TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics.
The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for anal...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3377657?pdf=render |
| _version_ | 1818143575976706048 |
|---|---|
| author | Reed S Beaman Greg H Traub Christopher A Dell Nestor Santiago Jin Koh Nico Cellinese |
| author_facet | Reed S Beaman Greg H Traub Christopher A Dell Nestor Santiago Jin Koh Nico Cellinese |
| author_sort | Reed S Beaman |
| collection | DOAJ |
| description | The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email. |
| first_indexed | 2024-12-11T11:33:51Z |
| format | Article |
| id | doaj.art-3eb59896436c4d73b09effd4f5163d61 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T11:33:51Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-3eb59896436c4d73b09effd4f5163d612022-12-22T01:08:48ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0176e3935210.1371/journal.pone.0039352TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics.Reed S BeamanGreg H TraubChristopher A DellNestor SantiagoJin KohNico CellineseThe development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email.http://europepmc.org/articles/PMC3377657?pdf=render |
| spellingShingle | Reed S Beaman Greg H Traub Christopher A Dell Nestor Santiago Jin Koh Nico Cellinese TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics. PLoS ONE |
| title | TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics. |
| title_full | TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics. |
| title_fullStr | TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics. |
| title_full_unstemmed | TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics. |
| title_short | TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics. |
| title_sort | tolkin tree of life knowledge and information network filling a gap for collaborative research in biological systematics |
| url | http://europepmc.org/articles/PMC3377657?pdf=render |
| work_keys_str_mv | AT reedsbeaman tolkintreeoflifeknowledgeandinformationnetworkfillingagapforcollaborativeresearchinbiologicalsystematics AT greghtraub tolkintreeoflifeknowledgeandinformationnetworkfillingagapforcollaborativeresearchinbiologicalsystematics AT christopheradell tolkintreeoflifeknowledgeandinformationnetworkfillingagapforcollaborativeresearchinbiologicalsystematics AT nestorsantiago tolkintreeoflifeknowledgeandinformationnetworkfillingagapforcollaborativeresearchinbiologicalsystematics AT jinkoh tolkintreeoflifeknowledgeandinformationnetworkfillingagapforcollaborativeresearchinbiologicalsystematics AT nicocellinese tolkintreeoflifeknowledgeandinformationnetworkfillingagapforcollaborativeresearchinbiologicalsystematics |