Limits...
The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource.

Sherwood AR, Wang N, Carlile AL, Neumann JM, Wolfgruber TK, Presting GG - BMC Ecol. (2012)

Bottom Line: HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011.These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages.Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Botany, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, Hawaii 96822, USA. asherwoo@hawaii.edu

ABSTRACT

Background: Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species.

Description: The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers ("Isolate Accession"), the first five of which correspond to the collection site ("Environmental Accession"). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages.

Conclusions: HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences. It is publicly available at http://algae.manoa.hawaii.edu/hfwadb/.

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Example database isolate accession page. Screenshot of an Isolate Accession page illustrating the types of data stored for individually identified algae.
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Related In: Results  -  Collection

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Figure 3: Example database isolate accession page. Screenshot of an Isolate Accession page illustrating the types of data stored for individually identified algae.

Mentions: The results page returned from any query includes eight columns of information: Environmental Accession, Isolate Accession, Organism (genus and species), Region (island), Details (collection location), Collected (date), Isolated (date) and Sequences (total number of DNA sequences). Users may select either the Environmental Accession to display information about the collecting location, or the Isolate Accession to display the full range of data available for a particular identification. The Environmental Accession page (Figure 2) includes details of when and where the sample was collected, the geo-referenced collection site displayed using the Yahoo! Maps service API embedded within the website, an indication of habitat type and any field notes that were taken, and at least one photograph of the collection site (which can be viewed at higher resolution by selecting it). The Isolate Accession page (Figure 3) includes both Environmental and Isolate Accession details pertaining to that particular sample. Environmental Accession data are displayed at the top of the page (under pink heading bars), in much the same way as for an Environmental Accession page, while Isolate Accession data are displayed toward the bottom of the page (under green heading bars). The full taxonomy and taxonomic authority of the identified alga are displayed on the left-hand side under the thumbnail images of the Environmental and Isolate Accessions. Details of where the alga is stored [Collection (Isolate)] along with the Curator of the collection, the Identifier of the sample and the date it was identified (Date Isolated) are shown under the Environmental Accession data. Notes that may be helpful to others in identifying the alga are included under Isolate Sample Note, followed by information on the type of voucher (Herbarium Sheet, Liquid Voucher, Photo Only, Dried Voucher and/or Culture) and thumbnail images of key characters of the taxon with compound light or dissecting microscopy (which are displayed at higher resolution and with scale bars when selected). At the bottom of the panel is a list of DNA sequences (Isolate DNA Sequences) associated with that alga, which may include one or more loci from the nucleus (or principal chromosome, as in the cyanobacteria) (ITS = Internal Transcribed Spacer region(s) [7], LSU = nuclear ribosomal large subunit gene [8], SSU = nuclear ribosomal small subunit gene [9], 16S = gene encoding the ribosomal small subunit in prokaryotes including cyanobacteria [10]), plastid (rbcL = gene encoding the large subunit of the Rubisco enzyme [11], tufA = gene encoding elongation factor Tu [12], UPA = Universal Plastid Amplicon [13,14], ) or mitochondrion (COI = 5′ cytochrome oxidase subunit I gene [15]).


The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource.

Sherwood AR, Wang N, Carlile AL, Neumann JM, Wolfgruber TK, Presting GG - BMC Ecol. (2012)

Example database isolate accession page. Screenshot of an Isolate Accession page illustrating the types of data stored for individually identified algae.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3526539&req=5

Figure 3: Example database isolate accession page. Screenshot of an Isolate Accession page illustrating the types of data stored for individually identified algae.
Mentions: The results page returned from any query includes eight columns of information: Environmental Accession, Isolate Accession, Organism (genus and species), Region (island), Details (collection location), Collected (date), Isolated (date) and Sequences (total number of DNA sequences). Users may select either the Environmental Accession to display information about the collecting location, or the Isolate Accession to display the full range of data available for a particular identification. The Environmental Accession page (Figure 2) includes details of when and where the sample was collected, the geo-referenced collection site displayed using the Yahoo! Maps service API embedded within the website, an indication of habitat type and any field notes that were taken, and at least one photograph of the collection site (which can be viewed at higher resolution by selecting it). The Isolate Accession page (Figure 3) includes both Environmental and Isolate Accession details pertaining to that particular sample. Environmental Accession data are displayed at the top of the page (under pink heading bars), in much the same way as for an Environmental Accession page, while Isolate Accession data are displayed toward the bottom of the page (under green heading bars). The full taxonomy and taxonomic authority of the identified alga are displayed on the left-hand side under the thumbnail images of the Environmental and Isolate Accessions. Details of where the alga is stored [Collection (Isolate)] along with the Curator of the collection, the Identifier of the sample and the date it was identified (Date Isolated) are shown under the Environmental Accession data. Notes that may be helpful to others in identifying the alga are included under Isolate Sample Note, followed by information on the type of voucher (Herbarium Sheet, Liquid Voucher, Photo Only, Dried Voucher and/or Culture) and thumbnail images of key characters of the taxon with compound light or dissecting microscopy (which are displayed at higher resolution and with scale bars when selected). At the bottom of the panel is a list of DNA sequences (Isolate DNA Sequences) associated with that alga, which may include one or more loci from the nucleus (or principal chromosome, as in the cyanobacteria) (ITS = Internal Transcribed Spacer region(s) [7], LSU = nuclear ribosomal large subunit gene [8], SSU = nuclear ribosomal small subunit gene [9], 16S = gene encoding the ribosomal small subunit in prokaryotes including cyanobacteria [10]), plastid (rbcL = gene encoding the large subunit of the Rubisco enzyme [11], tufA = gene encoding elongation factor Tu [12], UPA = Universal Plastid Amplicon [13,14], ) or mitochondrion (COI = 5′ cytochrome oxidase subunit I gene [15]).

Bottom Line: HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011.These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages.Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Botany, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, Hawaii 96822, USA. asherwoo@hawaii.edu

ABSTRACT

Background: Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species.

Description: The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers ("Isolate Accession"), the first five of which correspond to the collection site ("Environmental Accession"). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages.

Conclusions: HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences. It is publicly available at http://algae.manoa.hawaii.edu/hfwadb/.

Show MeSH