After a wonderful week in Montpellier, France and listening to some very interesting talks it’s time to get back to the daily grind and continue our developments. Before we do, I wanted to recap on some of the activities SilverBiology was involved in.
Another session of Nomina has been concluded. EOL was nice enough to again host this workshop at the Marine Biological Laboratory in Woods Hole. This time the focus was on methods for reconciling heterogeneous taxonomic data. The group this time was made up of myself from SilverBiology, GBif, EOL, and Atlas of Living Australia (ALA).
SilverBiology will be exhibiting again this year at the SPNHC 2009. The conference is to take place on July 6th - 11th, 2009 in Leiden, Netherlands.
Bridging Continents presents new, large-scaled infrastructure projects in natural history collections, the state-of-art in collection care and best practice, the latest on digitization of collections and much more. http://www.spnhc2009.org
We will be showcasing our newest version of SilverCollection, our web portal for biological collections. We have a new api and some great new features we are excited to show off.
We have also been doing research in fuzzy matching for scientific names and will be showing how TAXAMATCH web service can be used to help with scientific literature.
If your museum has an Arthropod, Herbarium, or other start to a digital collection we really want to speak with you during the meeting. We have some additional tools coming out this year that should help with imaging and processing scientific data.
We strive to build good working relationships with museums to improve our software, create open source tools, and offer custom solutions to your specific needs.
See you there!
Last week was the fourth gathering for Nomina. These meetings have been created by EOL & GBIF in collaboration with BHL (Biodiverstiy Heritage Library). The goal for this meeting was to improve Taxonomic Name Recognition, discover the tools and algorithms that are currently being used and how to merge and improve what we are currently doing to make things faster and better. With over 35,000 books and more then 14 million scientific pages from the BHL it is important to provide the most accurate tools to help discover information from the past.
The workspace used for this meeting includes links to web applications, source code, shared dictionaries, test files, and other useful resources for those in need of tools and services for finding, parsing, and processing taxonomic names. http://code.google.com/p/taxon-name-processing
The meeting was very productive and as changes and improvements are made to the individual projects the overall goals will be one step closer.
SilverBiology’s purpose at this meeting was to demonstrate and see how our TAXAMATCH web service can be used with fuzzy matching on scientific names that are misspelled. Our goal is to implement this with the Global Names Index (globalnames.org) and GBIF’s species checklist. These will be public web services so anyone can use to search for scientific names.
TAXAMATCH was originally developed by Tony Rees at OBIS and developed in PL/SQL. Our open source version is a PHP/MySql implementation of the algorithm with a few additional configurations. To learn more about Tony’s project and the continuation of our project just follow the links below.
If you would like to see more about the past Nomina workshops you can find them here:
SilverBiology is pleased to announce the expansion of our company to the European Universities and Museums to support their biological collections. Our new office is located in Sevilla, Spain. At the moment we are looking at the current status of collections and will be introducing ourselves to many of the universities in the near future.
We are excited to introduce Maciej Wyszkowski to our team. He is the European Regional Manager of SilverBiology and will be overseeing the biodiversity needs in this part of the world. If you are interested in speaking with him on how SilverCollection, our web portal for scientific collections, can work with your collection please contact us now. To view a full list of all our current services please visit: http://www.silverbiology.com/products
You are also welcome to discuss any projects that you need help with or integrating with current standards and technologies. Our focus is to provide open source and licensed based software tools to provide solutions for scientific goals throughout the world.
You may contact us at: http://www.silverbiology.com/company/contactus.php
We will be attending the SPNHC2009 (6 - 11 July 2009, Leiden, The Netherlands). You can also find out about our future events at: http://www.silverbiology.com/company/events.html
I am pleased to announce that SilverBiology has accepted the task of building a Php Port of Tony Rees’ Taxamatch (http://www.cmar.csiro.au/datacentre/taxamatch.htm). TAXAMATCH is a “fuzzy” matching algorithm for taxon names and potential applications in taxonomic databases developed by Tony Rees at the CSIRO Marine and Atmospheric Research in Australia.
SilverBiology’s initial interest in providing an API service is in anticipation for our upcoming product called “SilverArchive” (http://www.silverbiology.com/products/silverarchive), where we help process herbarium specimen data using a human distribution model approach. Having this tool to accurately spell check for scientific names will be highly useful for the efficiency of our software and our clients. Our other goal is to provide services to easily inspect and clean scientific names.
This web service is an open source project and is being developed to allow unique computer aided solutions for a variety of applications. The API will be a RESTful service that will initially support the JSON format. We hope to extend this to XML and other requested formats.
You can find more about our project at: http://taxamatch.silverbiology.com as we continue to develop this service. The project’s source code is located at: http://code.google.com/p/taxamatch-webservice. If anyone is interested in testing this service and getting involved or would like to use this service when it is completed, we would love to hear from you. Our goal is to build a service that is useful for everyone so all types of input is welcome.
This project is still in progress so no release date has been set. We are hoping to have an Alpha release, in May 2009, with some real world examples of using the system. We will post additional announcements as we progress with this service. Anyone that is interested in getting involved please contact Mike Giddens (mikegiddens <at> silverbiology.com)
We want to thank David Remsen and everyone else that has already contacted us about testing and using the service. The more initial tests and uses we come up with the better the service will become.
SilverBiology is proud to announce that they have been selected by CyberFlora Louisiana to design, manage, develop, and provide technical guidance on the digitization of more then 1 million herbarium specimen sheets. SilverCollection will be the official web portal for the herbarium collections in Louisiana.
SilverCollection is a webportal for biological collections and will be the primary interface to over 1.3 million herbarium specimens. There will be custom features designed to focus on the CyberFlora project goals and a highly useful “api/web service” to interact with the data.
SilverBiology will be also introducing new software products this year in conjunction with the Cyberflora project. Our goal is to develop new tools during the development of the Louisiana Herbarium Database to show as a model and ways for other consortia can follow.
This is a big endeavor and our team is excited to be working with Cyberflora Louisiana.
To find out more about the project you can monitor the official Cyberflora Louisiana Blog at: http://news.cyberfloralouisiana.com
Have you ever been doing field research, had your GPS, and searched for a locality or species? Well, what happens when you find and record the coordinates then later have no idea which county you where in?
There has been some recent discussion on associating the geographical coordinate of a collection or museum. If you are interested in updating your information in the Biodiversity Collection Index and not sure how to go about finding your coordinate you can follow this simple tutorial to get your location without any GPS device. Read the rest of this entry »
Ever wanted to know where all the historical plants are stored? How about bugs, insects, spiders, butterflies, or fish? Well with the help of Biodiversity Collection Index (BCI) and their wonderful resources of information we are finally able to get a true interactive visualization of how our world is collected and where that information is housed.
Research into biodiversity relies on the use of specimens. These specimens are held in reference collections around the world. BCI is a central index to these collections. With the help of BCI’s Web Services, SilverBiology was able to use its new open source web tool SilverMapper to easily map the location of these collections.
This data source is directly based on the data from the Biodiversity Collection Index (BCI) and all geospatial data is estimated on Google Maps reverse geocoding service to establish a latitude and longitude.
Why did we do this?
We wanted to show a real world example of our new program SilverMapper and at the same time provide something useful for the community. Comments and suggestions are welcome. I would also like to thank Roger Hyam for all his hard work over at the Royal Botanic Garden in Edinburgh for really bringing the Biodiversity Collection Index together. I hope this little demonstration will encourage collection managers to update their information with the exact latitude and longitude position at BCI to help provide the precise location of where people can find their collection.