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The taxonomic name resolution service: an online tool for automated standardization of plant names

Brad Boyle, Nicole Hopkins, Zhenyuan Lu, Juan Antonio Raygoza Garay, Dmitry Mozzherin, Tony Rees, Naim Matasci, Martha L Narro, William H Piel, Sheldon J Mckay, Sonya Lowry, Chris Freeland (+2 others)
2013 BMC Bioinformatics  
The TNRS is accessible via a web interface at and as a RESTful web service and application programming interface.  ...  Conclusions: We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names.  ...  interface).  ... 
doi:10.1186/1471-2105-14-16 pmid:23324024 pmcid:PMC3554605 fatcat:oef6eseme5aflg6cgxb463uhbm

A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control

Anton Güntsch, Cherian Mathew, Matthias Obst, Saverio Vicario, Robert Haines, Alan Williams, Yde de Jong, Carole Goble
2014 Biodiversity Data Journal  
We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system  ...  This request is then transformed into specific REST API calls to a number of online taxonomic checklists that provide web services to resolve scientific names.  ...  This workflow section provides an interface for functionality related to taxonomic data aggregation and this aspect can be greatly improved in the future.  ... 
doi:10.3897/bdj.2.e4221 pmid:25535486 pmcid:PMC4267104 fatcat:36j5scfgknbgdd3uzzjwgznmgu

The META-Frame: An environment for flexible tool management [chapter]

Bernhard Steffen, Tiziana Margaria, Andreas Claßen
1995 Lecture Notes in Computer Science  
Special care has been taken in the design of an adequate, almost natural-language specification language, a user-friendly graphical interface, a hypertext based navigation tool, the repository management  ...  , and global constraints fixing ordering, precedence, eventuality and conditional occurrence, 2. transforming specifications automatically into executable programs by means of a minimal model generator  ...  conditions, and global constraints fixing ordering, precedence, eventuality and conditional occurrence, 2. transforming specifications automatically into executable programs by means of a minimal model  ... 
doi:10.1007/3-540-59293-8_236 fatcat:snkjohed7bf3lcgressx2kswqa

The LifeWatch approach to the exploration of distributed species information

Daniel Fuentes, Nicola Fiore
2014 ZooKeys  
The approach improves data quality, avoiding taxonomic and nomenclature errors whilst increasing the availability and accessibility of the information.  ...  This paper introduces a new method of automatically extracting, integrating and presenting information regarding species from the most relevant online taxonomic resources.  ...  Three separate transformations are defined because both ways to query data and the XML structure in responses are different in these taxonomic resources.  ... 
doi:10.3897/zookeys.463.8397 pmid:25589865 pmcid:PMC4294304 fatcat:43aijozxgnd4jnhb44gdzoty4m

microViz: an R package for microbiome data visualization and statistics

David Barnett, Ilja Arts, John Penders
2021 Journal of Open Source Software  
aggregation and transformation information.  ...  These "taxonomic association trees" facilitate direct comparison of the direction, strength and significance of microbial associations between covariates and across multiple taxonomic ranks.  ...  aggregation and transformation information.  ... 
doi:10.21105/joss.03201 fatcat:fp2is2nmqvbcnlw5msa75qhwz4

Abundance and Taxonomic Diversity of Bacteria Inhabiting the Sediment-Water Interface in a Marine Harbor Channel

Piotr Perliński, Zbigniew J. Mudryk, Marta Zdanowicz
2019 Ocean Science Journal  
The abundance of bacteria inhabiting the sedimentwater interface and their taxonomic composition were determined with the fluorescence in situ hybridization (FISH) method in a marine harbor channel in  ...  Phylogenetic diversity of bacterial community inhabiting the sediment-water interface in the marine harbor in Ustka showed that Gammaproteobacteria dominated among the studied taxonomic groups.  ...  These reactions include such processes as dissolution, degradation, mineralization and demineralization, deposition, sorption and desorption, migration, transformation, oxidation and reduction, and enzymatic  ... 
doi:10.1007/s12601-019-0023-9 fatcat:4rcpo7f2vrgxdbkusoymt4th4y

ODB-Tools: A description logics based tool for schema validation and semantic query optimization in object oriented databases [chapter]

Sonia Bergamaschi, Claudio Sartori, Domenico Beneventano, Maurizio Vincini
1997 Lecture Notes in Computer Science  
The optimizer tentatively applies all the possible transformations and delays the choice of bene cial transformation till the end.  ...  ODB-Tools is a integrated environment for the object oriented database (OODB) validation, preserving taxonomy coherence and performing taxonomic inferences, and semantic query optimization.  ...  The optimizer tentatively applies all the possible transformations and delays the choice of bene cial transformation till the end.  ... 
doi:10.1007/3-540-63576-9_130 fatcat:brelyhs7ffdljgww6ob6ntf33i

