The Barcode of Life Data Portal: Bridging the Biodiversity Informatics Divide for DNA Barcoding

Sarkar, Indra Neil; Trizna, Michael

doi:10.1371/journal.pone.0014689

Cited by 27 publications

(19 citation statements)

References 18 publications

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“…nih.gov/) using BLAST (Altschul et al 1990) and BOLD (www.barcodinglife.org) with the default identification engine (Ratnasingham and Hebert 2007). For GenBank, an e-value of < 1.0e-1671.0e-167 was used to determine a positive identification of a blood meal, and a 96-100% identity of vertebrate host used for BOLD (Sarkar and Trizna 2011).…”

Section: Molecular Identification Of Vertebrate Source Of Blood Mealmentioning

confidence: 99%

Blood Meal Analysis and Virus Detection in Blood-Fed Mosquitoes Collected During the 2006–2007 Rift Valley Fever Outbreak in Kenya

Lutomiah

Omondi²,

Masiga³

et al. 2014

Vector-Borne and Zoonotic Diseases

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Section: Molecular Identification Of Vertebrate Source Of Blood Mealmentioning

confidence: 99%

Blood Meal Analysis and Virus Detection in Blood-Fed Mosquitoes Collected During the 2006–2007 Rift Valley Fever Outbreak in Kenya

Lutomiah

Omondi²,

Masiga³

et al. 2014

Vector-Borne and Zoonotic Diseases

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“…Equally, greater integration of different data types can be accompanied by a shared analytical toolbox. For example, the Barcode of Life Data Portal (Sarkar and Trizna 2011) currently makes available a range of tools specifically for analysis of DNA barcoding data, but also could take advantage of tools commonly used for other data types.…”

Section: Extending Data Types and Applicationsmentioning

confidence: 99%

Bridging the biodiversity data gaps: Recommendations to meet users’ data needs

Faith¹,

Collen²,

Ariño³

et al. 2013

Biodiv. Inf.

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-Freely available high quality, data on species occurrence and associated variables are needed in order to track changes in biodiversity. One of the main issues surrounding the provision of such data is that sources vary in quality, scope, and accuracy. Publishers of such data must face the challenge of maximizing quality, utility and breadth of data coverage, in order to make such data useful to users. With the Global Biodiversity Information Facility (GBIF), we recently conducted a content needs assessment survey to consolidate and synthesize major user needs regarding biodiversity data. We find a broad range of recommendations from the survey respondents, principally concerning issues such as data quality, bias, and coverage, and ease of access. We recommend a candidate set of actions for the GBIF that fall into three classes: 1) addressing data gaps, data volume, and data quality, 2) aggregating data types that are relatively new to GBIF, to support emerging new applications, and 3) promoting ease-of-use and providing incentives for wider use. Addressing the challenge of providing high quality primary biodiversity data potentially can serve the needs of national and international biodiversity initiatives. These include the "flexible framework" for addressing the new 2020 biodiversity targets of the Convention on Biological Diversity, the global biodiversity observation network (GEO BON) and the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES). Each of these presents opportunities for countries to define appropriate actions and corresponding data needs, with links from local to global scales.

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“…The Barcode of Life Data System (BOLD) is notably the largest initiative in establishing a worldwide DNA barcode library, signifying its importance and popularity for the scientific community [7], [8], [9]. The usefulness of DNA barcoding is evident when dealing with taxa displaying phenotypic plasticity throughout diphasic or triphasic life cycles as well as taxa involving cryptic species.…”

Section: Introductionmentioning

confidence: 99%

Assessment of Four Molecular Markers as Potential DNA Barcodes for Red Algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta)

et al. 2012

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DNA barcoding has been a major advancement in the field of taxonomy, seeing much effort put into the barcoding of wide taxa of organisms, macro and microalgae included. The mitochondrial-encoded cox1 and plastid-encoded rbcL has been proposed as potential DNA barcodes for rhodophytes, but are yet to be tested on the commercially important carrageenophytes Kappaphycus and Eucheuma. This study gauges the effectiveness of four markers, namely the mitochondrial cox1, cox2, cox2-3 spacer and the plastid rbcL in DNA barcoding on selected Kappaphycus and Eucheuma from Southeast Asia. Marker assessments were performed using established distance and tree-based identification criteria from earlier studies. Barcoding patterns on a larger scale were simulated by empirically testing on the commonly used cox2-3 spacer. The phylogeny of these rhodophytes was also briefly described. In this study, the cox2 marker which satisfies the prerequisites of DNA barcodes was found to exhibit moderately high interspecific divergences with no intraspecific variations, thus a promising marker for the DNA barcoding of Kappaphycus and Eucheuma. However, the already extensively used cox2-3 spacer was deemed to be in overall more appropriate as a DNA barcode for these two genera. On a wider scale, cox1 and rbcL were still better DNA barcodes across the rhodophyte taxa when practicality and cost-efficiency were taken into account. The phylogeny of Kappaphycus and Eucheuma were generally similar to those earlier reported. Still, the application of DNA barcoding has demonstrated our relatively poor taxonomic comprehension of these seaweeds, thus suggesting more in-depth efforts in taxonomic restructuring as well as establishment.

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The Barcode of Life Data Portal: Bridging the Biodiversity Informatics Divide for DNA Barcoding

Cited by 27 publications

References 18 publications

Blood Meal Analysis and Virus Detection in Blood-Fed Mosquitoes Collected During the 2006–2007 Rift Valley Fever Outbreak in Kenya

Blood Meal Analysis and Virus Detection in Blood-Fed Mosquitoes Collected During the 2006–2007 Rift Valley Fever Outbreak in Kenya

Bridging the biodiversity data gaps: Recommendations to meet users’ data needs

Assessment of Four Molecular Markers as Potential DNA Barcodes for Red Algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta)

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