Resolving taxonmic discrepancies: Role of Electronic Catalogues of Known Organisms

Chavan, Vishwas; Rane, Nilesh; Watve, Aparna; Ruggiero, Michael T.

doi:10.17161/bi.v2i0.16

Cited by 8 publications

(5 citation statements)

References 6 publications

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“…Perhaps influenced by open‐source software development, many phyloinformatics pipelines are fully open, although in practice they differ greatly in components, overall complexity and applicability. Second, there is a trade‐off between reproducibility and manual processing; human oversight of big data is variously required (Chavan, 2007) but undermines the goal of reproducibility through introducing ambiguity and subjectivity. Herein, manual checks during preliminary analyses inform on the necessary changes or additions to the protocol (e.g.…”

Section: Outlook and Conclusionmentioning

confidence: 99%

Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects

Chesters

Ferrari

et al. 2023

Molecular Ecology Resources

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The Holy Grail of an Insect Tree of Life can only be ‘discovered’ through extensive collaboration among taxon specialists, phylogeneticists and centralized frameworks such as Open Tree of Life, but insufficient effort from stakeholders has so far hampered this promising approach. The resultant unavailability of synthesis phylogenies is an unfortunate situation given the numerous practical usages of phylogenies in the near term and against the backdrop of the ongoing biodiversity crisis. To resolve this issue, we establish a new online hub that centralizes the collation of relevant phylogenetic data and provides the resultant synthesis molecular phylogenies. This is achieved through key developments in a proposed pipeline for the construction of a species‐level insect phylogeny. The functionality of the framework is demonstrated through the construction of a highly supported, species‐comprehensive phylogeny of Diptera, built from integrated omics data, COI DNA barcodes, and a compiled database of over 100 standardized, published Diptera phylogenies. Machine‐readable forms of the phylogeny (and subsets thereof) are publicly available at insectphylo.org, a new public repository for species‐comprehensive phylogenies for biological research.

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Section: Outlook and Conclusionmentioning

confidence: 99%

Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects

Chesters

Ferrari

et al. 2023

Molecular Ecology Resources

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“…Large scientific repositories are supported by powerful databases and are now focusing on the sharing of information between organizations. A problematic barrier is found in taxonomic differences and data model inconsistencies (Chavan et al, 2005); for this reason many repositories are contributing to the definition of standards to share and transfer their information. The use of spatial data is also becoming common, as the information on the location and distribution of specimens is valuable for research in this field.…”

Section: Existing Systemsmentioning

confidence: 99%

Biodiversity Information Systems Using Georeferencing and Physical Identification

Lira¹,

Ribeiro²,

Lopes³

2011

Proceedings of the 7th International Conference on Web Information Systems and Technologies

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Abstract:Biodiversity information can be found in diverse information systems, ranging from large technical repositories for research purposes to dedicated databases supporting the web presence of natural sites. To deal with individual botanical objects, it is important to adopt the established scientific taxonomy. Providing a satisfying experience with current interface devices is also mandatory. Two problems have been addressed in this work: the unique identification of the objects and the representation of their physical location. The former has been tackled with QR code, a two-dimensional barcode standard, and the latter with the use of a PostgreSQL/PostGIS spatial database. The paper describes the development and test of a Web information system integrating physical identification and geo-referencing. The application in biodiversity information management shows that low-cost, state-ofthe-art technologies can provide appropriate solutions even for small-and medium-sized natural sites, incorporating existing scientific information on species and contributing for a growing record of their occurrences. The system was tested on a university garden and can be used by site maintainers, visitors and researchers. The dataset collected in the site can be exported according to the Darwin Core biodiversity standard for research purposes.

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“…This was because the genus Paralia is used both in the Ebenaceae and for a genus of phytoplankton [16]. Other such examples are cited by Page [17,18] and Chavan et al [19]. A second major issue is the inconsistent use of valid names as accepted names or as synonyms.…”

Section: Taxonomic Disambiguationmentioning

confidence: 99%

Knowledge-Based and Intelligent Information and Engineering Systems

2010

Lecture Notes in Computer Science

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To construct Biodiversity richness maps from Environmental Niche Models (ENMs) of thousands of species is time consuming. A separate species occurrence data pre-processing phase enables the experimenter to control test AUC score variance due to species dataset size. Besides, removing duplicate occurrences and points with missing environmental data, we discuss the need for coordinate precision, wide dispersion, temporal and synonymity filters. After species data filtering, the final task of a pre-processing phase should be the automatic generation of species occurrence datasets which can then be directly 'plugged-in' to the ENM. A software application capable of carrying out all these tasks will be a valuable time-saver particularly for large scale biodiversity studies.

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Resolving taxonmic discrepancies: Role of Electronic Catalogues of Known Organisms

Cited by 8 publications

References 6 publications

Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects

Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects

Biodiversity Information Systems Using Georeferencing and Physical Identification

Knowledge-Based and Intelligent Information and Engineering Systems

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