Integration of Biodiversity Linked Data and Web APIs using SPARQL Micro-Services

Franck Michel, Catherine Faron-Zucker, Fabien Gandon
2018 Biodiversity Information Science and Standards  
A SPARQL micro-service provides access to a small RDF graph, typically resource-centric, that it builds at run-time by transforming a fraction of the whole dataset served by the Web API into RDF triples  ...  The SPARQL Micro-Service architecture (Michel et al. 2018) tackles the goal of reconciling Linked Data interfaces and Web APIs.  ...  The SPARQL Micro-Service architecture (Michel et al. 2018 ) tackles the goal of reconciling Linked Data interfaces and Web APIs.  ... 
doi:10.3897/biss.2.25481 fatcat:sm3lisqenvggtmpvw7jrm5y2xa

Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification [article]

Florian P Breitwieser, Steven L Salzberg
2016 bioRxiv   pre-print
With Pavian, researchers can analyze, display and transform results from the Kraken, Centrifuge and MetaPhlAn using interactive tables and plots.  ...  The data can be transformed by total sum scaling, variance-stabilizing transformation, and a robust z-score statistic. The results can also be displayed as an interactive heatmap.  ...  By default, read counts at all taxonomy levels are shown, but it is possible to show only specific taxonomical levels.  ... 
doi:10.1101/084715 fatcat:cuztmblv5nhedipejoctekjeri

A Taxonomic Search Engine: federating taxonomic databases using web services

Roderic D M Page
2005 BMC Bioinformatics  
The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format  ...  The Taxonomic Search Engine is available at and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic  ...  The XML summary of the search is transformed into HTML using an XSLT transformation.  ... 
doi:10.1186/1471-2105-6-48 pmid:15757517 pmcid:PMC555944 fatcat:pxzcc5o5arfntkz2tzwymq3wp4

MatrixConverter: Facilitating Construction of Phenomic Character Matrices

Jing Liu, Lorena Endara, J. Gordon Burleigh
2015 Applications in Plant Sciences  
In the user interface under "Step 2: Choose a Character," the user can select a character from the dropdown list.  ...  On a Mac or Windows computer, to open the user interface ( Fig. 1 ) , the user just has to click the executable JAR fi le.  ... 
doi:10.3732/apps.1400088 pmid:25699217 pmcid:PMC4332142 fatcat:y4begnjncna33k35cnqtrkccty

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements: Fig. 1

Kishori M. Konwar, Niels W. Hanson, Maya P. Bhatia, Dongjae Kim, Shang-Ju Wu, Aria S. Hahn, Connor Morgan-Lang, Hiu Kan Cheung, Steven J. Hallam
2015 Bioinformatics  
Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database.  ...  We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure  ...  ., , 2002a , there have been improvements to the software via the Knowledge Engine data structure, a graphical user interface (GUI) for data management and browsing and a master-worker model for task distribution  ... 
doi:10.1093/bioinformatics/btv361 pmid:26076725 pmcid:PMC4595896 fatcat:4i5aoaxbcjcefkbdtbctwzbdru

Visualization of information: a proposal to improve the search and access to digital resources in repositories

Paulo Alonso Gaona García, Salvador Sánchez Alonso, Carlos Montenegro Marin
2014 Ingeniería e Investigación  
Palabras clave: Técnicas de visualización, visualización de datos, interfaces de usuarios, repositorios y recursos digitales.  ...  Sin embargo, una de las áreas con pocos estudios en este campo, es el estudio de interfaces visuales que proporcionen acceso a los materiales relevantes en repositorios digitales.  ...  Figure 1 . 1 Tree interface Figure 2 . 2 Radial interface Figure 3 . 3 Hyperbolic interface Figure 4 . 4 Category interface Fig. 5 5 presents the work model for the data transformation process  ... 
doi:10.15446/ing.investig.v34n1.39449 fatcat:e2uq4yaeijfprjop5xfpjw2u5u

DNA is preserved and maintains transforming potential after contact with brines of the deep anoxic hypersaline lakes of the Eastern Mediterranean Sea

Sara Borin, Elena Crotti, Francesca Mapelli, Isabella Tamagnini, Cesare Corselli, Daniele Daffonchio
2008 Saline Systems  
Results: Seven strains belonging to different taxonomic groups isolated from the seawater-brine interface of four hypersaline lakes were grown at medium salinity and then incubated in the brines.  ...  Free DNA has the genetic potential to be acquired by living competent cells by horizontal gene transfer mediated by natural transformation.  ...  Results and discussion Survival in the brines of bacteria isolated from the seawater-brine interface The interface between deep sea-water and the hypersaline anoxic brines is a thin layer of few meters  ... 
doi:10.1186/1746-1448-4-10 pmid:18681968 pmcid:PMC2531117 fatcat:pc5w6cdkhbcdpm7pjlwvrvolqi

An integrated approach to database visualization

Dennis P. Groth, Edward L. Robertson
2002 Proceedings of the Working Conference on Advanced Visual Interfaces - AVI '02  
Our approach presents an abstraction of this transformation process, which we call mapping.  ...  Taxonomic approaches to describing data transformations is presented by Shneiderman in 5 and Chi in 3 . preparing and transforming data for the purposes of visualization.  ...  Using the application manager interface, a user adds various objects to the desktop. A screen capture from the system is shown in Figure 2 .  ... 
doi:10.1145/1556262.1556324 dblp:conf/avi/GrothR02 fatcat:5sxujr34jbad3mx4zg4i25f4k4
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