I am offline?

Still, I suspect there are opportunities here to merge diverse data sets to provide users with “hyper-personalized opportunities,” so long as it doesn’t interrupt one “hyper-personalized” situation to advise of another, potential “hyper-personalized” opportunity.

That would be like a phone call from an ex-girlfriend at an inopportune time. Bad joss.

Biological and Environmental Research (BER) Abstracts Database

Monday, October 17th, 2011

Biological and Environmental Research (BER) Abstracts Database

From the webpage:

Since 1995, OSTI has provided assistance and support to the Office of Biological and Environmental Research (BER) by developing and maintaining a database of BER research project information. Called the BER Abstracts Database (http://www.osti.gov/oberabstracts/index.jsp), it contains summaries of research projects supported by the program. Made up of two divisions, Biological Systems Science Division and Climate and Environmental Sciences Division, BER is responsible for world-class biological and environmental research programs and scientific user facilities. BER’s research program is closely aligned with DOE’s mission goals and focuses on two main areas: the Nation’s Energy Security (developing cost-effective cellulosic biofuels) and the Nation’s Environmental Future (improving the ability to understand, predict, and mitigate the impacts of energy production and use on climate change).

The BER Abstracts Database is publicly available to scientists, researchers, and interested citizens. Each BER research project is represented in the database, including both current/active projects and historical projects dating back to 1995. The information available on each research project includes: project title, abstract, principal investigator, research institution, research area, project term, and funding. Users may conduct basic or advanced searches, and various sorting and downloading options are available.

The BER Abstracts Database serves as a tool for BER program managers and a valuable resource for the public. The database also meets the Department’s strategic goals to disseminate research information and results. Over the past 16 years, over 6,000 project records have been created for the database, offering a fascinating look into the BER research program and how it has evolved. BER played a major role in the development of genomics-based systems biology and in the biotechnology revolution occurring over this period, while also supporting ground-breaking research on the impacts of energy production and use on the environment. The BER Abstracts Database, made available through the collaborative partnership between BER and OSTI, highlights these scientific advancements and maximizes the public value of BER’s research.

Particularly if this is an area of interest for you, take some time to become familiar with the interface.

  1. What do you think about the basic vs. advanced search?
  2. Does the advanced search offer any substantial advantages or do you have to start off with more complete information?
  3. What advantages (if any) does the use of abstracts offer over full text searching?

CITRIS – Center for Information Technology Research in the Interest of Society

Wednesday, September 21st, 2011

CITRIS – Center for Information Technology Research in the Interest of Society

The mission statement:

The Center for Information Technology Research in the Interest of Society (CITRIS) creates information technology solutions for many of our most pressing social, environmental, and health care problems.

CITRIS was created to “shorten the pipeline” between world-class laboratory research and the creation of start-ups, larger companies, and whole industries. CITRIS facilitates partnerships and collaborations among more than 300 faculty members and thousands of students from numerous departments at four University of California campuses (Berkeley, Davis, Merced, and Santa Cruz) with industrial researchers from over 60 corporations. Together the groups are thinking about information technology in ways its never been thought of before.

CITRIS works to find solutions to many of the concerns that face all of us today, from monitoring the environment and finding viable, sustainable energy alternatives to simplifying health care delivery and developing secure systems for electronic medical records and remote diagnosis, all of which will ultimately boost economic productivity. CITRIS represents a bold and exciting vision that leverages one of the top university systems in the world with highly successful corporate partners and government resources.

I mentioned CITRIS as an aside (News: Summarization and Visualization) yesterday but then decided it needed more attention.

Its grants are limited the four University of California campuses mentioned above. Shades of EU funding restrictions. Location has a hand in the selection process.

Still, the projects funded by CITRIS could likely profit from the use of topic maps and as they say, a rising tide lifts all boats.